Table 3 Prediction results from CNICS validation set.

From: Genomic risk prediction of type 2 diabetes in people living with and without HIV

Ancestry

Model

AUC (95% CI) in %

Full Model R2 in %

PRS R2 in %

NRI (95% CI) in %

AFR

Model 1

70.16 (68.36, 71.97)

14.67

-

Ref.

 

Model 2

79.67 (78.16, 81.18)

30.19

-

16.59 (12.88, 20.80)

 

Model 3

80.41 (78.91, 81.9)

31.80

1.88

18.59 (15.27, 22.09)

 

Model 4

80.31 (78.81, 81.81)

31.66

1.75

18.31 (14.67, 21.98)

 

Model 5

80.44 (78.94, 81.93)

31.83

1.91

18.94 (15.08, 22.77)

EUR

Model 1

68.7 (66.22, 71.18)

10.24

-

Ref.

 

Model 2

76.51 (74.34, 78.68)

21.31

-

15.48 (10.47, 20.51)

 

Model 3

78.28 (76.15, 80.4)

24.44

3.18

17.09 (11.72, 22.60)

 

Model 4

78.32 (76.20, 80.44)

24.48

3.20

16.57 (11.49, 22.17)

 

Model 5

78.11 (75.98, 80.24)

24.15

2.87

15.72 (10.07, 21.17)

  1. Model 1 adjusts for age, age squared, sex, 10 PCs, and genotyping array.
  2. Model 2 adjusts for Model 1 plus ART use, statin use, BMI, SBP, and cigarette smoking.
  3. Model 3 adjusts for Model 2 plus single-trait T2D PRS per SD.
  4. Model 4 adjusts for Model 2 plus meta-inflammation PRS per SD.
  5. Model 5 adjusts for Model 2 plus meta-lipids PRS per SD.
  6. AUC = area under the ROC curve; PRS = polygenic risk score; AFR = African ancestry; EUR = European ancestry; NRI = net reclassification improvement; ART = antiretroviral therapy; BMI = body mass index; SBP = systolic blood pressure
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