Table 3.

PRSice-2 polygenic risk score (PRS) prediction results for UK Biobank target samples, for optimal p value threshold.

Measure pair	Target sample	Threshold	PRS R2	Full R2	Null R2	Coefficient	Standard error	p	No. of SNP	Empirical p
HAID–HAID	AA	0.36	0.0104	0.0248	0.0144	112,697	40,950.5	0.0059	132,397	0.0701
HAID–HD	AA	0.017	0.0033	0.0991	0.0958	−7664.44	2951.83	0.0094	11,338	1
HD–HAID	AA	0.016	0.0015	0.0159	0.0144	4257.94	4092.96	0.2982	15,955	1
HD–HD	AA	0.019	0.0006	0.0964	0.0958	−2025.13	1827.21	0.2677	17,932	1
HAID–HAID	CH	0.14005	0.0041	0.0212	0.0172	31,395.8	27,561.6	0.2547	42,704	1
HAID–HD	CH	0.0003	0.0025	0.0687	0.0662	−730.731	569.454	0.1994	317	1
HD–HAID	CH	0.0091	0.0210	0.0382	0.0172	10,772.2	4188.19	0.0101	7853	0.1025
HD–HD	CH	0.015	0.0095	0.0757	0.0662	5924.37	2355.89	0.0119	11,034	0.1085
HAID–HAID	EA	0.0092	0.0017	0.0701	0.0684	15,670.8	3775.81	3.320E−05	10,648	0.0009
HAID–HD	EA	0.35	0.0013	0.0468	0.0455	53,336.3	10,047.5	1.106E−07	183,790	<0.0001
HD–HAID	EA	0.019	0.0027	0.0711	0.0684	13207	2506.83	1.376E−07	24,107	<0.0001
HD–HD	EA	0.018	0.0124	0.0579	0.0455	18,389.9	1111.69	1.821E−61	23,187	<0.0001
HAID–HAID	SA	0.045	0.0032	0.0424	0.0392	−19,437.9	7590.78	0.0104	28,737	1
HAID–HD	SA	0.1	0.0007	0.0457	0.0450	−9085.58	5864.3	0.1213	55,832	1
HD–HAID	SA	0.0037	0.0014	0.0407	0.0392	−2137.48	1241.07	0.0850	5932	1
HD–HD	SA	0.28005	0.0075	0.0525	0.0450	24,413.7	4746.59	2.698E−07	123,566	<0.0001

Measure pair denotes base sample polygenic risk scores constructed from UK Biobank genome-wide association study on British samples of either wearing a hearing aid (HAID) or having hearing difficulties (HD), respectively, predicting the UK Biobank target phenotypes HAID and HD, respectively. Target sample refers to the four UK Biobank subpopulations, African (AA), Chinese (CH), European (EA), and South Asian (SA), described in the text. Threshold is the p value threshold for SNP inclusion that maximised variance explained in the respective target phenotype. PRS R² is the variance in the target phenotype explained by the PRS. Full R² is the variance explained by the full-model regression, which includes the PRS as well as the covariates age and sex, while Null R² does not include the PRS, just the covariates. Coefficient is the regression coefficient for the PRS term, with standard error and p its corresponding standard error and p value. No. of SNP is the number of SNPs included in the PRS and empirical p is the p value obtained from simulation, which corrects for both multiple thresholds tested in order to obtain the optimal threshold and for relatedness in the sample, such as the inclusion of DZ twin pairs.