{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:08Z","timestamp":1753875788783,"version":"3.41.2"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,1]],"date-time":"2022-12-01T00:00:00Z","timestamp":1669852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Wetenschappelijk Fonds Willy Gepts"},{"name":"Universitair Ziekenhuis Brussel"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Intragenic exonic deletions are known to contribute to genetic diseases and are often flanked by regions of homology.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In order to get a more clear view of these interspersed repeats encompassing a coding sequence, we have developed EDIR (Exome Database of Interspersed Repeats) which contains the positions of these structures within the human exome. EDIR has been calculated by an inductive strategy, rather than by a brute force approach and can be queried through an R\/Bioconductor package or a web interface allowing the per-gene rapid extraction of homology-flanked sequences throughout the exome.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The code used to compile EDIR can be found at https:\/\/github.com\/lauravongoc\/EDIR. The full dataset of EDIR can be queried via an Rshiny application at http:\/\/193.70.34.71:3857\/edir\/. The R package for querying EDIR is called \u2018EDIRquery\u2019 and is available on Bioconductor. The full EDIR dataset can be downloaded from https:\/\/osf.io\/m3gvx\/ or http:\/\/193.70.34.71\/EDIR.tar.gz.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac771","type":"journal-article","created":{"date-parts":[[2022,12,1]],"date-time":"2022-12-01T13:37:28Z","timestamp":1669901848000},"source":"Crossref","is-referenced-by-count":0,"title":["EDIR: exome database of interspersed repeats"],"prefix":"10.1093","volume":"39","author":[{"given":"Laura D T","family":"Vo Ngoc","sequence":"first","affiliation":[{"name":"Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics , Brussels 1090, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Randy","family":"Osei","sequence":"additional","affiliation":[{"name":"Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics , Brussels 1090, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katrin","family":"Dohr","sequence":"additional","affiliation":[{"name":"Department of Paediatrics and Adolescent Medicine, Research Unit of Analytical Mass Spectrometry, Cell Biology and Biochemistry of Inborn Errors of Metabolism , Graz 8010, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Catharina","family":"Olsen","sequence":"additional","affiliation":[{"name":"Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics , Brussels 1090, Belgium"},{"name":"Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), VUB-ULB , Brussels 1090, Belgium"},{"name":"Interuniversity Institute of Bioinformatics in Brussels (IB)2, VUB-ULB , Brussels 1050, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sara","family":"Seneca","sequence":"additional","affiliation":[{"name":"Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics , Brussels 1090, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8320-1961","authenticated-orcid":false,"given":"Alexander","family":"Gheldof","sequence":"additional","affiliation":[{"name":"Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics , Brussels 1090, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,12,1]]},"reference":[{"key":"2023010107533297500_btac771-B1","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/s41431-017-0087-x","article-title":"Recessive loss of function PIGN alleles, including an intragenic deletion with founder effect in La R\u00e9union island, in patients with Fryns syndrome","volume":"26","author":"Alessandri","year":"2018","journal-title":"Eur. J. Hum. Genet"},{"key":"2023010107533297500_btac771-B2","doi-asserted-by":"crossref","first-page":"e152","DOI":"10.1212\/NXG.0000000000000152","article-title":"Intragenic DOK7 deletion detected by whole-genome sequencing in congenital myasthenic syndromes","volume":"3","author":"Azuma","year":"2017","journal-title":"Neurol. Genet"},{"key":"2023010107533297500_btac771-B3","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1038\/jhg.2017.32","article-title":"Intragenic multi-exon deletion in the FBN1 gene in a child with mildly dilated aortic sinus: a retrotransposal event","volume":"62","author":"Brett","year":"2017","journal-title":"J. Hum. Genet"},{"key":"2023010107533297500_btac771-B4","doi-asserted-by":"crossref","first-page":"443","DOI":"10.3389\/fgene.2021.636900","article-title":"A novel FLCN intragenic deletion identified by NGS in a BHDS family and literature review","volume":"12","author":"Cai","year":"2021","journal-title":"Front. Genet"},{"key":"2023010107533297500_btac771-B5","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1038\/nrg.2015.25","article-title":"Mechanisms underlying structural variant formation in genomic disorders","volume":"17","author":"Carvalho","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023010107533297500_btac771-B6","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.parkreldis.2019.01.001","article-title":"Contribution of intragenic deletions to mutation spectrum in Chinese patients with Wilson\u2019s disease and possible mechanism underlying ATP7B gross deletions","volume":"62","author":"Chen","year":"2019","journal-title":"Parkinsonism Relat. Disord"},{"key":"2023010107533297500_btac771-B7","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1002\/jmd2.12107","article-title":"Early-onset coenzyme Q10 deficiency associated with ataxia and respiratory chain dysfunction due to novel pathogenic COQ8A variants, including a large intragenic deletion","volume":"54","author":"Cotta","year":"2020","journal-title":"JIMD Rep"},{"key":"2023010107533297500_btac771-B8","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1038\/s41431-018-0122-6","article-title":"\u03b3-Glutamyl transpeptidase