{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:04Z","timestamp":1753875724597,"version":"3.41.2"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T00:00:00Z","timestamp":1693180800000},"content-version":"vor","delay-in-days":2,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM138184","R01CA241930","2217515","2326879"],"award-info":[{"award-number":["R35GM138184","R01CA241930","2217515","2326879"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"University of Texas Health Science Centerat Houston"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Microhomology-mediated end joining (MMEJ), an error-prone DNA damage repair mechanism, frequently leads to chromosomal rearrangements due to its ability to engage in promiscuous end joining of genomic instability and also leads to increasing mutational load at the sequences flanking the breakpoints (BPs). In this study, we systematically investigated the homology sequences around the genomic breakpoint area of human fusion genes, which were formed by the chromosomal rearrangements initiated by DNA double-strand breakage. Since the RNA-seq data is the typical data set to check the fusion genes, for the known exon junction fusion breakpoints identified from RNA-seq data, we have to infer the high chance of genomic breakpoint regions. For this, we utilized the high feature importance score area calculated from our recently developed fusion BP prediction model, FusionAI and identified 151\u00a0K microhomologies among ~24\u00a0K fusion BPs in 20\u00a0K fusion genes. From our multiple bioinformatics studies, we found a relationship between sequence homologies and the immune system. This in-silico study will provide novel knowledge on the sequence homologies around the coded structural variants.<\/jats:p>","DOI":"10.1093\/bib\/bbad314","type":"journal-article","created":{"date-parts":[[2023,8,28]],"date-time":"2023-08-28T05:56:57Z","timestamp":1693202217000},"source":"Crossref","is-referenced-by-count":0,"title":["Systematic investigation of the homology sequences around the human fusion gene breakpoints in pan-cancer \u2013 bioinformatics study for a potential link to MMEJ"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8321-6864","authenticated-orcid":false,"given":"Pora","family":"Kim","sequence":"first","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4335-4517","authenticated-orcid":false,"given":"Himansu","family":"Kumar","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengyuan","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Public Health Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruihan","family":"Luo","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiajia","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaobo","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX 77030 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,8,26]]},"reference":[{"key":"2023092216570464100_ref1","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.mrfmmm.2017.07.002","article-title":"Microhomology-mediated end joining: good, bad and ugly","volume":"809","author":"Seol","year":"2018","journal-title":"Mutat Res"},{"key":"2023092216570464100_ref2","doi-asserted-by":"crossref","first-page":"e1006714","DOI":"10.1371\/journal.pgen.1006714","article-title":"Microhomology-mediated end joining induces hypermutagenesis at breakpoint 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