Enumeration and targeted analysis of KRAS , BRAF and PIK3CA mutations in CTCs captured by a label-free platform: Comparison to ctDNA and tissue in metastatic colorectal cancer

// Evelyn Kidess-Sigal 1, 2, * , Haiyan E. Liu 3, * , Melanie M. Triboulet 2 , James Che 3 , Vishnu C. Ramani 2 , Brendan C. Visser 2 , George A. Poultsides 2 , Teri A. Longacre 4 , Andre Marziali 5 , Valentina Vysotskaia 6 , Matthew Wiggin 5 , Kyra Heirich 2 , Violet Hanft 2 , Ulrich Keilholz 7 , Ingeborg Tinhofer 8 , Jeffrey A. Norton 2 , Mark Lee 9 , Elodie Sollier-Christen 3 , Stefanie S. Jeffrey 2 1 Department of Medicine, Division of Hepatology and Gastroenterology, Charite University Hospital, Berlin, Germany 2 Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA 3 Vortex BioSciences, Inc., Menlo Park, CA, USA 4 Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA 5 Boreal Genomics, Vancouver, BC, Canada 6 Counsyl Inc., San Francisco, CA, USA 7 Comprehensive Cancer Center Charite, Berlin, Germany 8 Department of Radiooncology and Radiotherapy, Charite University Hospital, Berlin, Germany 9 GRAIL, Redwood City, CA, USA * These authors have contributed equally to this work Correspondence to: Stefanie S. Jeffrey, email: ssj@stanford.edu Keywords: colorectal cancer, circulating tumor cells, circulating tumor DNA, liquid biopsy, Vortex Received: June 30, 2016      Accepted: October 26, 2016      Published: November 15, 2016 ABSTRACT Treatment of advanced colorectal cancer (CRC) requires multimodal therapeutic approaches and need for monitoring tumor plasticity. Liquid biopsy biomarkers, including CTCs and ctDNA, hold promise for evaluating treatment response in real-time and guiding therapeutic modifications. From 15 patients with advanced CRC undergoing liver metastasectomy with curative intent, we collected 41 blood samples at different time points before and after surgery for CTC isolation and quantification using label-free Vortex technology. For mutational profiling, KRAS, BRAF, and PIK3CA hotspot mutations were analyzed in CTCs and ctDNA from 23 samples, nine matched liver metastases and three primary tumor samples. Mutational patterns were compared. 80% of patient blood samples were positive for CTCs, using a healthy baseline value as threshold (0.4 CTCs/mL), and 81.4% of captured cells were EpCAM+ CTCs. At least one mutation was detected in 78% of our blood samples. Among 23 matched CTC and ctDNA samples, we found a concordance of 78.2% for KRAS, 73.9% for BRAF and 91.3% for PIK3CA mutations. In several cases, CTCs exhibited a mutation that was not detected in ctDNA, and vice versa. Complementary assessment of both CTCs and ctDNA appears advantageous to assess dynamic tumor profiles.