Abstract A15: Detection of genome-wide copy number alterations in tumor tissue and cell-free DNA of pancreatic cancer patients
Authors: Greet Wieme, Frederik Berrevoet, Aude Vanlander, Jo Van Dorpe, Anne Hoorens, Bram Parton, Jurgen Van Limmen, Ann De Bruyne, Marc De Man, Karen Geboes, Kathleen Claes
Journal: Clinical Cancer Research (2020)

Abstract Pancreatic cancer is considered one of the deadliest malignancies, with only an 8% 5-year survival. The diagnosis of pancreatic cancer is very challenging since early-stage pancreatic cancer is associated with nonspecific and rarely noticeable symptoms. Additionally, the current diagnostic tools (such as imaging and the measurement of serum tumor marker CA19-9 levels) have limitations. Liquid biopsies make it possible to detect tumor-specific molecular alterations by analysis of cell-free DNA (cfDNA) isolated from plasma, which contains circulating tumor DNA (ctDNA). Large genomic rearrangements have become evident as key mutagenic events in the progression of solid tumors. In this study we evaluated the prevalence of large-scale genomic rearrangements in pancreatic resections and cell-free DNA (cfDNA) of pancreatic cancer patients. Genome-wide copy number profiles were derived from shallow whole-genome sequencing (sWGS). We applied sWGS to cfDNA samples from all patients at different time points. Concordance of the profiles was evaluated between cfDNA and matched FFPE tumor tissue in samples of operable pancreatic cancer patients. Clear copy number variations (CNVs) were observed in 13 FFPE tumor samples of 16 resectable patients (81%). This indicates that chromosomal instability is a frequent mechanism in pancreatic cancer. We then evaluated if CNVs could be detected in cfDNA of operable patients. Unfortunately, in none of the 50 operable patients were CNVs established. In contrast, cfDNA analysis in metastatic patients revealed clear CNVs in 66.7% (10/15) of the patients at the time of diagnosis. Although cfDNA concentrations were not statistically significantly increased compared to operable patients, remarkably higher CA19-9 values were determined in nonoperable patients. Preliminary data indicate that this approach can predict recurrence. For instance, a copy number change in a follow-up sample (1-year post-surgery; 6-months post-chemotherapy) was observed in a borderline-operative patient diagnosed with a liver metastasis. The CNV profiles obtained in both FFPE resections as well as in cfDNA were patient unique, but some recurrent alterations on chromosome 9 (region with CDKN2A and CDKN2B) and on chromosome 12 (region with KRAS) were ascertained. These results demonstrate detection of tumor-derived CNVs in cfDNA of advanced pancreatic cancer cases. We also show that there is potential to use cfDNA-derived profiles to monitor treatment response. Based on the results of this proof-of-concept study, additional patients are currently being analyzed. Citation Format: Greet Wieme, Frederik Berrevoet, Aude Vanlander, Jo Van Dorpe, Anne Hoorens, Bram Parton, Jurgen Van Limmen, Ann De Bruyne, Marc De Man, Karen Geboes, Kathleen Claes. Detection of genome-wide copy number alterations in tumor tissue and cell-free DNA of pancreatic cancer patients [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A15.