{"id":"https://openalex.org/W4386783705","doi":"https://doi.org/10.7717/peerj.16026","title":"DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing","display_name":"DEVOUR: Deleterious Variants on Uncovered Regions in Whole-Exome Sequencing","publication_year":2023,"publication_date":"2023-09-15","ids":{"openalex":"https://openalex.org/W4386783705","doi":"https://doi.org/10.7717/peerj.16026","pmid":"https://pubmed.ncbi.nlm.nih.gov/37727687","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/10506587"},"language":"en","primary_location":{"id":"doi:10.7717/peerj.16026","doi":"https://doi.org/10.7717/peerj.16026","is_oa":true,"landing_page_url":"http://dx.doi.org/10.7717/peerj.16026","pdf_url":null,"source":{"id":"https://openalex.org/S1983995261","display_name":"PeerJ","issn_l":"2167-8359","issn":["2167-8359"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320104","host_organization_name":"PeerJ, Inc.","host_organization_lineage":["https://openalex.org/P4310320104"],"host_organization_lineage_names":["PeerJ, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PeerJ","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"http://dx.doi.org/10.7717/peerj.16026","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088442993","display_name":"Erdem T\u00fcrk","orcid":"https://orcid.org/0000-0003-0898-6778","observed_orcids":["https://orcid.org/0000-0003-0898-6778"]},"institutions":[{"id":"https://openalex.org/I79946792","display_name":"Mu\u011fla University","ror":"https://ror.org/05n2cz176","country_code":"TR","type":"education","lineage":["https://openalex.org/I79946792"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Erdem T\u00fcrk","raw_affiliation_strings":["Bioinformatics Graduate Program, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey","Department of Computer Engineering, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Graduate Program, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey","institution_ids":["https://openalex.org/I79946792"]},{"raw_affiliation_string":"Department of Computer Engineering, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey","institution_ids":["https://openalex.org/I79946792"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077398037","display_name":"Akif Ayaz","orcid":"https://orcid.org/0000-0001-6930-7148","observed_orcids":["https://orcid.org/0000-0001-6930-7148"]},"institutions":[{"id":"https://openalex.org/I3125470973","display_name":"Istanbul Medipol University","ror":"https://ror.org/037jwzz50","country_code":"TR","type":"education","lineage":["https://openalex.org/I3125470973"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Akif Ayaz","raw_affiliation_strings":["Department of Medical Genetics, School of Medicine, \u0130stanbul Medipol University, \u0130stanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Genetics, School of Medicine, \u0130stanbul Medipol University, \u0130stanbul, Turkey","institution_ids":["https://openalex.org/I3125470973"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092880763","display_name":"Ayhan Y\u00fcksek","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I79946792","display_name":"Mu\u011fla University","ror":"https://ror.org/05n2cz176","country_code":"TR","type":"education","lineage":["https://openalex.org/I79946792"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ayhan Y\u00fcksek","raw_affiliation_strings":["Department of Computer Engineering, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey","institution_ids":["https://openalex.org/I79946792"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042134761","display_name":"Bar\u0131\u015f Ethem S\u00fczek","orcid":"https://orcid.org/0000-0002-1521-4306","observed_orcids":["https://orcid.org/0000-0002-1521-4306"]},"institutions":[{"id":"https://openalex.org/I79946792","display_name":"Mu\u011fla University","ror":"https://ror.org/05n2cz176","country_code":"TR","type":"education","lineage":["https://openalex.org/I79946792"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Bar\u0131\u015f E. S\u00fczek","raw_affiliation_strings":["Bioinformatics Graduate Program, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey","Department of Computer Engineering, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Graduate Program, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey","institution_ids":["https://openalex.org/I79946792"]},{"raw_affiliation_string":"Department of Computer Engineering, Mu\u011fla\u00a0S\u0131tk\u0131\u00a0Ko\u00e7man University, Mu\u011fla, Turkey","institution_ids":["https://openalex.org/I79946792"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5088442993"],"corresponding_institution_ids":["https://openalex.org/I79946792"],"apc_list":{"value":1395,"currency":"USD","value_usd":1395},"apc_paid":{"value":1395,"currency":"USD","value_usd":1395},"fwci":0.1657,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.47713863,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":96},"biblio":{"volume":"11","issue":null,"first_page":"e16026","last_page":"e16026"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.000699999975040555,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/deleterious-mutations","display_name":"deleterious mutations","score":0.8859999775886536},{"id":"https://openalex.org/keywords/whole-exome-sequencing","display_name":"exome sequencing","score":0.8700000047683716},{"id":"https://openalex.org/keywords/variant-calling","display_name":"variant calling","score":0.5419999957084656},{"id":"https://openalex.org/keywords/hirschsprung-disease","display_name":"Hirschsprung disease","score":0.9160000085830688},{"id":"https://openalex.org/keywords/desktop-application","display_name":"desktop application","score":0.7620000243186951},{"id":"https://openalex.org/keywords/genetic-diagnosis","display_name":"genetic diagnosis","score":0.41499999165534973}],"concepts":[{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.7194677591323853},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.6694669723510742},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6198137998580933},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6069808602333069},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5779702067375183},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5703042149543762},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.524231493473053},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.4903709888458252},{"id":"https://openalex.org/C3020646490","wikidata":"https://www.wikidata.org/wiki/Q25203551","display_name":"Clinical