Human Population Genomics Laboratory

Understanding human diversity through large-scale genomic analysis

教員

KAWAI, Yousuke

Professor

ykawai@nig.ac.jp

researchmap

Research Summary

1. Human Genome Data Analysis

We develop and apply advanced computational methods to analyze human genome sequencing data, with a primary focus on whole-genome sequencing (WGS). Our work spans the entire analytical spectrum—from raw data processing and variant discovery to functional annotation—emphasizing the creation of robust, scalable, and reproducible workflows.

We integrate diverse sequencing technologies, including short-read, long-read, and Hi-C, to enable the precise characterization of complex genomic regions and structural variations. Furthermore, we are actively engaged in telomere-to-telomere (T2T) genome analysis, aiming to resolve previously inaccessible regions such as centromeres and highly repetitive sequences.

By developing scalable pipelines and maintainable software, we establish the computational foundation necessary to support both large-scale research initiatives and clinical applications.

2. Human Evolution

Our research explores the history of human evolution by analyzing genetic variation across diverse populations. By leveraging genomic data from both modern and ancient individuals, we investigate population divergence, admixture, and migration patterns that have shaped contemporary human diversity.

Utilizing population genetics frameworks, we study allele frequency dynamics, signatures of natural selection, and gene flow to understand how environmental and cultural factors have influenced our species. These efforts help reconstruct human history and provide deeper insights into the genetic architecture of present-day populations.

3. Genomic Medicine

We strive to advance precision medicine by leveraging large-scale genomic data to elucidate the genetic basis of human diseases. A central focus of our research is the whole-genome sequencing of rare diseases, where we identify and interpret disease-associated variants to improve diagnostic yields and uncover underlying molecular mechanisms.

Our work is deeply integrated with national-scale genomic initiatives and clinical programs, allowing for the analysis of large cohorts paired with rich phenotypic data. This synergy enables the translation of genomic discoveries into improved diagnostic strategies and therapeutic insights. Additionally, we investigate common complex diseases through genome-wide association studies (GWAS) to identify genetic risk factors and develop risk prediction models tailored to individual genetic backgrounds.

We are also committed to developing population-specific genomic resources and infrastructure—with a particular emphasis on the Japanese population—to facilitate the seamless implementation of genomic medicine in clinical practice.

出版物

• Kulmanov M, Ashouri S, Liu Y, Abdelhakim M, Alsolme E, Nagasaki M, Ohkawa Y, Suzuki Y, Tawfiq R, Tokunaga K, Katayama T, Abedalthagafi M.S, Hoehndorf R, Kawai Y. Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia. Sci Data 2025: 12, 1316.
• Kawai Y, Watanabe Y, Omae Y, Miyahara R, Khor S-S, Noiri E, Kitajima K, Shimanuki H, Gatanaga H, Hata K, Hattori K, Iida A, Ishibashi-Ueda H, Kaname T, Kanto T, Matsumura R, Miyo K, Noguchi M, Ozaki K, Sugiyama S, Takahashi A, TokudaH ,Tomita T, Umezawa A, Watanabe H, Yoshida S, Goto Y, Maruoka Y, Matsubara Y, Niida S, Mizokami M,  Tokunaga K. Exploring the genetic diversity of the Japanese Population: Insights from a Large-Scale Whole Genome Sequencing Analysis. PLoS Genet 2023: 19(12): e1010625.
• Kawai Y, Hitomi Y, Ueta M, Khor SS, Nakatani K, Sotozono C, Kinoshita S, Nagasaki M, Tokunaga K. Mapping of susceptible variants for cold medicine-related Stevens–Johnson syndrome by whole-genome resequencing. npj Genomic Medicine. 2021;6(1):9-.
• Jinam T, Kawai Y (1^st coauthor), Kamatani Y, Sonoda S, Makisumi K, Sameshima H, Tokunaga K, Saitou N. Genome-wide SNP data of Izumo and Makurazaki populations support inner-dual structure model for origin of Yamato people. Journal of Human Genetics. 2021;66(7):681-7.
• Kawai Y, Mimori T, Kojima K, Nariai N, Danjoh I, Saito R, Yasuda J, Yamamoto M, Nagasaki M. Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals. Journal of Human Genetics. 2015;60(10):581-7.