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Robustness of Massively Parallel Sequencing Platforms.

Pınar Kavak1, Bayram Yüksel2, Soner Aksu2

  • 1Department 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.

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|September 19, 2015
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Summary

High-throughput sequencing (HTS) offers powerful clinical data, but variant calls from whole genome shotgun (WGS) data show discrepancies. Orthogonal validation is crucial for diagnostic and prognostic applications.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Clinical Sequencing

Background:

  • High-throughput sequencing (HTS) technologies have enabled large-scale clinical sequencing projects.
  • Ensuring accuracy and reproducibility is vital for using HTS data in diagnostics and prognostics.

Purpose of the Study:

  • To assess the robustness and clinical usability of a widely used HTS platform.
  • To evaluate the accuracy and reproducibility of variant calling from whole genome shotgun (WGS) data generated at different centers.

Main Methods:

  • Generated WGS sequence data from two human individuals across two genome sequencing centers.
  • Analyzed sequence data to characterize single nucleotide polymorphisms (SNPs) and insertions/deletions (indels).
  • Utilized standardized bioinformatics tools (BWA, SAMtools, GATK) for variant calling.

Main Results:

  • Observed significant discrepancies in variant call sets between the two sequencing centers.
  • Disagreements were predominantly located in genomic regions with repeats and segmental duplications.
  • A small fraction of discordant variants were found in functionally relevant regions like exons and promoters.

Conclusions:

  • HTS platforms provide sufficient data for initial clinical assessments.
  • Variant predictions from HTS require confirmation through orthogonal methods before clinical application.
  • Robustness of variant calling across different centers needs further improvement for reliable clinical use.