PT  - JOURNAL ARTICLE
AU  - Egor Dolzhenko
AU  - Mark F. Bennett
AU  - Phillip A. Richmond
AU  - Brett Trost
AU  - Sai Chen
AU  - Joke J.F.A. van Vugt
AU  - Charlotte Nguyen
AU  - Giuseppe Narzisi
AU  - Vladimir G. Gainullin
AU  - Andrew Gross
AU  - Bryan Lajoie
AU  - Ryan J. Taft
AU  - Wyeth W. Wasserman
AU  - Stephen W. Scherer
AU  - Jan H. Veldink
AU  - David R. Bentley
AU  - R.K.C. Yuen
AU  - Melanie Bahlo
AU  - Michael A. Eberle
TI  - ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data
AID  - 10.1101/863035
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 863035
4099  - http://biorxiv.org/content/early/2019/12/03/863035.short
4100  - http://biorxiv.org/content/early/2019/12/03/863035.full
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