Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA

Open AccessPublished:March 30, 2020DOI:https://doi.org/10.1016/j.annonc.2020.02.011

      Highlights

      • Targeted methylation analysis of cfDNA simultaneously detected and localized >50 cancer types, including high-mortality cancers that lack screening paradigms.
      • Cancers were detected across all stages (stage I–III sensitivity: 43.9%; stage I–IV sensitivity: 54.9%) at a specificity of >99% and a single false positive rate of <1%.
      • This targeted methylation approach localized the tissue of origin with >90% accuracy, which will be critical for directing follow-up care.
      • This supports the continued investigation of this test with the goal of population-scale early multi-cancer detection.

      Background

      Early cancer detection could identify tumors at a time when outcomes are superior and treatment is less morbid. This prospective case-control sub-study (from NCT02889978 and NCT03085888) assessed the performance of targeted methylation analysis of circulating cell-free DNA (cfDNA) to detect and localize multiple cancer types across all stages at high specificity.

      Participants and methods

      The 6689 participants [2482 cancer (>50 cancer types), 4207 non-cancer] were divided into training and validation sets. Plasma cfDNA underwent bisulfite sequencing targeting a panel of >100 000 informative methylation regions. A classifier was developed and validated for cancer detection and tissue of origin (TOO) localization.

      Results

      Performance was consistent in training and validation sets. In validation, specificity was 99.3% [95% confidence interval (CI): 98.3% to 99.8%; 0.7% false-positive rate (FPR)]. Stage I–III sensitivity was 67.3% (CI: 60.7% to 73.3%) in a pre-specified set of 12 cancer types (anus, bladder, colon/rectum, esophagus, head and neck, liver/bile-duct, lung, lymphoma, ovary, pancreas, plasma cell neoplasm, stomach), which account for ∼63% of US cancer deaths annually, and was 43.9% (CI: 39.4% to 48.5%) in all cancer types. Detection increased with increasing stage: in the pre-specified cancer types sensitivity was 39% (CI: 27% to 52%) in stage I, 69% (CI: 56% to 80%) in stage II, 83% (CI: 75% to 90%) in stage III, and 92% (CI: 86% to 96%) in stage IV. In all cancer types sensitivity was 18% (CI: 13% to 25%) in stage I, 43% (CI: 35% to 51%) in stage II, 81% (CI: 73% to 87%) in stage III, and 93% (CI: 87% to 96%) in stage IV. TOO was predicted in 96% of samples with cancer-like signal; of those, the TOO localization was accurate in 93%.

      Conclusions

      cfDNA sequencing leveraging informative methylation patterns detected more than 50 cancer types across stages. Considering the potential value of early detection in deadly malignancies, further evaluation of this test is justified in prospective population-level studies.

      Key words

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      Linked Article

      • Comment on ‘Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA’ by M. C. Liu et al.
        Annals of OncologyVol. 31Issue 9
        • In Brief
          Liu et al.1 reported the results of a study of targeted methylation analysis of circulating cell-free DNA as part of a project to develop a screening test for multiple cancers, supported by a company with the laudable mission ‘to detect cancer early, when it can be cured.’2 Unfortunately, methodological problems and misleading characterization of results detract from the usefulness of the authors’ report.
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      • A multi-cancer detection test: focus on the positive predictive value
        Annals of OncologyVol. 31Issue 9
        • In Brief
          Recently, Liu et al.1 published an important paper which evaluated the sensitivity and specificity of cell-free DNA (cfDNA) for early cancer detection. The test is based on analyzing methylation patterns of cfDNA by bisulfite sequencing at 100 000 informative sites followed by classifier analysis. Although >50 cancer types were evaluated, we will focus on average data and a selection of 12 cancers, due to space constraints. The report by Liu et al.1 represents an important extension of previous work by the same group; however, our previous work that identified important issues with this test was not discussed.
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      • Response to W.C. Taylor, and C. Fiala and E.P. Diamandis
        Annals of OncologyVol. 31Issue 9
        • In Brief
          We thank Taylor and Fiala and Diamandis for their comments on our recent manuscript (Liu et al.).1–3 In reviewing their comments, we re-emphasize that this study was a case-control study evaluating the specificity and sensitivity of a multi-cancer detection assay within a well-defined patient population, and was not intended to provide any specific claims on performance in an asymptomatic population being screened for cancer. Further, we agree that the development of useful screening tests requires rigorous and careful evaluation.
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