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  The landscape of human STR variation

Willems, T., Gymrek, M., Highnam, G., The 1000 Genomes Project, C., Herwig, R., Lehrach, H., et al. (2014). The landscape of human STR variation. Genome Research, 24(11), 1894-1904. doi:10.1101/gr.177774.114.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-A8AA-E Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-A8AB-C
Genre: Journal Article

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 Creators:
Willems, Thomas, Author
Gymrek, Melissa, Author
Highnam, Gareth, Author
The 1000 Genomes Project, Consortium, Author
Herwig, Ralf1, 2, Author              
Lehrach, Hans2, 3, Author              
Sudbrak, Ralf2, 3, Author              
Timmermann, Bernd2, 4, Author              
Mittelman, David, Author
Erlich, Yaniv, Author
Affiliations:
1Bioinformatics (Ralf Herwig), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479648              
2The 1000 Genomes Project Consortium, ou_persistent22              
3Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
4Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              

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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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Language(s): eng - English
 Dates: 2014-08-182014-11
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1101/gr.177774.114
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Title: Genome Research
Source Genre: Journal
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Publ. Info: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 24 (11) Sequence Number: - Start / End Page: 1894 - 1904 Identifier: ISSN: 1088-9051
CoNE: https://pure.mpg.de/cone/journals/resource/954926997202