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Evaluating a treatment for AIDS. Analyzing archival cancer samples. Tracking the RNA of a mutated gene known to cause cancer. Researchers recently met in San Diego to discuss these and many other ways they are using Bio-Rad Laboratories, Inc.’s QX100 Droplet Digital PCR system to achieve their research goals. Bio-Rad’s second QX100 User Group Meeting will be held Dec. 6–7, 2012 in Boston.
“Our first user group meeting demonstrated substantial traction for droplet digital PCR in applications that require unprecedented levels of sensitivity, precision, and reproducibility, such as the measurement of copy number variation and rare mutation/sequence detection,” said Viresh Patel, digital PCR marketing manager at Bio-Rad.
The research community has embraced the QX100 system since its release in October, 2011, as evidenced both by industry awards and the strong sales and market growth of the instrument, which is expected to continue. A recent survey conducted by The Scientist and research firm Frost & Sullivan found that 30 percent of non-digital PCR users plan to implement digital PCR in their labs in 2013. Frost & Sullivan believes the QX100 system will lead the digital PCR marketplace due to the instrument’s simplicity, performance, and affordability.
Researchers Share Droplet Digital Success Stories
During the first QX100 User Group Meeting in San Diego, academic, industry, and government researchers spoke about the benefits of droplet digital PCR (ddPCR™). Kerry Emslie, manager of the Bioanalysis Group at Australia’s National Measurement Institute, presented research published in Analytical Chemistry evaluating the performance of the QX100 system in quantifying DNA copy numbers. Using lambda genomic DNA as a model, she concluded that the system’s results are more precise than those typically observed using either real-time PCR or other digital PCR systems based on microfluidic chambers.
Dr. Hanlee Ji of the Stanford University School of Medicine spoke about his experience analyzing archival cancer samples using ddPCR analysis. In a recent report in Translational Medicine, Dr. Ji demonstrated that ddPCR improves accuracy and precision over real-time PCR when measuring copy number variation in genomic DNA from formalin-fixed paraffin-embedded (FFPE) cancer tissue.
“We run droplet digital PCR routinely,” said Dr. Ji. “It’s part of our set of genome technologies that allow us to conduct translational studies that have clinical implications.”
Users also presented research demonstrating the ultra-sensitivity of ddPCR for detecting rare events. Highlights included a contract research organization that screens for EGFR mutations in circulating nucleic acids, biotech researchers who quantify rare HIV DNA targets, and the development of a laboratory test that tracks the transcript of a fusion gene that activates cancer.
For more information about the upcoming Boston user group meeting, please contact Viresh Patel at viresh_patel(at)bio-rad.com or 925-474-8602.
“People are different from each other in ways that are fascinating and medically important, and to understand the ways in which variations in our genome give rise to those differences presents an important and interesting set of questions,” says Dr Steve McCarroll, faculty member and principal investigator with the Department of Genetics at Harvard Medical School and the Broad Institute of Harvard and MIT. The McCarroll laboratory studies the biological effects of human genome polymorphism, seeking to define how genome variation influences gene expression and risk of disease. Their work requires them to accurately measure the copy number of a genomic sequence with integer precision in hundreds of people. While real-time PCR and CGH (comparative genomic hybridization) arrays are useful for measuring simple deletions and duplications, these techniques simply weren’t sufficient for obtaining single-molecule resolution of target sequences with extreme precision and accuracy. That’s where Droplet Digital PCR entered the story.
Timothy Ray Brown is the only person who has been cured of HIV to date (Pollack 2011). Dubbed the Berlin Patient, the now 46-year-old Brown was living with HIV and leukemia in Berlin, Germany when he received two bone marrow stem cell transplants from a donor who carried, in both copies of his CCR5 gene, a well-characterized natural defect, the CCR5-∆ 32 mutation. (CCR5 is a major co-receptor used by HIV to enter and infect CD4+ cells.) The CCR5-∆ 32 mutation rendered the CCR5 protein inactive and thus made the donor’s cells naturally resistant to HIV. After completing the transplants in 2007 and 2008, Brown immediately stopped taking antiviral drugs and has remained HIV-free ever since, igniting considerable interest within the cure research community.