BEAMing Technology Effectively Detects Cancer-Linked Mutations in Liquid Biopsy Samples

Liquid biopsy using BEAMing technology was found to be an effective method for analyzing tumor genotypes in real time and identifying significant mutations that occur during the course of disease and are not detected by tissue biopsy.

Rapid developments in the technology and protocols required for reliably isolating and analyzing circulating tumor DNA (ctDNA) in peripheral blood are making it easier to obtain the necessary samples without the need for physical biopsies. One such method, developed by Sysmex-Inostics (Kobe, Japan), utilizes digital PCR to detect somatic tumor mutations in ctDNA with high sensitivity. The technique combines emulsion digital PCR and flow cytometry. Known as BEAMing, it employs a combination of beads, emulsification, amplification, and magnetics to achieve the necessary level of sensitivity.

The BEAMing process starts with isolating and purifying the DNA present in blood plasma, which then goes through a pre-amplification step using conventional PCR to amplify the genetic section of interest using primers incorporating known tag sequences. These DNA templates are then amplified again via emulsion PCR, employing primers directed at these sequence tags and covalently bound to magnetic microbeads via streptavidin–biotin interactions. By designing the system this way, the PCR products generated in each emulsion droplet will remain physically affixed to the microbeads at the end of the reaction, allowing them to be easily separated and purified using a magnet. The method also provides a digital readout of copy number, as it has been experimentally optimized to ensure that each emulsion droplet will contain a maximum of one microbead and one DNA template molecule. This makes it possible to detect even very rare mutant templates at copy ratios greater than 1:10,000.

BEAMing technology was used to analyze the DNA in 503 blood samples acquired from patients with metastatic colorectal cancer participating in the CORRECT (previously treated metastatic colorectal cancer) phase III trial.

Results revealed that tumor-associated mutations could readily be detected by BEAMing of plasma DNA, with KRAS mutations identified in 69% of patients, PIK3CA mutations in 17% of patients, and BRAF mutations in 3% of patients. The results also showed that the drug regorafenib seemed to be consistently associated with a clinical benefit in a range of patient subgroups based on mutational status and protein biomarker concentrations.

Regorafenib (commercial name Stivarga) is an oral multi-kinase inhibitor, which targets angiogenic, stromal, and oncogenic receptor tyrosine kinase (RTK). Regorafenib shows antiangiogenic activity due to its dual targeted VEGFR2-TIE2 (vascular endothelial growth factor receptor 2 - tyrosine kinase with immunoglobulin-like and EGF-like domains 2) tyrosine kinase inhibition. Regorafenib has been shown to increase the overall survival of patients with metastatic colorectal cancer and is currently being studied as a potential treatment option in multiple tumor types.

"This is the first large clinical trial to compare liquid versus conventional tissue biopsy data, and the results show the former (BEAMing technology) obtain more data on tumor mutation throughout the course of the disease, enabling us to better target therapy to the specificities of patient's tumor; this could have a considerable impact on clinical practice, as novel applications of this technology could be further investigated and developed," said first author Dr. Josep Tabernero, head of the medical oncology department at the Vall d'Hebron Institute of Oncology (Barcelona, Spain).

The CORRECT BEAMing study was published in the July 13, 2015, online edition of the journal the Lancet Oncology.

Related Links:
Sysmex-Inostics
Vall d'Hebron Institute of Oncology