Methylation analysis of serum cfDNA pooled samples for the discovery of non-invasive biomarkers for colorectal cancer

We explored the differential methylation patterns found in cfDNA between no neoplasia (NN; individuals with no colorectal findings, benign pathologies and non-advanced adenomas) and patients with advanced neoplasia (AN; advanced adenomas and colorectal cancer) using pooled samples, for the discovery of non-invasive methylation biomarkers for CRC screening. cfDNA was extracted from serum samples and methylation measurements were assessed with the Infinium MethylationEPIC BeadChip. Data was mainly preprocessed and analyzed with R/Bioconductor packages. We explored the differential methylation patterns found in cfDNA between no neoplasia and advanced neoplasia using pooled samples. cfDNA was extracted from 280 serum samples with a modifed phenol-chlorophorm protocol. A total of 28 cfDNA pooled samples were constructed using equal amounts of cfDNA from 5 men and 5 women with the same colorectal pathology as described in Gallardo-Gómez et al., Clinical Epigenetics 2018;10:53 (PMID: 29686738). cfDNA was bisulfite treated and was analyzed with the Infinium MethylationEPIC BeadChip microarray, covering over 850,000 CpG sites across the genome.