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The Landscape of Human STR Variation

Thomas Willems, Melissa Gymrek, Gareth Highnam, The 1000 Genomes Project, David Mittelman, Yaniv Erlich
doi: https://doi.org/10.1101/004671
Thomas Willems
1Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
2Computational and Systems Biology Program, MIT, Cambridge, MA 02139, USA
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Melissa Gymrek
1Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
3Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, MA 02139, USA
4Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
5Department of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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Gareth Highnam
6Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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7Membership of The 1000 Genomes Project can be found in the acknowledgments or at
David Mittelman
6Virginia Bioinformatics Institute and Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
8Gene by Gene, Ltd., Houston, Texas
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Yaniv Erlich
1Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142
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  • For correspondence: yaniv@wi.mit.edu
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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 over 1,000 individuals in phase 1 of the 1000 Genomes Project. This process nearly saturated common STR variations. After employing a series of quality controls, 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. The resource is publicly available at http://strcat.teamerlich.org/ both in raw format and via a graphical interface.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 01, 2014.
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The Landscape of Human STR Variation
Thomas Willems, Melissa Gymrek, Gareth Highnam, The 1000 Genomes Project, David Mittelman, Yaniv Erlich
bioRxiv 004671; doi: https://doi.org/10.1101/004671
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The Landscape of Human STR Variation
Thomas Willems, Melissa Gymrek, Gareth Highnam, The 1000 Genomes Project, David Mittelman, Yaniv Erlich
bioRxiv 004671; doi: https://doi.org/10.1101/004671

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