DNA methylation signatures of bilateral hippocampal volume, asymmetry and atrophy: a cross-omics analysis in the general population.
The 2 matches
- [1] § Methods › Statistics › Cohort-level epigenome-wide association analyses (EWAS) ↔ Run_EWAS_script.R, lines 50–128 · score 0.72 · smoking status, eTIV, variable, Covariates, technical, education
- [2] § Methods › Statistics ↔ Run_EWAS_script.R, lines 1–48 · score 0.56 · identifying DNA methylation, bilateral hippocampal volume, signatures associated, omics, EWAS, asymmetry
Paper
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The authors' code
R · 309 lines · 9.2 KB · CC-BY-4.0 · 2 matches
- #!/usr/bin/env Rscript
- ## =========================================================
- ##Integrative cross-omics analysis identifies DNA methylation signatures associated with bilateral hippocampal volume, asymmetry and atrophy rate in the general population
- ##
- ## Usage:
- ## Rscript run_ewas_per_study.R <MODEL> <PHENOTYPE> <STRATA>
- ##
- ## Example:
- ## Rscript run_ewas_per_study.R M2 LHCV All
- ##
- ## MODEL options:
- ## M1, M2, M3
- ##
- ## PHENOTYPE options:
- ## Example: LHCV, RHCV, HCasy
- ##
- ## STRATA options:
- ## All, f, m
- ## =========================================================
- args <- commandArgs(trailingOnly = TRUE)
- if (length(args) < 3) {
- stop("Usage: Rscript run_ewas_per_study.R <MODEL> <PHENOTYPE> <STRATA>")
- }
- Model <- args[1]
- Pheno <- args[2]
- Strata <- args[3]
- if (!Model %in% c("M1", "M2", "M3")) {
- stop("MODEL must be one of: M1, M2, M3")
- }
- if (!Strata %in% c("All", "f", "m")) {
- stop("STRATA must be one of: All, f, m")
- }
- ## =========================================================
- ## Load packages
- ## =========================================================
- suppressPackageStartupMessages({
- library(parallel)
- library(doParallel)
- library(data.table)
- library(dplyr)
- })
- ## =========================================================
- ## Parallel environment
- ## =========================================================
- nnodes <- as.integer(Sys.getenv("SLURM_NNODES", unset = "1"))
- nid <- as.integer(Sys.getenv("SLURM_NODEID", unset = "0"))
- ncpus <- as.integer(Sys.getenv("SLURM_CPUS_PER_TASK", unset = parallel::detectCores()))
- message("Model: ", Model)
- message("Phenotype: ", Pheno)
- message("Strata: ", Strata)
- message("Nodes: ", nnodes, " | Node ID: ", nid, " | CPUs: ", ncpus)
- ## =========================================================
- ## User-defined paths
- ## =========================================================
- data_dir <- "path/to/data"
- output_dir <- "path/to/output"
- if (!dir.exists(output_dir)) {
- dir.create(output_dir, recursive = TRUE)
- }
- ## =========================================================
- ## Input files
- ## =========================================================
- main_data_file <- file.path(data_dir, "main_dataset.RData")
- ## =========================================================
- ## Load data
- ##
- ## Expected objects:
- ## phenotype_data : data.frame with one row per participant
- ## methylation_mat : matrix/data.frame of CpGs x samples
- ##
- ## Replace the object names below as needed.
