Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads
Satomi Mitsuhashi, Martin C Frith, Takeshi Mizuguchi, Satoko Miyatake, Tomoko Toyota, Hiroaki Adachi, Yoko Oma, Yoshihiro Kino, Hiroaki Mitsuhashi, Naomichi Matsumoto, Satomi Mitsuhashi, Martin C Frith, Takeshi Mizuguchi, Satoko Miyatake, Tomoko Toyota, Hiroaki Adachi, Yoko Oma, Yoshihiro Kino, Hiroaki Mitsuhashi, Naomichi Matsumoto
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.
Keywords: Long-read sequencing; Nanopore; PacBio; Repeat diseases; Tandem repeat.
Conflict of interest statement
Ethics approval and consent to participateThe Institutional Review Board of Yokohama City University of Medicine approved the experimental protocols (IRB approval number: A180800011). Written informed consent was obtained from the patient, in accordance with Japanese regulatory requirements. Experimental methods comply with the Helsinki Declaration.
Consent for publicationNot applicable.
Competing interestsThe authors declare that they have no competing interests.
Publisher’s NoteSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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