Fig. 2: Comparison of RRBS data from different sample types.

a–d RRBS libraries were generated using the paired FF and FFPE tissues from 19 patients with primary cancer. a Size distributions for the two library types. FFPE-RRBS (red line), FF-RRBS (blue line). b Mean coverage of CpGs within CGIs for the two library types. FFPE-RRBS (red rectangle), FF-RRBS (blue rectangle). c Coverage uniformity of CpGs within CGIs. FFPE-RRBS (red line), FF-RRBS (blue line). d Comparison of the mean correlation of different DNA methylation metrics for paired (yellow rectangle) and unpaired (green rectangle) sample groups (n = 38). DNA methylation of CGIs was assessed using different methods, including beta value, CHALM, MHL, and PDR, as described in the Methods section. e–h RRBS libraries were constructed using the FFPE tissues from the primary and matched metastatic tissues of cancer patients (n = 8). e Size distributions for the FFPE-RRBS libraries derived from the primary (blue line) and matched metastatic (red line) tissues. f Mean coverage of the FFPE-RRBS libraries constructed using the primary (blue rectangle) and matched metastatic (red rectangle) tissues. g Coverage uniformity for the RRBS libraries of two tissue groups. Primary tissues (blue line); metastatic tissues (red line). h Comparison of the mean correlation of different DNA methylation metrics for paired (yellow rectangle) and unpaired (green rectangle) sample groups (n = 16). DNA methylation of CGIs was evaluated using different methods, including beta value, CHALM, MHL, and PDR, as described in the Methods section. In the box plots of b, d, f, and g, the center line, box limits and whiskers represent the median, upper and lower quartiles, and 1.5-fold interquartile range, respectively. Asterisks ∗ and ∗∗∗ indicate a significant difference at P < 0.05 and P < 0.001, respectively, as determined by the two-sided Wilcoxon rank sum test. Source data are available in a supplementary file.