GAVIN: Gene-Aware Variant INterpretation for medical sequencing.

van der Velde, K Joeri; de Boer, Eddy N; van Diemen, Cleo C; Sikkema-Raddatz, Birgit; Abbott, Kristin M; Knopperts, Alain; Franke, Lude; Sijmons, Rolf H; de Koning, Tom J; Wijmenga, Cisca; Sinke, Richard J; Swertz, Morris A

van der Velde, K Joeri; de Boer, Eddy N; van Diemen, Cleo C; Sikkema-Raddatz, Birgit; Abbott, Kristin M; Knopperts, Alain; Franke, Lude; Sijmons, Rolf H; de Koning, Tom J; Wijmenga, Cisca; Sinke, Richard J; Swertz, Morris A.

Afiliação

van der Velde KJ; University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.
de Boer EN; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
van Diemen CC; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Sikkema-Raddatz B; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Abbott KM; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Knopperts A; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Franke L; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Sijmons RH; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
de Koning TJ; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Wijmenga C; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Sinke RJ; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
Swertz MA; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.

Genome Biol ; 18(1): 6, 2017 01 16.

Article em En | MEDLINE | ID: mdl-28093075

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 .

Assuntos

Biologia Computacional/métodos; Variação Genética; Software; Frequência do Gene; Estudos de Associação Genética/métodos; Estudo de Associação Genômica Ampla/métodos; Humanos

Palavras-chave

Allele frequency; Automated protocol; Clinical next-generation sequencing; Gene-specific calibration; Pathogenicity prediction; Protein impact; Variant classification

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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Variação Genética / Software / Biologia Computacional Tipo de estudo: Prognostic_studies Limite: Humans Idioma: En Ano de publicação: 2017 Tipo de documento: Article

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