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bioRxiv · 10.1101/367607

WEScover: whole exome sequencing vs. gene panel testing

Alvarez, W. J.·Lee, I.-H.·Hernandez-Ferrer, C.·Negron La Rosa, J.·Mandl, K.·Kong, S. W.
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Abstract

MotivationWhole exome sequencing (WES) is widely adopted in clinical and research settings. However, there is potential for false negatives due to incomplete breadth and depth of coverage for several exons in clinically implicated genes. In some cases, a targeted gene panel testing may be a dependable option to ascertain true negatives for genomic variants in known phenotype associated genes. We developed a tool for quickly gauging whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should instead be considered to minimize false negatives in candidate genes. ResultsWEScover is a novel web application that provides an interface for discovering breadth and depth of coverage across population scale WES datasets, searching either by phenotype, by targeted gene panels and by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage. ConclusionWEScover allows users to efficiently query genes and phenotype for exome coverage of associated exons, and recommends use of panel tests for genes that are potentially not well covered by WES.

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Alvarez, W. J., Lee, I.-H., Hernandez-Ferrer, C., Negron La Rosa, J., Mandl, K., Kong, S. W.. 2018-07-27. WEScover: whole exome sequencing vs. gene panel testing. https://doi.org/10.1101/367607

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