Overall, this direct comparison of two commonly used BSS methods for FSHD indicates that the Jones et al. methodology produces an accurate assessment of the DNA methylation state of the FSHD-associated chromosome 4q35 D4Z4 array that is consistent with prior epigenetic analyses of FSHD using other methods [6,7,9,13,31,46], and accurately distinguishes FSHD from healthy, as well as distinguishing FSHD1 from FSHD2. Here, SMCHD1 is linked to facioscapulohumeral muscular dystrophy.