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https://ahro.austin.org.au/austinjspui/handle/1/23103| Title: | ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data. | Austin Authors: | 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 | Affiliation: | Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 2E5, Canada Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada The Centre for Applied Genomics, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada The McLaughlin Centre, University of Toronto, 686 Bay Street, Toronto, ON, M5G 0A4, Canada Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia Department of Medical Biology, The University of Melbourne, 1G Royal Parade, Parkville, VIC, 3052, Australia Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia Genetics and Genome Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON, M5G 0A4, Canada Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands New York Genome Center, 101 Avenue of the Americas, New York, 10013, USA Department of Neurology, UMC Utrecht Brain Center, Utrecht University, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands Illumina Cambridge Ltd, Illumina Centre, 19 Granta Park, Great Abington, Cambridge, CB21 6DF, UK Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA |
Issue Date: | 28-Apr-2020 | Date: | 2020-04-28 | Publication information: | Genome biology 2020; 21(1): 102 | 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. | URI: | https://ahro.austin.org.au/austinjspui/handle/1/23103 | DOI: | 10.1186/s13059-020-02017-z | Journal: | Genome biology | PubMed URL: | 32345345 | Type: | Journal Article | Subjects: | Fragile X syndrome Friedreich ataxia Genome-wide analysis Huntington disease Myotonic dystrophy type 1 Repeat expansions Short tandem repeats Whole-genome sequencing data |
| Appears in Collections: | Journal articles |
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