Abstract CT164: Circulating tumor DNA analysis for predictive and prognostic factors in patients with metastatic colorectal cancer: An exploratory analysis from the phase III PARADIGM study
Authors: Tsuchihara Katsuya , Muro Kei , Yoshino Takayuki , Shitara Kohei , Yamazaki Kentaro , Ota Mitsuyoshi , Oki Eiji , Sato Takeo , Naitoh Takeshi , Komatsu Yoshito , Kato Takeshi , Yamanaka Kazunori , Mori Ikuo , Hihara Masamitsu , Soeda Jumpei , Badola Sunita , Shin Hyunjin , Yamanaka Takeharu , Akagi Kiwamu , Ochiai Atsushi , Uetake Hiroyuki 
Published: August 2018

Abstract
Introduction Circulating tumor DNA (ctDNA) is an emerging biomarker used to track disease progression and treatment response. To investigate mechanisms of resistance to panitumumab and bevacizumab, we performed an exploratory analysis of ctDNA from patients (pts) with metastatic colorectal cancer (mCRC) in the ongoing phase III PARADIGM study (NCT02394834). We present an initial feasibility report of this analysis using a next generation sequencing-based platform.
Methods Pts with chemotherapy-naïve RAS wild-type mCRC were randomized 1:1 to receive mFOLFOX6 plus either panitumumab or bevacizumab. Plasma samples were taken pre- and post-treatment. Samples with a DNA yield of &gt;10ng/mL and &gt;10nM (assessed using an Agilent 2100 Bioanalyzer) were sequenced using an mCRC-focused ctDNA sequencing panel (PlasmaSELECTTM-R 91, PGDx) to detect mutations, amplifications, and rearrangements for 90, 26, and 3 genes, respectively, and microsatellite instability with 250kb targeted regions. Selected genes covered known pathways and functions related to CRC and sensitivity/resistance to anti-EGFR/VEGF therapies. Sequenced DNA required &gt;12,500x average coverage, &gt;15% mapping to regions of interest, and &gt;75x average high quality distinct coverage; analytical validity of the panel was established using standard samples. Pre-treatment archival tissue samples were collected and analyzed by the Broad Institute Solid Tumor panel, which covers 1,072 genes with 7.3Mb targeted regions.
Results Between May 29th 2015 and June 8th 2017, 823 pts were enrolled at 197 sites. Pre-treatment plasma samples and tissue samples were collected from 756 pts (92%); &gt;99.9% of plasma samples met the pre-specified quality criteria (QC). At the time of this feasibility analysis, 337 pre-treatment plasma samples that fulfilled the QC had been sequenced. In sensitivity validation, 92% of mutations were detected at the 0.1% mutant allele fraction (MAF) and 100% were detected at the &gt;0.5% MAF with &gt;99.9% specificity. In total, 25 tissue- and plasma-matched samples and 5 plasma samples without matched tissue samples were analyzed. Using individual mutations in tissue DNA as the denominator, genetic concordance was 100% (3/3) with BRAF and 70% (7/10) with TP53 between plasma and tissue samples for common TCGA mutations. Mechanisms of resistance to each therapy will be assessed by sub-clone analysis of pre- and post-treatment samples using the validated ultra-deep ctDNA sequencing panel. Collection of post-treatment samples is ongoing.
Conclusion Initial data confirms the analytical feasibility of this method and supports the use of ctDNA to track clonal evolution. Further analyses are warranted in all pts to explore the underlying mechanisms of response to treatment with anti-EGFR/VEGF therapies.
Citation Format: Katsuya Tsuchihara, Kei Muro, Takayuki Yoshino, Kohei Shitara, Kentaro Yamazaki, Mitsuyoshi Ota, Eiji Oki, Takeo Sato, Takeshi Naitoh, Yoshito Komatsu, Takeshi Kato, Kazunori Yamanaka, Ikuo Mori, Masamitsu Hihara, Jumpei Soeda, Sunita Badola, Hyunjin Shin, Takeharu Yamanaka, Kiwamu Akagi, Atsushi Ochiai, Hiroyuki Uetake. Circulating tumor DNA analysis for predictive and prognostic factors in patients with metastatic colorectal cancer: An exploratory analysis from the phase III PARADIGM study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr CT164.