GeneXpert DX System Operator Manual v4.8 Revk

GeneXpert Dx System
Operator Manual
Software Version 4.8
301-0045, Rev. K August 2016

Preface
About this Manual

The GeneXpert® Dx System Operator Manual provides instructions on how to operate
the GeneXpert Dx system. The software-related instructions in this operator manual
assume you have basic computer skills. You should be familiar with the Microsoft®
Windows® graphical user interface. If you do not have these skills, refer to the
documentation for Windows.
Safety Information
Chapter 8, Hazards in this manual provides important safety information that should be
used when operating the GeneXpert Dx system. Read and understand the safety
information thoroughly before beginning to operate the instrument. Using the instrument
without reading the hazard chapter or without proper training can result in serious injury,
damage to the instrument, invalid results, or loss of data.
Warning
A warning indicates a possibility of adverse reactions, injury, or death to the user or other
personnel if the precautions or instructions are not observed.
Caution
A caution indicates that damage to the system, loss of data, or invalid results could occur if
the user fails to comply with the advice given.
Important indicators highlight information that is critical for the completion of a task or the
Important
optimal performance of the system.
Note A note identifies information that applies only to specific cases or tasks.
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Preface
Symbols Used in the Manual and on GeneXpert Dx

System Labels
The following symbols and icons are used in this manual and on the GeneXpert Dx
system labels:
Symbol Meaning
In vitro diagnostic medical device
CE marking – European Conformity
Do not reuse
Consult instructions for use
Manufacturer
Authorized representative in the European Community
Separate collection for electrical and electronic equipment waste per Directive
2002/96/EC in the European Union.
This type of warning label indicates a potential biological hazard risk. Biological
samples such as tissues, body fluids, and blood of humans and/or animals
have the potential to transmit infectious diseases. Follow your local, state/
provincial, and national safety regulations for handling and disposing the
samples.
This type of warning label indicates that hazardous high voltage sections are
present in the electrical system in the GeneXpert Dx system. Do not remove
covers with this warning label.
This type of symbol indicates a possibility of loss of data or data corruption if

proper procedures are not followed. Read any additional information following
the symbol to avoid the data loss.
This type of symbol indicates a Warning or Caution for which there is no other
identified symbol. Read the instructions following the symbol to avoid injury or
equipment damage.
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Preface
Cepheid Headquarters Locations
Corporate Headquarters European Headquarters

Cepheid Cepheid Europe SAS
904 Caribbean Drive Vira Solelh
Sunnyvale, CA 94089-1189 USA 81470 Maurens-Scopont
France
Telephone: +1 408.541.4191 Telephone: +33 563 825 300
Fax: +1 408.541.4192 Fax: +33 563 825 301
www.cepheid.com www.cepheidinternational.com
Technical Assistance
Before contacting Cepheid Technical Support, collect the following information:
• Product name
• Lot number
• Serial number of the instrument
• Error messages (if any)
• Software version and, if applicable, Computer Service Tag number
Region Telephone Email

US + 1 888 838 3222 [email protected]
Australia and + 1800 107 884
New Zealand + 0800 001 028 [email protected]
Brazil and Latin America + 55 11 3524 8373 [email protected]
China + 86 021 5406 5387 [email protected]
France + 33 563 825 319 [email protected]
Germany + 49 69 710 480 480 [email protected]
India, Bangladesh, Bhutan, Nepal,
and Sri Lanka + 91 11 48353010 [email protected]
Italy + 39 800 902 567 [email protected]
Japan + 0120 95 4886 [email protected]
South Africa + 27 861 22 76 35 [email protected]
United Kingdom + 44 3303 332 533 [email protected]
Other European, Middle East, + 33 563 825 319 [email protected]
and African countries + 971 4 253 3218
Other countries not listed above +1 408.400.8495 [email protected]
Contact information for other Cepheid offices is available on our website at

www.cepheid.com, www.cepheidjapan.com or www.cepheidinternational.com under the
SUPPORT tab. Select the Contact Us option.
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Preface
EC REP
Cepheid Europe SAS
Vira Solelh Cepheid
81470 Maurens-Scopont 904 Caribbean Drive
France Sunnyvale, CA 94089
Telephone: +33 563 825 300 USA
Fax: +33 563 825 301 Tel: +1.408.541.4191
www.cepheidinternational.com Fax: +1.408.541.4192
Warranty
The following information constitutes the Product-specific warranties referenced in the purchase
agreement (typically bearing a title such as “Purchase Agreement” or “Sales Agreement”) under
which the GeneXpert® Instrument and Software described herein were purchased from Cepheid®.
Purchaser must not alter or remove any labels, signs, symbols, serial numbers, copyright, patent,
trademark, trade secret, proprietary and/or other legal notices contained on or in this Manual, the
GeneXpert Instrument, GeneXpert Software, and related documentation.
GeneXpert Instrument Limited Warranty

Cepheid warrants that (i) the GeneXpert Instrument (the “Instrument”) is free from defects in material
and workmanship, (ii) the Instrument together with the GeneXpert Dx System Software (the
“Product”) conforms to Cepheid's published specifications, and (iii) the Product conforms to the
labeling claims that accompany the Instrument. This Warranty is for a period of 12 months from the
date of shipment to the Purchaser (the Warranty Period). During the Warranty Period, if the
Instrument's hardware is found to be defective or if the Product is found to be non-conforming under
item (ii) or (iii) above, Cepheid will repair or replace it, at a site determined by Cepheid at Cepheids
expense. This warranty extends to Purchaser only and not to any other parties, except as agreed to
in writing by Cepheid, and applies only to new products manufactured by Cepheid.
Cepheid does not warrant any defects in the Instrument caused by (i) improper installation, removal
or testing, (ii) Purchaser's failure to provide a suitable operating environment for the Instrument, (iii)
use of the Instrument for purposes other than that for which it was designed, (iv) unauthorized
attachments, (v) unusual physical or electrical stress, (vi) modifications or repairs done by other than
Cepheid or a Cepheid authorized service provider, or (vii) any other abuse, misuse, or neglect of the
Instrument. The Instrument is designed and certified with applicable regulatory authorities as part of
an integrated instrument/reagent/consumable system. Use of unapproved parts, reagents or other
materials with the Instrument will void any warranty and any service contract between Cepheid and
the Purchaser that pertains to the Instrument.
OTHER THAN ANY EXPRESS WARRANTY PROVIDED IN THE ORIGINAL PURCHASE
AGREEMENT WITH CEPHEID, THERE ARE NO WARRANTIES WHICH EXTEND BEYOND THE
FACE HEREOF, AND CEPHEID DISCLAIMS ALL OTHER REPRESENTATIONS AND
WARRANTIES, WHETHER EXPRESS OR IMPLIED, REGARDING THE PRODUCT, INCLUDING
ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR
PURPOSE. CEPHEID AND ITS DIRECTORS, OFFICERS, EMPLOYEES AND AGENTS SHALL
HAVE NO LIABILITY FOR GENERAL, CONSEQUENTIAL, INCIDENTAL OR SPECIAL DAMAGES
ARISING FROM A DEFECT IN THE INSTRUMENT. FURTHERMORE, CEPHEID SHALL HAVE NO
STRICT LIABILITY, PRODUCTS LIABILITY OR NEGLIGENCE LIABILITY, WHETHER ACTIVE OR
PASSIVE, AS TO THE PURCHASER.
Purchaser's exclusive remedy for any defective Instrument or non-conforming Product is limited to
the repair or replacement of any defective Instrument. If Cepheid cannot or does not repair or
replace a defective Instrument or non-conforming Product, Cepheid will remove same and return the
purchase price. If Cepheid cannot or does not repair or replace any defective Instrument or non-
conforming Product or if Purchaser's exclusive remedy fails of its essential purpose, Cepheid's
entire liability shall in no event exceed the purchase price for any defective Instrument or non-
conforming Product.
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Preface
Cepheid GeneXpert Dx System Software License Agreement

Cepheid is the exclusive owner of the Cepheid GeneXpert Dx System Software program (the
“Software”), related documentation and physical media, and of all copyright, trade secret, patent,
trademark and other intellectual or industrial property rights therein. Physical media and copies of
the Software, whether in diskette, tape, paper or other form, shall remain the property of Cepheid,
and such copies are deemed to be on loan to Purchaser during the term of the License granted
hereby. Purchaser expressly acknowledges that no title to or ownership of the Software, or any copy
or portion thereof, is transferred to Purchaser. The ideas and expressions thereof contained in the
Software are confidential, proprietary information and trade secrets of Cepheid that are provided to
Purchaser. Purchaser shall not cause or permit decompilation, disassembly, or reverse engineering
of the Software or disclosure, copying, display, loan, publication, transfer of possession (whether by
sales, exchange, gift, operation of law or otherwise) or other dissemination of the Software and
related documentation, in whole or part, to any third party without the prior written consent of
Cepheid.
License Grant: Cepheid grants Purchaser a non-exclusive, non-transferable license (the “License”)
to use only one (1) copy of the Software on the computer provided by Cepheid with the GeneXpert
Instrument(s) and connected to the GeneXpert Instrument(s), and to make only one (1) copy solely
for back-up purposes. Purchaser shall not otherwise copy and shall not modify, duplicate, translate,
disassemble, or decompile the Software without Cepheid's prior written consent. If the Software is
used on a computer other than the one provided by Cepheid for the GeneXpert Instrument, Cepheid
will not guarantee performance and cannot provide technical support for problems arising therefrom.
Purchaser may not use this single-user product on a network. This License entitles Purchaser to use
toll-free telephone support as provided by Cepheid. This License is effective until terminated.
Cepheid may terminate this License if Purchaser fails to comply with any of the terms or conditions
of this License or of the original purchase agreement. If this License is terminated, Purchaser must
destroy all copies of the Software and its related documentation.
For Government Purchasers, the Software is commercial computer software subject to restricted
rights under FAR 52.227-19 (C) (1, 2).
The end user license agreement is located at C:\program files\cepheid\genexpert
4.0\resources\en_us\files\DxLicenseAgreement.pdf.
For software version 4.4 and earlier, if you cannot locate your license, you may obtain a copy from
Cepheid Technical Support.
Patent Statements
NOTICE TO PURCHASER
Licensed under all applicable claims of U.S. Patent Nos. 5,589,136, 6,524,532, and 6,602,473, and
corresponding claims in their non-U.S. counterparts.
The purchase of this instrument includes a limited, non-transferable license under U.S. Patents Nos.
6,787,338; 6,503,720 and 6,303,305, and claims 9, 10, 11, 56, 76, 80 and 107 of U.S. Patent No.
6,174,670, and corresponding claims in patents and patent applications outside the United States,
owned by the University of Utah Research Foundation and licensed to Idaho Technology, Inc. No
right is conveyed, expressly, by implication or estoppel, under any other patent or patent claims
owned by the University of Utah Research Foundation or Idaho Technology, Inc. Without limiting the
foregoing, no right, title or license is herein granted with respect to the uses that are proprietary to
Idaho Technology or the University of Utah Research Foundation of fluorescent double stranded
nucleic acid binding dyes, specifically including but not limited to SYBR® Green I, LCGreen® I, or
LCGreen® Plus.
NO OTHER RIGHTS ARE CONVEYED EXPRESSLY, BY IMPLICATION OR BY ESTOPPEL TO
ANY OTHER PATENTS. FURTHERMORE, NO RIGHTS FOR RESALE ARE CONFERRED WITH
THE PURCHASE OF THIS PRODUCT.
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Preface
Trademark and Copyright Statements

Cepheid®, the Cepheid logo, GeneXpert® and I-CORE® are trademarks of Cepheid.
Adobe® and Acrobat® are registered trademarks of Adobe Systems Incorporated.
Dacron® is a registered trademark of EI Dupont de Nemours and Company.
Ethernet® is a registered trademark of Xerox Corporation.
Microsoft® and Windows® are registered trademarks of Microsoft Corporation.
All other trademarks are the property of their respective owners.
This Manual contains information protected by copyright. No part of this Manual may be photocopied
or reproduced in any form without prior written consent from Cepheid.
© Cepheid 2016 — All rights reserved.
Disclaimers
All examples (printouts, graphics, displays, screens, etc.) are for information and illustration
purposes only and shall not be used for clinical or maintenance evaluations. Data shown in sample
printouts and screens do not reflect actual patient names or test results. Labels depicted in the
manual may appear different from actual product labels. Cepheid makes no representations or
warranties about the accuracy and reliability of the information contained in the GeneXpert Dx
System Operator Manual. The information was developed to be used by persons trained and
knowledgeable in GeneXpert operation or under the direct supervision of Cepheid Technical Support
or service representatives. Updates to this Operator Manual may be issued periodically and should
be maintained with this original manual.
Not all products described in this Manual are available in all countries.
Note REACH Directive 1907/2006/EC exempts in vitro diagnostic medical devices.
California Proposition 65 Warning

This instrument may contain chemicals known to the State of California to cause cancer and birth
defects or other reproductive harm.
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Table of Contents
1 Introduction—Use or Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.1 Intended Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.2 Terms Used for System Descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
1.3 Models of GeneXpert Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.4 System Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2
1.4.1 GeneXpert Dx System Components. . . . . . . . . . . . . . . . . . . . . 1-3
1.5 GeneXpert Cartridges. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
1.6 GeneXpert Dx Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
1.7 Workflow Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
1.7.1 Installation and Setup Workflow . . . . . . . . . . . . . . . . . . . . . . . . 1-7
1.7.2 Test Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7
1.8 Before Operating the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-8
2 Installation Procedures and Special Requirements . . . . . . . . . . . . . . . . . . 2-1

2.1 GeneXpert Dx System Package Contents . . . . . . . . . . . . . . . . . . . . . . 2-1
2.2 Required Materials for Use with the System
(But Not Provided) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.3 System Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.3.1 System Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
2.3.2 Network Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
2.3.3 Microsoft Software CDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
2.4 Installing the GeneXpert Dx System. . . . . . . . . . . . . . . . . . . . . . . . . . . 2-3
2.4.1 To Install a GeneXpert Dx System . . . . . . . . . . . . . . . . . . . . . . 2-4
2.4.2 To Install Additional Instruments. . . . . . . . . . . . . . . . . . . . . . . . 2-7
2.5 Turning On The Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8
2.5.1 Anti-Virus Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
2.6 Windows Language and Keyboard Configuration . . . . . . . . . . . . . . . 2-11
2.7 Configuring the Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
2.7.1 Selecting the Power Management Settings . . . . . . . . . . . . . . 2-12
2.7.2 Setting the Local Date and Time . . . . . . . . . . . . . . . . . . . . . . 2-16
2.7.3 Setting the IP Address . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-17
2.8 Starting the Software for the First Time . . . . . . . . . . . . . . . . . . . . . . . 2-22
2.9 Assigning Instrument Letters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-24
2.9.1 To Assign Instrument Letters (GX-I, GX-II and
GX-IV Instruments) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-24
2.9.2 To Assign Instrument Letters (GX-XVI Instruments) . . . . . . . 2-31
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2.10 Defining Users and Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-39

2.10.1 User Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-39
2.10.2 Specifying User Permissions . . . . . . . . . . . . . . . . . . . . . . . . . 2-39
2.10.3 Managing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-42
2.10.3.1 Adding New Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-42
2.10.3.2 Editing User Profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-43
2.10.3.3 Removing Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-44
2.11 Configuring the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-45
2.11.1 General Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-45
2.11.2 Archive Settings Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-49
2.11.3 Folders Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-50
2.11.4 Xpress Setting Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-51
2.11.5 Host Communication Settings Tab . . . . . . . . . . . . . . . . . . . . . 2-51
2.11.5.1 Configuring Host Communications for an LIS . . . . . . . . . . 2-51
2.11.5.2 Configuring Host Communications for Cepheid Link . . . . . 2-54
2.11.6 Configuring Assay for Order and Result Upload . . . . . . . . . . 2-57
2.11.6.1 Configuring a Single-Result Assay for Order and
Result Upload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-57
2.11.6.2 Configuring a Multiple-Result Assay for Order and
Result Upload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-58
2.12 Verifying Proper Installation and Setup . . . . . . . . . . . . . . . . . . . . . . . 2-59
2.13 Managing Assay Definitions and Lot Specific Parameters . . . . . . . . . 2-63
2.13.1 The DVD Drive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-63
2.13.2 Importing Assay Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . 2-64
2.13.3 Deleting Assay Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-65
2.13.4 Importing Lot Specific Parameters Manually . . . . . . . . . . . . . 2-67
2.13.5 Deleting Lot Specific Parameters . . . . . . . . . . . . . . . . . . . . . . 2-69
2.14 Restarting the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-70
2.14.1 Shutting the System Down . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-70
2.14.1.1 Archive Overdue Reminder . . . . . . . . . . . . . . . . . . . . . . . . 2-70
2.14.1.2 Database Management Reminder . . . . . . . . . . . . . . . . . . . 2-72
2.14.1.3 Final Shutdown Steps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-73
2.14.2 Restart the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-73
2.15 Uninstalling or Reinstalling GeneXpert Dx Software . . . . . . . . . . . . . 2-73
3 Principles of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

3.1 System Operation Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
3.2 GeneXpert Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.3 GeneXpert Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
3.4 I-CORE Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
3.5 Heating and Cooling Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
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3.6 Explanation of Experimental Methods . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

3.7 Optical System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-7
3.8 System Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
4 Performance Characteristics and Specifications . . . . . . . . . . . . . . . . . . . . 4-1

4.1 Instrument Classification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
4.2 General Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2
4.2.1 General Specifications for GeneXpert R1 Instruments . . . . . . . 4-2
4.2.2 General Specifications for GeneXpert R2 Instruments . . . . . . . 4-2
4.3 Operational Environmental Parameters . . . . . . . . . . . . . . . . . . . . . . . . 4-3
4.4 Environmental Conditions - Storage and Transport . . . . . . . . . . . . . . . 4-3
4.5 Sound Pressure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.6 European Union Directives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-4
4.7 Product Energy Consumption Information . . . . . . . . . . . . . . . . . . . . . . 4-4
5 Operating Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1

5.1 Typical Workflow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1
5.2 Getting Started . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
5.2.1 Powering the Instrument On and Off . . . . . . . . . . . . . . . . . . . . 5-2
5.2.2 Turning On The Computer . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
5.2.3 Starting the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5
5.2.3.1 Database Management Reminder . . . . . . . . . . . . . . . . . . . . .5-6
5.2.3.2 Archive Overdue Reminder . . . . . . . . . . . . . . . . . . . . . . . . . .5-8
5.2.4 Logging On with Software Running . . . . . . . . . . . . . . . . . . . . . 5-9
5.2.5 Logging Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
5.2.6 Changing Your Password . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
5.3 Using the System Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
5.4 Checking the List of Available Assay Definitions . . . . . . . . . . . . . . . . 5-13
5.5 Barcode Scanner Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
5.6 Creating a Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
5.7 Loading a Cartridge into an Instrument Module . . . . . . . . . . . . . . . . . 5-24
5.8 Starting the Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
5.9 Monitoring the Test Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-27
5.10 Stopping a Test in Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28
5.11 Viewing the Test Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-29
5.11.1 Displaying the Test Results . . . . . . . . . . . . . . . . . . . . . . . . . . 5-29
5.11.2 Basic User View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-31
5.11.2.1 Results Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-31
5.11.2.2 Errors Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-33
5.11.2.3 Support Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-34

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5.11.3 Detail User and Administrator View . . . . . . . . . . . . . . . . . . . . 5-35

5.11.3.1 Test Result Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-36
5.11.3.2 Analyte Result Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-37
5.11.3.3 Detail Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-38
5.11.3.4 Errors Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-40
5.11.3.5 History Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-41
5.11.3.6 Support Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-42
5.12 Editing the Test Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-43
5.13 Generating Test Result Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-47
5.14 Exporting the Test Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-52
5.15 Uploading Test Results to the Host . . . . . . . . . . . . . . . . . . . . . . . . . . 5-58
5.16 Managing the Test Results Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-58
5.16.1 Archiving the Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-59
5.16.2 Retrieving Data from an Archive File . . . . . . . . . . . . . . . . . . . 5-61
5.17 Performing Database Management Tasks . . . . . . . . . . . . . . . . . . . . . 5-63
5.17.1 Backing up the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-63
5.17.2 Restoring the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-65
5.17.3 Compacting the Database . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-68
5.17.4 Checking the Integrity of the Database . . . . . . . . . . . . . . . . . 5-69
5.18 Purging Tests from the Database. . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-70
5.19 Viewing and Printing Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-70
5.19.1 Specimen Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-71
5.19.2 Patient Report (If Enabled) . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-74
5.19.3 Patient Trend Report (If Enabled). . . . . . . . . . . . . . . . . . . . . . 5-76
5.19.4 Control Trend Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-80
5.19.5 System Log. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-80
5.19.6 Assay Statistics Report. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-80
5.19.7 Installation Qualification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-83
5.20 Operating with Host Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-83
5.20.1 Creating a Test with Host Connectivity. . . . . . . . . . . . . . . . . . 5-83
5.20.1.1 Creating a Test by Selecting from a List of Test Orders
Downloaded by the Host Automatically . . . . . . . . . . . . . . . 5-85
5.20.1.2 Creating a Test by Manually Requesting Test Orders and
Selecting From the List of Test Orders. . . . . . . . . . . . . . . . 5-86
5.20.1.3 Creating a Test by Querying the Host with Sample ID . . . . 5-87
5.20.1.4 Aborting a Query . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-88
5.20.1.5 Deleting a Host Downloaded Test Order . . . . . . . . . . . . . . 5-89
5.20.2 Uploading a Test Result to the Host . . . . . . . . . . . . . . . . . . . . 5-90
5.20.2.1 Automatically Uploading the Test Result to the Host . . . . . 5-90
5.20.2.2 Manually Uploading a Test Result to the Host . . . . . . . . . . 5-91
5.20.2.3 Uploading an External Control Result to the Host . . . . . . . 5-93

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5.20.3 Troubleshooting Host Connectivity . . . . . . . . . . . . . . . . . . . . . 5-93

5.21 Operating with Cepheid Link Connectivity . . . . . . . . . . . . . . . . . . . . . 5-94
5.21.1 Scanning a Sample and Cartridge using Cepheid Link . . . . . 5-94
5.21.2 Running Cartridges Scanned from Cepheid Link . . . . . . . . . 5-103
5.22 System Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-106
6 Calibration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1

6.1 Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.2 Quality Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
6.3 External Quality Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
6.4 Qualitative Assays vs. Quantitative Assays . . . . . . . . . . . . . . . . . . . . . 6-2
6.5 Control Trend Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
7 Operational Precautions and Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

7.1 Security Precautions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.2 Laboratory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1
7.3 Instrument and Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.4 Assay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
7.5 Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
8 Hazards . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.1 General Safety Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1
8.2 Precautionary Statements Used in this Manual . . . . . . . . . . . . . . . . . . 8-1
8.3 Moving the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3
8.4 Safety Labels on the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-3
8.5 Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-4
8.6 Chemical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-4
8.7 Biological Hazard Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-5
8.8 Environmental Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-5
9 Service and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

9.1 Maintenance Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-2
9.2 Maintenance Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-2
9.3 Power Down the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-4
9.4 Guidelines for Cleaning and Disinfecting . . . . . . . . . . . . . . . . . . . . . . . 9-4
9.5 Cleaning the Work Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-4
9.6 Close Module Doors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-5
9.7 Discard Used Cartridges. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-5
9.8 Cleaning the Instrument Surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-5
9.8.1 Quarterly Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-6

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9.8.2 In Case of Spill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-6

9.9 Cleaning the Plunger Rods and Cartridge Bays. . . . . . . . . . . . . . . . . . 9-7
9.10 Cleaning and Replacing the Fan Filters . . . . . . . . . . . . . . . . . . . . . . . 9-11
9.10.1 GX-II and GX-IV Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . . . 9-11
9.10.2 User-Serviceable GX-II and GX-IV Fan Filters . . . . . . . . . . . . 9-11
9.10.3 GeneXpert GX-XVI Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . 9-14
9.10.3.1 Procedure to Clean and Replace GX-XVI R1
Fan Filters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-14
9.10.3.2 Procedure to Clean and Replace GX-XVI R2
Fan Filters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-17
9.10.4 High Efficiency (HE) Filter Replacement Instructions . . . . . . . 9-20
9.11 Annual Instrument Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-24
9.12 Using Module Reporters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-25
9.13 Performing a Manual Self-Test. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-25
9.14 Excluding Modules from Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-27
9.15 Generating the System Log Report . . . . . . . . . . . . . . . . . . . . . . . . . . 9-29
9.16 Replacing Instrument Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-32
9.17 Repairing the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-32
9.18 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-33
9.18.1 Hardware Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-33
9.18.2 Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-34
9.18.2.1 Run-Time Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-36
9.18.2.2 Operation Terminated Errors . . . . . . . . . . . . . . . . . . . . . . . 9-39
9.18.2.3 Cartridge Loading Errors . . . . . . . . . . . . . . . . . . . . . . . . . . 9-42
9.18.2.4 Self-Test Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-43
9.18.2.5 Post-Run Analysis Errors . . . . . . . . . . . . . . . . . . . . . . . . . . 9-45
9.18.2.6 Communication Loss/Recovery Errors . . . . . . . . . . . . . . . . 9-48
9.18.3 Troubleshooting Host Connectivity . . . . . . . . . . . . . . . . . . . . . 9-49
9.18.3.1 Host Connectivity Indicator. . . . . . . . . . . . . . . . . . . . . . . . . 9-49
9.18.3.2 Host Communication Buffer . . . . . . . . . . . . . . . . . . . . . . . . 9-50
9.18.4 Troubleshooting the LIS Interface . . . . . . . . . . . . . . . . . . . . . 9-50
A Quick Reference. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1
B Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . B-1
C GeneXpert Dx Software International Configuration Instructions. . . . . . . C-1

C.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-1
C.2 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-1
C.3 Before You Begin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-1
C.4 Windows 7 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-2
C.4.1 Configuring the Windows 7 Language Setting . . . . . . . . . . . . . C-2

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C.4.2 Configuring the Keyboard - Windows 7 . . . . . . . . . . . . . . . . . . C-5

C.4.3 Configuring the Windows 7 Welcome Screen
Keyboard Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-9
C.4.4 Windows Login Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-12
C.5 Configuring and Testing the Barcode Scanner. . . . . . . . . . . . . . . . . . C-13
C.5.1 Configuring the Symbol Model DS6708 Scanner . . . . . . . . . . C-13
C.5.2 Configuring the JADAK Model JDK-2201 Scanner. . . . . . . . . C-14
C.5.3 Testing the Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-15
C.6 Date and Time Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-17
D Apache OpenOffice (AOO)

Initial Configuration Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D-1
D.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D-1
D.2 Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . D-1

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301-0045, Rev. K August 2016
List of Figures
Figure 1-1 GeneXpert GX-I Hardware Components (Shown with the
Desktop Computer) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3
Figure 1-2 GeneXpert GX-II Hardware Components (Shown with the
Figure 1-3 GeneXpert GX-IV Hardware Components (Shown with the
Figure 1-4 GeneXpert GX-XVI Hardware Components (Shown with the
Figure 1-5 GeneXpert Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5
Figure 1-6 The GeneXpert Dx Software Features . . . . . . . . . . . . . . . . . . . . . 1-6
Figure 1-7 GeneXpert Dx System Window and the Typical Test Workflow . . 1-8
Figure 2-1 Connecting the GX-I Instrument to the Computer . . . . . . . . . . . . . 2-5
Figure 2-2 Connecting the GX-II Instrument to the Computer . . . . . . . . . . . . 2-5
Figure 2-3 Connecting the GX-IV Instrument to the Computer . . . . . . . . . . . . 2-6
Figure 2-4 Connecting the GX-XVI Instrument to the Computer. . . . . . . . . . . 2-6
Figure 2-5 Connecting Multiple GX-IV Instruments to the Computer . . . . . . . 2-8
Figure 2-6 Windows Account Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
Figure 2-7 Windows Password Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-10
Figure 2-8 GeneXpert Dx System Shortcut Icon. . . . . . . . . . . . . . . . . . . . . . 2-10
Figure 2-9 All Control Panel Items Window . . . . . . . . . . . . . . . . . . . . . . . . . 2-12
Figure 2-10 Power Options Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Figure 2-11 Edit Plan Settings Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
Figure 2-12 Power Options—Advance settings Window . . . . . . . . . . . . . . . . 2-14
Figure 2-13 Power Options Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
Figure 2-14 System Settings Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-15
Figure 2-15 Date and Time Properties Dialog Box . . . . . . . . . . . . . . . . . . . . . 2-16
Figure 2-16 Date and Time Settings Dialog Box. . . . . . . . . . . . . . . . . . . . . . . 2-16
Figure 2-17 Time Zone Settings Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . 2-17
Figure 2-18 All Control Panel Items Window - Category View . . . . . . . . . . . . 2-18
Figure 2-19 Network and Sharing Center Screen . . . . . . . . . . . . . . . . . . . . . . 2-18
Figure 2-20 Network Connections Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-19
Figure 2-21 Network Connections Screen with Drop-Down Menu . . . . . . . . . 2-19
Figure 2-22 GeneXpert Connection Properties Screen . . . . . . . . . . . . . . . . . 2-20
Figure 2-23 GeneXpert Connection Properties Screen . . . . . . . . . . . . . . . . . 2-20
GeneXpert Dx System Operator Manual LOF-1

301-0045, Rev. K August 2016
List of Figures
Figure 2-24 Internet Protocol Version 4 (TCP/IPv4) Properties Screen . . . . . 2-21

Figure 2-25 GeneXpert Dx System Shortcut Icon . . . . . . . . . . . . . . . . . . . . . . 2-22
Figure 2-26 GeneXpert Dx System Window . . . . . . . . . . . . . . . . . . . . . . . . . . 2-23
Figure 2-27 GeneXpert Dx System Window with Assign Instrument Letter
Dialog Box Overlay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-24
Figure 2-28 GeneXpert Dx System Window with Database Management
Figure 2-30 GeneXpert Dx System Window, showing the Setup Drop-
Down Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-27
Figure 2-32 GeneXpert Dx System Window with Change Letter Dialog
Box Overlay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-28
Figure 2-34 GeneXpert Dx System Window showing User Drop-Down
Menu and Exit Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-29
Figure 2-35 GeneXpert Dx System Window at System Restart . . . . . . . . . . . 2-30
Figure 2-36 Quadrant Assigned Letters (GX-XVI Shown) . . . . . . . . . . . . . . . 2-31
Figure 2-38 GeneXpert Dx System Window with Database Management
Figure 2-40 GeneXpert Dx System Window showing Setup Drop-
Down Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-34
Figure 2-42 GeneXpert Dx System Window with Change Letter Dialog
Box Overlay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-35
Figure 2-44 GeneXpert Dx System Window showing User Drop-Down
Menu and Exit Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-37
Figure 2-45 GeneXpert Dx System Window showing New Module
Letter Assignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-38
Figure 2-46 User Administration Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . 2-42
Figure 2-47 Add User Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-43
Figure 2-48 Edit User Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-43
LOF-2 GeneXpert Dx System Operator Manual

301-0045, Rev. K August 2016
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Figure 2-49 User Administration Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . 2-44

Figure 2-50 User Administration Dialog Box selecting User to
be Removed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-44
Figure 2-51 User Admin Dialog Box after User Removal . . . . . . . . . . . . . . . . 2-45
Figure 2-52 System Configuration Dialog Box (General Tab). . . . . . . . . . . . . 2-46
Figure 2-53 System Configuration Dialog Box (Archive Settings Tab) . . . . . . 2-49
Figure 2-54 System Configuration Dialog Box (Folders Tab) . . . . . . . . . . . . . 2-50
Figure 2-55 System Configuration Dialog Box (Host Communication
Settings Tab) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-52
Figure 2-56 Host Communication Settings Workspace Configured for
Cepheid Link . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-55
Figure 2-57 Define Test Code Dialog Box for a Single-Result Assay . . . . . . . 2-57
Figure 2-58 Define Test Code Dialog Box for a Multi-Result Assay . . . . . . . . 2-58
Figure 2-59 GeneXpert Dx System Window showing Reports Drop-Down
Menu and Installation Qualification Selection . . . . . . . . . . . . . . . 2-59
Figure 2-60 Example Installation Qualification Report - Page 1 . . . . . . . . . . . 2-61
Figure 2-61 Example Installation Qualification Report - Page 2 . . . . . . . . . . . 2-62
Figure 2-62 System - Define Assays Window (Detail User View). . . . . . . . . . 2-64
Figure 2-63 Import Assay Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-65
Figure 2-64 GeneXpert Dx System - Define Assays Window
(Administrator User View) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-66
Figure 2-65 Define Assays Window, showing Need Lot Specific
Parameters Box Checked . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-67
Figure 2-66 Reagent Lot Specific Parameters Dialog Box . . . . . . . . . . . . . . . 2-68
Figure 2-67 Import Reagent Lot Specific Parameters Dialog Box . . . . . . . . . 2-69
Figure 2-68 Test Archive Reminder Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 2-70
Figure 2-69 Select Test(s) To Be Archived Screen. . . . . . . . . . . . . . . . . . . . . 2-71
Figure 2-70 Database Management Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 2-72
Figure 3-1 Example PCR Cycle Diagram for I-CORE Module Heating
and Fan Cooling (Temperature Durations not to Scale) . . . . . . . . 3-2
Figure 3-2 GeneXpert Cartridge Components . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Figure 3-3 I-CORE Module (6-Color Module Shown) . . . . . . . . . . . . . . . . . . . 3-5
Figure 3-4 Amplification Curve and Cycle Threshold (Ct). . . . . . . . . . . . . . . . 3-7
Figure 5-1 Windows Account Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
Figure 5-2 Windows Password Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4
Figure 5-3 GeneXpert Dx System Shortcut Icon. . . . . . . . . . . . . . . . . . . . . . . 5-5
Figure 5-4 Login Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5

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List of Figures
Figure 5-5 GeneXpert Dx System Window . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6

Figure 5-6 Database Management Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Figure 5-7 Database Management Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Figure 5-8 Test Archive Reminder Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Figure 5-9 Select Test(s) To Be Archived Screen . . . . . . . . . . . . . . . . . . . . . . 5-8
Figure 5-10 User Menu (Login) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Figure 5-11 User Menu (Logout) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Figure 5-12 User Menu (Change Password) . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Figure 5-13 Change Password Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Figure 5-15 GeneXpert Dx System - Define Assays Window . . . . . . . . . . . . . 5-14
Figure 5-16 Scanning a Cartridge Barcode . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
Figure 5-17 Create Test Window and Scan Patient ID Barcode
Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Figure 5-18 Create Test Window and Scan Sample ID Barcode
Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
Figure 5-19 Scan Cartridge Barcode Dialog Box . . . . . . . . . . . . . . . . . . . . . . 5-19
Figure 5-20 GeneXpert Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
Figure 5-21 Create Test Dialog Box with the Patient ID and Sample ID
Fields Shown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
Figure 5-22 Create Test Dialog Box with the Date of Birth Field and
Calendar Shown. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
Figure 5-23 Create Test Dialog Box with the Ethnicity Field Shown . . . . . . . . 5-22
Figure 5-24 Create Test Dialog Box with the Gender Field Shown . . . . . . . . . 5-23
Figure 5-25 Cartridge Showing Body and Reaction Tube . . . . . . . . . . . . . . . . 5-24
Figure 5-26 Create Test Dialog Box, Ready to Start Test . . . . . . . . . . . . . . . . 5-25
Figure 5-27 GeneXpert Cartridge, Positioned at the Heel of the Module
Bay Floor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-26
Figure 5-28 GeneXpert Dx System Window, Displaying the Status of a
Run in Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-27
Figure 5-29 Stop Test Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-28
Figure 5-30 GeneXpert Dx View Results Window (Detail and
Administrator View) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-30
Figure 5-31 Select Test to be Viewed Dialog Box . . . . . . . . . . . . . . . . . . . . . . 5-30
Figure 5-32 GeneXpert Dx View Results Window—Results Tab
(Basic Users View) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-31
Figure 5-33 GeneXpert Dx View Results Window—Errors Tab
(Basic Users View) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-33

301-0045, Rev. K August 2016
List of Figures
Figure 5-34 GeneXpert Dx View Results Window—Support Tab

(Basic Users View) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-34
Figure 5-35 GeneXpert Dx View Results Window—Test Result Tab
(Detail Users and Administrator View). . . . . . . . . . . . . . . . . . . . . 5-36
Figure 5-36 GeneXpert Dx View Results Window —Analyte Result Tab
Figure 5-37 GeneXpert Dx View Results Window—Detail Tab
Figure 5-38 GeneXpert Dx System - View Results Window—Errors Tab
Figure 5-39 GeneXpert Dx View Results Window—History Tab
Figure 5-40 GeneXpert Dx View Results Window—Support Tab
Figure 5-41 GeneXpert Dx View Results Window (Detail Users and
Administrator View) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-44
Figure 5-42 GeneXpert Dx System, View Results Window— (Detail Users
and Administrator View). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-44
Figure 5-43 GeneXpert Dx View Results Window, History Tab Selected . . . . 5-45
Figure 5-44 GeneXpert Dx View Results Window—Test Type Changed . . . . 5-45
Figure 5-45 Save Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-46
Figure 5-46 History Tab showing Change from Specimen to Negative
Control Test Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-46
Figure 5-47 Test Report Dialog Box (Detail User and Administrator Only). . . 5-47
Figure 5-48 Select Analyte Result Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 5-48
Figure 5-49 Example Test Report – Page 1 . . . . . . . . . . . . . . . . . . . . . . . . . . 5-50
Figure 5-50 Example Test Report – Page 2 . . . . . . . . . . . . . . . . . . . . . . . . . . 5-51
Figure 5-51 Export Data Dialog Box (Detail Users and
Administrator Only) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-52
Figure 5-52 Result Export Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-53
Figure 5-53 Opening a .csv File to Configure AOO (Example) . . . . . . . . . . . . 5-54
Figure 5-54 Text Import Screen with New Settings Selected . . . . . . . . . . . . . 5-55
Figure 5-55 All Cells Selected. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-56
Figure 5-56 Drop-Down Menu to select Column Width. . . . . . . . . . . . . . . . . . 5-56
Figure 5-57 Column Width Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-57
Figure 5-58 Example Exported Test Results . . . . . . . . . . . . . . . . . . . . . . . . . 5-57
Figure 5-59 Upload Test Results to the Host . . . . . . . . . . . . . . . . . . . . . . . . . 5-58
Figure 5-60 Select Test(s) To Be Archived Dialog Box. . . . . . . . . . . . . . . . . . 5-59
Figure 5-61 Select Test(s) to Be Retrieved Dialog Box . . . . . . . . . . . . . . . . . 5-62

301-0045, Rev. K August 2016
List of Figures

Figure 5-63 Database Management Window . . . . . . . . . . . . . . . . . . . . . . . . . 5-64
Figure 5-64 Backup File Naming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-64
Figure 5-65 Backup Completed Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-65
Figure 5-66 Database Management Window . . . . . . . . . . . . . . . . . . . . . . . . . 5-65
Figure 5-67 Database Restore Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-66
Figure 5-68 Database Backup Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-66
Figure 5-69 Backup Completed Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-67
Figure 5-70 Select File to Restore the Database Screen, with Filename . . . . 5-67
Figure 5-71 Database Restore Confirmation Dialog Box . . . . . . . . . . . . . . . . 5-67
Figure 5-72 Database Restore Completed Confirmation Screen . . . . . . . . . . 5-68
Figure 5-73 Compact Database Confirmation Dialog Box. . . . . . . . . . . . . . . . 5-68
Figure 5-74 Compact Database Completed Dialog Box . . . . . . . . . . . . . . . . . 5-68
Figure 5-75 Check Database Integrity Confirmation Dialog Box . . . . . . . . . . . 5-69
Figure 5-76 Check Database Integrity Completed Dialog Box . . . . . . . . . . . . 5-69
Figure 5-77 GeneXpert Dx System Window—Reports Drop-Down Menu . . . 5-71
Figure 5-78 Specimen Report Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-72
Figure 5-79 Example Specimen Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-73
Figure 5-80 Patient Report Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-74
Figure 5-81 Example Patient Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-75
Figure 5-82 Patient Trend Report Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . 5-76
Figure 5-83 Example Patient Trend Report (Page 1) . . . . . . . . . . . . . . . . . . . 5-78
Figure 5-84 Example Patient Trend Report (Page 2) . . . . . . . . . . . . . . . . . . . 5-79
Figure 5-85 Assay Statistics Report Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 5-80
Figure 5-86 Example Assay Statistics Report . . . . . . . . . . . . . . . . . . . . . . . . . 5-82
Figure 5-87 Create Test Window with Host Test Order Table. . . . . . . . . . . . . 5-84
Figure 5-88 Automatic Test Order Download Selected . . . . . . . . . . . . . . . . . . 5-85
Figure 5-89 Menu Bar Indicating Plus Sign on Create Test Button . . . . . . . . . 5-85
Figure 5-90 Host Query Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-87
Figure 5-91 Create Test Window showing the Abort Query Button. . . . . . . . . 5-88
Figure 5-92 Deleting a Host Download Test Order . . . . . . . . . . . . . . . . . . . . . 5-89
Figure 5-93 Automatic Result Upload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-90
Figure 5-94 Host Upload Shown in the Test Information Area of the
View Result Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-91
Figure 5-95 Select Test(s) to be Uploaded to the Host Window . . . . . . . . . . . 5-92
Figure 5-96 Cepheid Link Scanner Login Screen . . . . . . . . . . . . . . . . . . . . . . 5-95

