We quantified cell subfraction percentages for CD8 T cells, CD4 T cells, B cells, monocytes and granulocytes by inputting DNA methylation signatures of 473 loci into an algorithm designed for quantification of the above cell types using DNA methylation proxies from HM450 arrays.20 Before cell-type proportion calculation for the prepartum depressed cohort, DNA methylation values at the 473 loci were transformed by subtracting the residuals from a linear model of the mean DNA methylation values of three cross-batch controls from the prepartum euthymic cohort (batch 1) vs the mean DNA methylation values from two replicates of the same sample run in the prepartum depressed cohort (batch 2).
