Fig. 3

Technical Validation of Differentially Methylated Regions. A Selection of EdgeR-based testing results for differential methylation between responders and non-responders both in EXT and STD arm, prior to validation. B Validation criteria are exemplarily illustrated for the 500 bp region assigned to WNT10A and its corresponding probe cg22587479. For this probe, a strong and distinct correlation between beta values and RPKM exists (Spearman’s rank correlation coefficient > 0.8). Differences in beta regression levels between resp. and non-resp. patients showed statistical significance and overall methylation differences showed congruency in the change between modalities, i.e. hypermethylation in patients with refractory disease both in the MCIp-seq and 450k assay. CR Complete Response; RD Refractory Disease; RPKM Reads per kilobase per million mapped reads