301-0045, Rev. K August 2016
List of Figures
Figure 5-97 Cepheid Link Scan Sample Screen . . . . . . . . . . . . . . . . . . . . . . . 5-96

Figure 5-98 Cepheid Link Scanner Success (Green Check Mark) Screen. . . 5-96
Figure 5-99 Cepheid Link Scanner Error (Order Not Found
(Red X)) Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-97
Figure 5-100 Sample ID Manual Barcode Entry . . . . . . . . . . . . . . . . . . . . . . . . 5-97
Figure 5-101 Cepheid Link Scan Cartridge Screen . . . . . . . . . . . . . . . . . . . . . 5-98
Figure 5-102 Cepheid Link Scanned Cartridge Information Screen . . . . . . . . . 5-99
Figure 5-103 Cepheid Link Scanned Cartridge Error Screen . . . . . . . . . . . . . 5-100
Figure 5-104 Cepheid Link Scan Aliquot Screen . . . . . . . . . . . . . . . . . . . . . . 5-100
Figure 5-105 Cepheid Link Confirmation Screen . . . . . . . . . . . . . . . . . . . . . . 5-101
Figure 5-106 Cepheid Link Scanner Drop Down Menu . . . . . . . . . . . . . . . . . 5-102
Figure 5-107 Cepheid Link Scanner Logout Dialog . . . . . . . . . . . . . . . . . . . . 5-102
Figure 5-108 GeneXpert Dx Home Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-103
Figure 5-109 Orders Table with Scan Cartridge Barcode Overlay Screen . . . 5-104
Figure 5-110 Create Test Screen, showing Cartridge Query Completed . . . . 5-105
Figure 5-111 GeneXpert Home Screen, showing the Cartridge
Loading Message . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-106
Figure 5-112 GeneXpert Dx System—About Drop-Down Menu. . . . . . . . . . . 5-107
Figure 5-113 About GeneXpert Dx System Window. . . . . . . . . . . . . . . . . . . . 5-108
Figure 6-1 GeneXpert Dx System Screen Displaying Reports Menu . . . . . . . 6-3
Figure 6-2 Control Trend Report Dialog Box Showing Qualitative
Assay Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Figure 6-3 Select Analytes Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
Figure 6-4 Control Trend Report Dialog Box Showing Quantitative
Assay Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-6
Figure 6-5 Customize Graph Limits Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 6-6
Figure 6-6 Generate Report File Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . 6-7
Figure 6-7 Example Control Trend Report in the Adobe Reader Window . . . 6-8
Figure 6-8 Control Trend Report Qualitative Assay Example
(C. difficile G2), Page 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-9
Figure 6-9 Control Trend Report Qualitative Assay Example
(C. difficile G2) Page 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-10
Figure 6-10 Control Trend Report Quantitative Assay Example
(HIV-1 Viral Load), Page 1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-11
Figure 6-11 Control Trend Report Quantitative Assay Example
(HIV-1 Viral Load), Page 2. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-12
Figure 9-1 Maintenance Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-3
Figure 9-2 GeneXpert Dx System Window . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-8

301-0045, Rev. K August 2016
List of Figures
Figure 9-3 The Plunger Rod Maintenance Dialog Box . . . . . . . . . . . . . . . . . . 9-8

Figure 9-4 Plunger Rod Cleaning Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . 9-9
Figure 9-5 Plunger Rod Lowered into Cartridge Bay. . . . . . . . . . . . . . . . . . . . 9-9
Figure 9-6 Old-Style Filters (Not User-Serviceable) . . . . . . . . . . . . . . . . . . . 9-11
Figure 9-7 GeneXpert GX-II and GeneXpert GX-IV Instruments
Positioned for Access to Fans . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-12
Figure 9-8 Removing Fan Filter Guard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-13
Figure 9-9 Filter Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-13
Figure 9-10 Installing the Fan Filter Guard . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-14
Figure 9-11 GeneXpert GX-XVI R1 Instrument Positioned for
Access to Fans. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-15
Figure 9-12 Removing Fan Filter Guard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-16
Figure 9-13 Replacement Filter and Guard Installed. . . . . . . . . . . . . . . . . . . . 9-16
Figure 9-14 GeneXpert GX-XVI R2 Fan Filters . . . . . . . . . . . . . . . . . . . . . . . . 9-17
Figure 9-15 Removing the Fan Filter Guard and Filter . . . . . . . . . . . . . . . . . . 9-18
Figure 9-16 Replacing the Filter and Guard . . . . . . . . . . . . . . . . . . . . . . . . . . 9-19
Figure 9-17 GX-IV Instrument Positioned for Access to Filter . . . . . . . . . . . . . 9-20
Figure 9-18 Removing the Prefilter Retainer . . . . . . . . . . . . . . . . . . . . . . . . . . 9-21
Figure 9-19 Removing the Prefilter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-21
Figure 9-20 Removing the HE Filter Retainer . . . . . . . . . . . . . . . . . . . . . . . . . 9-22
Figure 9-21 Removing the HE Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-22
Figure 9-22 Replacing the HE Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-23
Figure 9-23 Replacing the HE Filter Retainer . . . . . . . . . . . . . . . . . . . . . . . . . 9-23
Figure 9-24 Replacing the Prefilter and the Prefilter Retainer . . . . . . . . . . . . . 9-24
Figure 9-25 Module Reporters Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-25
Figure 9-26 Module Self-Test Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-26
Figure 9-27 Self-Test Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-26
Figure 9-29 Exclude Modules From Test Dialog Box . . . . . . . . . . . . . . . . . . . 9-28
Figure 9-30 System Log Report Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-29
Figure 9-31 An Example of a System Log Report . . . . . . . . . . . . . . . . . . . . . . 9-31
Figure 9-32 GeneXpert Dx System - Check Status Window . . . . . . . . . . . . . . 9-35
Figure 9-33 GeneXpert Dx System - View Results Window - Errors Tab
(Detail Users and Administrator View) . . . . . . . . . . . . . . . . . . . . . 9-36
Figure 9-34 Check Status Button Normal (Check Mark Symbol) . . . . . . . . . . 9-49
Figure 9-35 Check Status Button Symbol Changed to X and
Messages Displayed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-49

301-0045, Rev. K August 2016
List of Figures
Figure 9-36 Upload Result To Host Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 9-50

Figure C-1 Control Panel Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-2
Figure C-2 Clock, Language, and Region Window . . . . . . . . . . . . . . . . . . . . . C-3
Figure C-3 Region and Language Window - Formats Tab . . . . . . . . . . . . . . . C-3
Figure C-4 Region and Language Screen - Language Selected. . . . . . . . . . . C-4
Figure C-5 Region and Language Screen with the New
Language Displayed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-5
Figure C-6 Region and Language Drop-Down Window . . . . . . . . . . . . . . . . . C-6
Figure C-7 Region and Language and Text Services and Input
Languages Screens. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-6
Figure C-8 Add Input Language Screen with French Selected (Example) . . . C-7
Figure C-9 The Add Input Languages Window with all Entries . . . . . . . . . . . . C-7
Figure C-10 Text Services and Region and Language Screen -
General Tab. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-8
Figure C-11 Region and Language Screen - Keyboards and
Languages Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-8
Figure C-12 Control Panel Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-9
Figure C-13 Clock, Language, and Region Window . . . . . . . . . . . . . . . . . . . . . C-9
Figure C-14 Region and Language Drop-Down Window - Formats Tab. . . . . C-10
Figure C-15 Region and Language Screen - Administrative Tab . . . . . . . . . . C-10
Figure C-16 Welcome Screen and New User Account Settings Screen . . . . . C-11
Figure C-17 Windows 7 Login Screen Showing Two-Country Designation. . . C-12
Figure C-18 Drop-Down Language Menu - Welcome Screen (Windows 7) . . C-12
Figure C-19 Barcode 1: *HID Keyboard Emulation . . . . . . . . . . . . . . . . . . . . . C-13
Figure C-20 Barcode 2: *North American Standard USB Keyboard . . . . . . . . C-13
Figure C-21 Barcode 3: Enable Keypad Emulation . . . . . . . . . . . . . . . . . . . . . C-14
Figure C-22 Barcode 4: Enable Keypad Emulation with Leading Zero . . . . . . C-14
Figure C-23 Barcode 5: Enable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-14
Figure C-24 International Configuration Barcode . . . . . . . . . . . . . . . . . . . . . . C-14
Figure C-25 North American Configuration Barcode . . . . . . . . . . . . . . . . . . . . C-15
Figure C-26 French Sample Barcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-15
Figure C-27 Italian Sample Barcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-15
Figure C-28 German Sample Barcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-16
Figure C-29 Portuguese Sample Barcode. . . . . . . . . . . . . . . . . . . . . . . . . . . . C-16
Figure C-30 Spanish Sample Barcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-16
Figure C-31 Chinese Sample Barcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-16
Figure C-32 Russian Sample Barcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-17

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List of Figures
Figure C-33 Japanese Sample Barcode . . . . . . . . . . . . . . . . . . . . . . . . . . . . .C-17

Figure D-1 Opening a .csv File to Configure AOO (Example) . . . . . . . . . . . . .D-1
Figure D-2 AOO Registration Screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D-2
Figure D-3 Text Import Screen, showing Default Settings . . . . . . . . . . . . . . . .D-3
Figure D-4 Text Import Screen with New Settings Selected . . . . . . . . . . . . . .D-4
Figure D-5 All Cells Selected . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D-4
Figure D-6 Drop-Down Menu to select Column Width . . . . . . . . . . . . . . . . . . .D-5
Figure D-7 Column Width Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D-5
Figure D-8 Final View of File with Columns Adjusted . . . . . . . . . . . . . . . . . . .D-6
Figure D-9 Format Saving Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .D-6

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List of Tables
Table 1-1 Workflow for Installing and Setting Up the System . . . . . . . . . . . .1-7
Table 1-2 Typical Test Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-7
Table 2-1 Example User Permission Policy for In Vitro Diagnostic Use . . .2-39
Table 2-2 User Task Descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-40
Table 3-1 GeneXpert Module Excitation and Emission Ranges
(6-Color Shown). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-8
Table 4-1 Dimensions and Weight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-2
Table 4-2 Rated Current and Fuse Rating . . . . . . . . . . . . . . . . . . . . . . . . . . .4-2
Table 4-3 Dimensions and Weight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-2
Table 4-4 Rated Current and Fuse Rating . . . . . . . . . . . . . . . . . . . . . . . . . . .4-3
Table 5-1 Typical Workflow for Processing a Specimen . . . . . . . . . . . . . . . .5-2
Table 8-1 Electrical Safety Labels on the Instruments. . . . . . . . . . . . . . . . . .8-3
Table 8-2 Other Safety Labels on the Instruments . . . . . . . . . . . . . . . . . . . .8-3
Table 9-1 Maintenance Tasks and Frequency. . . . . . . . . . . . . . . . . . . . . . . .9-2
Table 9-2 Hardware Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-33
Table 9-3 Errors that Occurred During a Test that is Not Aborted . . . . . . . .9-36
Table 9-4 Errors that Might Appear When a Test is Aborted . . . . . . . . . . . .9-39
Table 9-5 Errors that Might Appear During the Cartridge
Loading Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-42
Table 9-6 Error Messages that Might Appear During the Self-
Test Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-43
Table 9-7 Data Reduction Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9-45
Table 9-8 Communication Loss/Recovery Errors . . . . . . . . . . . . . . . . . . . .9-48
Table 9-9 System Configuration Problems . . . . . . . . . . . . . . . . . . . . . . . . .9-50
Table A-1 User . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1
Table A-2 Data Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1
Table A-3 Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2
Table A-4 Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2
Table A-5 About . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2
Table A-6 Create Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-2
Table A-7 Stop Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-3
Table A-8 View Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-3
Table A-9 Define Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-3
Table A-10 Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-3
GeneXpert Dx System Operator Manual LOT-1

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List of Tables
LOT-2 GeneXpert Dx System Operator Manual

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1 Introduction—Use or Function
This chapter provides an overview of the GeneXpert Dx system. The topics are:
• Section 1.1, Intended Use
• Section 1.2, Terms Used for System Descriptions
• Section 1.3, Models of GeneXpert Instruments
• Section 1.4, System Components
• Section 1.5, GeneXpert Cartridges
• Section 1.6, GeneXpert Dx Software
• Section 1.7, Workflow Overview
• Section 1.8, Before Operating the Instrument
GeneXpert Dx software version 4.8 supports the Microsoft Windows 7 operating system. Should
Note
you need any assistance, please contact your regional Cepheid Technical Support center.
1.1 Intended Use

The GeneXpert Dx system automates and integrates sample preparation, nucleic acid
amplification, and detection of the target sequence in simple or complex samples using
real-time Polymerase Chain Reaction (PCR). The system is suited for in vitro diagnostic
applications that require hands-off processing of patient samples (specimens) and
provides both summarized and detailed test results data in tabular and graphic formats.
The GeneXpert Dx System is designed exclusively for the use of Cepheid Xpert® assay
applications. It allows a laboratory healthcare professional to run tests on the GeneXpert
Dx platform using predefined assays.
1.2 Terms Used for System Descriptions

In this manual, the following terms are used to describe the GeneXpert Dx systems:
• GeneXpert Dx system refers to the complete system including the computer,
GeneXpert instrument and barcode scanner.
• GeneXpert instrument refers only to the components used to process the samples.
See Figure 1-1, Figure 1-2, Figure 1-3 and Figure 1-4 for examples of GeneXpert
instruments.
GeneXpert Dx System Operator Manual 1-1

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Introduction—Use or Function
1.3 Models of GeneXpert Instruments

There are three different GeneXpert R1 instruments:
• The GeneXpert GX-I instrument consists of one module (or one site) to process one
sample. Up to four GeneXpert GX-I instruments can be connected to one computer.
• The GeneXpert GX-IV instrument consists of up to four modules. Each module
processes one sample. Up to four GeneXpert GX-IV instruments can be connected
to one computer.
• The GeneXpert GX-XVI instrument consists of up to sixteen modules. Each module
processes one sample.
There are four different models of GeneXpert R2 instruments:
• The GeneXpert GX-I instrument consists of one module (or one site) to process one
sample. Up to four GeneXpert GX-I instruments can be connected to one computer.
• The GeneXpert GX-II instrument consists of one or two modules. Each module
processes one sample. Up to four GeneXpert GX-II instruments can be connected to
one computer.
• The GeneXpert GX-IV instrument consists of up to four modules. Each module
processes one sample. Up to four GeneXpert GX-IV instruments can be connected
to one computer.
• The GeneXpert GX-XVI instrument consists of up to sixteen modules. Each module
processes one sample. One GeneXpert GX-XVI instrument can be connected to one
computer.
For purposes of this document, the GeneXpert Dx systems function identically and will
not be identified as R1 or R2 unless there is a specific difference noted.
1.4 System Components

The components of the GeneXpert Dx systems are as follows:
• GeneXpert Instrument—Accepts the GeneXpert cartridges that are loaded into the
instrument, lyses the samples in the cartridges, releases the nucleic acids, and
amplifies the target sequences. Because the system allows control of the modules
independently, different samples can be processed using different assay definitions
in the same instrument at the same time.
• Desktop or Laptop Computer—Allows you to run the GeneXpert Dx system
software and hosts the GeneXpert Dx system results database. The software allows
the selection of assay definitions, monitoring of test process, viewing results, and
exporting of selected data to downstream software, such as Microsoft Excel, for
additional analysis. The software also allows the archiving and retrieval of the
results data and management of the database. Cepheid Link connectivity is provided
to enable cartridge traceability.
• Barcode Scanner—Facilitates data entry in the system.
1-2 GeneXpert Dx System Operator Manual

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1.4.1 GeneXpert Dx System Components

GeneXpert GX-I Instrument Desktop Computer Monitor
Barcode Scanner
Figure 1-1. GeneXpert GX-I Hardware Components (Shown with the Desktop Computer)
GeneXpert GX-II Instrument Desktop Computer Monitor
Barcode Scanner
Figure 1-2. GeneXpert GX-II Hardware Components (Shown with the Desktop Computer)

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GeneXpert GX-IV Instrument Desktop Computer Monitor
Barcode Scanner
Figure 1-3. GeneXpert GX-IV Hardware Components (Shown with the Desktop Computer)
GeneXpert GX-XVI Instrument Desktop Computer Monitor
Barcode Scanner
Figure 1-4. GeneXpert GX-XVI Hardware Components (Shown with the Desktop Computer)

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1.5 GeneXpert Cartridges

• The samples are prepared and processed in single-use, assay-specific GeneXpert
cartridges (see Figure 1-5). The sample and applicable reagents are inserted into a
cartridge and then the cartridge is loaded into one of the available instrument
modules.
• The cartridges are not supplied with the system and must be purchased separately.
For ordering information, contact Cepheid. See the Technical Assistance section in
the Preface for the contact information.
Figure 1-5. GeneXpert Cartridge
1.6 GeneXpert Dx Software

The GeneXpert Dx software is installed on the supplied computer and can accommodate
a variety of applications. This section describes the software features that are for in vitro
diagnostic use (Figure 1-6):
• Administrative tasks—Configure the system to accommodate the organization's
preferences, define system users and set up permissions (access privileges), import
and delete in vitro diagnostic assay definitions, generate external control trend
reports, and manage the test data in the database.
• Test tasks—Create and start an in vitro diagnostic test, stop a test in progress,
monitor a test in progress, view the test results, edit test information, and generate
test reports.
• Maintenance tasks—Perform various maintenance tasks which include using the
Module Reporters tool and Plunger controls for cleaning the module plungers,
performing a self-test manually for troubleshooting and checking the calibration and
test counts, and utilizing commands for opening a module door or updating the
EEPROM.
For a summary of the workflows for in vitro diagnostic use, see Section 1.7, Workflow
Overview.

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Test Administration Maintenance
Figure 1-6. The GeneXpert Dx Software Features
1.7 Workflow Overview

The GeneXpert Dx system workflow covers the following tasks:
• Section 1.7.1, Installation and Setup Workflow
• Section 1.7.2, Test Workflow

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1.7.1 Installation and Setup Workflow

Table 1-1 lists the tasks for installing and setting up the GeneXpert Dx system. Note that
although in vitro diagnostic assay definition files can be imported, the GeneXpert Dx
system software does not allow the modification of the assay definitions.
Table 1-1. Workflow for Installing and Setting Up the System
Step Task Section

1. Install the GeneXpert Dx system. Section 2.4
2. Turning on the computer. Section 2.5
3. Start the software. Section 2.8
4. Assign instrument letters. (Optional) Section 2.9
5. Define users and permissions. Section 2.10
6. Configure the system. Section 2.11
7. Verify proper installation and setup. Section 2.12
8. Manage assay definition files. Section 2.13
After the system is installed and running, the following tasks can be performed:
• Add new users (see Section 2.10.3.1, Adding New Users).
• Install additional GeneXpert instruments (see Section 2.4.2, To Install Additional
Instruments).
1.7.2 Test Workflow

Table 1-2 lists the tasks for processing a specimen sample using the GeneXpert Dx
system. Note that although in vitro diagnostic assay definition files can be imported, the
GeneXpert Dx software does not allow modification of the assay definitions (see
Section 1.6, GeneXpert Dx Software). For systems connected to a host, see Section 5.20,
Operating with Host Connectivity for the test workflow.
Table 1-2. Typical Test Workflow
Step Task Section

1. Start the GeneXpert Dx system. Section 5.2
2. Check the list of assays available. Import the assay definition files if Section 5.4 and
necessary. Section 2.13
3. Create a test. Section 5.6
4. Load a cartridge into an instrument module. Section 5.7
5. Start the test. Section 5.8
6. Monitor the test progress. Section 5.9
7. View the test results. Section 5.11
8. Manage the test results data. Section 5.16
9. Maintain the system. Chapter 9

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Figure 1-7 is a graphical overview of the test workflow.

1. Check the list of assays (Section 5.4)
2. Create and start a test (Section 5.6 and Section 5.8)
3. Monitor the test progress (Section 5.9)
4. View the results (Section 5.11)
Figure 1-7. GeneXpert Dx System Window and the Typical Test Workflow
1.8 Before Operating the Instrument

Read the entire manual and become familiar with the safety information in Chapter 8,
Hazards before starting to operate the instrument.
Warning
Using the instrument without reading the manual or without proper training can result in
serious injury, damage to the equipment or loss of data.

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2 Installation Procedures and Special
Requirements
This chapter describes how to install and set up the system. Except when noted, the
procedures in this chapter are for the GeneXpert Dx system administrator or equivalent
personnel. The topics are as follows:
• Section 2.1, GeneXpert Dx System Package Contents
• Section 2.2, Required Materials for Use with the System (But Not Provided)
• Section 2.3, System Notes
• Section 2.4, Installing the GeneXpert Dx System
• Section 2.5, Turning On The Computer
• Section 2.6, Windows Language and Keyboard Configuration
• Section 2.7, Configuring the Computer
• Section 2.8, Starting the Software for the First Time
• Section 2.9, Assigning Instrument Letters
• Section 2.10, Defining Users and Permissions
• Section 2.11, Configuring the System
• Section 2.12, Verifying Proper Installation and Setup
• Section 2.13, Managing Assay Definitions and Lot Specific Parameters
• Section 2.14, Restarting the System
• Section 2.15, Uninstalling or Reinstalling GeneXpert Dx Software
2.1 GeneXpert Dx System Package Contents

• The GeneXpert Dx system package contains the following items:
• GeneXpert instrument
• Desktop or laptop computer, preloaded with the GeneXpert Dx software and other
required software
• Network switch (included if the system has two or more instruments)
• 2D barcode scanner

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Installation Procedures and Special Requirements
• Power cord, type: IEC-320-13, 10A/125V North America or 10A/250V

International for:
• GeneXpert GX-I R1
• GeneXpert GX-IV R1/R2, and
• GeneXpert GX-XVI R1/R2)
• DC Adapter Power cable (for GeneXpert GX-I R2 and GeneXpert GX-II R2)
• CAT-5 Ethernet® crossover cable
• GeneXpert Dx System Operator Manual CD
• Certificate of Compliance
2.2 Required Materials for Use with the System

(But Not Provided)
The following items are required for use with the GeneXpert Dx system but are not
included in the package:
• Assay-specific GeneXpert cartridges
• Assay-specific requirements (refer to the assay package insert or your local and
national regulatory guidelines)
• Surge protector
• Printer
To order the GeneXpert cartridges or printer, contact Cepheid. See the Technical
Assistance section in the Preface for the contact information.
2.3 System Notes

2.3.1 System Components
Cepheid tested and qualified the GeneXpert Dx system components to provide optimal
performance.
Do not alter the computer settings, pre-installed software, and other system components
unless instructed by Cepheid to do so. Do not install non-approved software. Do not replace
Caution
system parts without assistance from Cepheid.
Altering the computer settings, pre-installed software, or other system components without
guidance from Cepheid can result in the loss of data, impact system performance, damage
the instrument, and void your warranty.

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2.3.2 Network Connection

The GeneXpert Dx system computer contains two Ethernet cards. The card that is
configured for the GeneXpert instrument is labeled on the back of the computer. Use
only the supplied Ethernet cable to connect the computer to the instrument. See
Section 2.4.1, To Install a GeneXpert Dx System, for detailed installation instructions.
Caution
Do not change the Internet Protocol (IP) setting for the Ethernet connection to the GeneXpert
Dx system. Changing the IP setting can cause instrument communication failure.
2.3.3 Microsoft Software CDs

Microsoft Windows 7 has been installed and activated on the GeneXpert Dx system
computer. The Microsoft software CDs are included in the computer shipping box.
Store the Microsoft software CDs in a safe place in the original packaging. If you must
reinstall the Microsoft software, the original CDs will be needed. In addition, to reactivate the
Important
software, the product key (located on the Certificate of Authenticity that is on the installation
diskette packaging) will also be needed.
2.4 Installing the GeneXpert Dx System

A 6-color GeneXpert Dx system and modules require software version 2.1 (or above) and a
10-color GeneXpert Dx system and modules require software version 4.7b and above.
Caution
To avoid hardware failures, GeneXpert Dx 2.1 (or above) software must be installed BEFORE
connecting and powering up a 6-color instrument or upgrade modules, and GeneXpert Dx
4.7b (and above) software must be installed BEFORE connecting and powering up a
10-color instrument or upgrade modules.
See the weights table in Section 4.2, General Specifications for GeneXpert instrument
Warning
weights. Use care when unpacking the instrument. Do not attempt to lift the instrument
without proper safety training and assistance. Lifting or moving the instrument without
proper training and assistance can cause personal injury, damage the instrument, and void
your warranty.
Before installing the instrument, read Chapter 4, Performance Characteristics and

Important Specifications and Chapter 7, Operational Precautions and Limitations to become familiar
with the system specifications and requirements.

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2.4.1 To Install a GeneXpert Dx System

The following sections describe the installation of GeneXpert Dx systems.
1. Unpack the system and make sure the package contains the items in Section 2.1.
2. Place the instrument on a hard, sturdy, level surface. Make sure the power cord
connection and the power switch (on the back side) are easily accessible.
Caution
Provide at least 5 cm (2 in) of clearance on each side of the instrument. Do not block the fan
exhaust on the lower back side or the air intake on the upper back side. The lack of proper
ventilation can cause the instrument to malfunction.
3. Connect one end of the supplied Ethernet cable to the network port on the back side
of the computer (depending on the GeneXpert model, see Figure 2-1, Figure 2-2,
Figure 2-3 or Figure 2-4). A label indicates that the port is for use with the
GeneXpert instrument.
Use the supplied Ethernet cable to connect the GeneXpert instrument and the computer. If
the cable is missing or an additional cable is needed, contact Cepheid Technical Support.
Important
See the Technical Assistance section in the Preface for the contact information.
See Section 9.16, Replacing Instrument Parts for the part number.
Caution
Do not change the Internet Protocol (IP) setting for the Ethernet connection to the GeneXpert
instrument. Changing the IP setting can cause an instrument communication failure.
The computer supplied with the GeneXpert instrument should have been set to the correct IP
Note address before it left the factory, but if the computer is not communicating with the instrument,
perform the steps shown in Section 2.7.3, Setting the IP Address.
4. Connect the other end of the Ethernet cable to the network port on the lower back
panel of the instrument (see Figure 2-1, Figure 2-2, Figure 2-3, or Figure 2-4).
5. Connect the supplied power cords (or DC adapter power cable) to the instrument and
the computer, and then connect the power cords to a surge protector.
Caution
Make sure the surge protector is connected to a properly grounded circuit. Using a non-
grounded circuit can cause damage to the instrument.
6. Perform the steps provided in Section 2.5, Turning On The Computer, or if multiple
instruments are being set up, perform the steps provided in Section 2.4.2, To Install
Additional Instruments.

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GX-I Instrument (Back View)
Connect with Supplied Ethernet Cable Power

Switch
Computer (Back View) DC Adapter

Power Cable
Connect to the
Connect to the Surge Protector
Surge Protector
Figure 2-1. Connecting the GX-I Instrument to the Computer
GX-II Instrument (Back View)
Connect with Supplied Ethernet Cable Power

Switch
Computer (Back View)
DC Adapter
Connect to Power Cable
the Surge
Protector
Connect to the
Surge Protector
Figure 2-2. Connecting the GX-II Instrument to the Computer

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GX-IV Instrument (Back View)
Power
Computer (Back View) Switch
Connect to the
Surge Protector
Connect to the
Surge Protector
Connect with Supplied Ethernet Cable
Figure 2-3. Connecting the GX-IV Instrument to the Computer
GX-XVI Instrument (Back View)
Power
Computer (Back View) Switch
Connect to the
Surge Protector
Connect with Supplied Ethernet Cable
Figure 2-4. Connecting the GX-XVI Instrument to the Computer

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2.4.2 To Install Additional Instruments

Caution
Before installing additional instruments, make sure the GeneXpert Dx software is not
running.
A 6-color GeneXpert Dx system and modules require software version 2,1 (or above). and a
10-color GeneXpert Dx system and modules require software version 4.7b and above.
Caution
To avoid hardware failures, GeneXpert Dx 2.1 (or above) software must be installed BEFORE
connecting and powering up a 6-color instrument or upgrade modules, and GeneXpert Dx
4.7b (and above) software must be installed BEFORE connecting and powering up a
10-color instrument or upgrade modules.
Note The computer does not have to be turned off to connect additional instruments.
Up to four GeneXpert GX-I, GeneXpert GX-II, or GeneXpert GX-IV instruments can be

connected to a single computer. In the multiple-instrument setup, connect the computer
to the supplied network switch, and then connect the instruments to the switch. See
Figure 2-5.
1. Unpack the additional instrument(s), power cords, network switch, and Ethernet
cables.
2. If the GeneXpert Dx software is currently running, quit the software.
3. Disconnect the Ethernet cable from the back of the previously installed instrument.
Keep the Ethernet cable connected to the computer.
4. Connect the free end of the Ethernet cable in Step 3 to any of the available ports in
the network switch. The Ethernet cable is used to connect the computer to the
network switch.
5. Using a second Ethernet cable, connect the additional instrument to any available
port in the network switch. One end of the Ethernet cable connects to the network
port on the back of the instrument, and the other end connects to a free port of the
network switch.
6. Repeat Step 5 to connect additional instruments to the network switch.
7. Connect the supplied power cord to the additional instrument, and then connect the
power cord into a surge protector. Repeat this step for each additional instrument.
Note Leave the instruments OFF until the computer is set up.
8. Connect the barcode scanner directly to an available computer USB port. Do not
connect the scanner to a USB hub.
9. Perform the steps given in Section 2.5, Turning On The Computer.

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Instrument Instrument
Power Power
Switch Switch
Computer (Back View)
Connect to the Connect to the Connect to the

Surge Protector Surge Protector Surge Protector
Network Switch
(Back View)
Connect with Supplied Ethernet Cables
Figure 2-5. Connecting Multiple GX-IV Instruments to the Computer
2.5 Turning On The Computer

After the GeneXpert DX system computer has been installed, use the following
procedure to turn the computer on and log onto the computer.
1. Turn on the GeneXpert Dx system computer.
2. Wait for the system to boot. The Windows Account screen will be displayed. See
Figure 2-6.
3. On the Windows Account screen, select the Cepheid user account (see Figure 2-6).
The Windows Password screen will be displayed. See Figure 2-7.
The GeneXpert Dx system computer is configured with two Windows accounts. The
Cepheid-Admin account is for administrator tasks such as software updates, system
configuration and normal operation; and the Cepheid- Techsupport account is for use
only by Cepheid Technical Support See Figure 2-6.
Caution
You must be logged on using the preconfigured account. If you log on using a different user
name and profile, the power management settings will be incorrect.

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Figure 2-6. Windows Account Screen

The initial login password is provided below. You will be required to change the
password upon first login. Do not change the user name or profile settings. When
logging on, use the following:
• Account name: Cepheid-Admin
• Password: cphd
4. On the Windows Password screen (see Figure 2-7), enter the password. The default
password is cphd and must be changed upon initial login (as instructed by the
software). After the password has been changed by the system administrator, enter
the assigned password for future logins.

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Figure 2-7. Windows Password Screen
On the initial login to the GeneXpert system for the Cepheid-Admin account, after entering the
cphd password, a prompt will be immediately displayed to change the password. Follow the on-
screen instructions to change the password. Enter the old password (cphd) for the account then
Note enter the new password two times. Remember to record and store the new password information in
a safe location.
After the first login to the system, there will be no additional prompts to change the password.
Caution
Do not change the Cepheid user profile. Changing the profile can cause loss of data during a
test.
5. The GeneXpert Dx software starts automatically on system startup. A GeneXpert Dx

icon on the Windows desktop allows for manual software initiation. See Figure 2-8.
Figure 2-8. GeneXpert Dx System Shortcut Icon

6. Exit the GeneXpert Dx software by clicking Exit under the File menu.

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2.5.1 Anti-Virus Software

In order to protect the GeneXpert Dx system computer from viruses that could cause
data corruption or disrupt normal functionality, Cepheid strongly recommends installing
and maintaining an updated anti-virus program. Computer viruses can be introduced by
connecting the computer to a local or wide area network or from extracting data using
external memory devices.
Cepheid has validated several commercially available off-the-shelf solutions from
Symantec Corporation, Trend Micro Inc. and McAfee Inc.
If the software is purchased from a commercial supplier, install the software by
following the instructions in the user documentation provided with the software program
chosen. Activation of the anti-virus software is usually accomplished by connecting to
the Internet. Follow the specific activation instructions in the software dialog screens or
documentation.
The computer usually must be connected to the Internet to activate the anti-virus software. Be sure
Note
any updating is scheduled when no data is being collected.
If your institution requires the use of another type of anti-virus software other than the
programs listed above, then the institution is responsible for validating the solutions
compatibility with Cepheid product offerings.
Maintain an active anti-virus subscription and download updates regularly. If the GeneXpert
Dx system computer is used to access the Internet, run anti-virus software before resuming
Important
the use of the GeneXpert Dx software and confirm that the results from the system match the
results output to any connected LIS.
Caution
The GeneXpert Dx system computer is set up to use Windows Firewall so the Windows
firewall can remain turned on. Do not turn on or use other non-Windows firewall products.
Doing so can prevent data collection.
Caution Cepheid tests and qualifies our system components to provide optimal performance. Do not
alter the computer settings, pre-installed software, or other system components unless
instructed by Cepheid. Do not install non-approved software. Do not replace the system
network connection.
2.6 Windows Language and Keyboard Configuration

The computer, as shipped, is configured for the English-language Windows software and
keyboard. However, if language and keyboard settings need to be reconfigured to
another language, refer to Appendix C, GeneXpert Dx Software International
Configuration Instructions.

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2.7 Configuring the Computer

GeneXpert Dx software version 4.8 supports both Microsoft Windows 7 and Windows XP operating
Note systems. Windows XP settings will not be affected when doing a software update. Should you need
any assistance, please contact your regional Cepheid Technical Support center.
In this section, perform the following steps:

• Select the correct computer power management setting to ensure proper operation of
the system. See Section 2.7.1, Selecting the Power Management Settings.
• Set the computer date and time to ensure accurate time-stamping when the system is
in use. See Section 2.7.2, Setting the Local Date and Time.
• Check the IP address settings to ensure the proper operation of the system. See
Section 2.7.3, Setting the IP Address.
2.7.1 Selecting the Power Management Settings

The computer is already configured with the correct power management settings. If it
needs to be reset:
1. On the Windows taskbar, click on the Windows icon.
2. Select Control Panel. If the view is set for Small icons, the All Control Panel Items
window appears as shown in Figure 2-9. Click on Power Options.
Figure 2-9. All Control Panel Items Window

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Figure 2-10. Power Options Window

3. Under the Cepheid Setup - Do Not Alter section, click Change plan settings. See
Figure 2-10. The Edit Plan Settings windows appears. See Figure 2-11.
Figure 2-11. Edit Plan Settings Window

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4. Make sure the Dim the Display, Turn off the display and Put the computer to sleep
features are set to Never for both On battery and Plugged in options. See Figure 2-11.
5. Click on Change advanced power settings (see Figure 2-11). The Power Options
Advance settings window appears. See Figure 2-12.
Figure 2-12. Power Options—Advance settings Window

6. In the Power Options Advance settings window, double-click Sleep to expand the
view, and then double-click Hibernate after. See Figure 2-12.
A. Desktop Computers: Verify that Setting value is set to zero (0) or Never. If not,
change the Setting value to zero (0) or Never.
B. Laptops Only: Verify On battery and Plugged in values are set to Never. If not,
click ON battery and/or Plugged in, and then use the up/down arrow keys to set
their values to zero (0) on the selectable option.
7. Click Apply and then OK to close the Power Options window. The Edit Plan Settings
window reappears.
8. Click Cancel to close the Edit Plan Settings window. The Power Options window is
displayed (see Figure 2-13.
9. Laptops Only: On the Power Options window, click the Choose what closing the lid
does entry. The System Settings window appears (see Figure 2-14). Set the When I
close the lid setting to Do nothing, and set all other settings to Sleep and click Save
Changes.

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Figure 2-13. Power Options Window
Figure 2-14. System Settings Window

10. Laptops Only: Click Cancel to close the Edit Plan Settings window. The Power
Options window is displayed (see Figure 2-10).
11. Click the red X in the upper right-hand corner of the window to exit the Power
Options settings and close the Control Panel window.

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2.7.2 Setting the Local Date and Time

To set date and time, perform the following procedure:
1. Click Control Panel > Date and Time. The Date and Time dialog box appears. See
Figure 2-15.
Figure 2-15. Date and Time Properties Dialog Box

2. Click the Change Date and Time... button. The Date and Time Settings dialog box
appears. See Figure 2-16.
Figure 2-16. Date and Time Settings Dialog Box

3. Set the correct local date and time.
4. Click OK to return to the Date and Time dialog box. See Figure 2-15.

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5. Click the Change Time Zone... button. The Time Zone Settings dialog box appears.
See Figure 2-17.
Figure 2-17. Time Zone Settings Dialog Box

6. Select the correct local time zone and check the Automatically adjust clock for
Daylight Saving Time check box, if applicable.
7. Click OK to close the Time Zone Settings dialog box, and then click OK to close the
Date and Time dialog box.
Caution
Do not change time or date settings when a test is in progress.
2.7.3 Setting the IP Address
To perform the steps in this section, you must either be logged on as Cepheid-Admin or you need
Note
to enter the Cepheid-Admin password.
The computer is already configured with the correct IP address when the GeneXpert Dx
system is shipped. If it needs to be reset:
1. Log onto the system as Cepheid-Admin or enter the Cepheid-Admin password when
requested to do so.
2. On the Windows taskbar, click on the Windows icon.
3. Select Control Panel. If the view is set for Category, the screen appears as shown in
Figure 2-18. Click on View Network Status and Tasks.

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Figure 2-18. All Control Panel Items Window - Category View

4. When the Network and Sharing Center screen appears, as shown in Figure 2-19.
Click on Change adapter settings.
Figure 2-19. Network and Sharing Center Screen

5. The Network Connections screen appears. See Figure 2-20.

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Figure 2-20. Network Connections Screen

6. Right click on the GeneXpert Connection entry. A drop-down menu appears (see
Figure 2-21).
Figure 2-21. Network Connections Screen with Drop-Down Menu

7. Click Properties on the drop-down menu. The screen shown in Figure 2-22 is
displayed.

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Figure 2-22. GeneXpert Connection Properties Screen

8. On the GeneXpert Connection Properties Screen (shown in Figure 2-23) uncheck
the box next to Internet Protocol Version 6 (TCP/IPv6). Highlight Internet Protocol
Version 4 (TCP/IPv4), and then click Properties. The Internet Protocol Version 4
(TCP/IPv4) Properties screen appears.
Figure 2-23. GeneXpert Connection Properties Screen

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Figure 2-24. Internet Protocol Version 4 (TCP/IPv4) Properties Screen

9. On this screen, select Use the following IP address:.
10. Enter:
IP Address: 10 . 11 . 14 . 1
Subnet Mask: 255 . 255 . 255 . 224
11. After you have verified that all numbers are entered correctly, click OK to close the
GeneXpert Connection Properties window.
12. Click Close to close the GeneXpert Connection Properties window.
13. Close the Control Panel window by clicking the X in the upper right corner of the
window.
14. If you were logged into the Cepheid-Admin account at the beginning of this
configuration section, then you must log off that account.

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2.8 Starting the Software for the First Time

Turn on the GeneXpert instrument(s). The small blue light on the front of the instrument
will turn on.
The GeneXpert instrument must be powered up before the GeneXpert software is started. If the
Note
instrument is not powered up first, it will not be recognized by the software.
After installing the system and setting up the computer, the GeneXpert Dx application
software will start automatically upon logging into the Cepheid or Cepheid-Admin user
accounts.
The first time the software starts, a user name and password do not have to be provided.
After defining the administrator profile (see Section 2.10, Defining Users and
Permissions), the software will ask for a user name and password each time the software
is started (see Section 5.2.3, Starting the Software).
As the software is starting, the green light above each module door flashes briefly, then
turns off.
The first time the software starts after installation, an Assign Instrument Letter
confirmation dialog box appears (see Figure 2-26).
After automatic instrument letter assignment, and every time the software starts thereafter, the
GeneXpert Dx System window appears without the Assign Instrument Letter confirmation dialog
Note
box. You will, however, see the assign instrument letter dialog box if you connect a new instrument
and then launch the software.
Whenever you exit the GeneXpert Dx application without powering down the computer, you must
Note
double-click the GeneXpert Dx icon to restart the application.
Important Do not load any new version of Microsoft SQL applications.
1. Start the GeneXpert Dx software:

• On the Windows desktop, double-click the GeneXpert Dx icon (see
Figure 2-25).

or
• On the Windows taskbar, click the Start icon, and select
All Programs >Cepheid >GeneXpert Dx.
The GeneXpert Dx System window appears. See Figure 2-26.

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Figure 2-26. GeneXpert Dx System Window
An update overlay screen may appear, stating Updating module firmware. This updating process
Note
must complete before you can proceed.
2. The Assign Instrument Letter overlay appears, indicating the automatic assigning of
the instrument(s) has completed. To continue, click OK to acknowledge this action
and close the dialog box.
3. After the Assign Instrument Letter box closes, the database management dialog box
(previously hidden by the Assign Instrument Letter overlay) becomes visible. Click
No on the Database Management dialog box to proceed.
Note Since this is the initial startup of the software, there are no database management tasks to perform.

