Taiwan Precision Medicine Initiative Elucidates Genetic Variants and Disease Risk in Han Chinese Population

TAIPEI, TAIWAN, Oct. 30, 2025- Two studies published in Nature have provided comprehensive insights into the genetic architecture and disease risk factors of Han Chinese individuals through data generated by the Taiwan Precision Medicine Initiative (TPMI), one of the largest precision health research efforts in Asia.

The first study, led by researchers from Academia Sinica, the University of California, San Francisco, and collaborating institutions, details the establishment of the TPMI cohort, which comprises approximately 565,400 participants recruited from 16 medical centers across Taiwan between 2019 and 2023. The initiative was designed to address the historical underrepresentation of Han Chinese individuals—who constitute nearly one-fifth of the global population—in genomic studies.

Participants, ranging in age from 20 to 90 years, including over 160 centenarians, contributed blood samples and granted access to their electronic medical records (EMRs). Genetic profiling was performed using single-nucleotide polymorphism (SNP) arrays optimized for Han Chinese ancestry, enabling genome-wide association studies (GWAS), phenome-wide association studies (PheWAS), and the calculation of polygenic risk scores (PRS) for assessing disease susceptibility and pharmacogenomic responses.

All participants consented to receive future health management recommendations based on individual genetic findings and to take part in TPMI-related research. The resulting genetic and clinical data are made available to qualified investigators through the TPMI Data Access Platform, which integrates genomic information with longitudinal medical data.

As a large-scale, non-European ancestry cohort that links genetic profiles to clinical outcomes, TPMI serves as an essential resource for validating genetic risk prediction models, conducting risk-based clinical trials, and supporting public health policy development. The project is expected to provide a foundational model for future population-based precision medicine initiatives worldwide.

The second study, also published in Nature, examined genetic data and EMR-derived phenotypes from 486,956 participants within the TPMI. The analysis integrated genotypic and phenotypic information to perform extensive GWAS on 24 quantitative traits and 695 disease-related phenotypes, referred to as phecodes.

Through these analyses, the research team identified 2,656 independent associations between genetic variants and clinical traits. This included 1,347 associations related to quantitative traits and more than 1,300 linked to disease phenotypes. Fine-mapping and colocalization analyses further elucidated the biological pathways and mechanisms underlying multiple complex diseases, contributing valuable insights into genetic contributions to health and disease in East Asian populations.

Based on these findings, the researchers developed Han Chinese–specific polygenic risk scores for a range of conditions, including cardiometabolic diseases, cancers, autoimmune disorders, and infectious diseases. The predictive performance of these PRS models was subsequently validated using independent datasets from the Taiwan Biobank, UK Biobank, and the All of Us project, confirming their reliability and cross-population applicability.

It was estimated that genetic factors account for approximately 10.3 percent of the variance in health outcomes, measured through hospitalization duration, among TPMI participants. Nonetheless, the authors noted that disease prevalence and ascertainment bias could influence the apparent magnitude of genetic effects.

Overall, the TPMI represents a critical advancement in the understanding of population-specific genetic variation and its relationship to disease risk. By integrating large-scale genomic data with detailed clinical information, the initiative provides a robust foundation for the development of precision medicine in Han Chinese and other East Asian populations, while also contributing to the broader global effort to achieve equitable genomic representation in medical research.

Reference

[1] Taiwan Precision Medicine Initiative

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