Figure 7.

Efficiency of SNP genotyping assay affected by the presence of non-canonical DNA methylation. (A) Synthetic single-stranded templates were used in an in vitro assay involving competitive annealing of ASO probes (3′ T or C colored gray) followed by extension and ligation to an LSO probe. A wild-type FVB template was used for all reactions and mixed with an unmodified BALB template (shown) or templates synthesized to contain one or two 5-methylcytosines or 5-hydroxymethylcytosines (locations indicated by C*). The reactions create a new strand that is amplified and sequenced (B) to reveal how template strand modification affected ASO-dependent allelic ratios. Results shown are from one of three independent experiments; statistics are for the pooled data.