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

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Bibliographic Details
Title:	ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data
Authors:	Stephen W. Scherer, Sai Chen, Ryan K. C. Yuen, David R. Bentley, Ryan J. Taft, Wyeth W. Wasserman, Bryan R. Lajoie, Egor Dolzhenko, Brett Trost, Jan H. Veldink, Vladimir G. Gainullin, Phillip A. Richmond, Michael A. Eberle, Giuseppe Narzisi, Melanie Bahlo, Charlotte Nguyen, Joke J.F.A. van Vugt, Andrew M. Gross, Mark F. Bennett
Contributors:	Neurogenetica, ZL Neuromusculaire Ziekten Medisch, Brain
Source:	Genome Biol Genome Biology, Vol 21, Iss 1, Pp 1-14 (2020) Genome Biology
Publication Status:	Preprint
Publisher Information:	Cold Spring Harbor Laboratory, 2019.
Publication Year:	2019
Subject Terms:	QH301-705.5, Method, QH426-470, Genome-wide analysis, Journal Article, Repeat expansions, Genetics, Humans, Myotonic Dystrophy, Biology (General), Huntington Disease/genetics, Ecology, Evolution, Behavior and Systematics, DNA Repeat Expansion, Whole Genome Sequencing, Myotonic dystrophy type 1, Research Support, Non-U.S. Gov't, High-Throughput Nucleotide Sequencing, Cell Biology, Huntington disease, Friedreich Ataxia/genetics, 3. Good health, Myotonic Dystrophy/genetics, Fragile X Syndrome/genetics, Huntington Disease, Short tandem repeats, Friedreich ataxia, Friedreich Ataxia, Case-Control Studies, Fragile X Syndrome, Whole-genome sequencing data, Software, Fragile X syndrome, Microsatellite Repeats
Description:	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
Document Type:	Article Other literature type
File Description:	application/pdf
ISSN:	1474-760X
DOI:	10.1101/863035
DOI:	10.1186/s13059-020-02017-z
DOI:	10.14288/1.0390018
Access URL:	https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-02017-z https://pubmed.ncbi.nlm.nih.gov/32345345 https://doaj.org/article/e6a0e5f3dd2f430489a30306e1ab55af https://www.biorxiv.org/content/biorxiv/early/2019/12/03/863035.full.pdf https://www.biorxiv.org/content/10.1101/863035v1.article-metrics https://www.biorxiv.org/content/10.1101/863035v1 https://minerva-access.unimelb.edu.au/bitstream/handle/11343/246361/PMC7187524.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187524 https://minerva-access.unimelb.edu.au/handle/11343/246361 https://open.library.ubc.ca/cIRcle/collections/52383/items/1.0390018 https://link.springer.com/article/10.1186/s13059-020-02017-z; https://ahro.austin.org.au/austinjspui/handle/1/23103 https://dspace.library.uu.nl/handle/1874/439831
Rights:	CC BY
Accession Number:	edsair.doi.dedup.....a1b9e7dd3234f362e4b51cf4a117f942
Database:	OpenAIRE

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