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

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...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) CA), 2023-09, Vol.11, p.e16026-e16026, Article e16026
Main Authors: Türk, Erdem, Ayaz, Akif, Yüksek, Ayhan, Süzek, Baris E
Format: Article
Language:English
Subjects:
Analysis
Bioinformatics
Computational Biology
Computational Science
Genetic diseases
Genetic disposition to disease
Genetic variants
Medical colleges
Medical genetics
Next-generation sequence (NGS) analysis
Whole-exome sequencing (WES) analysis
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Summary: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:
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.16026