Article
Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction.
Nature communications - 26 Mar 2020
Sakaue Saori, Hirata Jun, Kanai Masahiro, Suzuki Ken, Akiyama Masato, Lai Too Chun, Arayssi Thurayya, Hammoudeh Mohammed, Al Emadi Samar, Masri Basel K, Halabi Hussein, Badsha Humeira, Uthman Imad W, Saxena Richa, Padyukov Leonid, Hirata Makoto, Matsuda Koichi, Murakami Yoshinori, Kamatani Yoichiro, Okada Yukinori
Abstract excerpt
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...
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