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Comparing strategie...
Comparing strategies to fine-map the association of common SNPs at chromosome 9p21 with type 2 diabetes and myocardial infarction
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Shea, Jessica (author)
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Agarwala, Vineeta (author)
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Philippakis, Anthony A. (author)
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Maguire, Jared (author)
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Banks, Eric (author)
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DePristo, Mark (author)
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Thomson, Brian (author)
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Guiducci, Candace (author)
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Onofrio, Robert C. (author)
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Kathiresan, Sekar (author)
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Gabriel, Stacey (author)
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Burtt, Noel P. (author)
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Daly, Mark J. (author)
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- Groop, Leif (author)
- Lund University,Lunds universitet,Genomik, diabetes och endokrinologi,Forskargrupper vid Lunds universitet,Genomics, Diabetes and Endocrinology,Lund University Research Groups
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Altshuler, David (author)
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(creator_code:org_t)
- 2011-07-24
- 2011
- English.
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 43:8, s. 114-801
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Abstract
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- Noncoding variants at human chromosome 9p21 near CDKN2A and CDKN2B are associated with type 2 diabetes(1-4), myocardial infarction(5-7), aneurysm(8), vertical cup disc ratio(9) and at least five cancers(10-16). Here we compare approaches to more comprehensively assess genetic variation in the region. We carried out targeted sequencing at high coverage in 47 individuals and compared the results to pilot data from the 1000 Genomes Project. We imputed variants into type 2 diabetes and myocardial infarction cohorts directly from targeted sequencing, from a genotyped reference panel derived from sequencing and from 1000 Genomes Project low-coverage data. Polymorphisms with frequency >5% were captured well by all strategies. Imputation of intermediate-frequency polymorphisms required a higher density of tag SNPs in disease samples than is available on first-generation genome-wide association study (GWAS) arrays. Our association analyses identified more comprehensive sets of variants showing equivalent statistical association with type 2 diabetes or myocardial infarction, but did not identify stronger associations than the original GWAS signals.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Endokrinologi och diabetes (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Endocrinology and Diabetes (hsv//eng)
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- art (subject category)
- ref (subject category)
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- By the author/editor
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Shea, Jessica
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Agarwala, Vineet ...
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Philippakis, Ant ...
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Maguire, Jared
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Banks, Eric
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DePristo, Mark
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show more...
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Thomson, Brian
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Guiducci, Candac ...
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Onofrio, Robert ...
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Kathiresan, Seka ...
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Gabriel, Stacey
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Burtt, Noel P.
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Daly, Mark J.
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Groop, Leif
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Altshuler, David
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show less...
- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Endocrinology an ...
- Articles in the publication
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Nature Genetics
- By the university
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Lund University