Abstract A20: Detection and quantification of ctDNA KRAS mutations from patients with unresectable pancreatic cancer
Authors: Inna Chen, Victoria M. Raymond, Jennifer A. Geis, Sandeep Pingle, Eric A. Collisson, Vlada Melnikova, Mark G. Erlander, Julia A. Johansen, Fernando Blanco
Journal: Cancer Research (2016)

Abstract Introduction: An estimated 90% of pancreatic cancers harbor somatic KRAS G12/G13 mutations. The presence of circulating tumor DNA (ctDNA) KRAS mutations at diagnosis has prognostic implications, however, recent studies on small numbers of patients demonstrate widely variable KRAS ctDNA sensitivity (27 – 71%). Accurate identification of both the presence of ctDNA KRAS mutations and quantification of the number of ctDNA KRAS mutant copies would be an improved therapeutic response biomarker over CA19-9 which is known to be uninformative in 5-10% of patients with pancreatic cancer. A diagnostic and prognostic tool with very high analytical and clinical sensitivity, along with quantification, is needed for therapeutic response monitoring. Patients and Methods: Pretreatment (baseline) and longitudinal plasma samples were prospectively collected from 239 patients with unresectable pancreatic cancer through the Danish Biomarkers in Patients with Pancreatic Cancer (BIOPAC) study. The median age at diagnosis was 67 years (range 42 – 89 years) and 51.9% (N = 112) of patients were male. The majority of patients were metastatic at diagnosis (79.6%; N=172). ctDNA KRAS G12A/C/D/R/S/V, and G13D mutations were PCR enriched, sequenced by next generation sequencing (NGS), quantified and standardized. This was achieved by generating standard curves from a sample set with known numbers of spike-in copies for mutant KRAS molecules. These sample sets were assayed in parallel with patient samples starting with PCR enrichment of mutant KRAS DNA followed by NGS. The number of mutant copies detected was standardized by normalizing the number of copies detected in the sample to a constant number of calculated genome equivalents (GEqs) of wild type DNA across all samples evaluated. Baseline KRAS mutant levels were assessed. Additional metrics analyzed include age, gender, stage, and CA19-9 levels. Results: Two-hundred and sixteen patients (90.4%) had baseline plasma samples which passed quality control metrics. Baseline serum CA19-9 levels were available for 160 patients and ranged from 2.5 – 608,500 U/mL (median 202 U/mL). Eighteen patients (11.3%) had serum CA19-9 levels below the diagnostic threshold (&amp;lt;37 U/mL), and 76 patients (47.5%) had serum CA19-9 levels below the prognostic threshold (&amp;lt;1000 U/mL). Overall, 87% of patients were positive for a KRAS mutation at baseline by ctDNA analysis, with a median of 88.51 copies per 100,000 GEqs. Patients presenting with metastatic disease had a significantly higher median number of KRAS mutations (104.2 versus 23.9 copies per 100,000 GEqs; p&amp;lt;0.0001) and serum CA19-9 levels (1702.0 versus 303.0 U/mL; p&amp;lt;0.0001) at baseline than those with locally advanced cancer. Conclusion: In this large, prospective dataset of 216 patients with unresectable pancreatic cancer, ctDNA analysis was KRAS positive in 87.0% of patients. This detection rate closely matches the published prevalence of KRAS in pancreatic cancer (90%), and out performs previous studies, demonstrating the superior assay sensitivity. ctDNA analysis offers a viable tissue biopsy alternative for determining KRAS mutation status, especially in late stage patients. Given that approximately 48% of patients had CA19-9 levels below the prognostic threshold, quantification of KRAS mutant copy load may provide a more informative biomarker. Other clinical variables, baseline and longitudinal KRAS mutant levels, and patient outcomes will be examined and presented. Citation Format: Inna Chen, Victoria M. Raymond, Jennifer A. Geis, Sandeep Pingle, Eric A. Collisson, Vlada Melnikova, Mark G. Erlander, Julia A. Johansen, Fernando Blanco.{Authors}. Detection and quantification of ctDNA KRAS mutations from patients with unresectable pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A20.