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Microdroplet PCR Technology Well Suited for Performing Sequence-Based Association Studies

Data generated using microdroplet PCR technology as an enrichment method is particularly well suited for performing sequence-based association studies, according to a paper published today by researchers at the Scripps Translational Science Institute, the University of California, San Diego School of Medicine, and RainDance Technologies, Inc.

The study, led by Kelly A. Frazer, Ph.D., Professor of Pediatrics and Chief, Division of Genome Information Sciences, UC San Diego Department of Pediatrics, evaluated microdroplet PCR’s advantages in performing sequence enrichment for targeted sequencing over the gold-standard traditional PCR approach. “These benefits translated into a much higher efficiency of sequencing and a much more cost-effective way to do population studies,” Frazer said, in commenting about the paper.

Entitled “Microdroplet-based PCR Enrichment for Large-Scale Targeted Sequencing,” the paper was published today on Nature Biotechnology’s Web site at Microdroplet-based PCR enrichment for large-scale targeted sequencing : Abstract : Nature Biotechnology ( and will appear in the November issue of the magazine.

“I believe this new technology will be used to study the basic underpinnings of diseases and to understand their root causes,” said Eric J. Topol, M.D., Director of the Scripps Translational Science Institute and a co-author. “For instance, we’re now using it to understand the causes of anorexia nervosa. We also can use the technology to comprehend a disease’s response to a therapy or to determine a drug’s side effects. We even can employ it to study the healthy aging process. These are all applications for microdroplet PCR that will help us understand the vital aspects of human health and disease,” said Dr. Topol, in commenting on the paper.

The paper said that to efficiently perform population-based sequencing studies using next-generation sequencing platforms, it is important to be able to simultaneously examine large numbers of targeted sequences. “These results indicate that even when simultaneously amplifying 3,976 targeted sequences, microdroplet PCR generates a high ratio of target sequence to background sequence,” the authors said. The study concluded that data quality is independent of the number of amplicons. A path to scale to 20,000 amplicons while maintaining high performance was also demonstrated.

The paper’s authors said the microdroplet PCR process proved to be extremely efficient, with more than 99.6% of all amplicons being successful and with highly reproducible amplification of targeted sequences between samples. The data also showed that equivalently accurate SNP calling can be performed using microdroplet PCR whether the DNA is unamplified or whole-genome amplified from nanogram quantities. The allelic bias error rate of approximately 0.1% resulted in few known variants to be incorrectly called, further attesting to the robustness of the process.

“We were impressed with how well the technology worked,” said Dr. Frazer. “Compared to other types of sequence enrichment, we were able to generate greater uniform coverage of targeted sequences. In addition, the problems we typically encounter with standard PCR, such as difficult primer design and high allelic bias, were not observed with the microdroplet-based PCR workflow.”

“Efficient targeted sequencing will be critical as researchers study genetic variation in large populations to determine the causes of cancer and other complex diseases,” said Christopher McNary, President and Chief Executive Officer, RainDance Technologies. “This study confirms that our innovative RDT 1000 microdroplet-based platform is able to detect substantially higher numbers of variants in the targeted sequences than either solution-based hybridization or molecular inversion probes. This platform provides scientists with an exciting and highly effective new technology that accelerates research into the causes of these devastating diseases,” said McNary.

To view the paper, visit Microdroplet-based PCR enrichment for large-scale targeted sequencing : Abstract : Nature Biotechnology ( or see the November 2009 issue of Nature Biotechnology: “Microdroplet-based PCR Enrichment for Large-Scale Targeted Sequencing.” Authors: Ryan Tewhey1,2, Jason Warner3, Masakazu Nakano1,4, Brian Libby3, Martina Medkova3, Patricia David3, Steve Kotsopoulos3, Michael Samuels3, J. Brian Hutchinson3, Jonathan W. Larson3, Eric J. Topol1, Michael P. Weiner3, Olivier Harismendy1,4, Jeff Olson3, Darren R. Link3, and Kelly A. Frazer1,4. DOI:10.1038/nbt.1583.

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