Hydroxymethylation profile of cell free DNA is a biomarker for early colorectal cancer

Abstract Early detection of colorectal cancer (CRC) will improve survival rates. We created a classifier to detect CRC, based on 5-hydroxymethylcytosine levels in cell free DNA isolated from blood samples of 2198 individuals. Our classifier discriminated CRC samples from controls with an area under the receiver operating characteristic curve (AUC) of 90% (sensitivity was 55% at 95% specificity). Performance was similar for early stage 1 (AUC 89%) and late stage 4 CRC (AUC 94%). Performance was independent of the proportion of tumor-DNA in the cell free DNA. We expanded the classifier to include information about cell free DNA fragment size and abundance across the genome. Overall performance was similar (AUC 91%), with gains in sensitivity (63% at 95% specificity). The 5-hydroxymethylcytosine signal allows detection of CRC, even in cell free DNA samples with undetectable tumor DNA. Including 5-hydroxymethylcytosine in multi-analyte screening, will improve sensitivity for early-stage cancer.