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Genome Res. 2014 Nov;24(11):1894-904. doi: 10.1101/gr.177774.114. Epub 2014 Aug 18.

The landscape of human STR variation.

Author information

1
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; Computational and Systems Biology Program, MIT, Cambridge, Massachusetts 02139, USA;
2
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts 02139, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; Department of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA;
3
Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA;
4
Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia 24061, USA; Gene by Gene, Ltd., Houston, Texas 77008, USA.
5
Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA; yaniv@wi.mit.edu.

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.

PMID:
25135957
PMCID:
PMC4216929
DOI:
10.1101/gr.177774.114
[Indexed for MEDLINE]
Free PMC Article
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