GWAS summary statistics for milk HMO concentrations

GWAS summary statistics for the paper "Host and environmental determinants of human milk oligosaccharides and microbiota in the Lifelines NEXT cohort" by Spreckels et al. 2025 (https://doi.org/10.1016/j.celrep.2025.116124). GWAS were performed to investigate the effect of maternal genetics on HMO concentrations. For each timepoint (0.5–6 months), a separate GWAS was performed using PLINK version 2.0120. We used inverse rank-transformed HMO data and added the first two genotype principal components as covariates to the PLINK GWAS model to correct for population stratification. Only bi-allelic genetic variants with imputation quality >0.5, minor allele frequency >0.05, call rate >0.95, and a Hardy-Weinberg equilibrium p-value >10−4 were used. To correct for multiple testing, we used the Bonferroni correction method, with a p-value <1.79e−9 considered significant. The shared files are tar archives per timepoint, which contain separate GWAS summary statistics files for each HMO measured at that timepoint.