Table 2 ∣.
Summary of multivariate GWAS results
| Multivariate GWAS target | Effective n | Mean χ2(1) |
LDSC univariate intercept |
Independent hits (LD with Q hits) |
LD with univariate trait hits (LD with Q hits) |
Unique from univariate trait hits (LD with Q hits) |
|---|---|---|---|---|---|---|
| Multivariate GWAS | ||||||
| Factor 1 (Compulsive) | 19,108 | 1.209 | 0.973 | 1 (0) | 1 (0) | 0 (0) |
| Factor 2 (Psychotic) | 87,138 | 1.869 | 0.975 | 108 (1) | 96 (1) | 12 (0) |
| Factor 3 (Neurodevelopmental) | 55,932 | 1.301 | 1.022 | 9 (0) | 7 (0) | 2 (0) |
| Factor 4 (Internalizing) | 455,340 | 1.635 | 0.997 | 44 (0) | 38 (0) | 6 (0) |
| Total hits across Factors 1-4 | - | - | - | 153 (1) | 133 (1) | 20 (0) |
| Hierarchical p factor | 667,343 | 1.795 | 0.955 | 2 (1) | 2 (1) | 0 (0) |
| Bifactor p factor | 666,557 | 1.985 | 0.982 | 66 (8) | 58 (8) | 8 (0) |
| Unstructured meta-analysis | - | 2.216 | 0.883 | 184 | 145 (−) | 39 (−) |
| Heterogeneity index (QSNP) | ||||||
| Factor 1 (Compulsive) QSNP | - | 1.113 | 1.001 | 2 | 1 | 1 |
| Factor 2 (Psychotic) QSNP | - | 1.251 | 0.994 | 6 | 4 | 2 |
| Factor 3 (Neurodevelopmental) QSNP | - | 1.246 | 0.980 | 7 | 4 | 3 |
| Factor 4 (Internalizing) QSNP | - | 1.142 | 0.977 | 3 | 3 | 0 |
| Total QSNP hits across Factors 1-4 | - | - | - | 9 | 5 | 4 |
| Hierarchical p factor QSNP | - | 1.667 | 0.928 | 69 | 58 | 11 |
| Bifactor p factor QSNP | - | 1.645 | 0.936 | 76 | 59 | 17 |
Independent hits were defined using a pruning window of 250 kb and r2 < 0.1. Hits are considered in LD if their LD was r2 > 0.10 or within a 250-kb window of one another. Values in parentheses indicate whether any of the hits were in LD with hits for factor-specific QSNP hits from the respective model. Factor-specific QSNP indexes whether a particular SNP is unlikely to operate through the identified factor structure, as will often be the case when a SNP effect is highly specific to an individual disorder. To facilitate comparison across mean χ2 values reported in each row, all χ2 statistics with df > 1 (i.e. those for QSNP and those for the unstructured multivariate GWAS) were converted to χ2(1) statistics before taking their means. For all GWAS analyses, we correct for multiple testing by employing the field standard significance threshold of P < 5 × 10−8.