e/pQTL-GWAS coloc and TWAS/PWAS results for sCJD GWAS

This dataset is part of the manuscript "Multiomic analyses direct hypotheses for Creutzfeldt-Jakob disease risk genes" by Küçükali & Hill et al. Brain 2025.

Publication link: https://academic.oup.com/brain/advance-article/doi/10.1093/brain/awaf032/7981667

For details, please see the publication. For any questions, please contact Fahri Küçükali (fahri.kucukali@uantwerpen.be) and Kristel Sleegers (Kristel.Sleegers@uantwerpen.be).

Directories containing eQTL, pQTL, and ct-eQTL coloc results, and eTWAS and PWAS results were zipped respectively into separate files shared in this repository.

eQTL/ct-eQTL/pQTL coloc files contain colocalization results across all autosomes between eQTL/ct-eQTL/pQTL signals for genes/proteins and sCJD GWAS association signals. The data shows the colocalization probability results for the eQTL/ct-eQTL/pQTL signals, including the number of variants compared and the calculated posterior probabilities (PP) for 5 different hypotheses between two signals compared: H0 (no causal variant for both traits), H1 (causal variant only for sCJD GWAS), H2 (causal variant only for eQTL/ct-eQTL/pQTL), H3 (two distinct causal variants) and H4 (common causal variant shared between sCJD GWAS and eQTL/ct-eQTL/pQTL catalogue). In addition, we provided gene chromosome, start, end, gene name, ENSG ID, gene type and gene strand information based on following references: GENCODE v39 for Bryois et al. and Young et al. ct-eQTL coloc results, GENCODE v30 for GTEx eQTL coloc results, UniProt for pQTL coloc results, and GENCODE v24 for AMP-AD cohorts (MayoRNASeq, ROSMAP, MSBB) eQTL coloc results, all in GRCh38 human reference genome (with GRCh37 human coordinate columns are additionally present for pQTL coloc results from the original study).

eTWAS/PWAS files contain expression eTWAS and PWAS results of genes/proteins across all autosomes for sCJD GWAS, showing information on these results including the eTWAS/PWAS Z-scores and p-values. In addition, we provided gene chromosome, start, end, gene name, ENSG ID, gene type and gene strand information based on following references: GENCODE v24 for AMP-AD cohorts (MayoRNASeq, ROSMAP, MSBB), GTEx eTWAS results and for ROSMAP and Banner PWAS results, all in GRCh38 human reference genome coordinates. Moreover, in ancillary eTWAS results we provide these for PsychENCODE and eQTLGen based on GENCODE v19 (GRCh37) and for MetaBrain based on GENCODE v24 (GRCh38). Furthermore, in the eQTLGen and MetaBrain ancillary eTWAS result files, the "model" column shows the TWAS model-specific eTWAS results.

Contents of the zipped directories are as below, each explained in detail in Küçükali & Hill et al.:

eQTL_coloc:
sCJDgwas2020.GTEx_v8_Brain_Anterior_cingulate_cortex_BA24.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.GTEx_v8_Brain_Cortex.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.GTEx_v8_Brain_Frontal_Cortex_BA9.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.GTEx_v8_Brain_Hippocampus.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MayoRNAseq_TCX.eQTLcolocResults.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MSBB_BA10.eQTLcolocResults.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MSBB_BA22.eQTLcolocResults.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MSBB_BA36.eQTLcolocResults.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MSBB_BA44.eQTLcolocResults.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.ROSMAP_DLPFC.eQTLcolocResults.eQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.Young_etal_Microglia.eQTLcolocResults.chrALL.tsv.gz

pQTL_coloc:
sCJDgwas2020.ROSMAP_DLPFC.pQTLcolocResults.chrALL.tsv.gz

cteQTL_coloc:
sCJDgwas2020.Bryois_etal_Astrocytes.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.Bryois_etal_Endothelial_cells.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.Bryois_etal_Excitatory_neurons.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.Bryois_etal_Inhibitory_neurons.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.Bryois_etal_Microglia.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.Bryois_etal_Oligodendrocytes.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.Bryois_etal_OPCs_COPs.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.Bryois_etal_Pericytes.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.metaMiGA_Microglia.eQTLcolocResults.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MiGA_MFG_Microglia.eQTLcolocResults.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MiGA_STG_Microglia.eQTLcolocResults.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MiGA_SVZ_Microglia.eQTLcolocResults.cteQTLcolocResults.chrALL.tsv.gz
sCJDgwas2020.MiGA_THA_Microglia.eQTLcolocResults.cteQTLcolocResults.chrALL.tsv.gz

eTWAS:
sCJDgwas2020.GTEx_BA24.PrediXcanMASHR.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.GTEx_Cortex.PrediXcanMASHR.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.GTEx_FrontalCortex.PrediXcanMASHR.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.GTEx_Hippocampus.PrediXcanMASHR.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.MayoRNASeq_TCX.FUSION.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.MSBB_BA10.FUSION.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.MSBB_BA22.FUSION.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.MSBB_BA36.FUSION.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.MSBB_BA44.FUSION.eTWASresults.chrALL.tsv.gz
sCJDgwas2020.ROSMAP_DLPFC.FUSION.eTWASresults.chrALL.tsv.gz

PWAS:
sCJDgwas2020.Banner_DLPFC.FUSION.PWASresults.chrALL.tsv.gz
sCJDgwas2020.ROSMAP_DLPFC.FUSION.PWASresults.chrALL.tsv.gz

ancillary_eTWAS:
sCJDgwas2020.eQTLGen_Blood.summaryLevelFUSION.ancillary_eTWASresults.chrALL.tsv.gz
sCJDgwas2020.MetaBrain_Cortex.summaryLevelFUSION.ancillary_eTWASresults.chrALL.tsv.gz
sCJDgwas2020.PsychENCODE_DLPFC.FUSION.ancillary_eTWASresults.chrALL.tsv.gz