Bio-Rad this week launched the QX200 Droplet Digital PCR system, the next generation of the company's QX100 system.
The new platform, Bio-Rad said, is the only digital PCR platform that works with both EvaGreen fluorescent DNA dyes and TaqMan hydrolysis probes, providing users with greater flexibility in designing their digital PCR experiments, Bio-Rad said.
In addition, Bio-Rad believes that the expanded capability opens up a number of new applications for droplet digital PCR, in particular new gene expression, copy number variation, and multiplexing approaches, Bio-Rad representatives told PCR Insider at the American Association for Clinical Chemistry meeting this week in Houston.
Bio-Rad moved into the digital PCR space nearly two years ago when it acquired QuantaLife, which had developed a droplet-based digital PCR system, the first of its kind (PCR Insider, 10/6/2011).
Bio-Rad rebranded the platform as the QX100 Droplet Digital PCR system, and has been successfully ramping up sales of the system to researchers looking to use the technology for applications such as detection of rare alleles or CNVs.
The QX100 has been cited in multiple peer-reviewed research studies, and some labs have even explored using it for clinical diagnostic test development. However, the QX100 was only compatible with TaqMan hydrolysis probes – a well-vetted technology that nevertheless is viewed as prohibitively expensive by some.
As such, Bio-Rad responded to customer demand by making the new instrument, the QX200, capable of running both TaqMan probes and EvaGreen fluorescent dyes. According to biotech research products firm Biotium, which offers EvaGreen dyes, the product is brighter than SYBR Green I for detecting amplification due to a novel 'release-on-demand' DNA-binding mechanism; has low PCR inhibition, which permits the use of saturation dye concentration for maximal signal; and is compatible with multiplex PCR, among other features.
"We expanded the applications [on the QX200] to include EvaGreen intercalating dye," Annette Tumolo, vice president and general manager of Bio-Rad's Digital Biology Center, told PCR Insider. "We're good at optimizing emulsion chemistries, and we wanted to provide the best possible chemistry to accommodate these intercalating dyes."
EvaGreen, she added, "is cheaper and easier [than TaqMan probes] – you don't have to buy or design probes. You just have to design good primers, which you should be doing anyway."
Ben Ho Park, an associate professor of oncology in the breast cancer program at the Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, was an early adopter of the QX100 platform.
In an email to PCR Insider this week, Park noted that his group has been a beta tester of the QX200 and is looking to make the switch to the new platform.
"We are using ddPCR for a number of applications including detecting microscopic tumor burden in breast cancer patients by detecting plasma tumor DNA at various time points before, during, and after therapies," Park said. "Currently we are using mutations to track [plasma tumor] DNA [using] TaqMan probes with the QX100. Our hope is to facilitate faster marker development by using PCR primers that only amplify cancer DNA due to genetic rearrangements and use EvaGreen with the new QX200. This will allow us to forego probe design and allow for a much faster method of validating biomarkers for each individual's cancer and therefore [plasma tumor] DNA detection."
Tumolo noted that Bio-Rad has been a bit surprised at the types of applications that early-access users of the QX200 have been interested in.
"We thought the pull would be for gene expression, but we're finding that people are doing things like CNV, and looking at ways of multiplexing," she said. Tumolo also noted that cancer researchers looking to conduct research similar to that of Park's have been evaluating the QX200.
Tumolo said that current users of the QX100 would have an "upgrade path" to the QX200 if desired. Bio-Rad declined to comment on the price differential between the QX100 and QX200.
In addition, Tumolo noted that Bio-Rad is "already working on a third-generation platform," as well as an automation system for droplet formation that is "completely hands-off" and should be available by the end of this year.
The QX100 has made headway in the clinical genomics space, as several customers like Park are either using or evaluating the platform as a potential tool to develop and even run clinical diagnostic assays. The most publicized example to date is Trovagene, which PCR Insider reported in November was using the QX100 to develop its first CLIA molecular diagnostic test, a transrenal assay for KRAS mutations (PCR Insider, 11/29/2012).
However, TrovaGene said this week that it is now using the RainDance RainDrop digital PCR system for its test development, muddying the future of the QX100 in that program (see related story, this issue).
Nevertheless, Bio-Rad expects that the QX100 and QX200 will continue to be used in clinical development programs.
"People are using it for clinical assay development," Tumolo said. "Part of the idea of the Digital Biology Center was to help move the technology to both the research and clinical markets."
Early indications are that the platforms will be useful in residual disease monitoring, so-called "liquid biopsies," and newer applications such as early detection of transplant rejection, she added.
Also, "internally [Bio-Rad] is using the platform to develop diagnostics," she said. "We don't have a big molecular diagnostics presence now, but this could be technology that brings us there."