BrainXcan results for SCZ_PGC_2020
1 BrainXcan results
In this analysis, we tested 327 structural and diffusion MRI-derived phenotypes with cross validated spearman correlation >= 0.101.
For the main analysis we focused on 261 IDPs, which include 48 cortical volumes, 10 sub-cortical volumes, 13 sub-cortical gray matter volumes. In below, we show the overall number of IDP by IDP subtype in the main results.
| subtype | n |
|---|---|
| Brainstem | 1 |
| FA | 46 |
| Gray-Brainstem | 1 |
| Gray-Cerebellum | 27 |
| Gray-Cortical | 48 |
| Gray-Subcortical | 13 |
| ICVF | 44 |
| ISOVF | 13 |
| OD | 45 |
| PC-Cerebellum-1 | 1 |
| PC-Cortical-1 | 1 |
| PC-FA-TBSS-1 | 1 |
| PC-ICVF-TBSS-1 | 1 |
| PC-ISOVF-TBSS-1 | 1 |
| PC-OD-TBSS-1 | 1 |
| PC-Subcortical_GMvol-1 | 1 |
| PC-Subcortical_vol-1 | 1 |
| Subcortical | 10 |
| Total | 5 |
Among 261 IDPs (109 T1 and 109 diffusion MRI, including the subtype-specific PCs), 46 were significantly associated with SCZ_PGC_2020 (pval < \(1.92\times 10^{-4}\) = 0.05 / 261).
The top 20 associations for dMRI are
| IDP | subtype | region | zscore | pval | IDP -> Phenotype | Phenotype -> IDP | link |
|---|---|---|---|---|---|---|---|
| PC-ICVF-TBSS-1 | PC-ICVF-TBSS-1 | PC-ICVF-TBSS-1 | -6.628 | 3.411e-11 | 0.2727 | 0.003107 | MR plot |
| PC-FA-TBSS-1 | PC-FA-TBSS-1 | PC-FA-TBSS-1 | -6.176 | 6.571e-10 | 0.4237 | 0.009543 | MR plot |
| IDP-25359 | ICVF | cerebral peduncle | 5.798 | 6.696e-09 | 0.02073 | 0.001075 | MR plot |
| IDP-25407 | OD | cerebral peduncle | 5.422 | 5.887e-08 | 0.9039 | 0.0001649 | MR plot |
| IDP-25361 | ICVF | anterior limb of internal capsule | 5.144 | 2.683e-07 | 0.07922 | 0.002379 | MR plot |
| IDP-25487 | ISOVF | tapetum | 4.964 | 6.921e-07 | 0.009887 | 0.4492 | MR plot |
| IDP-25098 | FA | superior fronto-occipital fasciculus | -4.963 | 6.956e-07 | 0.002534 | 0.03965 | MR plot |
| IDP-25410 | OD | posterior limb of internal capsule | -4.847 | 1.25e-06 | NA | NA | NA |
| IDP-25456 | ISOVF | anterior limb of internal capsule | 4.829 | 1.369e-06 | NA | NA | NA |
| IDP-25434 | OD | superior fronto-occipital fasciculus | 4.822 | 1.422e-06 | NA | NA | NA |
| IDP-25397 | OD | fornix | 4.767 | 1.868e-06 | NA | NA | NA |
| IDP-25453 | ISOVF | superior cerebellar peduncle | 4.727 | 2.281e-06 | NA | NA | NA |
| IDP-25411 | OD | posterior limb of internal capsule | -4.711 | 2.461e-06 | NA | NA | NA |
| IDP-25452 | ISOVF | superior cerebellar peduncle | 4.61 | 4.026e-06 | NA | NA | NA |
| IDP-25474 | ISOVF | cingulum cingulate gyrus | -4.529 | 5.916e-06 | NA | NA | NA |
| IDP-25372 | ICVF | posterior thalamic radiation | -4.491 | 7.091e-06 | NA | NA | NA |
| IDP-25100 | FA | uncinate fasciculus | 4.475 | 7.625e-06 | NA | NA | NA |
| IDP-25085 | FA | posterior thalamic radiation | -4.439 | 9.022e-06 | NA | NA | NA |
