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Current diagnostic assays include laborious lab experiments, including repeat\u2010primed PCR and Southern blotting, that still cannot precisely determine the exact length of very long repeat expansions. Optical genome mapping (OGM) is a cost\u2010effective and easy\u2010to\u2010use alternative to traditional cytogenetic techniques and allows the comprehensive detection of chromosomal aberrations and structural variants &gt;500 bp in length, including insertions, deletions, duplications, inversions, translocations, and copy number variants. Here, we provide methodological guidance for preparing samples and performing OGM as well as running the analysis pipelines and using the specific repeat expansion workflows to determine the exact repeat length of repeat expansions expanded beyond 500 bp. Together these protocols provide all details needed to analyze the length and stability of any repeat expansion with an expected repeat size difference from the expected wild\u2010type allele of &gt;500 bp. \u00a9 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.<\/jats:p><jats:p><jats:bold>Basic Protocol 1<\/jats:bold>: Genomic ultra\u2010high\u2010molecular\u2010weight DNA isolation, labeling, and staining<\/jats:p><jats:p><jats:bold>Basic Protocol 2<\/jats:bold>: Data generation and genome mapping using the Bionano Saphyr\u00ae System<\/jats:p><jats:p><jats:bold>Basic Protocol 3<\/jats:bold>: Manual <jats:italic>De Novo<\/jats:italic> Assembly workflow<\/jats:p><jats:p><jats:bold>Basic Protocol 4<\/jats:bold>: Local guided assembly workflow<\/jats:p><jats:p><jats:bold>Basic Protocol 5<\/jats:bold>: EnFocus Fragile X workflow<\/jats:p><jats:p><jats:bold>Basic Protocol 6<\/jats:bold>: Molecule distance script workflow<\/jats:p>","DOI":"10.1002\/cpz1.1094","type":"journal-article","created":{"date-parts":[[2024,7,5]],"date-time":"2024-07-05T04:12:57Z","timestamp":1720152777000},"source":"Crossref","is-referenced-by-count":11,"title":["Optical Genome Mapping for Applications in Repeat Expansion Disorders"],"prefix":"10.1002","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0546-1351","authenticated-orcid":false,"given":"Bart","family":"van der Sanden","sequence":"first","affiliation":[{"name":"Department of Human Genetics, Research Institute for Medical Innovation Radboud University Medical Center  Nijmegen the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kornelia","family":"Neveling","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Research Institute for Medical Innovation Radboud University Medical Center  Nijmegen the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andy Wing Chun","family":"Pang","sequence":"additional","affiliation":[{"name":"Bionano Genomics Clinical and Scientific Affairs  San Diego California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Syukri","family":"Shukor","sequence":"additional","affiliation":[{"name":"Bionano Genomics Clinical and Scientific Affairs  San Diego California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael D.","family":"Gallagher","sequence":"additional","affiliation":[{"name":"Bionano Genomics Clinical and Scientific Affairs  San Diego California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephanie L.","family":"Burke","sequence":"additional","affiliation":[{"name":"Bionano Genomics Clinical and Scientific Affairs  San Diego California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik\u2010Jan","family":"Kamsteeg","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Research Institute for Medical Innovation Radboud University Medical Center  Nijmegen the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Hastie","sequence":"additional","affiliation":[{"name":"Bionano Genomics Clinical and Scientific Affairs  San Diego California"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8072-4476","authenticated-orcid":false,"given":"Alexander","family":"Hoischen","sequence":"additional","affiliation":[{"name":"Department of Human Genetics, Research Institute for Medical Innovation Radboud University Medical Center  Nijmegen the Netherlands"},{"name":"Department of Internal Medicine, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI) Radboud University Medical Center  Nijmegen the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,7,5]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.3390\/genes14101868"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-0716-2357-2_9"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/978\u2010981\u201013\u20106037\u20104_7"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00439\u2010023\u201002522\u20108"},{"key":"e_1_2_11_6_1","unstructured":"Broeckel U.(2024).Optical genome mapping for constitutional disorder applications.Current Protocols(in 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