Sequencing-free On-chip detection of lung cancer by fluorescent enzymatic profiling of cfDNA methylation

We present a highly sensitive, low-cost approach for detecting lung cancer and monitoring response to therapy, based on sequencing-free detection of methylation biomarkers in cell-free DNA. After bisulfite treatment and PCR amplification of cell-free DNA, an engineered methyltransferase is used to fluorescently label all originally methylated CpG sites. Labeled cell-free DNA is then analyzed on a standard hybridization microarray. In a proof-of-concept lung cancer study involving 103 participants, we distinguished patients with cancer from healthy individuals with both sensitivity and specificity exceeding 90% for stage 2-4 lung cancer.