Fig. 3

Example of a bi-modal pattern of β values distribution. a. Upper panel: Individual β values for 36 cell lines examined using the type I probe (cg16310958) interrogating CpG site with a SNP (G>A) in the second position. High β values are observed in cell lines with CpG (blue) and CpG/TpA (red) genotypes, low—in lines with CpA (TpA in converted DNA; yellow) genotypes. Similar bi-modal distributions were also observed when CpG sites with SNPs in the second position were interrogated by type II probes (not shown). Lower panel: Fluorescence readouts for the probe cg16310958. Signals are detected as a result of the extension of probes M (green) and U (red). All lines with homozygous CpG genotypes display strong green and no red signal, indicating methylated status. In heterozygotes the only readable signal is that from M probes. In lines with homozygous CpA (TpA in converted DNA) genotypes, fluorescence signals from both M and U probes are very low. b. Sequences of the cg16310958 probes M and U, aligned with the genomic sequence with the G>A substitution in the second position of the interrogated dinucleotide (TpA allele- bold and underlined). Additional CpG site under the probes (marked in red) appear to have the same methylation status as the CpG allele in the interrogated site. Neither U nor M probe would hybridize efficiently to the TpG allele