- ## =========================================================
- load(main_data_file)
- ## ---------------------------------------------------------
- ## Rename loaded objects here
- ## Replace these with the actual object names in your .RData
- ## ---------------------------------------------------------
- phenotype_data <- pheno_data
- methylation_mat <- beta_data
- ## Optional cleanup
- # rm(pheno_data, beta_data)
- ## =========================================================
- ## Study metadata
- ## Replace as needed
- ## =========================================================
- study_name <- "STUDY"
- array_type <- "ARRAY"
- ancestry <- "ANCESTRY"
- tissue <- "TISSUE"
- run_date <- Sys.Date()
- ## =========================================================
- ## Generic variable definitions
- ##
- ## Replace these variable names with those in your dataset
- ## =========================================================
- ## Sample ID column in phenotype_data matching methylation matrix columns
- sample_id_var <- "sample_id"
- ## Outcome/covariate variable names
- sex_var <- "sex"
- age_var <- "age"
- etiv_var <- "eTIV"
- smoking_var <- "smoking_status"
- education_var <- "education"
- handedness_var <- "handedness"
- ## Optional covariate groups
- cell_type_vars <- c("celltype1", "celltype2", "celltype3", "celltype4", "celltype5", "celltype6")
- technical_vars <- c("technical_covariate1", "technical_covariate2")
- genetic_pc_vars <- paste0("genetic_PC", 1:10)
- ## =========================================================
- ## Helper: keep only covariates that exist in the dataset
- ## =========================================================
- keep_existing <- function(vars, dat) {
- vars[vars %in% colnames(dat)]
- }
- cell_type_vars <- keep_existing(cell_type_vars, phenotype_data)
- technical_vars <- keep_existing(technical_vars, phenotype_data)
- genetic_pc_vars <- keep_existing(genetic_pc_vars, phenotype_data)
- ## =========================================================
- ## Build model formula
- ## =========================================================
- base_terms <- c("meth_beta", age_var, etiv_var)
- if (length(cell_type_vars) > 0) {
- base_terms <- c(base_terms, cell_type_vars)
- }
- if (length(technical_vars) > 0) {
- base_terms <- c(base_terms, technical_vars)
- }
- if (length(genetic_pc_vars) > 0) {
- base_terms <- c(base_terms, genetic_pc_vars)
- }
- if (Model == "M1") {
- model_terms <- c(base_terms, paste0("as.factor(", sex_var, ")"))
- } else if (Model == "M2") {
- model_terms <- c(
- base_terms,
- paste0("as.factor(", sex_var, ")"),
- paste0("as.factor(", smoking_var, ")"),
- paste0("as.factor(", education_var, ")")
- )
- } else if (Model == "M3") {
- model_terms <- c(
- base_terms,
- paste0("as.factor(", sex_var, ")"),
- paste0("as.factor(", smoking_var, ")"),
- paste0("as.factor(", education_var, ")"),
- paste0("as.factor(", handedness_var, ")")
- )
- }
- model_formula <- paste("outcome_var ~", paste(model_terms, collapse = " + "))
- message("Model formula: ", model_formula)
- ## =========================================================
- ## Subset by strata
- ## =========================================================
- if (Strata == "All") {
- cdat <- phenotype_data
- } else if (Strata == "f") {
- cdat <- phenotype_data[phenotype_data[[sex_var]] == "f", , drop = FALSE]
- } else if (Strata == "m") {
- cdat <- phenotype_data[phenotype_data[[sex_var]] == "m", , drop = FALSE]
- }
- samples <- cdat[[sample_id_var]]
- ## Keep only samples present in both datasets
- samples <- intersect(samples, colnames(methylation_mat))
- cdat <- cdat[cdat[[sample_id_var]] %in% samples, , drop = FALSE]
- cdat <- cdat[match(samples, cdat[[sample_id_var]]), , drop = FALSE]
- methylation_mat <- methylation_mat[, samples, drop = FALSE]
- stopifnot(identical(colnames(methylation_mat), cdat[[sample_id_var]]))
- ## =========================================================
- ## Split CpGs across nodes
- ## =========================================================
- n_rows <- nrow(methylation_mat)
- node_indices <- lapply(seq_len(nnodes), function(node) {
- start <- ((node - 1) * floor(n_rows / nnodes)) + 1
- end <- if (node == nnodes) n_rows else start + floor(n_rows / nnodes) - 1
- start:end
- })
- current_idx <- unlist(node_indices[nid + 1])
- meth_chunk <- methylation_mat[current_idx, , drop = FALSE]
- message("Running on node ", nid, ": ", nrow(meth_chunk), " CpGs x ", ncol(meth_chunk), " samples")
- ## =========================================================
- ## Set up parallel cluster
- ## =========================================================
- cl <- makeCluster(ncpus)
- registerDoParallel(cl)
- ## =========================================================
- ## EWAS function
- ## =========================================================
- run_mod <- function(outcome, clindat, methdat, filename, cl, model_formula) {
- stopifnot(identical(colnames(methdat), clindat[[sample_id_var]]))
- clindat$outcome_var <- clindat[[outcome]]
- clusterEvalQ(cl, {
- library(stats)
- NULL
- })
- clusterExport(
- cl,
- varlist = c("methdat", "clindat", "model_formula"),
- envir = environment()