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2.9 Assigning Instrument Letters

2.9.1 To Assign Instrument Letters (GX-I, GX-II and
GX-IV Instruments)
This section describes tasks that only the GeneXpert Dx system administrator and users with the
Note
appropriate privileges can perform.
The first time the software starts after installation, the software will automatically assign
instrument letters. By default, the software automatically assigns a letter (A, B, etc.) to
identify each instrument connected to the computer. In addition, the software also
assigns a number (1, 2, 3 or 4) to each module that is installed, from left to right. For
example, A1 is the first or left-most module of the A instrument. The instrument and
module identification appears in the Module Name column in all the software windows.
See Figure 2-27.
Figure 2-27. GeneXpert Dx System Window with Assign Instrument Letter Dialog Box Overlay

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1. In the Assign Instrument Dialog box, click OK to acknowledge the assignment of the
instrument letter(s), which closes the dialog box. The Database Management dialog
box appears (see Figure 2-28).
You will have an opportunity to change the instrument letter assignment later in this section, if
Note
needed.
Note The examples in this section shows how to change instrument letter “B” to “A.”
Figure 2-28. GeneXpert Dx System Window with Database Management Dialog Box Overlay
2. In the Database management dialog box, click NO to proceed. The GeneXpert Dx
System screen appears (see Figure 2-29).

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3. In the GeneXpert Dx System window, click Setup in the menu bar, and then select
Assign Instrument Letter. The Assign Instrument Letter dialog box appears. See
Figure 2-30. At the same time, the green LED indicators of four modules that
comprise the selected quadrant will flash.
4. To change the assignment letter, click to select the instrument to change and then
click Change Letter in the Assign Instrument Letter dialog box (see Figure 2-30).
The Change Letter dialog box appears, as shown in Figure 2-31. Select the letter to
be assigned to the module(s) by using the up and down arrows of the Change Letter
dialog box.

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Figure 2-30. GeneXpert Dx System Window, showing the Setup Drop-Down Menu

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Figure 2-32. GeneXpert Dx System Window with Change Letter Dialog Box Overlay
5. After changing the assignment letter, click OK. See Figure 2-32.
6. Click Close to close the Assign Instrument Letter dialog box (see Figure 2-32).
7. Click Close and another dialog box will appear, indicating that updated instrument
letters will be effective after the software is restarted (see Figure 2-33)
8. Acknowledge the overlay message about restarting the software (see Figure 2-33) by
clicking OK.
9. On the User Drop-Down menu on theGeneXpert Dx system window, click Exit to
shut down the software (see Figure 2-34).

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Figure 2-34. GeneXpert Dx System Window showing User Drop-Down Menu and Exit Selection

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10. The Database Management dialog box will display on top of the GeneXpert Dx
System window (see Figure 2-28). Click No in the Database Management dialog box
to continue with the software shut down.
11. Restart the system by double-clicking the GeneXpert Dx Icon on the desktop.
12. When the software restarts, the GeneXpert Dx system window will be displayed
showing the updated instrument letter assignment(s). The Database Management
dialog box will be displayed on top of the GeneXpert Dx System window (see
Figure 2-28). Click No in the Database Management dialog box to continue.
The GeneXpert Dx system window will be displayed, showing the updated letter
assignments (see Figure 2-35).
Figure 2-35. GeneXpert Dx System Window at System Restart

Configure the software and additional computer components. For details, see
Section 2.10, Defining Users and Permissions.

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2.9.2 To Assign Instrument Letters (GX-XVI Instruments)
Only a GeneXpert Dx system administrator or users with the appropriate privileges can assign
Note
instrument letters.
The GeneXpert Dx software automatically assigns a letter (A, B, C or D) to identify

each quadrant of the GeneXpert GX-XVI instrument connected to the computer.
Figure 2-36 shows how each quadrant of the GX-XVI is seen by the system.
Quadrant C Quadrant D
Quadrant A Quadrant B
Figure 2-36. Quadrant Assigned Letters (GX-XVI Shown)

In addition to assigning instrument letters, the software also assigns a number (1, 2, 3 or
4) to each module that is installed. For example, C1 is the first or left-most module of
the C instrument (quadrant C). The instrument and module identification appears in the
Module Name column in all the software windows.
The first time the software is started after installation, the software will automatically
assign instrument letters (shown in the Modules column on the left of the GeneXpert Dx
System window). See Figure 2-37.
In the screen examples shown in this section, the GeneXpert GX-XVI only has eight modules
Note
installed and active (not the full complement of 16 modules).

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1. In the Assign Instrument Dialog box, click OK to acknowledge the assignment of
instrument letters. When the Assign Instrument Dialog box closes, the Database
Management dialog box appears (see Figure 2-38).
You will have an opportunity to change these instrument letter assignments later in this section, if
Note
needed.
Note The examples in this section shows how to change instrument letter “C” to “B.”

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Figure 2-38. GeneXpert Dx System Window with Database Management Dialog Box Overlay
2. In the Database management dialog box, click NO to proceed. The GeneXpert Dx
System screen appears (see Figure 2-39).

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3. To ensure that letter assignments match the GeneXpert GX-XVI instrument, click
Setup in the menu bar, on the GeneXpert Dx System window (see Figure 2-40), and
then select Assign Instrument Letter from the drop-down menu. The Assign
Instrument Letter dialog box is displayed (see Figure 2-41). At the same time, the
green LED indicators of four modules that comprise the selected quadrant will flash.
Figure 2-40. GeneXpert Dx System Window showing Setup Drop-Down Menu

4. To change the assignment letter, click to select the instrument to change and then
click Change Letter in the Assign Instrument Letter dialog box (see Figure 2-41).
The Change Letter dialog box appears, as shown in Figure 2-42. Select the letter to
be assigned to the module(s) by using the up and down arrows of the Change Letter
dialog box. Select the letter that corresponds to the quadrant defined by the four
flashing modules. For example, if the lower-right set of modules (Quadrant B in
Figure 2-36) is flashing, select B as the new letter.

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Figure 2-42. GeneXpert Dx System Window with Change Letter Dialog Box Overlay
5. After changing the assignment letter, click OK. See Figure 2-42.

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6. Click Close to close the Assign Instrument Letter dialog box (see Figure 2-41).
7. Continue to assign instrument letters until all four quadrants are correctly assigned
to the letters A, B, C and D. The new assignment letter will be displayed in the table
in the Assign Instrument Letter dialog box.
8. Click Close and another dialog box will appear, indicating that updated instrument
letters will be effective after the software is restarted (see Figure 2-43)
9. Acknowledge the overlay message about restarting the software (see Figure 2-43) by
clicking OK.
10. On the User Drop-Down menu on the GeneXpert Dx system window, click Exit to
shut down the software (see Figure 2-44).

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Figure 2-44. GeneXpert Dx System Window showing User Drop-Down Menu and Exit Selection
11. The Database Management dialog box will display on top of the GeneXpert Dx
System window (see Figure 2-38). Click No in the Database Management dialog box
to continue with the software shut down.
12. Restart the system by double-clicking the GeneXpert Dx Icon on the desktop.
13. When the software restarts, the GeneXpert Dx system window will be displayed
showing the updated instrument letter assignment(s). The Database Management
dialog box will be displayed on top of the GeneXpert Dx System window (see
Figure 2-38). Click No in the Database Management dialog box to continue.
The GeneXpert Dx system window will be displayed, showing the updated letter
assignments (see Figure 2-45).

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Figure 2-45. GeneXpert Dx System Window showing New Module Letter Assignments
Configure the software and additional computer components, if needed. For details, see

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2.10 Defining Users and Permissions

Only a GeneXpert Dx system administrator or users with the appropriate privileges can define users
Note
and permissions.
Before starting to use the GeneXpert Dx system software, the GeneXpert Dx system
administrator and other system users must be defined. All the administrator functions are
accessible from the Setup menu in the GeneXpert Dx System window. See Figure 2-29.
2.10.1 User Types

The GeneXpert Dx system allows the Administrator to set up task permissions for
different user types, such as Basic and Detail. As the system administrator, you can use
this feature to limit access to the software functions based on your organization's
policies. For example, you might want to set up the policy presented in Table 2-1.
Table 2-1. Example User Permission Policy for In Vitro Diagnostic Use
Perform
Administrative
Perform and System
User Type Run Test View Results Maintenance Functions
Basic Yes Summary Only No No
Detail Yes All Details Limited No
Administrator* Yes All Details All Yes
*The Administrator user type has permissions to perform all the tasks, and the permissions of the
Administrator cannot be changed.
2.10.2 Specifying User Permissions

To specify permitted tasks for each user type, in the GeneXpert Dx System window, on
the Setup menu, click User Type Configuration. The User Type Configuration dialog box
appears and displays a permissions table.
• To allow a user type to perform certain tasks, select the task check boxes in the user
type column. See Table 2-2 for a complete list and description of the tasks.
• To remove a permission, clear the task check box in the user type column.
• To return all three user types to the default permission selections, click Reset to
Default.
After specifying the permissions, click OK to save the changes and close the dialog box.
Table 2-2 lists the tasks as they appear in the User Type Configuration dialog box. The
table provides a description of each task.

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Table 2-2. User Task Descriptions
Task Description Default User Settings

Basic Detail Admin.
Create/Start Test Allows an in vitro diagnostic test to be created and started X X X
(see Section 5.6 and Section 5.8).
Stop One Test or All Tests Allows stopping one or more tests in progress (see X X X
Section 5.10).
View Detailed Research Assay Allows the user to view detailed research assay test results X X
Test Result and Report and reports (not used for IVD diagnostic tests).
View Detailed Template Assay Allows the user to view detailed template assay test results X X
View Detailed Reference Assay Allows the user to view detailed reference assay test results X X
Edit Test Details Allows editing the in vitro diagnostic test information (see X X X
Section 5.12).
Create, Rename and Edit Allows the user to create, rename and edit research assays X
Research Assay (not used for IVD diagnostic tests).
Duplicate Research Assay into Allows the user to duplicate a research assay into another X
Research Assay research assay (not used for IVD diagnostic tests).
Duplicate Template Assay into Allows the user to duplicate a template assay into a X
Duplicate Reference Assay into Allows the user to duplicate a reference assay into a X
Delete Assay and Lot Specific Allows the deletion of an assay definition or lot specific X X
Parameters parameter (see Section 2.13).
Manage Assay Definition Allows the user to import assay definition (.gxa) and lot X X X
specific parameter (.gxr) files (see Section 2.13).
Export Research Assay Allows the user to export a research assay (not used for IVD X
diagnostic tests).
Export Template Assay Allows the user to export a research assay (not used for IVD X
diagnostic tests).
Export Reference Assay Allows the user to export a reference assay (not used for X
IVD diagnostic tests).
Convert Research Assay to Allows the user to convert a research assay to a reference X
Reference Assay assay (not used for IVD diagnostic tests).
Edit Graphs Allows the user to edit graphs for a research assay (not X
used for IVD diagnostic tests).
Archive Test Allows the archiving and deletion of (optional) test data (see X X X
Section 5.16.1).
Purge Test Allows the purging of a test from the database (see X X
Section 5.16.1).
Retrieve Test Allows test data to be retrieved from the test archives (see X X
Section 5.16.2).
Backup Database Allows the backing up of the database (see Section 5.17.1). X X X
Restore Database Allows the restoration of the database (see Section 5.17.2). X
Compact DB and Run Database Allows compacting of the database and the running of data X
Integrity Check integrity checks (see Section 5.17.3).

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Table 2-2. User Task Descriptions (Continued)
Task Description Default User Settings

Basic Detail Admin.
View Specimen, Patient and Allows the display of an overview of the test results for the X X X
Patient Trend Reports selected specimen in the database, and the display of test
results for samples for one patient according to the Patient
ID in the database.
View Control Trend and Assay Allows the creation and display of the external-control trend X X
Statistics Reports reports (see Section 6.4), and the display of a report
showing the number of tests performed for each assay over
a period of time with monthly breakdown values.
View System Log Allows the creation and display of a report about recent self- X X
tests and instrument errors.
Edit System Configuration Allows modification of the system configuration information X
(see Section 2.11).
Assign Instrument Letter Allows the changing of the instrument letter assignment (see X X
Section 2.9).
View IQ Report Allows the viewing of the installation qualification report (see X X X
Section 2.12).
View Module Reporter Allows the display of the reporters available in a module. X X
Run Plunger Rod Maintenance Allows the lowering of the plunger in the instrument for X X X
cleaning (see Section 9.4).
Run Self-Test Allows performing an instrument module self-test (see X X X
Section 9.13).
Open Door Allows unlocking and opening an instrument module door X
and updating cross-platform ICORE EEPROM format.
Exclude Modules from Test Allows the user to exclude modules from being used for X X X
running a test if they are suspected to have a problem (see
Section 9.14)
View About Box Allows the user to display the About window, view the X X X
software version number, copyright information and software
license agreement.

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2.10.3 Managing Users

The GeneXpert Dx system administrator can add users to the system and categorize
them as different user types, edit the user profiles or remove users from the system.
2.10.3.1 Adding New Users
The first user to be added must be the administrator. Having the administrator profile allows
Important
other users to be added and the system to be configured.
Until the administrator profile has been defined, anyone using the software has full access to all of
Note
the tasks.
To add users:
1. In the GeneXpert Dx System window (see Figure 2-30), on the Setup menu, click
User Administration. The User Administration dialog box appears. See Figure 2-46.
Figure 2-46. User Administration Dialog Box

2. Click Add. The Add User dialog box appears. See Figure 2-47.
3. In the User Name box, type a unique user name containing 6 to 10 characters that can
include spaces. For example, the first user to be added is the administrator, so enter
admin1 (or an equivalent user name).
4. (Optional) In the Full Name box, type the full or actual name of the user. For this
example, the full name of the administrator will be Administration User. The full
name can contain a maximum of 32 characters. Do not use special characters, such
as the quotation marks (" "). If a name is not provided, the software will
automatically insert the user name in this box. This name appears in the test reports.
5. In the Password and Confirm Password boxes, type the password for the user. The
password must contain 6 to 10 characters.
6. In the User Type list, select the type you want, to categorize the user. See
Section 2.10.1, User Types.

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7. When finished, click OK to save the changes and close the Add User dialog box and
display the User Administration dialog box. The new user will appear in the User
Administration dialog box.
Figure 2-47. Add User Dialog Box

8. Repeat Step 2 through Step 7 until all users have been added to the system.
9. Click Close to close the User Administration dialog box.
2.10.3.2 Editing User Profiles

To change a user name or password, or to make other changes to a user profile:
2. In the User Administration dialog box, in the User Name column, select the user
profile to be edited.
3. Click Edit. The Edit User dialog box appears. See Figure 2-48.
4. Revise the information, as desired, and then click OK to save the changes and close
the Edit User dialog box.
5. Click Close to close the User Administration dialog box.
Figure 2-48. Edit User Dialog Box

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2.10.3.3 Removing Users
Note When removing a user, the tests created by that user will remain in the database.
To remove a user:
Figure 2-49. User Administration Dialog Box

2. Click to select the user to be removed. See Figure 2-50.
Figure 2-50. User Administration Dialog Box selecting User to be Removed

3. Click Remove. The user is removed. See Figure 2-51.
4. To remove additional users, repeat Step 2 and Step 3. If you are done removing
users, click Close (see Figure 2-50).

301-0045, Rev. K August 2016
Figure 2-51. User Admin Dialog Box after User Removal
2.11 Configuring the System

Using the System Configuration function, the following can be specified:
• a name for the system (General tab)
• the date and time formats (General tab)
• options for creating a test (General tab)
• control of how the archive reminder is performed (Archive Settings tab)
• default folder paths for the exported test data, reports, and other information
(Folders tab)
• LIS interface (Host Communication Settings tab)
2.11.1 General Tab

1. In the GeneXpert Dx System window (see Figure 2-30), click Setup on the menu
bar, then click System Configuration. The System Configuration dialog box and the
General tab appears. See Figure 2-52.
2. Provide the requested information for the General tab as follows:
• System Name box—Type a unique name for the system. The system name will
be displayed in all of the reports.
• Date Format list—Select the format to be used to display the month, day and
year.
• Time Format list—Select the 24-hour or the 12-hour format.

301-0045, Rev. K August 2016
Figure 2-52. System Configuration Dialog Box (General Tab)

• Use Patient ID—If Patient ID is enabled, the Scan Patient ID Barcode can be
selected and used. Patient ID is available in Create Test and View Results.
Selecting Use Patient ID will enable the check boxes below it to become active:
• Patient ID - If Use Patient ID is enabled, Patient ID will also be enabled and
cannot be unchecked. The Patient ID field can contain up to 32
alphanumeric characters excluding illegal filename characters.
• Patient ID 2 – If Use Patient ID is enabled, Patient ID 2 may be enabled to
allow entry of additional patient identification. This field is optional and
does not require an entry if there is no additional patient ID. Select the
check box to enable Patient ID 2. The Patient ID 2 field can contain up to 32
alphanumeric characters excluding illegal filename characters.
• Patient Name – If Use Patient ID is enabled, Patient Name may be enabled to
allow entry of the patient’s name. This field is optional and does not require
an entry if you do not want to enter a patient name. Select the check box to
enable Patient Name.
The Patient Name Last Name field can contain up to 194 alphanumeric
characters excluding illegal filename characters. The Patient Name First
Name field can contain up to 30 alphanumeric characters excluding illegal
filename characters.

301-0045, Rev. K August 2016
The following symbols cannot be used for Sample ID, Patient ID, Patient ID2, First Name,
Important
Last Name, Other Sample Type, or Notes: | @ ^ ~ \ & / : * ? " < > ' $ % ! ; ( ) ‐
For screenshots and reports shown later in this manual, the Patient ID field will be shown as
Note
enabled.
• Patient Demographics—Select to enable the visibility of the Patient

Demographics. Demographics data is associated with the corresponding
patient’s test result.
Upon test creation, patient demographic information (Patient Name, Date
of Birth, Ethnicity, Gender and Postal Code) will be encrypted and saved in
the GeneXpert Dx database and will not be shown in the software.
The checkbox for Patient Demographics will be unchecked by default in System Configuration.
Note Only the system administrator can check or uncheck the Patient Demographics option.
Demographics data can only be used in future connectivity solutions.
• Scan Patient ID Barcode—Select to enable the software to prompt for the Patient
ID barcode to be scanned. Clear the check box to disable the prompt for the
Patient ID barcode.
• Scan Sample ID Barcode—Select to enable the software to prompt for the
Sample ID barcode to be scanned. Clear the check box to disable the prompt for
the Sample ID barcode.
• Scan Cartridge Barcode—Select to enable the software to automatically prompt
the cartridge barcode to be scanned (recommended). Clear the check box to
disable the prompt for the cartridge barcode.
• Require Start Test Login—This option allows the system administrator to
configure if Start Test Login is required for traceability of the person who
started a test and the period for the Start Test Login.
The options provided to the administrator are:
• Never – Start Test Login screen is never displayed when the Start Test
button is pressed in the Create Test screen.
• Always – This option is the default. Start Test Login screen is always
displayed if there is a custom-defined user and when the Start Test button is
pressed in the Create Test screen.
• Start Test Login Timeout (In Minutes) – If this option is selected and if there
is a custom-defined user, the system monitors the time lag since the most
recent user login or Start Test Login. After this amount of time elapses and
the user presses the Start Test button in Create Test window, then the Start
Test Login dialog box appears.

301-0045, Rev. K August 2016
The timeout counter will be reset when any user logs in. The system
administrator can select from 1 to 60 minutes using the drop-down list or
enter a value in the same range. The default is 30 minutes.
3. Select or clear the following check boxes:
• Audio At End of Test—If the user turns on the audio option, a short tone will be
provided at the end of the test. This feature utilizes the Windows default beep
sound and settings.
• Print Test Report At End of Test—This option allows a test report to be
automatically printed to the Windows system default printer in the default
format.
If the printer is out of paper, the test report is still present even though the report has not printed.
Note Depending on the printer, when paper is loaded and the paper tray is closed, the waiting reports will
automatically start printing, and it may not be necessary to manually print the test report.
• Assay Statistics Deletion Reminder—The user can enable or disable the Assay
Statistics Deletion Reminder. The default is enabled.
• Database Management Reminders—The user can enable or disable the Database
Management Reminders. The default is enabled.
If Database Management Reminders are enabled, the user is prompted on
startup and shutdown whether to perform database management tasks. The
prompt appears only if the user has privileges to perform these tasks. If the user
does not have any of these privileges or if Database Management Reminders
are disabled, the prompt will be skipped.
4. Click OK to save the changes and close the window.

301-0045, Rev. K August 2016
2.11.2 Archive Settings Tab

This tab provides the settings that control how the archive reminder is performed. The
time interval can be selected or when to be reminded to archive files: Never, Weekly, or
Monthly.
bar, then click System Configuration.
2. Select the Archive Settings tab. The Archive Settings tab information appears. See
Figure 2-53.
Figure 2-53. System Configuration Dialog Box (Archive Settings Tab)

3. Select the desired options:
• Manually—If this option is selected, archiving has to be performed manually by
the user, at the user’s convenience, and will follow the manual archive process.
Manually, With Reminder—If this option is selected, a reminder will be
displayed if the user has Archive Test privilege. This reminder is not displayed
for the users who do not have Archive Test privilege.
The user can choose to receive reminders weekly or monthly. The default will
be weekly.

301-0045, Rev. K August 2016
The system will attempt to remind the user to perform an overdue archive if the
last archive was performed in the last week or the last month (depending on the
reminder period selected). The last week or the last month is defined as being
the day prior to the first day of the current week/month. The first day of a week
is considered to be Monday. The first day of a month is the first of each month.
In such an event, the reminder is displayed to the user when:
• GeneXpert Dx application starts
• GeneXpert Dx application normally terminates
• user logs in (excluding start test login)
If the user accepts the archive reminder prompt, the Archive Test dialog will be
shown immediately.
If the user dismisses the reminder prompt, the software will proceed normally,
and the user will be reminded the next time the reminder criteria are met.
2.11.3 Folders Tab

bar, then click System Configuration.
2. Click the Folders tab. The Folders tab appears. See Figure 2-54.
Figure 2-54. System Configuration Dialog Box (Folders Tab)

3. Provide the requested information for the Folders tab as follows:

301-0045, Rev. K August 2016
• Export Folder box—Type the path to the folder in which all of the exported test
data will reside. Alternatively, the default path supplied can be used.
• Report Folder box—Type the path to the folder in which all of the reports will
reside. Alternatively, the default path supplied can be used.
• Backup Folder box—Type the path to the folder in which the backup database
will reside. Alternatively, the default path supplied can be used.
• DB Log Folder box—Type the path to the folder in which the database log files
will reside. Alternatively, the default path supplied can be used.
Caution The default locations for each of the folders is located on the computer hard drive. To guard
against loss of data, the files in the export folder should be periodically copied to a different
computer or server. If the GeneXpert Dx system is connected to a network, it is possible to
archive files directly to a server.
2.11.4 Xpress Settings Tab

The Xpress Settings tab is not to be used in the normal operation of the system. Do not
make any changes to the settings on this tab.
2.11.5 Host Communication Settings Tab

The Host Communication Settings tab is used to configure the system software when a
GeneXpert Dx is connected to a Laboratory Information System (LIS) host computer or
Cepheid Link.
Note No configuration of this tab is required if an LIS system is not being used with the system.
To configure the host communication settings for an LIS, see Section 2.11.5.1, Configuring Host
Note Communications for an LIS. To configure the host communication settings for Cepheid Link, see
Section 2.11.5.2, Configuring Host Communications for Cepheid Link.
2.11.5.1 Configuring Host Communications for an LIS

bar, then click System Configuration (see Figure 2-30).
2. Click the Host Communication Settings tab. The Host Communication Settings tab

301-0045, Rev. K August 2016
Figure 2-55. System Configuration Dialog Box (Host Communication

Settings Tab)
Note If the LIS is being enabled on a new system, there will be no assays shown.
Caution
Within the hospital or laboratory network, each GeneXpert Dx system should have a unique
system name, which is used for host communication. The LIS host administrator should
control the process for defining system names.
Do not check the Use Cepheid Link checkbox when configuring the host communication
Important
settings for a hospital LIS system.
3. Provide the settings to configure the communication between the GeneXpert Dx

software and a Laboratory Information System (LIS):
• Enable Host Communication—Select to enable the GeneXpert Dx software
connected to a host. Clear to disable the host communication.
• Host ID— Type in a unique host name to identify an LIS or Data
Management System (DMS) that is connected to this GeneXpert Dx
system. The maximum number of characters is 20.

301-0045, Rev. K August 2016
• Automatic Host Query After Sample ID Scan—Select to enable the

GeneXpert Dx system to query for test orders associated with the scanned
or entered Sample ID.
• Automatic Test Order Download—Select to enable the GeneXpert Dx
system to periodically query all test orders from the host.
If the Host is connected to multiple GeneXpert Systems, you may want to:
Caution  Use Automatic Host Query After Sample ID Scan instead of Automatic Test Order Download
to minimize duplicate orders to multiple GeneXpert systems.
 The host should download order to a specific GeneXpert System.
 If orders are sent to multiple GeneXpert systems, the host should cancel pending orders
when completed result is received.
• Automatic Result Upload—As soon as the test is completed, the results are
uploaded.
• Use Instrument Specimen ID—Select to enable the GeneXpert Dx system to
generate a unique specimen ID, which is returned to the host. The
Instrument Specimen ID is a unique ID for this sample. It should be stored
in the host and used for future communication for this sample. This option
is applicable if the facility does not provide unique sample identification.
If the facility provides unique sample identification, this setting should be
disabled.
• Communication Settings box—Select or clear the following check boxes:
• Protocol—Select HL7–compatible or ASTM–compatible protocol.
• Run Host As—For socket connection between the two systems. Select
to run the host as a server or a client.
• Server IP Address—If Run Host As Server option is selected, an IP
address with 4-part value (N.N.N.N) should be entered. The value
should match the IP address of the host server. N is between 0-255. If
Run Host As Client option is selected, the IP address of the network
card available for host connectivity is displayed.
• Port #—The port number should be between 1024 to 65535.
Caution
The network port that is dedicated for the GeneXpert instrument should not be used for the
host connection. The second NIC available on each GeneXpert computer should be used to
connect the GeneXpert Dx system to the host.
• Order/Result Management—Click the appropriate buttons:

• Delete Canceled Orders—Click to delete canceled orders. This is useful
to remove redundant orders during host communication testing.
• Expire Results—Click to expire results pending upload for tests that
should no longer upload to the host.

301-0045, Rev. K August 2016
Caution
Do not use Reset Communication Buffer (discussed below) during normal operation;
otherwise, you will have to re-download orders and re-upload results.
• Reset Communication Buffer—To clear the data between the GeneXpert Dx

system and the host. This is useful to remove data during host
communication testing.
• Host Test Code table—This look up table allows the host administrator to
type in the test code that was entered into the host, so it can be translated
into the GeneXpert Dx system for test order processing and result
reporting.
• Enable—Indicates if the assay has been set up for test order download
and result reporting.
• Assay—Assay name available for host connectivity.
• Host Test Code—the test code which the host used for download of test
order and upload of test result.
You cannot edit the test code for old versions of an assay. If you update the test code, the
Important update will only apply to the new version of the assay; therefore, you must change the test
code before upgrading an assay.
Caution
Be careful to not use the same test code for tests from two different assays.
4. Click Edit button to enable the assay for host use and to define host test codes for
that assay. See Section 2.11.6 to configure the assay for order and result upload and
to define host test codes.
2.11.5.2 Configuring Host Communications for Cepheid Link

Once the system has been configured for Cepheid Link, it cannot be used for non-LIS
originated test orders or for running external controls without disabling Cepheid Link.
Important
Cepheid Link may be enabled again after running non-LIS originated test orders or external
controls.
To enable and configure host communications for the GeneXpert Dx systems to Cepheid
Link:
1. On the GeneXpert Dx system window (see Figure 2-29), select the SETUP button,
then select the SYSTEM CONFIGURATION button (see Figure 2-30).
2. Select the HOST COMMUNICATIONS SETTINGS button (see Figure 2-30) to display
the Host Communications Settings workspace. See Figure 2-55.

301-0045, Rev. K August 2016
3. To enable host communication, select the Enable Host Communication check box in
the upper left corner of the workspace (see Figure 2-56). This allows other options to
be selected on the Host Communication Settings screen.
Within the hospital or laboratory network, each GeneXpert system should have a unique
Important system name which is used in the communication. The host administrator should control the
process for defining system names.
Figure 2-56. Host Communication Settings Workspace Configured for Cepheid Link
All of the information to be entered into this workspace must be provided by the LIS network
Important
administrator. It is not provided by Cepheid.
4. Select the Use Cepheid Link checkbox to set up the host communication for Cepheid
Link. After selecting the Use Cepheid Link checkbox, most of the configuration will
be automatically set up. See Figure 2-56.
5. In the General section of the Host Communication Settings workspace, enter the
appropriate information and select the appropriate items to interface with the LIS
network.
• Host ID field – Type in a unique host name to identify this GeneXpert Dx
system. The maximum number of characters is 20.

301-0045, Rev. K August 2016
• Automatic Host Query After Sample ID Scan check box – This check box is
disabled when connecting to Cepheid Link,
• Automatic Test Order Download check box – This check box is disabled when
connecting to Cepheid Link,
• Automatic Result Upload check box – This check box is enabled when
connecting to Cepheid Link,
• Use Instrument Specimen ID check box – Select to enable the GeneXpert system
to generate a unique specimen ID which is returned to the host. The Instrument
Specimen ID is a unique ID for this sample. It should be stored in the host and
used for future communication for this sample. This option is applicable if the
facility does not provide unique sample identification.
If the facility provides unique sample identification, this setting should be
disabled.
6. In the Protocol section of the Host Communication Settings workspace, select either
HL7-compatible or ASTM-compatible protocol.
7. In the Communication Settings section of the Host Communication Settings
workspace, the host must be set to Server to communicate with Cepheid Link.
• Server IP Address field – An IP address with 4-part value (N.N.N.N) should be
entered. The value should match the IP address of the Cepheid Link server. N is
between 0-255.
• Port # field – The port number must be 3000 to communicate with the Cepheid
Link server.
8. After you have set up the host communications for the Cepheid Link server, select
the OK button. See Figure 2-56.
Select the Cancel button if you do not want to save the host communication settings.
Cepheid recommends to always confirm that LIS or HIS uploaded results match GeneXpert results
after any changes to the GeneXpert or host system, including, but not limited to, changes to the
following:
• GeneXpert software version
Note
• GeneXpert assay definition files and version
• GeneXpert host communication settings
• Host middleware software or configuration changes
• LIS software or configuration changes

301-0045, Rev. K August 2016
2.11.6 Configuring Assay for Order and Result Upload

Caution
In order to perform the required assay, the same test code should be entered in the host, the
GeneXpert Dx system and the Cepheid Link system, if applicable.
Caution
Do not change test orders until all test results have been uploaded.
2.11.6.1 Configuring a Single-Result Assay for Order and Result Upload

1. In the Host Test Code table section of the Host Communication Settings tab (see
Figure 2-56), click the desired Edit button to change the setting. The Define Test
Code dialog box appears. See Figure 2-57.
Figure 2-57. Define Test Code Dialog Box for a Single-Result Assay
2. Click the Enable checkbox to allow the host to download test orders and GeneXpert
Dx system to upload results to the host using the defined assay test code.
3. In the Assay Host Test Code field of the Define Test Code dialog box, enter the same
test code that was entered into the host system and the Cepheid Link system, if
applicable.(the test code entered for the GeneXpert Dx system must be the same as
the test code entered for host system and the Cepheid Link system) Enter in 1 to 15
characters.
4. Click OK to save the setting for this assay. The software will check for uniqueness of
the test code before saving.
Cepheid recommends that you use the same test code for the new version of the same assay.
Note However, if you want to change the test code of the current assay, make the change before
importing the next version.

301-0045, Rev. K August 2016
2.11.6.2 Configuring a Multiple-Result Assay for Order and Result Upload

The multiple-result assay provides results for multiple organism and genes.
1. In the Host Test Code table section of the Host Communication Settings tab (see
Figure 2-56), click the desired Edit button to change the setting. The Define Test
Code dialog box appears. See Figure 2-58.
2. Click the Enable checkbox to allow the host to download test orders and the
GeneXpert Dx system to upload results to the host using the defined assay test code.
3. In the Assay Host Test Code field, enter the same test code that was entered into the
host system and the Cepheid Link system, if applicable (the test code entered for the
GeneXpert Dx system must be the same as the test code entered for host system and
the Cepheid Link system). You can enter 1 to 15 characters.
4. The result names reported by the assay are listed in the Result Name field. See
Figure 2-58.
5. Type in the result test code in the Result Test Code field (see Figure 2-58)
corresponding to each result name that can be reported by this assay.
+
Figure 2-58. Define Test Code Dialog Box for a Multi-Result Assay

301-0045, Rev. K August 2016
2.12 Verifying Proper Installation and Setup

This section describes tasks that all users with the appropriate permissions can perform. See
Note
After the instrument installation is complete (computer has been set up, the users and
permissions have been defined and the system configured), verify that the system is
properly installed and set up by running an Installation Qualification report to verify the
installation. To do this:
1. In the GeneXpert Dx System window, on the Reports menu, click Installation
Qualification. See Figure 2-59.
Figure 2-59. GeneXpert Dx System Window showing Reports Drop-Down Menu and Installation
Qualification Selection

301-0045, Rev. K August 2016
2. The Adobe® Reader window appears and displays the GeneXpert Dx System
Installation Qualification Report. See Figure 2-60.
3. Print the report. If the computer is not connected to a printer, save the file to a
location where the report can be printed.
4. Review the following sections in the report:
• System Information—Check that the Status column displays Pass in each row.
• Instrument Information—For each instrument connected to the computer, the
report shows the instrument serial number, the firmware installed, and the status
of each operational module. If a Reporter is out of calibration or a Not Available
message is shown, call Cepheid Technical Support. See the Technical
Assistance section in the Preface for the contact information.
• Available Assays—Check the assays in the list. If the No Assays message is
shown, see the instructions provided with the in vitro diagnostics assay kit and
Section 2.13.2, Importing Assay Definitions for instructions on how to import
assay definition files.
If this report is run after system installation but before assays have been
installed on the system, the No Assays message will be displayed. If the No
Assays message is shown after importing the assay definition files, call Cepheid
Technical Support. See the Technical Assistance section in the Preface for the
contact information.
5. Sign the Installation Qualification Report and file a copy of the report for your
records. See Figure 2-61.

301-0045, Rev. K August 2016
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301-0045, Rev. K August 2016
2.13 Managing Assay Definitions and Lot Specific

Parameters
This section describes tasks that all users with the appropriate permissions can perform.User
Note permissions are described in Section 2.10, Defining Users and Permissions. For this section, the
screen shots will show a Detail user level.
An assay definition contains a series of programmed steps that the GeneXpert Dx system
uses to perform sample preparation, amplification and detection procedures. In vitro
diagnostic assay definition (.gxa) files can be obtained from Cepheid and imported into
the software (see Section 2.13.2, Importing Assay Definitions). Assay definitions that are
no longer in use can also be deleted (see Section 2.13.3, Deleting Assay Definitions).
Some assay definitions require lot specific parameters to determine the test results. The
2D cartridge barcodes contain the lot specific parameter information that is automatically
imported when a barcode is scanned. If, for some reason, the barcode scanner is not
working or is not available, the lot specific parameter information can be supplied
manually by importing the .gxr file (see Section 2.13.4, Importing Lot Specific
Parameters Manually). The lot specific parameter information that is no longer in use
can also be deleted (see Section 2.13.5, Deleting Lot Specific Parameters).
2.13.1 The DVD Drive

The usual way to import assay definitions from the CDROM is by using the DVD drive
installed in the system.
1. Locate the DVD drive. The drive is installed on the GeneXpert Dx system computer
but the location of the drive will vary:
• On a desktop computer, the drive will be accessed from the front of the
computer, and
• on a laptop, the drive will be on the side of the laptop.
2. Press the Eject button on the front of the DVD drive to open the door.
3. The CDROM is located in the assay kit. Insert the assay definitions CD into the
DVD drive and close the DVD drive door. The green light on the front of the DVD
drive will flash while the drive reads the CD.
Import the assay definitions following the procedure in Section 2.13.2.

301-0045, Rev. K August 2016
2.13.2 Importing Assay Definitions
Although in vitro diagnostic assay definitions can be imported, the GeneXpert Dx software does not
Note
allow the assay definitions to be modified.
To import new assay definitions:

1. In the GeneXpert Dx System window, click Define Assays on the menu bar. The
Define Assays window appears. Figure 2-64 shows the Define Assay window for the
GeneXpert Dx system administrator. The window for Detail and Basic users has
fewer functions (see Figure 2-62).
Click to Define Assays
Click to Import Assay
Figure 2-62. System - Define Assays Window (Detail User View)

2. Click Import. The Import Assay dialog box appears. See Figure 2-63.

301-0045, Rev. K August 2016
Figure 2-63. Import Assay Dialog Box

3. Navigate to the DVD folder. Locate and select the assay definition (.gxa) file, and
then click Import. The new assay name and version number appear in the Assay list
(on the left side of the window) and details about the assay appear to the right of the
list. See Figure 2-62.
4. Check the assay name and version number to make sure the correct assay definition
has been imported.
5. If you need to import additional assay definition files from the same CD, repeat
Step 2 through Step 4.
For combination assays that have multiple .gxa files, import only the assay definition files for assays
Note
that will be performed in your lab.
6. Remove the CD from the DVD drive and store the CD in a safe location in the event
it is needed in the future.
Note After importing a quantitative assay, the Quantitative Result Unit can be changed. See Figure 2-64.
2.13.3 Deleting Assay Definitions

Caution
Deleting assay definitions from the system is a permanent operation. Ensure that the assay
definitions are no longer needed. If they are needed, they will need to be imported again from
the assay definitions CDROM.
1. To delete an assay definition file, in the Define Assays window (see Figure 2-64),
select the assay name in the Assay list (on the left side of the window), and then
click Delete. A confirmation message appears.
2. Click Yes to delete the assay definition. The assay definition file will be deleted and
is removed from the list of assays.

301-0045, Rev. K August 2016
Click to Delete Assays
Figure 2-64. GeneXpert Dx System - Define Assays Window (Administrator User View)

301-0045, Rev. K August 2016
2.13.4 Importing Lot Specific Parameters Manually

Some assay definitions require lot specific parameters to determine the test results. The
cartridge barcodes contain the lot specific parameter information that is automatically
imported when you scan the barcode when creating a test or defining assay. If, for some
reason, the barcode scanner is not working or is not available, you can supply the lot
specific parameter information manually by importing the .gxr file.
Contact Cepheid Technical Support to obtain the .gxr files. After obtaining the .gxr files, store them
Note
on the computer and note where the files are located (typically stored in the export folder).
To check if a specific assay requires Lot Specific Parameters, see if the box is checked
for the assay to the left of the Need Lot Specific Parameters entry on the Define Assays
screen.
Click to Import Lot Specific Parameters

Figure 2-65. Define Assays Window, showing Need Lot Specific Parameters Box Checked

301-0045, Rev. K August 2016
To import lot specific parameters manually:

1. In the Define Assays window (see Figure 2-65), select the assay name in the Assay
list (on the left side of the window).
2. Click Lot. The Reagent Lot Specific Parameters dialog box appears. See
Figure 2-66.
3. Click Import. The Import Reagent Lot Specific Parameters dialog box appears.
Figure 2-66 shows the common Reagent Lot Number before importing specific lots. If assays and/or
Note lot specific parameters have already been imported into the system, the reagent lot numbers will be
displayed.
Figure 2-66. Reagent Lot Specific Parameters Dialog Box

4. Using the Look In: file viewing area, (see Figure 2-67) locate and select the .gxr file
obtained from Technical Support previously, and then click Open. The new lot
number appears in the Reagent Lot Specific Parameters dialog box. Click Close in
the Reagent Lot Specific Parameters dialog box to return to the Define Assays
window.

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Figure 2-67. Import Reagent Lot Specific Parameters Dialog Box
2.13.5 Deleting Lot Specific Parameters

To delete lot specific parameters:
1. In the Define Assays window (see Figure 2-65), click Lot. The Reagent Lot Specific
Parameters dialog box appears. See Figure 2-66.
Note Be aware that you cannot delete the common lot.
2. Select the lot number to be deleted, and then click Delete. A confirmation message
appears.
3. Click OK to delete the lot specific parameters.
4. Click Close to close the Reagent Lot Specific Parameters dialog box.

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2.14 Restarting the System

Note This section describes tasks that all user types can perform.
Under some troubleshooting scenarios (see Section 9.18.2, Error Messages), the system
may need to be restarted. To do this, perform the steps in Section 2.14.1 through
Section 2.14.2.
2.14.1 Shutting the System Down

1. Make sure the instrument is not currently processing any samples. Wait for the
instrument to finish all processes before shutting down or restarting the system.
2. Remove the cartridges from the instrument modules.
3. Close the GeneXpert Dx software by clicking Exit on the User menu.
2.14.1.1 Archive Overdue Reminder

If an archive is not overdue, or if an archive setting in Figure 2-53 is not selected,
Figure 2-68 will not appear, and you can skip directly to Section 2.14.1.2.
If an archive is overdue, the Test Archive Reminder dialog box will appear (see
Figure 2-68).
Figure 2-68. Test Archive Reminder Dialog Box

• If you do not want to archive, click No in the Test Archive Reminder dialog box (see
Figure 2-68). Continue the shutdown sequence without archiving, in
Section 2.14.1.2.
or
• If you would like to archive, click Yes in the Test Archive Reminder dialog box (see
Figure 2-68) to continue the shutdown sequence with archiving. The Select Test(s)
To Be Archived screen appears. See Figure 2-69.

