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      • Department of Computer Engineering
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      Robustness of massively parallel sequencing platforms

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      Author
      Kavak P.
      Yüksel, B.
      Aksu, S.
      Kulekci, M.O.
      Güngör, T.
      Hach F.
      Şahinalp, S.C.
      Alkan, C.
      Saʇiroʇlu, M.Ş.
      Date
      2015
      Source Title
      PLoS ONE
      Print ISSN
      19326203
      Publisher
      Public Library of Science
      Volume
      10
      Issue
      9
      Language
      English
      Type
      Article
      Item Usage Stats
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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 report
      DNA structure
      exon
      genome
      high throughput sequencing
      human
      indel mutation
      prediction
      promoter region
      segmental duplication
      single nucleotide polymorphism
      Permalink
      http://hdl.handle.net/11693/20992
      Published Version (Please cite this version)
      http://dx.doi.org/10.1371/journal.pone.0138259
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