RT Journal Article
SR Electronic
T1 ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 863035
DO 10.1101/863035
A1 Egor Dolzhenko
A1 Mark F. Bennett
A1 Phillip A. Richmond
A1 Brett Trost
A1 Sai Chen
A1 Joke J.F.A. van Vugt
A1 Charlotte Nguyen
A1 Giuseppe Narzisi
A1 Vladimir G. Gainullin
A1 Andrew Gross
A1 Bryan Lajoie
A1 Ryan J. Taft
A1 Wyeth W. Wasserman
A1 Stephen W. Scherer
A1 Jan H. Veldink
A1 David R. Bentley
A1 R.K.C. Yuen
A1 Melanie Bahlo
A1 Michael A. Eberle
YR 2019
UL http://biorxiv.org/content/early/2019/12/03/863035.abstract
AB Expansions of short tandem repeats are responsible for over 40 monogenic disorders, and undoubtedly many more pathogenic repeat expansions (REs) remain to be discovered. Existing methods for detecting REs in short read sequencing data require predefined repeat catalogs. However recent discoveries have emphasized the need for detection methods that do not require candidate repeats to be specified in advance. To address this need, we introduce ExpansionHunter Denovo, an efficient catalog-free method for genome-wide detection of REs. Analysis of real and simulated data shows that our method can identify large expansions of 41 out of 43 pathogenic repeats, including nine recently reported non-reference REs not discoverable via existing methods.ExpansionHunter Denovo is freely available at https://github.com/Illumina/ExpansionHunterDenovo