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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.
Dolzhenko, Egor; Deshpande, Viraj; Schlesinger, Felix; Krusche, Peter; Petrovski, Roman; Chen, Sai; Emig-Agius, Dorothea; Gross, Andrew; Narzisi, Giuseppe; Bowman, Brett; Scheffler, Konrad; van Vugt, Joke J F A; French, Courtney; Sanchis-Juan, Alba; Ibáñez, Kristina; Tucci, Arianna; Lajoie, Bryan R; Veldink, Jan H; Raymond, F Lucy; Taft, Ryan J; Bentley, David R; Eberle, Michael A.
Afiliación
  • Dolzhenko E; Illumina Inc., San Diego, CA 92122, USA.
  • Deshpande V; Illumina Inc., San Diego, CA 92122, USA.
  • Schlesinger F; Illumina Inc., San Diego, CA 92122, USA.
  • Krusche P; Illumina Cambridge Ltd, Illumina Centre, 19 Granta Park, Great Abington, Cambridge CB21 6DF, UK.
  • Petrovski R; Illumina Cambridge Ltd, Illumina Centre, 19 Granta Park, Great Abington, Cambridge CB21 6DF, UK.
  • Chen S; Illumina Inc., San Diego, CA 92122, USA.
  • Emig-Agius D; Illumina Inc., San Diego, CA 92122, USA.
  • Gross A; Illumina Inc., San Diego, CA 92122, USA.
  • Narzisi G; Computational Biology, New York Genome Center, New York, NY 10013, USA.
  • Bowman B; Illumina Inc., San Diego, CA 92122, USA.
  • Scheffler K; Illumina Inc., San Diego, CA 92122, USA.
  • van Vugt JJFA; UMC Utrecht Brain Center, Utrecht University, 3508 AB Utrecht, The Netherlands.
  • French C; Department of Medical Genetics, NHS Blood and Transplant Centre, Cambridge, CB2 0PT, UK.
  • Sanchis-Juan A; Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, CB2 0PT, UK.
  • Ibáñez K; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
  • Tucci A; Genomics England, Queen Mary University London, London EC1M 6BQ, UK.
  • Lajoie BR; Genomics England, Queen Mary University London, London EC1M 6BQ, UK.
  • Veldink JH; Illumina Inc., San Diego, CA 92122, USA.
  • Raymond FL; UMC Utrecht Brain Center, Utrecht University, 3508 AB Utrecht, The Netherlands.
  • Taft RJ; Department of Medical Genetics, NHS Blood and Transplant Centre, Cambridge, CB2 0PT, UK.
  • Bentley DR; Illumina Inc., San Diego, CA 92122, USA.
  • Eberle MA; Illumina Cambridge Ltd, Illumina Centre, 19 Granta Park, Great Abington, Cambridge CB21 6DF, UK.
Bioinformatics ; 35(22): 4754-4756, 2019 11 01.
Article en En | MEDLINE | ID: mdl-31134279
ABSTRACT

SUMMARY:

We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. AVAILABILITY AND IMPLEMENTATION ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https//github.com/Illumina/ExpansionHunter/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Repeticiones de Microsatélite Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Repeticiones de Microsatélite Idioma: En Revista: Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos