A single nucleotide polymorphism (SNP) assay for population stratification test between eastern Asians in association studies

Abstract

Population subdivision or recent admixture of populations can lead to spurious associations between the certain phenotypes and unlinked candidate loci in case-control and cohort studies of association. False positive associations due to population stratification can be controlled by genotyping a few dozen unlinked genetic markers. Lots of researches have reported SNP markers with high ethnic differentiation among African and European populations, but very few SNP panels can test stratification among Asians, especially in eastern Asians. Therefore, we developed the first SNP assay to test stratification between Chinese and Japanese populations living in East Asia. The ancestry informative SNP markers (AIMs) were selected from HapMap Affymetrix 500K data and evaluated on 113 unrelated subjects recruited from Xi’an City, located Northwest of China. This SNP based assay has proven very reliable, and made it possible to perform population stratification analyses with Sequenom MassARRAY SNP genotyping technology. The SNP assay showed excellent promise as a highly potential application to test population stratification in case-control studies of association in Eastern Asians.

Key words: Chinese, Japanese, population stratification, ancestry informative markers (AIMs).