By: Francisco J. Rojas, Ph.D.
For the first time, the US Food and Drug Administration (FDA) has cleared a next generation sequencing (NGS)-based companion diagnostic that identifies multiple lung cancer mutations. The clearance marks the start of a new era in diagnostics, as the sequencing-based kit can be distributed to laboratories throughout the US, in contrast to ‘home brew’ tests, which are run only by the laboratories that developed them.
The new lung cancer diagnostic, named Oncomine Dx Target Test, was developed by Thermo Fisher Scientific (Waltham, Massachusetts), in collaboration with Novartis (Basel, Switzerland) and Pfizer (New York). Oncomine detects 369 variants in 23 genes in a single assay using one tumor specimen. Any of the variants on the panel can help an oncologist to make a treatment decision. In addition, the test acts as a companion diagnostic for some specific drugs including the combination of the drugs Tafinlar and Mekinist for the BRAF mutations, which the FDA approved on June to treat non-small-cell lung cancer patients.
The Oncomine platform is based on Thermo Fisher’s Ion ApliSeq technology, which requires 10 ng of nucleic acid to screen a tumor sample for multiple genetic markers. Although the technology is not as amenable for whole genome or whole exome sequencing, it’s very good at targeted sequencing from limited tumor specimens. Metastatic lung cancer biopsy samples are uniquely challenging because tumor biopsies often yield minute amounts. So the Oncomine’s minimal DNA/RNA requirement makes the panel testing for lung cancer feasible.
Researchers are particularly pleased that the kit was originally focused on in vitro diagnostic for lung cancer because this disease has many different molecular subtypes, which are targeted by a number of drugs or drugs in development. So the new test offers an analytically validated set of genes that allows understanding of the physiopathology of lung cancer and testing for the efficacy of new treatments and drugs.
We hope that Thermo Fisher will quickly expand the use of the new kit as a companion diagnostic tool for in vitro colon and other types of cancer covered by the genes on the panel.
Nature Biotechnology, 35: 699, 2017.
Nature Biotechnology, 34: 895, 2016