The Taiwan Precision Medicine Initiative provides a cohort for large-scale studies

Figures

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  Fig. 1. Map of medical centres, their satellite hospitals and sample sizes. Locations of 16 partner medical centres and 33 affiliated hospitals, along with the numbers of DNA samples, genotyped samples, individuals with EMRs received, individuals with EMRs stored in the TPMI Data Lake and individuals with both genotype and EMR data. Source Data.

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  Fig. 2. Cohort characteristics. a, Sex-specific age distribution. b, Top 20 most prevalent ICD-10 codes: E78 (disorders of lipoprotein metabolism and other lipidaemias), I10 (EHT), E11 (type 2 diabetes mellitus), K21 (gastro-oesophageal reflux disease), J30 (vasomotor and allergic rhinitis), G47 (sleep disorders), K05 (gingivitis and periodontal diseases), N39 (other urinary disorders), M47 (spondylosis), K59 (other functional intestinal disorders), M79 (other and unspecified soft tissue disorders), R10 (abdominal and pelvic pain), H10 (conjunctivitis), I25 (chronic ischaemic heart disease), N40 (enlarged prostate), L30 (other and unspecified dermatitis), I11 (hypertensive heart disease), H04 (lacrimal system disorders), N18 (chronic kidney disease) and R07 (pain in throat or chest). c, Age of onset for the top 20 diseases. Onset ages in male individuals (blue) and female individuals (pink) are presented as box plots, ordered by median. Box plots represent minima, first quartile, median, third quartile and maxima. Values and sample sizes are in the Source Data. d, Top 20 most prevalent laboratory tests: creatinine_B (blood creatinine), WBC (white blood cell count), SGPT (serum glutamic…

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  Fig. 3. Population structure. a, PCA analysis. The TPMI cohort was compared with TWB, SGDP and 1KGP samples. The top-left inset compares TPMI participants born before 1950 with those born after 1950; the top-right inset compares the TPMI and the 1KGP. The main figure shows TPMI, TWB and two Taiwan Indigenous tribes (SGDP). Admixture fraction plots show ancestry fractions from ten ancestral populations (K = 10), with principal component (PC) 1 on the bottom axis and PC2 on the right. b, Coancestry and fine-scale structure. The coancestry heat map shows individuals (rows, columns) clustered by shared haplotypes, with colour intensity indicating haplotype copying. Darker blue or red indicates higher coancestry; yellow or light orange indicates lower. Diagonal blocks mark within-group sharing: K1–K6 show strong within-group haplotype sharing; K1–K2 (Han Chinese-enriched) exhibit strong coancestry with each other but less with K3–K6 (Indigenous-enriched), reflecting genetic differentiation; K3–K6 form distinct blocks, with some asymmetric sharing suggesting admixture or shared ancestry. The dendrogram shows clustering consistent with subgroup distinctions. c, Admixture graph depicting…

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  Fig. 4. Comparison of T2D GWAS results in the TPMI with those from four biobanks. a, Comparison of GWAS results from the TPMI and the PheWebs of the Biobank Japan (BBJ), China Kadoorie Biobank (CKB), the Korean Genome and Epidemiology Study (KoGES) and the UK Biobank (UKB). A Firth logistic regression was applied for the T2D GWAS in the TPMI. All statistical tests were two-sided. Multiple-testing adjustment was applied using a genome-wide significance threshold of P < 1 × 10−8. Novel T2D-associated SNPs identified in our GWAS but absent in biobanks at the genome-wide significance level are shown. b, Pairwise comparison with each biobank. Different statistical methods were applied across cohorts. For BBJ, CKB and KoGES, a generalized linear mixed model was implemented using SAIGE; for UKB: linear regression was used. All tests were two-sided. Bonferroni correction was applied for multiple-testing adjustment across loci. The four graphs (from top to bottom) show T2D-associated SNPs identified in the TPMI but not in BBJ, CKB, KoGES and UKB, respectively. Source Data.

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  Fig. 5. PRS analysis for T2D. a, AUC of PRS (red curve) and of PRS, age, sex and BMI (blue curve). b, Dose–response effect of PRS levels on the odds ratio (OR) of T2D. Dose–response effect of PRS (red line) and of a combination of PRS, age, sex and BMI (blue curve) with n = 205,779 independent samples. Error bars represent the 95% confidence interval, calculated as exp (β ± Z0.025 × s.e.), based on maximum likelihood estimation from a logistic regression model with different decile intervals of PRS values included as covariates. The estimated coefficient (β) is provided in column B (‘Estimate’) and the standard error (s.e.) is provided in column C (‘Std. Error’) in the Source Data for b. Source Data.