Genomic Landscape of Cell-Free DNA in Patients with Colorectal Cancer

Abstract

ABSTRACT"Liquid biopsy" approaches analyzing cell-free DNA (cfDNA) from the blood of patients with cancer are increasingly utilized in clinical practice. However, it is not yet known whether cfDNA sequencing from large cohorts of patients with cancer can detect genomic alterations at frequencies similar to those observed by direct tumor sequencing, and whether this approach can generate novel insights. Here, we report next-generation sequencing data from cfDNA of 1,397 patients with colorectal cancer. Overall, frequencies of genomic alterations detected in cfDNA were comparable to those observed in three independent tissue-based colorectal cancer sequencing compendia. Our analysis also identifi ed a novel cluster of extracellular domain (ECD) mutations in EGFR , mediating resistance by blocking binding of anti-EGFR antibodies. Patients with EGFR ECD mutations displayed striking tumor heterogeneity, with 91% harboring multiple distinct resistance alterations (range, 1-13; median, 4). These results suggest that cfDNA profi ling can effectively defi ne the genomic landscape of cancer and yield important biological insights. SIGNIFICANCE:This study provides one of the fi rst examples of how large-scale genomic profi ling of cfDNA from patients with colorectal cancer can detect genomic alterations at frequencies comparable to those observed by direct tumor sequencing. Sequencing of cfDNA also generated insights into tumor heterogeneity and therapeutic resistance and identifi ed novel EGFR ectodomain mutations. Cancer Discov; 8(2);

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

“…Evidence of ctDNA in the blood, as estimated by MSAF > 0, was detected in 82% of cases, similar to recent studies in colon cancer (21, 22). Among cases with evidence of ctDNA, at least one reportable GA was detected in 89% of cases with an average of 2.28 reportable alterations per case.…”

“…Of note, EGFR mutations were more common in the other two published tissue studies examined relative to FoundationCORE; however, this may be expected as these datasets included only colorectal carcinoma cases and excluded other gastrointestinal-type malignancies less likely to have received anti-EGFR therapies. Similar observations regarding subclonal EGFR ECD mutations were noted in a recent large study of blood-based cell-free DNA samples in colorectal carcinoma, including recurrent mutations at EGFR V441D/G, which had not been previously reported (22). This study also noted treatment history with EGFR antibodies in all patients with samples harboring these mutations for whom clinical data were available, further suggesting a role for ECD mutations in cetuximab/panitumumab resistance.…”

“…In contrast, the spectrum and incidence of genes with short variant alterations was similar to that observed in tissue samples from patients with gastrointestinal cancers, supporting the ability of ctDNA profiling to reflect tissue-based characterization. In recent studies comparing ctDNA and tissue samples in colorectal carcinoma patients, similar rates of short variant alterations to those seen here were also observed for frequently altered genes (21, 22). However, in one study (21), reported frequencies of EGFR and MET amplification in ctDNA samples were notably enriched compared with ctDNA results observed here and relative to published tissue studies of colorectal carcinoma (21).…”

“…However, in one study (21), reported frequencies of EGFR and MET amplification in ctDNA samples were notably enriched compared with ctDNA results observed here and relative to published tissue studies of colorectal carcinoma (21). In another study (22), although short variant alteration frequencies were reported, the prevalence of gene amplifications and fusions detected in cell-free DNA samples were not included for the majority of cases (22). …”

“…Strickler and colleagues recently reported cell-free DNA genomic profiling results for over 1,000 colorectal carcinoma patients, but analysis was largely focused on short variant alterations, and no comparison with paired tissue samples was available (22). Alternative applications for ctDNA, including detection of residual disease and early recurrence, rather than identification of actionable GAs, have been the focus of other studies and are not formally examined in our analysis (35, 36).…”