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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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Titel: ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data
Autoren: 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
Weitere Verfasser: Neurogenetica, ZL Neuromusculaire Ziekten Medisch, Brain
Quelle: Genome Biol
Genome Biology, Vol 21, Iss 1, Pp 1-14 (2020)
Genome Biology
Publication Status: Preprint
Verlagsinformationen: Cold Spring Harbor Laboratory, 2019.
Publikationsjahr: 2019
Schlagwörter: 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
Beschreibung: 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
Publikationsart: Article
Other literature type
Dateibeschreibung: application/pdf
ISSN: 1474-760X
DOI: 10.1101/863035
DOI: 10.1186/s13059-020-02017-z
DOI: 10.14288/1.0390018
Zugangs-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
Dokumentencode: edsair.doi.dedup.....a1b9e7dd3234f362e4b51cf4a117f942
Datenbank: OpenAIRE
Beschreibung
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
ISSN:1474760X
DOI:10.1101/863035