Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads.
Long-read sequencing
Nanopore
PacBio
Repeat diseases
Tandem repeat
Journal
Genome biology
ISSN: 1474-760X
Titre abrégé: Genome Biol
Pays: England
ID NLM: 100960660
Informations de publication
Date de publication:
19 03 2019
19 03 2019
Historique:
received:
14
08
2018
accepted:
01
03
2019
entrez:
21
3
2019
pubmed:
21
3
2019
medline:
17
8
2019
Statut:
epublish
Résumé
Tandemly repeated DNA is highly mutable and causes at least 31 diseases, but it is hard to detect pathogenic repeat expansions genome-wide. Here, we report robust detection of human repeat expansions from careful alignments of long but error-prone (PacBio and nanopore) reads to a reference genome. Our method is robust to systematic sequencing errors, inexact repeats with fuzzy boundaries, and low sequencing coverage. By comparing to healthy controls, we prioritize pathogenic expansions within the top 10 out of 700,000 tandem repeats in whole genome sequencing data. This may help to elucidate the many genetic diseases whose causes remain unknown.
Identifiants
pubmed: 30890163
doi: 10.1186/s13059-019-1667-6
pii: 10.1186/s13059-019-1667-6
pmc: PMC6425644
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Pagination
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