Papers by ALESSANDRA MINGRINO
Unbalanced Structural Variants (uSVs) play important roles in the pathogenesis of several genetic... more Unbalanced Structural Variants (uSVs) play important roles in the pathogenesis of several genetic syndromes. Traditional and molecular karyotyping are considered the first-tier diagnostic tests to detect macroscopic and cryptic deletions/duplications. However, their time-consuming and laborious experimental protocols protract diagnostic times from three to fifteen days. Long read sequencing approaches, such as Oxford Nanopore Technologies (ONT), have the ability to reduce time to results for the detection of uSVs with the same resolution of current state-of-the-art diagnostic tests.Here we compared ONT to molecular karyotyping for the detection of pathogenic uSVs of 7 patients with previously diagnosed causative CNVs of different sizes and allelic fractions. Larger chromosomal anomalies included trisomy 21 and mosaic tetrasomy 12p. Among smaller CNVs we tested two reciprocal genomic imbalances in 7q11.23 (1.367 Mb), a 170 kb deletion encompassing NRXN1 and mosaic 6q27 (1.231 Mb) and...
Additional file 1: Methods and supplementary results. Pdf file including more detailed informatio... more Additional file 1: Methods and supplementary results. Pdf file including more detailed information on methods and results.
Additional file 2: Supplementary tables. Spreadsheet file including analyzed data and statistics.... more Additional file 2: Supplementary tables. Spreadsheet file including analyzed data and statistics. Table S1. Case series and run statistics. Table S2. Performance of NanoGLADIATOR pipeline in "nocontrol" and "paired" mode. Table S3. Correlation of Illumina and Nanopore results. Table S4. Sensitivity, Specificity, Accuracy and Precision test of Nanopore approach. Table S5. Correlation of Nanopore results: subsampled BAMs (2 M reads) Vs full BAMs ("nocontrol" and "paired" mode). Table S6. Correlation of Illumina results: paired-end Vs single-end, and subsampled BAMs (2 M reads) Vs full BAMs. Table S7. Genes and genomic regions CNV results. Table S8. CNV detection performance at different tumor fractions.
Additional file 3: Supplementary Figures. Fig. S1. Segmentation results of cancer patients, "... more Additional file 3: Supplementary Figures. Fig. S1. Segmentation results of cancer patients, "nocontrol" mode. Fig. S2. Segmentation results of healthy subjects, "nocontrol" mode. Fig. S3. Technical artifacts in healthy samples. Venn diagram reporting recurring genomic bins with altered log2ratio in healthy samples. Fig. S4. Segmentation results of HM1 white blood cells. Fig. S5. Segment mean and segment length of Nanopore results. Correlation of segment mean and length in nocontrol (A) and paired mode (B). Every dot represents a segment. Segment mean is reported on the x-axis and segment length (number of bins per segment) on the y axis. Vertical lines indicate the threshold used to discriminate artifacts from CNVs (log ratio ± 0.04). The lower range of the segments is shown in the lower plot for each sample. Fig. S6. Correlation of short- and long-read sequencing results. (A) Correlation plot of short (sheared DNA) and long (non-sheared DNA) sequencing. Each gen...
ABSTRACTAlterations in the genetic content, such as Copy Number Variations (CNVs) is one of the h... more ABSTRACTAlterations in the genetic content, such as Copy Number Variations (CNVs) is one of the hallmarks of cancer and their detection is used to recognize tumoral DNA. Analysis of cell-free DNA from plasma is a powerful tool for non-invasive disease monitoring in cancer patients. Here we exploit third generation sequencing (Nanopore) to obtain a CNVs profile of tumoral DNA from plasma, where cancer-related chromosomal alterations are readily identifiable.Compared to Illumina sequencing -the only available alternative- Nanopore sequencing represents a viable approach to characterize the molecular phenotype, both for its ease of use, costs and rapid turnaround (6 hours).
Bioinformatics, 2019
Motivation The past few years have seen the emergence of nanopore-based sequencing technologies w... more Motivation The past few years have seen the emergence of nanopore-based sequencing technologies which interrogate single molecule of DNA and generate reads sequentially. Results In this paper, we demonstrate that, thanks to the sequentiality of the nanopore process, the data generated in the first tens of minutes of a typical MinION/GridION run can be exploited to resolve the alterations of a human genome at a karyotype level with a resolution in the order of tens of Mb, while the data produced in the first 6–12 h allow to obtain a resolution comparable to currently available array-based technologies, and thanks to a novel probabilistic approach are capable to predict the allelic fraction of genomic alteration with high accuracy. To exploit the unique characteristics of nanopore sequencing data we developed a novel software tool, Nano-GLADIATOR, that is capable to perform copy number variants/alterations detection and allelic fraction prediction during the sequencing run (‘On-line’ ...
