ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
| Autor: | Sai Chen, Ryan K. C. Yuen, David R. Bentley, Stephen W. Scherer, Vladimir G. Gainullin, Phillip A. Richmond, Jan H. Veldink, Mark F. Bennett, Egor Dolzhenko, Giuseppe Narzisi, Charlotte Nguyen, Melanie Bahlo, Bryan R. Lajoie, Andrew M. Gross, Michael A. Eberle, Wyeth W. Wasserman, Ryan J. Taft, Joke J.F.A. van Vugt, Brett Trost |
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| Rok vydání: | 2020 |
| Předmět: |
lcsh:QH426-470
Computer science Sequencing data Method Computational biology Biology Genome 03 medical and health sciences 0302 clinical medicine Genome-wide analysis Repeat expansions Humans Myotonic Dystrophy lcsh:QH301-705.5 030304 developmental biology Whole genome sequencing 0303 health sciences DNA Repeat Expansion Whole Genome Sequencing Myotonic dystrophy type 1 High-Throughput Nucleotide Sequencing Huntington disease Short read lcsh:Genetics Short tandem repeats Friedreich ataxia lcsh:Biology (General) Case-Control Studies Fragile X Syndrome Simulated data Microsatellite Human genome Trinucleotide repeat expansion Software Whole-genome sequencing data 030217 neurology & neurosurgery Microsatellite Repeats |
| Zdroj: | Genome Biology Genome Biology, Vol 21, Iss 1, Pp 1-14 (2020) |
| ISSN: | 1474-760X |
| DOI: | 10.1186/s13059-020-02017-z |
| Popis: | 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 44 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 |
| Databáze: | OpenAIRE |
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