ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions

Egor Dolzhenko(Illumina (United States)), Viraj Deshpande(Illumina (United States)), Felix Schlesinger(Illumina (United States)), Peter Krusche(Illumina (United Kingdom)), Roman Petrovski(Illumina (United Kingdom)), Sai Chen(Illumina (United States)), Dorothea Emig-Agius(Illumina (United States)), Andrew M. Gross(Illumina (United States)), Giuseppe Narzisi(New York Genome Center), Brett Bowman(Illumina (United States)), Konrad Scheffler(Illumina (United States)), Joke J.F.A. van Vugt(Utrecht University), Courtney E. French(NHS Blood and Transplant), Alba Sanchis‐Juan(NHS Blood and Transplant), Kristina Ibáñez(Genomics England), Arianna Tucci(Genomics England), Bryan R. Lajoie(Illumina (United States)), Jan H. Veldink(Utrecht University), F. Lucy Raymond(NHS Blood and Transplant), Ryan J. Taft(Illumina (United States)), David Bentley(Illumina (United Kingdom)), Michael A. Eberle(Illumina (United States))
Bioinformatics
May 23, 2019
10.1093/bioinformatics/btz431
Cited by 406Open Access
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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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