Human Population Genomics Laboratory
Kawai Group
Understanding human diversity through large-scale genomic analysis
Faculty
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
- Masao Nagasaki, Toshiaki Katayama, Yuki Moriya, Yayoi Sekiya, Shuichi Kawashima, Ryo Teraoka, Shuto Machida, Taichi Matsubara, Hiroki Hashimoto, Akihiro Asakura, Akio Nagano, Riu Yamashita, Toyoyuki Takada, Nobutaka Mitsuhashi, Mayumi Kamada, Yasuyuki Ohkawa, Katsushi Tokunaga, Yosuke Kawai.JoGo 1.0: the ACTG hierarchical nomenclature and database covering 4.7 million haplotypes across 19,194 human genes.. 2025年11月29日. Nucleic acids research :, 10.1093/nar/gkaf1232
- Kohei Hamanaka, Atsushi Fujita, Satoko Miyatake, Kazuharu Misawa, Eriko Koshimizu, Yuri Uchiyama, Naomi Tsuchida, Rie Seyama, Masamune Sakamoto, Kazuhiro Iwama, Naoto Nishimura, Yasuhiro Utsuno, Li Fu, Marina Takizawa, Qiaowei Liang, Toshiyuki Itai, Ken Saida, Sachiko Ohori, Shinichi Kameyama, Hiromi Fukuda, Yukina Hayashi, Yuta Inoue, Tomohide Goto, Kazushi Ichikawa, Ichiro Kuki, Masataka Fukuoka, Kiyohiro Kim, Tadashi Shiohama, Konomi Shimoda, Kosuke Otsuka, Yuki Ueda, Kazutoshi Cho, Kotaro Yuge, Nobutada Tachi, Masaki Yoshida, Atsuro Daida, Kyoko Hirasawa, Tomoe Yanagishita, Toshiyuki Yamamoto, Kentaro Shirai, Tammar Fixler Mehr, Aviva Fattal-Valevski, Dorit Lev, Haruna Yokoyama, Emi Iwabuchi, Yoshihiko Saito, Masaki Miura, Kenji Sugai, Akihiko Ishiyama, Masayuki Sasaki, Yoshihiro Watanabe, Jun-ichi Takanashi, Chong Ae Kim, Kenji Yokochi, Jun Tohyama, Tatsuo Mori, Yuishin Izumi, Yuiko Hasegawa, Nobuhiko Okamoto, Takahiro Ikeda, Hitoshi Osaka, Yosuke Kawai, Yosuke Omae, Katsushi Tokunaga, Mitsuhiro Kato, Takeshi Mizuguchi, Naomichi Matsumoto.Genome sequencing provides high diagnostic yield and new etiological insights for intellectual disability and developmental delay. 2025年8月26日. NPJ GENOMIC MEDICINE 10:(1), 10.1038/s41525-025-00521-4
- Maxat Kulmanov, Saeideh Ashouri, Yang Liu, Marwa Abdelhakim, Ebtehal Alsolme, Masao Nagasaki, Yasuyuki Ohkawa, Yutaka Suzuki, Rund Tawfiq, Katsushi Tokunaga, Toshiaki Katayama, Malak S Abedalthagafi, Robert Hoehndorf, Yosuke Kawai.Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia.. 2025年8月12日. Scientific data 12:(1), 1316-1316, 10.1038/s41597-025-05652-y
- Yosuke Omae, Seik-Soon Khor, Mihoko Shimada, Yosuke Kawai, Taihei Yamaguchi, Maiko Yagi, Masashi Ebisawa, Junko S Takeuchi, Tetsuya Mizoue, Wataru Sugiura, Katsushi Tokunaga.Genome-wide association study of common side effects following COVID-19 booster vaccination in a cohort of corporate employees in Japan.. 2025年4月13日. Scientific reports 15:(1), 12728-12728, 10.1038/s41598-025-90787-6
- Masao Nagasaki, Kouyuki Hirayasu, Seik-Soon Khor, Ryoko Otokozawa, Yayoi Sekiya, Yosuke Kawai, Katsushi Tokunaga.JoGo-LILR caller: Unveiling and navigating the complex diversity of LILRB3-LILRA6 copy number haplotype structures with whole-genome sequencing.. 2025年3月6日. Human immunology 86:(3), 111272-111272 , 10.1016/j.humimm.2025.111272
- Seik-Soon Khor, Kouyuki Hirayasu, Yosuke Kawai, Hie Lim Kim, Masao Nagasaki, Katsushi Tokunaga.LILR genotype imputation with attribute bagging (LIBAG): leukocyte immunoglobulin-like receptor copy number imputation system.. 2025年. Frontiers in immunology 16:, 1559301-1559301, 10.3389/fimmu.2025.1559301