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
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.
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