Table 2.
Summary of the source GWAS and number of causal mRNAs identified through TWAS, SMR/HEIDI, and COLOC
| GWAS statistics | Causal mRNA counts | Causal mRNAs shared among traits | ||||||
|---|---|---|---|---|---|---|---|---|
| N | significant SNPs | cis | trans | total | Psychiatric | Neuro-degenerative | Brain structure | |
| Psychiatric | ||||||||
| Major depressive disorder | 807,553 | 9744 | 160 | 11 | 171 | 37% | 2% | 4% |
| Bipolar disorder | 51,710 | 240 | 88 | 0 | 88 | 47% | 1% | 2% |
| Schizophrenia | 77,096 | 14,724 | 243 | 5 | 248 | 25% | 3% | 4% |
| Anxiety | 175,163 | 166 | 11 | 0 | 11 | 82% | 46% | 27% |
| Post-traumatic stress disorder | 214,408 | 4607 | 37 | 0 | 37 | 43% | 8% | 11% |
| Alcoholism | 300,789 | 1857 | 23 | 0 | 23 | 48% | 26% | 13% |
| Neuroticism | 390,278 | 7759 | 154 | 5 | 159 | 40% | 8% | 8% |
| Insomnia | 386,533 | 463 | 30 | 0 | 30 | 30% | 13% | 7% |
| Neurodegenerative | ||||||||
| Alzheimer’s disease (AD1) | 455,258 | 2357 | 28 | 0 | 28 | 46% | 25% | 4% |
| Alzheimer’s disease (AD2) | 63,926 | 1506 | 12 | 2 | 14 | 36% | 29% | 0% |
| Frontotemporal dementia | 12,908 | 29 | 0 | 0 | 0 | – | – | – |
| Amyotrophic lateral sclerosis | 80,610 | 182 | 4 | 0 | 4 | 25% | 0% | 0% |
| Lewy body dementia | 6,618 | 189 | 0 | 0 | 0 | – | – | – |
| Parkinson’s disease | 482,730 | 3464 | 25 | 0 | 25 | 32% | 12% | 28% |
| Brain structure | ||||||||
| Hippocampal volume | 26,814 | 461 | 0 | 0 | 0 | – | – | – |
| Nucleus accumbens volume | 32,562 | 138 | 0 | 0 | 0 | – | – | – |
| Amygdala volume | 34,431 | 0 | 0 | 0 | 0 | – | – | – |
| Putamen volume | 37,571 | 1465 | 9 | 0 | 9 | 33% | 22% | 44% |
| Brainstem volume | 28,809 | 1063 | 20 | 0 | 20 | 30% | 10% | 10% |
| Caudate nucleus volume | 37,741 | 141 | 15 | 0 | 15 | 20% | 0% | 27% |
| Globus pallidus volume | 34,413 | 272 | 12 | 0 | 12 | 8% | 0% | 42% |
| Thalamus volume | 34,464 | 50 | 3 | 0 | 3 | 0% | 0% | 0% |
| Cortical thickness | 33,992 | 370 | 10 | 0 | 10 | 40% | 40% | 30% |
| White matter hyperintensity | 48,454 | 1340 | 29 | 0 | 29 | 31% | 10% | 14% |
| Cortical surface area | 33,992 | 1127 | 29 | 0 | 29 | 35% | 17% | 14% |
The sample size (N) for each trait is the number of samples that contributed to the GWAS results used in our analysis, which may be smaller than the sample reported in the original GWAS publication due to data access limitations or restricting to samples of European ancestry. GWAS-significant SNPs were defined as SNPs with p value < 5 × 10−8. A mRNA is considered shared within a trait group if it is also causal for any other trait in that group. Since different traits have different number of identified causal mRNAs, we examined the percentage of the causal mRNAs of each trait that is shared within a trait group or between two trait groups.