Recommendations for Specimen and Therapy Selection in Colorectal Cancer

Abstract

Introduction: Next-generation sequencing has emerged as a clinical tool for the identification of actionable mutations to triage advanced colorectal cancer patients for targeted therapies. The literature is conflicted as to whether primaries or their metastases should be selected for sequencing. Some authors suggest that either site may be sequenced, whereas others recommend sequencing the primary, the metastasis, or even both tumors. Here, we address this issue head on with a meta-analysis and provide for the first time a set of sensible recommendations to make this determination.

Methods: From our own series, we include 43 tumors from 13 patients including 14 primaries, 10 regional lymph node metastases, 17 distant metastases, and two anastomotic recurrences sequenced using the 50 gene Ion AmpliSeq cancer NGS panel v2.

Results: Based on our new cohort and a meta-analysis, we found that ~ 77% of patient-matched primary-metastatic pairs have identical alterations in these 50 cancer-associated genes.

Conclusions: Low tumor cellularity, tumor heterogeneity, clonal evolution, treatment status, sample quality, and/or size of the sequencing panel accounted for a proportion of the differential detection of mutations at primary and metastatic sites. The therapeutic implications of the most frequently discordant alterations (TP53, APC, PIK3CA, and SMAD4) are discussed. Our meta-analysis indicates that a subset of patients who fail initial therapy may benefit from sequencing of additional sites to identify new actionable genomic abnormalities not present in the initial analysis. Evidence-based recommendations are proposed.

Keywords: Colorectal cancer; Next-generation sequencing; Paired primary and metastatic tumors; Patient-matched tumors; Specimen selection; Therapy selection; Tumor heterogeneity.

Fig. 1

Distribution of samples. PTs primary tumors, RLNs regional lymph node metastases, DLNs distant lymph node metastases, DMs distant organ metastases. Note that one patient had two synchronous primaries

Fig. 2

Prevalence of mutations across primary and metastatic tumors. PTs primary tumors, RLNs = regional lymph node metastases, DLNs distant lymph node metastases, DMs distant organ metastases

Fig. 3

Mutational concordance between tumor pairs across six studies. a Studies examining genetic differences in primary and metastatic CRCs were compared for variables that potentially explain differences in their results. Brannon et al. also performed WGS on four of their 69 patients. Kim et al. had one patient with two primary-metastatic pairs and two patients with only metastatic-metastatic pairs, all of which were included in the analysis below. b Most studies find that patient-matched tumor pairs are highly concordant for mutations in common cancer genes. Numbers in bars represent the number of pairs in the respective category. WGS whole genome sequencing, WES whole exome sequencing, *Kim et al. and Lee et al. studies reanalyzed after including only 50 genes interrogated in the current study. Compared studies are boxed in