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Estimating exome genotyping accuracy by comparing to data from large scale sequencing projects.

ABSTRACT: With exome sequencing becoming a tool for mutation detection in routine diagnostics there is an increasing need for platform-independent methods of quality control. We present a genotype-weighted metric that allows comparison of all the variant calls of an exome to a high-quality reference dataset of an ethnically matched population. The exome-wide genotyping accuracy is estimated from the distance to this reference set, and does not require any further knowledge about data generation or the bioinformatics involved. The distances of our metric are visualized by non-metric multidimensional scaling and serve as an intuitive, standardizable score for the quality assessment of exome data.

SUBMITTER: Heinrich V

PROVIDER: S-EPMC3978951 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Estimating exome genotyping accuracy by comparing to data from large scale sequencing projects.

Heinrich Verena V Kamphans Tom T Stange Jens J Parkhomchuk Dmitri D Hecht Jochen J Dickhaus Thorsten T Robinson Peter N PN Krawitz Peter M PM

Genome medicine 20130731 7

With exome sequencing becoming a tool for mutation detection in routine diagnostics there is an increasing need for platform-independent methods of quality control. We present a genotype-weighted metric that allows comparison of all the variant calls of an exome to a high-quality reference dataset of an ethnically matched population. The exome-wide genotyping accuracy is estimated from the distance to this reference set, and does not require any further knowledge about data generation or the bio ...[more]

PMID: 23902830

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