학술논문
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
Document Type
article
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
Source
Genome Biology, Vol 21, Iss 1, Pp 1-14 (2020)
Subject
Language
English
ISSN
1474-760X
Abstract
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.