Abstract 4027: XNA-Based OptiSeqTMlung and colorectal cancer mini panel, a high sensitivity method for cancer early detection

The identification of genetic variants with low allelic frequency using next-generation sequencing method is confounded by the complexity of human genome sequence and by bias that arise during library preparation, sequencing and analysis. Herein, we introduce a novel molecule, Xenonucleic Acid (XNA) for NGS application. XNA is able to selectively suppress primer directed amplification of DNA with wild type alleles and only amplify DNA target templates containing mutant alleles. Mutants with low allelic frequency will be easily detectable without deep sequencing after enrichment by adding XNA in multiplex PCR. The 17 actionable mutants related to lung or colorectal cancer diseases at different VAF% were investigated in this study. Upon XNA blocking of wild type alleles, enriched variant allelic frequency (VAF) can be increased by ~32 fold from 10 ng of gDNA samples containing mutants as low as 0.10% VAF. Analytical sensitivity of Limit of Detection (LOD) is about 0.10% VAF. These 17 actionable mutants were tested and verified by using tissue biopsy (FFPE) and liquid biopsy (cfDNA) of lung or colon cancer patient samples. Clinical sensitivity for FFPE sample is about 100% for lung cancer and colorectal cancer samples respectively, comparing to without XNA NGS about 85.7% for lung cancer and 70% for colon cancer. For cfDNA sample its clinical sensitivity is about 100% for lung and colon cancer, but without XNA mediated enrichment NGS is only about 70% for lung cancer and undetectable for early colon cancer. This method provides a simple, robust, accurate, faster turnaround, highly sensitive and low cost alternative compared conventional NGS employing deep sequencing. This technology will greatly enhance the adaptability of NGS as a clinically useful platform for every modern pathology laboratory. Citation Format: Michael Y. Sha, Wenjing Feng, Qing Sun, Ke Zhan, Michael J. Powell, Aiguo Zhang. XNA-Based OptiSeqTMlung and colorectal cancer mini panel, a high sensitivity method for cancer early detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4027.