Abstract 29: Concordance of somatic mutations found in primary tumors and plasma circulating-free DNA from early and late-stage colorectal cancer patients

Abstract

Abstract Circulating-free DNA (cfDNA) holds great potential for non-invasive somatic mutation detection in cancer patients as a so-called “liquid biopsy”. A liquid biopsy is especially valuable when tumor tissue is not available and for longitudinal monitoring of tumor burden or emerging resistance. In such cases, tumor-specific mutations are not known a priori and in order to detect tumor-derived somatic mutations it is best to interrogate a broad panel of cancer genes. The primary obstacle to sequencing cfDNA with broad mutation panels is achieving the necessary limit of detection to identify small amounts of tumor-derived cfDNA relative to the predominant wild-type cfDNA in the plasma of cancer patients. Tumor-derived cfDNA levels correlate with tumor stage, also making it an important consideration when investigating the sensitivity of this approach. We demonstrate the detection of somatic variants in several cancer genes in the plasma of early and late-stage colorectal cancer (CRC) patients by deep sequencing (> 8,000X) the cfDNA and matched normal DNA of N=33 CRC patients using the AmpliSeq cancer panel. The AmpliSeq panel requires less than 10ng of input DNA and amplifies hotspot loci of 50 known cancer genes for next-generation sequencing (NGS). We observe at least one somatic mutation with greater than 0.1% variant allele frequency in the cfDNA of all 33 CRC patients. We also show the sensitivity of detecting tumor-derived somatic mutations in cfDNA by exome sequencing of the primary tumor tissue. We find higher sensitivity for tumor mutations in cfDNA of late-stage patients compared to early-stage patients. Overall, we demonstrate the feasibility of using NGS on a small sized cancer panel for identifying somatic mutations, including those with low variant allele frequency, in cfDNA of early and late-stage CRC patients. Although a cfDNA approach holds promise as a tool to aid in pre-clinical and clinical research, more work is needed to understand its performance under different assay and disease conditions. Citation Format: Steven M. Bray, Philip J. Ebert, John N. Calley, Richard E. Higgs, Isabella H. Wulur, Swee Seong Wong, Candice L. Horn, Ricardo Martinez, Christoph Reinhard. Concordance of somatic mutations found in primary tumors and plasma circulating-free DNA from early and late-stage colorectal cancer patients. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 29.