Table 2 Comparison of Polygenic risk score estimated from PGC BP1 GWAS summary statistic between BP1 individuals and controls.

From: Contribution of common and rare variants to bipolar disorder susceptibility in extended pedigrees from population isolates

GWAS threshold

NSNPs, NSNPsPGC, NSNPsPGCInCOCR

LM beta (BP)

LM P value (BP)

LM Beta (AdMix)

LM P value (AdMix)

LR Log OR (QNPRS)

LR P value (QNPRS)

OR for 1-unit increase in QNPRS

LR Log or (AdMix)

LR P value (AdMix)

Nagelkerke R2

0.01

26868, 189221, 171166

0.27

0.0014

−4.11

2.13E-09

0.39

0.0027

1.477

5.53

5.12E-05

0.0151

0.001

4241, 36855, 34460

0.25

0.0069

−3.24

2.92E-05

0.23

0.0539

1.262

4.90

2.27E-04

0.0046

0.0001

789, 9457, 9017

0.06

0.4842

−2.83

1.23E-04

0.13

0.2704

1.143

4.54

4.52E-04

0.0007

0.000001

65, 896, 855

0.09

0.3421

−0.44

5.81E-01

0.03

0.7740

1.034

4.29

7.48E-04

0.0002

0.00000005

13, 126, 124

0.05

0.6136

−0.74

3.67E-01

0.00

0.9709

0.996

4.27

7.94E-04

0.0003

  1. P values are computed using linear and logistic regression models by taking into account relatedness. Nagelkerke R2 calculation assumed independence among individuals. NSNPs the number of SNPs used in PRS calculation after LD clumping, NSNPsPGC the number of SNPs in the PGC data without LD clumping, NSNPsPGCInCOCR the number of SNPs from the PGC data present in CO/CR pedigrees without LD clumping, BP coefficients and p values for BP1 status, AdMix coefficients and p values for global admixture proportions of European ancestry, LM linear model, LR logistic regression, QNPRS quantile-normalized polygenic risk scores.
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