Broad, Hybrid Capture-Based Next-Generation Sequencing Identifies Actionable Genomic Alterations in Lung Adenocarcinomas Otherwise Negative for Such Alterations by Other Genomic Testing Approaches

Abstract

Purpose: Broad, hybrid capture-based next-generation sequencing (NGS), as a clinical test, uses less tissue to identify more clinically relevant genomic alterations compared with profiling with multiple non-NGS tests. We set out to determine the frequency of such genomic alterations via this approach in tumors in which previous extensive non-NGS testing had not yielded a targetable driver alteration.

Experimental design: We enrolled patients with lung adenocarcinoma with a ≤ 15 pack-year smoking history whose tumors previously tested "negative" for alterations in 11 genes (mutations in EGFR, ERBB2, KRAS, NRAS, BRAF, MAP2K1, PIK3CA, and AKT1 and fusions involving ALK, ROS1, and RET) via multiple non-NGS methods. We performed hybridization capture of the coding exons of 287 cancer-related genes and 47 introns of 19 frequently rearranged genes and sequenced these to deep, uniform coverage.

Results: Actionable genomic alterations with a targeted agent based on NCCN guidelines were identified in 26% [8 of 31: EGFR G719A, BRAF V600E, SOCS5-ALK, HIP1-ALK, CD74-ROS1, KIF5B-RET (n = 2), CCDC6-RET]. Seven of these patients either received or are candidates for targeted therapy. Comprehensive genomic profiling using this method also identified a genomic alteration with a targeted agent available on a clinical trial in an additional 39% (12 of 31).

Conclusions: Broad, hybrid capture-based NGS identified actionable genomic alterations in 65% [95% confidence interval (CI), 48%-82%] of tumors from never or light smokers with lung cancers deemed without targetable genomic alterations by earlier extensive non-NGS testing. These findings support first-line profiling of lung adenocarcinomas using this approach as a more comprehensive and efficient strategy compared with non-NGS testing. See related commentary by McCutcheon and Giaccone, p. 3584.

Figure 1. Frequency of genomic alterations (GAs) identified via next-generation sequencing

A total of 96 GAs were identified in 31 lung adenocarcinomas. GAs were divided into six categories: base substitution, amplification, insertion/deletion, rearrangement, homozygous loss, and splice site mutation. The frequency of each of these categories is depicted in the pie chart on the right. The frequency of each of the most commonly involved genes under each category is detailed on the left.

Figure 2. Clinical next-generation sequencing (NGS) and targeted therapy use

The results of NGS of lung adenocarcinomas that harbored no genomic alterations (GAs) in 11 genes (EGFR, ERBB2, KRAS, NRAS, BRAF, MAP2K1, PIK3CA, AKT1, ALK, ROS1, and RET) via a focused panel of non-NGS testing in never or ≤15 pack-year smokers are shown. The percentage of patients with results that fall into one of four categories is depicted in the pie chart.