Interrogating DNA methylation associated with Lewy body pathology in a cross brain-region and multi-cohort study

The following data was used in analysis for the paper " "Interrogating DNA methylation associated with Lewy body pathology in a cross brain-region and multi-cohort study" J. Harvey, J. Imm et al. (2025) For analysis code used please refer to "https://github.com/UoE-Dementia-Genomics/LB-Meta-Analysis" Data is organised into compressed directories as follows. UKBBN: Processed DNA methylation matrices (PFC = Prefrontal Cortex, CNG = Anterior Cingulate Cortex), pheno files and Epigenome wide association study summary statistic outputs for the UK- Brain Bank Network cohort. Files are labelled as follows: betasCNG.Rdata - normalised betas for the Anterior cingulate cortex betasPFC.Rdata - normalised betas for the Prefrontal cortex ewasPheno.Rdata - phenotyping and processing covariate data. Brain_Region collumn is coded such that 1 = Anterior Cingulate and 2 = Prefrontal Cortex res_UKBBN_cng.Rdata - EWAS summary statistics for the Anterior Cingulate res_UKBBN_pfc.Rdata - EWAS summary statistics for the Prefrontal Cortex res_UKBBN_CrossCortex.Rdata - EWAS summary statistics for the cross cortex mixed model, all viable samples res_UKBBN_CrossCortex_Filtered.Rdata - EWAS summary statistics for the cross cortex mixed model, samples for the "Pure LB" subset (Braak NFT < 3) res_UKBBN_CrossCortex_Filtered.Rdata - EWAS summary statistics for the cross cortex mixed model, including Thal as a covariate NBB: Pheno files and Epigenome wide association study summary statistic outputs for the Netherlands Brain Bank cohort. Processed DNA methylation data available at GEO GSE203332 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE203332 NBB_pheno.txt - phenotyping and processing covariate data, base file NBB_pheno_cellsJoined.csv - phenotyping and processing covariate data, including deconvoluted cell type proportions NBB_knownCovar_SV3.Rdata - EWAS summary statistics, all viable samples NBB_knownCovar_SV3_filtered.Rdata - EWAS summary statistics, samples for the "Pure LB" subset (Braak NFT < 3) NBB_knownCovar_SV3_Thal.Rdata - EWAS summary statistics, including Thal as a covariate BDR: Processed DNA methylation matrices (PFC = Prefrontal Cortex), pheno files and Epigenome wide association study summary statistic outputs for the Brains for dementia research cohort. BDR_LB_Betas.Rdata - normalised beta matrix for the samples utilised in primary discovery EWAS BDR_LB_Pheno.Rdata - phenotyping file including all relavent covariated for discovery EWAS BDR_Res_SV1.Rdata - EWAS summary statistics, all viable samples NBB_Res_Thal_SV1.Rdata - EWAS summary statistics, including Thal as a covariate Meta: Meta analysis summary statistics used in analysis. MultiMeta_FullCohort.Rdata - EWAS meta analysis results - all viable samples MultiMeta_PureLB.Rdata - EWAS meta analysis results - samples for the "Pure LB" subset (Braak NFT < 3) MultiMeta_ThalControlled.Rdata -EWAS meta analysis results, including Thal as a covariate PFC_Meta_FullCohort.Rdata -EWAS meta analysis results, PFC Specific Reference testing files: Additional reference files utilised in genomic enrichment and colocalisation testing analysis. alldataresultswithCB.csv - EWAS Meta analysis summary statistics from Smith et al. testing NFT associated methylation. EC_PAPER_model2_bacon_EPIC.RData - EWAS summary statistics Wheildon et al. testing HD assocation methylation in the entorhinal cortex STR_PAPER_model2_bacon_EPIC.RData - EWAS summary statistics Wheildon et al. testing HD assocation methylation in the striatum inputsFormatted - GWAS and QTL summary statistics for the SNCA region derived from Chia et al, Pihlstrom et al and methylation QTL discovery analysis conducted in this cohort PD_Regions2024.csv - Formatted genomic regions from the Kim et al GWAS into Parkinsons disease used as input for the Brown's Genomic Region Enrichment analysis