Abstract 982: Variation of cell-free DNA concentrations in liquid biopsies
Authors: Sarah Short, Akshaya V. Annapragada, Jamie E. Medina, Zachariah H. Foda, Dimitrios Mathios, Carolyn Hruban, Elaine J. Chiao, Kavya Boyapati, Adrianna Bartolomucci, Keerti Boyapati, Vilmos Adleff, Robert B. Scharpf, Victor E. Velculescu, Jillian Phallen
Journal: Cancer Research (2024)

Abstract Introduction: Liquid biopsies are promising noninvasive tools for cancer detection. Variation in cell-free DNA concentrations (cfDNA-conc) has been observed between individuals with and without cancer. We assessed cfDNA-conc in 2287 treatment-naive individuals including those without cancer, with benign or high-risk conditions, or with one of eight cancer types. Methods: Plasma (0.3 to 9.8 mL) was separated from whole blood collected in Streck or EDTA tubes from individuals with bile duct, breast, colorectal, gastric, ovarian, liver, lung, pancreatic, or metastatic cancer (n=23, 54, 28, 26, 264, 75, 180, 31, 22, respectively) as well as benign or high-risk conditions (n=550, 133, respectively) such as cirrhosis or hepatitis B or C virus infection (HBV/HCV), and without cancer (n=901). cfDNA was extracted using the Qiagen QIAamp Circulating Nucleic Acid Kit. Quality and quantity were assessed using the High Sensitivity DNA assay on the Agilent Bioanalyzer. Total amount (ng) of cfDNA from all nucleosomal peaks was evaluated per volume (mL) of plasma to assess significance across cohorts using unpaired two-sample Wilcoxon tests. Results: We observed that in individuals without cancer, cfDNA-conc increased with age (Pearson R2=0.59; 18-40yrs vs 41-55yrs, vs 56-65yrs, vs 66-85yrs; p=2.31E-09, 1.50E-12, 8.31E-17, respectively). No difference was observed between cfDNA-conc from EDTA and Streck plasma from the same individual (n=9, p=0.359, Wilcoxon signed-rank test two-tailed). Individuals with benign adnexal masses or cirrhosis had similar cfDNA-conc compared to those without cancer while individuals with benign lung lesions or HBV/HCV had significantly different cfDNA-conc (p=0.70, 0.35, 6.96E-04, 1.88E-09, respectively). These observations were not affected by age. Individuals with cancer had significantly higher cfDNA-conc compared to those without cancer (bile duct p=2.08E-14, breast p=4.44E-16, colorectal p=6.04E-10, gastric p=5.93E-04, ovarian p=9.99E-16, liver p=1.22E-15, lung p=0, pancreatic p=8.57E-03, metastatic p=1.18E-06). Ovarian cancer exhibited higher cfDNA-conc than benign adnexal masses which was more pronounced in later stage disease (I/II p=3.83E-06, III/IV p=8.18E-08). Compared to cirrhosis or HBV/HCV we observed a stepwise increase in cfDNA-conc in liver cancer with progressing stage (0/A p= 6.50E-04, B p= 5.69E-10, C p= 1.47E-08). Higher cfDNA-conc were also observed with higher stage of lung cancer compared to benign lung lesions (I/II p=4.99E-03, III/IV p=3.89E-06). Using cfDNA-conc (ng/mL) as a single feature, we distinguished individuals with and without cancer with an AUC of 0.72 (95% CI=0.70-0.75). Conclusions: In a cohort of 2287 individuals, we observed cfDNA-conc increases with age and cancer stage that varied across cancer types. As a classifier, cfDNA-conc can be predictive of cancer status, yet further work is needed to understand the contribution of other comorbidities. Citation Format: Sarah Short, Akshaya V. Annapragada, Jamie E. Medina, Zachariah H. Foda, Dimitrios Mathios, Carolyn Hruban, Elaine J. Chiao, Kavya Boyapati, Adrianna Bartolomucci, Keerti Boyapati, Vilmos Adleff, Robert B. Scharpf, Victor E. Velculescu, Jillian Phallen. Variation of cell-free DNA concentrations in liquid biopsies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 982.