Illustration of measuring DNA methylation using the MethyLight technology. A) Example DNA from an experimental sample and an M.Sss I-treated control sample. In the M.Sss I-treated control sample all unmethylated MLH1 molecules become methylated. B) Sampling of DNA fragments. A large number of fragments sampled results in a very low real-time PCR cycle threshold (ALU C(t) value). A very small number of fragments sampled results in a high ALU C(t) value. C) The formula to compute Percent Methylated Reference (PMR), a ratio of methylated alleles in the experimental sample (black balls) over the quantity of input DNA (grey balls) in the experimental and reference samples.