Abstract 1992: Improved somatic classification and detection of tumor heterogeneity using ctDNA based liquid biopsy compared to tumor-only tissue in colorectal cancer
Authors: Zheng Feng, Dennis Merkle, Danyi Wang, Dennis O'Rourke, Allysia Mak, Juergen Scheuenpflug
Journal: Cancer Research (2020)

Abstract Purpose Tumor cells and white blood cells shed DNA into the blood at different rates, resulting in easily distinguishable somatic and germline mutant allele frequency (MAF)s in plasma. Liquid biopsy (LBx) can robustly detect somatic and germline variants enabling paired germline-somatic evaluation. Previous comparisons of plasma and tissue samples mainly focused on somatic variant calls; we investigate the clinical utility of LBx by comparing somatic and germline variant agreement between matched plasma and tissue samples in colorectal cancer (CRC). Procedure Circulating free DNA was extracted from plasma of 25 treatment-naïve patients with stage III/IV CRC and tested using the GuardantOMNI™ (500 gene, 2.145Mb) panel for reporting SNVS, Indels, CNVs, fusions, MSI-High status, and tumor mutation burden. Somatic classification &amp; status for SNVs and Indels is performed by a beta-binomial model that incorporates genomic context and MAF (Nance AACR 2018). Matched FFPE tissue was analyzed by whole Exome sequencing (WES). To determine variant-level agreement between plasma and tissue, results from both assays were restricted to the common panel space. For SNVs and Indels, agreement was defined as the presence of identical alterations at a given position. Digital droplet PCR (ddPCR) was performed to assess selected clinically relevant somatic variants which were detected only in plasma by GuardantOMNI . Data Summary ctDNA was detected in 23/25 (92%) samples after excluding variants commonly associated with clonal hematopoiesis. In the common panel space, 108 somatic mutations were detected only in plasma across the 23 plasma samples at an average MAF of 4.35%. For variants detected only in plasma, ddPCR was conducted on four clinically relevant mutations thus far; PIK3CA C420R, FBXW7 R505C, KRAS G12D, and TP53 R273C. GuardantOMNI reported these mutations at MAFs of 29.15%, 60.39%, 28.91%, and 49.95%, respectively; ddPCR detected these variants at 27.8%, 62.8%, 33.7%, and 51.6%, respectively. ddPCR assessment of additional lower MAF variants is ongoing. 225 variants called germline by GuardantOMNI were also called in tissue, however, 176 (78%) were called somatic in tissue. In plasma, these variants were easily distinguishable from the tumor fraction (TF), with an average MAF difference of 40% higher than the TF as estimated by Max MAF. Conclusion: GuardantOMNI panel determines somatic status by leveraging local genomic context of common germline MAFs that provides a holistic view to reflect tumor heterogeneity. The ddPCR confirmatory results suggest that tissue of origin&amp;lt metastasis may attribute to the observed disagreement between plasma ctDNA and matched tissue. Data also suggest that LBx and multiple site tumor tissue biopsy can serve as an alternative cross reference for corroborating metastasis and therapeutically relevant genetic evolution. Citation Format: Zheng Feng, Dennis Merkle, Danyi Wang, Dennis O'Rourke, Allysia Mak, Juergen Scheuenpflug. Improved somatic classification and detection of tumor heterogeneity using ctDNA based liquid biopsy compared to tumor-only tissue in colorectal cancer [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 1992.