Company News: Highly Sensitive Assessment Of Common Somatic Mutations In Pulmonary Non-Small Cell Carcinoma With The MassARRAY® System
Agena Bioscience today announced a comparative study published in PLOS ONE highlighting the use of its mass spectrometry-based platform and new, highly sensitive iPLEX® HS chemistry for detection of somatic mutations in EGFR, KRAS, BRAF, and NRAS occurring in non-small cell lung cancer (NSCLC).
Lung cancers are frequently biopsied using minimally invasive technologies such as thin needle core biopsies and cytology cell blocks which result in small, heterogeneous sample specimens with minimal tumor tissue. A large portion of the available specimen is used up for immunohistochemical studies to determine the histologic tumor types, leaving minimal amounts for molecular analysis. Most technologies such as Sanger sequencing and NGS require a minimum of 20 – 40% tumor content to detect mutations as low as 5% – 20% variant allele frequency (VAF). Thus, disqualifying several samples due to insufficient tumor content.
In this proof-of-principle study, 179 archived clinical specimens of NSCLC from The Medical Foundation were tested using Agena Bioscience’s iPLEX HS Lung Panel, which has a limit of detection of 1% VAF and requires only 5-10ng of input DNA. The specimens were previously tested for EGFR, KRAS, NRAS, and BRAF mutations using Agena Bioscience’s OncoFOCUS™ v2.0 or v3.0 panels on the MassARRAY System, which have a limit of detection of 5-10% VAF. With the increased sensitivity of the iPLEX HS chemistry, an additional 17 (or 9.5% more mutations) previously undetected KRAS, NRAS, BRAF, and EGFR mutations were identified. These additional mutations were mostly detected in core needle biopsies and cytology cell blocks.
The iPLEX® HS Lung Panel runs on the MassARRAY System, using amplification and single-base extension followed by analysis on the mass spectrometer. Higher sensitivity is achieved by depleting the wild type terminator in the extension reaction, thereby reducing the wild type signal in the specimen and enabling the quantification of the mutant signal down to very low allele frequencies. All mutations identified by the iPLEX HS Lung panel that were previously undetected were positively confirmed by digital droplet PCR.
“The increased limit of detection and low DNA input requirements of the iPLEX HS Lung panel make it an ideal candidate to use for testing NSCLC specimens with limited tumor content,” commented Dr. Darryl Irwin, Senior Director, Scientific Affairs at Agena Bioscience.
The Medical Foundation stated that “Furthermore, with an 8-hour turnaround time and low per sample cost, we can perform targeted screens on more samples with a higher level of detection and thereby potentially discover mutations at an earlier stage.”
The full publication may be accessed at PLOS ONE.
The iPLEX® HS Panel and MassARRAY® System are for Research Use Only.