Fig. 3

Methylation profile consistent with maternal imprinting in UPD region. a Ideogram of chromosome 14q displays location of DUP-TRP/INV-DUP and AOH segment (top). Two out of three differential methylated regions (DMR) located at 14q32.2 (bottom) were assayed by Infinium Human Methylation450 Beadchip (Illumina). *DMR not assayed. b Beta value (β, i.e., percentage of methylation of a given cytosine) plots: β > 0.8 methylated, 0.2 > β < 0.8 partially methylated, β < 0.2 unmethylated. X-axis indicates genomic coordinates for each CpG dinucleotide assayed by the array for MEG3-DMR and MEG8-DMR (hg19). Color-matched dashed lines display β values for three groups of assayed individuals: blue, UPD(14)pat individuals (BAB7706); green, UPD(14)mat individuals (BAB489, BAB7704, BAB7705); red, controls without UPD(14) (BAB7085, BAB7086, BAB7087, BAB7088, BAB7291, BAB7292). Black line displays BAB7004 results. In both MEG3-DMR and MEG8-DMR, BAB7004 displays methylation profile consistent with UPD(14)mat. c Plot displays the methylation log-likelihood ratio (LLR) for the CpGs spanning the MEG3-DMR locus calculated using Nanopolish [36] in BAB7004 and control NA12878. Positive LLR indicates methylated CpG. Haplotypes are color-matched. For BAB7004, both haplotype alleles show skewed lack of methylation across MEG3-DMR consistent with maternal imprinting whereas control NA12878 shows a haplotype pattern expected for a non-UPD sample. Genomic coordinates are in hg19