Table 6 |.

Polygenic risk scores and non-vascular outcomes

Outcometype	Outcome	T2D PRS decile	n Cases	n Controls	OR	95%CI lower	95%CI upper	P	P for linear trend
Non-vascular	Retinopathy	0–10%	792	4,533	1.00	Ref	Ref	-	3.1E-32
		10–20%	832	4,533	1.08	0.97	1.20	0.158
		20–30%	795	4,533	1.05	0.94	1.17	0.364
		30–40%	852	4,533	1.14	1.02	1.26	0.019
		40–50%	814	4,533	1.08	0.97	1.20	0.152
		50–60%	891	4,533	1.20	1.08	1.33	6.8E-04
		60–70%	901	4,533	1.25	1.13	1.39	3.1E-05
		70–80%	936	4,533	1.30	1.17	1.45	6.8E-07
		80–90%	1,031	4,533	1.47	1.33	1.63	2.2E-13
		90–100%	1,069	4,533	1.59	1.44	1.77	4.2E-19
	Chronic kidney	0–10%	3,446	3,391	1.00	Ref	Ref	-	7.3E-06
	disease	10–20%	3,490	3,391	1.03	0.93	1.15	0.508
		20–30%	3,439	3,391	1.04	0.94	1.14	0.488
		30–40%	3,463	3,391	1.05	0.95	1.16	0.323
		40–50%	3,370	3,391	1.04	0.95	1.14	0.409
		50–60%	3,362	3,391	1.07	0.97	1.17	0.166
		60–70%	3,389	3,391	1.07	0.98	1.17	0.129
		70–80%	3,285	3,391	1.07	0.98	1.17	0.121
		80–90%	3,373	3,391	1.07	0.98	1.16	0.151
		90–100%	3,326	3,391	1.16	1.07	1.26	5.9E-04
	Neuropathy	0–10%	2,176	3,814	1.00	Ref	Ref	-	7.9E-08
		10–20%	2,193	3,814	1.03	0.96	1.11	0.436
		20–30%	2,217	3,814	1.07	0.99	1.15	0.075
		30–40%	2,218	3,814	1.06	0.99	1.15	0.110
		40–50%	2,217	3,814	1.05	0.98	1.13	0.192
		50–60%	2,293	3,814	1.11	1.03	1.20	0.006
		60–70%	2,261	3,814	1.10	1.02	1.18	0.014
		70–80%	2,253	3,814	1.10	1.02	1.19	0.009
		80–90%	2,265	3,814	1.11	1.03	1.19	0.007
		90–100%	2,377	3,814	1.21	1.12	1.30	9.7E-07

Genome-wide polygenic risk scores (gPRS) for T2D were generated in the MVP participants of European ancestry with T2D by calculating a linear combination of weights derived from the Europeans in the DIAMANTE Consortium using the prune and threshold method in PRSice-2 software (pruning r² = 0.8, P = 0.05). The gPRSs were divided into deciles and the risk of T2D-related non-vascular outcomes was assessed using a logistic regression model using the lowest decile (0–10%) as the reference category, together with the potential confounding factors of age, gender, and the first 10 PCs of European ancestry. The decile-specific P-values are shown in the column labeled P. In a separate logistic regression analysis, the continuous PRS was set as the dependent variable together with age, gender, and the first 10 PCs, and the P-value for linear trend is shown in the column labeled P for linear trend. For chronic kidney disease, a CKD PRS (from CKDgen consortium) is included in the regression model as an additional covariate. T2D, type 2 diabetes; PRS, polygenic risk score; n Cases, number of cases with the respective non-vascular outcome; n Controls, number of unaffected controls for the respective non-vascular outcome; OR, odds ratio; CI, confidence interval.