Abstract 3117: Early detection of CRC Biomarker matched FFPE DNA and plasma cell-free DNA from CRC patients using a highly sensitive NGS panel
Authors: Franklin Chin, Vidyodhaya Sundaram, Vinh Q. Lam, Dong Liu
Journal: Cancer Research (2020)

Abstract Background: Patients with later stage colorectal cancer (CRC) exhibit relatively poor prognosis, and resistance to drug treatment remains an important factor in the shorter survival rate. Particularly well known is the resistance to anti-EGFR therapy caused by the presence of mutations in the KRAS oncogene. The BRAF V600E mutation is also linked to shorter survival. Therefore, it is essential to obtain a patient's mutational profile based on a set of biomarker genes, especially in the early stages of oncogenesis. Obtaining this information is also critical for the application of companion diagnostics, where the effective use of a drug is analyzed for each patient. BioChain Institute, Inc. is currently screening formalin-fixed paraffin-embedded (FFPE) tissue along with the same donor's plasma for the ability to detect hotspot mutations in a panel of CRC-related biomarker genes. Methods: FFPE tissues from five donors exhibiting various stages of colorectal cancer were provided by BioChain. These tissues consist of primary tumor and adjacent normal for comparison purposes. For each donor, matched plasma samples were also procured. FFPE DNA was extracted from the tissues using BioChain's AnaPrep FFPE DNA Extraction kit and cell-free DNA (cfDNA) was isolated from plasma using BioChain's cfPure V2 Cell Free DNA Extraction kit. Both the FFPE DNA and cfDNA were then analyzed using Diacarta's XNA-Based OptiSeq™ Lung and Colorectal Cancer Panel. This assay provides high sensitivity for the detection of 17 hotspots in 7 genes (APC, BRAF, CTNNB1, EGFR, KRAS, NRAS, and PIK3CA) that are frequently mutated in colorectal cancer. Results: Using the aforementioned cancer panel, we detected hotspot mutations in not only the FFPE DNA isolated from cancer tissues but in the plasma-derived cfDNA as well. Among the detected hotspots are the frequently mutated G12 in the KRAS oncogene. Interestingly, the BRAF V600E mutation was also detected in the cfDNA of all five selected donors, demonstrating the utility of liquid biopsy as both diagnostic and prognostic tools in oncogenesis. Conclusions: BioChain has demonstrated the ability to detect hotspot mutations in patients of colorectal cancer not only in the tissue sample but also in the same donor's circulating cfDNA. The detection of mutants such as BRAF V600E in plasma samples highlights the application of liquid biopsy in early diagnosis of cancer and provides the basis for the application of companion diagnostics to personalize drug treatment for each unique patient profile. For example, the detection of the BRAF V600E mutation may lead to a prescription of the BRAF inhibitor vemurafenib. By providing access to a plethora of tissue types, such as colon, along with proprietary kits that deliver the highest quality cfDNA samples possible, BioChain will be able to provide researchers with powerful tools that facilitate applications of liquid biopsy along with companion diagnostics and promote biomarker discovery. Citation Format: Franklin Chin, Vidyodhaya Sundaram, Vinh Q. Lam, Dong Liu. Early detection of CRC Biomarker matched FFPE DNA and plasma cell-free DNA from CRC patients using a highly sensitive NGS panel [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3117.