Consistent Association of Type 2 Diabetes Risk Variants Found in Europeans in Diverse Racial and Ethnic Groups
Open accessAbstract
It has been recently hypothesized that many of the signals detected in genome-wide association studies (GWAS) to T2D and other diseases, despite being observed to common variants, might in fact result from causal mutations that are rare. One prediction of this hypothesis is that the allelic associations should be population-specific, as the causal mutations arose after the migrations that established different populations around the world. We selected 19 common variants found to be reproducibly associated to T2D risk in European populations and studied them in a large multiethnic case-control study (6,142 cases and 7,403 controls) among men and women from 5 racial/ethnic groups (European Americans, African Americans, Latinos, Japanese Americans, and Native Hawaiians). In analysis pooled across ethnic groups, the allelic associations were in the same direction as the original report for all 19 variants, and 14 of the 19 were significantly associated with risk. In summing the number of risk alleles for each individual, the per-allele associations were highly statistically significant (P<10(-4)) and similar in all populations (odds ratios 1.09-1.12) except in Japanese Americans the estimated effect per allele was larger than in the other populations (1.20; P(het) = 3.8×10(-4)). We did not observe ethnic differences in the distribution of risk that would explain the increased prevalence of type 2 diabetes in these groups as compared to European Americans. The consistency of allelic associations in diverse racial/ethnic groups is not predicted under the hypothesis of Goldstein regarding "synthetic associations" of rare mutations in T2D.
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LD differences drive differences in effect size estimates from GWAS across populations in proportion to LD between tagging and causal SNP pairs, even when causal effects are the same.
“These LD differences in turn drive differences in effect size estimates (i.e. predictors) from GWAS across populations in proportion to LD between tagging and causal SNP pairs, even when causal effects are the same35,37–40 (Supplementary Note).”
From Clinical use of current polygenic risk scores may exacerbate health disparities (2019) · cites this paper as [39]
The Discussion (page not provided) says weaker associations across racial and ethnic groups may be due to differences in linkage disequilibrium, and suggests lower LD between a marker and a biologically relevant allele for two loci. It does not establish that LD drives effect-size differences in proportion to LD between tagging and causal SNPs, or test that relationship while holding causal effects constant. (LLM, conf=0.86)
Experimental — accuracy not yet measuredLinkage disequilibrium differentiates marginal effect size estimates for polygenic traits across populations, even when causal variants are the same.
“2) linkage disequilibrium (LD) differentiates marginal effect size estimates for polygenic traits across populations, even when causal variants are the same;”
From Clinical use of current polygenic risk scores may exacerbate health disparities (2019) · cites this paper as [39]
The Discussion (page unavailable) says weaker associations across racial and ethnic groups may reflect differences in linkage disequilibrium, among other factors, and suggests lower linkage disequilibrium could explain two marker-SNP results. It does not establish that linkage disequilibrium causes differences in marginal effect estimates generally across polygenic traits; it also says the causal alleles at the studied type 2 diabetes loci have yet to be found. (LLM, conf=0.86)
Experimental — accuracy not yet measuredCommon variants are often consistent across populations, such as between Caucasians and Asians, despite differences in allele frequencies.
“common variants are often consistent across populations — such as between Caucasians and Asians — despite differences in allele frequencies65,66.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [65]
T2DM and breast cancer loci identified in European samples tend to replicate in samples of East Asian ancestry.
“For example, T2DM and breast cancer loci identified in European samples tend to replicate in samples of East Asian ancestry. 150,151”
From Genetic architectures of psychiatric disorders: the emerging picture and its implications (2012) · cites this paper as [151]
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- Authors
- Waters, K. M., Stram, D. O., Hassanein, M. T., Le Marchand, L., Wilkens, L. R., Maskarinec, G., Monroe, K. R., Kolonel, L. N., Altshuler, D., Henderson, B. E., & Haiman, C. A.
- Affiliations
- University of Southern California (US)
- USC Norris Comprehensive Cancer Center (US)
- University of Hawaiʻi at Mānoa (US)
- Broad Institute (US)
- Corresponding author
- Waters, Kevin M.
- Haiman, Christopher A.
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-08-26
- Volume
- 6
- Issue
- 8
- Pages
- e1001078
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC2928808
- OpenAlex
- W2145604455
- Cited by
- 191
- References
- 33
- Citations by year
- 2026: 6 · 2025: 2 · 2024: 7 · 2023: 9 · 2022: 8 · 2021: 8 · 2020: 3 · 2019: 10 · 2018: 7 · 2017: 10 · 2016: 16 · 2015: 7 · 2014: 23 · 2013: 18 · 2012: 33
- FWCI
- 13.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- National Human Genome Research Institute (U01HG004802)
- National Cancer Institute (CA63464, U01CA063464, R37CA054281, R01CA054281, R01CA063464, CA 54281)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- type 2 diabetes, genetic risk variants, common genetic variants, European Americans, African Americans, Hispanic Americans, Japanese Americans, Native Hawaiians, ethnic differences in diabetes risk
- MeSH terms
- Adult, Aged, Alleles, Diabetes Mellitus, Type 2, Ethnicity, Europe, Female, Humans, Male, Middle Aged, Genetic Variation, Case-Control Studies, Genetic Predisposition to Disease, Genome-Wide Association Study
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