WEScover: selection between clinical whole exome sequencing and gene panel testing

BMC Bioinformatics

In-Hee Lee¹  Yufei Lin¹  William Jefferson Alvarez²  Carles Hernandez-Ferrer³  Sek Won Kong⁴  Kenneth D. Mandl⁵ 

[1] Computational Health Informatics Program, Boston Children’s Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, 02115, Boston, MA, USA;Computational Health Informatics Program, Boston Children’s Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, 02115, Boston, MA, USA;Agios Pharmaceuticals, Boston, MA, USA;Computational Health Informatics Program, Boston Children’s Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, 02115, Boston, MA, USA;Centre Nacional d’Anàlisi Genòmica (CNAG-CRG), Barcelona, Spain;Computational Health Informatics Program, Boston Children’s Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, 02115, Boston, MA, USA;Department of Pediatrics, Harvard Medical School, 02115, Boston, MA, USA;Computational Health Informatics Program, Boston Children’s Hospital, 401 Park Drive, Mail Stop BCH3187, LM5528.4, 02115, Boston, MA, USA;Department of Pediatrics, Harvard Medical School, 02115, Boston, MA, USA;Department of Biomedical Informatics, Harvard Medical School, 02115, Boston, MA, USA;

关键词: Genetic testing;    False negative;    Coverage;    Whole exome sequencing;    Gene panel testing;   

DOI  :  10.1186/s12859-021-04178-5

来源: Springer

【 摘 要 】

BackgroundWhole exome sequencing (WES) is widely adopted in clinical and research settings; however, one of the practical concerns is the potential 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 disease-associated genes. We developed a web-based tool to quickly gauge whether all genes of interest would be reliably covered by WES or whether targeted gene panel testing should be considered instead to minimize false negatives in candidate genes.ResultsWEScover is a novel web application that provides an intuitive user interface for discovering breadth and depth of coverage across population-scale WES datasets, searching either by phenotype, by targeted gene panel(s) or by gene(s). Moreover, the application shows metrics from the Genome Aggregation Database to provide gene-centric view on breadth of coverage.ConclusionsWEScover allows users to efficiently query genes and phenotypes for the coverage of associated exons by WES and recommends use of panel tests for the genes with potential incomplete coverage by WES.

【 授权许可】

CC BY