DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing

Author:

Türk Erdem12,Ayaz Akif3,Yüksek Ayhan1,Süzek Barış E.12

Affiliation:

1. Department of Computer Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey

2. Bioinformatics Graduate Program, Muğla Sıtkı Koçman University, Muğla, Turkey

3. Department of Medical Genetics, School of Medicine, İstanbul Medipol University, İstanbul, Turkey

Abstract

The discovery of low-coverage (i.e. uncovered) regions containing clinically significant variants, especially when they are related to the patient’s clinical phenotype, is critical for whole-exome sequencing (WES) based clinical diagnosis. Therefore, it is essential to develop tools to identify the existence of clinically important variants in low-coverage regions. Here, we introduce a desktop application, namely DEVOUR (DEleterious Variants On Uncovered Regions), that analyzes read alignments for WES experiments, identifies genomic regions with no or low-coverage (read depth < 5) and then annotates known variants in the low-coverage regions using clinical variant annotation databases. As a proof of concept, DEVOUR was used to analyze a total of 28 samples from a publicly available Hirschsprung disease-related WES project (NCBI Bioproject: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB19327), revealing the potential existence of 98 disease-associated variants in low-coverage regions. DEVOUR is available from https://github.com/projectDevour/DEVOUR under the MIT license.

Funder

Scientific and Technological Research Council of Turkey

Publisher

PeerJ

Subject

General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

Reference25 articles.

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