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Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads.

Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads.

Authors :
Mitsuhashi S
Frith MC
Mizuguchi T
Miyatake S
Toyota T
Adachi H
Oma Y
Kino Y
Mitsuhashi H
Matsumoto N
Source :
Genome biology [Genome Biol] 2019 Mar 19; Vol. 20 (1), pp. 58. Date of Electronic Publication: 2019 Mar 19.
Publication Year :
2019

Abstract

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.

Details

Language :
English
ISSN :
1474-760X
Volume :
20
Issue :
1
Database :
MEDLINE
Journal :
Genome biology
Publication Type :
Academic Journal
Accession number :
30890163
Full Text :
https://doi.org/10.1186/s13059-019-1667-6