- )
- all_cpgs <- parApply(cl, data.frame(methdat), 1, function(mrow) {
- tmp_dat <- clindat
- tmp_dat$meth_beta <- as.numeric(mrow)
- mean_cpg <- mean(tmp_dat$meth_beta, na.rm = TRUE)
- sd_cpg <- sd(tmp_dat$meth_beta, na.rm = TRUE)
- mod <- tryCatch(
- lm(as.formula(model_formula), data = tmp_dat),
- error = function(e) NULL
- )
- if (is.null(mod)) {
- res <- rep(NA, 5)
- } else {
- coef_tab <- summary(mod)$coefficients
- res <- c(coef_tab[2, ], nobs(mod))
- }
- res <- c(res, mean_cpg, sd_cpg)
- names(res) <- c("beta", "se", "t_val", "p_val", "N", "mean", "sd")
- res
- })
- all_cpgs <- t(all_cpgs)
- all_cpgs <- as.data.frame(all_cpgs, stringsAsFactors = FALSE)
- all_cpgs$cpg <- rownames(methdat)
- write.table(all_cpgs, file = filename, sep = "\t", quote = FALSE, row.names = FALSE)
- return("Success")
- }
- ## =========================================================
- ## Output filename
- ## =========================================================
- outfile <- file.path(
- output_dir,
- paste0(
- study_name, "_", array_type, "_", ancestry, "_",
- Pheno, "_", Model, "_", Strata, "_",
- tissue, "_", run_date, "_Node_", nid, ".txt"
- )
- )
- ## =========================================================
- ## Run EWAS
- ## =========================================================
- message("Starting EWAS on node ", nid)
- result <- run_mod(
- outcome = Pheno,
- clindat = cdat,
- methdat = meth_chunk,
- filename = outfile,
- cl = cl,
- model_formula = model_formula
- )
- message("Finished EWAS on node ", nid, " | Result: ", result)
- ## =========================================================
- ## Clean up
- ## =========================================================
- stopCluster(cl)
- message("Output written to: ", outfile)
- message("Combine node-level output files after all jobs finish.")
Run_EWAS_script.R, under CC-BY-4.0 · at the source
Overview
and 6 other authors
P. Eline Slagboom6,13, Simon R. Cox5, Hans Jörgen Grabe3,14, Qiong Yang2,15, N. Ahmad Aziz1,16, Monique M.B. Breteler1,1717 affiliations
- Population Health Sciences, German Centre for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489, Greifswald, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, 17475, Germany
- Lothian Birth Cohorts, Department of Psychology, The University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Molecular Epidemiology, Department of Biomedical Data Science, Leiden University Medical Centre, 233 ZA, Leiden, the Netherlands
- Mathematics and Statistics, Curtin University, 6845, Perth, Australia
- Artificial Intelligence in Medical Imaging, German Centre for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- Institute for Community Medicine, University Medicine Greifswald, 17489, Greifswald, Germany
- Institute of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, 17489, Greifswald, Germany
- Brain Research Imaging Centre, The University of Edinburgh, Edinburgh, EH8 9AB, UK
- Centre for Healthy Brain Ageing, Discipline of Psychiatry and Mental Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, 2052, Australia
- Max Planck Institute for Biology of Ageing, 50931, Cologne, Germany
- German Centre for Neurodegenerative Diseases (DZNE), Partner Site Rostock/Greifswald, 17489, Greifswald, Germany
- The Framingham Heart Study, Framingham, MA, 01701, USA
- Department of Neurology, Faculty of Medicine, University of Bonn, 53127, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty of Medicine, University of Bonn, 53127, Bonn, Germany
Abstract
Background: Left-right hippocampal volumetric asymmetry and atrophy are implicated in neurodegenerative and neuropsychiatric disorders, yet their molecular basis in healthy adults remains poorly understood.
Methods: We conducted a meta-analysis of epigenome-wide association studies across six population-based cohorts (n = 8156; 53% women; mean age = 60.7 years) to identify DNA methylation signatures associated with left and right hippocampal volumes (LHCV, RHCV) and hippocampal asymmetry (i.e, differences between left and right volumes divided by their sums).
Findings: We identified five CpGs and 262 differentially methylated regions associated with LHCV, nine CpGs and 246 regions with RHCV, one CpG and 16 regions with asymmetry. Cross-omics integration uncovered 15 LHCV-related and 13 RHCV-related methylation-gene expression pairs, with five overlapping genes primarily involved in immune regulation. LHCV-specific genes were involved in cellular signalling, and Mendelian randomisation (MR) analyses supported a potential causal association between brain expression of DIP2C and increased risk of major depressive disorder. RHCV-specific genes were involved in neuronal differentiation pathways, with MR analyses suggesting that brain-tissue expression of BAIAP2, MACF1, SLC16A5, and CORO1B was associated with neuropsychiatric disorders. We also identified sex-specific patterns with hippocampal asymmetry. Notably, baseline methylation at these sites predicted hippocampal atrophy rates, explaining >10% of the variation. Associations with multiple healthy dietary patterns suggest modifiable influences on hippocampal structure.
