Comparison of a large NGS panel to hot-spot testing and small panels for the ability to accurately stratify advanced colorectal cancer patients to appropriate treatment pathways.

Abstract

510 Background: It is well established that KRAS mutations confer resistance to anti-EGFR therapy for colorectal cancer patients. More recently, other RAS mutations (NRAS and BRAF) have been determined to cause similar resistance and treatment guidelines are changing to incorporate testing of these genes as well. In addition, evidence suggests that mutations outside of hot-spot regions (Codons 12 & 13 of KRAS and NRAS; BRAF V600E) can also mediate therapeutic response. Recent data also suggest that other genes are relevant for treatment planning. We evaluated the ability of a 415 gene panel, CancerPlex, to accurately stratify colorectal cancer patients to appropriate treatment pathways compared to single gene “hot-spot” testing and small gene panels ( ≤ 50 genes). Methods: 70 colorectal cancer samples were analyzed by a large NGS panel of 415 genes that includes full-gene sequencing for SNPs, short insertions and deletions, and CNVs. All actionable mutations for each patient were recorded. We calculated relative frequencies of variants present in key oncogenic drivers to compare the effectiveness of current single gene testing with data obtained using a large panel. Testing was performed in a CLIA-certified laboratory (KEW Group Inc, Cambridge, MA). Results: 40% of samples contained a KRAS hot-spot mutation. When expanded to NRAS and BRAF hot-spots, an additional 8% of patients were identified as resistant to anti-EGFR therapy. An additional 15% of clinically significant variants were captured by full-gene sequencing of these 3 genes. Thus, > 25% of mutations lie outside traditional hot-spot regions. The majority of BRAF mutations were not V600E. The 415 gene panel identified clinically significant driver mutations in 99% of patients, while in smaller panels missed a significant number of actionable changes. In very few patients were actionable changes limited to KRAS, NRAS and BRAF hot-spots. Conclusions: Hot-spot testing and small gene panels can miss clinically significant genomic alterations. The detection of mutations outside of small panels and hot-spots may lead to more appropriate and successful treatment of colorectal cancers.