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Self-reported ethnicity, genetic structure and the impact of population stratification in a multiethnic study.

ABSTRACT: It is well-known that population substructure may lead to confounding in case-control association studies. Here, we examined genetic structure in a large racially and ethnically diverse sample consisting of five ethnic groups of the Multiethnic Cohort study (African Americans, Japanese Americans, Latinos, European Americans and Native Hawaiians) using 2,509 SNPs distributed across the genome. Principal component analysis on 6,213 study participants, 18 Native Americans and 11 HapMap III populations revealed four important principal components (PCs): the first two separated Asians, Europeans and Africans, and the third and fourth corresponded to Native American and Native Hawaiian (Polynesian) ancestry, respectively. Individual ethnic composition derived from self-reported parental information matched well to genetic ancestry for Japanese and European Americans. STRUCTURE-estimated individual ancestral proportions for African Americans and Latinos are consistent with previous reports. We quantified the East Asian (mean 27%), European (mean 27%) and Polynesian (mean 46%) ancestral proportions for the first time, to our knowledge, for Native Hawaiians. Simulations based on realistic settings of case-control studies nested in the Multiethnic Cohort found that the effect of population stratification was modest and readily corrected by adjusting for race/ethnicity or by adjusting for top PCs derived from all SNPs or from ancestry informative markers; the power of these approaches was similar when averaged across causal variants simulated based on allele frequencies of the 2,509 genotyped markers. The bias may be large in case-only analysis of gene by gene interactions but it can be corrected by top PCs derived from all SNPs.

SUBMITTER: Wang H

PROVIDER: S-EPMC3057055 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature

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Self-reported ethnicity, genetic structure and the impact of population stratification in a multiethnic study.

Wang Hansong H Haiman Christopher A CA Kolonel Laurence N LN Henderson Brian E BE Wilkens Lynne R LR Le Marchand Loïc L Stram Daniel O DO

Human genetics 20100525 2

It is well-known that population substructure may lead to confounding in case-control association studies. Here, we examined genetic structure in a large racially and ethnically diverse sample consisting of five ethnic groups of the Multiethnic Cohort study (African Americans, Japanese Americans, Latinos, European Americans and Native Hawaiians) using 2,509 SNPs distributed across the genome. Principal component analysis on 6,213 study participants, 18 Native Americans and 11 HapMap III populati ...[more]

PMID: 20499252

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Project description:There is a growing recognition of the health benefits of the natural environment. Whilst domestic gardens account for a significant proportion of greenspace in urban areas, few studies, and no population level studies, have investigated their potential health benefits. With gardens offering immediate interaction with nature on our doorsteps, we hypothesise that garden size will affect general health-with smaller domestic gardens associated with poorer health.A small area ecological design was undertaken using two separate analyses based on data from the 2001 and 2011 UK census. The urban population of England was classified into 'quintiles' based on deprivation (Index of Multiple Deprivation) and average garden size (Generalised Land Use Database). Self-reported general health was obtained from the UK population census. We controlled for greenspace exposure, population density, air pollution, house prices, smoking, and geographic location. Models were stratified to explore the associations.Smaller domestic gardens were associated with a higher prevalence of self-reported poor health. The adjusted prevalence ratio of poor self-reported general health for the quintile with smallest average garden size was 1.13 (95% CI 1.12-1.14) relative to the quintile with the largest gardens. Additionally, the analysis suggested that income-related inequalities in health were greater in areas with smaller gardens. The adjusted prevalence ratio for poor self-reported general health for the most income deprived quintile compared against the least deprived was 1.72 (95% CI 1.64-1.79) in the areas with the smallest gardens, compared to 1.31 (95% CI 1.21-1.42) in areas with the largest gardens.Residents of areas with small domestic gardens have the highest levels of poor health/health inequality related to income deprivation. Although causality needs to be confirmed, the implications for new housing are that adequate garden sizes may be an important means of reducing socioeconomic health inequalities. These findings suggest that the trend for continued urban densification and new housing with minimal gardens could have adverse impacts on health.

Dataset Information

Self-reported ethnicity, genetic structure and the impact of population stratification in a multiethnic study.

Publications

Self-reported ethnicity, genetic structure and the impact of population stratification in a multiethnic study.

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