PT  - JOURNAL ARTICLE
AU  - K. Joeri van der Velde
AU  - Eddy N. de Boer
AU  - Cleo C. van Diemen
AU  - Birgit Sikkema-Raddatz
AU  - Kristin M. Abbott
AU  - Alain Knopperts
AU  - Lude Franke
AU  - Rolf H. Sijmons
AU  - Tom J. de Koning
AU  - Cisca Wijmenga
AU  - Richard J. Sinke
AU  - Morris A. Swertz
TI  - GAVIN - Gene-Aware Variant INterpretation for medical sequencing
AID  - 10.1101/072330
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 072330
4099  - http://biorxiv.org/content/early/2016/08/30/072330.short
4100  - http://biorxiv.org/content/early/2016/08/30/072330.full
AB  - Here, we present GAVIN, a new method that delivers accurate classification of variants for next-generation sequencing molecular diagnostics. It is based on gene-specific calibrations of allele frequencies (from the ExAC database), effect impact (using SnpEff) and estimated deleteriousness (CADD scores) for >3,000 genes. In a benchmark on 18 clinical gene sets, we achieved a sensitivity of 91.6%, with a specificity of 78.2%. This accuracy was unmatched by 12 other tools we tested. We provide GAVIN as an online MOLGENIS service to annotate VCF files, and as open source executable for use in bioinformatic pipelines. It can be found at http://molgenis.org/gavin.