Please use this identifier to cite or link to this item: http://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.
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
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
Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC, V5Z 4H4, 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
EDate: 2020-04-28
Citation: 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: http://ahro.austin.org.au/austinjspui/handle/1/23103
DOI: 10.1186/s13059-020-02017-z
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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