Fig. 3: A sscf-MeDIP-Seq procedure to analyze methylomes of plasma cell free DNA (cfDNA).
From: Tumor detection by analysis of both symmetric- and hemi-methylation of plasma cell-free DNA
a An outline of the sscf-MeDIP-Seq method for analyzing cfDNA methylomes. SM symmetric DNA methylation, HM hemi-methylation. Please note that DNA methylation on single-stranded (ss) DNA would be regarded as HMR. Based on 8 input samples, the number of HMRs that arose from ssDNAs was likely to be small. b A snapshot of cfDNA DMR at the TBX2 gene locus. The shaded area highlight DMRs identified using 10 cfDNA samples from liver tumor patients compared to 10 cfDNA samples from controls, with only two samples from each group shown. Also shown are sequence reads of two input samples in which methylated DNA immunoprecipitation was also not performed. c Heatmap of cfDNA DMRs from 10 plasma samples of liver cancer and 10 plasma samples of non-tumor controls. The Z score, shown in color, represents log2 (RPKM) of sscf-MeDIP-Seq signals. Violin plot (d) and bar plot (e) showing overlaps between liver tumor cfDNA DMRs identified by sscf-MeDIP-Seq and liver tumor DNA DMRs identified in this study using ssg-MeDIP-seq. Violin plots represent the random distribution of overlaps from 100 permutations and P values were computed using random permutation distribution in a one-side way. Green diamonds represent observed overlaps. Fisher test was used for statistical analysis of the bar plot in a two-side way. f Heatmap of plasma cfDNA DHMRs of 10 liver cancer samples and 10 controls. The hemi-methylation score, shown in color, was calculated using formula shown in Fig. 2a and represents HM levels. g Overlap of plasma cfDNA DMRs and cfDNA DHMRs of the same 10 liver cancer samples compared to 10 controls.
