methylation between the prepartum euthymic and depressed cohorts was assessed in two separate batches, as all initial analyses were performed on the euthymic cohort only. To control for this, we normalized DNA methylation levels at all 473 loci used for blood count proxy analysis using a cross-batch control. The predicted cell-type proportions at these controls showed moderate but nonsignificant batch effects between cohorts (Supplementary Table 4); however, the effects were in the opposite direction to the prepartum mood status association observed, suggesting that this association is a true effect of prepartum mood status. In addition, the significant correlation observed with CBC-derived values adds confidence to assertion that the proxy-derived values are representative of actual cell subtype proportions. Finally, the linear model incorporating CBC-derived cell proportions generated a highly accurate prediction of PPD status (AUC=0.96). Owing to the small size of the subsample used for this prediction, larger prospective cohorts will be required to validate the predictive efficacy of this model. Cumulatively, our data suggest that cell count information in combination with DNA methylation at HP1BP3 and TTC9B successfully and accurately predicts PPD status independent of prepartum mood status.
