73P Multi-cancer early detection through evaluation of aneuploidy, methylation, and protein biomarkers in plasma

Multi-cancer early detection (MCED) using a blood test represents a rapidly emerging, potentially transformative advance in preventive oncology. Given the complexity of carcinogenesis across organs, simultaneous analysis of several biomarkers will maximize assay performance, particularly for early stage tumors. Previously, we demonstrated the performance of blood tests that incorporated the detection of DNA mutations plus proteins and combining DNA methylation and proteins, respectively. In the current study, we assessed the combination of aneuploidy, DNA methylation, and proteins. To assess aneuploidy, we used the Repetitive Element AneupLoidy Sequencing System (REALSeqS). In addition, we explored in silico sequencing features from REALSeqS beyond aneuploidy to increase detection sensitivities. DNA methylation testing was performed on a refined panel of markers using the Target Enrichment Long-probe Quantitative Amplified Signal (TELQAS) assay on bisulfite converted cell-free DNA. For protein quantification we applied an immunoassay to quantify six extensively documented biomarkers. To assess the performance of these biomarkers, we designed a retrospectively-assembled, case-control study consisting of 600 cancers (12 organ types, all stages) and 1,920 non-cancers. From the total samples, 2,386 have been analyzed for all biomarkers. Using a stratified 5-fold cross-validation, we found that the combined markers can detect cancer across all 12 organ types and stages with a mean overall sensitivity of 52.6% (95% CI: 47.0%-58.2%) at mean specificity of 98.7% (95% CI: 98.3%-99.2%). By stage the following sensitivities were determined: Stage I/II: 32.8%, Stage III 59.9%, and stage IV 87.7%. The cancer-specific sensitivities were lowest for prostate and kidney cancers and highest for liver and ovarian cancers. In summary, these three biomarker classes provide complementary and highly specific components for a multi-cancer early detection test. When combining a diverse set of analytes, we believe that a single blood test has the potential to effectively detect a large number of cancer types, particularly in earlier stage disease.