BSS analysis identifies distinct epigenetic signatures for FSHD1 and healthy controls that are similar between genomic DNA samples isolated from blood and saliva. Genomic DNAs isolated from PBMCs or saliva from the same four subjects were analyzed using the (A) 4qA BSS assay and 4qA-L BSS assay, and (B) the DUX4 5’ assay. 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 at the expected site. The DNA methylation for the Q1 is indicated along with the range from the lowest percentage methylation to the highest percentage methylation in the set. *Neither the 4qA BS PCR nor the 4qA-L BS PCR produced a product from this subject, indicating that no 4qA or 4qA-L alleles were present; therefore, an alternative BSS protocol (4q/10q BSS) that amplifies both 4qA and 10qA alleles was performed (see Methods). The white boxes indicate no CpGs were detected at positions #16 and #55, which suggested these sequences were derived from 10qA. However, analysis of the complete BSS sequence data provided an additional non-CpG polymorphism that identified all sequences as being derived from 4C166H chromosomes.