DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing.
Clinical NGS informatics
Genetic diseases
Genetic disposition to disease
Genetic variants
Medical genetics
Next-generation sequence (NGS) analysis
Whole-exome sequencing (WES) analysis
Journal
PeerJ
ISSN: 2167-8359
Titre abrégé: PeerJ
Pays: United States
ID NLM: 101603425
Informations de publication
Date de publication:
2023
2023
Historique:
received:
09
05
2023
accepted:
13
08
2023
medline:
21
9
2023
pubmed:
20
9
2023
entrez:
20
9
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37727687
doi: 10.7717/peerj.16026
pii: 16026
pmc: PMC10506587
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e16026Informations de copyright
©2023 Türk et al.
Déclaration de conflit d'intérêts
The authors declare there are no competing interests.
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