Plasma cell-free DNA (cfDNA) assays for early multi-cancer detection: The circulating cell-free genome atlas (CCGA) study

Abstract

Background: A noninvasive cfDNA blood test detecting multiple high-mortality cancers at early stages when treatment is more likely effective could decrease cancer mortality. CCGA (NCT02889978) is a prospective multi-center observational study to develop a plasma cfDNA-based multi-cancer detection assay. Methods: Prospectively collected clinically evaluable samples (N = 2402) from non-cancer controls (C) and participants with newly diagnosed untreated cancer (pts; 20 tumor types, all stages) were divided into training (n = 1458; 580 C, 878 pts) and test (n = 944; 368 C, 576 pts) sets and analyzed as a preplanned substudy. Prototype sequencing assays included paired cfDNA/white blood cell (WBC, 60000X) targeted sequencing, paired cfDNA/WBC whole genome sequencing (30X), cfDNA whole genome bisulfite sequencing (WGBS, 30X). Sensitivity was estimated at 98% specificity. Cancers with >5 pts in training and test are reported. Results: Overall, pts (all stages) and C had similar age, smoking status, and gender. WGBS returned the highest sensitivity and is included here; results were consistent across the targeted, WGS, and WGBS assays, and will be reported in full. WBC signal was used to correct for clonal hematopoiesis. Stage I-IV cancer detection was consistent in training and test sets. In training, cancer-specific sensitivities (high-signal cancers) ranged from 54-92% and will be reported in detail. In individual cancers in the test set, numbers and sensitivity (95% CI) were: 22 hormone receptor negative breast (36%, 17-59), 45 colorectal (60%, 44-74), 7 esophageal (43%, 10-82), 12 head & neck (50%, 21-79), 15 hepatobiliary (73%, 45-92), 47 lung (70%, 55-83), 22 lymphoma (64%, 41-83), 7 ovarian (71%, 29-96) and 23 pancreatic (74%, 52-90). Results were also consistent between training and test sets in stage I-III and stage IV cancers. Conclusions: A cfDNA-based blood test detected multiple cancers at various stages consistently in training and test sets. This approach is promising as a multi-cancer early detection test, including for high mortality unscreened cancers where stage shift can impact mortality. Further assay and clinical development of a multi-cancer cfDNA test in large-scale clinical studies, including CCGA, is ongoing. Clinical trial identification: NCT02889978. Editorial acknowledgement: Writing support provided by Megan P. Hall, PhD (GRAIL, Inc., Menlo Park, CA). Legal entity responsible for the study: GRAIL, Inc. Funding: GRAIL, Inc. Disclosure: M.C. Liu: Advisory board member: GRAIL, Inc. E. Klein: Consultant: GRAIL Inc., GenomicHealth, GenomeDx. E. Hubbell: Employee: GRAIL, Inc. with options to hold stock; Stock: ThermoFisher. T. Maddala, A.M. Aravanis, J.F. Beausang, D. Filippova, S. Gross, L. Shen, N. Zhang, O. Venn, J. Yecies, S. Patel, A-R. Hartman: Employee: GRAIL, Inc. with options to hold stock in the company. A. Jamshidi, K. Kurtzman: Employee: GRAIL, Inc. with options to hold stock in the company; Stock: Illumina. M. Seiden: Employee and stocks: McKesson. G.Oxnard: Advisory board member, consultant: Inivata; Honorarium: Guardant Health, Sysmex, BioRad; Consultant: DropWorks, AstraZeneca, GRAIL, Inc. All other authors have declared no conflicts of interest.