GAVIN: Gene-Aware Variant INterpretation for medical sequencing.
GAVIN: Gene-Aware Variant INterpretation for medical sequencing.
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DOI：
10.1186/s13059-016-1141-7
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发表时间：
2017-01-16
期刊：
影响因子：
12.3
通讯作者：
Swertz MA
中科院分区：
文献类型：
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作者：
van der Velde KJ;de Boer EN;van Diemen CC;Sikkema-Raddatz B;Abbott KM;Knopperts A;Franke L;Sijmons RH;de Koning TJ;Wijmenga C;Sinke RJ;Swertz MA
我们提出了基因感知变异解释(Gavin)，这是一种新的方法，可以准确地将变异分类用于临床诊断目的。分类是基于Exac数据库中等位基因频率的特定基因校准，使用SnpEff可能的变异影响，以及基于>；3000基因的CADD分数估计的有害程度。在18个临床基因集上的基准测试中，我们获得了91.4%的灵敏度和76.9%的特异度。这一精度是其他12种工具无法比拟的。我们提供Gavin作为在线MOLGENIS服务来注释VCF文件，并作为用于生物信息管道的开源可执行文件。它可以在http://molgenis.org/gavin.上找到本文的在线版本(doi：10.1186/s13059-0161141-7)包含补充材料，授权用户可以使用。
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. The online version of this article (doi:10.1186/s13059-016-1141-7) contains supplementary material, which is available to authorized users.