| IDP-25101 | FA | uncinate fasciculus | 4.336 | 1.452e-05 | NA | NA | NA |
| IDP-25419 | OD | posterior corona radiata | -4.33 | 1.492e-05 | NA | NA | NA |
The top 20 associations for T1 are
| IDP | subtype | region | zscore | pval | IDP -> Phenotype | Phenotype -> IDP | link |
|---|---|---|---|---|---|---|---|
| IDP-25020 | Subcortical | hippocampus | 8.37 | 5.786e-17 | 0.5365 | 0.7089 | MR plot |
| IDP-25847 | Gray-Cortical | frontal orbital cortex | 5.542 | 2.991e-08 | 0.06336 | 0.5993 | MR plot |
| IDP-25004 | Total | all | 5.488 | 4.06e-08 | 0.02596 | 0.1907 | MR plot |
| IDP-25869 | Gray-Cortical | planum polare | -5.457 | 4.853e-08 | 0.9056 | 0.06819 | MR plot |
| IDP-25838 | Gray-Cortical | cingulate gyrus, anterior division | 5.251 | 1.515e-07 | 0.2068 | 0.3745 | MR plot |
| IDP-25857 | Gray-Cortical | temporal fusiform cortex, posterior division | 4.61 | 4.024e-06 | NA | NA | NA |
| IDP-25888 | Gray-Subcortical | amygdala | -4.425 | 9.634e-06 | NA | NA | NA |
| IDP-25011 | Subcortical | thalamus | -4.326 | 1.517e-05 | NA | NA | NA |
| IDP-25811 | Gray-Cortical | inferior temporal gyrus, posterior division | 4.311 | 1.623e-05 | NA | NA | NA |
| IDP-25012 | Subcortical | thalamus | -4.298 | 1.72e-05 | NA | NA | NA |
| IDP-25845 | Gray-Cortical | cuneal cortex | 4.287 | 1.811e-05 | NA | NA | NA |
| IDP-25846 | Gray-Cortical | frontal orbital cortex | 3.902 | 9.559e-05 | NA | NA | NA |
| IDP-25852 | Gray-Cortical | lingual gyrus | 3.853 | 0.0001165 | NA | NA | NA |
| IDP-25784 | Gray-Cortical | insular cortex | -3.778 | 0.0001582 | NA | NA | NA |
2 Visualization of associations in the brain
2.1 T1
2.2 dMRI
3 BrainXcan MR Figures
3.1 IDP-25098
Mean FA (fractional anisotropy) in superior fronto-occipital fasciculus (right) on FA skeleton (from dMRI data)
3.2 IDP-25359
Mean ICVF (intra-cellular volume fraction) in cerebral peduncle (left) on FA (fractional anisotropy) skeleton (from dMRI data)
3.3 IDP-25361
Mean ICVF (intra-cellular volume fraction) in anterior limb of internal capsule (left) on FA (fractional anisotropy) skeleton (from dMRI data)
3.4 IDP-25407
Mean OD (orientation dispersion index) in cerebral peduncle (left) on FA (fractional anisotropy) skeleton (from dMRI data)
3.5 IDP-25487
Mean ISOVF (isotropic or free water volume fraction) in tapetum (left) on FA (fractional anisotropy) skeleton (from dMRI data)
3.6 PC-FA-TBSS-1
PC-FA-TBSS-1
3.7 PC-ICVF-TBSS-1
PC-ICVF-TBSS-1
3.8 IDP-25004
Volume of ventricular cerebrospinal fluid (from T1 brain image)
3.9 IDP-25020
Volume of right hippocampus (from T1 brain image)
3.10 IDP-25838
Volume of grey matter in Left Cingulate Gyrus, anterior division
3.11 IDP-25847
Volume of grey matter in Right Frontal Orbital Cortex
3.12 IDP-25869
Volume of grey matter in Right Planum Polare
