The landscape of human STR variation
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Abstract
Short tandem repeats are among the most polymorphic loci in the human genome. These loci play a role in the etiology of a range of genetic diseases and have been frequently utilized in forensics, population genetics, and genetic genealogy. Despite this plethora of applications, little is known about the variation of most STRs in the human population. Here, we report the largest-scale analysis of human STR variation to date. We collected information for nearly 700,000 STR loci across more than 1000 individuals in Phase 1 of the 1000 Genomes Project. Extensive quality controls show that reliable allelic spectra can be obtained for close to 90% of the STR loci in the genome. We utilize this call set to analyze determinants of STR variation, assess the human reference genome’s representation of STR alleles, find STR loci with common loss-of-function alleles, and obtain initial estimates of the linkage disequilibrium between STRs and common SNPs. Overall, these analyses further elucidate the scale of genetic variation beyond classical point mutations.
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Tandem repeat regions were enriched in known polymorphic simple sequence repeat regions (OR=6.24; p<2.2×10−16).
“they were prevalent in known polymorphic simple sequence repeat regions previously detected by Tandem Repeats Finder35 in 1,031,708 locations in the human reference genome (odds ratio (OR)=6.24; p<2.2×10−16)36.”
From Genome-wide detection of tandem DNA repeats that are expanded in autism (2020) · cites this paper as [36]
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- Authors
- Willems, T., Gymrek, M., Highnam, G., The 1000 Genomes Project Consortium, Mittelman, D., & Erlich, Y.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- Broad Institute (US)
- Virginia Tech (US)
- Corresponding author
- Erlich, Yaniv
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2014-08-18
- Volume
- 24
- Issue
- 11
- Pages
- 1894-1904
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC4216929
- OpenAlex
- W2124561138
- Cited by
- 283
- References
- 74
- Citations by year
- 2026: 21 · 2025: 24 · 2024: 30 · 2023: 25 · 2022: 21 · 2021: 27 · 2020: 17 · 2019: 27 · 2018: 32 · 2017: 23 · 2016: 15 · 2015: 14 · 2014: 7
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- HighWire Press Open Archive (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Funders
- Burroughs Wellcome Fund
- National Defense Science and Engineering Graduate
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- microsatellite markers, human genetic variation, 1000 Genomes Project, loss-of-function alleles, linkage disequilibrium, population genetics
- MeSH terms
- Alleles, Gene Frequency, Genetics, Population, Genotype, Humans, Genetic Variation, Linkage Disequilibrium, Genome, Human, Microsatellite Repeats, Polymorphism, Single Nucleotide, Genomics
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