Epigenomic Profiling of Circulating cfDNA in Ovarian Cancer

Circulating cfDNA (cFDNA) was profiled using Illumina Infinium MethylationEPIC BeadChip arrays (Illumina, San Diego, CA). In this prospective case–control study, we compared the methylation profile of OC patients with matched age grouped controls. The study was approved by the Institutional Review Board of Beaumont Health System, Royal Oak, MI, USA (IRB#2018-306) and performed in accordance with the Declaration of Helsinki. All participants provided written informed consent. CfDNA was extracted using the blood from 5 OC female cases and 12 female controls. Blood samples were collected in Streck Cell-Free DNA BCT^® tubes^{19 (link)}. Samples were deidentified and processed within 24 h of sample collection. For the primary processing, these were centrifuged at 3000×g for 15 min and the plasma was aliquoted into cryogenic vials. The aliquoted plasma samples were stored at − 80 °C until further process. Using QIAamp circulating nucleic acid kit (Qiagen Cat # 55114) the ccfDNA was extracted. All samples were bisulfite converted using EZ DNA Methylation Kit (Zymo, USA) per the manufacturer’s standardized method. Illumina Infinium MethylationEPIC BeadChip arrays (~ 850,000 CpG loci genome-wide) was used for methylation analysis based on manufacturer’s standardized protocol^{20 (link)}.