Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population

• Published in: BMC medical genomics Vol. 14; no. 1; pp. 17 - 12
• Main Authors: Mitsuhashi, Satomi, Frith, Martin C, Matsumoto, Naomichi
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 07.01.2021; BioMed Central; BMC
• Subjects: 5' Untranslated Regions; Amyotrophic lateral sclerosis; Copy number; Datasets; Disease; DNA sequencing; Genetic polymorphisms; Genetic Predisposition to Disease; Genetic research; Genome, Human; Genome-wide analysis; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genotypes; Health aspects; Humans; Medical genetics; Nanopore long read sequencing; Nanopore Sequencing; Nucleotide sequence; Nucleotide sequencing; Polyglutamine; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Proteins; Single-nucleotide polymorphism; Tandem Repeat Sequences - genetics; Tandem repeats; Trinucleotide repeats; Triplet repeat disease; Japan; Tandem repeats; Triplet repeat disease; Nanopore long read sequencing; Genome-wide analysis
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/s12920-020-00853-3

Tandem repeats are highly mutable and contribute to the development of human disease by a variety of mechanisms. It is difficult to predict which tandem repeats may cause a disease. One hypothesis is that changeable tandem repeats are the source of genetic diseases, because disease-causing repeats are polymorphic in healthy individuals. However, it is not clear whether disease-causing repeats are more polymorphic than other repeats. We performed a genome-wide survey of the millions of human tandem repeats using publicly available long read genome sequencing data from 21 humans. We measured tandem repeat copy number changes using tandem-genotypes. Length variation of known disease-associated repeats was compared to other repeat loci. We found that known Mendelian disease-causing or disease-associated repeats, especially CAG and 5'UTR GGC repeats, are relatively long and polymorphic in the general population. We also show that repeat lengths of two disease-causing tandem repeats, in ATXN3 and GLS, are correlated with near-by GWAS SNP genotypes. We provide a catalog of polymorphic tandem repeats across a variety of repeat unit lengths and sequences, from long read sequencing data. This method especially if used in genome wide association study, may indicate possible new candidates of pathogenic or biologically important tandem repeats in human genomes.