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    CGE Course Johanne

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    razib126
    This document discusses using whole genome data to construct phylogenetic trees. It describes single nucleotide polymorphism (SNP) methods like snpTree and CSI Phylogeny that call SNPs to differentiate strains, as well as nucleotide difference (ND) methods like NDtree that count differences between sequences. These methods are used to classify taxonomy and detect disease outbreaks. The document also discusses a controlled evolution study constructed phylogenetic trees of descendants using different methods.

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    CGE Course Johanne

    Uploaded by

    razib126
    46 views24 pages
    This document discusses using whole genome data to construct phylogenetic trees. It describes single nucleotide polymorphism (SNP) methods like snpTree and CSI Phylogeny that call SNPs to differentiate strains, as well as nucleotide difference (ND) methods like NDtree that count differences between sequences. These methods are used to classify taxonomy and detect disease outbreaks. The document also discusses a controlled evolution study constructed phylogenetic trees of descendants using different methods.

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    This document discusses using whole genome data to construct phylogenetic trees. It describes single nucleotide polymorphism (SNP) methods like snpTree and CSI Phylogeny that call SNPs to differentiate strains, as well as nucleotide difference (ND) methods like NDtree that count differences between sequences. These methods are used to classify taxonomy and detect disease outbreaks. The document also discusses a controlled evolution study constructed phylogenetic trees of descendants using different methods.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    46 views24 pages

    CGE Course Johanne

    Uploaded by

    razib126
    This document discusses using whole genome data to construct phylogenetic trees. It describes single nucleotide polymorphism (SNP) methods like snpTree and CSI Phylogeny that call SNPs to differentiate strains, as well as nucleotide difference (ND) methods like NDtree that count differences between sequences. These methods are used to classify taxonomy and detect disease outbreaks. The document also discusses a controlled evolution study constructed phylogenetic trees of descendants using different methods.

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    © All Rights Reserved
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    Download as pptx, pdf, or txt
    of 24

    Phylogeny

    - based on whole genome data

    Johanne Ahrenfeldt
    Research Assistant
    Overview

    • What is Phylogeny and what can it be used for


    • Single Nucleotide Polymorphism (SNP) methods
    - snpTree and CSI Phylogeny
    • Nucleotide Differences
    - NDtree
    • Controlled Evolution study
    • What services for which data
    What is phylogenetic trees

    • Trees are traditionally made using aligned sequences


    of single genes or proteins
    • Whole genome data may be used to create trees
    based on
    – SNP calling
    – K-mer overlap
    What is a SNP

    • A Single Nucleotide Polymorphism (SNP) is a DNA


    sequence variation occurring commonly* within a
    population (e.g. 1%) in which a Single Nucleotide
    — A, T, C or G — in the genome (or other shared
    sequence) differs between members of a biological
    species or paired chromosomes.
    What is phylogeny used for

    • Classify taxonomy – the classic use


    • Outbreak detection – becoming more increasing
    with WGS data
    How does it work

    Strain A ATTCAGTA
    Strain B ATGCAGTC
    Strain C ATGCAATC
    Strain D ATTCAGTC
    Construct distance matrix
    Strain A ATTCAGTA
    Strain B ATGCAGTC
    Strain C ATGCAATC
    Strain D ATTCAGTC
    A B C D
    A 0 2 3 1
    B 2 0 1 1
    C 3 1 0 2
    D 1 1 2 0
    Make Tree
    Strain A ATTCAGTA
    Strain B ATGCAGTC
    Strain C ATGCAATC
    Strain D ATTCAGTC
    A B C D
    A 0 2 3 1
    B 2 0 1 1
    C 3 1 0 2
    D 1 1 2 0

    A B
    C
    D
    snpTree

    • First online webserver for constructing phylogenetic


    trees based on whole genome sequencing

    snpTree--a web-server to identify and construct SNP trees from whole genome sequence data. Leekitcharoenphon P,
    Kaas RS, Thomsen MC, Friis C, Rasmussen S, Aarestrup FM. BMC Genomics. 2012;13 Suppl 7:S6.
    snpTree flow
    snpTree output
    CSIPhylogeny

    • Finds SNPs in the same manner as snpTree


    • More strict sorting of SNPs
    • Requires all SNPs to be significant
    – Z-score higher than 1.96 for all SNPs

    X -Y
    Z=
    X+Y
    • X is the number of reads, of the most common
    nucleotide at that position, and Y the number of reads
    with any other nucleotide.
    NDtree

    • A different approach where the main distinction is


    not between if a SNP should be called or not, but
    between whether there is solid evidence for what
    nucleotide should be called or not.
    NDtree
    • When all reads had been mapped the significance of the
    base call at each position was evaluates by calculating the
    number of reads X having the most common nucleotide at
    that position, and the number of reads Y supporting other
    nucleotides.
    • A Z-score threshold was calculated as:
    X - Y > 1.96 (or 3.29)
    Z=
    X+Y

    • >90% of reads supporting the same base


    NDtree

    • Count nucleotide differences


    – Method 1: Each pair of sequences was compared and
    the number of nucleotide differences in positions called
    in all sequences was counted.
    • More accurate (Z=1.96 is used as threshold)
    – Method 2: Each pair of sequences was compared and
    the number of nucleotide differences in positions called
    in both sequences was counted.
    • More robust (Z=3.29 is used as threshold)
    NDtree

    • A matrix with these numbers was given as input to a


    UPGMA algorithm implemented in the neighbor
    program.
    • Simplest method:
    – First cluster closest strains
    • Merge those strains to one point
    – Distance of cluster to another strain is average of distances for each
    member in cluster to that strain
    – Then merge second closest
    – Repeat until all strains are clustered
    Controlled Evolution study

    This study was performed as part of my Master Thesis


    Naming the descendants
    Mutations
    Phylogenetic tree using NDtree
    (UPGMA)
    Phylogenetic tree using
    Neighbor Joining
    UPGMA vs. Neighbor Joining

    • UPGMA works well when samples have been taken


    the same time

    • Neighbor joining is better when samples have been


    taken at different times
    CSI Phylogeny
    d_1_1_1_2_2
    b_1_1_1_1_2
    b_1_2_2
    1_2_1_1
    i_1_2_1_1_1
    j_1_2_1_1_2
    1_1_1_1
    1_1_1_2
    1_1_1
    1_1_2_1
    1_1_2_2
    1_1_2
    1_1
    1_2_1
    1_2_2_1
    1_2_2_2
    1_2_2
    1_2
    1
    c_1_1_1_2_1
    e_1_1_2_1_1
    f_1_1_2_1_2
    f_2_1_1
    g_1_1_2_2_1
    h_1_1_2_2_2
    m_1_2_2_1_1
    n_1_2_2_1_2
    o_1_2_2_2_1
    1_2_1_2
    k_1_2_1_2_1
    l_1_2_1_2_2
    a_1_1_1_1_1

    0.2
    So… What should I use when?

    • CSI Phylogeny is advantageous to use when you


    expect the differences between the samples to be
    larger than 5-10 mutations
    • NDtree on the other hand is able to find these small
    differences, but may not be strict enough to handle
    very large differences.

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