Fig. 1: cfMethyl-Seq assay.
From: Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer
a Diagram of the cfMethyl-Seq protocol. b Typical TBE-UREA PAGE image of cfMethyl-Seq libraries made from cfDNA, compared with conventional RRBS with cfDNA or intact genomic DNA as input material. The non-specific ligation product from cfDNA fragments with the conventional RRBS protocol is indicated by an arrow. This technical validation experiment was repeated independently twice and showed similar results. For cfMethyl-Seq assays generating data for analysis, each sample was constructed into library without replicate. c The percentage of reads with MspI sites on both ends, on only one end, and on neither end from WGBS assay, our cfMethyl-Seq assay, and RRBS assay on cfDNA. Source data are provided as a Source Data file. d The percentage of mapped fragments that fall in CpG islands, CpG island shores, CpG island shelves, and open sea regions is shown for cfMethyl-Seq libraries, RRBS libraries, and WGBS libraries on cfDNA. Source data are provided as a Source Data file. e Methylation concordance between a genomic DNA sample sequenced with RRBS, and sheared and sequenced with cfMethyl-Seq, increases with depth of coverage. Pearson correlation (y-axis) of the methylation rate (beta value) in the two datasets was calculated on the CpG sites that are covered by both datasets at minimum depth of coverage specified on the x-axis. Source data are provided as a Source Data file. Abbreviations: RRBS Reduced representation bisulfite sequencing.