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Figure 2-69. Select Test(s) To Be Archived Screen

To archive tests, perform Step 2 through Step 7 of the procedure in Section 5.16.1,
Archiving the Tests. When you are finished with the archiving, continue with
Section 2.14.1.2.

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2.14.1.2 Database Management Reminder

• If the Database Management Reminders box on the System Configuration dialog box
(see Figure 2-52) is not checked, the Database Management Dialog Box (see
Figure 2-70) will not appear, and no further action will be required. The software
will close when the Exit button is clicked in Section 2.14.1, Step 3, and you can skip
to Section 2.14.1.3 to complete the shutdown sequence.
or
• If the Database Management Reminders box on the System Configuration dialog
screen (see Figure 2-52) is checked, the Database Management dialog box (see
Figure 2-70) will then appear on top of the GeneXpert Dx System window., asking if
you want to perform Database Management tasks.
Figure 2-70. Database Management Dialog Box
A. If you click No on the Database Management dialog box (see Figure 2-70), the
GeneXpert Dx software closes and you can proceed to Section 2.14.1.3 to
complete the shutdown sequence.
or
B. Click Yes in the Database Management dialog box (see Figure 2-70), and you
will be asked to select the task to be performed (see Figure 2-71).
Depending on the user’s privileges, all (or some) of the four options in the Database Management
Note
dialog box may not be visible. See Figure 2-71.

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See Section 5.17, Performing Database Management Tasks for details on how to perform
each of the database management tasks. After completion of the Database Management
tasks, the GeneXpert Dx software closes and the Windows desktop is displayed.
Proceed to Section 2.14.1.3.
2.14.1.3 Final Shutdown Steps

1. Turn off the instrument
2. Shut down the GeneXpert Dx system computer.
2.14.2 Restart the System

To restart the system, follow the procedure in Section 5.2.2, Turning On The Computer.
After the system has been powered off, wait two minutes before turning the system back on.
Important
The system may not boot up correctly if it is turned back on in less than two minutes.
2.15 Uninstalling or Reinstalling GeneXpert Dx Software

The GeneXpert Dx software is already installed on the supplied computer but may need
to be reinstalled in certain situations, with assistance from Cepheid Technical Support.
Caution If the software becomes corrupted or there is a system failure, do not attempt to reinstall the
software. Call Cepheid Technical Support for assistance to minimize the chance of
permanent data loss. See the Technical Assistance section in the Preface for the contact
information.

301-0045, Rev. K August 2016

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3 Principles of Operation
This chapter explains how the GeneXpert Dx system works. The topics are as follows:
• Section 3.1, System Operation Overview
• Section 3.2, GeneXpert Module
• Section 3.3, GeneXpert Cartridge
• Section 3.4, I-CORE Module
• Section 3.5, Heating and Cooling Mechanisms
• Section 3.6, Explanation of Experimental Methods
• Section 3.7, Optical System
• Section 3.8, System Calibration
3.1 System Operation Overview

GeneXpert Dx systems automate and integrate sample purification, nucleic acid
amplification, and detection of the target sequence using real-time reverse transcriptase
PCR (RT-PCR) and real-time PCR assays.
Each GeneXpert Dx module processes one sample. The sample and applicable reagents
are inserted into a GeneXpert cartridge and a test is created on the GeneXpert Dx system
(see Section 5.6, Creating a Test) to run the test. The cartridge is then loaded into an
available instrument module (see Section 5.7, Loading a Cartridge into an Instrument
Module) and then is started (see Section 5.8, Starting the Test). During the test, the
system performs the following steps:
1. Moves the sample and reagents into different chambers in the cartridge for sample
preparation.
2. Hydrates the reagent beads.
3. Performs probe checks to ensure that the sample preparation is successful (only if
the assay definition requires this step).
4. Moves the sample and the reagent mixture which contains reverse transcription (if
applicable) and real-time PCR specific components into the reaction tube.
5. Starts the RT-PCR (if applicable) and PCR cycles and real-time detection (see
Figure 3-1).
The GeneXpert Dx System uses the I-CORE® module heating and fan cooling system to
perform the real-time polymerase chain reaction used to exponentially amplify and
detect the organism’s DNA or cDNA sequence of interest.

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Principles of Operation
Polymerase chain reaction is an amplification method that increases quantities of specific

copies of DNA or cDNA sequences. Real-time polymerase chain reaction uses
fluorescence to detect the specific sequences and includes a mechanism to determine the
cycle at which the DNA or cDNA of interest first appears at appreciable copies (called
the cycle threshold).
Polymerase chain reaction consists of a series of cycles during which the DNA or cDNA
is heated and cooled at specific temperatures for a certain duration.
After Initial Denaturation (when the polymerase used to amplify the DNA or cDNA is
activated) a cycle occurs, which is usually a three-step process, consisting of:
1. The Denaturation step which divides the DNA strands.
2. An Annealing step in which a primer is needed by the polymerase to amplify the
DNA. The primer will bind to the DNA or cDNA sequence if complementary.
3. The Extension step, where the DNA strands will be extended.
Initial Denaturation Denaturation
95 °C 95 °C
Extension
72 °C
Annealing
120 Sec. 5 Sec. 60 °C
10 Sec.
30 Sec.
Figure 3-1. Example PCR Cycle Diagram for I-CORE Module Heating and Fan Cooling
(Temperature Durations not to Scale)

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3.2 GeneXpert Module

The PCR cycle diagrammed in Figure 3-1 indicates 40 cycles performed by the I-CORE
module. The denaturation temperature is 95 °C; the annealing temperature is 60 °C; and,
the extension temperature is 72 °C. Each of these temperatures must be held by the
module for a specific duration, as indicated in Figure 3-1. The initial denaturation takes
place for 120 seconds for one cycle. The denaturation (5 seconds), annealing (30
seconds) and extension (10 seconds) steps cycle consecutively forty times before the
polymerase chain reaction is finally completed.
Each instrument module contains the following components that enable automated
sample processing in the cartridge and filling of the tube with the sample-reagent
mixture for PCR:
• Valve Drive – Rotates the cartridge valve body to address the different cartridge
chambers.
• Plunger Rod – Dispenses fluids into the different cartridge chambers.
• Ultrasonic Horn – Lyses the sample (if applicable).
• I-CORE Module – Performs PCR amplification and detection.
A cartridge loading and unloading mechanism assures the proper movement of the
cartridge in the instrument. In addition, the system is designed to perform a self-test
before each test starts to verify that the system is functioning properly.
3.3 GeneXpert Cartridge

The disposable, single-use GeneXpert cartridge holds the samples and reagents that are
to be processed in the GeneXpert Dx system. Each cartridge consists of the following
components (see Figure 3-2):
• Processing Chambers – Hold the samples, reagents, processed sample, and waste
solutions. One chamber is designated as an air chamber to equilibrate pressures
within the cartridge.
• Valve Body – Rotates and allows fluid to move to different cartridge chambers and to
the reaction tube. Within the valve body, the specimen is isolated, PCR inhibitors are
removed, and specimens are ultrasonically lysed (if applicable). After the sample is
processed, it is mixed with PCR reagents and moved into the integrated reaction
tube.
• Reaction Tube – Enables rapid thermal cycling and optical excitation and detection of
the tube contents. The reaction tube is automatically inserted into the I-CORE
module when the cartridge is loaded into the instrument.

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The cartridge is designed to keep the reagent contained within the cartridge. It is a
closed-system vessel.
The GeneXpert cartridges are not supplied with the system. To order the assay-specific
cartridges, contact Cepheid. See the Technical Assistance section in the Preface for the
Processing
Chambers
Reaction
Tube
Valve
Body
Figure 3-2. GeneXpert Cartridge Components

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3.4 I-CORE Module

The I-CORE (Intelligent Cooling/Heating Optical Reaction) module is the hardware
component within each instrument module that performs PCR amplification and
fluorescence detection. As part of the cartridge load process, the reactor tube is inserted
into the I-CORE module (see Figure 3-3). The sample and reagent mixture are pushed
from the cartridge into the reaction tube. During the amplification process, the I-CORE
heater heats up and the fan cools down the reaction tube contents. The optical blocks
excite the dye molecules and detect the fluorescence emitted.
I-CORE Module (Side View)

Fan
Cartridge
Inserts into the I-CORE
Heater Reaction Tube
Reaction Tube
Optical Blocks
(Inside the I-CORE)
Figure 3-3. I-CORE Module (6-Color Module Shown)

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3.5 Heating and Cooling Mechanisms

Within the I-CORE, the heater consists of two ceramic plates that have high thermal
conductivity to assure temperature uniformity and rapid heat transfer (see Figure 3-3).
Resistive heater elements are deposited on the ceramic plates using thick film
technologies and a thermistor attached directly to each plate monitors its temperature. A
high-efficiency fan cools the reaction tube contents by moving ambient air across the
heater plates. During thermocycling, the instrument firmware controls the temperature
inside the instrument module. The firmware incorporates a control loop to ensure rapid
heating of the plates while minimizing the temperature overshoot around the desired
target temperature.
3.6 Explanation of Experimental Methods

The GeneXpert system uses real-time polymerase chain reaction (real-time PCR) to
detect the organism’s DNA of interest.
Real-time polymerase chain reaction is a variant of polymerase chain reaction and uses
the same method of PCR with denaturation, annealing and extension at specified time
durations to amplify DNA. Real-time PCR uses fluorescence in the form of either
intercalating dyes or probes to detect amplified copies of the DNA of interest and to
visualize and monitor the amplified product in real time.
In real-time PCR, primers specifically designed to be complementary to the organism’s
DNA bind to the DNA and extend it. For example in 5’-nuclease technology, a probe
which has a reporter dye and quencher attached to it is also complementary to the
organism’s DNA and binds to the DNA downstream to the primer. The primer and probe
together add a higher level of specificity to identify a sequence specific to the organism.
As the DNA strand gets extended, the probe is destroyed and the reporter and quencher
are dissociated and become free in solution. The fluorescent signal becomes detected and
increases with each amplification.
The cycle at which the fluorescence becomes detected after appreciable copies of the
DNA are made is the cycle threshold (Ct). The most basic definition of a cycle threshold
is the first cycle in which there is significant increase in fluorescence above the
background fluorescence (see Figure 3-4).
The real-time PCR generates a growth curve with number of cycles on the x-axis and
fluorescence on the y-axis. The increase in fluorescence is proportional to the amount of
amplicon generated and can be used to define cycle threshold. As the growth curve
plateaus, it will reach a fluorescent end-point at which other factors are rate-limiting. If
the organism’s DNA is not detected by the real-time PCR reaction, the growth curve will
be flat.

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PLATEAU
ENDPOINT
FLUORESCENCE
CYCLE THRESHOLD
Fluorescence
THRESHOLD LINE
(Fluorescence Units) LOG LINEAR
BASELINE
Cycles
Figure 3-4. Amplification Curve and Cycle Threshold (Ct)
3.7 Optical System

Within the I-CORE, the optical system consists of two blocks (see Figure 3-3):
• Six-color exciter module – Contains high intensity light-emitting diodes (LEDs) to
excite the reporter dye molecules.
• Six-color detector module – Contains silicon photodetectors and filters to detect the
six spectral bands.
The optical blocks are positioned within the I-CORE such that their apertures mate with
the optical windows of the reaction tube, allowing excitation and emission detection of
the reaction mixture. By using probes labeled with different fluorescent reporter dyes, up
to six targets can be detected simultaneously in a single reaction tube. The emission
spectra of fluorescent dyes can overlap, and a particular dye could produce a signal in
more than one channel. To compensate for the spectral overlap, the system uses
appropriate calibration and data analysis algorithms to determine the concentrations of
each reporter dye. Table 3-1 shows the excitation and detection spectral bands for the six
channels.

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Table 3-1. GeneXpert Module Excitation and Emission Ranges (6-Color Shown)
Optical Channel Excitation (nm) Emission (nm)

1 375-405 420-480
2 450-495 510-535
3 500-550 565-590
4 555-590 606-650
5 630-650 665-685
6 630-650 >700
3.8 System Calibration

The thermal reaction chamber thermistors are calibrated to ±1.0 °C using National
Institute of Standards and Technology (NIST) - traceable standards. During the
manufacturing process, the temperature of the heating system is measured at two
temperatures: 60 °C and 95 °C. Calibration coefficients that correct for small errors in
the raw thermistor readings of the heaters are stored in the memory of each I-CORE
module.
The optical system is calibrated using standard concentrations of individual unquenched
fluorescent dye-oligos. For each optical channel, the signal produced by a tube alone (the
blank signal) is subtracted from the raw signal produced by the dye-oligo standard to
determine the spectral characteristics. Using the individual spectral characteristics of the
pure dye-oligos, signals from an unknown mixture of dye-oligos can be resolved into
corrected signals for the individual dye-oligos in the mixture.

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4 Performance Characteristics and
Specifications
This chapter presents the GeneXpert Dx system performance characteristics and

specifications. The topics are as follows:
• Section 4.1, Instrument Classification
• Section 4.2, General Specifications
• Section 4.3, Operational Environmental Parameters
• Section 4.4, Environmental Conditions - Storage and Transport
• Section 4.5, Sound Pressure
• Section 4.6, European Union Directives
• Section 4.7, Product Energy Consumption Information
4.1 Instrument Classification

The GeneXpert Dx system is:
• An Industrial Scientific Medical Device (ISM) instrument, medium-sized, for
industrial and laboratory use.
• Designed for stationary operation.
• Intended for worldwide use.
• Intended for evaluating preprocessed biological material.

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Performance Characteristics and Specifications
4.2 General Specifications

4.2.1 General Specifications for GeneXpert R1 Instruments
The GeneXpert R1 instruments have the following specifications:
• Dimensions and Weight:
Table 4-1. Dimensions and Weight
Instrument Width Height Depth Weight

10.8 cm 34.29 cm 34.29 cm 8.16 kg
GX-I R1
(4.2 in) (13.5 in) (13.5 in) (18 lb)
29.8 cm 35.6 cm 31.1 cm 12 kg
GX-IV R1
(11.75 in) (14 in) (12.25 in) (26 lb)
53 cm 76 cm 38 cm 57 kg
GX-XVI R1
(21 in) (30 in) (15 in) (125 lb)
• Power Supply: Auto-ranging

• Rated AC Voltage Range: 100–240 V~, 50–60Hz
• Mains Supply Fluctuations: Up to ± 10% of the nominal voltage
• Transient Over-Voltages: Up to 2500 V peak (impulse withstand category II)
• Rated Current and Fuse Rating:
Table 4-2. Rated Current and Fuse Rating
Instrument Rated Current Fuse Rating

GX-I R1 1.5A @ 100V~, 0.75A @ 200V~ 250 V~ T2A (IEC 60127 time-delay type)
GX-IV R1 1.9A @ 100V~, 0.95A @ 200V~ 250 V~ T3A (IEC 60127 time-delay type)
GX-XVI R1 8.24A @ 100V~, 4.12A @ 200V~ 250 V~ T6.3A (IEC 60127 time-delay type)
4.2.2 General Specifications for GeneXpert R2 Instruments

The GeneXpert R2 instruments have the following specifications:
• Dimensions and Weight:
Table 4-3. Dimensions and Weight
Instrument Width Height Depth Weight

9.4 cm 30.5 cm 29.7 cm 4 kg
GX-I R2
(3.7 in) (12 in) (11.7 in) (9 lb)
16.3 cm 30.7 cm 29.7 cm 6.5 kg
GX-II R2
(6.4 in) (12.1 in) (11.7 in) (15 lb)
28.2 cm 30.5 cm 29.7 cm 11.4 kg
GX-IV R2
(11.1 in) (12 in) (11.7 in) (25 lb)
71.1 cm 65.8 cm 33.8 cm 57 kg
GX-XVI R2
(28 in) (25.9 in) (13.3 in) (125 lb)

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• Power Supply: Auto-ranging

• Rated AC Voltage Range: 100–240 V~, 50–60Hz
• Mains Supply Fluctuations: Up to ± 10% of the nominal voltage
• Transient Over-Voltages: Up to 2500 V peak (impulse withstand category II)
• Rated Current and Fuse Rating:
Table 4-4. Rated Current and Fuse Rating
Instrument Rated Current Fuse Rating

1.5A @ 100V~
GX-I R2 No serviceable fuse
(AC Adapter Output 2.5A @ 24Vdc)
1.5A @ 100V~
GX-II R2 No serviceable fuse
(AC Adapter Output 2.5A @ 24Vdc)
250V~ T3A
GX-IV R2 1.4A @ 100V~
(IEC 60127 time-delay type)
250V~ T6.3A
GX-XVI R2 6.16A @ 100V~
(IEC 60127 time-delay type)
4.3 Operational Environmental Parameters

Your laboratory must meet the following requirements:
• General Environment: Indoor only
• Pollution Degree: 2
• Operating Temperature: 15–30 °C
• Operating Temperature Required for Maximum Thermal Ramp Rates:
20–25 °C
• Relative Humidity: 10%–95%, non-condensing
Place the GeneXpert Dx system away from heat and air conditioning ducts. Do not place
the instrument directly under an air vent or in direct sunlight. Always keep the
instrument module doors closed when not in use.
4.4 Environmental Conditions - Storage and Transport

The required storage conditions are as follows:
• Temperature: -30 °C to +45 °C
• Humidity: 0%–95% relative humidity, non-condensing

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4.5 Sound Pressure

The sound pressure specifications are as follows:
• Audible Sound Pressure Range: < 85 dB (reference level 20 µPa)
• Ultrasonic Sound Pressure Between 20kHz to 100kHz: < 94.5 dB SPL
(reference level 20 µPa)
• Maximum Sound Pressure: Contained in the 40 kHz one-third octave bands
4.6 European Union Directives

The GeneXpert Dx systems comply with the following standards for laboratory
equipment:
• IVD In-Vitro Device Directive 98/79/EC
• EMC Directive 2004/108/EC
• Low Voltage Directive 2014/35/EU
• WEEE Directive 2002/96/EC label
• Energy Labeling Directive 2010/30/EU
• Machinery Directive 2006/42/EC
• Packaging Waste Directive 2006/62/EC
• Restriction of Hazardous Substances (RoHS2) Directive 2011/65/EU
Note REACH Directive 1907/2006/EC exempts in vitro diagnostic medical devices.
4.7 Product Energy Consumption Information

Energy Annual Energy
Supplier Model Efficiency On Mode Power Consumption Standby Power
Supplier Name Identifier Class Consumption (W) (KWh) Consumption (W)
Cepheid GeneXpert GX-I G 61 263 58
Cepheid GeneXpert GX-II G 85 372 71
Cepheid GeneXpert GX-IV G 100 489 83
Cepheid GeneXpert GX-XVI G 270 1168 170

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5 Operating Instructions
This chapter explains how to use the GeneXpert Dx system to run an in vitro diagnostic
(IVD) test and manage the results data. The topics are as follows:
• Section 5.1, Typical Workflow
• Section 5.2, Getting Started
• Section 5.3, Using the System Window
• Section 5.4, Checking the List of Available Assay Definitions
• Section 5.5, Barcode Scanner Usage
• Section 5.6, Creating a Test
• Section 5.7, Loading a Cartridge into an Instrument Module
• Section 5.8, Starting the Test
• Section 5.9, Monitoring the Test Process
• Section 5.10, Stopping a Test in Progress
• Section 5.11, Viewing the Test Results
• Section 5.12, Editing the Test Information
• Section 5.13, Generating Test Result Reports
• Section 5.14, Exporting the Test Results
• Section 5.15, Uploading Test Results to the Host
• Section 5.16, Managing the Test Results Data
• Section 5.17, Performing Database Management Tasks
• Section 5.18, Purging Tests from the Database
• Section 5.19, Viewing and Printing Reports
• Section 5.20, Operating with Host Connectivity
• Section 5.21, Operating with Cepheid Link Connectivity
• Section 5.22, System Information
5.1 Typical Workflow

Table 5-1 shows the typical workflow for processing a specimen sample using the
GeneXpert Dx system.

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Operating Instructions
Table 5-1. Typical Workflow for Processing a Specimen
Step Task Section

1. Start the GeneXpert Dx System. Section 5.4
2. Perform Database Management Tasks. Section 5.2.3.1
Check the list of assays available. Import the assay definition files if Section 5.4 and
3.
necessary. Section 2.13
See the Package Insert that
4. Prepare the assay-specific GeneXpert cartridge
is shipped with the cartridge.
5. Create a test. Section 5.6
6. Load a cartridge into an instrument module. Section 5.7
7. Start the test. Section 5.8
8. Monitor the test progress. Section 5.9
9. View the test results. Section 5.11
10. Generate test result reports. Section 5.13
11. Export the test results. Section 5.14
12. Manage the test results data. Section 5.16
5.2 Getting Started

This section describes the basic system tasks.
• Section 5.2.1, Powering the Instrument On and Off
• Section 5.2.2, Turning On The Computer
• Section 5.2.3, Starting the Software
• Section 5.2.4, Logging On with Software Running
• Section 5.2.5, Logging Off
• Section 5.2.6, Changing Your Password
5.2.1 Powering the Instrument On and Off
The GeneXpert instrument must be powered up before the GeneXpert software is started. If the
Note
instrument is not powered up first, it will not be recognized by the software.
The power switch is located on the lower back side of the instrument. From the front of
the instrument, the switch can be reached from either side.
To turn on the instrument(s), press the switch to the on position (|). The small blue light
on the front of the instrument will turn on.
To turn off the instrument, press the switch to the off position (O).
Important Cepheid recommends powering down the instrument and computer at least once per week.

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5.2.2 Turning On The Computer

After the GeneXpert Dx system computer has been installed, use the following
procedure to turn the computer on and log onto the computer.
1. Turn on the GeneXpert Dx system computer.
2. Wait for the system to boot. The Windows Account screen will be displayed. See
Figure 5-1.
Figure 5-1. Windows Account Screen

3. On the Windows Account screen, select the Cepheid -Admin user account (see
Figure 5-1). The Windows Password screen will be displayed. See Figure 5-2.
The GeneXpert Dx system computer is configured with two Windows accounts. The
Cepheid-Admin account is for administrator tasks such as software updates, system
configuration and for normal operation; and the Cepheid-Techsupport account is for
use only by Cepheid Technical Support. See Figure 5-1.
Caution
You must be logged on using the preconfigured Cepheid account. If you log on using a
different user name and profile, the power management settings will be incorrect.

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Figure 5-2. Windows Password Screen

4. On the Windows Password screen (see Figure 5-2), enter the password assigned by
your system administrator.
The default password is cphd and must be changed upon initial login. After the
password has been changed by the system administrator, enter the assigned
password for future logins.
On the initial login to the GeneXpert system for the Cepheid account, after entering the cphd
password, a prompt will be immediately displayed to change the password. Follow the on-screen
instructions to change the password. Remember to record and store the new password information
Note
in a safe location.
After the first login to the system, there will be no additional prompts to change the password.
Caution
Do not change the Cepheid user profile. Changing the profile can cause loss of data during a
test.

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5.2.3 Starting the Software

Always turn on the instrument before starting the software.
Note
Always end a software session before turning off the instrument.
The GeneXpert Dx software starts automatically after logging into Windows. If the
GeneXpert Dx software is closed manually, the software can be started in one of two
ways:
1. On the Windows desktop, double-click the GeneXpert Dx icon. See Figure 5-3.

or
On the Windows taskbar, click the Windows icon, and select All Programs >
Cepheid >GeneXpert Dx.
2. The Login screen appears.
Each time the software is started, the Login dialog box appears and asks for a user
name and password (see Figure 5-4). In the User Name box, type your GeneXpert Dx
user name. In the Password box, type your password. Click OK to log on and start
the software.
Figure 5-4. Login Dialog Box

The GeneXpert Dx System Window is displayed. See Figure 5-5.
If the Login dialog box does not appear during the software startup, contact your GeneXpert
Important
Dx system administrator.
If you forget your password, contact your GeneXpert Dx system administrator.

If you are the GeneXpert Dx system administrator and you forget your password, contact Cepheid
Note Technical Support. See the Technical Assistance section in the Preface for the contact information.
Cepheid Technical Support will supply a temporary password to allow you to log on and change the
password. The temporary password expires after 1 day.

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Most of the screens shown in this manual will be at a detail user login. Basic user login will be
Note shown when needed to show screens relating to that specific user and administrator user login will
be shown, where required.
5.2.3.1 Database Management Reminder

1. If the Database Management Reminders box on the System Configuration dialog box
(see Figure 2-52) is not checked, the Database Management Dialog Box (see
Figure 5-6) will not appear and no action concerning the database will be required.
The software will continue to load and you can skip to Section 5.2.3.2 to continue
the startup sequence.
or
2. If the Database Management Reminders box on the System Configuration dialog
screen (see Figure 2-52) is checked, the Database Management dialog box (see
Figure 5-6) will then appear on top of the GeneXpert Dx System window asking if
you want to perform Database Management tasks.

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A. If you click No on the Database Management dialog box (see Figure 5-6). The
GeneXpert Dx software continues to load and you can proceed to
Section 5.2.3.2.
or
B. Click Yes in the Database Management dialog box (see Figure 5-6) and you will
be asked to select the task to be performed (see Figure 5-7).
Depending on the user’s privileges, all (or any) of the four options in the Database Management
Note
dialog box may not be visible. See Figure 5-7.

3. Select the applicable button for the database management tasks desired (i.e.,
Database Backup, Database Restore, Compact Database or Check Database Integrity).
See Section 5.17, Performing Database Management Tasks for details on how to
perform each of the database management tasks.
4. Click the Proceed button (see Figure 5-7) to start performing the desired database
management task.
5. When the database management task is complete, a confirmation dialog box appears.
Click OK, and then the Cancel button in the Database Management dialog box.
The Database Management dialog box disappears from the GeneXpert Dx System
window. Continue with Section 5.2.3.2.

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5.2.3.2 Archive Overdue Reminder

If an archive is not overdue, or if the archive setting in Figure 2-53 is set to Manually,
Figure 5-8 will not appear, and you can skip directly to Section 5.3.
If an archive is overdue, the Test Archive Reminder dialog box will appear (see
Figure 5-8).
Figure 5-8. Test Archive Reminder Dialog Box

If you do not want to archive, click No in the Test Archive Reminder dialog box (see
Figure 5-8). Continue the startup sequence without archiving, in Section 5.3.
or
If you would like to archive, click Yes in the Test Archive Reminder dialog box (see
Figure 5-8) to continue the startup sequence with archiving. The Select Test(s) To Be
Archived screen appears. See Figure 5-9.
Figure 5-9. Select Test(s) To Be Archived Screen

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To archive tests, perform Step 2 through Step 7 of the procedure in Section 5.16.1,
Archiving the Tests. When you are finished with the archiving, continue with
Section 5.3.
5.2.4 Logging On with Software Running

If another user is logged onto the system, it is not necessary to log the other user out
before logging in. To log on to the software while the software is running: on the User
menu, click Login. See Figure 5-10.
Enter your information into the Login dialog box (see Figure 5-4). You will be logged
onto the system and the other use will be automatically logged out.
Figure 5-10. User Menu (Login)

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5.2.5 Logging Off

To log off the software: in the GeneXpert Dx System window, on the User menu, click
Logout. See Figure 5-11.
Figure 5-11. User Menu (Logout)

The GeneXpert Dx System window changes to the No User mode. You should log off if
you are going to be away from the system for an extended period of time. Logging off
prevents the software from recording other users’ activities under your account.
Note If you log out while a test is in progress, the system will finish the test and save the results.

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5.2.6 Changing Your Password
Important In order to maintain system security, users should change their password every 90 days.
Cepheid recommends that users change their password every 90 days to protect their
identity on the GeneXpert Dx system. Your institution may have additional requirements
for changing passwords. Follow your institution’s policies regarding passwords. To
change your GeneXpert Dx software password:
1. In the GeneXpert Dx System window, on the User menu, click Change Password.
See Figure 5-12. The Change Password dialog box is displayed (see
Figure 5-13).
Figure 5-12. User Menu (Change Password)

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Figure 5-13. Change Password Dialog Box

2. In the Current Password box, type your current password.
3. In the New Password and Confirm New Password boxes, type your new password
(must be 6 to 10 characters).
4. Click OK to save the change.
5. A dialog box will be displayed indicating that the password was successfully
changed. Click OK to close the dialog box.
If the password does not meet the minimum requirements, a dialog box will be
displayed indicating the requirements. Click OK to return to the Change Password
dialog box and close the dialog box.
5.3 Using the System Window

When you start the GeneXpert Dx software, the GeneXpert Dx System window appears.
Figure 5-14 shows an example of the GeneXpert Dx System window.
Depending on the permissions you have, the window in Figure 5-14 might vary slightly.
For information about your user profile and permissions, see your GeneXpert Dx system
administrator.
When you click Check Status, View Results, Define Assays, or Maintenance on the menu
bar, the window contents change and a new menu appears on the menu bar. For example,
if you click View Results, the View Results window displaces the current window
contents. In addition, the View Results menu appears on the menu bar so that you have
the option of accessing the View Results functions from the menu.

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5.4 Checking the List of Available Assay Definitions

Before starting an in vitro diagnostic test, check that the assay definition you want to use
is already loaded into the software. To do this:
1. In the GeneXpert Dx System window, click Define Assays. The Define Assays
window appears (see Figure 5-15).
2. In the Assay list (on the left side of the window), verify that the assay definition you
want to use is present. Cartridges will not run with an assay version that does not
match the cartridge barcode information. Make sure to use the latest version of the
assay definition file.
3. If the assay is not listed, import the assay definition file. See Section 2.13.2,
Importing Assay Definitions. You must have permission to import assay definitions.
If you do not have such permission, contact your GeneXpert Dx system
administrator.

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List of Available Assays
Figure 5-15. GeneXpert Dx System - Define Assays Window

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5.5 Barcode Scanner Usage

Using the hand-held scanner is similar for all scanning operations, such as scanning the Patient ID,
Note the Sample ID and the cartridge barcode, although this section describes the scanning of the
cartridge barcode. See Figure 5-16.
To scan a cartridge barcode, follow the instructions in this section.
1. Scan the barcode by holding the scanner about 8 to 10 inches from the barcode,
aligning the laser on the scanner to the barcode image. Figure 5-16 shows a cartridge
barcode being scanned.
2. When aiming is correct, press the trigger control on the scanner. An audible beep
will sound.
If the barcode on the cartridge is damaged or smudged and cannot be scanned, skip the cartridge
Note and contact Cepheid Technical Support for a replacement cartridge, if necessary. If the barcode
scanner is damaged, missing or incorrectly configured, contact Cepheid Technical Support.
Scanner
Figure 5-16. Scanning a Cartridge Barcode

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5.6 Creating a Test

Caution
The Information you provide in the Create Test dialog box is automatically saved when you
start the test. If you close the Create Test dialog box before you start the test, all information
will be lost.
For screenshots shown in this manual, the Patient ID field will be shown as enabled and the
Patient ID 2 and Patient Name fields will also be enabled. The Patient ID, Patient ID 2 and
Patient Name fields are optional and may be left blank if they are not required. If these options are
not enabled in the system configuration screen, they will not be displayed. In addition, Patient
Note Demographics will be displayed only if enabled by your GeneXpert Dx system administrator (see
Section 2.11, Configuring the System).
Scanning the Patient ID, Sample ID, and cartridge label reduces typing errors and helps ensure that
the Patient ID, Sample ID, and test results are properly linked. If the barcode scanning options are
not turned on, the Patient ID, Sample ID, and assay information can be provided manually.
The following symbols cannot be used for Sample ID, Patient ID, Patient ID2, First Name,
Important
Last Name, Other Sample Type, or Notes: | @ ^ ~ \ & / : * ? " < > ' $ % ! ; ( ) ‐
When a test is being created, a record of how a specimen is processed is being created.
The record includes Patient ID, Sample ID, cartridge information, the assay information,
instrument module ID, and test type. In addition, Patient ID 2, First Name, Last Name, and
Patient Demographic information is also included, if enabled (checked) in the system
configuration.
Note Patient Demographic data cannot be edited after data entry.
For screens shown in this example, Patient ID 2, First Name, Last Name and Patient
Note Demographics are enabled. If some of these options are not enabled, screens will vary in
appearance.
To create a test:
1. In the GeneXpert Dx System window, click Create Test on the menu bar. The Scan
Patient ID Barcode dialog box appears. See Figure 5-17.

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Figure 5-17. Create Test Window and Scan Patient ID Barcode Dialog Box
2. Scan the Patient ID barcode using the supplied barcode scanner. See Section 5.5.
The Scan Sample ID dialog box appears. See Figure 5-18.
To enter the Patient ID barcode manually, click the Manual Entry button. The Manual
Patient ID Barcode Entry dialog box will be displayed. Enter the patient ID barcode
into the Patient ID Barcode field and click OK.

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Figure 5-18. Create Test Window and Scan Sample ID Barcode Dialog Box
3. Scan the Sample ID barcode using the supplied barcode scanner. See Section 5.5.
The Scan Cartridge Barcode dialog box appears. See Figure 5-19.
To enter the Sample ID barcode manually, click the Manual Entry button. The
Manual Sample ID Barcode Entry dialog box will be displayed. Enter the sample ID
barcode into the Sample ID Barcode field and click OK.

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Figure 5-19. Scan Cartridge Barcode Dialog Box

4. Scan the cartridge barcode using the supplied barcode scanner. See Section 5.5. The
Create Test dialog box appears as shown in Figure 5-21. Note that the software
automatically fills the required information into the Create Test window.
To enter the cartridge barcode manually, click the Manual Entry button. The Manual
Cartridge Barcode Entry dialog box will be displayed. Enter the cartridge barcode
into the Cartridge Barcode field and click OK.
Reagent Lot ID
Expiration Date
Assay
Cartridge Barcode
(All numbers including
cartridge serial number)
Cartridge Serial Number
Figure 5-20. GeneXpert Cartridge
Type in the cartridge information accurately. This information will appear on all patient and
Important
results reports.

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To ensure the accuracy of test results, be sure to use the same cartridge in the test. (Do not
Important
switch or substitute cartridges after scanning and other preparations have begun.)
Important If you see multiple assays in the drop-down menu, select the desired assay.
5. (Optional) If Patient ID 2 is enabled, place the cursor in the field. The Patient ID 2 can
be either scanned or entered manually into the field.
6. (Optional) If Patient Name is enabled, place the cursor in the Last Name field and
enter the patient's last name then place the cursor in the First Name field and enter the
patient's first name (see Figure 5-21).
Figure 5-21. Create Test Dialog Box with the Patient ID and Sample ID Fields Shown

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7. (Optional) If Patient Demographics is enabled, follow the steps below to enter the
desired data:
A. Date of Birth - Click the drop-down arrow in the Date of Birth box to display the
calendar.
Using the <<Previous and Next>> buttons, scroll through the calendar to display
the appropriate year and month. Select the patient’s birth date and click OK (see
Figure 5-22).
Figure 5-22. Create Test Dialog Box with the Date of Birth Field and Calendar Shown

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B. Ethnicity - Click the drop-down arrow in the Ethnicity box and select the
appropriate ethnicity from the drop-down menu (see Figure 5-23).
Figure 5-23. Create Test Dialog Box with the Ethnicity Field Shown

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C. Gender - Click the drop-down arrow in the Gender box and select the
appropriate gender from the drop-down menu that appears (see Figure 5-24).
Figure 5-24. Create Test Dialog Box with the Gender Field Shown
D. Postal Code - Type the postal code (the entry may be left blank). The GeneXpert
Dx software does not validate the postal code. In the United States, the postal
code is referred to as the zip code.
8. (Optional) In the Select Module list, select the available instrument module. By
default, the software displays the module that is least used.
Only modules with the correct calibration and that are not busy running another test
will be selectable. You can change the selected module by clicking on the drop down
menu.
9. Select the Test Type (Specimen or External Controls).
10. Type any additional information about the test in the Notes box.
The Cepheid barcode scanner has been qualified to be used with Codabar, Code 39, Code 128a,
Note
Code 128b, Code 128c or interleaved 2 of 5 barcode symbologies.
For customers planning to use the interleaved 2 of 5 symbology, note that due to the
Caution construction of the interleaved 2 of 5 symbology, it is possible for a scan line covering only a
portion of the code to be interpreted as a complete scan, yielding less data than is encoded
in the bar code. To prevent this, select specific lengths (interleaved 2 of 5 - One Discrete
Length) for interleaved 2 of 5 applications. For assistance, call Cepheid Technical Support.
See the Technical Assistance section in the Preface for the contact information.

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Make sure you scan or type the correct Sample ID, Patient ID, or Patient ID 2. The Sample ID,
Caution Patient ID, or Patient ID 2 is associated with the test results and is shown in the View Results
window and all the reports.
The following symbols cannot be used for Sample ID, Patient ID, or Patient ID2: | @ ^ ~ \ &
/ : * ? " < > ' $ % ! ; ( ) ‐
5.7 Loading a Cartridge into an Instrument Module

Caution Do not load a GeneXpert cartridge that has been dropped or shaken after the lid of the
cartridge has been opened. Dropping or shaking the cartridge after it has been opened can
cause invalid results. Bent or broken reaction tubes can also produce invalid results. Do not
re-use spent cartridges.
Caution
Always pick up the cartridge by its body. Do not pick up the cartridge by the protruding
reaction tube (see Figure 5-25).
Body
Reaction Tube
Figure 5-25. Cartridge Showing Body and Reaction Tube

This section assumes that you have inserted the specimen and reagents into the
GeneXpert cartridge. See the assay-specific package insert or quality-control labeling
document for instructions.

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5.8 Starting the Test

Caution
Do not run other software while a test is in progress. Doing so might interfere with the test
process and cause the loss of data.
If you log out while a test is in progress, the system will continue to finish the test and save the
Note
results.
To start the test:

1. In the Create Test dialog box (see Figure 5-26), click Start Test. The software asks
for your password (if a password is required to start a test).
Note If your user name is not displayed, type both your user name and password.
Figure 5-26. Create Test Dialog Box, Ready to Start Test

2. Type your password, and then click OK. In the Check Status window, the instrument
module progress changes to Waiting. The green light above the instrument module
door flashes.
3. Open the instrument module door below the module with the flashing green light.
4. Place the cartridge on the module bay floor. See Figure 5-27. The cartridge label
should face out. Make sure the cartridge sits level on the bay floor and is positioned
at the heel of the bay.

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5. Close the instrument module door all the way. The door latches and the green light
stops flashing and stays on. The test starts.
Figure 5-27. GeneXpert Cartridge, Positioned at the Heel of the Module Bay Floor
During the first few minutes after you start the test, the system moves the cartridge
contents and rehydrates the reagent beads. If applicable to the assay definition, the
system also performs a probe check to see if the master mix is reconstituted properly and
that the probes are present in the master mix.
• If the probe check fails, the test will abort. You can check the error message to
review the cause of the probe check failure. See Section 9.18.2, Error Messages.
• If the probe check passes, the test continues.
When the test finishes, the instrument module door unlatches and the green light turns
off. In the GeneXpert Dx System window, the Progress column in the Modules area
shows the module is available.

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5.9 Monitoring the Test Process

You can monitor the test process or other status indicators in the following areas of the
GeneXpert Dx System window. See Figure 5-28:
• Modules—Displays the assay definition used, the Sample ID, the progress or phase
of the test (for example, 3/45 means the test is on the third PCR cycle out of 45
cycles), the status of the test phase, and the amount of time remaining until the end
of the test. If the Status column displays Error or Warning, look in the Messages area
of the window for a description of the problem.
• Messages—Displays the date and time you started the software, the software version
number, and any error messages that were encountered since the software started.
Check the Module Area for Test Status
Figure 5-28. GeneXpert Dx System Window, Displaying the Status of a Run in Progress
When a test is in progress, NO RESULT is shown in the Result column.
The right side of the screen, Tests Since Launch, displays tests since the most current launch of
Note
the GeneXpert Dx software.

