WGBS of ctDNA
cfDNA (5ng) and germline DNA (100ng) were sonicated using a Covaris S220 to approximately 180–220 bp and bisulfite converted using the EZ DNA Methylation-Gold Kit. The single-stranded DNA obtained was processed for library construction using the Accel-NGS Methyl-seq DNA Library kit as per manufacturer instructions. Truncated adapter sequences were incorporated to the single-stranded DNA in a template-independent reaction through sequential steps using the Adaptase module (Swift BioSciences). DNA was then enriched using PCR with primers compatible with Illumina sequencing, 9 cycles for cfDNA, and 6 cycles for genomic DNA.