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The Taiwan Biobank (TWB) provides a large-scale genomic resource for characterizing population-specific variants. Leveraging whole-genome sequencing from TWB participants, we generated high-confidence variant profiles spanning single-nucleotide variants, small insertions and deletions, mitochondrial variants, and larger structural changes, and refined allele frequency estimates for variants of clinical and functional interest. We then integrated these multiple variant types with extensive lifestyle and clinically relevant phenotypes to evaluate the disease risk across a broad spectrum of complex traits. Our analyses highlight Taiwanese-specific and East Asian–enriched variants that are underrepresented in global reference databases, including pathogenic and likely pathogenic alleles in Mendelian disease genes and mitochondrial loci, and show how their frequencies and effect sizes differ from those observed in European-based cohorts. Collectively, this work illustrates how systematically combining multiple genomic variant types with rich phenotypes in the Taiwan Biobank can advance both rare and common disease genomics, and provides a scalable framework for population-tailored precision medicine in East Asia.