{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T19:04:27Z","timestamp":1790881467561,"version":"4.1.0"},"reference-count":0,"publisher":"Cold Spring Harbor Laboratory","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genome Res."],"accepted":{"date-parts":[[2026,9,3]]},"abstract":"<jats:p>\n                    Somatic variants are a prominent cause of epilepsy-associated cortical malformations, but about half of patients undergoing genetic testing have no finding due partly to limitations in variant detection. Most studies have focused on single-nucleotide variants or small indels that are accessible to short-read sequencing technologies, but somatic structural variants are also emerging as important contributors despite their unique detection challenges. Optical genome mapping (OGM) is a promising methodology for the detection of structural variants, but requires high quality, high molecular weight DNA from clinical specimens. Here we successfully optimize a protocol for OGM of surgically-resected patient brain tissue which yields ~450\u00d7 effective coverage suitable for detecting somatic variants at low allele fractions. We apply this approach to brain specimens from four patients with epilepsy. OGM identifies large and complex structural variants, most of which are not captured by short-read exome sequencing of the same specimen. In one patient with a known germline\n                    <jats:italic>DEPDC5<\/jats:italic>\n                    variant, OGM reveals a somatic variant, a 13.2kb deletion in\n                    <jats:italic>DEPDC5<\/jats:italic>\n                    at approximately 20% VAF, consistent with the established two-hit model in\n                    <jats:italic>DEPDC5<\/jats:italic>\n                    -associated lesional epilepsies. By resolving the breakpoints in PacBio HiFi sequencing data, we identify a mechanism for this somatic deletion, mediated by recombination of two\n                    <jats:italic>Alu<\/jats:italic>\n                    elements flanking the region. Our findings demonstrate that OGM is a robust and complementary tool for detecting somatic structural variation in human brain tissue, with potential to improve diagnostic yield and refine genotype-phenotype correlations in neurological disorders.\n                  <\/jats:p>","DOI":"10.1101\/gr.281418.125","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T18:20:16Z","timestamp":1790878816000},"page":"gr.281418.125","source":"Crossref","is-referenced-by-count":0,"title":["Optical genome mapping identifies clinically relevant somatic structural variation in epilepsy-affected brain tissue"],"prefix":"10.1101","author":[{"given":"Anthony R","family":"Miller","sequence":"first","affiliation":[{"name":"Nationwide Children's Hospital;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James J","family":"Anderson","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Elena","family":"Hernandez Gonzalez","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lakshmi Prakruthi","family":"Rao Venkata","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eileen","family":"Stonerock","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lauren","family":"Mashburn-Warren","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Allison","family":"Daley","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey","family":"Leonard","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathan","family":"Pindrik","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ammar","family":"Shaikhouni","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel R","family":"Boue","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diana L","family":"Thomas","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher R","family":"Pierson","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9994-6650","authenticated-orcid":false,"given":"Adam P","family":"Ostendorf","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5892-1553","authenticated-orcid":false,"given":"Elaine R","family":"Mardis","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel C","family":"Koboldt","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katherine E","family":"Miller","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tracy A","family":"Bedrosian","sequence":"additional","affiliation":[{"name":"Nationwide Children's Hospital, The Ohio State University College of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"246","published-online":{"date-parts":[[2026,10,1]]},"container-title":["Genome Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/gr.281418.125","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T18:20:16Z","timestamp":1790878816000},"score":1,"resource":{"primary":{"URL":"http:\/\/genome.cshlp.org\/lookup\/doi\/10.1101\/gr.281418.125"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,1]]},"references-count":0,"alternative-id":["10.1101\/gr.281418.125"],"URL":"https:\/\/doi.org\/10.1101\/gr.281418.125","relation":{},"ISSN":["1088-9051"],"issn-type":[{"value":"1088-9051","type":"print"}],"subject":[],"published":{"date-parts":[[2026,10,1]]}}}