Swiss molecular diagnostics firm Biocartis said last week that it is collaborating with the Wellcome Trust Sanger Institute and Philips Research to develop a workflow to extract and amplify circulating tumor DNA from blood samples for downstream analysis on Biocartis' multiplex detection platform.
The work, which is being supported by a Strategic Translation award from the Wellcome Trust, is expected to enable Biocartis' DMAT platform to detect and identify chromosomal rearrangement mutations as biomarkers for cancer progression or recurrence, a Biocartis official said this week.
In addition, the project could eventually result in a panel of clinically validated biomarkers to help personalize and guide cancer therapy using Biocartis' Apollo platform, which the company is developing for in vitro diagnostic use, according to the official.
Biocartis did not disclose the duration and amount of the Wellcome Trust award. However, it noted that it would retain full rights to any intellectual property created during the project.
The overarching goal of the collaborative effort is to create a fast and efficient workflow for extracting circulating tumor DNA from large volumes of plasma — on the order of 1 mL — from cancer patients so that it can be analyzed using the DMAT system, which is currently under development at Biocartis.
DMAT, or Dynamic Multi-Analyte Technology, is the internal working name of the assay platform, which uses disposable, microfluidic cartridges to rapidly and sensitively detect up to 1,000 different analytes from a single sample. The platform achieves this using proprietary microfluidics and microfabrication technologies, Patrick van den Bogaard, director of life science research at Biocartis, told PCR Insider this week.
"We are creating these silicon particles that [have] embedded coding that is unambiguous, and … we can functionalize these microparticles [so that] each particle has a different analyte and has a different code," van den Bogaard said.
"These can then be mixed and matched in an array similar to a bead array, although we do all our reactions inside the same … platform as we do our detection," he added. "We are able to flow the analytes over [the array] and simultaneously detect the signal, and we can do this in a highly multiplexed fashion, basically up to 1,000 [analytes]."
However, the DMAT platform does not currently have an integrated sample prep component, limiting its use as a high-throughput biomarker identification and assay development platform.
"We would like to provide two feasibility models for a clinical workflow," van den Bogaard said. "Either the amplification is going to be done at the end of the extraction, so all tumor DNA is … extracted and specifically amplified, and then transferred to [the DMAT] platform [for] highly multiplexed detection.
"The other scenario is that we transfer the extracted nucleic acids [to DMAT] then do amplification and real-time detection … on the platform," he added. "That would create the most simple and versatile workflow, so that's our favorite scenario."
Van den Bogaard noted that the amplification component could use PCR or some isothermal amplification method, details that are to be determined over the course of the project.
"These are not going to be full commercial platforms at the end of the project, but [we will] basically show the feasibility of such new laboratory workflows and decide within the project what would be more suitable," he said.
Concurrently, a group led by Peter Campbell, head of cancer genetics and genomics at the Wellcome Trust Sanger Institute, is working under another Wellcome Trust award to clinically validate the use of chromosomal rearrangements as biomarkers for personalized cancer therapy.
The major focus of the Campbell group is large-scale sequencing of cancer genomes and developing informatics tools to identify cancer mutations like the chromosomal rearrangements.
"Sequencing is becoming more abundant in these types of workflows, but it's still not really penetrated very well, only specialized labs use it, and it's still far off from being a generic tool, which may take a lot of time," van den Bogaard said.
"[W]e propose having the oncogenome sequenced only once. Then, we develop for this particular patient an assay that can be used in the local hospital," he added. "That's where it gets decentralized. Every time a patient comes in for another round of therapy, we could measure on the spot within hours the cancer load, and look at the response of the tumor."
It is at this theoretical stage of the project that Biocartis' second analysis platform, Apollo — also an internal development codename — could come into play.
Biocartis, based in Lausanne, acquired the underlying technology for the Apollo platform from Royal Philips Electronics in 2010; and the companies have since worked together to develop the system. Inspired by various semiconductor technologies and design elements from the consumer electronics industry, Apollo is being designed as a compact, benchtop system comprising an instrument, communication console, and single-use, disposable cartridges (PCR Insider, 2/11/2010).
"The Apollo platform basically uses very robust and mature technologies for sample preparation and extraction, and for amplification and detection. It's just a smart integration of these technologies," van den Bogaard said. "That will be an IVD instrument that really handles validated biomarkers in an IVD setting … [while the DMAT] is going to be pre-diagnostics, and basically how we go from larger [biomarker] panels in an extremely flexible way, to reduced panels. This is where we see a pipeline going from pre-clinical assay development and biomarker analysis, for nucleic acids at least, all the way to validated assays with the Apollo."
Biocartis is also currently developing Apollo for infectious disease testing in partnership with other molecular diagnostic developers such as BioMérieux. In November, after closing a Series C financing round worth €71 million ($96 million at the time) to back development of Apollo, Biocartis said that it expected to begin various clinical trials on the platform this year with an eye toward commercialization in 2013 (PCR Insider, 11/17/2011).
Van den Bogaard declined to provide a commercialization timeline for the Apollo platform.