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

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.

SUBMITTER: Mitsuhashi S

PROVIDER: S-EPMC6425644 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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

Mitsuhashi Satomi S Frith Martin C MC Mizuguchi Takeshi T Miyatake Satoko S Toyota Tomoko T Adachi Hiroaki H Oma Yoko Y Kino Yoshihiro Y Mitsuhashi Hiroaki H Matsumoto Naomichi N

Genome biology 20190319 1

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 th ...[more]

PMID: 30890163

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