801 ORAL High Throughput Molecular Analyses to Select Patients for Targeted Agents

Abstract

Background: Rapid advancements in genomics paired with significant growth in the availability of targeted therapies offers clinicians expanding opportunities to provide increasingly effective cancer treatment. Currently, individual gene sequencing (e.g. EGFR) from formalin-fixed paraffinembedded (FFPE) tissue is widely used in cancer diagnosis. Shifting this paradigm towards NGS-based, comprehensive mutation testing in routinely collected FFPE cancer specimens will enable more complete and accurate characterization of patients’ cancers for individualized targeted therapy selection. Materials and Methods: DNA was extracted from 2×20micron sections of 83 specimens consisting of colorectal cancer, non-small cell lung cancer and melanoma. Hybridization-capture of 2574 exons across 176 oncogenes, tumour suppressor genes and ADME-related genes was performed to produce libraries appropriate for paired-end sequence analysis on the Illumina HiSeq2000 platform. Results: In-depth sequence analysis of 176 genes in 50 CRC, 29 NSCLC, and 4 melanoma specimens with median coverage averaging 213-fold (range 8 to 461) detected a per-sample average of 2 previously-described mutations, 7 novel mutations and 2 CNAs in the colon specimens, including frequent alterations in TP53 (33), APC (27), KRAS (12) and BRAF (6). The lung specimens averaged 1 previously described mutation, 8 novel mutations and 1 CNA per sample, most frequently KRAS (10), TP53 (7), JAK2 (3), EGFR (2) and BRAF (2). The melanoma cases exhibited on average 1 previously described mutation, 7 novel mutations and 3 CNAs including TP53 (4) and BRAF (2). In addition to validated clinically actionable mutations in EGFR, KRAS, and BRAF, and multiple alterations in well-known cancer genes such as TP53, STK11, APC,MLH1, BRCA2, and SMAD4, we detected many other mutations that are plausibly clinically actionable. These included activating mutations in the PI3 kinase subunit gene PIK3CA, as well as mutations in MET , KIT , ERBB2 and CDKN2A. Conclusions: It is feasible to perform highly sensitive and specific sequence analysis of hundreds of genes from routinely collected FFPE tissues. This approach detects not only the “hot spot” mutations commonly tested for in CRC, NSCLC and melanoma but also many additional mutations that could plausibly inform therapeutic decision-making. We suggest that clinical-grade next-generation sequencing should become a routine part of all clinical trials, and increasingly, of clinical care.