Fig. 2: DNA methylation profiles in AH cfDNAs are highly concordant with paired primary RB tumors.
From: Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy
A Violin plot showing the global DNA methylation level of sonicated DNA from the HCT116 cell line. DNA input amounts for EPIC methylation array assays are shown at the bottom. Non-sonicated bulk DNA (200 ng) was used as control. The median methylation values are shown in dots for each sample. B Smooth Kernel scatter plots showing the DNA methylation patterns of different amounts of sonicated DNA input DNA (y-axis) compared to the bulk DNA sample (x-axis). The r2 values are displayed for each plot. C MDS plot indicating the concordance of individual CHLA RB primary tumor sample (RB_CHLA, n = 4) and the paired AH cfDNA sample (AH_CHLA, n = 4) demonstrating AH is a valid substrate to assay tumor methylation signature. Top 10,000 most variably methylated probes were used to generate the plot. D Unsupervised hierarchical clustering analysis and heatmap representation of the methylation of the probes used in panel C.
