File:PCA of Chinese populations.png

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English: Principal component analysis (PCA) of the 10,588 participants in the ChinaMAP with the 1KGP and HapMap project as a reference to distinguish the ethnic and geographic ancestry of Chinese and other populations.
  • (b) PCA of the ChinaMAP and other populations in the 1KGP and HapMap project.
  • (c) PCA of East Asians in different geographical areas. d PCA of the Chinese Han population.
  • (e) PCA of the Chinese populations in 27 provinces and 7 geographical divisions.
PCA was performed using a subset of autosomal bi-allelic SNPs. Several restrictions were employed to select the final 1,409,151 SNPs for PCA analysis, including minor allele frequency (MAF) ≥ 1% (common and low-frequency variants), genotyping rate ≥ 90%, Hardy-Weinberg-Equilibrium (HWE) P > 0.000001, and removing one SNP from each pair with r2 ≥ 0.5 (in windows of 50 SNPs with steps of 5 SNPs). The PCA was performed with the final SNPs using PLINK68 (v1.9) and EIGENSOFT (v7.2.1). When compared to 1KGP and CHD population in HapMap, the overlapping 124,900 SNPs between the ChinaMAP, 1KGP and CHD in HapMap Project were used for PCA analysis. Restricting PCA of CHD in HapMap, EAS populations in 1KGP and ChinaMAP was based on the overlapping 124,900 SNPs.
Date Published: 30 April 2020
Source Cao, Y., Li, L., Xu, M. et al. The ChinaMAP analytics of deep whole genome sequences in 10,588 individuals. Cell Res 30, 717–731 (2020). https://doi.org/10.1038/s41422-020-0322-9
Author Yanan Cao, Lin Li, Min Xu, Zhimin Feng, Xiaohui Sun, Jieli Lu, Yu Xu, Peina Du, Tiange Wang, Ruying Hu, Zhen Ye, Lixin Shi, Xulei Tang, Li Yan, Zhengnan Gao, Gang Chen, Yinfei Zhang, Lulu Chen, Guang Ning, Yufang Bi, Weiqing Wang & The ChinaMAP Consortium
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current10:42, 29 December 2020Thumbnail for version as of 10:42, 29 December 20201,717 × 1,331 (832 KB)Was a bee (talk | contribs){{Information |Description={{en|1=Principal component analysis (PCA) of the 10,588 participants in the ChinaMAP with the 1KGP and HapMap project as a reference to distinguish the ethnic and geographic ancestry of Chinese and other populations. *(b) PCA of the ChinaMAP and other populations in the 1KGP and HapMap project. *(c) PCA of East Asians in different geographical areas. d PCA of the Chinese Han population. *(e) PCA of the Chinese populations in 27 provinces and 7 geographical divisions...

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