5639 - Simultaneous multi-cancer detection and tissue of origin (TOO) localization using targeted bisulfite sequencing of plasma cell-free DNA (cfDNA)

Background

Our previous discovery work identified whole-genome bisulfite sequencing as outperforming whole-genome and targeted sequencing approaches for multi-cancer detection. We developed a targeted methylation assay for multi-cancer detection and tissue of origin (TOO) localization.

Methods

Participants were from Circulating Cell-free Genome Atlas (CCGA; NCT02889978) and STRIVE (NCT03085888), both prospective, multi-center, observational studies with longitudinal follow-up. cfDNA from 3,583 evaluable samples (1,530 cancer, 2,053 non-cancer) spanned >20 tumor types of all stages; a prespecified subset of these comprised the “multi-cancer” group: anorectal, hormone-receptor (HR)-negative breast, colorectal, esophageal, gallbladder, gastric, head and neck, hepatobiliary, lung, lymphoid leukemia, lymphoma, multiple myeloma, ovarian, and pancreatic (937 cancer [all stages]). A cross-validated targeted methylation test evaluated cfDNA for predictability of cancer presence and TOO; precision defined as the fraction of correct calls. Breast and lung cancer subtypes were also assessed. All analyses targeted 99.4% specificity (0.6% false-positive rate).

Results

Participants with and without cancer were similar in age. Specificity was set to 99.4%. For the prespecified multi-cancer group, overall sensitivity was 76% (73-78): stage I 32% (25-40), stage II 76% (69-82), stage III 85% (80-89), and stage IV 93% (89-95). Among all samples, overall sensitivity was 55% (52-57%): stage I 19% (15-23%), stage II 43% (38-48%), stage III 78% (73-82%), and stage IV 90% (86-93%). Overall TOO precision for the multi-cancer group and all samples was 89%, and was similar across stages. Squamous-cell and small-cell lung cancer had higher sensitivity than adenocarcinoma: 84% (75-91) vs 83% (69-92) vs 58% (49-67); HR-negative had higher sensitivity than HR-positive breast cancer: 66% (53-77) vs 20% (15-27).

Conclusions

This targeted methylation assay detected cancer signal across >20 cancer types with a single, fixed, low false positive rate and highly accurate TOO localization. These data support the feasibility of a single test that can screen for multiple cancers.

Clinical trial identification

NCT02889978, NCT03085888.

Editorial acknowledgement

Sarah Prins, PhD (GRAIL, Inc.), and Megan P. Hall, PhD (GRAIL, Inc.).

Legal entity responsible for the study

GRAIL, Inc.

Funding

GRAIL, Inc.

Disclosure

G.R. Oxnard: Advisory / Consultancy, Officer / Board of Directors: Inivata; Honoraria (self): Guardant Health; Honoraria (self): Sysmex; Honoraria (self): Bio-Rad; Advisory / Consultancy: DropWorks; Advisory / Consultancy: AstraZeneca; Advisory / Consultancy: GRAIL, Inc.. E.A. Klein: Advisory / Consultancy: GRAIL, Inc.; Advisory / Consultancy: Genomic Health; Advisory / Consultancy: GenomeDx Biosciences. M.V. Seiden: Shareholder / Stockholder / Stock options, Full / Part-time employment: McKesson. E. Hubbell: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. O. Venn: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. A. Jamshidi: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc.; Shareholder / Stockholder / Stock options: Illumina. N. Zhang: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. J.F. Beausang: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. S. Gross: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. K.N. Kurtzman: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc.; Shareholder / Stockholder / Stock options: Illumina. E.T. Fung: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. B. Allen: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. A.P. Fields: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. H. Liu: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. A.M. Aravanis: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. A. Hartman: Shareholder / Stockholder / Stock options, Full / Part-time employment: GRAIL, Inc. M.C. Liu: Honoraria (institution): GRAIL, Inc. All other authors have declared no conflicts of interest.