GLI1 and cancer: To determine how the methylation differences contributed to the differential transcriptional activity of the Ptch alleles in RMS, we initially examined the binding of Gli1, a known activator of Ptch in cancer, in SM and RMS from 5 Ptch+/− mice and consecutively amplified the fragments 1–4 and a 197 bp fragment covering the polymorphism by qPCR (Supplemental Fig. S5 and data not shown).