Robustness of Massively Parallel Sequencing Platforms

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic an...

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Main Authors:	Kavak, Pınar, Yüksel, Bayram, Aksu, Soner, Kulekci, M. Oguzhan, Güngör, Tunga, Hach, Faraz, Şahinalp, S. Cenk, Alkan, Can, Sağıroğlu, Mahmut Şamil
Format:	Online
Language:	English
Published:	Public Library of Science 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4575192/

id	pubmed-4575192
recordtype	oai_dc
spelling	pubmed-45751922015-09-25 Robustness of Massively Parallel Sequencing Platforms Kavak, Pınar Yüksel, Bayram Aksu, Soner Kulekci, M. Oguzhan Güngör, Tunga Hach, Faraz Şahinalp, S. Cenk Alkan, Can Sağıroğlu, Mahmut Şamil Research Article The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications. Public Library of Science 2015-09-18 /pmc/articles/PMC4575192/ /pubmed/26382624 http://dx.doi.org/10.1371/journal.pone.0138259 Text en © 2015 Kavak et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Kavak, Pınar Yüksel, Bayram Aksu, Soner Kulekci, M. Oguzhan Güngör, Tunga Hach, Faraz Şahinalp, S. Cenk Alkan, Can Sağıroğlu, Mahmut Şamil
spellingShingle	Kavak, Pınar Yüksel, Bayram Aksu, Soner Kulekci, M. Oguzhan Güngör, Tunga Hach, Faraz Şahinalp, S. Cenk Alkan, Can Sağıroğlu, Mahmut Şamil Robustness of Massively Parallel Sequencing Platforms
author_facet	Kavak, Pınar Yüksel, Bayram Aksu, Soner Kulekci, M. Oguzhan Güngör, Tunga Hach, Faraz Şahinalp, S. Cenk Alkan, Can Sağıroğlu, Mahmut Şamil
author_sort	Kavak, Pınar
title	Robustness of Massively Parallel Sequencing Platforms
title_short	Robustness of Massively Parallel Sequencing Platforms
title_full	Robustness of Massively Parallel Sequencing Platforms
title_fullStr	Robustness of Massively Parallel Sequencing Platforms
title_full_unstemmed	Robustness of Massively Parallel Sequencing Platforms
title_sort	robustness of massively parallel sequencing platforms
description	The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications.
publisher	Public Library of Science
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4575192/
_version_	1613477333204729856

Robustness of Massively Parallel Sequencing Platforms

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