Since our unbiased analyses showed frequent differences in DNA methylation in regions of genomic imprinting between hPSCs and somatic samples, as well as variability in these regions among hPSC samples, we examined imprinted loci separately. We identified 49 CpGs from the 27K DNA Methylation array that were assigned to known imprinted genes (geneimprint.org), and also displayed methylation patterns consistent with gametic imprints (Figure 4A). These loci were partially methylated in tissue samples, and were reciprocally methylated in gynogenetic samples (our parthenogenetic hESCs and previously published data from an ovarian teratoma (Choufani et al., 2011)) and androgenetic samples (previously published data from hydatidiform moles (Choufani et al., 2011)) (Table S5A, Figure S3A–D, Experimental Procedures). Analysis of the DNA methylation status of these imprinted CpGs in pluripotent cells compared to somatic cells showed recurrent hypermethylation of CpGs associated with the genes DIRAS3, NAP1L5, MEST, H19, and ZIM2/PEG3. In a small number of hPSC samples, hypomethylation occurred in PLAGL1 and GRB10. For GNAS, some hPSCs showed a gynogenetic pattern, while other hPSCs showed an androgenetic pattern.
