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Your search keyword '"Whole-genome sequencing data"' showing total 3 results
Start Over Descriptor "Whole-genome sequencing data" Journal genome biology
3 results on '"Whole-genome sequencing data"'

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

Author

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 M. Gross, Bryan R. Lajoie, Ryan J. Taft, Wyeth W. Wasserman, Stephen W. Scherer, Jan H. Veldink, David R. Bentley, Ryan K. C. Yuen, Melanie Bahlo, and Michael A. Eberle

Subjects
Repeat expansions, Short tandem repeats, Whole-genome sequencing data, Genome-wide analysis, Friedreich ataxia, Myotonic dystrophy type 1, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

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.

Published
2020
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2. ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data

Author

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, and Eberle, Michael A.

Published
2020
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3. ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data

Author

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, and Brett Trost

Subjects
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
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

Published
2020
Full Text
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