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5.10 Stopping a Test in Progress

Caution
After you stop a test in progress, the system halts the sample processing activities and
terminates data collection. The cartridge cannot be reused.
To stop a test that is currently in progress, in the GeneXpert Dx System window, click
Stop Test on the menu bar. The Stop Test dialog box appears. See Figure 5-29. You can
do one of the following:
• Stop Individual Tests—Select the tests you want to stop, and then click Stop. The
confirmation dialog box appears. Click Yes to confirm or click No to cancel.
• Stop All Tests in Progress—Click Select Running to select all tests currently in
progress, and then click Stop. The confirmation dialog box appears. Click Yes to
confirm or click No to cancel.
• To clear all of the test selections, click Deselect All.
• Click Cancel to close the Stop Test dialog box.
Figure 5-29. Stop Test Dialog Box

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5.11 Viewing the Test Results

To ensure all data is displayed correctly, reports must be generated in the same language
Important
that was used when the test results were collected.
You can display and view the test results in the View Results window. See
Section 5.11.1, Displaying the Test Results. The features in the View Results window
vary by user type:
• Basic users (see Section 5.11.2, Basic User View)
• Detail users and the administrator (see Section 5.11.3, Detail User and Administrator
View)
5.11.1 Displaying the Test Results

To select and display the test results:
1. In the GeneXpert Dx System window, click View Results on the menu bar. The View
Results window appears. See Figure 5-30.
The View Results window displays different features for different user types. Section 5.11.2, Basic
User View describes the View Results window for the Basic users. Section 5.11.3, Detail User and
Note
Administrator View describes the View Results window for the Detail users and Administrator users.
Figure 5-30 shows a View Results window for Detail users and Administrator users.
To select a test, click View Test. The Select Test To Be Viewed dialog box appears.
See Figure 5-31.
2. Select the test to be viewed. To sort the list of tests by a column, click the column
heading.
3. Click OK. The results of the selected test is displayed in the View Results window.
Sometimes only part of the result information is shown in the Result column of the Select
Important Test to be Viewed dialog box. To see the rest of the result information, move the mouse’s
cursor over the Result column.

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Figure 5-30. GeneXpert Dx View Results Window (Detail and Administrator View)
Figure 5-31. Select Test to be Viewed Dialog Box

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5.11.2 Basic User View

Figure 5-32 shows the View Results window for Basic users. The window contains three
tabs: Results, Errors, and Support.
5.11.2.1 Results Tab

The Results tab displays the following information for a test (see Figure 5-32):
Figure 5-32. GeneXpert Dx View Results Window—Results Tab (Basic Users View)
Note Editable fields are shown on a white background. Non-editable fields have a gray background.
• Patient ID—This field is available if the Use Patient ID option is enabled. It is user-
editable if it was not originated from a host order. If there is an asterisk (*) next to
the field, the Patient ID was scanned.
• Patient ID 2—This field is available if the Use Patient ID 2 option is enabled. It is
user-editable if it was not originated from a host order.
• Sample ID—This field is user-editable if it was not originated from a host order. If
there is an asterisk (*) next to the field, the Patient ID was scanned.
• Assay—Assay name. This field is not editable.

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• Version—The assay version number. This field is not editable.

• Result—The test results shown in the Basic View Results window will be expanded
to display all lines for multiple line results to support the maximum number of
results for organism, genotyping, or % ratio assays. If the expansion is such that
other information will no longer fit on the window, a scroll bar will allow viewing of
the other information. The result is not editable.
• User—This field displays the name of the system operator who performed the test. It
is not editable.
• Sample Type—This field is editable using a drop-down list of assay specific sample
types.
• Other Sample Type—The Other Sample Type will contain text entered during the
Create Test process or as a result of editing a test. It is editable if the Sample Type is
Other; otherwise, it is not editable.
• Notes—This field displays any notes entered when the test was submitted. If
additional notes are required, add or change the note information.
• Start Time—This non-editable field displays the test start date and time in the system
configuration format.
• End Time—This non-editable field displays the test end date and time in the system
configuration format.
• Status— The operational status of the test is displayed in this non-editable field. It
will display Done if the test has completed. It may also display RUNNING if the test
has not completed yet or INCOMPLETE if there were problems while running the test.
• Upload Status—(if host communication is enabled) – If host communication is
enabled, a field will be shown indicating the upload status of the results. This field is
not editable. It will display Uploaded if the test results have been uploaded or it may
also display Pending Upload if the test has completed but the results have not been
uploaded yet. This field is not displayed if host communication is not enabled.
• Disclaimer—This non-editable disclaimer text is shown after the test result is
available depending on the assay and the result.
Some fields are editable if the system administrator has set up the system User Type
Configuration to allow basic users to edit test details. To edit those fields:
1. Place the cursor in the desired field(s) and edit the fields, as needed.
2. Press the Save Changes button. The Save dialog box will be displayed.
3. Check that the Save Test radial button is enabled.
4. Press the Yes button to save the changes. Pressing the Cancel button returns to the
View Results screen with the entered changes displayed. Pressing the No button
returns to the View Results screen and discards the entered changes.

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5.11.2.2 Errors Tab

The Errors tab lists the errors encountered during the test process and provides the
following information (see Figure 5-33).
Figure 5-33. GeneXpert Dx View Results Window—Errors Tab (Basic Users View)
• #—The number that indicates the sequence in which the errors appeared during the
test. It is not user-editable.
• Description—A description of the error type is displayed. It is not user-editable.
• Detail—Additional error information is provided about the error (e.g. Error 2002:
Could not find calibration......). It is not user-editable.
• Time—The time the error occurred is displayed. It is not user-editable.
See Section 9.18.2, Error Messages for a description of the error messages and the
possible causes and potential solutions to the errors.
If there were no errors during the test, the Errors tab displays a blank table.

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5.11.2.3 Support Tab

The Support tab displays the following information for a test (see Figure 5-34):
Figure 5-34. GeneXpert Dx View Results Window—Support Tab (Basic Users View)
• Assay Type—This is a non-editable field that displays the type of diagnostic test that
was run. For most tests, it will display In Vitro Diagnostic.
• Test Type—This editable field displays type of test that was run. The drop-down can
be set to either Specimen or various types of external controls.
• Reagent Lot ID–This field displays the reagent lot ID. If there is an asterisk (*) next
to the field, the reagent lot ID was scanned from the cartridge. It is not editable if the
associated assay is a factory assay that requires lot specific parameters or the
cartridge barcode is scanned.
• Expiration Date—This non-editable field displays the cartridge expiration date. If
there is an asterisk (*) next to the field, the cartridge expiration date was scanned
from the cartridge.
• Cartridge S/N—This non-editable field displays the cartridge serial number. If there
is an asterisk (*) next to the field, the cartridge serial number was scanned from the
cartridge.

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• Error Status—This non-editable field indicates if there were any errors during the
test run. No errors are indicated by OK. If an error occurred while the test was
running, the error status will be Error.
• S/W Version—This non-editable field displays the software version installed on the
system at the time the test was run.
• Module Name—This non-editable field displays the name of the module in which the
test was run (i.e. A1).
• Instrument S/N—This non-editable field displays the serial number of the instrument
in which the test was run.
• Module S/N—This non-editable field displays the serial number of the module in
which the test was run.
Editable if the system administrator has set up the system User Type Configuration to
allow basic users to edit test details. To edit this field:
1. Click the drop down box for the Test Type field and select the desire test type.
2. Press the Save Changes button. The Save dialog box will be displayed.
3. Check that the Save Test radial button is enabled.
4. Press the Yes button to save the changes. Pressing the Cancel button returns to the
View Results screen with the entered changes displayed. Pressing the No button
returns to the View Results screen and discards the entered changes.
Note Editable fields are shown on a white background. Non-editable fields have a gray background.
5.11.3 Detail User and Administrator View

Figure 5-35 shows the View Results window for Detail and Administrator users. The
window is divided into four areas:
• Test Information Area—Displays information provided when you created the test,
including the module used in the test, the Patient ID or Patient ID 2 (if they are
enabled), Sample ID, assay information, and cartridge information. You can edit and
save the Patient ID, Patient ID 2, Sample ID, Test Type information, Sample Type,
Other Sample Type, and text in the Notes box (see Section 5.12, Editing the Test
Information). Do not use the following symbols in this area: | @ ^ ~ \ & / : * ? " < > ' $
% ! ; ( ) -.
• Views Area—Allows you to arrange the display of the results and growth curve
areas. For example, you can display the growth curve area above the results area.
• Results Area—Allows you to view the information in the following tabs: Test Result,
Analyte Result, Detail, Errors, History, and Support.

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• Growth Curve Area—Displays a graph that plots the number of cycles on the X-axis
and the fluorescence units on the Y-axis for each analyte. The graph reflects the
curve analysis specified in the assay definition. Using this graph, you can visually
inspect the rate at which the fluorescence signal increases.
To display or hide an analyte graph, select the analyte name in the graph legend to
the right of the graph. In addition, you can change the magnification of the graph in
the X or Y direction by clicking and dragging the horizontal or vertical slider next to
the X- and/or Y-axes.
5.11.3.1 Test Result Tab

The Test Result tab of the View Results window displays the following information for a
test (see Figure 5-35).
Test Information Area Views Area Results Area Growth Curve Area
Figure 5-35. GeneXpert Dx View Results Window—Test Result Tab (Detail Users and Administrator
View)
• Assay Name—The name of the assay. This field is not editable.
• Version—The assay version number. This field is not editable.

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• Test Result—The test results shown in the Detail View Results will be expanded to
display all lines for multiple line results to support the maximum number of results
for organism, genotyping, or % ratio assays. If the expansion is such that other
information will no longer fit on the window, a scroll bar will allow viewing of the
other information. The Test Result is not editable.
• Disclaimer—This non-editable disclaimer text is shown after the test result is
available depending on the assay and the result.
Note There are no editable fields on the Test Result tab.
5.11.3.2 Analyte Result Tab

The Analyte Result tab displays the following information in tabular form (see
Figure 5-36.
Figure 5-36. GeneXpert Dx View Results Window —Analyte Result Tab (Detail Users and Administrator
View)
• Analyte Name—The analyte that was tracked during the test process. The possible
analytes are the name of the test target, IC (internal control), or SPC (sample
processing control), and EC (endogenous control).

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• Ct—The first cycle in which the fluorescence signal reaches a specified threshold.
The threshold cycle (Ct) is determined from the growth curve.
• EndPt—The endpoint value of the growth curve in fluorescence units.
• Analyte Result—The result for each analyte processed. The results are displayed
after the test is finished.
• Probe Check Result—The result of the probe check, the process that verifies
presence and integrity of the probes in the master mix. Possible values are PASS,
FAIL and NA if the assay does not include a probe check. The probe check passes if
the measured fluorescence values together meet the predetermined validated
acceptance criteria.
Note There are no editable fields on the Analyte Result tab.
5.11.3.3 Detail Tab

The Detail tab displays the detailed probe check results if the assay specifies the use of a
probe check (see Figure 5-37). In addition, the second derivative peak height value (for
the combination curve), melt peaks, and curve fit result are available if the assay
definition specified their use.
Figure 5-37. GeneXpert Dx View Results Window—Detail Tab (Detail Users and Administrator View)

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As shown in Figure 5-37, the Detail tab of the View Results window provides the
following miscellaneous data for test results:
• Analyte Name—Description of the reference targets that aid in the detection of a
specific assay.
• Prb Chk 1—Probe check 1 data are the results of fluorescent measurements of dye
specific to each analyte.
• Probe Check Result—Before the start of the PCR reaction, the GeneXpert Dx system
measures the fluorescence signal from the probes to monitor bead rehydration,
reaction-tube filling, probe integrity and dye stability. Probe Check passes if it meets
the assigned acceptance criteria.
• 2nd Derivative Peak Height—The highest peak of the 2nd derivative represents the
point of maximum curvature of the growth curve. The threshold defines only a
minimum peak height for determining Ct. If the 2nd derivative peak is above the
threshold, a Ct is reported. If the peak is below the threshold, no Ct is reported.
• Curve Fit—This section is selected by default in the dialog. Curve Fit substitutes the
modeled curve fit data to reduce false positives that may occur due to optical noise,
drift or other curve anomalies, by smoothing the curve. For example a noise spike in
a curve could trigger the primary threshold, indicating a positive whereas an
experienced operator would call the result as a negative.
Note There are no editable fields on the Detail tab.

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5.11.3.4 Errors Tab

The Errors tab lists the errors encountered during the test process and provides the
following information (see Figure 5-38).
Figure 5-38. GeneXpert Dx System - View Results Window—Errors Tab (Detail Users and Administrator
View)
• #—The number that indicates the sequence in which the errors appeared during the
test. It is not user-editable.
• Description—A description of the error type is displayed. It is not user-editable.
• Detail—Additional error information is provided about the error (e.g. Error 2002:
Could not find calibration......). It is not user-editable.
• Time—The time at which the error occurred is displayed. It is not user-editable.
See Section 9.18.2, Error Messages for a description of the error messages and the
possible causes and potential solutions to the errors.
If there were no errors during the test, the Errors tab displays a blank table.

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5.11.3.5 History Tab

The History tab displays a log of revisions made to the test information (see
Figure 5-39). The log includes the original information, the revised information, the user
who revised the information, and the date and time of the revision.
Figure 5-39. GeneXpert Dx View Results Window—History Tab (Detail Users and Administrator View)
See Section 5.12, Editing the Test Information for instructions on how to edit
information in the View Results window and save the change(s) into the History tab
window.

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5.11.3.6 Support Tab

The Support tab for the Detail users and Administrator users displays the following
information for a test (see Figure 5-40):
• Assay Type—This is a non-editable field that displays the type of diagnostic test that
was run. For most tests, it will display In Vitro Diagnostic.
• Cartridge S/N—This non-editable field displays the cartridge serial number. If there
is an asterisk (*) next to the field, the cartridge serial number was scanned from the
cartridge.
• Expiration Date—This non-editable field displays the cartridge expiration date. If
there is an asterisk (*) next to the field, the cartridge expiration date was scanned
from the cartridge.
Figure 5-40. GeneXpert Dx View Results Window—Support Tab (Detail Users and Administrator View)

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• Error Status—This non-editable field indicates if there were any errors during the
test run. No errors are indicated by OK. If an error occurred while the test was
running, the error status will be Error.
• S/W Version—This non-editable field displays the software version installed on the
system at the time the test was run
• Instrument S/N—This non-editable field displays the serial number of the instrument
in which the test was run
• Module S/N—This non-editable field displays the serial number of the module in
which the test was run.
Note There are no user-editable fields on the Support tab.
5.12 Editing the Test Information

Make sure you scan or type the correct Sample ID, Patient ID and Patient ID2. The Sample ID,
Important Patient ID and Patient ID2 is associated with the test results and is shown in the View Results
window and all the reports.
For each test, you can edit the Patient ID and Patient ID 2 (if they are enabled), Sample
ID, Test Type, Sample Type, Other Sample Type, and Notes. To do this, in the View
Results window (see Figure 5-41), edit the Sample ID, Test Type, Sample Type, Other
Sample Type and Notes (see Figure 5-41). Sample IDs cannot include the following
characters: | @ ^ ~ & / : * ? " < > ’ $ % ! ; ( ) -.
To demonstrate the History tab feature:
1. In the GeneXpert Dx System window, click View Results on the menu bar. The Test
Result tab is displayed. See Figure 5-41.
2. Click the History tab in the View Results screen (see Figure 5-42). The History tab is
displayed, showing that no changes have been made to the test. See Figure 5-43.

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Figure 5-41. GeneXpert Dx View Results Window (Detail Users and Administrator View)
Figure 5-42. GeneXpert Dx System, View Results Window— (Detail Users and Administrator View)

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Figure 5-43. GeneXpert Dx View Results Window, History Tab Selected

3. Change Test Type to Negative Control as shown in Figure 5-44.
Figure 5-44. GeneXpert Dx View Results Window—Test Type Changed

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4. Click the Save Changes button located at the bottom of the View Results window
(see Figure 5-44). The Save Test dialog box appears. See Figure 5-45.
Figure 5-45. Save Dialog Box

5. Click Yes to save the changes and proceed. The software tracks the change history
(see Figure 5-46).
Click No to not save changes. The previous screen is displayed and all edits are
discarded.
Click Cancel to not proceed and stay in the same window. Any edits made to the
window will remain but will not be saved.
If changes have been made to a window, the Save dialog box will be displayed for any operation
Note
that will open another window.
Figure 5-46. History Tab showing Change from Specimen to Negative Control Test Type

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5.13 Generating Test Result Reports

Important
To generate a PDF file containing the test results, in the View Results window (see
Figure 5-32 or Figure 5-35), click the Report button.
For Basic users, the software creates a PDF file and displays the file in the Adobe
Reader window. You can save and print the PDF file from the Adobe Reader software.
For instructions on how to use Adobe Reader, click the Adobe Reader Help selection
under the Adobe Reader Help menu.
For Detail users and the administrator, the software displays the Test Report dialog box
(see Figure 5-47). Select one or more test reports to print by selecting the check box to
the left of the report(s).
Figure 5-47. Test Report Dialog Box (Detail User and Administrator Only)
Sometimes only part of the result information is shown in the Result column of the Test
Important Report dialog box. To see the rest of the result information, move the mouse’s cursor over
the Result column.

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In the upper left-hand corner of the dialog box, several types of information are
available. Select the information you want to include in the report by clicking the check
box(es) to the left of the item(s):
• Detail—Select to include information from the Detail tab in the report such as analyte
names, probe check values and results, second derivative peak height and curve fit.
• Melt Peaks—Select to include melt peaks in the report, if applicable.
• Error Details—Select to include any error details from the Errors tab, if applicable.
• Troubleshoot—Select to include troubleshooting information in the report, if
applicable.
• Messages—Select to include messages in the report relating to the test, if applicable.
• History—Select to include any changes made to the test results from the History tab,
if applicable.
The Analyte Result button allows the user to select specific information to include in the
Analyte Result section of the report (see Figure 5-48).
Figure 5-48. Select Analyte Result Dialog Box

To include specific analyte data in the report, select one or more of the items from the
Available column and click the right arrow button to move them to the Selected column.
To exclude specific analyte data from the report, select one or more of the items from the
Selected column and click the left arrow button to move them to the Available column.
All items can be either included or excluded by the report by clicking the double right
arrow button or the double left arrow button. After selecting the analyte data items, click
the OK button to close the Select Analyte Result dialog box.

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When all selections have been made, click one or both of the following buttons on the
Test Report dialog box:
• Generate Report File—Creates a PDF file and saves it in the default location or a
location you specify.
• Click the Generate Report File button on Test Report workspace (see
Figure 5-47) to create the PDF file of the test report. The Generate Report File
dialog box will appear, which enables you to save the file to a specified
location. Click Save once you have navigated to the specified location.
• Optionally, to print the report, go to the saved location, open the test report and
print it. A test report similar to the test report shown in Figure 5-49 and
Figure 5-50 will be printed. The last page of the test report contains a signature
block for approval of printed test reports.
The test report shown in Figure 5-49 and Figure 5-50 have all options selected. Specific test reports
Note
may be longer or shorter depending upon the options selected and the items applicable to the test.
• Preview PDF—Creates a PDF file and displays the file in the Adobe Reader window.
The PDF file can be saved or printed from the Acrobat software. For instructions on
how to use Adobe Reader, click the Adobe Reader Help selection under the Adobe
Reader Help menu.
• Close—After generating the test report(s), click Close to close the Test Report
window.
If Print Test Report At End of Test is enabled, the report will automatically print each test
report after the test is completed. See Section 2.11, Configuring the System.

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5.14 Exporting the Test Results

Important
To export the test results to a comma-separated value (.csv) file, in the View Results
window (see Figure 5-32 or Figure 5-35), click Export.
Basic users can only export the test result for the test currently displayed. For Basic
users, the Result Export dialog box appears (see Figure 5-52). Locate and select the
folder where the file is to be exported, type a file name, and then click Save.
Detail and Administrator users can select and export results for multiple tests at one
time. Various options can also be selected for export. For Detail and Administrator users,
the Export Data dialog box appears. See Figure 5-51.
Figure 5-51. Export Data Dialog Box (Detail Users and Administrator Only)

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In the upper left-hand corner of the dialog box, several types of information are
available. Select the information you want to include in the export by clicking the check
box(es) to the left of the item(s):
• Analysis Settings—Select to include analysis settings in the report.
• Test Result—Select to include the test result in the report.
• Optical Data—Select to include optical data in the report.
• Melt Data—Select to include melt data in the report.
• Pressure—Select to include pressure information in the report.
• Ultrasonic Horn Amplitude, Frequency and Duty Cycle—Select to include ultrasonic
horn amplitude, frequency and duty cycle in the report.
• Heater Temperature—Select to include heater temperature information in the report.
Select the test results and the associated information you want to export. The four
buttons at the bottom of the screen, Select All, Deselect All, Select Highlighted and
Deselect Highlighted provide shortcuts to making selections. Click Export when you have
made your selection. The Result Export dialog box appears (see Figure 5-52). Locate and
select the folder where the file is to be exported, type a file name, and then click Save.
The export folder is the default folder. When a report file is exported, the software will remember the
Note
last directory used.
Figure 5-52. Result Export Dialog Box

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Opening and Viewing a .csv File

The exported test results can be opened using Apache OpenOffice (AOO) or other
software program that supports .csv files. The following instructions describe the use of
AOO for opening and viewing a .csv file.
Refer to Appendix D for in-depth instructions for configuring Apache OpenOffice.
Note GeneXpert Dx systems shipped prior to November 30, 2015 may have Microsoft Office installed,
and .csv files can be opened and viewed using the Excel program available in that software suite as
well.
1. In the GeneXpert folder on your system, navigate to the Export folder. Right click on
the .csv file you want to open. When the drop-down menu appears, click Open with
and select OpenOffice Calc. See Figure 5-53.
Figure 5-53. Opening a .csv File to Configure AOO (Example)

2. The Text Import screen will appear. On this screen, verify the checkboxes to the left
of Comma and Quoted field as text have been checked. See Figure 5-54.
In the Character Set drop-down menu:

For single-byte languages (English, French, Spanish, Portuguese, Italian, German,
Russian) select Unicode (UTF-8).
For multi-byte languages (Japanese and Chinese) select Unicode.

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Figure 5-54. Text Import Screen with New Settings Selected

3. After verifying the Separator and other options, click OK. The .csv file will be
displayed.
4. Once the file is open, click on the upper left corner of the worksheet to highlight all
the cells, as shown in Figure 5-55.

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Figure 5-55. All Cells Selected

5. Right click on the column header. A drop-down menu will appear at the right of the
column (see Figure 5-56).
6. In this drop-down menu, select Column Width.
Right-
Click in
Column
Header
Figure 5-56. Drop-Down Menu to select Column Width

7. The Column Width dialog box appears. See Figure 5-57

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Figure 5-57. Column Width Dialog Box

8. Click the checkbox to the left of Default value, and then click OK to close the dialog
box. The column widths will then adjust and the file will be formatted, as shown in
Figure 5-58. Click anywhere in the blank columns to “deselect” the blue cells and
turn the cells white again.
Figure 5-58. Example Exported Test Results

9. Click Save under the File menu to save the document.

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5.15 Uploading Test Results to the Host

If your host connectivity is enabled, the Upload Test button (see Figure 5-59) is available
for use to select test(s) for uploading to the host. For details, see Section 5.20, Operating
with Host Connectivity.
Figure 5-59. Upload Test Results to the Host
5.16 Managing the Test Results Data

The GeneXpert Dx system includes a database that stores all of the saved test results.
You can:
• Manage the test result data:
• Archive tests and then purge archived tests to save database space (see
Section 5.16.1, Archiving the Tests).
• Retrieve tests from an archived file (see Section 5.16.2, Retrieving Data from
an Archive File).
• Perform database management tasks (only during system startup and shutdown):
• Back up the database (see Section 5.17.1, Backing up the Database).

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• Restore the database (see Section 5.17.2, Restoring the Database).

• Compact the database (see Section 5.17.3, Compacting the Database).
• Check the integrity of the database (see Section 5.17.4, Checking the Integrity
of the Database).
The GeneXpert Dx system administrator specifies whether you have the permissions for
the data management tasks. See Section 2.10, Defining Users and Permissions. See your
GeneXpert Dx system administrator to adjust the permissions to meet your requirements.
5.16.1 Archiving the Tests

Archiving tests allows you to move your data and, if desired, free up space in the
database. You can archive multiple tests at a time. In addition to serving as a
safe-keeping mechanism, you can provide the archive files to Cepheid for analysis when
troubleshooting. The archive process creates a copy of the test and saves the data in a
.gxx file.
Some e-mail filters may block files with .gxx extensions. Adjust your email filter, if possible,
Important
or change the extensions, if required.
To archive the test data:

1. In the GeneXpert Dx System window, on the Data Management menu, click Archive
Test. The Select Test(s) To Be Archived dialog box appears. See Figure 5-60.
Figure 5-60. Select Test(s) To Be Archived Dialog Box

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2. Select the test(s) you want to archive. Click the check box that is adjacent to each
test you want to archive. See Figure 5-60. You can select the individual tests one-by-
one, or select a large number of tests by clicking one of the following buttons at the
bottom of the Select Tests To Be Archived screen:
• Select All – Selects all of the tests in the table.
• Select Highlighted – Selects the tests you highlighted.
• Select New Archive – Selects only the tests that have not been archived before.
You can also hold the Shift or Ctrl keys to highlight continuous and discontinuous multiple tests on
Note
the Select Tests To Be Archived screen.
After selecting tests on the Select Tests To Be Archived screen, click one of the
following buttons to deselect some or all tests:
• Deselect All – Deselects all of the test selections in the window.
• Deselect Highlighted – Deselects the tests you highlighted.
In addition to selecting the tests to archive, there are two check boxes located near
the top of the Select Tests To Be Archived screen that may need to be selected:
• Cloak IDs – Select this check box if you want to send Cepheid Technical
Support some data in question, but want to hide patient-sensitive information.
See Masking Patient and Sample IDs During Test Archive (below) for more
information.
• Purge Selected Tests from List After Archiving (Recommended monthly)– Select
this check box to free up space on the computer. After the selected tests have
been successfully archived, they are removed from the database.
3. Click OK. A message appears and asks you to confirm the archive request.
4. Click Proceed. The Save dialog box appears.
Click Cancel to not perform the Archive Test operation.
5. Locate and select the folder in which you want to store the archive (.gxx) file, type a
name for the archive file, and then click Save.
Caution The default archive location is the export folder which is located on the computer hard drive.
To guard against loss of data, the files in the export folder should be periodically copied to a
different computer or server. If the GeneXpert Dx system is connected to a network, it is
possible to archive files directly to a server. To configure the archive location, see
Section 2.11.2, Archive Settings Tab.
6. After the files have been archived, the Archive Test(s) dialog box is displayed
indicating that the tests have been successfully archived. Click OK.

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7. If you selected the Purge Selected Tests from List After Archiving (Recommended
Monthly) option, a Purge Test(s) dialog box appears indicating that the selected
test(s) will be deleted from the database. Click Yes to confirm or click No to not
delete the selected test(s) from the database.
Caution
If data is archived and purged from the database, then the archive files will only include the
Patient ID and not the patient demographic data. Therefore, it will not be available again and
cannot be used in future connectivity solutions.
It is important to understand that when tests have been archived, they have not been
permanently deleted from the computer. They have been removed from the main system
database and saved to an archive file when the Purge Selected Tests from List After
Important
Archiving (Recommended Monthly) option has been selected. Tests may be retrieved from
the archive file if needed for later use. See Section 5.16.2, Retrieving Data from an Archive
File.
Masking Patient and Sample IDs During Test Archive

Masking sample and Patient IDs allow customers to send Cepheid Technical Support
some data in question, but hides patient-sensitive information.
When the Cloak IDs check box, located in the top left area of the Select Test(s) To Be
Archived dialog box, (see Figure 5-60) is checked, all information about the sample ID
and patient ID is masked.
Caution
Once you mask sample and or patient ID information for an archived test, if you retrieve the
test information, the sample and patient ID information will still be masked. You should
maintain an on-site copy of the archived test information without the masked information.
5.16.2 Retrieving Data from an Archive File

Caution
If a test you are retrieving already exists in the current database, the software will overwrite it
and existing data will be lost.
You can retrieve test data from an archived file. To do this:

1. In the GeneXpert Dx System window, on the Data Management menu, click Retrieve
Test. The Open dialog box appears.
2. Locate and select the archive (.gxx) file, and then click Open to retrieve the selected
test(s) from the archive file.
If there are tests in the archive that already exist in the database, the Retrieve Test(s)
dialog box will be displayed indicating the number of duplicate tests. Click OK.

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3. The Select Test(s) To Be Retrieved From dialog box appears (see Figure 5-61). The
tests that already exist in the current database appear in red text.
Click Cancel in the Open dialog box to not retrieve any archived tests.
Figure 5-61. Select Test(s) to Be Retrieved Dialog Box

4. Select the tests you want to retrieve. You can select the individual tests one-by-one,
or select multiple tests by clicking one of the following:
• Select All—Selects all of the tests in the table.
• Select Highlighted—Selects the tests you highlighted.
• Select With No Duplicate—Selects only the tests that do not exist in the current
database.
• After selecting tests in the Select Tests to Retrieved From dialog box, click one
of the following buttons to deselect some or all tests:
• Click Deselect All to clear all of the selections in the dialog box.
• Click Deselect Highlighted to clear the tests you highlighted.
5. Click OK to retrieve the selected test(s). The Retrieve Test(s) dialog box appears and
asks you to confirm the retrieval.
Click Cancel to not retrieve the selected test(s) from the database.
6. In the Retrieve Test(s) dialog box, click Proceed. The selected test)s) are retrieved
and a message appears and confirms that the tests are retrieved.
7. In the Retrieve Test(s) confirmation dialog box, click OK.

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5.17 Performing Database Management Tasks

The database management tasks can only be performed during system startup and
shutdown.
• Back up the database (see Section 5.17.1, Backing up the Database).
• Restore the database (see Section 5.17.2, Restoring the Database).
• Compact the database (see Section 5.17.3, Compacting the Database).
• Check the integrity of the database (see Section 5.17.4, Checking the Integrity of the
Database).
The GeneXpert Dx system administrator specifies whether you have permission for the
data management tasks. See Section 2.10, Defining Users and Permissions. See the
GeneXpert Dx system administrator to adjust the permissions to meet your requirements.
If Database Management Reminders are enabled, the user is prompted on startup whether
to perform database management. The prompt appears only if the user has privileges to
perform these tasks. If the user does not have any of these privileges or if Database
Management Reminders are disabled, the prompt will not be displayed. See Figure 5-62.

8. If you do not want to perform database management tasks, click No in the
Database Management dialog box (see Figure 5-62).and skip to Section 5.18,
Purging Tests from the Database.
If you want to perform database management tasks, click Yes in the Database
Management dialog box (see Figure 5-62). The Database Management window
5.17.1 Backing up the Database

You should back up the entire database periodically and store the backup on a different
computer or on a different storage medium. If the computer fails, you can restore the
entire database using the backup copy.
To back up the database:
1. Select Database Backup on the Database Management window (see Figure 5-63).
2. Click Proceed.

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Figure 5-63. Database Management Window

3. Locate and select the folder in which you want to store the backup file, type a name
for the backup file (or use the default file name), and then click Save. The backup
process creates a .zip file in the location you specified (see Figure 5-64).
Figure 5-64. Backup File Naming

4. The backup process varies, depending on the amount of data in the database and the
speed of the computer (older computers may take longer).
It has been found that 1000 tests takes less than 30 seconds, and 3000 tests takes less than a
Note
minute.
For large database backups, a progress bar will be displayed. When the backup
process is finished, a process completion message appears (see Figure 5-65).

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Figure 5-65. Backup Completed Screen
Caution The default database backup location is the export folder which is located on the computer
hard drive. To guard against loss of data, the files in the export folder should be periodically
copied to a different computer or server. If the GeneXpert Dx system is connected to a
network, it is possible to back up the files directly to a server. To configure the database
backup location, see Section 2.11.3, Folders Tab.
5.17.2 Restoring the Database

Caution
The database restore process overwrites the data in the current database. Do not restore a
database unless the current database is corrupted or needs to be replaced.
You can restore the entire database using the backup database file. Because the restore
process overwrites the data in the current database, first archive any test data to be
retained (see Section 5.16.1, Archiving the Tests), restore the database, and then retrieve
the data from the archive file (see Section 5.16.2, Retrieving Data from an Archive File).
To restore the database:
1. Select Database Restore on the Database Management window. See Figure 5-66.
Figure 5-66. Database Management Window

2. Click Proceed. A dialog box appears asking if you want to back up the current
database (recommended) before restoring. See Figure 5-67.

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Figure 5-67. Database Restore Dialog Box

3. Click Proceed in the Database Restore confirmation dialog box to continue with the
database backup (see Figure 5-67). The Database Backup dialog will be displayed.
See Figure 5-68.
Click Cancel to not back up the database and proceed directly to the Select File To
Restore the Database screen (see Figure 5-70).
Figure 5-68. Database Backup Dialog Box

4. Locate and select the folder in which you want to store the backup file, type a name
for the backup file (or use the default filename) and click Save. See Figure 5-68
5. The database will be backed up to the selected location. The Backup process time
varies, depending on the amount of data in the database and the speed of the
computer (older computers may take longer).
Note
minute.
For large database backups, a progress bar will be displayed. The Backup completed
screen appears when the database backup is complete. See Figure 5-69.

301-0045, Rev. K August 2016
Figure 5-69. Backup Completed Screen

6. Click OK. The Select File to Restore the Database screen appears. See Figure 5-70.
Figure 5-70. Select File to Restore the Database Screen, with Filename
7. Select the file to restore, and then click the Open button.
8. The Database Restore confirmation dialog box appears. See Figure 5-71.
Figure 5-71. Database Restore Confirmation Dialog Box

9. Either click Proceed in the Database Restore confirmation dialog box to continue, or
click Cancel to discontinue and return to the Database Management screen (see
Figure 5-66).
10. If you clicked Proceed, the restore process will begin. The restore process time
varies, depending on the amount of data in the database and the speed of the
computer (older computers may take longer).
Note
minute.

301-0045, Rev. K August 2016
For large database restores, a progress bar will be displayed. When the restoration
process is finished, a process completion message appears (see Figure 5-72).
Figure 5-72. Database Restore Completed Confirmation Screen

11. Click OK to close the GeneXpert Dx software application.
12. If desired, restart the GeneXpert Dx software. For details on starting the software,
see Section 5.2.3, Starting the Software.
5.17.3 Compacting the Database

Compact the database periodically to ensure efficient use of the space in the database
and to save hard disk space.
To compact the database:
1. Select Compact Database on the Database Management window. See Figure 5-66.
2. Click Proceed on the Database Management window. The Compact Database
confirmation dialog box appears. See Figure 5-73.
Figure 5-73. Compact Database Confirmation Dialog Box

3. Click Proceed to compact the database. When the database compacting has
completed, the Compact Database complete dialog box will appear. See Figure 5-74.
Figure 5-74. Compact Database Completed Dialog Box

4. Click OK.

301-0045, Rev. K August 2016
In addition to compacting the database, you can also save space by purging tests from the
Note database after archiving. For details on deleting archived tests, see Section 5.16.1, Archiving the
Tests.
5. Click Cancel to close the Database Management window.
5.17.4 Checking the Integrity of the Database

The software automatically checks the integrity of the database at start-up. To manually
check the integrity of the database, perform the following steps:
1. Click on Check Database Integrity on the Database Management window. See
Figure 5-66.
2. Click Proceed. The Check Database Integrity confirmation dialog box appears (see
Figure 5-75), asking to confirm the check request.
Figure 5-75. Check Database Integrity Confirmation Dialog Box

3. Click Proceed to start the integrity check. If the software finds integrity errors, a
message alert will appear. Click Proceed to repair the database.
4. When the check database integrity is successfully completed, the Check Database
Integrity complete dialog will appear. See Figure 5-76.
Figure 5-76. Check Database Integrity Completed Dialog Box

5. Click OK.
6. Click Cancel to close the Database Management window.

301-0045, Rev. K August 2016
5.18 Purging Tests from the Database

Tests may be purged from the active database after they have been archived (see Section
5.16.1, Archiving the Tests for details).
When tests have been archived, they have not been permanently deleted from the computer.
They have been removed from the main system database and saved to an archive file when
Important the Purge Selected Tests from List After Archiving (Recommended Monthly) option has been
selected. Tests may be retrieved from the archive file if needed for later use. See Section
5.16.2, Retrieving Data from an Archive File.
5.19 Viewing and Printing Reports

Important
The Reports menu (see Figure 5-77) provides the following menu options:
• Specimen Report (see Section 5.19.1)
• Patient Report (see Section 5.19.2)
• Patient Trend Report (see Section 5.19.3)
• Control Trend Report (see Section 5.19.4)
• System Log (see Section 5.19.5)
• Assay Statistics Report (see Section 5.19.6)
• Installation Qualification (see Section 5.19.7)

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Figure 5-77. GeneXpert Dx System Window—Reports Drop-Down Menu
5.19.1 Specimen Report

The Specimen Report provides an overview of the test results for the selected specimen
in the database. This menu item is available to all users unless it has been restricted by
the system administrator.
To view the specimen report:
1. In the GeneXpert Dx System window, on the Reports menu (see Figure 5-77), click
Specimen Report. The Specimen Report dialog box appears. See Figure 5-78.
2. Specify the following criteria to view the specimen report of interest:
• Date Range—Click All to view all dates or click Select to view report(s) for a
specific date range.
• Sample ID—You can enter the exact sample ID, a single-character wildcard
combined in exact characters or a multiple-character wildcard (%) with or
without exact characters.

301-0045, Rev. K August 2016
Figure 5-78. Specimen Report Dialog Box

3. When the criteria selection has been completed, click one of the following buttons:
A. Generate Report File—Creates a PDF file and saves it to the location you
specify.
1) Click the Generate Report File button on the Specimen Report screen (see
Figure 5-78) to create the PDF file of the report. The Generate Report File
location. Click Save once you have navigated to the specific location.
2) Optionally, to print the report, go to the saved location, open the test report
and print it. A test report similar to the report shown in Figure 5-79 will be
printed.
B. Preview PDF—Creates a PDF file and displays the file in the Adobe Reader
window. See Figure 5-79. You can save and print the PDF file from the Adobe
Reader software.
4. After selecting one of the two buttons in Step 3, a Specimen Report dialog box will
be displayed indicating the number of matching Sample IDs found. Click OK. The
Specimen Report will be created in the specified format.
5. After generating the Specimen Report, click Close to close the Specimen Report
dialog box.

301-0045, Rev. K August 2016
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5.19.2 Patient Report (If Enabled)

The Patient Report provides test results for samples for one patient according to the
Patient ID in the database. This menu item is available to all users unless it has been
restricted by the system administrator.
To view the patient report:
Patient Report. The Patient Report dialog box appears. See Figure 5-80.
Figure 5-80. Patient Report Dialog Box

2. Specify the following criteria to view the patient report of interest:
• Date Range—Click All to view all reports or click Select to view report(s) for a
specific date range.
• Patient ID – the user can enter the exact patient ID, a single-character wildcard _
combined in exact characters or a multiple-character wildcard (%) with or
3. When you finish selecting the criteria, click one of the following buttons:
A. Generate Report File—Creates a PDF file and saves it to the specified location.
1) Click the GENERATE REPORT FILE button on Patient Report screen (see
Figure 5-80) to create the PDF file of the report. The Generate Report File
location. Click Save once you have navigated to the specific location.
printed.
Reader software.
4. After selecting one of the two buttons in Step 3, a Patient Report dialog box will be
displayed indicating the number of matching Patient IDs found. Click OK. The
Patient Report will be created in the specified format.

301-0045, Rev. K August 2016
5. After generating the Patient Report, click Close to close the Patient Report dialog
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5.19.3 Patient Trend Report (If Enabled)

The Patient Trend Report provides test results for samples for quantitative assays for one
patient according to the Patient ID in the database. This menu item is available to all
users unless it has been restricted by the system administrator.
To view the patient trend report:
Patient Trend Report. The Patient Trend Report dialog box appears. See Figure 5-82.
Figure 5-82. Patient Trend Report Dialog Box

2. Specify the following criteria to view or print a Patient Trend of interest that
includes the desired data range and assay:
• Date Range – Click All to view all dates or click Select to view report(s) for a
specific date range. If you click on Select, enter the desired date range.
• Patient ID – The user can enter the exact patient ID, or perform a look-up using
the Find Patient ID dialog box, accessible by clicking the [...] button. A lookup
is performed in the Find Patient ID dialog box with a single-character wildcard
_ combined in exact characters or a multiple-character wildcard (%) with or
• Select Assay – Select the desired assay from the drop down box. Assays are
shown in alphabetical order. Only quantitative assays are shown.
• Show target reference line at – Enter the value for the desired target reference
line. The value must be larger than the Lower Quantitative Level (LQL) value
and less than the Upper Quantitative Level (UQL) value.
• Specify y-axis maximum value – Check the check box and enter this optional
value for the Y-axis of the graph. Entering or changing this value allows the
user to zoom in or out on the graph.

301-0045, Rev. K August 2016
• Plot quantitative value in log format – If this option is checked, the graph will be
plotted using the log-10 value of the quantitative value. The default for this
option is checked.
3. When you finish selecting the criteria, click one of the following buttons:
A. Generate Report File—Creates a PDF file and saves it to the location you
specify.
1) Click the Generate Report File button on the Patient Trend Report screen
(see Figure 5-82) to create the PDF file of the report. The Generate Report
File dialog box will appear, which enables you to save the file to a
specified location. Click Save once you have navigated to the specific
location.
printed.
window (see Figure 5-83 and Figure 5-84). You can save and print the PDF file
from the Adobe Reader software.
4. After selecting one of the two buttons in Step 3, a Patient Trend Report dialog box
will be displayed indicating the number of matching Patient IDs found. Click OK.
The Patient Trend Report will be created in the specified format.
Information may vary depending upon the options selected in the system. For example, the report
Note may contain the Patient ID and Patient ID 2 if these options are enabled in the System
Configuration General window.
5. View Graph – Clicking on this button opens the Patient Trend Graph screen and
displays a graph of all results that meet the selection criteria for a specific patient.
Test results of ERROR, INVALID and NO RESULT are excluded from the graph.
Press the OK button after viewing the graph to return to the Patient Trend Report
screen.
6. After generating the Patient Trend Report, click Close to close the Patient Trend
Report dialog box.
An example of a printed Patient Trend Report is shown in Figure 5-83 and Figure 5-84.

