Abstract
BackgroundOncology applications of cell-free DNA analysis are often limited by the amount of circulating tumor DNA and the fraction of cell-free DNA derived from tumor cells in a blood sample. This circulating tumor fraction varies widely between individuals and cancer types. Clinical factors that influence tumor fraction have not been completely elucidated.Methods and findingsCirculating tumor fraction was determined for breast, lung, and colorectal cancer participant samples in the first substudy of the Circulating Cell-free Genome Atlas study (CCGA; NCT02889978; multi-cancer early detection test development) and was related to tumor and patient characteristics. Linear models were created to determine the influence of tumor size combined with mitotic or metabolic activity (as tumor mitotic volume or excessive lesion glycolysis, respectively), histologic type, histologic grade, and lymph node status on tumor fraction. For breast and lung cancer, tumor mitotic volume and excessive lesion glycolysis (primary lesion volume scaled by percentage positive for Ki-67 or PET standardized uptake value minus 1.0, respectively) were the only statistically significant covariates. For colorectal cancer, the surface area of tumors invading beyond the subserosa was the only significant covariate. The models were validated with cases from the second CCGA substudy and show that these clinical correlates of circulating tumor fraction can predict and explain the performance of a multi-cancer early detection test.ConclusionsPrognostic clinical variables, including mitotic or metabolic activity and depth of invasion, were identified as correlates of circulating tumor DNA by linear models that relate clinical covariates to tumor fraction. The identified correlates indicate that faster growing tumors have higher tumor fractions. Early cancer detection from assays that analyze cell-free DNA is determined by circulating tumor fraction. Results support that early detection is particularly sensitive for faster growing, aggressive tumors with high mortality, many of which have no available screening today.
Highlights
An inherent limitation of circulating tumor DNA analysis techniques is the proportion of cell-free DNA that is derived from tumor cells in a blood sample [1]
Cancer detection from assays that analyze cell-free DNA is determined by circulating tumor fraction
Current evidence suggests that the origin of circulating tumor DNA (ctDNA) in a blood sample is biased towards tumor cells that are aggressive or susceptible to treatment, which lead to proliferation- or treatment-induced apoptosis and cell-free DNA (cfDNA) shedding [14]
Summary
An inherent limitation of circulating tumor DNA (ctDNA) analysis techniques is the proportion of cell-free DNA (cfDNA) that is derived from tumor cells in a blood sample [1]. CTF varies widely between individuals, cancer types [3], and clinical stage [5] These variations have important implications for a wide range of clinical applications of ctDNA-based assays, including multicancer early detection (MCED) tests [6,7,8,9] and minimal residual disease detection [10,11,12,13]; the factors that influence cTF have not been completely elucidated. Clinical factors that influence tumor fraction have not been completely elucidated
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