Sep 19, 2015

Robustness of Massively Parallel Sequencing Platforms

PloS One
Pınar KavakMahmut Şamil Sağıroğlu

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...Continue Reading

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Citations

Mentioned in this Paper

Exons
Genome
Segmental Duplications, Genomic
Clinical Enzyme Tests (Procedure)
Promoter
Euthyroid Sick Syndromes
Genomics
Sequencing
Massively-Parallel Sequencing
BWA 4C

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