Company News: Multiplexed Analysis of ALK, ROS1, and RET Rearrangements in Lung Cancer Enabled by the MassARRAY® System

Agena Bioscience today announced a comparative study published in Scientific Reports highlighting the use of its mass spec-based platform for transcriptome analysis of ALK, ROS1, and RET gene fusions in lung cancer.

While Fluorescence In Situ Hybridization (FISH) is the gold standard for gene fusion detection due to its high sensitivity and specificity, it is also labor intensive, subjective in analysis, and unable to screen a larger number of gene fusions. Alternate transcriptome-based methods can offer multiplexing and compatibility with diagnostic workflows.

In this proof-of-principle study conducted at the Peter MacCullum Cancer Centre in Australia, Pfizer Oncology Research in San Diego, CA, and Agena Bioscience, fifty-one clinical specimens were tested using three different transcriptome analysis platforms. The study included the Agena Bioscience LungFUSION™ Panel, Nanostring Elements, and a Thermo Fisher Scientific NGS fusion panel. Results were measured against historical FISH and immunohistochemistry (IHC) data with concordance ranging from 86-96% depending upon the platform used.

The LungFUSION Panel runs on the MassARRAY System, and requires an initial cDNA synthesis step, followed by two rounds of amplification, and spectrometry. The method utilizes imbalance to discover new fusions with known partners. The Agena Bioscience LungFUSION Panel demonstrated a 95% positive percent agreement and a 93% negative percent agreement with FISH. Interestingly, it was the only platform to detect a FISH positive RET fusion in the most degraded sample.

“Molecular laboratories now have a number of sensitive and robust options to complement their clinical diagnostic testing,” commented Dr. Darryl Irwin, Senior Director, Applications Development at Agena Bioscience. “We are pleased to be part of this formative study that demonstrated the capability and sensitivity of the MassARRAY System, in particular for detection of fusions as important predictive biomarkers for tyrosine kinase inhibitors in lung cancer.”

While further evaluation in a larger cohort of patients will be required to assess clinical accuracy, the MassARRAY System is a highly cost-effective, high throughput platform that will be able to accommodate these studies.

Dr. Irwin further explained that the company’s system enables tens to hundreds of actionable or known predictive genetic variants to be screened across 100s of samples in a single day. The flexibility and scalability of the platform permit mid- to large-scale sample throughput which provides the means for highly-efficient lab production.