Comparison of CpG methylation patterns in cRCC (VHL and sporadic wtVHL) and pRCC demonstrated that (at a 1% significance level using log-likelihood G-test) one gene (CDH1) was more methylated in the cRCC (29% vs 0%; p < 0.01) and 14 genes were more methylated in the papillary RCC (RASSF1, SERPINE1, HOXA11, HOXC6, JAK3, PDGFRB, MMP2, ITGB1, CREB1, MYOD1, GSTM2, TNFRSF10C, SMARCA3 and COL1A1 (see Additional file 2). The gene discussed is HOXA11; the disease is chromophobe renal cell carcinoma.