Abstract A083: Automated Processing of Up to 50 mL Urine Enhances Recovery of Low-Abundance KRAS G12V ctDNA for Early Detection of Pancreatic Cancer
Nafiseh Jafari, Jason Saenz, Carlos Hernandez, Daniel Cedeno, Cameron Van Dieren, William Lewis, Mayer SaidianAbstract
Introduction:
Pancreatic ductal adenocarcinoma (PDAC) is frequently diagnosed at advanced stages due to the lack of sensitive, noninvasive screening methods. Urine is an attractive liquid biopsy specimen because it can be collected noninvasively and repeatedly; however, tumor-derived cell-free DNA is highly diluted in urine and is often present at extremely low abundance, particularly in early-stage disease. Consequently, conventional workflows that process limited urine volumes may fail to recover sufficient mutant cfDNA for reliable detection. We evaluated whether automated processing of up to 50 mL of urine improves recovery of low-abundance KRAS cfDNA, supporting more sensitive urine-based liquid biopsy assays for early pancreatic cancer detection.
Methods:
Healthy donor urine was spiked with synthetic KRAS G12V mutant cfDNA to simulate low-abundance pancreatic cancer-derived biomarkers. Urine input volumes ranging from 1 to 50 mL were processed using the nRichDX Revolution Pro automated sample preparation system. Recovered cell-free DNA was quantified by Qubit fluorometry, and KRAS G12V mutant copies were measured using qPCR. Recovery efficiency, assay precision, and analytical linearity were evaluated across all urine input volumes.
Results:
The automated workflow successfully processed urine volumes from 1 to 50 mL in a single extraction without sample pooling or manual intervention. Recovery of KRAS mutant cfDNA remained consistently high (>80%) across all evaluated input volumes with excellent reproducibility (CV <3%). The number of recovered mutant copies increased proportionally with urine input volume, demonstrating near-linear analytical performance. Because urine is a dilute specimen, processing larger sample volumes substantially increased recovery of rare mutant cfDNA molecules, improving the analytical sensitivity for detecting low-abundance KRAS biomarkers representative of early pancreatic cancer.
Conclusions:
Automated processing of up to 50 mL of urine enables sensitive and reproducible recovery of low-abundance KRAS cfDNA from a dilute liquid biopsy specimen. By maximizing recovery of rare mutant molecules that may otherwise remain undetectable in smaller urine inputs, this approach has the potential to improve the sensitivity of urine-based liquid biopsy assays for early detection of pancreatic cancer and supports future clinical validation in patients at risk for early-stage disease.
Disclosure:
Artificial intelligence was used solely to assist with drafting and editing the manuscript. All scientific concepts, study design, data interpretation, and final content were reviewed, verified, and approved by the authors.
Citation Format:
Nafiseh Jafari, Jason Saenz, Carlos Hernandez, Daniel Cedeno, Cameron Van Dieren, William Lewis, Mayer Saidian. Automated Processing of Up to 50 mL Urine Enhances Recovery of Low-Abundance KRAS G12V ctDNA for Early Detection of Pancreatic Cancer [abstract]. In: Proceedings of the AACR Conference on Pancreatic Cancer: New Frontiers in Biology and Therapeutic Development; 2026 Sep 25-28; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(18_Suppl_2):Abstract nr A083.