Analysis of cfDNA in cancer patients using tissue-specific methylation markers

We have developed an approach to identify the tissue origins of cfDNA, based on tissue-specific methylation patterns. We have combined public methylome datasets with locally-generated methylome of sorted primary cell types, to generate an extensive human methylome atlas. By interrogating this atlas we have identified multiple cytosines whose methylation pattern is unique to specific cell types, and used these loci as biomarkers to detect cfDNA derived from specific cell types. In the context of cancer, we use tissue-specific methylation patterns as a universal biomarker regardless of individual mutations. We demonstrate elevated breast cfDNA in patients with local breast cancer pre or post treatment, exocrine pancreas cfDNA in patients with pancreatic cancer, and intestinal epithelial cfDNA in patients with colorectal cancer. Strikingly, patients with metastases to the liver or brain have elevated brain and hepatocyte cfDNA, suggesting that cfDNA can be used to monitor damage to the tissue hosting tumor metastases. We also show the identification of the tissue of origin in cancer of unknown primary (CUP), based on methylation patterns of cfDNA. cfDNA methylation patterns offer a non-invasive window into normal human tissue dynamics and into a broad spectrum of human pathologies.