Table 1.
LD Score regression results for all studies analyzed that either did not apply meta-analysis level GC correction or listed λGC in the relevant publication. The column labeled “GC” indicates how many rounds of GC correction were performed. For GWAS that applied meta-analysis level GC correction and listed λGC, we re-inflated all test statistics by the meta-analysis level λGC. LD Score regression performed on GC-corrected summary statistics will generally yield an intercept less than one. Note that GC correction at the individual study level will also push the expected intercept in the absence of confounding slightly below one (Supplementary Note). Standard errors were obtained via a block jackknife over blocks of ~2000 adjacent SNPs, which provides a robust estimate of standard error in the presence of correlated, heteroskedastic error terms. The column labeled “Type” indicates whether the study was a mega-(raw genotypes shared between studies) or meta-analysis (only summary statistics shared between all contributing studies).
| Phenotype | Mean χ2 | λGC | Intercept (SE) |
Type | GC | Ref |
|---|---|---|---|---|---|---|
| Inflammatory bowel disease | 1.247 | 1.164 | 1.095 (0.010) | mega | 0 | 26 |
| Ulcerative Colitis | 1.174 | 1.128 | 1.079 (0.010) | mega | 0 | 26 |
| Crohn’s Disease | 1.185 | 1.122 | 1.059 (0.008) | mega | 0 | 26 |
| Schizophrenia | 1.613 | 1.484 | 1.070 (0.010) | mega | 0 | 33 |
| ADHD | 1.033 | 1.033 | 1.008 (0.006) | mega | 0 | 18 |
| Bipolar Disorder | 1.154 | 1.135 | 1.030 (0.008) | mega | 0 | 23 |
| PGC Cross-Disorder | 1.205 | 1.187 | 1.018 (0.008) | mega | 0 | 29 |
| Major Depression | 1.063 | 1.063 | 1.009 (0.006) | mega | 0 | 30 |
| Rheumatoid Arthritis | 1.063 | 1.033 | 0.980 (0.007) | mega | 2 | 20 |
| Coronary Artery Disease | 1.125 | 1.096 | 1.033 (0.008) | meta | 1 | 24 |
| Type-2 Diabetes | 1.116 | 1.097 | 1.025 (0.008) | meta | 1 | 28 |
| BMI-Adj. Fasting Insulin | 1.088 | 1.072 | 1.015 (0.007) | meta | 1 | 27 |
| Fasting Insulin | 1.079 | 1.067 | 1.021 (0.007) | meta | 1 | 27 |
| College (Yes/No) | 1.207 | 1.180 | 1.046 (0.009) | meta | 1 | 31 |
| Years of Education | 1.220 | 1.188 | 1.041 (0.009) | meta | 1 | 31 |
| Cigarettes Per Day | 1.047 | 1.047 | 0.998 (0.008) | meta | 1 | 21 |
| Ever Smoked | 1.097 | 1.083 | 1.008 (0.006) | meta | 1 | 21 |
| Former Smoker | 1.050 | 1.048 | 0.999 (0.007) | meta | 1 | 21 |
| Age-Onset (Smoking) | 1.025 | 1.030 | 0.998 (0.006) | meta | 1 | 21 |
| FN-BMD | 1.163 | 1.109 | 1.001 (0.009) | meta | 2 | 25 |
| LS-BMD | 1.174 | 1.112 | 1.032 (0.009) | meta | 2 | 25 |
| Waist-Hip Ratio | 1.417 | 1.330 | 1.040 (0.008) | meta | 2 | 16 |
| Height | 1.802 | 1.478 | 1.149 (0.021) | meta | 2 | 17 |
| Body-Mass Index | 1.130 | 1.090 | 1.033 (0.012) | meta | 2 | 19 |