Abstract 2141: Development of a highly-sensitive targeted cell-free DNA epigenomic assay for early-stage multi-cancer screening
Authors: Valouev Anton , Zotenko Elena , Snyder Matthew , Eid Charbel , Nguyen Ngan , Min Jun , He Yupeng , Jaimovich Ariel , Axelrod Haley , Natarajan Prashanthi , Hartwig Anna , Vardi Noam , Banh Tam , Kennedy Andrew , Greenleaf William , Mortimer Stefanie , Duenwald Sven , Chudova Darya , Talasaz AmirAli 
Published: June 2022

Background: A blood-based cancer screening test must exhibit performance metrics optimized for the cancer of interest based on associated clinical diagnostic pathways and demonstrate an ability to detect disease at an early stage when intervention has a meaningful impact on individual and net population health outcomes. We evaluated the performance of a blood-based cancer screening assay in select tumor types where we believe cancer screening can save lives. The assay interrogates cell-free DNA (cfDNA) methylation signatures for early-stage cancer (stage I/II) detection and tissue of origin identification.

Methods: Whole blood samples from individuals with (N &gt; 1,500) and without (N &gt; 1,800) cancer were obtained from multiple cohorts. Plasma-derived cfDNA was profiled using a custom assay that enriches fragments with dense CpG methylation and further depletes uninformative background molecules. A broad genomic panel (16 Mb) targeting regions with low rates of methylation in healthy individuals was used to capture and sequence tumor-associated molecules while maintaining high sensitivity at low sequencing cost per sample. A cross-validated analysis was used to estimate out of sample performance of the predictive model. Classification thresholds corresponding to 90% and 95% specificities were established using a set of samples from individuals without a cancer diagnosis.

Results: To evaluate the performance of this screening assay in cancers with guideline-directed screening protocols, colorectal and lung cancers, detection was assessed at 90% specificity. At this threshold, sensitivity for stage I/II colorectal and lung cancer was 90% and 87%, respectively. For other cancers with no current guideline-directed screening paradigms, pancreatic and bladder cancers, a specificity threshold of 95% was applied. Sensitivity was 73% and 52% for stage I/II pancreatic and bladder cancer, respectively. Tissue of origin prediction evaluated at 98% specificity had accurate identification in 99% of colorectal, 94% of lung, 88% of bladder, and 86% of pancreatic cancers.

Conclusions: This multi-cancer targeted screening assay provides robust and sensitive detection of early-stage cancer at thresholds optimized for current screening paradigms with accurate tissue of origin identification. The assay is undergoing further expansion of its detection capabilities to include additional cancer types where screening can save lives. Clinical evaluation in registrational screening trials is ongoing (NCT05117840).

Citation Format: Anton Valouev, Elena Zotenko, Matthew Snyder, Charbel Eid, Ngan Nguyen, Jun Min, Yupeng He, Ariel Jaimovich, Haley Axelrod, Prashanthi Natarajan, Anna Hartwig, Noam Vardi, Tam Banh, Andrew Kennedy, William Greenleaf, Stefanie Mortimer, Sven Duenwald, Darya Chudova, AmirAli Talasaz. Development of a highly-sensitive targeted cell-free DNA epigenomic assay for early-stage multi-cancer screening [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2141.