deficiency caused by a large homozygous intragenic deletion in GGT1","volume":"26","author":"Darin","year":"2018","journal-title":"Eur. J. Hum. Genet"},{"key":"2023010107533297500_btac771-B9","doi-asserted-by":"crossref","first-page":"e203","DOI":"10.1097\/HS9.0000000000000203","article-title":"Germline RUNX1 intragenic deletion: implications for accurate diagnosis of FPD\/AML","volume":"3","author":"Duployez","year":"2019","journal-title":"HemaSphere"},{"key":"2023010107533297500_btac771-B10","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1038\/jhg.2017.84","article-title":"Precise mapping of 17 deletion breakpoints within the Central hotspot deletion region (introns 50 and 51) of the DMD gene","volume":"62","author":"Esposito","year":"2017","journal-title":"J. Hum. Genet"},{"key":"2023010107533297500_btac771-B11","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/s13100-020-00208-w","article-title":"The UCSC repeat browser allows discovery and visualization of evolutionary conflict across repeat families","volume":"11","author":"Fernandes","year":"2020","journal-title":"Mob. DNA"},{"key":"2023010107533297500_btac771-B12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s10194-018-0891-x","article-title":"New CACNA1A deletions are associated to migraine phenotypes","volume":"19","author":"Grieco","year":"2018","journal-title":"J. Headache Pain"},{"key":"2023010107533297500_btac771-B13","first-page":"1","article-title":"Large intragenic deletion of CDC73 (exons 4\u201310) in a three-generation hyperparathyroidism-jaw tumor (HPT-JT) syndrome family","volume":"18","author":"Guarnieri","year":"2017","journal-title":"BMC Med. Genet"},{"key":"2023010107533297500_btac771-B14","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1002\/ajmg.a.38517","article-title":"DOCK3-related neurodevelopmental syndrome: biallelic intragenic deletion of DOCK3 in a boy with developmental delay and hypotonia","volume":"176","author":"Iwata-Otsubo","year":"2018","journal-title":"Am. J. Med. Genet. A"},{"key":"2023010107533297500_btac771-B15","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1038\/s41439-019-0070-x","article-title":"Breakpoint junction features of seven DMD deletion mutations","volume":"6","author":"Keegan","year":"2019","journal-title":"Hum. Genome Var"},{"key":"2023010107533297500_btac771-B16","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1002\/ajmg.a.38181","article-title":"Alu-mediated deletion of PIGL in a patient with CHIME syndrome","volume":"173","author":"Knight Johnson","year":"2017","journal-title":"Am. J. Med. Genet. A"},{"key":"2023010107533297500_btac771-B17","doi-asserted-by":"crossref","first-page":"e3197","DOI":"10.1210\/clinem\/dgaa286","article-title":"Intragenic deletions of GNAS in pseudohypoparathyroidism type 1A identify a new region affecting methylation of exon A\/B","volume":"105","author":"Li","year":"2020","journal-title":"J. Clin. Endocrinol. Metab"},{"key":"2023010107533297500_btac771-B18","doi-asserted-by":"crossref","first-page":"D236","DOI":"10.1093\/nar\/gkab1089","article-title":"msRepDB: a comprehensive repetitive sequence database of over 80 000 species","volume":"50","author":"Liao","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2023010107533297500_btac771-B19","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1016\/j.tig.2014.01.001","article-title":"The role of microhomology in genomic structural variation","volume":"30","author":"Ottaviani","year":"2014","journal-title":"Trends in Genetics"},{"key":"2023010107533297500_btac771-B20","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1002\/acn3.51345","article-title":"Novel SPTBN2 gene mutation and first intragenic deletion in early onset spinocerebellar ataxia type 5","volume":"8","author":"Romaniello","year":"2021","journal-title":"Ann. Clin. Transl. Neurol"},{"key":"2023010107533297500_btac771-B21","doi-asserted-by":"crossref","first-page":"104060","DOI":"10.1016\/j.ejmg.2020.104060","article-title":"TSC1 intragenic deletion transmitted from a mosaic father to two siblings with cardiac rhabdomyomas: identification of two aberrant transcripts","volume":"63","author":"Uchiyama","year":"2020","journal-title":"Eur. J. Med. Genet"},{"key":"2023010107533297500_btac771-B22","doi-asserted-by":"crossref","first-page":"3579","DOI":"10.1093\/hmg\/ddp306","article-title":"Rare pathogenic microdeletions and tandem duplications are microhomology-mediated and stimulated by local genomic architecture","volume":"18","author":"Vissers","year":"2009","journal-title":"Hum. Mol. Genet"},{"key":"2023010107533297500_btac771-B23","first-page":"495","article-title":"A novel homozygous exon2 deletion of TRIM32 gene in a Chinese patient with sarcotubular myopathy: a case report and literature review","volume":"21","author":"Wei","year":"2021","journal-title":"Bosn. J. Basic Med. Sci"},{"key":"2023010107533297500_btac771-B24","doi-asserted-by":"crossref","first-page":"44271","DOI":"10.1038\/srep44271","article-title":"A complex intragenic rearrangement of ERCC8 in Chinese siblings with cockayne syndrome","volume":"7","author":"Xie","year":"2017","journal-title":"Sci. Rep"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac771\/47749522\/btac771.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac771\/48448899\/btac771.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/1\/btac771\/48448899\/btac771.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T10:11:39Z","timestamp":1672567899000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btac771\/6858440"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,12,1]]},"references-count":24,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,12,1]]},"published-print":{"date-parts":[[2023,1,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac771","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2023,1,1]]},"published":{"date-parts":[[2022,12,1]]},"article-number":"btac771"}}