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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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Název: ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data
Autoři: 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
Přispěvatelé: Neurogenetica, ZL Neuromusculaire Ziekten Medisch, Brain
Zdroj: Genome Biol
Genome Biology, Vol 21, Iss 1, Pp 1-14 (2020)
Genome Biology
Publication Status: Preprint
Informace o vydavateli: Cold Spring Harbor Laboratory, 2019.
Rok vydání: 2019
Témata: 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
Popis: 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
Druh dokumentu: Article
Other literature type
Popis souboru: application/pdf
ISSN: 1474-760X
DOI: 10.1101/863035
DOI: 10.1186/s13059-020-02017-z
DOI: 10.14288/1.0390018
Přístupová URL adresa: 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
Přístupové číslo: edsair.doi.dedup.....a1b9e7dd3234f362e4b51cf4a117f942
Databáze: OpenAIRE
Popis
Abstrakt: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