The best possible marker combination to discriminate BC from controls was the combination CFTR, SALL3, and TWIST1. We confirmed that these genes (and specifically CpG dinucleotides analyzed here) are hypermethylated in the bladder cancer tissue using methylation data from the TCGA Research Network [20] (Additional file 9: Figure S6). Here, SALL3 is linked to urinary bladder cancer.