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ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data Dolzhenko, Egor; Bennett, Mark F.; Richmond, Phillip A.; Trost, Brett; Chen, Sai; van Vugt, Joke J. F. A.; Nguyen, Charlotte; Narzisi, Giuseppe; Gainullin, Vladimir G.; Gross, Andrew M.; Lajoie, Bryan R.; Taft, Ryan J.; Wasserman, Wyeth W.; Scherer, Stephen W.; Veldink, Jan H.; Bentley, David R.; Yuen, Ryan K. C.; Bahlo, Melanie; Eberle, Michael A.

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.

Item Metadata

Title
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
Creator
Dolzhenko, Egor; Bennett, Mark F.; Richmond, Phillip A.; Trost, Brett; Chen, Sai; van Vugt, Joke J. F. A.; Nguyen, Charlotte; Narzisi, Giuseppe; Gainullin, Vladimir G.; Gross, Andrew M.; Lajoie, Bryan R.; Taft, Ryan J.; Wasserman, Wyeth W.; Scherer, Stephen W.; Veldink, Jan H.; Bentley, David R.; Yuen, Ryan K. C.; Bahlo, Melanie; Eberle, Michael A.
Contributor
University of British Columbia. Centre for Molecular Medicine and Therapeutics
Publisher
BioMed Central
Date Issued
2020-04-28
Description
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.
Subject
Repeat expansions; Short tandem repeats; Whole-genome sequencing data; Genome-wide analysis; Friedreich ataxia; Myotonic dystrophy type 1; Huntington disease; Fragile X syndrome
Genre
Article
Type
Text
Language
eng
Date Available
2020-04-28
Provider
Vancouver : University of British Columbia Library
Rights
Attribution 4.0 International (CC BY 4.0)
DOI
10.14288/1.0390018
URI
http://hdl.handle.net/2429/74206
Affiliation
Other UBC; Non UBC
Citation
Genome Biology. 2020 Apr 28;21(1):102
Publisher DOI
10.1186/s13059-020-02017-z
Peer Review Status
Reviewed
Scholarly Level
Faculty
Copyright Holder
The Author(s)
Rights URI
http://creativecommons.org/licenses/by/4.0/
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Rights

Attribution 4.0 International (CC BY 4.0)