Hybrid Capture-Based Genomic Profiling of Circulating Tumor DNA from Patients with Advanced Cancers of the Gastrointestinal Tract or Anus

Abstract

Purpose: Genomic profiling of tumor biopsies from advanced gastrointestinal and anal cancers is increasingly used to inform treatment. In some cases, tissue biopsy can be prohibitive, and we sought to investigate whether analysis of blood-derived circulating tumor DNA (ctDNA) may provide a minimally invasive alternative.Experimental Design: Hybrid capture-based genomic profiling of 62 genes was performed on blood-based ctDNA from 417 patients with gastrointestinal carcinomas to assess the presence of genomic alterations (GA) and compare with matched tissue samples.Results: Evidence of ctDNA was detected in 344 of 417 samples (82%), and of these, ≥1 reportable GA was detected in 89% (306/344) of samples. Frequently altered genes were TP53 (72%), KRAS (35%), PIK3CA (14%), BRAF (8%), and EGFR (7%). In temporally matched ctDNA and tissue samples available from 25 patients, 86% of alterations detected in tissue were also detected in ctDNA, including 95% of short variants, but only 50% of amplifications. Conversely, 63% of alterations detected in ctDNA were also detected in matched tissue. Examples demonstrating clinical utility are presented.Conclusions: Genomic profiling of ctDNA detected potentially clinically relevant GAs in a significant subset of patients with gastrointestinal carcinomas. In these tumor types, most alterations detected in matched tissue were also detected in ctDNA, and with the exception of amplifications, ctDNA sequencing routinely detected additional alterations not found in matched tissue, consistent with tumor heterogeneity. These results suggest feasibility and utility of ctDNA testing in advanced gastrointestinal cancers as a complementary approach to tissue testing, and further investigation is warranted. Clin Cancer Res; 24(8); 1881-90. ©2018 AACR.

Figure 1.

ctDNA fraction estimated across gastrointestinal disease histologies. MSAF was used to estimate the ctDNA fraction in a given sample. MSAF was significantly greater for all gastrointestinal ctDNA cases versus gastric carcinoma ctDNA cases (*, P = 0.011) and in colorectal carcinoma ctDNA cases versus gastric ctDNA cases (**, P = 0.003). Box-and-whisker plots: box spans first and third quartiles, the median is denoted by the horizontal line in the box, and whiskers indicate maximum and minimum values within 1.5× the interquartile range.

Figure 2.

GAs identified in ctDNA from patients with gastrointestinal or anal carcinomas. Includes samples with evidence of ctDNA in the blood (MSAF >0). All gastrointestinal samples (n = 344), colorectal carcinoma (n = 258), GEJ (n = 36), gastric adenocarcinoma (n = 25). A, Longtail of frequently altered genes in carcinomas of the gastrointestinal tract or anus. B, Frequency of major pathway alterations across gastrointestinal disease histologies. RTK alterations include mutation, amplification, or fusion of EGFR; amplification or mutation of MET, ERBB2, FGFR1, and FGFR2; and fusion only of ALK, ROS1, RET, PDGFRA, and FGFR3. RAS/RAF/MEK pathway alterations include mutation or amplification of KRAS, NRAS, BRAF, RAF1, or MEK1. PI3K pathway alterations include amplification or mutation of PIK3CA, and mutation of AKT1 or PTEN. C, Distribution of individual gene alterations within pathways defined in B.

Figure 3.

GAs in ctDNA from patients with carcinomas of the gastrointestinal tract or anus compared with tissue. Comparison of the most frequently mutated (A) or amplified (B) genes observed in ctDNA in this study with tissue-based genomic profiling of carcinomas of the gastrointestinal tract of anus (FoundationCORE database) or with published tissue-based genomic profiling studies of primarily early-stage colorectal carcinoma (TCGA 2012 and Giannakis and colleagues 2016). Copy number data were not available in the Giannakis and colleagues study. Data from the TCGA and Giannakis studies were extracted from cBioPortal. *, TERT alterations were not assessed in the Giannakis (gray bars) or TCGA (blue bars) series.

Figure 4.

Concordance between GAs found in ctDNA and matched tissue from 25 patients with gastrointestinal carcinomas. A, Days between ctDNA and tissue collection, MSAF, and disease histology are shown. CR, colorectal adenocarcinoma; G, gastric adenocarcinoma; RE, rearrangement. Concordant/shared GAs are in blue, GAs found only in tissue are in red, and GAs found only in ctDNA are in pink. For samples with multiple unique mutations in a given gene, the number of mutations is indicated. B, Venn diagrams of concordant and discordant alterations by class. Blue, GAs found in both ctDNA and tissue; pink, GAs found only in ctDNA; red, GAs found only in tissue.