Figure 3.

Female subjects with SPEN-truncating mutations exhibit an X chromosome-specific episignature

(A) Samples from female individuals were compared to samples from healthy female control individuals processed alongside the SPEN-mutated samples (batch controls) and CpGs on the X chromosome were analyzed. The episignature was able to separate SPEN-truncated samples from control individuals as shown by hierarchical clustering (left) and multidimensional scaling (right) analyses.

(B) The X chromosome episignature was able to differentiate between females with SPEN mutations and control samples but not between males with SPEN mutations and control samples.

(C) Support vector machine-based methylation variant pathogenicity (MVP) scores showed that the X chromosome signature scored female samples differently from all the other tested samples.