Interpretation: These findings highlight distinct methylation profiles as potential biomarkers or therapeutic targets for neuropsychiatric and neurodegenerative conditions.
Funding: Institutional funds , 10.13039/
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.
Zenodo 18926492
Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)
- 28 September 2026: the link answers (HTTP 200)
1 file
- Run_EWAS_script.R, R, 309 lines, 2 matches
The paper's code and data availability statement is in the Data section.
Tracing map
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What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 1 script, each with its path and the digest of its content;
- 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data sharing statement
The data supporting the findings of this study are included in the manuscript and its supplementary materials. The complete EWAS summary statistics and analysis scripts are available via Zenodo (https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 2, 28 September 2026
- Authors: added Katharina Wittfeld (0000-0003-4383-5043); Nicola J. Armstrong (0000-0002-4477-293X); Santiago Estrada (0000-0003-0339-8870); N. Ahmad Aziz (0000-0001-6184-458X); Monique M.B. Breteler (0000-0002-0626-9305); removed Katharina Wittfeld; Nicola J. Armstrong; Santiago Estrada; N. Ahmad Aziz; Monique M.B. Breteler
Version 1, 28 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 26 authors, 6 keywords, 14 MeSH terms, 16 funders, 72 references.
Cite
This paper
Liu, D., Talevi, V., Tavares, J. F., Wang, R., Imtiaz, M. A., Melas, K., Teumer, A., Wittfeld, K., Hillary, R. F., Vojinovic, D., Beekman, M., Armstrong, N. J., Estrada, S., Völzke, H., Bülow, R., Royle, N. A., Wardlaw, J. M., Wen, W., Sachdev, P. S., . . . Breteler, M. M. (2026). DNA methylation signatures of bilateral hippocampal volume, asymmetry and atrophy: a cross-omics analysis in the general population. EBioMedicine, 128, 106289. https://
BibTeX
@article{liu2026dna,
author = {Liu, Dan and Talevi, Valentina and Tavares, Juliana F. and Wang, Ruiqi and Imtiaz, Mohammed A. and Melas, Konstantinos and Teumer, Alexander and Wittfeld, Katharina and Hillary, Robert F. and Vojinovic, Dina and Beekman, Marian and Armstrong, Nicola J. and Estrada, Santiago and Völzke, Henry and Bülow, Robin and Royle, Natalie A. and Wardlaw, Joanna M. and Wen, Wei and Sachdev, Perminder S. and Mather, Karen A. and Slagboom, P. Eline and Cox, Simon R. and Grabe, Hans Jörgen and Yang, Qiong and Aziz, N. Ahmad and Breteler, Monique M.B.},
title = {{DNA methylation signatures of bilateral hippocampal volume, asymmetry and atrophy: a cross-omics analysis in the general population}},
journal = {EBioMedicine},
year = {2026},
month = may,
volume = {128},
pages = {106289},
publisher = {Elsevier},
issn = {2352-3964},
doi = {10.1016/
url = {https://
pmid = {42114417},
pmcid = {PMC13191633}
}
RIS
TY - JOUR
AU - Liu, Dan
AU - Talevi, Valentina
AU - Tavares, Juliana F.
AU - Wang, Ruiqi
AU - Imtiaz, Mohammed A.
AU - Melas, Konstantinos
AU - Teumer, Alexander
AU - Wittfeld, Katharina
AU - Hillary, Robert F.
AU - Vojinovic, Dina
AU - Beekman, Marian
AU - Armstrong, Nicola J.
AU - Estrada, Santiago
AU - Völzke, Henry
AU - Bülow, Robin
AU - Royle, Natalie A.
AU - Wardlaw, Joanna M.
AU - Wen, Wei
AU - Sachdev, Perminder S.
AU - Mather, Karen A.
AU - Slagboom, P. Eline
AU - Cox, Simon R.
AU - Grabe, Hans Jörgen
AU - Yang, Qiong
AU - Aziz, N. Ahmad
AU - Breteler, Monique M.B.
TI - DNA methylation signatures of bilateral hippocampal volume, asymmetry and atrophy: a cross-omics analysis in the general population
T2 - EBioMedicine
J2 - EBioMedicine
PY - 2026
DA - 2026/
VL - 128
SP - 106289
SN - 2352-3964
PB - Elsevier
DO - 10.1016/
UR - https://
LA - en
ER -
CSL-JSON
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