phenotype","level":4,"score":0.41571077704429626},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.38331323862075806},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34016919136047363},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33591294288635254},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.3055071234703064},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22854739427566528},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.20418009161949158},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005086","descriptor_name":"Existentialism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006627","descriptor_name":"Hirschsprung Disease","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.7717/peerj.16026","doi":"https://doi.org/10.7717/peerj.16026","is_oa":true,"landing_page_url":"http://dx.doi.org/10.7717/peerj.16026","pdf_url":null,"source":{"id":"https://openalex.org/S1983995261","display_name":"PeerJ","issn_l":"2167-8359","issn":["2167-8359"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320104","host_organization_name":"PeerJ, Inc.","host_organization_lineage":["https://openalex.org/P4310320104"],"host_organization_lineage_names":["PeerJ, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PeerJ","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10506587","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10506587","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10506587/pdf/peerj-11-16026.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PeerJ","raw_type":"Text"},{"id":"pmid:37727687","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37727687","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PeerJ","raw_type":"Journal Article"},{"id":"pmh:oai:acikerisim.mu.edu.tr:20.500.12809/10975","doi":null,"is_oa":true,"landing_page_url":"https://doi.org/10.7717/peerj.16026","pdf_url":null,"source":{"id":"https://openalex.org/S7407055340","display_name":"Mu\u011fla S\u0131tk\u0131 Ko\u00e7man University Institutional Repository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:e57b288bc55841fc967faca0463f27dd","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/e57b288bc55841fc967faca0463f27dd","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PeerJ, Vol 11, p e16026 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.7717/peerj.16026","doi":"https://doi.org/10.7717/peerj.16026","is_oa":true,"landing_page_url":"http://dx.doi.org/10.7717/peerj.16026","pdf_url":null,"source":{"id":"https://openalex.org/S1983995261","display_name":"PeerJ","issn_l":"2167-8359","issn":["2167-8359"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320104","host_organization_name":"PeerJ, Inc.","host_organization_lineage":["https://openalex.org/P4310320104"],"host_organization_lineage_names":["PeerJ, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PeerJ","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5683000087738037,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G3656981112","display_name":"\u0130nsan T\u00fcm Ekzom Dizileme Tekniklerinin Kapsamad\u0131\u011f\u0131 Klinik \u00d6nemi Olan Varyantlar\u0131 Tespit Eden ve Anlamland\u0131ran Sistem","funder_award_id":"120E522","funder_id":"https://openalex.org/F4320322626","funder_display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu"}],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1596062789","https://openalex.org/W1676827377","https://openalex.org/W1971584645","https://openalex.org/W1984068087","https://openalex.org/W2018584963","https://openalex.org/W2029205619","https://openalex.org/W2030701454","https://openalex.org/W2060965924","https://openalex.org/W2104595023","https://openalex.org/W2116041602","https://openalex.org/W2119180969","https://openalex.org/W2121531763","https://openalex.org/W2152745352","https://openalex.org/W2594366209","https://openalex.org/W2755772215","https://openalex.org/W2797275307","https://openalex.org/W2808107434","https://openalex.org/W2950006249","https://openalex.org/W2964849163","https://openalex.org/W2990435446","https://openalex.org/W3007469223","https://openalex.org/W3109958717","https://openalex.org/W3131055609","https://openalex.org/W4319334504","https://openalex.org/W6969259846"],"related_works":["https://openalex.org/W2951038513","https://openalex.org/W3056775967","https://openalex.org/W4295353219","https://openalex.org/W4281641943","https://openalex.org/W6920712024","https://openalex.org/W4409786048","https://openalex.org/W3024000346","https://openalex.org/W4285239049","https://openalex.org/W7137107062","https://openalex.org/W2022714591"],"abstract_inverted_index":{"The":[0],"discovery":[1],"of":[2,41,96,105,123],"low-coverage":[3,46,74,86,128],"(i.e.":[4],"uncovered)":[5],"regions":[6,70,87],"containing":[7],"clinically":[8,42],"significant":[9],"variants,":[10],"especially":[11],"when":[12],"they":[13],"are":[14],"related":[15],"to":[16,34,37,101],"the":[17,39,85,120,136],"patient's":[18],"clinical":[19,28,89],"phenotype,":[20],"is":[21,32,131],"critical":[22],"for":[23,65],"whole-exome":[24],"sequencing":[25],"(WES)":[26],"based":[27],"diagnosis.":[29],"Therefore,":[30],"it":[31],"essential":[33],"develop":[35],"tools":[36],"identify":[38],"existence":[40,122],"important":[43],"variants":[44,83,126],"in":[45,84,127],"regions.":[47,129],"Here,":[48],"we":[49],"introduce":[50],"a":[51,94,103,109],"desktop":[52],"application,":[53],"namely":[54],"DEVOUR":[55,98,130],"(DEleterious":[56],"Variants":[57],"On":[58],"Uncovered":[59],"Regions),":[60],"that":[61],"analyzes":[62],"read":[63],"alignments":[64],"WES":[66,114],"experiments,":[67],"identifies":[68],"genomic":[69],"with":[71],"no":[72],"or":[73],"(read":[75],"depth":[76],"<":[77],"5)":[78],"and":[79],"then":[80],"annotates":[81],"known":[82],"using":[88],"variant":[90],"annotation":[91],"databases.":[92],"As":[93],"proof":[95],"concept,":[97],"was":[99],"used":[100],"analyze":[102],"total":[104],"28":[106],"samples":[107],"from":[108,133],"publicly":[110],"available":[111,132],"Hirschsprung":[112],"disease-related":[113],"project":[115],"(NCBI":[116],"Bioproject:":[117],"https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB19327),":[118],"revealing":[119],"potential":[121],"98":[124],"disease-associated":[125],"https://github.com/projectDevour/DEVOUR":[134],"under":[135],"MIT":[137],"license.":[138]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2023-09-16T00:00:00"}