The landscape of human STR variation
Name
Willems-2014-The landscape of hum.pdf
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4.1 MB
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Author(s)
Willems, Thomas Frederick
Gymrek, Melissa A.
Highnam, Gareth
1000 Genomes Project Consortium
Mittelman, David
Erlich, Yaniv
Date Issued
August 2014
Journal
Genome Research
Publisher
Cold Spring Harbor Laboratory Press
Citation
Willems, T., M. Gymrek, G. Highnam, D. Mittelman, and Y. Erlich. “The Landscape of Human STR Variation.” Genome Research (August 18, 2014).
Version
Final published version
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.
MIT Department
Harvard University--MIT Division of Health Sciences and Technology
Massachusetts Institute of Technology. Computational and Systems Biology Program
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1101/gr.177774.114
