Bisulfite (BS) PCRs using genomic DNAs from subjects with a range of 4q allelic combinations show the specificity of the three bisulfite sequencing (BSS) assays. Nested PCRs were performed using BS-converted genomic DNAs from seven subjects, five FSHD1 and two healthy, with varying 4q haplotypes (4qA/A, 4qA/B, 4qB/B, and 4qA/A-L, as indicated). The primer sets used are indicated to the right of each panel. The 4qA BS PCR (upper panel) amplified a product from all five subjects possessing at least 1 4qA allele and did not amplify any detectable product from the two subjects lacking a 4qA allele. The 4qA-L BS PCR (middle panel) only amplified a product from the one subject possessing a 4qA-L allele. The DUX4 5’ BS PCR (lower panel) amplified a product from all seven subjects. The identities of all BS PCR products were confirmed by sequencing.