Table 2.

Comparison of schizophrenia and bipolar disorder polygenic risk scores between patients with psychotic disorders and controls^a

Polygenic risk score	Polygenic risk score P-value thresholds
	5 × 10−08	1 × 10−04	0.05	1
Schizophrenia
P-value	1.3 × 10−06	6.8 × 10−21	7.6 × 10−40	5.7 × 10−40
Variance explained, %	1.1	4.4	9	9
Bipolar disorder
P-value	0.6	0.25	2.8 × 10−09	5.7 × 10−11
Variance explained, %	<0.1	<0.1	1.7	2.1

^a.Schizophrenia polygenic risk scores and bipolar disorder polygenic risk scores were calculated using as reference, respectively, the outcome of the schizophrenia and bipolar disorder mega-analyses conducted by the Psychiatric Genomics Consortium. We then compared the scores between 1168 case participants and 1472 controls using standard logistic regression at ten different P-value thresholds (P_T 5 × 10⁻⁰⁸, 1 × 10⁻⁰⁶, 1 × 10⁻⁰⁴, 1 × 10⁻⁰³, 0.01, 0.05, 0.1, 0.2, 0.5, 1). Regression models included the first three ancestry-based principal components and a cohort indicator as covariates. For clarity, here we report P-values and the variance explained in disease risk as measured by Nagelkerke's pseudo-R² at four P-value thresholds (P_T 5 × 10⁻⁰⁸, 1 × 10⁻⁰⁴, 0.05, 1). Results at each one of the ten different thresholds are available in Supplementary Table 6.