MinION and GridION X5 from Oxford Nanopore Technologies are devices for real-time DNA and RNA seq... more MinION and GridION X5 from Oxford Nanopore Technologies are devices for real-time DNA and RNA sequencing. While MinION is the only real-time, low cost and portable sequencing device and, thanks to its unique properties, is becoming more and more popular among biologists, GridION X5, mainly for its costs, is less widespread but highly suitable for researchers with large sequencing projects. Despite the fact that Oxford Nanopore Technologies’ devices have been increasingly used in the last few years, there is a lack of high-performing and user-friendly tools to handle the data outputted by both MinION and GridION X5 platforms. Here we present NanoR, a cross-platform R package designed with the purpose to simplify and improve nanopore data visualization. Indeed, NanoR is built on few functions but overcomes the capabilities of existing tools to extract meaningful informations from MinION sequencing data; in addition, as exclusive features, NanoR can deal with GridION X5 sequencing outp...
Briefings in bioinformatics, Jan 16, 2017
The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic po... more The nanopore sequencing process is based on the transit of a DNA molecule through a nanoscopic pore, and since the 90s is considered as one of the most promising approaches to detect polymeric molecules. In 2014, Oxford Nanopore Technologies (ONT) launched a beta-testing program that supplied the scientific community with the first prototype of a nanopore sequencer: the MinION. Thanks to this program, several research groups had the opportunity to evaluate the performance of this novel instrument and develop novel computational approaches for analyzing this new generation of data. Despite the short period of time from the release of the MinION, a large number of algorithms and tools have been developed for base calling, data handling, read mapping, de novo assembly and variant discovery. Here, we face the main computational challenges related to the analysis of nanopore data, and we carry out a comprehensive and up-to-date survey of the algorithmic solutions adopted by the bioinform...
Life Sciences, 1998
Human adrenomedullin (ADM) is a 52-amino acid hypotensive peptide, which possesses a disulfide br... more Human adrenomedullin (ADM) is a 52-amino acid hypotensive peptide, which possesses a disulfide bridge-formed six-membered ring in 16-21 position. The ring structure, and both the N-and C-terminal amino-acid sequences seem to play a key role in the vascular effects of ADM(l-52) and we have investigated whether the same is true for the inhibitory effect of this peptide on the aldosterone response of zona glomerulosa (ZG) cells to angiotensin-II (ANG-II). Autoradiography showed the presence of abundant ["'I]ADM(l-52) binding sites in the ZG of human adrenals, which were displaced not only by cold ADM(l-52) but also by both ADM(13-52) and ADM(22-52); ADM fragments 1-12, 15-22 and 16-3 1 were ineffective. ADM(l-52) and ADM(13-52) but not other fragments, concentration-dependently inhibited ANG-II-stimulated aldosterone secretion of dispersed human adrenocortical cells. The aldosterone antisecretagogue actions of ADM(l-52) and ADM(13-52) were counteracted by ADM(22-52) in a concentration-dependent manner, while other ADM fragments were ineffective. In light of these findings the following conclusions could be drawn: (i) human ZG cells are provided with ADM(22-52)~sensitive receptors; (ii) the six-membered ring structure and the C-terminal, but not N-terminal, amino-acid sequence are both essential for ADM(l-52) to exert its antimineralocorticoid action; and probably (iii) the C-terminal sequence is needed for ADM(l-52) to bind its ZG receptors, while the ring structure is required for the receptor activation.
Combination therapy is the mainstay of anticancer therapy due to the significant synergistic effe... more Combination therapy is the mainstay of anticancer therapy due to the significant synergistic effects achievable. Now that anticancer drug research turned toward a more molecular targeted approach, the design of dual-target drugs appears to be a new promising strategy with the potential to improve the therapeutic efficacy of the single drug and to reduce the probability of drug induced resistance and cross resistance. In our previous work, we found that 3’-C-methyl-adenosine (3’-Me-Ado), developed by us as a potent ribonucleotide reductase (RR) inhibitor with antitumor activity against both human leukemia and carcinoma cell lines, elicited significant growth inhibitory and apoptotic synergistic effects in promyelocytic leukemia cells in combination with some hydroxamic acid–derived histone deacetylase (HDAC) inhibitors. Also the antiepileptic agent valproic acid (VPA) was shown to inhibit HDAC in tumors and to synergize with a number of anticancer drugs including RR inhibitors. Since...
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Papers by ALESSANDRA MINGRINO