Utility Of Next-Generation Sequencing In Cancer Diagnosis

Next-generation sequencing (NGS) is arguably one of the latest technological advancements in biological sciences for the past few years. Research as well as diagnostics fields have witnessed a rapid revolution in sequencing technologies that already had an intense impact on the understanding of genetics and genome biology. A variety of research approaches are well-documented with NGS-based studies for de novo genome sequencing, transcriptome sequencing, DNA resequencing, and epigenomics. These research efforts are the basic strengths for the development of new experimental protocols as well as bioinformatics analysis pipelines. From a clinical standpoint, there is a high potential for NGS-mediated human health management. Clinical NGS is the use of genomic-level information generated by NGS technologies to diagnose the genomic alteration for selective treatment options and monitor its effects. Though far from routine, NGS is rapidly being integrated into medical practice.

In the context of solid tumors, the evolution of cancer therapies to more targeted approaches has led to the impetus for personalized medicine. Application of clinical NGS includes the molecular characterization of tumors. The targets for these therapies are largely based on the driving genetic alterations of the tumors. To track these multiple driving mutations NGS coupled with histological studies has the potential to deliver on the promises of personalized medicine. Comprehensive genomic profiling of tumors using NGS can detect mutation predictive of chemotherapy response and prognosis. Clinical NGS analysis of tumors uncovers the small changes characteristic of these mutations; small insertion, deletion, and point mutations as well as larger changes such as rearrangements and copy number changes. Recent advancements of NGS included translocations as well as fusions for different targetable genes. This may aid additional benefit in a tissue proficient manner. Additionally, this NGS-based analysis for fusions can reveal the exact position for translocation. However, FISH is the gold standard for targetable translocation studies.

In the United States of America, diagnostic tests provided to clinical laboratories are regulated by the US FDA. However, only a handful of NGS-based diagnostics tests have been approved. Among them two NGS-based tests have been approved this year. In June, Thermo Fisher Scientific obtained the FDA approval for the Oncomine DX target test, which is now available for use. Oncomine Dx can identify best responders to AstraZenica’s EGFR inhibitor Iressa (Gefitinib), Pfizers’s ALK and ROS1 inhibitor Xalkori (crizotinib), and the combination of Novartis’ MEK inhibitor Mekinist (tramatinib) and RAF inhibitor Tafinlar (Dabrafenib). In the same year in June, Illumina received FDA approval for the extended RAS panel. This panel will aid in clinicians’ decision making for patients eligibility for the treatment of metastatic colorectal cancer with Amgen’s Vectibx (Panitumumab). Earlier in December 2016, Foundation medicine obtained the FDA approval for the Foundation Focus CDxBRCA test, a companion diagnostic. The test was helpful for identifying women with ovarian cancer who may benefit from treatment with Rubbraca (rucaparib).

There is another way, different labs offer these NGS-based test as a laboratory developed test (LDT). An LDT is an in vitro diagnostics that is made and used only within the lab that developed it. There are ACMG standard guidelines available (year 2017) for validation of NGS-based LDT. When clinicians order an LDT, the lab offering the test receives the patient specimen, processes the test, and reports the result back to clinicians. FDA regulates tests sold as kits. In the present scenario, how may LDTs are actually on the market is difficult to estimate, but the numbers are quite high. With the current technologies, NGS can be better named as sample proficient techniques as it can accurately identify the variants of different genes from easily available blood samples at one go – just as a blood test. However, it is very important to remember that we need to validate LDTs based on instruments, sample, and available or custom-designed NGS panels.