UBC Faculty Research and Publications

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.; et al.

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.

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Attribution 4.0 International (CC BY 4.0)