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BioMed Central, Genome Biology, 1(18)

DOI: 10.1186/s13059-016-1141-7

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GAVIN: Gene-Aware Variant INterpretation for medical sequencing

Journal article published in 2017 by K. Joeri van der Velde, Eddy N. de Boer, Cleo C. van Diemen ORCID, Birgit Sikkema-Raddatz ORCID, Kristin M. Abbott ORCID, Alain Knopperts, Lude Franke ORCID, Rolf H. Sijmons ORCID, Tom J. de Koning ORCID, Cisca Wijmenga ORCID, Richard J. Sinke ORCID, Morris A. Swertz ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Abstract We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele frequencies from the ExAC database, likely variant impact using SnpEff, and estimated deleteriousness based on CADD scores for >3000 genes. In a benchmark on 18 clinical gene sets, we achieve a sensitivity of 91.4% and a specificity of 76.9%. This accuracy is unmatched by 12 other tools. We provide GAVIN as an online MOLGENIS service to annotate VCF files and as an open source executable for use in bioinformatic pipelines. It can be found at http://molgenis.org/gavin .