Clinical utility of comprehensive circulating tumor DNA genotyping compared with standard of care tissue testing in patients with newly diagnosed metastatic colorectal cancer

Abstract

Background: Comprehensive biomarker testing is essential in selecting optimal treatment for patients with metastatic colorectal cancer (mCRC); however, incomplete genotyping is widespread, with most patients not receiving testing for all guideline-recommended biomarkers, in part due to reliance on burdensome sequential tissue-based single-biomarker tests with long waiting times or availability of only archival tissue samples. We aimed to demonstrate that liquid biopsy, associated with rapid turnaround time (TAT) and lower patient burden, effectively identifies guideline-recommended biomarkers in mCRC relative to standard of care (SOC) tissue testing.

Patients and methods: Prospectively enrolled patients with previously untreated mCRC undergoing physician discretion SOC tissue genotyping submitted pretreatment blood samples for comprehensive circulating tumor DNA (ctDNA) analysis with Guardant360 and targeted RAS and BRAF analysis with OncoBEAM.

Results: Among 155 patients, physician discretion SOC tissue genotyping identified a guideline-recommended biomarker in 82 patients, versus 88 identified with comprehensive ctDNA (52.9% versus 56.8%, noninferiority demonstrated down to α = 0.005) and 69 identified with targeted PCR ctDNA analysis (52.9% versus 44.5%, noninferiority rejected at α = 0.05). Utilizing ctDNA in addition to tissue increased patient identification for a guideline-recommended biomarker by 19.5% by rescuing those without tissue results either due to tissue insufficiency, test failure, or false negatives. ctDNA median TAT was significantly faster than tissue testing when the complete process from sample acquisition to results was considered (median 10 versus 27 days, P < 0.0001), resulting in accelerated biomarker discovery, with 52.0% biomarker-positive patients identified by ctDNA versus 10.2% by SOC tissue 10 days after sample collection (P < 0.0001).

Conclusions: Comprehensive ctDNA genotyping accurately identifies guideline-recommended biomarkers in patients with mCRC at a rate at least as high as SOC tissue genotyping, in a much shorter time. Based on these findings, the addition of ctDNA genotyping to clinical practice has significant potential to improve the care of patients with mCRC.

Keywords: biomarker; circulating tumor DNA; genomic profiling; liquid biopsy; metastatic colorectal cancer; next-generation sequencing.

Figure 1

Patient accountability. ctDNA, circulating tumor DNA.

Figure 2

Biomarker discovery rate and turnaround time (TAT). (A) Biomarker discovery rate. Percent of total study patients with at least one guideline-recommended biomarker. (B) Relationship of patients positive by SOC tissue and comprehensive ctDNA testing. (C) Hypothetical sequencing of both orders of serial testing. Percent is out of total biomarker-positive patients identified. (D) Cumulative biomarker discovery rate as a function of time from sample collection to test result. (E) SOC tissue genotyping completion rate by biomarker. BRAF is BRAF V600E. ‘All’ includes RAS, BRAF V600E, and MSI status. (F) Clinical performance summary statistics for each testing method using the other as the comparator. Primary analysis population, all 155 patients on study; secondary analysis population, patients with valid results on both tests and tissue taken at stage IV. BDR, biomarker discovery rate; ctDNA, circulating tumor DNA; MSI, microsatellite instability; NGS, next-generation sequencing; NPA, negative percent agreement; OPA, overall percent agreement; PPA, positive percent agreement; SOC, standard of care.

Figure 3

Biomarker identity and concordance between comprehensive ctDNA and SOC tissue testing. (A) Biomarkers identified by comprehensive ctDNA and SOC tissue testing. (B) Clinical performance summary statistics for each test method using the other as the comparator for each biomarker. BRAF is BRAF V600E. (C) Concordance between test methods per biomarker. (D) Correlation between variant allelic fractions (VAFs) as determined by comprehensive ctDNA NGS and limited ctDNA PCR testing for KRAS.ctDNA, circulating tumor DNA; NGS, next-generation sequencing; SOC, standard of care.

Figure 4

Clinical correlates of ctDNA. (A) Biomarker discovery rate for tissue and comprehensive ctDNA testing by primary tumor location. (B) Maximum variant allelic fraction (VAF) by primary tumor location. (C) Biomarker prevalence by metastases in liver, lung, and peritoneum. (D) Maximum VAF by presence versus absence of metastases at site. (E) Maximum VAF by metastatic site with all metastatic site combinations represented. There were no patients without metastasis in at least one of the aforementioned sites.ctDNA, circulating tumor DNA.