DEVOUR: Deleterious variants on uncovered regions in whole-exome sequencing
| dc.authorid | 0000-0001-6930-7148 | |
| dc.contributor.author | Türk, Erdem | |
| dc.contributor.author | Ayaz, Akif | |
| dc.contributor.author | Yüksek, Ayhan | |
| dc.contributor.author | Süzek, Barış Ethem | |
| dc.date.accessioned | 2023-10-13T12:42:52Z | |
| dc.date.available | 2023-10-13T12:42:52Z | |
| dc.date.issued | 2023 | |
| dc.department | İstanbul Medipol Üniversitesi, Tıp Fakültesi, Dahili Tıp Bilimleri Bölümü, Tıbbi Genetik Ana Bilim Dalı | |
| dc.description.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. | |
| dc.identifier.citation | Türk, E., Ayaz, A., Yüksek, A. ve Süzek, B. E. (2023). DEVOUR: Deleterious variants on uncovered regions in whole-exome sequencing. PeerJ, 11. https://doi.org/10.7717/peerj.16026 | |
| dc.identifier.doi | 10.7717/peerj.16026 | |
| dc.identifier.issn | 2167-8359 | |
| dc.identifier.pmid | 37727687 | |
| dc.identifier.scopus | 2-s2.0-85173879175 | |
| dc.identifier.scopusquality | Q1 | |
| dc.identifier.uri | https://doi.org/10.7717/peerj.16026 | |
| dc.identifier.uri | https://hdl.handle.net/20.500.12511/11587 | |
| dc.identifier.volume | 11 | |
| dc.identifier.wos | 001074470400005 | en_US |
| dc.identifier.wosquality | Q2 | |
| dc.indekslendigikaynak | Web of Science | |
| dc.indekslendigikaynak | Scopus | |
| dc.indekslendigikaynak | PubMed | |
| dc.institutionauthor | Ayaz, Akif | |
| dc.language.iso | en | |
| dc.publisher | PeerJ Inc. | |
| dc.relation.ispartof | PeerJ | en_US |
| dc.relation.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | |
| dc.relation.tubitak | info:eu-repo/grantAgreement/TUBITAK/SOBAG/120E522 | |
| dc.rights | Attribution 4.0 International | * |
| dc.rights | info:eu-repo/semantics/openAccess | |
| dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | * |
| dc.subject | Next-Generation Sequence (NGS) Analysis | |
| dc.subject | Whole-Exome Sequencing (WES) Analysis | |
| dc.subject | Medical Genetics | |
| dc.subject | Genetic Disposition to Disease | |
| dc.subject | Genetic Diseases | |
| dc.subject | Genetic Variants | |
| dc.subject | Clinical NGS Informatics | |
| dc.title | DEVOUR: Deleterious variants on uncovered regions in whole-exome sequencing | |
| dc.type | Article |
