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ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data

View ORCID ProfileEgor Dolzhenko, View ORCID ProfileMark F. Bennett, Phillip A. Richmond, View ORCID ProfileBrett Trost, Sai Chen, Joke J.F.A. van Vugt, Charlotte Nguyen, Giuseppe Narzisi, Vladimir G. Gainullin, Andrew Gross, Bryan Lajoie, Ryan J. Taft, Wyeth W. Wasserman, Stephen W. Scherer, View ORCID ProfileJan H. Veldink, David R. Bentley, R K.C. Yuen, View ORCID ProfileMelanie Bahlo, View ORCID ProfileMichael A. Eberle
doi: https://doi.org/10.1101/863035
Egor Dolzhenko
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Mark F. Bennett
2Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia
3Department of Medical Biology, The University of Melbourne, 1G Royal Parade, Parkville VIC 3052, Australia
4Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, 245 Burgundy Street, Heidelberg VIC 3084, Australia
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Phillip A. Richmond
5Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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Brett Trost
6Genetics and Genome Biology, The Hospital for Sick Children, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
7The Center for Applied Genomics, The Hospital for Sick Children, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
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Sai Chen
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Joke J.F.A. van Vugt
8Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
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Charlotte Nguyen
6Genetics and Genome Biology, The Hospital for Sick Children, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
7The Center for Applied Genomics, The Hospital for Sick Children, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
9Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 2E5, Canada
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Giuseppe Narzisi
10New York Genome Center, 101 Avenue of the Americas, New York 10013, USA
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Vladimir G. Gainullin
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Andrew Gross
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Bryan Lajoie
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Ryan J. Taft
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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Wyeth W. Wasserman
5Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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Stephen W. Scherer
6Genetics and Genome Biology, The Hospital for Sick Children, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
7The Center for Applied Genomics, The Hospital for Sick Children, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
9Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 2E5, Canada
11The McLaughlin Centre, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
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Jan H. Veldink
8Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
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David R. Bentley
12Illumina Cambridge Ltd, Illumina Centre, 19 Granta Park, Great Abington, Cambridge CB21 6DF, UK
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R K.C. Yuen
6Genetics and Genome Biology, The Hospital for Sick Children, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
7The Center for Applied Genomics, The Hospital for Sick Children, University of Toronto, 686 Bay Street, Toronto, ON M5G 0A4, Canada
9Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 2E5, Canada
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Melanie Bahlo
2Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia
3Department of Medical Biology, The University of Melbourne, 1G Royal Parade, Parkville VIC 3052, Australia
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Michael A. Eberle
1Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
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  • ORCID record for Michael A. Eberle
  • For correspondence: meberle@illumina.com
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Abstract

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

Footnotes

  • https://github.com/Illumina/ExpansionHunterDenovo

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 13, 2019.
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ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data
Egor Dolzhenko, Mark F. Bennett, Phillip A. Richmond, Brett Trost, Sai Chen, Joke J.F.A. van Vugt, Charlotte Nguyen, Giuseppe Narzisi, Vladimir G. Gainullin, Andrew Gross, Bryan Lajoie, Ryan J. Taft, Wyeth W. Wasserman, Stephen W. Scherer, Jan H. Veldink, David R. Bentley, R K.C. Yuen, Melanie Bahlo, Michael A. Eberle
bioRxiv 863035; doi: https://doi.org/10.1101/863035
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ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data
Egor Dolzhenko, Mark F. Bennett, Phillip A. Richmond, Brett Trost, Sai Chen, Joke J.F.A. van Vugt, Charlotte Nguyen, Giuseppe Narzisi, Vladimir G. Gainullin, Andrew Gross, Bryan Lajoie, Ryan J. Taft, Wyeth W. Wasserman, Stephen W. Scherer, Jan H. Veldink, David R. Bentley, R K.C. Yuen, Melanie Bahlo, Michael A. Eberle
bioRxiv 863035; doi: https://doi.org/10.1101/863035

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