DNA methylation analysis was performed using DNA from 29 patients based on the UROMOL2016 classification with 10–11 samples from each class. After re-classification, we had 10 samples in class 1, 12 in class 2a/2b with a majority in class 2b and 6 in class 3. All tumors were selected to have a high silhouette score, and all were Ta high-grade tumors. We used 500 ng genomic DNA for bisulfite conversion followed by whole-genome amplification prior to hybridization to EPIC BeadChip (Illumina, San Diego, CA) overnight as described by the manufacturer and then scanned with the Illumina iSCAN system. Data was imported and processed using the RnBeads v2.2R package pipeline. For the preprocessing of the data, the normalization method was set to “illumina” and the background correction method to “methylumi.noob”.

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