Why NGS?

Since Dako Denmark received the first companion diagnostic FDA approval for its HercepTest in 1998, which analyzed BRCA ½ status, the FDA has largely adopted the “one drug/one biomarker” paradigm approach. This means that most studies have largely focused on assessing a single biomarker, often a highly penetrant or mutated gene, whose status for a particular neoplasm is meant to be utilized to inform the clinician therapeutic decision-making process. Traditional platforms utilized to interrogate single biomarker status include amplication-refractory mutation system (ARMS), fluorescence in situ hybridization (FISH), and immunohistochemistry (IHC). Although all these methods are highly reliable, they all feature the same shortcoming: they require a specific assay to be designed to analyze each individual genomic alteration. There are also additional limitations. ARMS can only be utilized in the detection of base substitutions and indels. FISH can detect rearrangements and amplification in DNA, however, it cannot differentiate between fusion variants. IHC is utilized to detect changes in gene expression on the protein level but does not always offer insights on what is occurring at a genomic level.

NGS is the single most powerful platform for the identification of multiple gene mutations, comprehensive profiling of the human genome, and providing actionable data metrics. In addition to NGS's unique ability to detect driver and resistance mutations, the unbiased probe design allows for additional identification of novel non-hotspot mutations. For example, in patients with NSCLC and secondary resistance to EGFR tyrosine kinase inhibitors, NGS can simultaneously analyze the acquisition of T790M mutations (the most prevalent mechanism for acquiring EGFR TKI resistance), as well as MET amplification, ERBB2 amplification, and small-cell lung carcinoma transformation.

Another promising biproduct of NGS adoption has been the emergence of complex biomarkers such as homologous recombination deficiency (HRD) status, tumor mutational burden (TMB), and microsatellite insatiability (MSI) which can only be calculated through the analysis of multiple genes concurrently. The importance of these complex biomarkers is best demonstrated by the shift in how patients with PD-L1 positive have been diagnosed in recent years. Traditionally the FDA has approved IHC-based companion diagnostics as the primary method for identifying PD-L1 expression and determining whether patients would have a positive clinical response to immune checkpoint inhibitor drugs (ICI). However, not all patients who meet the IHC cut off for PD-L1 respond favorably to immune checkpoint inhibitors, demonstrating that PD-L1 as a single biomarker is imperfect. TMB as a complementary complex biomarker analyzes the mutational load across the entire tumor genome and has shown to be a more accurate predictor of ICI efficacy for NSCLC patients. These research advancements, sparked by NGS, led to the FDA approving the administration of Keytruda for patients with TMB-H solid tumors in June of 2020.