GAVIN : Gene-Aware Variant INterpretation for medical sequencing
(2017) In Genome Biology 18(1).- 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.
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/236dffbe-a4cd-4a2b-a4de-b384d6ef03b4
- author
- publishing date
- 2017-01-16
- type
- Contribution to journal
- publication status
- published
- subject
- keywords
- Allele frequency, Automated protocol, Clinical next-generation sequencing, Gene-specific calibration, Pathogenicity prediction, Protein impact, Variant classification
- in
- Genome Biology
- volume
- 18
- issue
- 1
- article number
- 6
- publisher
- BioMed Central (BMC)
- external identifiers
-
- pmid:28093075
- scopus:85010014418
- ISSN
- 1474-7596
- DOI
- 10.1186/s13059-016-1141-7
- language
- English
- LU publication?
- no
- id
- 236dffbe-a4cd-4a2b-a4de-b384d6ef03b4
- date added to LUP
- 2020-02-26 09:51:53
- date last changed
- 2024-10-02 22:21:16
@article{236dffbe-a4cd-4a2b-a4de-b384d6ef03b4, abstract = {{<p>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.</p>}}, author = {{van der Velde, K. Joeri and de Boer, Eddy N. and van Diemen, Cleo C. and Sikkema-Raddatz, Birgit and Abbott, Kristin M. and Knopperts, Alain and Franke, Lude and Sijmons, Rolf H. and de Koning, Tom J. and Wijmenga, Cisca and Sinke, Richard J. and Swertz, Morris A.}}, issn = {{1474-7596}}, keywords = {{Allele frequency; Automated protocol; Clinical next-generation sequencing; Gene-specific calibration; Pathogenicity prediction; Protein impact; Variant classification}}, language = {{eng}}, month = {{01}}, number = {{1}}, publisher = {{BioMed Central (BMC)}}, series = {{Genome Biology}}, title = {{GAVIN : Gene-Aware Variant INterpretation for medical sequencing}}, url = {{http://dx.doi.org/10.1186/s13059-016-1141-7}}, doi = {{10.1186/s13059-016-1141-7}}, volume = {{18}}, year = {{2017}}, }