Fig. 1
DNA methylation analysis of molar tissue of a patient with a KHDC3L mutation. a Scatterplot of methylation values from the Illumina Human MethylationEPIC BeadChip array of 20-kb windows in the KHDC3Lc.1A>G mole compared with the grouped control placentas (n = 11). Highlighted are methylation levels of classic and placenta-specific maternal gDMRs. b UCSC browser screenshot of genomic methylation in KHDC3Lc.1A>G mole compared with the control placentas (n = 11). The zoomed-in view shows methylation over the KCNQ1OT1 imprinted domain with gDMR location highlighted in grey. Each vertical bar represents a single CpG on the array. c Heatmap showing methylation of maternal and paternal gDMRs in the KHDC3Lc.1A>G mole, control placentas (n = 11) and AnCHM. d, e Box and whisker plots showing methylation in the control placentas (n = 11) and KHDC3Lc.1A>G molar tissue at d maternal gDMRs (n = 43) and e placenta-specific methylated CGIs (n = 937), placenta-specific unmethylated CGIs (n = 11,728) and non-CGI windows (n = 48,581). Boxes represent the interquartile range; lines, the median; and dots beyond the whiskers, outliers. Comparisons in d and e are all statistically significant (p < 0.0001), although the effect size at maternal gDMRs is significantly greater (Additional file 3: Fig. S3E). Detailed statistical measures are given in Additional file 4: Table S3