CpG probes that were reciprocally methylated in gynogenetic (ovarian teratoma and parthenotes; entirely of maternal origin) and androgenetic (complete hydatidiform moles; entirely of paternal origin), partially methylated in tissue samples (stable imprinting) and associated with imprinted genes (according to geneimprint.com) were identified as gametic imprints (Figure S4). For range-scaled 27K DNA Methylation array data, we supplemented our data with published data from an ovarian teratoma and three hydatidiform mole samples46. All imprinted probes were partially methylated (0.25<β<0.75) in at least 75% of tissue samples. Maternal imprints were unmethylated (β<0.09) in at least 2 androgenetic samples and fully methylated (β>0.85) in at least 2 gynogenetic samples. Paternal imprints were unmethylated (β<0.09) in at least 2 gynogenetic samples and fully methylated (β>0.85) in at least 2 androgenetic samples (Table S5A). Due to differences in normalization, the criteria for identification of imprinted probes were slightly different for the 450K DNA Methylation array data. CpG probes were annotated to imprinted genes using the 450K DNA Methylation array manifest file, or if it fell within 5 kb upstream of the gene according to UCSC hg18.
