title: Robustness of Massively Parallel Sequencing Platforms.
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.
authors.affiliation: Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey; Advanced Genomics and Bioinformatics Research Group (İGBAM), BİLGEM, The Scientific and Technological Research Council of Turkey (TÜBİTAK), Gebze, Kocaeli, Turkey.
authors.forename: Pınar
authors.initials: P
authors.lastname: Kavak
authors.affiliation: TÜBİTAK - MAM - GMBE (The Scientific and Technological Research Council of Turkey, Genetic Engineering and Biotechnology Institute), Gebze, Kocaeli, Turkey.
authors.forename: Bayram
authors.initials: B
authors.lastname: Yüksel
authors.affiliation: TÜBİTAK - MAM - GMBE (The Scientific and Technological Research Council of Turkey, Genetic Engineering and Biotechnology Institute), Gebze, Kocaeli, Turkey.
authors.forename: Soner
authors.initials: S
authors.lastname: Aksu
authors.affiliation: Advanced Genomics and Bioinformatics Research Group (İGBAM), BİLGEM, The Scientific and Technological Research Council of Turkey (TÜBİTAK), Gebze, Kocaeli, Turkey.
authors.forename: M Oguzhan
authors.initials: MO
authors.lastname: Kulekci
authors.affiliation: Department of Computer Engineering, Boğaziçi University, İstanbul, Turkey.
authors.forename: Tunga
authors.initials: T
authors.lastname: Güngör
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.
authors.forename: Faraz
authors.initials: F
authors.lastname: Hach
authors.affiliation: School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.
authors.forename: S Cenk
authors.initials: SC
authors.lastname: Şahinalp
authors.affiliation: Department of Computer Engineering, Bilkent University, Ankara, Turkey.
authors.forename: Can
authors.initials: C
authors.lastname: Alkan
authors.affiliation: Advanced Genomics and Bioinformatics Research Group (İGBAM), BİLGEM, The Scientific and Technological Research Council of Turkey (TÜBİTAK), Gebze, Kocaeli, Turkey.
authors.forename: Mahmut Şamil
authors.initials: MŞ
authors.lastname: Sağıroğlu
mesh_terms: D004247:DNA / Q000235:genetics*; D015894:Genome, Human; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results
chemical_list: D004247:DNA