Using this approach, we identified lost and gained CTCF binding sites in each of the six cancer types (Additional file 4: Table S3) and confirmed that most identified lost/gained sites have significantly reduced/elevated CTCF binding levels (FDR ≤ 0.05, fold change ≥ 2) in that cancer compared to all other samples (Additional file 1: Fig. S2a), with absolute effect sizes ranging between 0.93 and 1.87 and an average of 1.46 (Additional file 1: Fig. S2b,c). The gene discussed is CTCF; the disease is cancer.