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Genome Med. 2013 Jul 31;5(7):69. doi: 10.1186/gm473. eCollection 2013.

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

Author information

1
Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
2
Smart Algos, Retzbacher Weg 83, 13189 Berlin, Germany.
3
Department of Mathematics, Humboldt-University Berlin, Unter den Linden 6, 10099 Berlin, Germany.
4
Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany ; Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.
5
Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany ; Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany.

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.

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