301-0045, Rev. K August 2016
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301-0045, Rev. K August 2016
5.19.4 Control Trend Report

See Section 6.5, Control Trend Reports.
5.19.5 System Log

See Section 9.15, Generating the System Log Report.
5.19.6 Assay Statistics Report

An Assay Statistics Report is a report showing the number of tests performed for each
assay over a period of time with monthly breakdown values. This menu item is available
to Detail and Administrator users unless it has been restricted by the system
administrator.
To view the assay statistics report:
Assay Statistics Report. The Assay Statistics Report dialog box appears. See
Figure 5-85.
Figure 5-85. Assay Statistics Report Dialog Box

301-0045, Rev. K August 2016
2. Specify the following criteria to view the assay statistics of interest:

• Date Range—Select Last 12 Months or Select for a specific date range.
• Assay—Select All to select all the listed assays or Select to select a specific
assay.
3. When you finish selecting the assay(s), click one or both of the following buttons:
• Generate Report File—Creates a PDF file and saves it to the location you
specify.
1) Click the Generate Report File button on the Assay Statistics Report screen
(see Figure 5-85) to create the PDF file of the report. The Generate Report
File dialog box will appear, which enables you to save the file to a
specified location. Click Save once you have navigated to the specific
location.
2) Optionally, to print the report, go to the saved location, open the report and
print it. A report similar to the report shown in Figure 5-86 will be printed.
C. Preview PDF—Creates a PDF file and displays the file in the Adobe Reader
Reader software.
4. After selecting one of the two buttons in Step 3, an Assay Statistics Report dialog
box will be displayed indicating the number of matching assays found. Click OK.
The Assay Statistics Report will be created in the specified format.
• After generating the Assay Statistics Report, click Close to close the Assay
Statistics dialog box.
• Preview PDF—Creates a PDF file and displays the file in the Adobe Reader
Reader software.

301-0045, Rev. K August 2016
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5.19.7 Installation Qualification

See Section 2.12, Verifying Proper Installation and Setup.
5.20 Operating with Host Connectivity

This section provides instructions on how to use the GeneXpert Dx host interface to:
• Configure Assay for order and result upload (Section 5.20.1, Creating a Test with
Host Connectivity)
• Create a test from downloaded test order (Section 5.20.1, Creating a Test with Host
Connectivity)
• Upload a test result (Section 5.20.2, Uploading a Test Result to the Host)
• Troubleshoot Host Connectivity (Section 5.20.3, Troubleshooting Host
Connectivity)
Cepheid recommends to always confirm that LIS uploaded results match GeneXpert Dx
system test results after any changes to the GeneXpert Dx system or host system, including
Caution (but not limited to) changes to the following:
-GeneXpert Dx software version
-GeneXpert Assay Definition version
-GeneXpert Dx Host Communication Settings
-Host middleware software or configuration changes
-LIS software or configuration changes
5.20.1 Creating a Test with Host Connectivity

When the host connectivity is enabled, test orders can be automatically downloaded from
the host by:
• The GeneXpert Dx system periodically requesting new orders
• Manual queries by GeneXpert Dx system user of new orders from the Create Test
dialog box
• Scanning or entering the Sample ID to perform host query for orders for a specific
Sample ID
The workflow in your laboratory will determine how a test is created.
Additional areas are available in Create Test dialog box. See Figure 5-87.

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Figure 5-87. Create Test Window with Host Test Order Table
• Host Test Order Table - New orders are shown in the table which can be sorted by
clicking the header. The table contains:
• Patient ID - Patient ID (s) for each test order.
• Sample ID - Sample ID (s) for each test order.
• Assay—Assay name and version number for each test order.
• STAT—Indicates whether it is STAT priority or Normal priority.
• Host Order Time—Time downloaded by the host or created by the GeneXpert
Dx system as time received.
• Delete button—Allows an order to be canceled.
• Host Query Status—Displays the current status for query for new orders.
• Manual Query button—Allows manual query of the host for any available new
orders.
To accept an order from the host, the test code for the assay must be set up by the host
Note
administrator. See Section 2.11.6, Configuring Assay for Order and Result Upload for details.

301-0045, Rev. K August 2016
5.20.1.1 Creating a Test by Selecting from a List of Test Orders Downloaded

by the Host Automatically
1. In the Host Communication Settings tab of the System Configuration dialog, click on
the Automatic Test Order Download check box to select and enable this function. See
Figure 5-88.
Figure 5-88. Automatic Test Order Download Selected

2. The GeneXpert Dx system periodically queries all test orders from the host.
The Create Test button is shown with a Plus (+) sign when there are new host orders
to be filled. See Figure 5-89.
Plus Symbol (+) Indicates a New Host Order
Figure 5-89. Menu Bar Indicating Plus Sign on Create Test Button

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3. Click Create Test. Scan or enter the optional Patient ID, Patient ID 2, Patient Name,
if enabled, and all three scan dialogs, if enabled (Patient ID, Sample ID, cartridge
barcode). Do not use the following symbols if manually entering the Patient ID: | @
^ ~ \ & / : * ? " < > ' $ % ! ; ( ) -.
4. The Scan Sample ID Barcode dialog box appears (see Figure 5-18 in Section 5.6,
Creating a Test).
5. Scan the sample ID barcode on the specimen container (see Figure 5-18 in
Section 5.6, Creating a Test).
6. New order for this optional Patient ID and Sample ID is selected in the Host Test
Order Table section of the Create Test window, which can be sorted by clicking the
table header.
7. The Scan Cartridge Barcode dialog will automatically display a prompt to scan the
barcode on the cartridge. This confirms that the correct assay will be run. Reagent
lot ID, expiration date, and cartridge serial number are processed and transferred.
8. The order for this Patient ID and Sample ID will be removed from the list of new
orders.
9. Insert the cartridge with the specimen and reagents according to the assay-specific
package insert. See Section 5.7, Loading a Cartridge into an Instrument Module.
10. Click on Start Test, load the cartridge, and close the module door by performing the
steps provided in Section 5.8, Starting the Test.
You cannot change the Patient ID, Patient ID 2, Patient Name, Sample ID, or the assay if it is
Note
selected from a host downloaded test order.
If only one order matches the Patient ID and Sample ID provided by the host, this order will be
Note
automatically selected.
5.20.1.2 Creating a Test by Manually Requesting Test Orders and Selecting

From the List of Test Orders
You can manually request new test orders from the host by clicking the Manual Query
button. After orders are downloaded from the host, proceed as instructed in
Section 5.20.1.1, Creating a Test by Selecting from a List of Test Orders Downloaded by
the Host Automatically.

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5.20.1.3 Creating a Test by Querying the Host with Sample ID

1. In the Host Communication Settings tab of the System Configuration dialog, click on
the Automatic Host Query After Sample ID Scan check box to select and enable this
function. See Figure 5-90.
Figure 5-90. Host Query Selected

2. Click Create Test. The Scan Sample ID Barcode dialog box appears (see Figure 5-18
in Section 5.6, Creating a Test).
3. Scan the sample ID barcode on the specimen container (see Figure 5-18 in
Section 5.6, Creating a Test).
4. Test orders for this Sample ID are downloaded from the host and are displayed in the
Host Test Order Table which can be sorted by clicking the header.
Other downloaded orders for different samples will not be displayed in the order table for a
Note
temporary period.
5. Select an order from the table. This will select the assay according to the test order.

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Note If only one order matches the given Sample ID, this order will be automatically selected.
6. The Scan Cartridge Barcode dialog will automatically display a prompt to scan the
barcode on the cartridge. This confirms that the correct assay will be run. The
reagent lot ID, expiration date, and cartridge serial number are processed and
transferred.
7. Insert the cartridge with the specimen and reagents according to the assay-specific
package insert (see Section 5.7, Loading a Cartridge into an Instrument Module).
8. Start the test, load the cartridge, and close the module door by performing steps
provided in Section 5.8, Starting the Test.
5.20.1.4 Aborting a Query

During the Manual Query described in Section 5.20.1.2, Creating a Test by Manually
Requesting Test Orders and Selecting From the List of Test Orders or Host Query
described in Section 5.20.1.3, Creating a Test by Querying the Host with Sample ID, the
Manual Query button becomes the Abort Query button. See Figure 5-91.
To start a test or close the dialog box, wait until the query is completed or click the Abort
Query button to cancel the operation.
Figure 5-91. Create Test Window showing the Abort Query Button

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5.20.1.5 Deleting a Host Downloaded Test Order

Occasionally, you may need to delete an order downloaded from the host.
1. Select the order from the Host Test Order Table.
2. Click the Delete button on the same row. See Figure 5-92.
Figure 5-92. Deleting a Host Download Test Order

3. A confirmation dialog is shown. Click OK to confirm the deletion.
• The order will be removed from the table.
• The host will be informed.

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5.20.2 Uploading a Test Result to the Host

Test results can be uploaded to the host either automatically or manually.
5.20.2.1 Automatically Uploading the Test Result to the Host

1. In the Host Communication Settings tab of the System Configuration dialog, click the
Automatic Result Upload check box so the result will be uploaded as soon as the test
is completed. See Figure 5-93.
Figure 5-93. Automatic Result Upload

2. Click OK. Upload status is shown in the Test Information area of the View Result
window.
After the test is completed, the result will be automatically uploaded. The Upload Status
is shown in the Test Information area of the View Result window. See Figure 5-94.

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Figure 5-94. Host Upload Shown in the Test Information Area of the View Result Window
5.20.2.2 Manually Uploading a Test Result to the Host

1. In the Host Communication Settings tab of the System Configuration dialog, make
sure Automatic Result Upload is deselected or disabled. See Figure 5-93.
2. Click Upload Test in the View Results window (see Figure 5-94). The Select Test(s)
To Be Uploaded To Host window appears, displaying the completed tests. See
Figure 5-95.

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Figure 5-95. Select Test(s) to be Uploaded to the Host Window

The possible host uploaded statuses are:
• Upload-pending – this result has not been uploaded.
• Uploading – this result is being uploaded.
• Re-Uploading – this result has been uploaded previously and currently being
uploaded again.
• Uploaded – this result has been received by the host.
• Review – this is an external control and it should be reviewed before manually
uploading.
• Expired – test has not been uploaded and will not be alerted to the user by the system
when exiting the software.
If an attempt to exit the software is made with results in the upload pending, uploading or re-
Note
uploading status, the software will alert the user.

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3. Select the test you want to upload. You can select the individual tests one-by-one or
select a large number of tests (up to 100 tests) by clicking one of the following:
• Select All – Selects all of the tests in the table.
• Select Highlighted – Selects the tests you highlighted.
• Select All Pending – Selects only the tests that have not been uploaded before.
4. Click Deselect All to clear all of the test selections in the window. Click Deselect
Highlighted to clear the tests you highlighted.
5. Click Upload. A message appears and asks for confirmation of the upload request.
6. Click Close.
5.20.2.3 Uploading an External Control Result to the Host

Regardless of the setting for Automatic Result Upload, an external control result is
manually uploaded. See Section 5.20.2.2, Manually Uploading a Test Result to the Host.
5.20.3 Troubleshooting Host Connectivity

If there are problems with host connectivity, see Section 9.18.3, Troubleshooting Host
Connectivity and Section 9.18.4, Troubleshooting the LIS Interface.

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5.21 Operating with Cepheid Link Connectivity

This section provides instructions on how to use Cepheid Link to scan samples and
cartridges and to run the tests on the GeneXpert Dx system. The workflow for using
Cepheid Link is that the test order is entered into the institution’s LIS system. The
Cepheid Link scanner is used to scan the samples and cartridges either near the
GeneXpert Dx system or remotely. The cartridges are then transported to the GeneXpert
Dx system to run the tests. Test results are uploaded to the institution’s LIS system.
Once the system has been configured for Cepheid Link, it cannot be used for non-LIS
originated test orders or for running external controls without disabling Cepheid Link.
Important Cepheid Link may be enabled again after running non-LIS originated test orders or external
controls. Configuration for Cepheid Link is described in Section 2.11.5.2, Configuring Host
Communications for Cepheid Link
• Section 5.21.1, Scanning a Sample and Cartridge using Cepheid Link

• Section 5.21.2, Running Cartridges Scanned from Cepheid Link
Cepheid recommends to always confirm that LIS uploaded results match GeneXpert test
results after any changes to the GeneXpert or host system, including (but not limited to)
changes to the following:
Caution
• GeneXpert software version
• GeneXpert Assay Definition version
• GeneXpert host communication settings
• Host middleware software or configuration changes
• LIS software or configuration settings
5.21.1 Scanning a Sample and Cartridge using Cepheid Link

After an order is entered into the LIS, system, use the Cepheid Link scanner to scan the
sample and cartridge. This procedure assumes that the Cepheid Link scanner has been
set up following the instructions in the Cepheid Link User Guide and the scanner has
already been powered on.
In order to scan a sample and cartridge, an order for the test must have been previously
Important
entered into the institution’s LIS system.
1. Remove the scanner from the docking station.

2. If the scanner screen is locked, swipe the screen upward vertically to unlock the
screen.
3. Log into the Cepheid Link scanner using your assigned user name and password (see
Figure 5-96). The Scan Sample screen will be displayed. See Figure 5-97.

301-0045, Rev. K August 2016
Figure 5-96. Cepheid Link Scanner Login Screen

4. Scan the sample ID using the scanner:
• To scan the sample ID:
1) Press and hold the blue scanner button (located on either side of the
barcode scanner) to scan the sample barcode. The sample barcode will be
scanned and Cepheid Link will check to see if there is a test order for the
sample.
2) If an order was found, the Success screen (green check mark) will be
displayed for a very short time (see Figure 5-98) and the Scan Cartridge
screen will be displayed. See Figure 5-101.
3) If an order was not found, the Error screen (Order Not Found (red X)) will
be displayed (see Figure 5-99). Touch the Ok button to return to the Scan
Sample screen.
• If a sample barcode is not available, to enter the sample ID manually:
1) Touch the Barcode area of the screen (see Figure 5-97). A keyboard will be
displayed (see Figure 5-100) to enter the sample ID manually.
2) Manually enter the sample ID using the keyboard.
3) Press the Submit button to submit the sample ID.
4) If an order was found, the Success screen (green check mark) will be
displayed for a very short time (see Figure 5-98) and the Scan Cartridge
screen will be displayed. See Figure 5-101.

301-0045, Rev. K August 2016
5) If an order was not found, the Error screen (Order Not Found (red X)) will
be displayed (see Figure 5-99). Touch the Ok button to return to the Scan
Sample screen.
Touch Here to Display

Scanner Menu
Touch Here to Manually

Enter Sample ID
Figure 5-97. Cepheid Link Scan Sample Screen
Figure 5-98. Cepheid Link Scanner Success (Green Check Mark) Screen

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Figure 5-99. Cepheid Link Scanner Error (Order Not Found (Red X)) Screen
Touch Submit Button

After Entering Sample ID
Figure 5-100. Sample ID Manual Barcode Entry

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Touch Start Over to

Return to the Scan
Sample Screen.
Figure 5-101. Cepheid Link Scan Cartridge Screen

5. Scan the cartridge barcode:
• Press the scanner button (located on either side of the barcode scanner) to scan
the cartridge barcode. After the cartridge barcode has been successfully
scanned, Cepheid Link will pair the cartridge with the sample. The scanner will
momentarily display the scanned cartridge information (see Figure 5-102).
If the cartridge is successfully paired with the sample, the Success screen (green
check mark) will be displayed for a very short time (see Figure 5-98).
• If the cartridge is not successfully paired with the sample, the Error (Red X)
screen will be displayed along with the error message (see Figure 5-103) for an
example. Touch the Ok button to return to the Scan Cartridge screen. The
scanner will return to the Scan Sample screen (see Figure 5-97).
• If aliquots are to be scanned, the Scan Aliquot screen will be displayed (see
Figure 5-104).
• The scanner will display the Confirmation screen (see Figure 5-105), if aliquots
are not required and if Confirmation is enabled, or will return to the Scan
Sample screen (see Figure 5-97).
• Touch Start Over to not scan the aliquot and return to the Scan Sample screen.
See Figure 5-97. A confirmation screen will be displayed after touching the
Start Over button.

301-0045, Rev. K August 2016
6. (Optional) If the sample requires an aliquot to be scanned, the Scan Aliquot screen
will be displayed (see Figure 5-104).
• Press the scanner button (located on either side of the barcode scanner) to scan
the aliquot barcode. The aliquot barcode will be scanned.
• If the aliquot is successfully scanned, the Success screen (green check mark)
will be displayed for a very short time (see Figure 5-98).
• If the assay is set up for aliquots but the sample has not been divided into
aliquots, touch Skip to skip scanning an aliquot. The scanner will display the
Confirmation screen (see Figure 5-105), if aliquots are not required and if
Confirmation is enabled, or will return to the Scan Sample screen (see
Figure 5-97).
• If aliquots are to scanned, the Scan Aliquot screen will be displayed (see
Figure 5-104).
• Touch Start Over to not scan the aliquot and return to the Scan Sample screen
(see Figure 5-97). A confirmation screen will be displayed after touching the
Start Over button.
7. (Optional) The scanner will display the Confirmation screen (see Figure 5-105), if
enabled, or will return to the Scan Sample screen (see Figure 5-97).
8. If the Confirmation screen is displayed, touch Start Over to go to the Scan Sample
screen. See Figure 5-97.
Figure 5-102. Cepheid Link Scanned Cartridge Information Screen

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Figure 5-103. Cepheid Link Scanned Cartridge Error Screen
Figure 5-104. Cepheid Link Scan Aliquot Screen

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Figure 5-105. Cepheid Link Confirmation Screen

9. To scan additional samples and cartridges, go to Step 4 on page 5-95.
10. When all samples and cartridges have been scanned, log off the Cepheid Link.
Access the scanner menu by touching the Menu icon in the drop down menu (see
Figure 5-97). The scanner menu will be displayed. See Figure 5-106.
11. On the scanner menu, touch Logout. The logout dialog will be displayed at the
bottom of the screen. See Figure 5-107.
12. On the logout dialog, touch OK to log off the scanner (see Figure 5-107). The
scanner Login screen will be displayed. See Figure 5-96.
Select Cancel if you do not want to log off the scanner.
13. Return the scanner to the docking station.

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Touch Logout to Display

the Logout Dialog
Figure 5-106. Cepheid Link Scanner Drop Down Menu
Touch OK to Log Off

the Scanner
Figure 5-107. Cepheid Link Scanner Logout Dialog

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5.21.2 Running Cartridges Scanned from Cepheid Link

After cartridges have been scanned using Cepheid Link, they are transported to the
GeneXpert Dx system to run the tests.
The system must be configured for Cepheid Link before running tests using this procedure.
Important Configuration for Cepheid Link is described inSection 2.11.5.2, Configuring Host
Communications for Cepheid Link
The ordering process will be demonstrated using a series of screenshots that direct you
to either scan or type in test information.
To run tests on the GeneXpert Dx system:
1. In the GeneXpert Dx system Home screen, select the Create Test button. See
Figure 5-108.
Figure 5-108. GeneXpert Dx Home Screen

2. The Host Test Order screen will be displayed with a Scan Cartridge Barcode overlay
screen. See Figure 5-109.
Select the Cancel button if you do not want to run a test.

301-0045, Rev. K August 2016
Even though the patient demographics fields are displayed in the host screens, data cannot be
Note
entered into the fields.
Figure 5-109. Orders Table with Scan Cartridge Barcode Overlay Screen
3. As instructed in Figure 5-109, scan the cartridge barcode using the supplied scanner.
The GeneXpert Dx system will query the Cepheid Link system to verify that the
order exists on the system. If the order exists, the order will be downloaded to the
GeneXpert Dx system. (see Figure 5-110).

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Figure 5-110. Create Test Screen, showing Cartridge Query Completed

4. On the Host Test Order Table section, (see Figure 5-110), review the order. Enter
additional information or notes, if necessary, then select the Start Test button. The
GeneXpert Home Screen appears, displaying a message to load the cartridge into the
module, which is highlighted in green. See Figure 5-111.
You cannot change the Patient ID (if enabled), Sample ID, patient demographics information or the
Note
assay if it is downloaded from a Link test order.
5. If required, log in to start the test.

You can monitor the test process or other status indicators in the Modules or
Messages areas of the GeneXpert Dx System window. See Figure 5-28.

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Figure 5-111. GeneXpert Home Screen, showing the Cartridge Loading Message
6. Continue scanning cartridges for testing by repeating Step 1 (page 5-103) through
Step 5 (page 5-105) until all cartridges have been processed.
5.22 System Information

Information about the system and software can be obtained by clicking on the About
menu at the top of the GeneXpert Dx System window (see Figure 5-112) and selecting
About GeneXpert® DX System. The About GeneXpert Dx System window will be
displayed. See Figure 5-113.

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Figure 5-112. GeneXpert Dx System—About Drop-Down Menu

The About GeneXpert Dx System window displays specific information about the
instrument and software such as:
• Software version number
• Copyright statement
• Various version numbers of software utilities used on the system
• Instrument serial numbers and firmware version
• Module numbers and firmware version numbers
To view the GeneXpert Dx software license agreement, click on the License button. See
Figure 5-113, About GeneXpert Dx System Window. You may read the complete
software license agreement by scrolling through the document in Adobe Reader. When
finished, close Adobe Reader.
Click Close to close the About GeneXpert Dx System window.

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Figure 5-113. About GeneXpert Dx System Window

301-0045, Rev. K August 2016
6 Calibration Procedures
This chapter describes the following:

• Section 6.1, Calibration
• Section 6.2, Quality Control
• Section 6.3, External Quality Controls
• Section 6.4, Qualitative Assays vs. Quantitative Assays
• Section 6.5, Control Trend Reports
6.1 Calibration
Calibration of the GeneXpert instrument is not required during the initial system setup.
Cepheid performs all of the necessary calibrations before the system is shipped.
However, Cepheid recommends that the system be checked for proper calibration on an
annual basis. Based upon the usage and care of each system, calibration checks may be
recommended more frequently. The system is designed to measure module performance
with the internal assay controls. In the event of a module failure, the replacement module
provided will have been calibrated prior to shipment.
The Cepheid Field Service Engineer or customer will perform the calibration checks
during annual maintenance or by the field service engineer if responding to a module
failure. Contact Cepheid Technical Support for information about calibration. See the
Technical Assistance section in the Preface for contact information.
6.2 Quality Control

Quality control is an important part of in vitro diagnostic testing because it helps ensure
you are performing the tests correctly and that your GeneXpert Dx system is working
properly. The GeneXpert Dx system automatically performs internal quality control for
each sample. During each test, the system uses one or more of the following controls that
must be positive to report a negative test result:
• Sample-Processing Control (SPC)—Helps ensure that a sample was correctly
processed. The sample-processing control, which is included in the cartridge, is
processed with the sample and detected by PCR.
• Internal Control (IC)—Helps verify the performance of the PCR reagents and the
absence of significant inhibition that would prevent PCR amplification
• Endogenous Control (EC)—Normalizes targets and/or helps ensure sufficient sample
is used in the test. The endogenous control is from the test sample.

301-0045, Rev. K August 2016
Calibration Procedures
In addition to the controls, the GeneXpert Dx system performs a probe check during the
first stage of the test. A probe check verifies the presence and the integrity of the labeled
probes. A probe-check status of Pass indicates that the probe check results meet the
acceptance criteria.
6.3 External Quality Controls

External controls may be used in accordance with local, state, or federal accrediting
organizations, as applicable. External controls can be trended if an external control test
type is assigned when the test is created. For additional information, see the quality label
or package insert for the specific assay. During Order Test, select the appropriate Test
Type for the controls being tested.
6.4 Qualitative Assays vs. Quantitative Assays

The Control Trend Report may be generated for both qualitative assays and quantitative
assays. After selecting the assay, to trend quantitative assay results, check the Use
Quantitative Data check box. For qualitative assays, the Use Quantitative Data check box
is grayed out.
It is possible to trend qualitative assay results on an assay that uses quantitative data. Do not check
Note
the Use Quantitative Data check box.
6.5 Control Trend Reports

The Control Trend reports can be used to verify the quality of the system, reagents or
specimens. For example, a negative-control trend report can be generated to check for
cross-contamination. Other external-control trend reports can be generated to check for
reagent degradation.
The following procedure shows how to perform both qualitative assay control trend reports and
Note
quantitative assay control trend reports.
To view the control trends:

1. In the GeneXpert Dx System window on the Reports menu, click Control Trend
Report (see Figure 6-1). The Control Trend Report dialog box is displayed. See
Figure 6-2.

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Figure 6-1. GeneXpert Dx System Screen Displaying Reports Menu

2. Select the Date Range. Select All to include all of the tests or click the Select button
to filter the tests by specifying a range of dates.
3. Select the assay to generate the Control Trend Report. See Figure 6-2 for a
qualitative assay selection and Figure 6-4 for a quantitative assay selection.
Note Control trending is not available for % Ratio quantitative assays.
4. If the assay selected is a qualitative assay, the Use Quantitative Data check box is not
displayed (see Figure 6-2). If the assay selected is a quantitative assay, the Use
Quantitative Data check box will be available (see Figure 6-4). Check the Use
Quantitative Data check box to generate the Control Trend Report using quantitative
data.
5. If the assay contains multiple reagent lot numbers, select the lot number to use for
the Control Trend Report using the Reagent Lot Number drop down.

301-0045, Rev. K August 2016
Figure 6-2. Control Trend Report Dialog Box Showing Qualitative Assay Selected
6. Specify the following criteria to view the trends of interest:
• Qualitative Assay Options (see Figure 6-2):
• Test Type(s)—Select the external-control trend types to be trended. For the
example in this chapter, Negative Control 1 was selected.
• Select Analytes button—Select the analytes. Press the Select Analytes
button to display the analytes applicable to this assay. The Select Analytes
dialog box is displayed. See Figure 6-3.
• Ensure that desired analytes are listed under the Selected Analytes
column.
• If additional analytes should be added to the Selected Analytes column,
highlight the analyte under the Available Analytes column, click the
Right Arrow key to move the analyte to the Selected Analytes column
and press the OK button. The Select Analytes dialog box closes.
• If analytes should be removed from the Selected Analytes column,
highlight the analyte under the Selected Analytes column, click the Left
Arrow key to move the analyte to the Available Analytes column and
press the OK button. The Select Analytes dialog box closes.

301-0045, Rev. K August 2016
Figure 6-3. Select Analytes Dialog Box

• Data Type—Select the data type. For this example, the Cycle Threshold and
EndPoint data are selected to be trended.
• Exclude tests in which any target analyte is positive check box—Select this
check box to not include tests in which the target analyte is positive from
the report.
• Quantitative Assay Options (see Figure 6-4):
• Test Type(s)—Select the external-control trend types to be trended. For the
example in this chapter, Positive Control 1 was selected.
• Plot quantitative value in log format check box—Select the format of the
data to be plotted. For the example in this chapter, Plot quantitative value in
log format was selected.
• Customize Graph Limits button—Select the data limits to be used for
plotting the data. Press the Customize Graph Limits button. The Customize
Graph Limits dialog box is displayed. See Figure 6-5.
For each Test Type selected, enter the Target, Upper Limit and Lower Limit.
For this example, the Target was set to 200.00, the Lower Limit was set to
96.00 and the Upper Limit was set to 991.00. The Target must be between the
Upper Limit and the Lower Limit.

301-0045, Rev. K August 2016
Figure 6-4. Control Trend Report Dialog Box Showing Quantitative Assay Selected
Figure 6-5. Customize Graph Limits Dialog Box

7. After selecting the trend criteria, click one or more of the following options:
specify. Click the Generate Report File button on the Control Trend Report
dialog box (see Figure 6-2 for qualitative assay trends and Figure 6-4 for
quantitative assay trends) to create the PDF file of the report. The Generate
Report File dialog box is displayed (see Figure 6-6), which enables you to save
the file to a specified location.
Click the Save button once you have navigated to the specific location. To view
the Control Trend Report, go to the location where you saved the report, open
the report and print it, if desired.
Click the Cancel button to not save the Control Trend Report, if desired.

301-0045, Rev. K August 2016
Note The default location for saving the Control Trend Report is the Report folder.
window. Click the Preview PDF button on the Control Trend Report dialog box
(see Figure 6-2 for qualitative assay trends and Figure 6-4 for quantitative assay
trends) to create the PDF file of the report (see Figure 6-7). The PDF file can be
saved and printed from the Adobe Reader software.
The length of the Control Trend Report can be very long depending upon the number of test types
Note
and data types selected.
• Close—Click Close when you are done to close the Control Trend Report dialog
box or if you do not wish to generate a Control Trend Report.
Figure 6-6. Generate Report File Dialog Box

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Figure 6-7. Example Control Trend Report in the Adobe Reader Window
The file from Adobe Reader may be saved in the Report folder or saved on another
device.
A sample control trend report for a qualitative assay (Xpert C. difficile G2) is shown in
Figure 6-8 and Figure 6-9. A sample control trend report for a quantitative assay (Xpert
HIV-1 Viral Load) is shown in Figure 6-10 and Figure 6-11.
Note The Xpert HIV-1 Viral Load test is not available in the United States.

301-0045, Rev. K August 2016
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301-0045, Rev. K August 2016
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301-0045, Rev. K August 2016
7 Operational Precautions and Limitations
You should be aware of the following system precautions and limitations to ensure
proper operation and results:
• Section 7.1, Security Precautions
• Section 7.2, Laboratory
• Section 7.3, Instrument and Software
• Section 7.4, Assay
• Section 7.5, Cartridge
7.1 Security Precautions

User data stored in the system may contain personal health information of patients, such
as name, patient ID, and test results. Cepheid strongly recommends that you implement
physical, technical, and administrative safeguards to protect the privacy and integrity of
patient data, such as restricting network and system access, enforcing user authentication
practices, maintaining antiviral software, and so on, in accordance with applicable data
privacy laws and regulations. In particular, unique, strong passwords should be
maintained for all system users and should not be disabled. Consult your facilities
security officer to ensure internal compliance with all applicable laws and regulations.
7.2 Laboratory
Before installing the GeneXpert Dx system, make sure your laboratory meets the
environmental requirements specified in Chapter 4, Performance Characteristics and
Specifications.
• Place the GeneXpert Dx system in a sheltered environment because it is designed for
indoor use only.
• Provide at least 5 cm (2 in) of clearance on each side of the GeneXpert instrument to
ensure adequate ventilation.
• Do not place the GeneXpert instrument close to the vents of other instruments or air
handling units.

301-0045, Rev. K August 2016
Operational Precautions and Limitations
7.3 Instrument and Software

Be sure to do the following:
• Connect the GeneXpert Dx system to a surge protector and a properly grounded AC
circuit. See Chapter 4, Performance Characteristics and Specifications for the
electrical requirements.
• Use the GeneXpert Dx system for in vitro diagnostic applications only.
• While a test is in progress:
• Do not move the instrument.
• Do not run other software.
• Do not change the date and time.
7.4 Assay
For each test, be sure to follow the instructions in the assay-specific package insert,
which specifies the test requirements.
7.5 Cartridge
The GeneXpert cartridges are designed for single-use only. To prevent cross-
contamination and biologically hazardous situations, use each cartridge only once.
If module communication loss occurs after a test has been ordered and assigned to a
module, but before the cartridge is loaded and the door is latched, an error message will
appear that advises not to proceed with loading the cartridge and latching the door. If the
Important message instructions are followed, the cartridge may be resubmitted to another module.
However, if the cartridge is loaded and the door latched when module communication loss
occurs, no result will be given when the test completes and the cartridge should not be
reused.

301-0045, Rev. K August 2016
8 Hazards
This chapter describes the possible safety hazards found in the GeneXpert Dx system. It
is imperative that you follow the precautions in this chapter for safe operation. The
topics are as follows:
• Section 8.1, General Safety Precautions
• Section 8.2, Precautionary Statements Used in this Manual
• Section 8.3, Moving the Instrument
• Section 8.4, Safety Labels on the Instrument
• Section 8.5, Electrical Safety
• Section 8.6, Chemical Safety
• Section 8.7, Biological Hazard Safety
• Section 8.8, Environmental Data
8.1 General Safety Precautions

Before starting to use the GeneXpert Dx system, read this operator manual entirely and
be familiar with the safety information provided. Using controls, making adjustments, or
performing procedures other than those specified in this manual can result in exposure to
hazards that can cause injury to personnel or damage to the system.
Protection provided by the equipment may be impaired if the equipment is used with
accessories not provided or recommended by the manufacturer, or used in a manner not
specified by the manufacturer. Do not use the equipment in hazardous atmospheres or
with hazardous materials for which the equipment is not designed.
8.2 Precautionary Statements Used in this Manual

There are a number of safety notations used in the manual to identify potential safety
hazards when operating or servicing the instrument. The types of precautionary
statements used in this manual are:
Warning
A warning indicates a possibility of adverse reactions, injury, or death to the user or other
personnel if the precautions or instructions are not observed.

301-0045, Rev. K August 2016
Hazards
Caution
A caution indicates that damage to the system, or invalid results could occur if the user fails
to comply with the advice provided.
Important indicators highlight information that is critical for the completion of a task or the
Important
optimal performance of the system.
Note A note identifies information that applies only to specific cases or tasks.
The following warnings are used in this manual:
Biological Risks
A biological risk warning indicates that it is possible for personnel or the instrument to be
exposed to biological hazards. Follow the instructions in the manual and use standard lab
biological hazard protocol to reduce the possibility of exposure.
Warning An electrical hazard warning indicates that there is a risk of electrical shock that can cause
injury or death to the user or other personnel. Follow the instructions in the manual and use
appropriate electrical precautions to avoid electrical shock. Operators should not attempt to
open or remove the instrument covers. Doing so can expose them to electrical hazards.
Warning
A general warning indicates a hazard for which there are no standard icons provided in the
manual. These warnings are accompanied by additional information about the hazard and
how to avoid the hazard in the manual.
Warning
A heavy object warning indicates an object is heavy and that it is possible for personnel to
be injured if they lift improperly. Follow instructions and observe proper lifting techniques or
use lifting aids when lifting heavy objects.
The following cautions are used in this manual:
Caution
A general caution indicates a possibility of equipment damage for which there are no
standard icons provided in the manual. These cautions are accompanied by additional
information about how to avoid the equipment damage in the manual.
Caution
A data loss caution indicates a possibility of loss of data or data corruption if proper
procedures are not followed. This caution will be accompanied by additional information
about how to avoid the data loss in the manual.

301-0045, Rev. K August 2016
Hazards
8.3 Moving the Instrument

Because of the GeneXpert GX-XVI instrument’s weight (see Weight in Section 4.2,
General Specifications), do not attempt to lift the instrument without proper safety
training and assistance. The weight of the GeneXpert GX-I, GeneXpert GX-II, and
GeneXpert GX-IV is not a hazard under normal conditions.
Warning
Lifting or moving the GeneXpert GX-XVI instrument without proper training and assistance
can cause personal injury or damage the instrument.
8.4 Safety Labels on the Instrument

Table 8-1 lists the electrical labels that may be found on the GeneXpert instruments.
Table 8-1. Electrical Safety Labels on the Instruments
Label Description
Indicates the ON position of the main power switch.
Indicates the OFF position of the main power switch.
Indicates the designated terminal either receives or delivers alternating current or

voltage.
Table 8-2 lists other safety labels that may be found on the GeneXpert instruments.
Table 8-2. Other Safety Labels on the Instruments
Label Description
Indicates a potential hazard that is not defined by other warning labels. Consult
the operator or service manual for further information or additional information
that may be included on the label. Proceed with appropriate caution.
Indicates a potential biological risk. Biological samples such as tissues, body

fluids, and blood of humans and other animals have the potential to transmit
infectious diseases. Follow your local, state/provincial, and national safety
regulations for handling and disposing the samples.
Indicates that there should be separate collection for electrical and electronic
waste per Directive 2002/96/EC in the European Union. Follow your local state/
provincial and national environmental regulations for disposing of electrical and
electronic waste.

301-0045, Rev. K August 2016
Hazards
8.5 Electrical Safety

Warning
Electrical hazards exist inside the GeneXpert instruments. Operators should not attempt to
remove the instrument covers. Doing so can expose them to electrical hazards and cause
injuries or death.
The GeneXpert instrument’s enclosure is designed to protect operators from electrical

shock hazards. Under normal operating conditions, you are protected from electrical
shock hazards.
Only trained service personnel should open the covers of the GeneXpert instruments.
Training is available from Cepheid.
8.6 Chemical Safety

• Follow standard laboratory safety procedures for working with chemicals.
• Consult your institution’s environmental waste personnel on proper disposal of used
cartridges, unused reagents, and disposal of instruments. This material may exhibit
characteristics of federal EPA Resource Conservation and Recovery Act (RCRA)
hazardous waste requiring specific disposal requirements. Check state and local
regulations as they may differ from federal disposal regulations. Institutions outside
the USA should check their country hazardous waste disposal requirements.
• Safety Data Sheets (SDS) for all reagents used with this system are available upon
request from Cepheid Technical Support and are available on Cepheid's websites
(www.cepheid.com and www.cepheidinternational.com).
• Refer to the Cepheid website for additional environmental health and safety
information on Cepheid products.

301-0045, Rev. K August 2016
Hazards
8.7 Biological Hazard Safety

Biological specimens, transfer devices, and used cartridges should be considered capable
of transmitting infectious agents requiring standard precautions. Follow your
institution’s environmental waste procedures for proper disposal of used cartridges and
unused reagents. These materials may exhibit characteristics of chemical hazardous
waste requiring specific national or regional disposal procedures. If country or regional
regulations do not provide clear direction on proper disposal, biological specimens and
used cartridges should be disposed per WHO [World Health Organization] medical waste
handling and disposal guidelines.
8.8 Environmental Data

• Recyclability of GeneXpert System: the WEEE mark is affixed to Cepheid
electronic products.
• Recyclability of packaging materials: many of the shipping packaging components
can be recycled.
• Additional information on the above, including EU and country directives
concerning packaging, energy consumption, RoHS, REACH, Prop. 65, etc. can be
found on the Cepheid website.

301-0045, Rev. K August 2016
Hazards

301-0045, Rev. K August 2016
9 Service and Maintenance
This chapter describes the basic maintenance procedures for the GeneXpert instruments
and lists the possible problems or error messages you might encounter. The topics in this
chapter are as follows:
• Section 9.1, Maintenance Tasks
• Section 9.2, Maintenance Log
• Section 9.3, Power Down the System
• Section 9.4, Guidelines for Cleaning and Disinfecting
• Section 9.5, Cleaning the Work Area
• Section 9.6, Close Module Doors
• Section 9.7, Discard Used Cartridges
• Section 9.8, Cleaning the Instrument Surfaces
• Section 9.9, Cleaning the Plunger Rods and Cartridge Bays
• Section 9.10, Cleaning and Replacing the Fan Filters
• Section 9.11, Annual Instrument Maintenance
• Section 9.12, Using Module Reporters
• Section 9.13, Performing a Manual Self-Test
• Section 9.14, Excluding Modules from Test
• Section 9.15, Generating the System Log Report
• Section 9.16, Replacing Instrument Parts
• Section 9.17, Repairing the Instrument
• Section 9.18, Troubleshooting

301-0045, Rev. K August 2016
Service and Maintenance
9.1 Maintenance Tasks

Although the system is designed to prevent cross-contamination and ensure accurate
results, the instrument can be checked and cleaned periodically as a precautionary
measure. Table 9-1 lists the basic maintenance tasks that can be performed.
Table 9-1. Maintenance Tasks and Frequency
Task Frequency Section

Clean work area Daily Section 9.5
Close all module doors Daily Section 9.6
Discard used cartridges Daily Section 9.7
Power down the GeneXpert instrument Weekly Section 9.3
Power down the GeneXpert computer Weekly Section 9.3
Archive tests Monthly Section 5.16.1
Purge tests Monthly Section 5.18
Replace the fan filters Monthly Section 9.10
Clean plunger rod and cartridge bay Quarterly Section 9.9
Clean the instrument surfaces Quarterly Section 9.6
Perform annual instrument maintenance Annually Section 9.11
Print system log report As necessary Section 9.15
Back up database As necessary Section 5.17.1
9.2 Maintenance Log

Complete the maintenance log shown in Figure 9-1 daily or whenever maintenance tasks
are performed on the system. Copies of this monthly log may be made to use, as
required. There is an electronic version of this file on the GeneXpert Dx System
Operator Manual CDROM that can be copied and used for monthly records. The
electronic version of this file is a pdf file that can be filled in and saved using Adobe
Reader or Adobe Acrobat.

