Highlights
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Targeted methylation analysis of cfDNA simultaneously detected and localized >50 cancer types, including high-mortality cancers that lack screening paradigms.
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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%.
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This targeted methylation approach localized the tissue of origin with >90% accuracy, which will be critical for directing follow-up care.
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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
References
NIH National Cancer Insitute. Surveillance, Epidemiology, and End Results (SEER) Program (www.seer.cancer.gov) SEER∗Stat Database: Incidence - SEER 18 Regs Research Data, Nov 2017 Sub (1973-2015) National Cancer Institute, DCCPS, Surveillance Research Program, released April 2018, based on the November 2017 submission. Statistic based on all invasive cancers, ages 50+ at diagnosis. [www.seer.cancer.gov].
Noone A, Howlander N, Krapcho M, et al., eds. SEER Cancer Statistics Review, 1975-2015, National Cancer Institute, software version 8.3.6. Bethesda. Available at: https://seer.cancer.gov/csr/1975_2015/.
- Colorectal cancer screening: the role of psychological, social and background factors in decision-making process.Clin Pract Epidemiol Ment Health. 2018; 14: 63-69
- Nationwide cross-sectional adherence to mammography screening guidelines: national behavioral risk factor surveillance system survey results.Breast Cancer Res Treat. 2017; 164: 719-725
- Adherence to annual lung cancer screening within the Veterans Health Administration lung cancer screening demonstration project.Chest. 2018; 154: 636A-637A
- Predictors of cervical cancer screening adherence in the United States: a systematic review.J Adv Pract Oncol. 2014; 5: 31-41
- Simultaneous multi-cancer detection and tissue of origin (TOO) localization using targeted bisulfite sequencing of plasma cell-free DNA (cfDNA).Ann Oncol. 2019; 30: LBA77
- Genome-wide cell-free DNA (cfDNA) methylation signatures and effect on tissue of origin (TOO) performance.J Clin Oncol. 2019; 37: 3049
- Detection and localization of surgically resectable cancers with a multi-analyte blood test.Science. 2018; 359: 926-930
- Genome-wide cell-free DNA fragmentation in patients with cancer.Nature. 2019; 570: 385-389
- Sensitive tumour detection and classification using plasma cell-free DNA methylomes.Nature. 2018; 563: 579-583
- Circulating tumor DNA analysis in patients with cancer: American Society of Clinical Oncology and College of American Pathologists joint review.J Clin Oncol. 2018; 36: 1631-1641
- High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants.Nat Med. 2019; 25: 1928-1937
- False-positive plasma genotyping due to clonal hematopoiesis.Clin Cancer Res. 2018; 24: 4437-4443
- Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing.Sci Transl Med. 2012; 4: 162ra154
- Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing.Proc Natl Acad Sci. 2013; 110: 18761-18768
- Plasma cell-free DNA (cfDNA) assays for early multi-cancer detection: the circulating cell-free genome atlas (CCGA) study.Ann Oncol. 2018; 29: 500
- Prevalence of clonal hematopoiesis of indeterminate potential (CHIP) measured by an ultra-sensitive sequencing assay: exploratory analysis of the Circulating Cancer Genome Atlas (CCGA) study.J Clin Oncol. 2018; 36: 12003
- Development of a comprehensive cell-free DNA (cfDNA) assay for early detection of multiple tumor types: the Circulating Cell-free Genome Atlas (CCGA) study.J Clin Oncol. 2018; 36: 12021
- The Eighth Edition AJCC Cancer Staging Manual: continuing to build a bridge from a population-based to a more ‘personalized’ approach to cancer staging.CA Cancer J Clin. 2017; 67: 93-99
Surveillance, Epidemiology, and End Results (SEER) Program SEER∗Stat Database: Mortality - All COD, Aggregated With State, Total U.S. (1969-2016) <Katrina/Rita Population Adjustment>, National Cancer Institute, DCCPS, Surveillance Research Program, released December 2018. Underlying mortality data provided by NCHS (www.cdc.gov/nchs). Statistic based on 2015-2016 data, all ages. [www.seer.cancer.gov].
- Initial sequencing and analysis of the human genome.Nature. 2001; 409: 860-921
- Cancer genome landscapes.Science. 2013; 339: 1546-1558
- The human genome browser at UCSC.Genome Research. 2002; 6: 996-1006
- Detection and localization of surgically resectable cancers with a multi-analyte blood test.Science. 2018; 359: 926-930
- Cumulative incidence of false-positive results in repeated, multimodal cancer screening.Ann Fam Med. 2009; 7: 212-222
- Surveillance, Epidemiology, and End Results SEER∗Stat software.(Available at:)
- National performance benchmarks for modern screening digital mammography: update from the Breast Cancer Surveillance Consortium.Radiology. 2017; 283: 49-58
- Cologuard Summary of Safety and Effectiveness Data (Premarket Approval Application P130017).2014 (Available at https://www.accessdata.fda.gov/cdrh_docs/pdf13/P130017B.pdf)
- Results of initial low-dose computed tomographic screening for lung cancer.N Engl J Med. 2013; 368: 1980-1991
- The Circulating Cell-free Genome Atlas (CCGA) study: follow-up (F/U) on non-cancer participants with cancer-like cell-free DNA signals.J Clin Oncol. 2019; 37: 5574
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Published online: March 30, 2020
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- 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 BriefLiu 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.
- Full-Text
- In Brief
- A multi-cancer detection test: focus on the positive predictive valueAnnals of OncologyVol. 31Issue 9
- In BriefRecently, 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.
- Full-Text
- In Brief
- Response to W.C. Taylor, and C. Fiala and E.P. DiamandisAnnals of OncologyVol. 31Issue 9
- In BriefWe 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.
- Full-Text
- In Brief
