ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
Abstract Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods for detecting repeat expansions in short-read sequencing data require predefined repeat catalogs. Recent discoveries emphasize the n...
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doaj-e6a0e5f3dd2f430489a30306e1ab55af2020-11-25T02:54:23ZengBMCGenome Biology1474-760X2020-04-0121111410.1186/s13059-020-02017-zExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing dataEgor Dolzhenko0Mark F. Bennett1Phillip A. Richmond2Brett Trost3Sai Chen4Joke J. F. A. van Vugt5Charlotte Nguyen6Giuseppe Narzisi7Vladimir G. Gainullin8Andrew M. Gross9Bryan R. Lajoie10Ryan J. Taft11Wyeth W. Wasserman12Stephen W. Scherer13Jan H. Veldink14David R. Bentley15Ryan K. C. Yuen16Melanie Bahlo17Michael A. Eberle18Illumina Inc.Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical ResearchCentre for Molecular Medicine and Therapeutics, BC Children’s Hospital, University of British ColumbiaGenetics and Genome Biology, The Hospital for Sick ChildrenIllumina Inc.Department of Neurology, UMC Utrecht Brain Center, Utrecht UniversityGenetics and Genome Biology, The Hospital for Sick ChildrenNew York Genome CenterIllumina Inc.Illumina Inc.Illumina Inc.Illumina Inc.Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital, University of British ColumbiaGenetics and Genome Biology, The Hospital for Sick ChildrenDepartment of Neurology, UMC Utrecht Brain Center, Utrecht UniversityIllumina Cambridge Ltd, Illumina CentreGenetics and Genome Biology, The Hospital for Sick ChildrenPopulation Health and Immunity Division, The Walter and Eliza Hall Institute of Medical ResearchIllumina Inc.Abstract Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods for detecting repeat expansions in short-read sequencing data require predefined repeat catalogs. Recent discoveries emphasize the need for methods that do not require pre-specified candidate repeats. To address this need, we introduce ExpansionHunter Denovo, an efficient catalog-free method for genome-wide repeat expansion detection. Analysis of real and simulated data shows that our method can identify large expansions of 41 out of 44 pathogenic repeats, including nine recently reported non-reference repeat expansions not discoverable via existing methods.http://link.springer.com/article/10.1186/s13059-020-02017-zRepeat expansionsShort tandem repeatsWhole-genome sequencing dataGenome-wide analysisFriedreich ataxiaMyotonic dystrophy type 1 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Egor Dolzhenko Mark F. Bennett Phillip A. Richmond Brett Trost Sai Chen Joke J. F. A. van Vugt Charlotte Nguyen Giuseppe Narzisi Vladimir G. Gainullin Andrew M. Gross Bryan R. Lajoie Ryan J. Taft Wyeth W. Wasserman Stephen W. Scherer Jan H. Veldink David R. Bentley Ryan K. C. Yuen Melanie Bahlo Michael A. Eberle |
spellingShingle |
Egor Dolzhenko Mark F. Bennett Phillip A. Richmond Brett Trost Sai Chen Joke J. F. A. van Vugt Charlotte Nguyen Giuseppe Narzisi Vladimir G. Gainullin Andrew M. Gross Bryan R. Lajoie Ryan J. Taft Wyeth W. Wasserman Stephen W. Scherer Jan H. Veldink David R. Bentley Ryan K. C. Yuen Melanie Bahlo Michael A. Eberle ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data Genome Biology Repeat expansions Short tandem repeats Whole-genome sequencing data Genome-wide analysis Friedreich ataxia Myotonic dystrophy type 1 |
author_facet |
Egor Dolzhenko Mark F. Bennett Phillip A. Richmond Brett Trost Sai Chen Joke J. F. A. van Vugt Charlotte Nguyen Giuseppe Narzisi Vladimir G. Gainullin Andrew M. Gross Bryan R. Lajoie Ryan J. Taft Wyeth W. Wasserman Stephen W. Scherer Jan H. Veldink David R. Bentley Ryan K. C. Yuen Melanie Bahlo Michael A. Eberle |
author_sort |
Egor Dolzhenko |
title |
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data |
title_short |
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data |
title_full |
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data |
title_fullStr |
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data |
title_full_unstemmed |
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data |
title_sort |
expansionhunter denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data |
publisher |
BMC |
series |
Genome Biology |
issn |
1474-760X |
publishDate |
2020-04-01 |
description |
Abstract Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods for detecting repeat expansions in short-read sequencing data require predefined repeat catalogs. Recent discoveries emphasize the need for methods that do not require pre-specified candidate repeats. To address this need, we introduce ExpansionHunter Denovo, an efficient catalog-free method for genome-wide repeat expansion detection. Analysis of real and simulated data shows that our method can identify large expansions of 41 out of 44 pathogenic repeats, including nine recently reported non-reference repeat expansions not discoverable via existing methods. |
topic |
Repeat expansions Short tandem repeats Whole-genome sequencing data Genome-wide analysis Friedreich ataxia Myotonic dystrophy type 1 |
url |
http://link.springer.com/article/10.1186/s13059-020-02017-z |
work_keys_str_mv |
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