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

Tian C, Kosoy R, Lee A, Ransom M, Belmont JW, Gregersen PK, Seldin MF - PLoS ONE (2008)

Bottom Line: Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease.For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations.PCA showed substructure both between different East Asian groups and within the Han Chinese population.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Rowe Program in Human Genetics, University of California Davis, Davis, California, United States of America.

ABSTRACT
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 <0.0025 with CHB). For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations. PCA showed substructure both between different East Asian groups and within the Han Chinese population. These studies have also identified a subset of East Asian substructure ancestry informative markers (EASTASAIMS) that may be useful for future complex genetic disease association studies in reducing type 1 errors and in identifying homogeneous groups that may increase the power of such studies.

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Related in: MedlinePlus

PCA analyses of Han Chinese and Chinese American population groups.A, Results from PCA performed together with EAS populations. B, PCA performed using only Chinese and Chinese American participants. The color coded population groups included the HapMap Han Chinese from Beijing (CHB), HGDP Han Chinese (HAN), HGDP North Han Chinese (HAN_N), Chinese American North (CHAN), Chinese American South (CHAS), Chinese American Central (CHAC), Taiwan Chinese American (TWN), Korean (KOR), and Hezhen (HEZ).
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pone-0003862-g004: PCA analyses of Han Chinese and Chinese American population groups.A, Results from PCA performed together with EAS populations. B, PCA performed using only Chinese and Chinese American participants. The color coded population groups included the HapMap Han Chinese from Beijing (CHB), HGDP Han Chinese (HAN), HGDP North Han Chinese (HAN_N), Chinese American North (CHAN), Chinese American South (CHAS), Chinese American Central (CHAC), Taiwan Chinese American (TWN), Korean (KOR), and Hezhen (HEZ).

Mentions: Similar analyses were also performed using population sets restricted to the more closely related Han Chinese, Japanese, and Korean groups, as well as a group restricted to Han Chinese and Chinese Americans (Table 2). These results as expected indicated substantially less substructure. However, even the subject set limited to Han Chinese and Chinese Americans showed substructure in PC1 using the split half reliability test and with the self identified groupings (ANOVA result). The relationship among the Han Chinese can be demonstrated in PCAs performed either including or excluding other EAS populations (Figure 4). Although there is variability in the distribution of many of the self-identified groups there was a general northwest/southeast gradient within these Chinese participants. In PC1 the North Han Chinese (HGDP from north central China[12]) were most separated from the southern Chinese participants including the Chinese American participants from Taiwan or with self-reported southern China origin.


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

Tian C, Kosoy R, Lee A, Ransom M, Belmont JW, Gregersen PK, Seldin MF - PLoS ONE (2008)

PCA analyses of Han Chinese and Chinese American population groups.A, Results from PCA performed together with EAS populations. B, PCA performed using only Chinese and Chinese American participants. The color coded population groups included the HapMap Han Chinese from Beijing (CHB), HGDP Han Chinese (HAN), HGDP North Han Chinese (HAN_N), Chinese American North (CHAN), Chinese American South (CHAS), Chinese American Central (CHAC), Taiwan Chinese American (TWN), Korean (KOR), and Hezhen (HEZ).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2587696&req=5

pone-0003862-g004: PCA analyses of Han Chinese and Chinese American population groups.A, Results from PCA performed together with EAS populations. B, PCA performed using only Chinese and Chinese American participants. The color coded population groups included the HapMap Han Chinese from Beijing (CHB), HGDP Han Chinese (HAN), HGDP North Han Chinese (HAN_N), Chinese American North (CHAN), Chinese American South (CHAS), Chinese American Central (CHAC), Taiwan Chinese American (TWN), Korean (KOR), and Hezhen (HEZ).
Mentions: Similar analyses were also performed using population sets restricted to the more closely related Han Chinese, Japanese, and Korean groups, as well as a group restricted to Han Chinese and Chinese Americans (Table 2). These results as expected indicated substantially less substructure. However, even the subject set limited to Han Chinese and Chinese Americans showed substructure in PC1 using the split half reliability test and with the self identified groupings (ANOVA result). The relationship among the Han Chinese can be demonstrated in PCAs performed either including or excluding other EAS populations (Figure 4). Although there is variability in the distribution of many of the self-identified groups there was a general northwest/southeast gradient within these Chinese participants. In PC1 the North Han Chinese (HGDP from north central China[12]) were most separated from the southern Chinese participants including the Chinese American participants from Taiwan or with self-reported southern China origin.

Bottom Line: Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease.For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations.PCA showed substructure both between different East Asian groups and within the Han Chinese population.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Rowe Program in Human Genetics, University of California Davis, Davis, California, United States of America.

ABSTRACT
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 <0.0025 with CHB). For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations. PCA showed substructure both between different East Asian groups and within the Han Chinese population. These studies have also identified a subset of East Asian substructure ancestry informative markers (EASTASAIMS) that may be useful for future complex genetic disease association studies in reducing type 1 errors and in identifying homogeneous groups that may increase the power of such studies.

Show MeSH
Related in: MedlinePlus