301-0045, Rev. K August 2016
GeneXpert® System Maintenance Log Month and Year:
GeneXpert Serial Number: Last Calibration Check Date:

Name of Institution
FAS Installation Date:
Instructions: 1. Enter the name of your institution, GeneXpert Serial Number, current Month and Year, Last Calibration Check date, and FAS Installation Date in
the fields above.
2. For each maintenance activity listed below check the box(es) under the day of the month that the activities were performed and enter your initials
301-0045, Rev. K August 2016

(2 characters maximum) in the bottom row.
3. Save the file after entering the data. We recommend saving one file each month for a complete record of activities.
Daily Maintenance 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31
Clean work area
GeneXpert Dx System Operator Manual

Close all module doors
Discard used cartridges
Weekly Maintenance
Power down the GeneXpert instrument1
Power down the GeneXpert computer1
Monthly Maintenance
Archive tests2
Purge tests2
Replace fan filters1
Quarterly Maintenance
Figure 9-1. Maintenance Log

Clean plunger rod and cartridge bays1
Clean instrument surfaces1
Yearly Maintenance
Check annual instrument maintenance1
As Necessary
Print system log report1
Back up database2
Technician Initials (Two Letters)
1. Refer to Chapter 9 (Service and Maintenance) in the Operator Manual for detailed procedure.
2. Refer to Chapter 5 (Operating Instructions) in the Operator Manual for detailed procedure.
These are minimum recommendations for cleaning. Your institution may require that maintenance be performed on a more frequent basis.
Reference: GeneXpert GX Dx Operator Manual (P/N 301-0045, Rev. K)
301-0748 Rev. G August 2016
9-3
9.3 Power Down the System

The GeneXpert instrument and computer should be powered down once per week to
refresh the system. This action clears out unwanted temporary files and guards against
computer memory corruption to prevent a malfunction of the system.
To exit the GeneXpert Dx software, see Section 5.2.5, Logging Off. Power down the
computer, wait two minutes, then restart the computer.
9.4 Guidelines for Cleaning and Disinfecting

Cleaning and disinfecting system components is crucial for proper system maintenance.
Disinfection is a chemical reaction. As a chemical reaction, it is affected by many factors
including the concentration of the disinfectant, contact time, temperature, nature of the
microbes present, amount of organic residue, surface properties, etc. With any
disinfectant, it is crucial that the entire area to be disinfected be in contact with the
disinfecting solution.
General guidelines for routine surface cleaning are:
• Use only 70% ethanol or denatured ethanol (70% ethanol containing 5% methanol
and 5% isopropanol).
General guidelines for cleaning combined with disinfection are:
• Use a final concentration of 1:10 dilution of household chlorine bleach (used within
1 day of preparation).
• Use sufficient disinfectant (bleach solution) and spread the disinfectant evenly. The
entire surface should be wet to completely disinfect the surface.
• Allow a minimum of two minutes contact time. More than five minutes is not
recommended.
• Remove remaining bleach residue with 70% ethanol or denatured ethanol (70%
ethanol containing 5% methanol and 5% isopropanol).
Caution
Failure to remove bleach residue from the system may cause damage to the instrument
components. Always perform a wipe down with ethanol after using bleach.
• Repeat the cleaning and disinfection with bleach three times (two minutes contact
time for each bleach application) followed by a final wipe with ethanol to remove
bleach residue.
9.5 Cleaning the Work Area

Clean the work area daily using good laboratory practices to avoid contamination of
specimens or reagents. Follow your institution’s guidelines for cleaning the work area.

301-0045, Rev. K August 2016
9.6 Close Module Doors

Check that all module doors are closed daily to avoid contamination of the modules.
9.7 Discard Used Cartridges

Discard used cartridges from the GeneXpert Dx system modules and on the surrounding
work surfaces. Follow your institution’s standard practices for disposal. See Section 8.6,
Chemical Safety and Section 8.7, Biological Hazard Safety for additional information
regarding cartridge disposal.
9.8 Cleaning the Instrument Surfaces

Clean the instrument surfaces quarterly (every three months) with ethanol. All outside
surfaces of the instrument housing should be cleaned including the top, sides, and
outside door of the module.
Before cleaning the instrument surfaces, read Section 9.4, Guidelines for Cleaning and
Disinfecting.
The materials required for this procedure are:
• 70% ethanol or denatured ethanol (70% ethanol containing 5% isopropanol and 5%
methanol).
Caution
Do not use 70% isopropyl alcohol for cleaning the instrument surfaces. Isopropyl alcohol
can degrade system components.
• A final concentration of 1:10 dilution of household chlorine bleach (used within 1

day of preparation).
Use the bleach solution only in the event of a spill. Wipe down the affected surface(s) with
Important bleach three separate times. Leave the bleach on the instrument surfaces for two minutes
each time before wiping the surfaces with ethanol to remove the bleach residue.
• Lint-free wipes
• Disposable gloves
• Eye protection
Biological Risks
Wear disposable gloves, eye protection and other personal protective equipment (PPE)
mandated by your institution’s safety policies while performing this cleaning procedure.
Wearing PPE prevents exposure to chemical and biologically hazardous materials.

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9.8.1 Quarterly Maintenance

Warning
Shut down the GeneXpert Dx system completely when cleaning the instrument surfaces.
Do not remove the instrument covers or use a vacuum cleaner inside the instrument at any
Important time. Remove debris from exterior instrument surfaces using lint-free wipes or paper towels
moistened with ethanol or bleach as described in the following procedure.
For routine cleaning of the instrument surfaces:

1. Thoroughly moisten a lint-free wipe or paper towel with the 70% ethanol solution.
2. Wipe all surfaces outside the instrument. Change lint-free wipes or paper towels
frequently while wiping.
3. Move the GeneXpert instrument and wipe the table surfaces underneath and around
the instrument. Change lint-free wipes or paper towels frequently while wiping.
4. Discard used wipes or paper towels according to your standard laboratory procedure.
9.8.2 In Case of Spill

Clean affected exterior instrument surfaces in the event of a spill.
If it is suspected that a spill has affected the interior of the instrument, do not remove any of
Important the exterior instrument covers. Instead, shut down the instrument and contact Cepheid
Technical Support for assistance.
To clean the affected instrument surfaces:

1. Thoroughly moisten a lint-free wipe or paper towel with the 1:10 bleach solution.
2. Wipe affected surfaces on the instrument. Change wipes or paper towels frequently
while wiping.
3. Allow the bleach solution to remain on the surfaces at least two minutes but no
longer than five minutes.
4. Repeat Step 1 through Step 3 two more times for a total of three times.
5. Thoroughly moisten a lint-free wipe or paper towel with the 70% ethanol solution.
6. Wipe affected surfaces on the instrument. Change wipes or paper towels frequently
while wiping.
7. Discard used wipes or paper towels according to your standard laboratory procedure.

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9.9 Cleaning the Plunger Rods and Cartridge Bays

Clean and disinfect the plunger rods and cartridge bays quarterly (every three months),
in the event of a spill, or if a negative control yields a positive result.
Before cleaning the plunger rods and cartridge bays, read Section 9.4, Guidelines for
Cleaning and Disinfecting.
The materials required for this procedure are:
• A final concentration of 1:10 dilution of household chlorine bleach (used within 1
day of preparation)
Perform the bleach wipe-down three separate times on the interior surfaces of the cartridge
bay, allowing the bleach to remain on the surfaces for two minutes after each wipe. After the
Important
final two minutes, remove the bleach residue by thoroughly wiping the cartridge bay and
plunger rod with ethanol.
• 70% ethanol or denatured ethanol (70% ethanol containing 5% isopropanol and 5%

methanol)
Caution
Do not use 70% isopropyl alcohol for cleaning the cartridge bay and plunger rod. Isopropyl
alcohol can degrade polycarbonate plastics.
• Lint-free wipes
• Eye protection
Biological Risks
Wear disposable gloves, eye protection and other personal protective equipment (PPE)
mandated by your institution’s safety policies while performing this cleaning procedure.
Wearing PPE prevents exposure to chemical and biologically hazardous materials.
To clean the plunger rod(s) and cartridge bay(s):

1. Remove cartridge(s) from the module(s) to be cleaned.
2. In the GeneXpert Dx System window, click the Maintenance icon (see Figure 9-2).
The Maintenance screen is displayed.
3. Click on Maintenance on the Menu Bar (see Figure 9-2), select Plunger Rod
Maintenance. The Plunger Rod Maintenance dialog box is displayed. See Figure 9-3.

301-0045, Rev. K August 2016
Figure 9-3. The Plunger Rod Maintenance Dialog Box

301-0045, Rev. K August 2016
For efficient cleaning of the cartridge bay(s) and plunger rod(s), choose the Clean All option, which
lowers all plunger rod(s), allowing the cleaning of all modules simultaneously.
Note
On the GeneXpert GX-XVI, for efficient cleaning of the cartridge bays and plunger rods, clean them
in groups of four modules.
4. In the Module table, select the module(s) to be cleaned and then select Clean or Clean
All (see Figure 9-3). The Plunger Rod Cleaning dialog box is displayed (see
Figure 9-4).
Figure 9-4. Plunger Rod Cleaning Dialog Box

5. Ensure that there are no cartridges in any of the modules, and click OK.
6. In the Plunger Rod Maintenance dialog box, the Clean button name changes to Move
Up (if the Clean All button is clicked, it changes to Move Up All). In the instrument,
the plunger rod(s) in the selected module(s) (or all modules if the Clean All button is
clicked) lowers into the cartridge bay(s). See Figure 9-5.
Cartridge Bay
Plunger Rod (Lowered)
Slit for I-CORE Module
Instrument Module Door (Opened)
Figure 9-5. Plunger Rod Lowered into Cartridge Bay

301-0045, Rev. K August 2016
7. Clean the plunger rod(s) and cartridge bay(s) as follows:

A. Thoroughly moisten a lint-free wipe with a 1:10 solution of household chlorine
bleach.
B. Vigorously wipe the plunger rod with the lint-free wipe. Wipe hard enough to
remove the black debris that accumulates on the plunger rod.
Using the same lint-free wipe, wipe the walls, ceiling, corners and edges of the
cartridge bay, then wipe the inside of the door and the top lip of the door and
discard the lint-free wipe.
Caution
Getting liquid inside the I-CORE module can damage the module. Do not touch the slit on the
I-CORE module where the cartridge reaction tube is inserted (see Figure 9-5).
Caution
Do not allow the bleach to remain on any surface for more than five minutes.
C. Wait 2 minutes after wiping with the bleach solution.

D. Use a new lint-free wipe thoroughly moistened with the 1:10 bleach solution
and wipe the plunger rod, walls, ceiling, corners and edges of the cartridge bay,
then wipe the inside of the door and the top lip of the door and discard the wipe.
E. Wait 2 minutes after wiping with the bleach solution.
F. Using another new lint-free wipe thoroughly moistened with the 1:10 bleach
solution, wipe the plunger rod, walls, ceiling, corners and edges of the cartridge
bay. Wipe the inside of the door and the top lip of the door and discard the lint-
free wipe.
G. Wait 2 minutes after wiping with the bleach solution.
H. Thoroughly moisten a lint-free wipe with the 70% ethanol solution.
I. Use the lint-free wipe thoroughly moistened with the 70% ethanol solution to
remove all residual bleach. Wipe the plunger rod, walls, ceiling, corners and
edges of the cartridge bay, then wipe the inside of the door and the top lip of the
door and discard the lint-free wipe.
8. After the plunger rod(s) and cartridge bay(s) have been cleaned, return to the
Plunger Maintenance dialog box and select the Move Up button. The plunger rod(s)
move(s) back up to the resting position.
9. Click Close to close the Plunger Maintenance dialog box.
10. Manually close the instrument module door(s).
11. This completes the procedures for cleaning the plunger rod(s) and cartridge bay(s).

301-0045, Rev. K August 2016
9.10 Cleaning and Replacing the Fan Filters

9.10.1 GX-II and GX-IV Fan Filters
There are two styles of fan filters on the GeneXpert GX-II and GeneXpert GX-IV
instruments. If the GeneXpert instrument has a rear panel such as the ones shown in
Figure 9-6, the fan filters are not user-serviceable and must be replaced by a Cepheid
Field Service Engineer. Request your Cepheid Field Service Engineer to replace the fan
filters on the next service call for the system.
GX-II GX-IV
Figure 9-6. Old-Style Filters (Not User-Serviceable)
If the rear panels look like the instruments shown in Figure 9-7, the fan filters can be
cleaned by performing the procedure below.
9.10.2 User-Serviceable GX-II and GX-IV Fan Filters
In order to minimize system downtime, Cepheid recommends that you have a spare fan filter
Note available to swap with the dirty fan filter being cleaned. After removing the fan filter, it may be
cleaned and re-used the next time that a fan filter is removed for cleaning.
Clean the fan filters monthly or more frequently, if necessary. There is one fan filter on
both the GeneXpert GX-II and the GeneXpert GX-IV instruments. Location of the fan
filters is on the back of the instruments (see Figure 9-7). The materials needed for the
procedure are as follows:
• Replacement fan filters:
• GeneXpert GX-II - Filter Part Number: 001-1271
• GeneXpert GX-IV - Filter Part Number: 001-1537
• Paper towels
• Water

301-0045, Rev. K August 2016
The GeneXpert instrument and computer must be powered down prior to performing the fan
Important
filter cleaning described below. This procedure must be performed on a monthly basis.
1. Make sure all tests have finished running before attempting to move the instrument.
2. Turn off the GX-II or GX-IV instrument and the computer following the instructions
in Section 5.2, Getting Started.
If needed, gently move the instrument when performing the following procedure for fan filter
Note
cleaning.
Warning
weights. Use care when moving the instrument. Do not attempt to lift the instrument without
proper safety training and assistance. Lifting or moving the instrument without proper
training and assistance can cause personal injury, damage the instrument, and void your
warranty.
Caution
Be careful not to drop the instrument.
3. Reposition the instrument so the fan filter can be easily accessed. See Figure 9-7.
Fans
Fans (4)
GeneXpert GX-II GeneXpert GX-IV

Figure 9-7. GeneXpert GX-II and GeneXpert GX-IV Instruments Positioned for Access to Fans
4. Gently take the fan filter guard off by unsnapping the guard from the fan housing
(see Figure 9-8) and place it aside for the remainder of the procedure for filter
removal and cleaning.

301-0045, Rev. K August 2016

Fan Filter Guard
Figure 9-8. Removing Fan Filter Guard

5. Remove the dirty filter for cleaning. See Figure 9-9.
Filter

Figure 9-9. Filter Removal
6. Place a clean filter into the fan filter guard.
7. Position the fan filter guard and filter into place as a unit. Press the sides of the guard
firmly onto the fan housing until the grip snaps securely onto the fan. Press the
bottom of the guard until the grip snaps securely onto the fan. See Figure 9-10.

301-0045, Rev. K August 2016
GX-II: Pressing the Bottom into Place GX-IV: Pressing the Sides into Place
Figure 9-10. Installing the Fan Filter Guard
8. Clean the old filter by washing it. Place this cleaned filter between two paper towels
and allow it to air-dry.
Caution
Never wash a fan filter and then put it back onto the system immediately. The fan filter must
be completely dry before installing it onto the system.
9. After the filter is dry, store it to use the following month, when you next remove the
filter for cleaning.
10. In the maintenance log (see Figure 9-1), fill in the date of the fan filter cleaning and
keep it for your records.
9.10.3 GeneXpert GX-XVI Fan Filters

9.10.3.1 Procedure to Clean and Replace GX-XVI R1 Fan Filters
In order to minimize system downtime, Cepheid recommends that you have spare fan filters
Note available to swap with the dirty fan filters being cleaned. After removing a fan filter, it may be
cleaned and re-used the next time that the fan filters are removed for cleaning.
Clean the fan filters monthly or more frequently, if necessary. There are four fan filters
on the GeneXpert GX-XVI R1. Location of the fan filters is on the back of the GX-
XVI R1. See Figure 9-11. The materials needed for the procedure are as follows:
• Replacement fan filters - Filter Part Number: 001-1271

301-0045, Rev. K August 2016
• Paper towels
• Water
The GeneXpert instrument and computer must be powered down prior to performing the fan
Important
filter cleaning described below. This procedure must be performed on a monthly basis.
2. Turn off the GX-XVI R1 instrument and the computer following the instructions in
Section 5.2, Getting Started.
If needed, gently move the instrument when performing the following fan filter replacement
Note
procedure.
Warning
warranty.
Caution
3. If there is not sufficient rear access to the instrument, slide the instrument around so
you can easily access the filter covers. See Figure 9-11.
Fans (4)
Fans
Figure 9-11. GeneXpert GX-XVI R1 Instrument Positioned for Access to Fans

301-0045, Rev. K August 2016
4. Gently take the fan filter guard off by unsnapping the guard from the fan housing
(see Figure 9-12), and place it aside for the remainder of the procedure for filter
Fan Filter Guard Filter
Figure 9-12. Removing Fan Filter Guard

5. Remove the dirty filter(s) for cleaning. See Figure 9-12.
6. Place a clean filter into the fan filter guard.
Filter in Fan Guard Filter Guard Installed
Figure 9-13. Replacement Filter and Guard Installed

8. Repeat Step 4 through Step 6 for the remaining fan filters (three additional filters).
9. Clean the old filters by washing them. Place each cleaned filter between two paper
towels and allow it to air-dry.
Caution
Never wash a fan filter and then put it back onto the system immediately. A fan filter must be
completely dry before installing it onto the system.

301-0045, Rev. K August 2016
10. After the filters are dry, store them to use the following month, when you next
remove the filters for cleaning.
9.10.3.2 Procedure to Clean and Replace GX-XVI R2 Fan Filters
In order to minimize system downtime, Cepheid recommends that you have spare fan filters
Note available to swap with the dirty fan filters being cleaned. After removing a fan filter, it may be
cleaned and re-used the next time that the fan filters are removed for cleaning.
Clean the fan filters monthly or more frequently, if necessary. There are four fan filters
on the GeneXpert GX-XVI R2. Location of the fan filters is on the back of the GX-XVI
R2. See Figure 9-14. The materials needed for the procedure are as follows:
• Replacement fan filters - Filter Part Number: 001-1537
• Paper towels
• Water
The GeneXpert instrument and computer must be powered down prior to performing the
Important
filter replacement described below. This procedure must be performed on a monthly basis.
Filters
(4 each)
Figure 9-14. GeneXpert GX-XVI R2 Fan Filters


301-0045, Rev. K August 2016
2. Turn off the GX-XVI R2 instrument and computer following the instructions in
Note If needed, gently move the instrument when performing the following fan filter cleaning procedure.
Warning
warranty.
Caution
3. If there is not sufficient rear access to the instrument, slide the instrument around so
you can easily access the filter covers.
4. Gently take the fan filter guard off by unsnapping the guard from the fan housing.
See Figure 9-15 and place it aside for the remainder of the procedure for filter
Filter Fan Filter Guard
Figure 9-15. Removing the Fan Filter Guard and Filter

301-0045, Rev. K August 2016
5. Remove the dirty filter(s) for cleaning.

6. Place a clean filter in the fan filter guard.
Filter in Fan Guard Filter and Fan Guard Installed
Figure 9-16. Replacing the Filter and Guard

8. Repeat Step 4 through Step 6 for the remaining fan filters (three additional filters).
9. Clean the old filters by washing them. Place each cleaned filter between two paper
towels and allow it to air-dry.
Caution
Never wash a fan filter and then put it back onto the system immediately. A fan filter must be
completely dry before installing it onto the system.
10. After the filters are dry, store them to use the following month, when you next
remove the filters for cleaning.

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9.10.4 High Efficiency (HE) Filter Replacement Instructions

This section provides instructions for the replacement of the HE filter and prefilter, and
applies only to specifically-configured GX-IV systems.
Location of the fan filters is on the back of the GX-IV (see Figure 9-17). The materials
needed for the procedure are as follows:
• Replacement Filter Kit - Part Number: GX-HE-FILTERKIT
• Contains Qty. 1 HE Filter and Qty. 6 Prefilters
Replace the Prefilter at a minimum of once every 2 to 3 months.
Replace the HE filter at a minimum of once every 12 months.
The GeneXpert instrument and computer must be powered down prior to performing the
Important
filter replacements described below.
2. Turn off the GX-IV instrument and the computer following the instructions in
Note If needed, gently move the instrument when performing the following filter replacement procedure.
Caution
3. Reposition your instrument so you can easily access the filter.
Figure 9-17. GX-IV Instrument Positioned for Access to Filter

301-0045, Rev. K August 2016
4. Gently remove the prefilter retainer using fingers at the corners. See Figure 9-18.
Figure 9-18. Removing the Prefilter Retainer

5. Remove the prefilter from the prefilter retainer. See Figure 9-19. Discard the old
prefilter.
Figure 9-19. Removing the Prefilter

6. Remove the HE filter retainer by releasing the clips on sides and top and bottom.
The filter retainer fits very tightly and may take effort to remove. See Figure 9-20.

301-0045, Rev. K August 2016
Figure 9-20. Removing the HE Filter Retainer

7. Tilt the GX-IV instrument to the surface toward you to remove the HE filter. The HE
filter should come out easily. See Figure 9-21. Discard the old HE filter.
Figure 9-21. Removing the HE Filter

301-0045, Rev. K August 2016
Installing the HE Filter, HE Filter Retainer, Prefilter and Prefilter Retainer

1. Place the new HE filter into the filter housing. The arrow on the HE filter points
inward toward the instrument. See Figure 9-22.
Figure 9-22. Replacing the HE Filter

2. Place the HE filter retainer on top of the HE filter. Using your fingers on the sides,
top and bottom, gently push the HE filter retainer so it fits tightly. The clips on the
sides, top and bottom need to engage fully. See Figure 9-23
Figure 9-23. Replacing the HE Filter Retainer

3. Place the prefilter underneath the prefilter retainer so that the two are directly in
contact together.
4. Place the assembled prefilter retainer and the prefilter together on top of the HE
filter retainer with fingers at sides, top and bottom so it fits tightly. See Figure 9-24.

301-0045, Rev. K August 2016
Figure 9-24. Replacing the Prefilter and the Prefilter Retainer

5. The HE filter is now fully replaced and assembled on the GX-IV instrument. The
filter on the instrument should resemble Figure 9-17.
9.11 Annual Instrument Maintenance

Calibration of the GeneXpert instrument is not required during the initial system startup.
Cepheid performs all of the necessary calibrations before the system is shipped.
However, Cepheid recommends that the system be checked for proper calibration on an
annual basis. Based upon the usage and care of each system, calibration checks may be
recommended more frequently. The system is designed to measure module performance
with the internal assay controls. In the event of a module failure, the replacement module
provided will have been calibrated prior to shipment.
The Cepheid Field Service Engineer or customer will perform the calibration checks
during annual maintenance or by the field service engineer if responding to a module
failure. Contact Cepheid Technical Support for information about calibration. See the
Technical Assistance section in the Preface for contact information.

301-0045, Rev. K August 2016
9.12 Using Module Reporters

Cepheid Technical Support may ask you to use the Module Reporters tool when
investigating the source of possible module-related problems. The Module Reporters tool
is also used to check the last date of calibration for the modules. It provides calibration
information and other data, shown in Figure 9-25.
To view the Module Reporters, go to the Maintenance screen. Click on Maintenance on
the menu bar and select Module Reporters. The Module Reporters window appears. See
Figure 9-25.
Click the drop-down menu to
view a different module.
Figure 9-25. Module Reporters Window
9.13 Performing a Manual Self-Test

Note No tests can be running in the GeneXpert Dx system when performing a manual self-test.
The GeneXpert Dx system automatically performs a self-test during startup. However, a

self-test can be manually initiated on any of the modules to reset and check for hardware
failure problems.
To start the self-test:
1. Remove cartridges from the modules to be checked.
2. In the GeneXpert Dx System window, click the Maintenance icon. The Maintenance
screen appears. See Figure 9-28.
3. Click on Maintenance on the menu bar and select Perform Self-Test. The Module
Self-Test dialog box appears. See Figure 9-26.

301-0045, Rev. K August 2016
Figure 9-26. Module Self-Test Dialog Box

4. Select the module to be checked.
5. Click Self-Test. The Self-Test dialog box appears. See Figure 9-27.
Figure 9-27. Self-Test Dialog Box

6. Follow the instructions in the Self-Test dialog box and click OK.
7. When the self-test finishes, the software changes the progress to Available, indicating
the self-test passed. If the message indicates the self-test failed, contact Cepheid
Technical Support. See the Technical Assistance section in the Preface for the

301-0045, Rev. K August 2016
9.14 Excluding Modules from Test

Modules may be excluded from testing, if desired, by following the instructions in this
section. Modules that are excluded will be listed as Disabled, and will not be used by the
system to run tests.
To exclude modules from a test:
1. In the GeneXpert Dx System window, click the Maintenance icon. The Maintenance
screen appears. See Figure 9-28.
2. Click on Maintenance on the menu bar and select Exclude Modules From Test. The
Exclude Modules From Test dialog box appears. See Figure 9-29.

301-0045, Rev. K August 2016
Figure 9-29. Exclude Modules From Test Dialog Box

3. Select the module(s) to be excluded from test by clicking on the adjacent check box.
4. Press the OK button to save changes to the Exclude Modules From Test dialog box
(see Figure 9-29).
Press the Cancel button to cancel changes.

301-0045, Rev. K August 2016
9.15 Generating the System Log Report

The System Log reports can be used to provide incidents of instrument module self-tests
and errors to Cepheid when a module failure has been encountered.
1. In the GeneXpert Dx System window, click Reports on the menu bar, and then click
System Log. The System Log Report window appears. See Figure 9-30.
Figure 9-30. System Log Report Window

2. Specify the following criteria to view the trends of interest:
• Date Range:
• All—Select to include all of the records.
• Select—Select to filter the records by specifying a range of dates. Entries
older than 1 year are automatically removed.
• Modules:
• Currently Connected Modules— Displays modules that are connected to the
system and are currently shown on Check Status screen. This is the default
option.
• All Logged Modules—Displays all modules which have self-test or error
entries in this system database within the last 1 year. This allows technical
support to obtain self-test/error entries for a module that is no longer
connected to the system.

301-0045, Rev. K August 2016
A list of modules is displayed in the table. Select the module to be included

in the system by selecting the individual modules one-by-one, or by using
one of the following buttons:
• Select All—Selects every module shown in the table by checking all
check boxes.
• Deselect All—Deselect every Module by clearing all check boxes.
• Select Highlighted—Selects the row(s) highlighted by the mouse.
• Deselect Highlighted—Deselect the highlighted rows and clear the
check boxes.
• Show:
• Errors Only—Displays only error entries in the generated report file.
• All Entries—Displays all self-test entries and error entries in the report.
3. When you finish selecting the log criteria, click one of the following buttons:
specify.
• Click the Generate Report File button on the System Log Report screen (see
Figure 9-30) to create the PDF file of the test report. The Generate Report
File dialog box will appear, which enables a file to be saved to a specified
location. Click Save after navigating to the specific location.
• Optionally, to print the report, go to the saved location, open the System
Log report and print it. A report similar to the System Log report shown in
Figure 9-31 will be printed.
window. See Figure 9-31. The PDF file can be saved and printed from the
Adobe Reader software.
4. After printing the System Log report, click Close to close the System Log Report
window.

301-0045, Rev. K August 2016
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301-0045, Rev. K August 2016
9.16 Replacing Instrument Parts

Caution
Do not attempt to replace the power cord or Ethernet cable using non-approved parts. Using
incompatible parts can damage the instrument, cause performance problems or cause loss
of data.
You can replace the following GeneXpert instrument parts:

• Power cord for GeneXpert GX-IV and GeneXpert GX-XVI
(Part Number: 100-1375)
• Ethernet cable (Part Number: 700-0555)
• DC Adapter Power Supply for GeneXpert GX-I R2 and GeneXpert GX-II R2
• Power Cord for GeneXpert GX-I R2 and GeneXpert GX-II R2
You can obtain the power cord, Ethernet cable, and DC adapter power supply from
Cepheid. See the Technical Assistance section in the Preface for the contact information.
9.17 Repairing the Instrument

Warning
Do not attempt to open or remove the instrument covers. Doing so can expose you to
electrical hazards and cause injuries or death.
Warning
Do not attempt to open or remove the instrument covers. Do not attempt to modify or repair
the system. Improper repairs and incorrect part replacements can cause injury, damage the
instrument, and void your warranty.
To protect your warranty and for proper operation, the GeneXpert Dx system should be
serviced only by an authorized Cepheid representative. If the instrument is not working
correctly, contact Cepheid Technical Support. See the Technical Assistance section in the
Preface for the contact information. When you call Cepheid Technical Support, be
prepared to supply the serial number of your instrument. You can find the serial number
label on the back side of the instrument.

301-0045, Rev. K August 2016
9.18 Troubleshooting
This section lists the possible problems or error messages you might encounter.
The topics are as follows:
• Section 9.18.1, Hardware Problems
• Section 9.18.2, Error Messages
9.18.1 Hardware Problems

Table 9-2 lists the possible hardware problems you might encounter. To contact Cepheid
Technical Support, see the Technical Assistance section in the Preface for the contact
information.
Table 9-2. Hardware Problems
Problem Possible Cause Solution

The system does not start. The instrument is not connected to the Check the instrument power
power outlet. connections.
Module not detected. Network cable not connected or Connect network cable
incorrect cable installed. (Cepheid P/N 700-0555).
Software launched before instrument Exit software and relaunch with
turned on. instrument powered on.
The IP address is not assigned Change IP Address Setting by
correctly. performing the steps provided in
Section 2.7.3, Setting the IP Address.
Hardware failure. Using software version less than 4.0 Turn system off and update software.
with 6-color instrument.
Barcode scanner failure. Symbology unsupported. GeneXpert Dx software supports Code
39, Codebar, Code 128 (A, B and C)
linear barcode symbologies and
Interleave 2 of 5.
Scanner barcode cable not plugged in. Unplug scanner and replug into
computer.
The cartridge is stuck inside the Module mechanical failure. To remove the cartridge:
instrument module. • In the GeneXpert Dx System
window, click Maintenance on the
toolbar.
• On the Maintenance menu, click
Open Module Door or Update
EEPROM.
• Select the module.
• Click Open Door to open the
module door.
If the door does not open, cycle the
instrument power and repeat the above
steps.

301-0045, Rev. K August 2016
Table 9-2. Hardware Problems (Continued)
Problem Possible Cause Solution

The instrument module red light is Module mechanical failure. Confirm no cartridge is in the module.
flashing. Perform a self-test manually (Section
9.13, Performing a Manual Self-Test).
If the error recurs, contact Cepheid
Technical Support.
Test report is not printed at the end of Printer off line. Check:
run. • Printer on-line.
Printer out of paper and/ • Paper present.
or toner. • Toner OK.
Unable to create a test. Modules not available. Check that assay is selected.
No assay selected. Calibrate with assay dyes.
Module not calibrated for reporters Check that the modules are not
used in assay. disabled.
The ambient temperature of the Check module temperature in
module is above 55 °C. Maintenance screen. If your room is in
the recommended temperature range
and the module is above 55 °C, contact
Unable to start test. Reporters out of calibration. Check module reporters in
maintenance window:
Reporter for assay are present.
Calibration status is valid.
9.18.2 Error Messages

This section lists the error messages and provides possible causes and solutions. The
error messages are grouped by the categories shown in the software:
• Section 9.18.2.1, Run-Time Errors—Errors that occur during a test. This list
includes five codes that were added to support assay development. If these codes are
encountered, the error status will be reported as OK.
• Section 9.18.2.2, Operation Terminated Errors —Errors that abort a test.
• Section 9.18.2.3, Cartridge Loading Errors —Errors that occur during a cartridge
loading process.
• Section 9.18.2.4, Self-Test Errors —Errors that occur during the self-test process.
• Section 9.18.2.5, Post-Run Analysis Errors —Errors that occur during the data
reduction process.You can view all of the errors in the Check Status window (see
Figure 9-32). Details for test-specific errors are also shown on the Errors tab of the
View Results window (see Figure 9-33).
• Section 9.18.2.6, Communication Loss/Recovery Errors —Errors that occur
during the self-test process.

301-0045, Rev. K August 2016
Figure 9-32. GeneXpert Dx System - Check Status Window

301-0045, Rev. K August 2016
Check the Description column Check the Detail column for the
for the error type. error message text.
Figure 9-33. GeneXpert Dx System - View Results Window - Errors Tab

(Detail Users and Administrator View)
9.18.2.1 Run-Time Errors

Table 9-3 lists errors that might appear during a test that is not aborted. Although the
system was able to finish the test and save the results, some non-critical errors occurred
and require attention. These error messages appear in the View Results window (see
Figure 9-33). To contact Cepheid Technical Support, see the Technical Assistance
section in the Preface for the contact information.
Table 9-3. Errors that Occurred During a Test that is Not Aborted
Error Error Message Possible Causes Solution

Code
1001 The actual temperature n °C has A heater component or a related Report the temperature value in the
drifted too far away from the setpoint component failed. error message to Cepheid Technical
of m °C. Support.
(n and m are temperature values Environment temperature is too Check room temperature.
that the software displays. The warm.
values can vary.) Fan Failure. Check fans are functional and fan
filters are clean.

301-0045, Rev. K August 2016
Table 9-3. Errors that Occurred During a Test that is Not Aborted (Continued)

Code
1002 The temperature difference of n °C The difference between the Call Cepheid Technical Support.
exceeds the limit of m °C. The temperatures of the two thermistors
temperatures for heaters A and B has exceeded the acceptable
are p °C and q °C. difference of 5 °C.
(n, m, p, and q are temperature
values that the software displays.
The values can vary.)
1004 The internal instrument temperature One or more of the following might Check the following:
n °C was out of range of m1 °C to have caused the error: • Verify the instrument has at
m2 °C. • The ambient temperature is not least 5 cm (2 in) of clearance on
(n, m1, and m2 are temperature within the required range. each side.
values that the software displays. • The environmental conditions • Verify the laboratory
The values can vary.) do not meet the requirements. environmental conditions meet
• The ambient temperature the requirements specified in
sensor failed. Chapter 4, Performance
• Broken or dirty fans Characteristics and
Specifications.
• Verify fans are moving.
• Clean fan filters.
If the instrument meets all the
requirements and the error persists,
call Cepheid Technical Support.
1005 Optic signal of n from detector #m One or more of the following might Try one or more of the following
using LED #p exceeded the limit have caused the error: solutions:
of q. • The signal from the reporter is • Use a different cartridge.
(n, m, p, and q are values that the too high. • Make sure the module door is
software displays. The values can • The module door is not closed closed completely.
vary.) properly. If the error recurs, call Cepheid
• A hardware component failed. Technical Support and provide the
information presented in the error
message.
1006 Detector #n dark signal of m The detector or the electronics Call Cepheid Technical Support and
exceeded the limit of p. failed. provide the information presented in
(n, m, and p are values that the the error message.
software displays. The values can
vary.)
1007 The n V power supply was detected The power supply voltage is out of Record the information in the error
to be m V. range. message. If the error recurs in
(n and m are voltage values that the multiple runs, call Cepheid Technical
software displays. The values can Support.
vary.)
1017 The measured temperature of the One or more of the following might Rerun the test.
optical system was n °C which was have caused the error: If the error recurs, call Cepheid
not within the acceptable range of • The optical block thermistor Technical Support.
m1 °C to m2 °C. failed.
(n, m1, and m2 are temperature • The ambient temperature is too
values that the software displays. high.

301-0045, Rev. K August 2016
Table 9-3. Errors that Occurred During a Test that is Not Aborted (Continued)

Code
1018 A valve positioning error of n A valve component failed. Rerun the test.
count(s) was detected at the end of Cartridge integrity compromised. If the error recurs, call Cepheid
the run. Technical Support
(n is a value that the software
displays. The value can vary.)
1096 Proceeded to Next Step #1: n, m, p, Assay specific cause. Rerun the test.
q If the error recurs, call Cepheid
(n, m, p, q values are assay specific) Technical Support.
1125 Possible Insufficient Volume Error: Possible Insufficient Volume Rerun the test.
n, m, p, q If the error recurs, call Cepheid

301-0045, Rev. K August 2016
9.18.2.2 Operation Terminated Errors

Table 9-4 lists errors that might appear when a test is aborted. The operation-terminated
error messages appear in the View Results window. See Figure 9-33. To contact Cepheid
information.
Table 9-4. Errors that Might Appear When a Test is Aborted

Code
2003 Module is already running a test with Software communication failed. Call Cepheid Technical Support.
test ID n while performing command ID
m.
(m and n are ID numbers that the
software displays. The number can
vary.)
2005 Motion of the syringe drive was not A syringe stall was detected. Try one or more of the following
detected. Detected motion started at solutions:
position n ul and transferred m ul at • Use a new cartridge.
valve position p with pressure q PSI.
• Restart the system. See
(n, m, p, and q are values that the Section 2.14, Restarting the
software displays. The values can vary.) System for instructions.
If the error persists, call Cepheid
Technical Support.
2006 Valve motion was not detected. Valve The valve drive failed. Try one or more of the following
started at position n. Last detected at solutions:
position m. • Open the module and reposition
Improper interface between
(n and m are values that the software cartridge and valve body. the cartridge.
displays. The values can vary.) • Use a new cartridge.
• Restart the system. See
Section 2.14, Restarting the
System for instructions.
Technical Support.
2008 Syringe pressure reading of f.f PSI One or more of the following Try one or more of the following
exceeds the protocol limit of f.f PSI, items might have caused the solutions:
command # [The command line number error: • Use a new cartridge.
in the ADF] • The filter is clogged by • Run a cartridge containing
(f.f is a value that the software displays. debris in sample. buffer only.
The value can vary.) • Pressure sensor failed. If the error persists, call Cepheid
Technical Support.
2009 Syringe pressure reading of f.f PSI is The filter is clogged. Try one or more of the following
below the protocol limit of f.f PSI, solutions:
command # [The command line number • Use a new cartridge.
in the ADF]
• Run a cartridge containing
(f.f is a value that the software displays. buffer only.
The value can vary.) If the error persists, call Cepheid
Technical Support.

301-0045, Rev. K August 2016
Table 9-4. Errors that Might Appear When a Test is Aborted (Continued)

Code
2012 An inaccurate valve move to position n A component of the valve drive Use a new cartridge. If the error
was detected. The valve was detected failed. persists, call Cepheid Technical
to stop at position m. Support.
(n and m are values that the software
displays. The values can vary.)
2014 The digital temperature reading of n for The heater A/heater B/module’s Check the following:
Thermistor A/Thermistor B/Ambient optical block thermistor failed. • The ambient temperature.
Thermistor/Optic Thermistor was not
• The internal temperature of the
within the acceptable range of m1 to
instrument.
m2.
• Two inches of clearance, refer
(n, m1, and m2 are temperature values to Chapter 2 (Installation).
that the software displays. The values
• If the ambient and internal
can vary.)
temperatures are within the
acceptable range and you
continue to see the error
message, call Cepheid
Technical Support.
2016 The system was unable to find the valve The valve position sensor failed. Perform self-test and try again with
home position. another cartridge.
Technical Support.
2017 The door latch sensor is still on after a One or more of the following To remove the cartridge:
cartridge eject operation. might have caused the error: • In the GeneXpert Dx System
• A syringe component failed. window, click Maintenance on
• The door or a related the toolbar.
component failed. • On the Maintenance menu,
• The door sensor failed. click Open Module Door or
Update EEPROM.
• Select the module.
• Click Open Door to open the
module door.
• After you remove the cartridge,
restart the system. See Section
2.14, Restarting the System for
instructions.
2022 Failed to get to desired temperature of n Environmental temperature is Check the following:
°C. The temperature reached m °C. above or below the acceptable • The ambient temperature
(n and m are temperature values that range.
• The internal temperature of the
the software displays. The values can instrument
vary.) • Two inches of clearance, refer
to Section 2.4.1 and Section
4.3, Operational Environmental
Parameters.
If the ambient and internal
temperatures are within the
acceptable range and you continue
to see the error message, call

301-0045, Rev. K August 2016
Table 9-4. Errors that Might Appear When a Test is Aborted (Continued)

Code
2024 An ultrasonic horn failure occurred with The ultrasonic horn failed. Use a new cartridge.
n% duty cycle, m Hz and actual p% If the problem persists, call Cepheid
amplitude. Setpoint amplitude was q%. Technical Support.
(n, m, p, and q are values that the
software displays. The values can vary.)
2026 The ultrasonic horn current was The ultrasonic horn failed. Call Cepheid Technical Support.
detected to be out of the normal range.
2032 The ultrasonic horn could not be tuned The ultrasonic horn failed. Use a new cartridge.
properly. The tuning frequency value If the problem persists, call Cepheid
was n Hz. Technical Support.
(n is a value the software displays. The
value can vary.)
2034 The optical signal from Detector n/LED One or more of the following Restart the test. If the error recurs,
n did not reach the expected value. might have caused the error: restart the system. See Section
Expected value=m, Actual value=p. • The LED is not working. 2.14, Restarting the System for
(n, m, and p are values that the software • instructions.
The detector is not working.
displays. The values can vary.) • The associated circuit is If the error persists, call Cepheid
experiencing problems. Technical Support.
2035 An ultrasonic failure occurred with n% One or more of the following Restart the test. If the error recurs,
duty cycle, m Hz and actual p% might have caused the error: restart the system. See Section
amplitude. Setpoint amplitude was q%. • Cartridge issue 2.14, Restarting the System for
(n, m, p, and q are values that the instructions.
• Dirt on the horn surface
software displays. The values can vary.) • The ultrasonic horn failed. If the error persists, call Cepheid
Technical Support.
2096 Assay-Specific Termination Error #1: n, Assay specific cause. Rerun the test.
m, p, q If the error recurs, call Cepheid
2125 Termination Error –Insufficient Volume: Insufficient Volume Rerun the test.
n, m, p, q If the error recurs, call Cepheid
2126 Module was reset. Intermittent power supply failure. Restart system.
Power supply cable or connector If problem persists, call Cepheid
failure. Technical Support.

