Genome-wide gene association analysis was performed using MAGMA v1.0815 (http://ctg.cncr.nl/software/magma ). All variants in the GWAS outside of the MHC region (GRCh37: 6:28,477,797–33,448,354) that positionally map within one of the 19,019 protein coding genes were included to estimate the significance value of that gene. Genes were considered significant if the P-value was <0.05 after Bonferroni correction for 19,019 genes. All MAGMA analyses utilized 1KG43 (link) LD information. MAGMA gene-set analysis was performed where variants map to 15,496 gene-sets from the MSigDB v7.0 database52 (link). Gene-sets were considered significant if the P-value was <0.05 after Bonferroni correction for the number of tested gene-sets. Forward selection of significantly associated gene-sets was performed using MAGMA v1.08 conditional analysis53 (link). Initially the most significant gene-set was selected as a covariate and the remaining gene-sets were analyzed. The most significant gene-set from this conditional analysis was added as a covariate in addition to the previous gene-set and a new analysis was run. This process was repeated until no gene-set met the significance threshold (PBonferroni<0.05). MAGMA tissue specificity analysis was performed in FUMA using 30 general tissue type gene expression profiles (from GTEx v8). Tissues were considered significant if the P-value was < 0.05 after Bonferroni correction for 30 tissues.
FUMA cell type specificity analysis16 (link) utilises the MAGMA gene association results to identify cell types enriched in expression of trait associated genes. We focused on brain and immune related cell types with the inclusion of pancreas as a control, therefore selecting the following scRNA-seq datasets: Allen_Human_LGN_level154 (link), Allen_Human_LGN_level254 (link), Allen_Human_MTG_level154 (link), Allen_Human_MTG_level254 (link), DroNc_Human_Hippocampus55 (link), DroNc_Mouse_Hippocampus55 (link), GSE104276_Human_Prefrontal_cortex_all_ages56 (link), GSE67835_Human_Cortex57 (link), GSE81547_Human_Pancreas58 (link), Linnarsson_GSE101601_Human_Temporal_cortex59 (link), MouseCellAtlas_all60 (link), PBMC_10x_68k61 (link), and PsychENCODE_Adult62 . Within-dataset corrected results were reported to indicate which single cells are most likely to be disease relevant. The gene-based and gene-set analyses were also performed without the larger APOE region (19:40000000–50000000).
FUMA cell type specificity analysis16 (link) utilises the MAGMA gene association results to identify cell types enriched in expression of trait associated genes. We focused on brain and immune related cell types with the inclusion of pancreas as a control, therefore selecting the following scRNA-seq datasets: Allen_Human_LGN_level154 (link), Allen_Human_LGN_level254 (link), Allen_Human_MTG_level154 (link), Allen_Human_MTG_level254 (link), DroNc_Human_Hippocampus55 (link), DroNc_Mouse_Hippocampus55 (link), GSE104276_Human_Prefrontal_cortex_all_ages56 (link), GSE67835_Human_Cortex57 (link), GSE81547_Human_Pancreas58 (link), Linnarsson_GSE101601_Human_Temporal_cortex59 (link), MouseCellAtlas_all60 (link), PBMC_10x_68k61 (link), and PsychENCODE_Adult62 . Within-dataset corrected results were reported to indicate which single cells are most likely to be disease relevant. The gene-based and gene-set analyses were also performed without the larger APOE region (19:40000000–50000000).
