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Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population
- Source :
- BMC Medical Genomics, Vol 14, Iss 1, Pp 1-12 (2021), BMC Medical Genomics
- Publication Year :
- 2019
- Publisher :
- Cold Spring Harbor Laboratory, 2019.
-
Abstract
- Background 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. Methods 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 . Length variation of known disease-associated repeats was compared to other repeat loci. Results 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. Conclusions 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.
- Subjects :
- lcsh:Internal medicine
lcsh:QH426-470
Population
Genome-wide association study
Computational biology
Biology
Genome
DNA sequencing
symbols.namesake
Tandem repeat
Genome-wide analysis
Genetics
lcsh:RC31-1245
education
Genetics (clinical)
Repeat unit
education.field_of_study
High-Throughput Nucleotide Sequencing
Tandem repeats
Sequence Analysis, DNA
Nanopore long read sequencing
Nanopore Sequencing
lcsh:Genetics
Triplet repeat disease
Mendelian inheritance
symbols
Human genome
Nanopore sequencing
Genome-Wide Association Study
Research Article
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- BMC Medical Genomics, Vol 14, Iss 1, Pp 1-12 (2021), BMC Medical Genomics
- Accession number :
- edsair.doi.dedup.....3616014e0c4a36c6704876d06b5e62d4
- Full Text :
- https://doi.org/10.1101/2019.12.19.883389