Table 1: Overview of 12 diseases in the UK Biobank.

We report the prevalence, parental prevalence, liability-scale SNP-heritability, and number of samples analyzed by GWAS, GWAX and LT-FH. GWAX sample sizes are lower than GWAS and LT-FH sample sizes due to incomplete family history data.

Trait	UKBB Prevalence	UKBB Parental Prevalence	${\widehat{\text{h}}}_{\text{g}}^2$	s.e. (${\widehat{\text{h}}}_{\text{g}}^2$)	NGWAS	NGWAX	NLT-FH
AD	0.001	0.065	0.12	0.11	381493	324512	381493
PD	0.003	0.020	0.15	0.05	381493	318792	381493
Lung cancer	0.006	0.064	0.10	0.03	381493	323838	381493
Bowel cancer	0.013	0.054	0.14	0.018	381493	322887	381493
Stroke	0.023	0.14	0.08	0.011	381493	332468	381493
COPD	0.035	0.082	0.17	0.0092	381493	329495	381493
Prostate cancer*	0.037	0.075	0.30	0.019	175450	331458	368940
T2D	0.042	0.092	0.36	0.0093	380180	330267	381390
Breast cancer*	0.061	0.082	0.20	0.012	206043	348170	371064
Depression	0.073	0.052	0.11	0.0058	381493	328186	381493
CAD	0.083	0.25	0.20	0.0058	381493	341810	381493
HTN	0.32	0.26	0.31	0.0037	381493	354208	381493

^*denotes sex-specific diseases (for which GWAX and LT-FH incorporate family history data from samples of both sexes). Estimates of (liability-scale) narrow-sense heritability (h²) from the literature, which are used by the LT-FH method, are reported in Supplementary Table 15. Diseases are listed in order of disease prevalence. AD: Alzheimer’s disease/dementia. PD: Parkinson’s disease. COPD: Chronic bronchitis/emphysema. T2D: Type 2 diabetes. CAD: Coronary artery disease. HTN: Hypertension.