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dc.contributor.authorKavak P.en_US
dc.contributor.authorYüksel, B.en_US
dc.contributor.authorAksu, S.en_US
dc.contributor.authorKulekci, M.O.en_US
dc.contributor.authorGüngör, T.en_US
dc.contributor.authorHach F.en_US
dc.contributor.authorŞahinalp, S.C.en_US
dc.contributor.authorAlkan, C.en_US
dc.contributor.authorSaʇiroʇlu, M.Ş.en_US
dc.date.accessioned2016-02-08T09:39:14Z
dc.date.available2016-02-08T09:39:14Z
dc.date.issued2015en_US
dc.identifier.issn19326203
dc.identifier.urihttp://hdl.handle.net/11693/20992
dc.description.abstractThe 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.en_US
dc.language.isoEnglishen_US
dc.source.titlePLoS ONEen_US
dc.relation.isversionofhttp://dx.doi.org/10.1371/journal.pone.0138259en_US
dc.subjectcase reporten_US
dc.subjectDNA structureen_US
dc.subjectexonen_US
dc.subjectgenomeen_US
dc.subjecthigh throughput sequencingen_US
dc.subjecthumanen_US
dc.subjectindel mutationen_US
dc.subjectpredictionen_US
dc.subjectpromoter regionen_US
dc.subjectsegmental duplicationen_US
dc.subjectsingle nucleotide polymorphismen_US
dc.titleRobustness of massively parallel sequencing platformsen_US
dc.typeArticleen_US
dc.departmentDepartment of Computer Engineering
dc.citation.volumeNumber10en_US
dc.citation.issueNumber9en_US
dc.identifier.doi10.1371/journal.pone.0138259en_US
dc.publisherPublic Library of Scienceen_US


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