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

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. O...

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Detalles Bibliográficos
Autores principales: Mitsuhashi, Satomi, Frith, Martin C., Mizuguchi, Takeshi, Miyatake, Satoko, Toyota, Tomoko, Adachi, Hiroaki, Oma, Yoko, Kino, Yoshihiro, Mitsuhashi, Hiroaki, Matsumoto, Naomichi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425644/
https://www.ncbi.nlm.nih.gov/pubmed/30890163
http://dx.doi.org/10.1186/s13059-019-1667-6
Descripción
Sumario: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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1667-6) contains supplementary material, which is available to authorized users.

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