The landscape of human STR variation
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...
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| Format: | Article |
| Language: | en_US |
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Cold Spring Harbor Laboratory Press
2014
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| Online Access: | http://hdl.handle.net/1721.1/90965 https://orcid.org/0000-0002-2293-7991 https://orcid.org/0000-0002-6086-3903 |
| _version_ | 1826205534326358016 |
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| author | Willems, Thomas Frederick Gymrek, Melissa A. Highnam, Gareth 1000 Genomes Project Consortium Mittelman, David Erlich, Yaniv |
| author2 | Harvard University--MIT Division of Health Sciences and Technology |
| author_facet | Harvard University--MIT Division of Health Sciences and Technology Willems, Thomas Frederick Gymrek, Melissa A. Highnam, Gareth 1000 Genomes Project Consortium Mittelman, David Erlich, Yaniv |
| author_sort | Willems, Thomas Frederick |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T13:14:35Z |
| format | Article |
| id | mit-1721.1/90965 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T13:14:35Z |
| publishDate | 2014 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | mit-1721.1/909652022-09-28T12:52:01Z The landscape of human STR variation Willems, Thomas Frederick Gymrek, Melissa A. Highnam, Gareth 1000 Genomes Project Consortium Mittelman, David Erlich, Yaniv Harvard University--MIT Division of Health Sciences and Technology Massachusetts Institute of Technology. Computational and Systems Biology Program Willems, Thomas Frederick Gymrek, Melissa A. 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. American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowship 2014-10-17T16:44:12Z 2014-10-17T16:44:12Z 2014-08 Article http://purl.org/eprint/type/JournalArticle 1088-9051 http://hdl.handle.net/1721.1/90965 Willems, T., M. Gymrek, G. Highnam, D. Mittelman, and Y. Erlich. “The Landscape of Human STR Variation.” Genome Research (August 18, 2014). https://orcid.org/0000-0002-2293-7991 https://orcid.org/0000-0002-6086-3903 en_US http://dx.doi.org/10.1101/gr.177774.114 Genome Research Creative Commons Attribution http://creativecommons.org/licenses/by/4.0 application/pdf Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press |
| spellingShingle | Willems, Thomas Frederick Gymrek, Melissa A. Highnam, Gareth 1000 Genomes Project Consortium Mittelman, David Erlich, Yaniv The landscape of human STR variation |
| title | The landscape of human STR variation |
| title_full | The landscape of human STR variation |
| title_fullStr | The landscape of human STR variation |
| title_full_unstemmed | The landscape of human STR variation |
| title_short | The landscape of human STR variation |
| title_sort | landscape of human str variation |
| url | http://hdl.handle.net/1721.1/90965 https://orcid.org/0000-0002-2293-7991 https://orcid.org/0000-0002-6086-3903 |
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