Analysis of East Asia genetic substructure using genome-wide SNP arrays

• Published in: PloS one 2008-12, Vol.3 (12), p.e3862-e3862
• Main Authors: Tian, Chao, Kosoy, Roman, Lee, Annette, Ransom, Michael, Belmont, John W, Gregersen, Peter K, Seldin, Michael F
• Format: Article
• Language: English
• Subjects: Analysis; Asian Americans; Asian Continental Ancestry Group - genetics; Biochemistry; Continents; Differentiation; Far East - ethnology; Genetic analysis; Genetic Markers - genetics; Genetic Predisposition to Disease; Genetic research; Genetics; Genetics and Genomics/Complex Traits; Genetics and Genomics/Genetics of Disease; Genetics and Genomics/Population Genetics; Genetics, Population; Genome, Human; Genome-Wide Association Study; Genomes; Genomics; Genotype; Genotype & phenotype; Genotypes; Geographical distribution; Humans; Inflammatory bowel disease; Medical research; Medicine; Minority & ethnic groups; Mutation; Oligonucleotide Array Sequence Analysis; Polymorphism, Single Nucleotide; Population; Population differentiation; Population genetics; Population studies; Populations; Principal Component Analysis; Principal components analysis; Single-nucleotide polymorphism; Studies
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0003862

Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, 00651; CHB/Vietnamese, 0.0065) with larger separation with Filipino (CHB/Filipino, 0.014). Low levels of differentiation were also observed between Dai and Vietnamese (0.0045) and between Vietnamese and Cambodian (0.0062). Similarly, small Fst's were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan (Fst's