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

Türk E., AYAZ A., Yüksek A., Süzek B. E.

PeerJ, cilt.11, 2023 (SCI-Expanded) identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 11
  • Basım Tarihi: 2023
  • Doi Numarası: 10.7717/peerj.16026
  • Dergi Adı: PeerJ
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, MEDLINE, Veterinary Science Database, Directory of Open Access Journals
  • Anahtar Kelimeler: Clinical NGS informatics, Genetic diseases, Genetic disposition to disease, Genetic variants, Medical genetics, Next-generation sequence (NGS) analysis, Whole-exome sequencing (WES) analysis
  • İstanbul Medipol Üniversitesi Adresli: Evet

Özet

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.