biostudies-literatureSakaue STakeda Science FoundationEPAJapan Agency for Medical Research and DevelopmentMinistry of Education, Culture, Sports, Science and TechnologyQatar National Research Fund1569https://www.ebi.ac.uk/biostudies/studies/S-EPMC7099015biostudies-literatureUnknown11(1)The diversity in our genome is crucial to understanding the demographic history of worldwide populations. However, we have yet to know whether subtle genetic differences within a population can be disentangled, or whether they have an impact on complex traits. Here we apply dimensionality reduction methods (PCA, t-SNE, PCA-t-SNE, UMAP, and PCA-UMAP) to biobank-derived genomic data of a Japanese population (n = 169,719). Dimensionality reduction reveals fine-scale population structure, conspicuously differentiating adjacent insular subpopulations. We further enluciate the demographic landscape of these Japanese subpopulations using population genetics analyses. Finally, we perform phenome-wide polygenic risk score (PRS) analyses on 67 complex traits. Differences in PRS between the deconvoluNature communicationsDimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction.PMC709901515H05911, 19H0102119gm6010001h0004, 19ek0410041h0003, 19ek0109413h0001, 19km0405211h0001EP-C-17-0174-344-3-105Kamatani YHammoudeh MAl Emadi SMurakami YSakaue SSaxena RPadyukov LSuzuki KLai Too CUthman IWHirata MArayssi TOkada YKanai MAkiyama MMasri BKHalabi HBadsha HMatsuda KHirata JfalseDimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction.The diversity in our genome is crucial to understanding the demographic history of worldwide populations. However, we have yet to know whether subtle genetic differences within a population can be disentangled, or whether they have an impact on complex traits. Here we apply dimensionality reduction methods (PCA, t-SNE, PCA-t-SNE, UMAP, and PCA-UMAP) to biobank-derived genomic data of a Japanese population (n = 169,719). Dimensionality reduction reveals fine-scale population structure, conspicuously differentiating adjacent insular subpopulations. We further enluciate the demographic landscape of these Japanese subpopulations using population genetics analyses. Finally, we perform phenome-wide polygenic risk score (PRS) analyses on 67 complex traits. Differences in PRS between the deconvolu2020-01-01T00:00:00Z2020 Mar2026-06-04T02:17:19.586Z2020-05-22T14:43:26ZS-EPMC70990153221844010.1038/s41467-020-15194-z