ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data.
Fragile X syndrome
Friedreich ataxia
Genome-wide analysis
Huntington disease
Myotonic dystrophy type 1
Repeat expansions
Short tandem repeats
Whole-genome sequencing data
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
28 04 2020
28 04 2020
Historique:
received:
20
12
2019
accepted:
14
04
2020
entrez:
30
4
2020
pubmed:
30
4
2020
medline:
24
2
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 32345345
doi: 10.1186/s13059-020-02017-z
pii: 10.1186/s13059-020-02017-z
pmc: PMC7187524
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
102Subventions
Organisme : CIHR
Pays : Canada
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