301-0045, Rev. K August 2016
9.18.2.3 Cartridge Loading Errors

Table 9-5 lists errors that might appear during a cartridge loading process. The cartridge-
loading error messages appear in the Check Status window. See Figure 9-32.
Because the software performs some self-test procedures during the loading process,
some of the error messages that appear during loading process are identical to the self-
test error messages. See Section 9.18.2.4, Self-Test Errors for the list of those messages.
To contact Cepheid Technical Support, see the Technical Assistance section in the
Preface for the contact information.
Table 9-5. Errors that Might Appear During the Cartridge Loading Process

Code
2011 Unable to initialize pressure sensor The force sensor failed. Restart the test. If the error recurs,
to n. Sensor value of m was restart the system. See Section 2.14,
obtained. Restarting the System for instructions.
(n and m are pressure values that If the error persists, call Cepheid
the software displays. The values Technical Support.
can vary.)
2018 Attempt to load a cartridge while the One of the following might have Restart the system. See Section 2.14,
door is still closed. caused the error: Restarting the System for instructions.
• The valve motor failed. Open door.
• A syringe component failed. If the error recurs, call Cepheid
• The door-latch sensor failed. Technical Support.
2025 One of the following messages is The plunger components or the To determine if the error is caused by a
displayed: force sensor failed. failed instrument module or a bad
The system failed to find the plunger cartridge:
home position. Plunger moved down • Restart the test using the same
looking for ADC = n. ADC value m cartridge and load it into the same
was detected and stall occurred. instrument module.
The system failed to find the plunger • If the error recurs, restart the test
home position. Upward move with using the same cartridge but load it
minimum force value of n was into a different instrument module.
completed without reaching force If the test progresses successfully
value less than m. in the new module, the previous
(n and m are values that the module requires repair. Call
software displays. The values can Cepheid Technical Support.
vary.) • If the error occurs in the second
instrument module, restart the test
using a new cartridge and load it
into the original module. If the test
progresses successfully, the
previous cartridge was bad.
Technical Support.
2037 The cartridge integrity test failed at The cartridge integrity test failed. Restart the system. See Section 2.14,
valve position <n>. The pressure Restarting the System for instructions.
change of f.ff PSI did not exceed the Open door.
requirement of f.f PSI. The pressure
If the error recurs, call Cepheid
increased from f.f PSI to f.f PSI
Technical Support.
during the test.

301-0045, Rev. K August 2016
9.18.2.4 Self-Test Errors

Table 9-6 lists errors that might appear during the self-test process. The self-test error
messages appear in the Check Status window. See Figure 9-32. To contact Cepheid
information.
Table 9-6. Error Messages that Might Appear During the Self-Test Process

Code
4001 A problem with the memory of the A hardware component failed Restart the system. See Section
I-CORE was detected. 2.14, Restarting the System for
instructions.
Open door, select module, and
update EEPROM.
Technical Support.
4002 A problem with the main memory of A hardware component failed. Restart the system. See Section
the GeneXpert module was 2.14, Restarting the System for
detected. instructions.
Technical Support.
4003 A problem of the ultrasonic horn The ultrasonic drive circuitry failed. Restart the system. See Section
system was detected. 2.14, Restarting the System for
instructions.
Technical Support.
4004 Valve motion was not detected. A component of the valve drive Remove any cartridges from the
failed. module, and then restart the system.
If the error recurs, perform a self-test
manually (see Section 9.13,
Performing a Manual Self-Test). If
the error persists, call Cepheid
Technical Support.
4006 Syringe drive movement was not The stall sensor failed during Restart the system. See Section
detected. cartridge loading because: 2.14, Restarting the System for
• The cartridge was not instructions.
positioned correctly. If the error persists, call Cepheid
• A component of the syringe Technical Support.
drive failed.
4008 The n-V power supply was detected Power supply failure. Restart the system. See Section
to be m V. 2.14, Restarting the System for
(n and m are voltage values that the instructions.
software displays. The values can If the error persists, call Cepheid
vary.) Technical Support.
4009 Heater A operation was not verified. A heater A component failed. Perform self-test. See Section 9.13,
Measured temperature changed Performing a Manual Self-Test.
from n °C to m °C. If the error persists, call Cepheid
(n and m are temperature values Technical Support.
that the software displays. The
values can vary.)

301-0045, Rev. K August 2016
Table 9-6. Error Messages that Might Appear During the Self-Test Process (Continued)

Code
4010 Cooling fan operation was not A cooling component failed. Make sure that the air vents are not
verified. Measured temperature of n blocked. The instrument must have
°C exceeded the limit of m °C. at least 5 cm (2 in) of clearance on
(n and m are temperature values each side.
that the software displays. The Perform self-test. See Section 9.13,
values can vary.) Performing a Manual Self-Test.
Technical Support.
4011 The reported dark value of n for The module door was not closed Make sure the module door is
detector m was too high. completely, or a hardware closed completely. If the error
(n and m are values that the component failed. recurs, record the value in the error
software displays. The values can message, and then call Cepheid
vary. Technical Support.
4012 Heater B operation was not verified. A heater B component failed. Perform self-test. See Section 9.13,
Measured temperature changed Performing a Manual Self-Test.
from n °C to m °C. If the error persists, call Cepheid
(n and m are temperature values Technical Support.
that the software displays. The value
can vary.)
4013 An inaccurate valve move was A valve error has occurred. If a cartridge is found in the module,
detected. The valve was remove it. Perform a self-test.See
programmed to stop at position n but Section 9.13, Performing a Manual
stopped at position m. Self-Test.
(n and m are position values that the If the error recurs, call Cepheid
software displays. The values can Technical Support.
vary.)
4014 The optical signal from Detector n/ An optics component failed. Call Cepheid Technical Support.
LED n did not reach the expected
value. Expected value = m, Actual
value = p.
(n, m, and p are optical signal values
that the software displays. The
values can vary.)
4015 The measured temperature of the An optical block thermistor failed. Restart the system. See Section
optical system is n which was not 2.14, Restarting the System for
within the acceptable range of m1 to instructions.
m2. If the error recurs, call Cepheid
(n, m1, and m2 are temperature Technical Support.
4016 GX module program corruption. • Possible RAM failure Call Cepheid Technical Support.
Unable to continue the test • Possible EMI
• Firmware defect

301-0045, Rev. K August 2016
Table 9-6. Error Messages that Might Appear During the Self-Test Process (Continued)

Code
4017 The digital temperature reading of n The heater A/heater B/module’s/ Restart the system. See Section
for Thermistor A/Thermistor B/ optical block thermistor failed. 2.14, Restarting the System for
Ambient Thermistor/Optic instructions.
Thermistor was not within the If the error recurs, call Cepheid
acceptable range of m1 to m2. Technical Support.
(n, m1, and m2 are temperature
4019 The optical ramp test for LED n LED is broken. Restart the system. See Section
resulted in non-monotonic results at 2.14, Restarting the System for
DAC setting of nnn. The reference instructions.
detector readings were nnn and nnn. If the error recurs, call Cepheid
Technical Support.
9.18.2.5 Post-Run Analysis Errors

Table 9-7 lists errors that might appear during the post-run analysis (data reduction)
process. The post-run analysis error messages appear in the View Results window (see
Figure 9-33). To contact Cepheid Technical Support, see the Technical Assistance
section in the Preface for the contact information.
Table 9-7. Data Reduction Errors

Code
5001 Unable to verify positive analyte [x] A component of the cartridge is Use a new cartridge.
using curve fitting. defective, causing the positive If the error recurs, call Cepheid
(x is the analyte name) growth curve to have an abnormal Technical Support and provide the
shape. information presented in the error
message.
5002 Failed to verify valid amplification A component of the cartridge is Use a new cartridge.
curve for reporter. The shape factor defective, causing the positive If the error recurs, call Cepheid
of n was below the minimum of m. amplification curve to have an Technical Support and provide the
(n and m are values that the abnormal shape. information presented in the error
software displays. The values can message.
vary.)
curve for reporter. The shape factor defective, causing the positive If the error recurs, call Cepheid
of n was higher than the maximum amplification curve to have an Technical Support and provide the
of m. abnormal shape. information presented in the error
(n and m are values that the message.
vary.)

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Table 9-7. Data Reduction Errors (Continued)

Code
curve for reporter. The normalized defective, causing the positive If the error recurs, call Cepheid
sum of errors of n was greater than amplification curve to have an Technical Support and provide the
the limit of m. abnormal shape. information presented in the error
vary.)
curve for reporter. The slope to defective, causing the positive If the error recurs, call Cepheid
vertical scaling ratio of n was higher amplification curve to have an Technical Support and provide the
than the limit of m. abnormal shape. information presented in the error
vary.)
5006 X probe check failed. Probe check One or more of the following might Check the following:
value of n for reading number m was have caused the error: • Reagents are added to the
above the maximum of p. • An incorrect amount of reagent cartridge correctly.
(x is the analyte name, n, m, and p was inserted into the cartridge. • Cartridges were stored
are values that the software • The reagent is defective. correctly.
displays. The values can vary.) • Fluid transfer failed. • Rerun the test using fresh
cartridges.
• If the error recurs, call Cepheid
Technical Support.
value of n for reading number m was have caused the error: • Reagents are added to the
below the minimum of p. • An incorrect amount of reagent cartridge correctly.
(x is the analyte name, n, m, and p was inserted into the cartridge. • Cartridges were stored
are values that the software • The reagent is defective. correctly.
displays. The values can vary.) • Fluid transfer failed. • Rerun the test using fresh
• The sample was processed cartridges.
incorrectly in the cartridge. • If the error recurs, call Cepheid
Technical Support.
delta value n between reading have caused the error: • Reagents are added to the
number m and reading number p • An incorrect amount of reagent cartridge correctly.
was below the minimum of q. was inserted into the cartridge. • Cartridges were stored
(x is the analyte name, n, m, and p • The reagent is defective. correctly.
are values that the software • Fluid transfer failed. • Rerun the test using fresh
displays. The values can vary.) cartridges.
Technical Support.

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Table 9-7. Data Reduction Errors (Continued)

Code
delta value n between reading have caused the error: • Reagents are added to the
number m and reading number p • An incorrect amount of reagent cartridge correctly.
was above the maximum of q. was inserted into the cartridge. • Cartridges were stored
(x is the analyte name, n, m, and p • The reagent is defective. correctly.
are values that the software • Fluid transfer failed. • Rerun the test using fresh
displays. The values can vary.) cartridges.
Technical Support.
5010 Unable to verify positive analyte [x] A component of the cartridge is Use a new cartridge.
using curve fitting. X readings were defective, causing the positive If the error recurs, call Cepheid
available, but the minimum number growth curve to have an abnormal Technical Support and provide the
of readings required is y. shape. information in the error message.
(x is the analyte name; y is a value
software displays)
5011 Signal loss detected in the Usually occurs when a fluorescent Use a new cartridge.
amplification curve for analyte [x]. n signal is so high that it bleeds into If the error recurs, call Cepheid
decrease in signal with m% another channel, causing the Technical Support and provide the
decrease at cycle p. second signal to go into negative information in the error message.
(X is the analyte name; n, m, and p curve.
are values that the software
displays. The values can vary.
5013 Quantitative value is too large to The base quantitative value or If the error recurs, call Cepheid
represent in application or database. quantitative value is too large to Technical Support.
display.
5014 Quantitative value is below the lower The quantitative value is less than If the error recurs, call Cepheid
calculation limit. 0.01. Technical Support.
5015 Failed to verify valid background High slope in optical background If the error recurs, call Cepheid
slope for analyte [analyte name]. region. Technical Support.
The absolute value of the slope of
f.f was above the maximum of f.f.
5016 Failed to verify valid background High RMS error in background If the error recurs, call Cepheid
error for analyte [analyte name]. The region. Technical Support.
RMS error of f.f was above the
maximum of f.f.
5017 X probe check failed. Probe check Cartridge issue. Use a new cartridge.
value of n for reading number m was If the error recurs, call Cepheid
below the valid level of p. Technical Support and provide the
information in the error message.
5018 Failed to verify valid probe check Cartridge issue. Use a new cartridge.
ratio for analyte [analyte name]. If the error recurs, call Cepheid
Probe check 1 = m, probe check 2 = Technical Support and provide the
n, ratio = f.ff greater than maximum information in the error message.
f.ff.
5019 Failed to verify valid probe check Cartridge issue. Use a new cartridge.
ratio for analyte [analyte name]. If the error recurs, call Cepheid
Probe check 1 = m, probe check 2 = Technical Support and provide the
n, ratio = f.ff less than minimum f.ff. information in the error message.

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9.18.2.6 Communication Loss/Recovery Errors
If module communication loss occurs after a test has been ordered and assigned to a
module, but before the cartridge is loaded and the door is latched, an error message will
appear that says not to proceed with loading the cartridge and latching the door. If the
Important
message instructions are followed, the cartridge may be resubmitted to another module.
However, if the cartridge is loaded and the door latched, no result will be given when the test
completes, and the cartridge should not be reused.
Table 9-8 lists communication errors that might appear while the module is idle, before
the module door is latched or when starting the test (test is aborted). To contact Cepheid
information.
Table 9-8. Communication Loss/Recovery Errors

Code
2120 Module X lost communication while Loose or faulty Ethernet cable Verify the Ethernet cable is
module was idle between the PC and the GeneXpert connected properly between the PC
instrument. and the GeneXpert instrument.
Technical Support and provide the
message.
2121 Module X lost communication before Loose or faulty Ethernet cable Verify the Ethernet cable is
module door was latched between the PC and the GeneXpert connected properly between the PC
message.
2122 Module X lost communication while Loose or faulty Ethernet cable Verify the Ethernet cable is
starting test, test aborted between the PC and the GeneXpert connected properly between the PC
message.
2124 Module X communication restored Communication restored from loose Not applicable.
or faulty Ethernet cable between the
PC and the GeneXpert instrument.

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9.18.3 Troubleshooting Host Connectivity

9.18.3.1 Host Connectivity Indicator
When the software starts, host connectivity is automatically established if it is enabled.
The Check Status button is shown as normal. See Figure 9-34.
Check Status
Figure 9-34. Check Status Button Normal (Check Mark Symbol)

If host connectivity is interrupted while the system is operating, the Check Status button
will change to an X sign and a message will be displayed in the Messages area of the
Check Status window (see Figure 9-35). Contact your host administrator to re-establish
the connection.
Figure 9-35. Check Status Button Symbol Changed to X and Messages Displayed

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9.18.3.2 Host Communication Buffer

If the communication between the GeneXpert Dx system and the host is slow, the data
may be filling up in the communication buffer. When the communication buffer is at and
above 75%, the system will stop uploading results and provide a warning to the user in
the Check Status screen.
When you click the Upload Result button in the View Results screen before the host
connection is established or when the communication buffer is filled up, the Upload
Result To Host dialog box appears. See Figure 9-36.
Figure 9-36. Upload Result To Host Dialog Box
9.18.4 Troubleshooting the LIS Interface

Table 9-9 lists the possible system configuration problems you might encounter. To
contact Cepheid Technical Support, see the Technical Assistance section in the Preface
for the contact information.
Table 9-9. System Configuration Problems
Problem Cause Solutions

Cannot edit test code for old versions Upgrade of assay to new version. Change the test code prior to upgrade
of an assay. If the LIS Administrator of assay.
updates the test code, it will only apply
to the new version of the assay.
Upload of test results with duplicate Duplicate system name. • System name must be unique.
System Name; cannot tell which • LIS interface to check for duplicate
instrument the results came from. instrument system names.
• LIS Administrator to control
process for defining system name.
User error in selecting the assay when User error in selecting the assay. LIS Administrator to configure correct
defining test codes. test code; for example, CPT code for
test or abbreviate assay name.

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A Quick Reference
This appendix provides a quick reference of the software menus and commands. In the
GeneXpert Dx System window, the menus are as follows:
• Table A-1, User
• Table A-2, Data Management
• Table A-3, Reports
• Table A-4, Setup
• Table A-5, About
• Table A-6, Create Test
• Table A-7, Stop Test
• Table A-8, View Results
• Table A-9, Define Assays
• Table A-10, Maintenance
Table A-1. User
Command Description
Login Logs you on to your GeneXpert Dx system account.
Change Password Changes your password.
Logout Logs you out of your GeneXpert Dx system account.
Exit Exits the GeneXpert Dx system software.
Table A-2. Data Management
Command Description
Archive Test Archives the tests you select.
Retrieve Test Retrieves the tests you select.
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Quick Reference
Table A-3. Reports
Command Description
Specimen Report Displays an overview of the test results for the selected specimen in
the database.
Patient Report Displays test results for samples for one patient according to the
patient ID in the database.
Patient Trend Report Displays and prints patient trend reports for quantitative assays based
on patient IDs.
Control Trend Report Displays and prints the external-control trend reports.
System Log Displays and prints the log of module self-test and module errors.
Assay Statistics Report Displays a report showing the number of tests performed for each
assay over a period of time with monthly breakdown values.
Installation Qualification Displays and prints the installation qualification report.
Table A-4. Setup
Command Description
User Administration Adds users, removes users, or edits user information.
User Type Configuration Specifies the user type permissions.
System Configuration Specifies the system name, date format, time format, and destination
folders for exported files, reports, database logs. You can also specify
other system settings.
Assign Instrument Letter Assigns an ID to each instrument and instrument module.
Table A-5. About
Command Description
About GeneXpert Dx Displays the software copyright and version number.
System
Table A-6. Create Test
Command Description
Scan Patient ID Use the barcode scanner to enter the Patient ID.
Scan Sample ID Use the barcode scanner to enter the Sample ID.
Patient ID 2 Must be entered manually
Patient Family or Last Name Must be entered manually.
Patient First Name Must be entered manually
Manual entry Use to manually enter the Patient ID, Sample ID, or cartridge information.
Scan Cartridge Barcode Use the scanner or choose Manual Entry to enter the cartridge barcode.
Start Test Begin the test.
Cancel Closes the dialog box, discarding the new test.
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Quick Reference
Table A-7. Stop Test
Command Description
Select Running Selects all tests in progress.
Deselect All Clears all selections.
Stop Stops selected tests.
Cancel Closes the dialog box.
Table A-8. View Results
Command Description
Save Changes Saves changes you make in the Patient ID, Patient ID 2, Sample ID,
Test Type, Sample Type, Other Sample Type, and Notes boxes.
Export Exports the selected results to a .csv file.
Report Saves the results in a PDF file.
Upload Test Upload selected results to LIS.
View Test Displays list of tests that can be viewed.
Table A-9. Define Assays
Command Description
Delete Deletes the assay definition file (.gxa) you select.
Move to Top Moves the currently selected assay to top of the assay list.
Lot Manages lot specific parameters for the selected assay definition.
Import Imports an assay definition into the database.
Report Displays or saves the assay definition in a PDF file.
Table A-10. Maintenance
Command Description
Module Reporters Displays optical calibration information about the instrument module.
Plunger Rod Maintenance Lowers the syringe plunger rod for cleaning.
Valve Maintenance This function is disabled for all users.
Perform Self-Test Performs the self-test to check the system functions.
Open Module Door or Opens the module door to eject a stuck cartridge and update
Update EEPROM cross-platform I-CORE EEPROM format.
Exclude Modules from Test Lists module(s) as Disabled, and they will not be used by the system to
command run tests.
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Quick Reference
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B Glossary
.gxa file – an assay definition file.

.gxr file – a lot specific parameter file.
.gxx file – an archive file that contains multiple tests.
amplification curve – a graph that plots the number of PCR cycles against
fluorescence detected. A real-time amplification curve has three distinct phases: baseline,
log-linear, and plateau. The increase in fluorescence is proportional to the amount of
amplicon generated and can be used to define the cycle threshold.
assay definition – a series of programmed steps to perform sample preparation,
amplification, and detection procedures.
curve fit – the determination of a curve that fits a specified set of data points on a
graph.
cycle threshold (Ct) – the first cycle in which the fluorescence reaches a specified
threshold. The Ct can be determined by analyzing the growth curve (Primary Curve) or
the second derivative of the growth curve (2nd Deriv).
data reduction – the process in which the system analyzes the raw data based on the
settings in the assay definition to determine the test result.
DMS (Data Management System) – could be a stand-alone small scale information
system or compliment an LIS in the same facility. A DMS is a software application
which handles receiving, processing and storing information.
endogenous control – a control (gene) from the test sample that is used to
normalize targets and/or help ensure that sufficient sample is used in the test.
endpoint – the fluorescence reading for the last cycle of a thermal cycling protocol.
instrument module – an individual hardware component within which fluidic and
thermocycling protocols occur. Each module consists of a bay for holding a cartridge, a
syringe drive, a valve drive, an ultrasonic horn, and an I-CORE module.
internal control (IC) – a control that helps verify the performance of the PCR
reagents and the absence of significant inhibition that would prevent PCR amplification.
LIS (Laboratory Information System) – is a software application which handles
receiving, processing, and storing information generated by medical laboratory
processes. These systems often must interface with instruments and other information
systems, such as hospital information systems (HIS). An LIS is a highly configurable
application which is customized to facilitate a wide variety of laboratory workflow
models.
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Glossary
lot specific parameters (LSP) – information about a reagent lot that is required by
some assay definitions to determine the test results. The lot specific parameters are
included in the GeneXpert cartridge 2D barcodes and in the lot specific parameter (.gxr)
files.
manual entry – entry of data into a field using the keyboard. Some fields provide a
choice between scanning the data or manually entering the data, such as Patient ID or
Sample ID.
module – see instrument module.
primary curve – a plot of fluorescence vs. cycle number. A real-time growth curve
should have three distinct phases: baseline, log-linear and plateau. The increase in
fluorescence is proportional to the amount of amplicon generated and can be used to
define the cycle threshold.
probe check – a stage during the test that checks for the presence and the integrity of
the labeled probes.
protocol – an assay command that defines the thermal cycling and optical data
collection parameters for an assay.
reporter – a fluorescent dye or dye complex used to detect specific amplification
products.
sample processing control (SPC) – a control that helps ensure that a sample was
correctly processed. The sample-processing control is processed with the sample and
detected by PCR.
site – see instrument module.
system log – a report of incidents of instrument module self-tests and errors.
test – the laboratory process used to determine the presence of a substance and
measure the amount of that substance. In the GeneXpert Dx system software, a test is a
record of how a specimen is processed. The record includes the instrument module ID,
the assay information, sample ID, test type, and notes about the test.
test type – the sample that is designated as a specimen, positive control, or negative
control in the test.
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C GeneXpert Dx Software International
Configuration Instructions
C.1 Introduction
This appendix provides instructions to configure the GeneXpert Dx software to display
in a non-English language. Instructions are also provided for configuring a non-English
keyboard and barcode scanner.
Use this document for new installations of the GeneXpert Dx software. For existing software
installations, the GeneXpert Dx system should be already configured for the correct
Important language settings. Installing an update of the GeneXpert Dx software will not change these
settings. If you need assistance, contact Cepheid Technical Support. See the Technical
Assistance section in the Preface for contact information.
The information in this document applies only to configuring the GeneXpert Dx system
for a non-English language.
GeneXpert Dx software version 4.8 supports both Microsoft Windows 7 and Windows XP operating
Note systems. Windows XP settings will not be affected when doing a software update. Should you need
any assistance, please contact your regional Cepheid Technical Support center.
C.2 Summary
Internationalization support was added in GeneXpert Dx software releases beginning
with version 4.4 and above. Systems that are updating to GeneXpert Dx version 4.8 from
earlier releases require additional steps that are not necessary on systems that are
installed with GeneXpert Dx version 4.4 and above:
• Configure the Windows language setting
• Configure the keyboard
• Configure the Barcode Scanner
C.3 Before You Begin

Ensure that you quit or close all applications.
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GeneXpert Dx Software International Configuration Instructions
C.4 Windows 7 Configuration

This section provides information on configuring the language setting, keyboard and the
welcome screen keyboard layout for Windows 7.
For each Windows 7 user account on the system, perform the procedures in Section C.4.1,
Note
Section C.4.2 and Section C.4.3.
C.4.1 Configuring the Windows 7 Language Setting

The Format and Keyboard settings must match each other in order to run the GeneXpert
Dx software. The valid language and keyboard combinations for Windows 7 are:
Format Keyboard
English (United States) English (United States) – US
Chinese (Simplified, PRC) Chinese (Simplified) – Microsoft Pinyin New Experience Input Style
French (France) French (France) – French
German (Germany) German (Germany) – German
Italian (Italy) Italian (Italy) – Italian
Japanese (Japan) Japanese (Japan) - Microsoft IME
Portuguese (Portugal) Portuguese (Portugal) – Portuguese
Russian (Russia) Russian (Russia) – Russian
Spanish (Spain) Spanish (Spain, International Sort) – Spanish
1. Log in to Windows 7 using the cepheid user account if not already logged on. See
2. If the GeneXpert Dx software starts, exit the software.
3. Open the Control Panel. Ensure that View by: is set to Category and then click Clock,
Language, and Region (see Figure C-1).
Figure C-1. Control Panel Window
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4. The Clock, Language, and Region window appears (see Figure C-2). Click Region
and Language.
Figure C-2. Clock, Language, and Region Window

5. The Region and Language window appears. See Figure C-3.
Figure C-3. Region and Language Window - Formats Tab

6. The Formats: drop-down box will have English (United States) selected. Click on the
drop-down (see Figure C-3 and Figure C-4) listing the language selections available.
Scroll the list to locate the desired language and click on that entry.

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Figure C-4. Region and Language Screen - Language Selected

7. After clicking on the new language, the drop-down list will close and the newly-
selected language will then appear in the Format drop-down box. In the example
shown, French is selected. The Region and Language screen will now display French
(France) in the Format drop-down box (see Figure C-5).

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Figure C-5. Region and Language Screen with the New Language Displayed
C.4.2 Configuring the Keyboard - Windows 7

If a non-English USB keyboard was provided, remove the existing English USB
keyboard and attach a new non-English USB keyboard to the computer. Use the
following steps to configure the keyboard in Windows 7.
1. On the Region and Languages screen, click the Keyboards and Languages tab (see
Figure C-6).

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Figure C-6. Region and Language Drop-Down Window

2. When the Keyboards and Languages tab appears, click the Change Keyboards…
button (see Figure C-7). An overlay window will appear, listing Installed Services
(the available language keyboards).
Overlay
Window
Figure C-7. Region and Language and Text Services and Input Languages Screens
3. If the desired language exists in the Installed Services box, go to Step 8.

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If the desired language does not exist in the Installed Services box, click the Add
button (see Figure C-7).
4. On the Add Input Language window, use the drop-down menu to select the desired
Language (Country) combination, click the + next to the Language (Country), and
then click the + next to the Keyboard (see Figure C-8).
Click “+”
Next to
Desired Click Box
Country Next to
Selected
Country
Keyboard
Figure C-8. Add Input Language Screen with French Selected (Example)
5. After selecting the new keyboard which corresponds to the language selected in
Figure C-8, a drop-down menu will appear beneath the keyboard selected (see
Figure C-9).
Figure C-9. The Add Input Languages Window with all Entries
6. Select from the choices presented by clicking the empty box to the left of the desired
entry and a check mark will appear for that entry. Click the OK button to add the
selected language. This Add Input Languages window will close, returning you to
the Text Services and Input Languages screen.
7. Click the General tab (see Figure C-10) and use the scrollable box in the Installed
services section to select the (new) desired keyboard and click the OK button.

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Figure C-10. Text Services and Region and Language Screen - General Tab
8. Return to the Keyboards and Languages tab (see Figure C-11) and click the OK
button to complete the keyboard language change.
Figure C-11. Region and Language Screen - Keyboards and Languages Tab
9. Close the Control Panel window and log off the computer.

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C.4.3 Configuring the Windows 7 Welcome Screen

Keyboard Layout
Perform this procedure to enable the switching of the configured keyboard layouts at the
Windows 7 login screen.
1. Log in to Windows 7 as Cepheid-Admin, if not already logged on.
2. If the GeneXpert Dx software starts, exit the software.
3. Open the Control Panel, and then click Clock, Language, and Region (see
Figure C-12).
Figure C-12. Control Panel Window

4. The Clock, Language, and Region window appears (see Figure C-13). Click on
Region and Language.
Figure C-13. Clock, Language, and Region Window

5. The Region and Language screen appears (see Figure C-14).

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Figure C-14. Region and Language Drop-Down Window - Formats Tab

6. Click the Administrative tab. The Administrative tab appears (see
Figure C-15).
Figure C-15. Region and Language Screen - Administrative Tab

7. On the Administrative tab, click the Copy settings... button.

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8. The Welcome screen and new user account settings screen appears
(see Figure C-16).
Figure C-16. Welcome Screen and New User Account Settings Screen
9. Verify that the Format fields match the language selected in Section C.4.1, and the
Input Language fields match the language selected in Section C.4.2 (see
Figure C-16).
10. Select the Welcome screen and system accounts check box.
11. When you are finished, click the OK button. The Region and Languages window will
be displayed.
12. Click the OK button to close the Region and Languages window.
13. Close the Control Panel window.
14. Restart the computer.
Note The new settings will apply after you restart the computer.

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C.4.4 Windows Login Screen

1. When restarting the computer (after completing the language and keyboard
additions), when the Windows 7 login screen appears there will be a two-letter icon
in the upper left corner of the screen showing the current (active) keyboard layout.
The active keyboard layout language can now be changed on this screen by clicking
this two letter icon (see Figure C-17).
Figure C-17. Windows 7 Login Screen Showing Two-Country Designation

2. Click the two-letter icon and a menu similar to that shown at the left in Figure C-18
will appear.
English (United States) The language designation also appears on the

task bar at the bottom of the screen after start-
German (Germany)
up. Moving the cursor over the letters displays
French (France) the complete country/language name.
Italian (Italy)
Russian (Russia)
Chinese (Simplified, PRC)
Portuguese (Portugal)
Spanish (Spain, International Sort)
Japanese (Japan)
Figure C-18. Drop-Down Language Menu - Welcome Screen (Windows 7)

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3. Click any of the languages displayed to change the language.
Changes to the keyboard layout will only apply at login, and will not affect the GeneXpert Dx
Note software. If the icon does not exist, or the desired language is not available, perform the procedure
in Section C.4.1 to add the keyboard language.
This completes the Windows 7 configuration. Go to Section C.5 to configure the barcode
scanner.
C.5 Configuring and Testing the Barcode Scanner

The barcode scanner must be configured and tested. Depending on the scanner model,
follow one of the two procedure below:
• Symbol, Model DS6708: Section C.5.1, Configuring the Symbol Model DS6708
Scanner
• JDK-2201: Section C.5.2, Configuring the JADAK Model JDK-2201 Scanner
C.5.1 Configuring the Symbol Model DS6708 Scanner

1. Verify the manufacturer and model of the scanner. The scanner must be a Symbol,
Model DS6708 scanner to use this procedure. This scanner is gray with a yellow
scan button.
The barcode scanner must be a Symbol (brand), Model DS6708 in order to support the
Note internationalized inputs shown below. If the scanner is a JDK-2201 scanner, see Section C.5.2,
Configuring the JADAK Model JDK-2201 Scanner.
2. Plug the barcode scanner into an available USB port and wait for it to initialize
(there will be a series of beeps).
3. Configure the barcode scanner by scanning the barcodes shown in Figure C-19
through Figure C-23, in order:
Figure C-19. Barcode 1: *HID Keyboard Emulation
Figure C-20. Barcode 2: *North American Standard USB Keyboard

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Figure C-21. Barcode 3: Enable Keypad Emulation
Figure C-22. Barcode 4: Enable Keypad Emulation with Leading Zero
Figure C-23. Barcode 5: Enable

4. Test the scanner by following the procedure in Section C.5.3, Testing the
Configuration.
C.5.2 Configuring the JADAK Model JDK-2201 Scanner

1. Verify the manufacturer and model of the scanner. The scanner must be a JADAK
Model JDK-2201 scanner to use this procedure. This scanner is white with a blue
scan button.
The barcode scanner must be a JADAK, Model JDK-2201 in order to support the internationalized
Note inputs shown below. If the scanner is a Symbol DS6708 scanner, see Section C.5.1, Configuring the
Symbol Model DS6708 Scanner.
2. Plug the barcode scanner into an available USB port and wait for it to initialize
(there will be a series of beeps).
3. Configure the barcode scanner by for international configuration by scanning the
barcode shown in Figure C-24.
Figure C-24. International Configuration Barcode

4. Test the scanner by following the procedure in Section C.5.3, Testing the
Configuration.

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If it is necessary to configure the barcode scanner back to the North American barcode
configuration, scan the barcode shown in Figure C-25.
Figure C-25. North American Configuration Barcode
C.5.3 Testing the Configuration

To test that the configuration was successful, launch the GeneXpert Dx software. Verify
each language using the barcodes below:
If any barcodes do not scan correctly, unplug the barcode scanner from the computer and repeat the
Note configuration procedure starting with Step 2 in Section C.5.1 or Step 2 in Section C.5.2 and rescan
the barcodes shown in Figure C-19 through Figure C-23.
French
Go to the Create Test screen and scan the barcode shown in Figure C-26 when prompted
to scan the Sample ID:
Figure C-26. French Sample Barcode

Verify that the Sample ID field is filled in with the string: ÀâÆæçéÈ êËÎîïôŒœ.
Italian
Figure C-27. Italian Sample Barcode

Verify that the Sample ID field is filled in with the string: àèéìíîòóùú.

301-0045, Rev. K August 2016
German
Figure C-28. German Sample Barcode

Verify that the Sample ID field is filled in with the string: ÄÖßÜ.
Portuguese
Figure C-29. Portuguese Sample Barcode

Verify that the Sample ID field is filled in with the string: ábêcêdêéóçãú.
Spanish
Figure C-30. Spanish Sample Barcode

Verify that the Sample ID field is filled in with the string: ñüñchllñrr.
Chinese
Figure C-31. Chinese Sample Barcode

Verify that the Sample ID field is filled in with the string: .

301-0045, Rev. K August 2016
Russian
Go to the Create Test screen and scan the barcode shown in Figure C-32 when
prompted to scan the Sample ID:
Figure C-32. Russian Sample Barcode

Verify that the Sample ID field is filled in with the string: .
Japanese
Figure C-33. Japanese Sample Barcode

Verify that the Sample ID field is filled in with the string:
.
C.6 Date and Time Format

The date and time format used by the GeneXpert Dx software is configured in the
System Configuration screen. See Section 2.7.2, Setting the Local Date and Time for
details.

301-0045, Rev. K August 2016

301-0045, Rev. K August 2016
D Apache OpenOffice (AOO)
Initial Configuration Instructions
D.1 Introduction
Apache Open Office (AOO) is an open source solution replacing Microsoft Office on
Cepheid customer computers, and is used for viewing, formatting and storing .csv files.
On initial startup, the program must be configured for proper display of the .csv files.
This appendix provides instructions for the opening and configuration of .csv files
generated on GeneXpert using AOO on your system.
For GeneXpert Dx systems using software versions prior to November 30, 2015, Microsoft Excel
(part of Microsoft Office software) is used for displaying .csv files, and no configuration is necessary
Note
for that software. If you need assistance, see the Technical Assistance section in the Preface for
D.2 Configuration
1. In the GeneXpert folder on your system, navigate to the Export folder. Right click on
the .csv file you want to open. When the drop-down menu appears, click Open with
and select OpenOffice Calc. See Figure D-1.
Figure D-1. Opening a .csv File to Configure AOO (Example)
GeneXpert Dx System Operator Manual D-1

301-0045, Rev. K August 2016
Apache OpenOffice (AOO) Initial Configuration Instructions
Figure D-2. AOO Registration Screen

2. On initial startup of AOO, a registration screen will appear. See Figure D-2.
3. Click Next. When the new screen appears, enter the requested information (name and
initials), and click Finish. The Text Import screen will appear. See Figure D-3.
In the Character Set drop-down menu:

For single-byte languages (English, French, Spanish, Portuguese, Italian, German,
Russian) select Unicode (UTF-8).
For multi-byte languages (Japanese and Chinese) select Unicode.
D-2 GeneXpert Dx System Operator Manual

301-0045, Rev. K August 2016
Figure D-3. Text Import Screen, showing Default Settings

4. On the default Text Import screen (see Figure D-3), uncheck Semicolon and Space.
5. Select the checkbox to the left of Comma and Quoted field as text. See Figure D-4.

301-0045, Rev. K August 2016
Figure D-4. Text Import Screen with New Settings Selected

6. After making selections, click OK. The .csv file will be displayed. See Figure D-5.
7. Once the file is open, click on the upper left corner of the worksheet to highlight all
the cells, as shown in Figure D-5.
Figure D-5. All Cells Selected

301-0045, Rev. K August 2016
8. Right click on the column header. A drop-down menu will appear at the right of the
column (see Figure D-6).
9. In this drop-down menu, select Column Width.
Right-
Click in
Column
Header
Figure D-6. Drop-Down Menu to select Column Width

10. The Column Width dialog box appears. See Figure D-7
Figure D-7. Column Width Dialog Box

11. Click the checkbox to the left of Default value, and then click OK to close the dialog
box. The column widths will then adjust and the file will be formatted, as shown in
Figure D-8. Click anywhere in the blank columns to “deselect” the blue cells and
turn the cells white again.

301-0045, Rev. K August 2016
Figure D-8. Final View of File with Columns Adjusted

12. Click Save under the File menu to save the document.
The document saving format screen shown in Figure D-9 may appear. If so, click
Keep Current Format, and the dialog box will close.
Figure D-9. Format Saving Dialog Box

13. This completes the configuration set-up for the initial .csv file.
For all subsequent .csv files no setup will be required, and it will only be necessary
to acknowledge the existing setting chosen in this procedure.

301-0045, Rev. K August 2016

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About this Manual

GeneXpert Dx System Operator Manual iii

Symbols Used in the Manual and on GeneXpert Dx

In vitro diagnostic medical device

CE marking – European Conformity

Consult instructions for use

Authorized representative in the European Community

This type of symbol indicates a possibility of loss of data or data corruption if

iv GeneXpert Dx System Operator Manual

Cepheid Headquarters Locations

Corporate Headquarters European Headquarters

Region Telephone Email

Contact information for other Cepheid offices is available on our website at

GeneXpert Dx System Operator Manual v

GeneXpert Instrument Limited Warranty

vi GeneXpert Dx System Operator Manual

Cepheid GeneXpert Dx System Software License Agreement

GeneXpert Dx System Operator Manual vii

Trademark and Copyright Statements

Note REACH Directive 1907/2006/EC exempts in vitro diagnostic medical devices.

California Proposition 65 Warning

viii GeneXpert Dx System Operator Manual

2 Installation Procedures and Special Requirements . . . . . . . . . . . . . . . . . . 2-1

GeneXpert Dx System Operator Manual TOC-1

2.10 Defining Users and Permissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-39

3 Principles of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

TOC-2 GeneXpert Dx System Operator Manual

3.6 Explanation of Experimental Methods . . . . . . . . . . . . . . . . . . . . . . . . . 3-6

4 Performance Characteristics and Specifications . . . . . . . . . . . . . . . . . . . . 4-1

5 Operating Instructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1

GeneXpert Dx System Operator Manual TOC-3

5.11.3 Detail User and Administrator View . . . . . . . . . . . . . . . . . . . . 5-35

TOC-4 GeneXpert Dx System Operator Manual

5.20.3 Troubleshooting Host Connectivity . . . . . . . . . . . . . . . . . . . . . 5-93

6 Calibration Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1

7 Operational Precautions and Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

9 Service and Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

GeneXpert Dx System Operator Manual TOC-5

9.8.2 In Case of Spill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-6

A Quick Reference. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A-1

C GeneXpert Dx Software International Configuration Instructions. . . . . . . C-1

TOC-6 GeneXpert Dx System Operator Manual

C.4.2 Configuring the Keyboard - Windows 7 . . . . . . . . . . . . . . . . . . C-5

D Apache OpenOffice (AOO)

GeneXpert Dx System Operator Manual TOC-7

TOC-8 GeneXpert Dx System Operator Manual

GeneXpert Dx System Operator Manual LOF-1

Figure 2-24 Internet Protocol Version 4 (TCP/IPv4) Properties Screen . . . . . 2-21

LOF-2 GeneXpert Dx System Operator Manual

Figure 2-49 User Administration Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . 2-44

GeneXpert Dx System Operator Manual LOF-3

Figure 5-5 GeneXpert Dx System Window . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6

LOF-4 GeneXpert Dx System Operator Manual

Figure 5-34 GeneXpert Dx View Results Window—Support Tab

GeneXpert Dx System Operator Manual LOF-5

Figure 5-62 Database Management Dialog Box . . . . . . . . . . . . . . . . . . . . . . . 5-63

LOF-6 GeneXpert Dx System Operator Manual