Post by Admin on Nov 25, 2024 18:14:03 GMT
Results
Inference for the tripartite ancestral structure in Biobank Japan dataset
To assess the fit of the tripartite model in contemporary populations, we used BBJ GWAS data, comprising participants from hospitals across seven geographic regions in Japan28,29 (Fig. 1a and Supplementary Data 1). The total number of participants is 171,287, with regional distribution from northeast to southwest throughout the archipelago as follows: Hokkaido = 7955, Tohoku = 11,013, Kanto-Koshinetsu = 94,981, Chubu-Hokuriku = 9489, Kinki = 25,200, Kyushu = 15,962, and Okinawa = 5804. Our PCA defines distinct clusters (Fig. 1b), with a separation of the Ryukyu cluster, primarily including individuals from Okinawa, from the rest of the populations as reported in previous studies17,18. There are also regional clusters observable from Tohoku, Kanto-Koshinetsu, Kinki, and Kyushu respectively. Based on the PCA results, we define five distinct genetic clusters in the Japanese populations: EastAsian_admix (EA_admix; n = 1019), Mainland (n = 159,642), Ryukyu_admix (n = 640), Ryukyu (n = 9847), and Hokkaido_sub (n = 139) (Fig. 1c). Population stratification is further evident even within the Ryukyu Islands, reflecting their geographic affinities in this local insular context (Fig. 1d, e, Yakushima; n = 431, Amami; n = 1531, Kikai; n = 561, Okinoerabu; n = 845, Tokunoshima; n = 476, Yoron; n = 167, Okinawa; n = 4795, Miyako; n = 827).
Fig. 1: Population structure of Biobank Japan.
a Seven geographic regions, each represented by a different color, indicate the locations where participants were registered at local hospitals. b A scatter plot of PCA for BBJ participants with 1KG EAS samples. The colors of the BBJ participants correspond to those used in (a). c Clustering results of BBJ participants based on PCA. d Geographic locations of the Ryukyu Islands. e Scatter plots of PCA for BBJ participants from the Ryukyu Islands. The individuals are colored differently according to the locations of their registered hospitals. In (a, d) the map of Japan is drawn using the R package “jpndistrict” (https://github.com/uribo/jpndistrict). PC Principal component, 1KG 1000 Genomes Project, JPT Japanese in Tokyo, CDX Chinese Dai in Xishuangbanna, CHB Han Chinese in Beijing, CHS Han Chinese South, KHV Kinh in Ho Chi Minh City, NEA Northeast Asian, EA East Asian.
Inference for the tripartite ancestral structure in Biobank Japan dataset
To assess the fit of the tripartite model in contemporary populations, we used BBJ GWAS data, comprising participants from hospitals across seven geographic regions in Japan28,29 (Fig. 1a and Supplementary Data 1). The total number of participants is 171,287, with regional distribution from northeast to southwest throughout the archipelago as follows: Hokkaido = 7955, Tohoku = 11,013, Kanto-Koshinetsu = 94,981, Chubu-Hokuriku = 9489, Kinki = 25,200, Kyushu = 15,962, and Okinawa = 5804. Our PCA defines distinct clusters (Fig. 1b), with a separation of the Ryukyu cluster, primarily including individuals from Okinawa, from the rest of the populations as reported in previous studies17,18. There are also regional clusters observable from Tohoku, Kanto-Koshinetsu, Kinki, and Kyushu respectively. Based on the PCA results, we define five distinct genetic clusters in the Japanese populations: EastAsian_admix (EA_admix; n = 1019), Mainland (n = 159,642), Ryukyu_admix (n = 640), Ryukyu (n = 9847), and Hokkaido_sub (n = 139) (Fig. 1c). Population stratification is further evident even within the Ryukyu Islands, reflecting their geographic affinities in this local insular context (Fig. 1d, e, Yakushima; n = 431, Amami; n = 1531, Kikai; n = 561, Okinoerabu; n = 845, Tokunoshima; n = 476, Yoron; n = 167, Okinawa; n = 4795, Miyako; n = 827).
Fig. 1: Population structure of Biobank Japan.
a Seven geographic regions, each represented by a different color, indicate the locations where participants were registered at local hospitals. b A scatter plot of PCA for BBJ participants with 1KG EAS samples. The colors of the BBJ participants correspond to those used in (a). c Clustering results of BBJ participants based on PCA. d Geographic locations of the Ryukyu Islands. e Scatter plots of PCA for BBJ participants from the Ryukyu Islands. The individuals are colored differently according to the locations of their registered hospitals. In (a, d) the map of Japan is drawn using the R package “jpndistrict” (https://github.com/uribo/jpndistrict). PC Principal component, 1KG 1000 Genomes Project, JPT Japanese in Tokyo, CDX Chinese Dai in Xishuangbanna, CHB Han Chinese in Beijing, CHS Han Chinese South, KHV Kinh in Ho Chi Minh City, NEA Northeast Asian, EA East Asian.