Our results from pyrosequencing that intronic sequences far downstream of the canonical promoter region (EGFR, LHX2, SOX9 and RFX1) and intergenic sequences upstream of the promoter (PAX3 and EN1) were significantly hypermethylated in breast cancer may be related to new understandings of the transcription-regulatory roles played by DNA methylation in intragenic and distant intergenic regions [2, 66]. Here, PAX3 is linked to breast carcinoma.