Fig. 3
Replication MWAS in Lothian Birth Cohort (LBC) 1921, LBC1936 and Avon Longitudinal Study of Parents and Children (ALSPAC) adults. a Manhattan plot for the replication MWAS for PRS of pT at 5 × 10−8. Each dot represents a CpG probe. X-axis represents the relative position of the probes in the genome. Y-axis represents −log10-transformed p-values. The red dashed line represents the significance threshold for Bonferroni correction. b Scatter plot showing the correlation of standardised regression coefficients between the discovery (GS) and replication (LCB1921+LBC1936+ALSPAC adults) analysis. Each dot represents a CpG probe. Probes shown in the figure are those associated with depression-PRS of pT at 5 × 10−8 in the discovery MWAS (in GS). Dots in green represent probes locate in the major histocompatibility complex (MHC) regions and those in red represent other probes that locate outside of the MHC region c Number of CpG probes significantly associated with polygenic risk scores (PRS) at nine different pTs for replication analysis. X-axis represents the pTs used for generating PRS. Y-axis shows the number of probes significant associated with the given PRS. The four different lines represent four types of methods to define significance