We performed a combined study using methylation data from Flower et al.36 (link) analysed by Infinium HumanMethylation450 BeadChip and data from the metEPICVal study previously described. First, we analysed HM450K array samples according to the methods described in the data pre-processing section. We retained methylation levels for 405,068 probes present in both metEPICVal and Flower et al.’s36 (link) HM450K study in a total of 64 samples (32 BCO samples, 32 from BCVY) that were used in the validation study.
Additionally, we used methylation data from independent breast tissue samples available from TCGA, that includes data for 485,577 probes in 720 BCO and 27 BCVY samples. Gene expression study for TCGA data was done with 50 permutations, and 50 samples were randomly selected and balanced by subtype.
Both studies were performed using the Illumina HM450K array, which includes only half of the probes present in the EPICarray. To validate our results from the BCVY-BCO study we selected differentially methylated miRNA probes that were included in HM450K and a Wilcoxon Rank Sum test was performed between BCVY and BCO tumour samples.
Additionally, we used methylation data from independent breast tissue samples available from TCGA, that includes data for 485,577 probes in 720 BCO and 27 BCVY samples. Gene expression study for TCGA data was done with 50 permutations, and 50 samples were randomly selected and balanced by subtype.
Both studies were performed using the Illumina HM450K array, which includes only half of the probes present in the EPICarray. To validate our results from the BCVY-BCO study we selected differentially methylated miRNA probes that were included in HM450K and a Wilcoxon Rank Sum test was performed between BCVY and BCO tumour samples.
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