Hypermethylation of H19 and GNAS was seen only in the late passage samples (in 8/11 and 1/11 fibroblast-derived clones, respectively), pointing to instability at these loci with time in culture. Losses in DNA methylation were also observed in HYMA1/PLAGL1, GRB10, KCNQ1, SNRPN and GNAS. Aberrant methylation of L3MBTL was present in 2/4 chondrocyte hiPSC clones. Analysis of an additional 22 hPSC, 60 tissue and 19 primary samples identified additional aberrations in methylation of DIRAS3, PEG10, and MEST in hPSCs, and demonstrated the relative stability of these loci in tissues and primary cell lines (Figure S3E).
