ArticleNature communications2020
Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 118 citations in OpenAlex.
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- Topological stratification of continuous genetic variation in large biobanks.PLoS genetics · 2026Article
- Empowering genetic discoveries and cardiovascular risk assessment by predicting electrocardiograms from genotype.NPJ digital medicine · 2026Article
- SPC: a SPectral Component approach leveraging Identity-by-Descent graphs to address recent population structure in genomic analysis.medRxiv : the preprint server for health sciences · 2025Article
- The Role of Polygenic Risk Score in the General Population: Current Status and Future Prospects.Journal of atherosclerosis and thrombosis · 2025Review
- A genealogy-based approach for revealing ancestry-specific structures in admixed populations.American journal of human genetics · 2025Article
- Intricate interactions between fine-scale genetic structure, lifestyle, and dietary habits in the Japanese population.Communications biology · 2025Article
- Fine-scale population structure of JapaneseMicrobial genomics · 2025Article
- A variant in HMMR/HMMR-AS1 is associated with serum alanine aminotransferase levels in the Ryukyu population.Scientific reports · 2025Article
- East Asian Gene flow bridged by northern coastal populations over past 6000 years.Nature communications · 2025Article
- A genealogy-based approach for revealing ancestry-specific structures in admixed populations.bioRxiv : the preprint server for biology · 2025Article
- GenoTools: an open-source Python package for efficient genotype data quality control and analysis.G3 (Bethesda, Md.) · 2025Article
- Leveraging haplotype information in heritability estimation and polygenic prediction.Nature communications · 2025Article
- Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations.Nature communications · 2024Article
- The genome landscape of the Xinglong buffalo.BMC genomics · 2024Article
- Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins.Bioinformatics (Oxford, England) · 2024Article
- Ancestral genetic components are consistently associated with the complex trait landscape in European biobanks.European journal of human genetics : EJHG · 2024Article
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Corrections and comments
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Authors and funding
20 authors at 15 institutions in 9 countries.
Funding
Abstract
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 deconvoluted subpopulations are not always concordant with those in the observed phenotypes, suggesting that the PRS differences might reflect biases from the uncorrected structure, in a trait-dependent manner. This study suggests that such an uncorrected structure can be a potential pitfall in the clinical application of PRS.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.