@article {329964,
	title = {Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing},
	journal = {Science Advances},
	volume = {10},
	year = {2024},
	note = {<p>doi: 10.1126/sciadv.adi8419</p>
},
	pages = {eadi8419},
	abstract = {<p>We generated Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), a high-depth whole-genome sequencing dataset comprising 3256 individuals from across Japan. Analysis of JEWEL revealed genetic characteristics of the Japanese population that were not discernible using microarray data. First, rare variant?based analysis revealed an unprecedented fine-scale genetic structure. Together with population genetics analysis, the present-day Japanese can be decomposed into three ancestral components. Second, we identified unreported loss-of-function (LoF) variants and observed that for specific genes, LoF variants appeared to be restricted to a more limited set of transcripts than would be expected by chance, with PTPRD as a notable example. Third, we identified 44 archaic segments linked to complex traits, including a Denisovan-derived segment at NKX6-1 associated with type 2 diabetes. Most of these segments are specific to East Asians. Fourth, we identified candidate genetic loci under recent natural selection. Overall, our work provided insights into genetic characteristics of the Japanese population. Whole-genome sequencing of 3256 Japanese individuals uncovered genetic characteristics of this population.We generated Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), a high-depth whole-genome sequencing dataset comprising 3256 individuals from across Japan. Analysis of JEWEL revealed genetic characteristics of the Japanese population that were not discernible using microarray data. First, rare variant?based analysis revealed an unprecedented fine-scale genetic structure. Together with population genetics analysis, the present-day Japanese can be decomposed into three ancestral components. Second, we identified unreported loss-of-function (LoF) variants and observed that for specific genes, LoF variants appeared to be restricted to a more limited set of transcripts than would be expected by chance, with PTPRD as a notable example. Third, we identified 44 archaic segments linked to complex traits, including a Denisovan-derived segment at NKX6-1 associated with type 2 diabetes. Most of these segments are specific to East Asians. Fourth, we identified candidate genetic loci under recent natural selection. Overall, our work provided insights into genetic characteristics of the Japanese population. Whole-genome sequencing of 3256 Japanese individuals uncovered genetic characteristics of this population.</p>
},
	doi = {https://doi.org/10.1126/sciadv.adi8419},
	url = {https://www.science.org/doi/10.1126/sciadv.adi8419},
	author = {Liu, Xiaoxi and Koyama, Satoshi and Tomizuka, Kohei and Takata, Sadaaki and Ishikawa, Yuki and Ito, Shuji and Kosugi, Shunichi and Suzuki, Kunihiko and Hikino, Keiko and Koido, Masaru and Koike, Yoshinao and Horikoshi, Momoko and Gakuhari, Takashi and Ikegawa, Shiro and Matsuda, Kochi and Momozawa, Yukihide and Ito, Kaoru and Kamatani, Yoichiro and Terao, Chikashi}
}
