ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions
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- Egor Dolzhenko
- Illumina Inc. , San Diego, CA 92122, USA
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- Viraj Deshpande
- Illumina Inc. , San Diego, CA 92122, USA
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- Felix Schlesinger
- Illumina Inc. , San Diego, CA 92122, USA
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- Peter Krusche
- Illumina Cambridge Ltd, Illumina Centre, 19 Granta Park, Great Abington , Cambridge CB21 6DF, UK
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- Roman Petrovski
- Illumina Cambridge Ltd, Illumina Centre, 19 Granta Park, Great Abington , Cambridge CB21 6DF, UK
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- Sai Chen
- Illumina Inc. , San Diego, CA 92122, USA
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- Dorothea Emig-Agius
- Illumina Inc. , San Diego, CA 92122, USA
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- Andrew Gross
- Illumina Inc. , San Diego, CA 92122, USA
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- Giuseppe Narzisi
- Computational Biology, New York Genome Center , New York, NY 10013, USA
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- Brett Bowman
- Illumina Inc. , San Diego, CA 92122, USA
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- Konrad Scheffler
- Illumina Inc. , San Diego, CA 92122, USA
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- Joke J F A van Vugt
- UMC Utrecht Brain Center, Utrecht University , 3508 AB Utrecht, The Netherlands
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- Courtney French
- Department of Medical Genetics, NHS Blood and Transplant Centre , Cambridge, CB2 0PT, UK
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- Alba Sanchis-Juan
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre , Cambridge, CB2 0PT, UK
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- Kristina Ibáñez
- Genomics England, Queen Mary University London , London EC1M 6BQ, UK
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- Arianna Tucci
- Genomics England, Queen Mary University London , London EC1M 6BQ, UK
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- Bryan R Lajoie
- Illumina Inc. , San Diego, CA 92122, USA
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- Jan H Veldink
- UMC Utrecht Brain Center, Utrecht University , 3508 AB Utrecht, The Netherlands
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- F Lucy Raymond
- Department of Medical Genetics, NHS Blood and Transplant Centre , Cambridge, CB2 0PT, UK
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- Ryan J Taft
- Illumina Inc. , San Diego, CA 92122, USA
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- David R Bentley
- Illumina Cambridge Ltd, Illumina Centre, 19 Granta Park, Great Abington , Cambridge CB21 6DF, UK
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- Michael A Eberle
- Illumina Inc. , San Diego, CA 92122, USA
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- Inanc Birol
- editor
説明
<jats:title>Abstract</jats:title> <jats:sec> <jats:title>Summary</jats:title> <jats:p>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.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>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/.</jats:p> </jats:sec> <jats:sec> <jats:title>Supplementary information</jats:title> <jats:p>Supplementary data are available at Bioinformatics online.</jats:p> </jats:sec>
収録刊行物
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- Bioinformatics
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Bioinformatics 35 (22), 4754-4756, 2019-05-27
Oxford University Press (OUP)
