The 4qA BSS analysis does not amplify from 10A176T or 4A166 alleles. (A) The 4qA BSS assay (upper panel) is specific for 4qA sequences (present in sample 17A) and does not amplify the non-permissive 10A176T or 4A166 alleles present in samples 27A and 27B. BSS PCR using oligonucleotide primers that do not distinguish between 4A and 10A176T (lower panel) amplifies robustly from all three samples. (B) Sequence analysis of the products from samples 27A and 27B confirmed their origins as being from a 10A176T allele. The lack of a detectable CpG at position #55 but the presence of a CpG at position #16 identifies these as derived from a chromosome with a 10A176T haplotype. Expected CpGs, based on predicted sequence composition of the unconverted region amplified, are listed in numerical order. Red boxes indicate methylated CpGs, blue boxes indicate unmethylated CpGs, and white boxes indicate no CpG detected at the expected site.