Genetic profiling of cancer aims to identify molecular variants in the tumor that might help guide patient management. For instance, it is recommended that KRAS and NRAS genes be genotyped in metastatic colon cancer tissue and patients with mutations in codons 12, 13 of exon 2, codons 59, 61 of exon 3, and codons 117 and 146 of exon 4 should not be treated with either cetuximab or panitumumab. Similarly, amplification of the MET gene is also associated with poor response to cetuximab and panitumumab therapy. Large clinical studies have found that a mutation in codon 600 of BRAF is a negative prognostic factor in metastatic colorectal cancer.
Increasing utility of multi-gene tumor profiling for patient management has led to an increase in the utilization of Next- Generation Sequencing (NGS) assays in order to identify clinically informative variants in multiple genes. These complex assays require careful planning on multiple design parameters: panel design (i.e. selection of genes and number of targets to include), assay type, NGS platforms, variant calling algorithms, thresholds to call Copy Number Variation (CNV) and rearrangements. Additionally, multiple interpretive considerations need to be included in this planning (e.g. how to interpret the oncogenicity of a variant, or its ability to activate a particular pathway, and what clinical utility to report for the variant based on literature assessment).