Fig. 4
From: Reduced representative methylome profiling of cell-free DNA for breast cancer detection
Breast cancer detection using RRMP analysis of cfDNA. a, b Plots show the number of CpG islands (a) or promoters (b) with at least 100-fold combined coverage as a function of sequencing depth (x axis) for 4-cut RRMP and EM-seq from two cfDNA samples NBC16 and BC11. Vertical gray line indicates break in x-axis scale. c, d Heat maps compare individual CpG methylation values between 4-cut RRMP and EM-seq for cfDNA samples NBC16 (c, r = 0.86) and BC11 (d, r = 0.87). Analysis limited to CpGs with at least tenfold coverage (n = 6358 and 7028 CpGs). Percentages indicate the fraction of CpGs that differed between conditions (difference in beta values > 0.5). e Receiver operator characteristic curves (ROC) and area under the curve (AUC) values. f LOO cancer prediction scores for BC and NBC. Dashed line represents probability score threshold. Samples with a probability score above this threshold were predicted as BC