Abstract
BackgroundCase-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia.ResultsIn this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups.ConclusionThese data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.
Highlights
Case-control genetic studies of complex human diseases can be confounded by population stratification
Populations studied The individuals used in these studies include those from the Human Genome Diversity Panel (HGDP), HapMap, the New York Cancer Project (NYCP) [6] and samples collected in the United States (Houston, Sacramento), Guatemala, Peru, Sweden. and
The previous genotypes included those from 128 European Americans, 88 African Americans, 60 CEPH Europeans (CEU), 56 Yoruban sub-Saharan Africans (YRI), 19 Bini sub-Saharan Africans, 23 Kanuri West Africans, 50 Mayan Amerindians, 26 Quechuan Amerindians, 29 Nahua Amerindians, 40 Mexican Americans (MAM), 26 Mexicans from Mexico City, 28 Puerto Rican Americans, 43 Chinese (CHB), 43 Chinese Americans, 43 Japanese (JPT), 3 Japanese Americans, 8 Vietnamese Americans, 1 Korean American, 45 Filipino Americans, 2 unspecified East Asian Americans, and 64 South Asian Indian Americans
Summary
Case-control genetic studies of complex human diseases can be confounded by population stratification. Our group has demonstrated the application of a set of SNP AIMs for discerning continental population information[4] These studies using a total of 128 SNPs and subsets derived from this panel showed the ability of small sets of SNPs to separate a variety of self-identified subjects of European, Amerindian, East Asian, and sub-Saharan African ancestry. Using these SNPs we were able to provide admixture information for sub-Saharan African, European and Amerindian admixed populations, and perform structured association testing in the context of mixed or admixed population groups. These studies showed that a subset of 96 AIMs performed well in TaqMan® assays, enabling potential wide application of these SNPs
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