Fig. 3

Targeted sodium bisulfite pyrosequencing validation of DNAm alterations in NCBRS-SMARCA2 signature cases. a-c DNAm was assessed for three sites in the DNAm signature in the promoters of RUNX2 (cg19109335), HIF3A (cg23548163), and CEP85L (cg18102862); the change in DNAm across these sites was: + 17%, + 26%, and − 19% respectively. d-f Additional neighboring CpG sites covered by the assays from a-c. The additional CpG site in the RUNX2 promoter is represented on the EPIC array, those in HIF3A and CEP85L are not; the change in DNAm across these sites was: + 16%, + 30%, and − 25% respectively. Statistical significance between NCBRS and control groups was assessed using a Student’s t-test, p-values were corrected for multiple CpG assessed *p < 0.05, **p < 0.01, ***p < 0.001