Leveraging information about methylation patterns from blood-based circulating tumor cell-free DNA (cfDNA) sequences may to detect cancer at early stages, though stage I detection sensitivity remains low, according to research being published in the Annals of Oncology.

While several studies interrogating cfDNA data have shown promise in improving early cancer detection, an optimal method of interrogation has not yet been confirmed. The Circulating Cell-Free Genome Atlas (CCGA; ClinicalTrials.gov Identifier: NCT02889978) was designed to evaluate different methods of cfDNA analysis, with some results suggesting that whole-genome bisulfite sequencing interrogating methylation patterns may be the most effective.

In the present paper, the authors reported “results from the second case-control sub-study designed to develop, train, and validate a methylation-based assay for simultaneous multi-cancer detection across stages as well as [tissue of origin] localization in preparation for clinical validation and utility studies.” A further study (ClinicalTrials.gov Identifier: NCT04241796), also reported in this paper, evaluated the effects of returning cfDNA data results to healthcare providers.

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A total of 6689 participants were assigned to either a machine learning training data set (4720 patients) or a validation data set (1969 patients); 2482 individuals had previously untreated cancer (representing > 50 cancer types) and 4207 did not have cancer. Bisulfite sequencing of plasma cfDNA targeted a panel of more than 100,000 methylation regions. The researchers also developed and validated a classifier for cancer detection and tissue of origin localization.

Targeted methylation cfDNA test performance was consistent in the training and validation cohorts, with an overall specificity of 99.8% in the training compared with 99.3% in the validation cohort. Overall sensitivity was also consistent in both cohorts, but low with a stage I to III sensitivity of 44.2% for the training set and a sensitivity of 43.9% for the validation set for all cancer types. Stage I to III sensitivities for a preselected group of 12 cancer types (anus, bladder, colon/rectum, esophagus, head and neck, liver/bile duct, lung, lymphoma, ovary, pancreas, plasma cell neoplasm, and stomach) were 69.8% and 67.3% for training and validation sets, respectively.

In addition, results suggested that sensitivity may be lower in early-stage disease; 18% for stage I in all cancer types, compared with 43%, 81%, and 93% in stages II, III, and IV, respectively.

The developed classified predicted tissue of origin in 96% of samples with a cancer-like signal, and was correct in 93% of these predictions.

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“In summary, cfDNA sequencing of informative methylation patterns detected a broad range of cancer types at metastatic and non-metastatic stages with specificity and sensitivity performance approaching the goal for population-level screening,” the authors concluded. “These results support the feasibility of employing this targeted methylation analysis of cfDNA in ongoing clinical trials in the intended use population for early cancer detection.”

Disclosures: Multiple authors declared affiliations with the pharmaceutical industry. Please refer to the reference for a complete list of authors’ disclosures.


Liu MC, Oxnard GR, Klein EA, Swanton C, Seiden MV for CCGA Consortium. Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA [published online March 30, 2020]. Ann Oncol. doi: 10.1016/j.annonc.2020.02.011