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Optical Genome Mapping for Applications in Repeat Expansion Disorders.
van der Sanden, Bart; Neveling, Kornelia; Pang, Andy Wing Chun; Shukor, Syukri; Gallagher, Michael D; Burke, Stephanie L; Kamsteeg, Erik-Jan; Hastie, Alex; Hoischen, Alexander.
Afiliación
  • van der Sanden B; Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands.
  • Neveling K; Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands.
  • Pang AWC; Bionano Genomics Clinical and Scientific Affairs, San Diego, California.
  • Shukor S; Bionano Genomics Clinical and Scientific Affairs, San Diego, California.
  • Gallagher MD; Bionano Genomics Clinical and Scientific Affairs, San Diego, California.
  • Burke SL; Bionano Genomics Clinical and Scientific Affairs, San Diego, California.
  • Kamsteeg EJ; Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands.
  • Hastie A; Bionano Genomics Clinical and Scientific Affairs, San Diego, California.
  • Hoischen A; Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands.
Curr Protoc ; 4(7): e1094, 2024 Jul.
Article en En | MEDLINE | ID: mdl-38966883
ABSTRACT
Short tandem repeat (STR) expansions are associated with more than 60 genetic disorders. The size and stability of these expansions correlate with the severity and age of onset of the disease. Therefore, being able to accurately detect the absolute length of STRs is important. Current diagnostic assays include laborious lab experiments, including repeat-primed PCR and Southern blotting, that still cannot precisely determine the exact length of very long repeat expansions. Optical genome mapping (OGM) is a cost-effective and easy-to-use alternative to traditional cytogenetic techniques and allows the comprehensive detection of chromosomal aberrations and structural variants >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-type allele of >500 bp. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1 Genomic ultra-high-molecular-weight DNA isolation, labeling, and staining Basic Protocol 2 Data generation and genome mapping using the Bionano Saphyr® System Basic Protocol 3 Manual De Novo Assembly workflow Basic Protocol 4 Local guided assembly workflow Basic Protocol 5 EnFocus Fragile X workflow Basic Protocol 6 Molecule distance script workflow.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Mapeo Cromosómico Límite: Humans Idioma: En Revista: Curr Protoc Año: 2024 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Estados Unidos
Texto completo
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Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Mapeo Cromosómico Límite: Humans Idioma: En Revista: Curr Protoc Año: 2024 Tipo del documento: Article País de afiliación: Países Bajos Pais de publicación: Estados Unidos