With development of high-throughput genotyping technologies, many genome-wide association studies on common diseases have been launched in Hong Kong. However, the population structure of Hong Kong population remains enigmatic. In GWAS, population stratification might cause problems of spurious associations. In this study, we report one of the first surveys of autosomal DNA diversity within the Hong Kong Chinese population. Principal component analysis results show that Hong Kong Chinese population is genetically closer to southern than northern Chinese populations. This pattern is consistent with geographic distribution and linguistic affiliation of Chinese population. There is also admixture of northern and southern Chinese genetic ancestries as indicated by stratification in the Hong Kong Chinese population, which is in accordance to known historical immigrations. At the SNP level, ancestry informative SNPs among Chinese populations, principal-component-correlated SNPs and SNPs showing significance in simulated case-control studies were identified. These variations characterize Hong Kong Chinese population which might have been affected by immigration, gene flow or natural selection. Thus, disease association results located on or near these loci are often not replicable in the second phase of GWAS, which may call for stratification adjustment using methods which have been evaluated and being implemented in practice. Our findings provide insights for designing GWAS, filtering out confounding results and correcting stratification in Hong Kong Chinese population.
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