PT  - JOURNAL ARTICLE
AU  - William Jefferson Alvarez
AU  - In-Hee Lee
AU  - Carles Hernandez-Ferrer
AU  - Kenneth D. Mandl
AU  - Sek Won Kong
TI  - <em>WEScover</em>: selection of whole exome sequencing vs. gene panel testing
AID  - 10.1101/367607
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 367607
4099  - http://biorxiv.org/content/early/2020/01/02/367607.short
4100  - http://biorxiv.org/content/early/2020/01/02/367607.full
AB  - Motivation Whole 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.Results WEScover 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.Conclusion WEScover 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.WESWhole exome sequencingWGSWhole genome sequencinggnomADGenome Aggregation DatabaseGTRGenetic Testing RegistryCCDSConsensus Coding Sequence1KGP1000 Genomes ProjectHPOHuman Phenotype Ontology