Assessing the clear cell Renal Cell Carcinoma (ccRCC) DNA-methylome by MethylCapSeq. Homo sapiens

MethylCap-Seq experiments of 4 ccRCC cell lines (SKRC1, SKRC10, SKRC52, SKRC59) and one "normal" kidney cell line (HK2) were performed, and used, in combination with DAC/TSA re-expression data, to mine the ccRCC specific cancer methylome. Identified candidate DNA-methylation markers were evaluated by MSP in two independent series, yielding 4 validated markers (GREM1, NEURL, LAD1, NEFH) of which promoter methylation was highly predictive of survival. Overall design: After enrichment of methylated DNA by MBD-based affinity purification, captured fragments were paired-end sequenced on the GAIIx.