Robustness of massively parallel sequencing platforms
Author
Kavak P.
Yüksel, B.
Aksu, S.
Kulekci, M.O.
Güngör, T.
Hach F.
Şahinalp, S.C.
Alkan, C.
Saʇiroʇlu, M.Ş.
Date
2015Source Title
PLoS ONE
Print ISSN
19326203
Publisher
Public Library of Science
Volume
10
Issue
9
Language
English
Type
ArticleItem Usage Stats
127
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Abstract
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. © 2015 Kavak et al. 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 credited.
Keywords
case reportDNA structure
exon
genome
high throughput sequencing
human
indel mutation
prediction
promoter region
segmental duplication
single nucleotide polymorphism