University of California, San Diego Uses RainDance's Technology to Detect Rare Somatic Mutations in Solid Tumors Undetectable by Current Sequencing Methods

January 11, 2012

New Genome Biology publication validates potential for cost-effective clinical sequencing with integrated RainDance and Illumina MiSeq(TM) workflow

LEXINGTON, Mass., Jan 11, 201 -- RainDance Technologies, Inc., the Digital Biology(TM) Company, today announced the publication of data from a collaboration with the University of California, San Diego (UC San Diego) and Prognosys Biosciences that further validates RainDance's "hotspot" approach for detecting low prevalence somatic mutations in heterogeneous tumor samples. The publication, entitled "Detection of Low Prevalence Somatic Mutations in Solid Tumors with Ultra-Deep Targeted Sequencing," was published online by Genome Biology on December 20, 2011.

To fully examine the low prevalence somatic mutations in breast, colon and ovarian tumors, the team at UC San Diego School of Medicine used a solution, which included RainDance's automated RDT 1000 system and cancer hotspot panel, as well as an ultra-deep targeted sequencing assay (UDT-Seq) and protocol that were co-developed by researchers from RainDance, UC San Diego, and Prognosys Biosciences. Using this method, researchers were able to create a high-performing streamlined workflow using Illumina's Genome Analyzer system, and, as part of a performance comparison, generate the first peer-reviewed publication featuring the combination of the RainDance platform with the Illumina MiSeq(TM) system for ultra-deep tumor sequencing.

The ultra-deep targeted sequencing assay used in this study enabled the detection of low prevalence mutations at more than 70,000 positions in the mutational hotspots of 42 cancer genes. Many other laboratories around the world are currently using the same cancer hotspot panel to investigate clinically relevant cancer related gene networks and pathways, such as BRAF, KRAS and EGFR. The breadth and depth of this ultra-deep sequencing method makes it a very effective tool for supporting more personalized cancer care and translational research projects.

"Clinical samples collected from surgery or biopsies are often contaminated with normal tissue or infiltrated with immune cells. Tumors can also be heterogeneous and it is not clear how the different subclones affect tumor progression or response to drugs," said Olivier Harismendy, Ph.D., Assistant Professor of Pediatrics at the UC San Diego Moores Cancer Center and lead author of the paper. "The approach outlined in the publication provides the necessary coverage, breadth and depth to allow for the more accurate selection of patients for targeted treatments or clinical trials, testing novel targeted therapies or repurposing of approved drugs."

The limit of detection achieved with this assay is much lower than current methods of similar or higher breadth, therefore making the majority of clinical samples amenable for DNA profiling. In this study, the researchers achieved true sensitivity and specificity (>94% and >99%, respectively) for low prevalence mutations as measured from blends of known DNA. The team was able to detect many mutations at a frequency as low as one percent of a heterogeneous sample. Such an assay will open up many research opportunities aimed at guiding clinical decisions and studying clonal selection in vivo.

"The ultra-deep targeted sequencing assay outlined in this publication forms the foundation of our DeepSeq(TM) FFPE Solution, which offers the required sensitivity to interrogate regions of the cancer genome at a resolution that cannot be achieved with next-generation sequencing alone," said Darren Link, Ph.D., Vice President, Research and Development at RainDance Technologies and a co-author on the paper. "In the near future, customers will be able to add more power to these types of cancer research projects by combining our innovative Digital PCR solution for downstream validation and characterization of mutations discovered by next-generation sequencing."

RainDance offers a complete portfolio of innovative microdroplet-based cancer research solutions that capture, interrogate and quantitate biological information. The full portfolio includes automated instrumentation, a sophisticated primer design pipeline, and consumables and reagents for applications such as Targeted DNA Sequencing, ultra-deep sequencing of FFPE samples (DeepSeq(TM) FFPE Solution), methylation analysis (MethylSeq(TM) Solution) and eventually, digital PCR and single cell analysis. The MethylSeq Solution was featured in two recent scientific publications in PLoS One and Genome Research, while the DeepSeq Solution was recently featured in the Journal of Translational Medicine.

For more information about the DeepSeq Solution and RainDance's complete line of cancer research products, please visit .


Harismendy O, Schwab RB, Bao L, Olson J, Rozenzhak S, Kotsopoulos SK, Pond S, Crain B, Chee MS, Messer K, Link DR, Frazer KA. Detection of Low Prevalence Somatic Mutations in Solid Tumors With Ultra-Deep Targeted Sequencing. Genome Biology. 2011, 12:R124. doi:10.1186/gb-2011-12-12-r124. To view abstract, please visit: .

Holbrook JD, Parker JS, Gallagher KT, Halsey WS, Hughes AM, Weigman V, Lebowitz PF, Kumar R. Deep Sequencing Of Gastric Carcinoma Reveals Somatic Mutations Relevant To Personalized Medicine. Journal of Translational Medicine. 2011, 9:119. doi:10.1186/1479-5876-9-119. To view abstract, please visit: .

About UC San Diego Moores Cancer Center

The UC San Diego Moores Cancer Center is one of the nation's 40 National Cancer Institute-designated Comprehensive Cancer Centers, combining research, clinical care and community outreach to advance the prevention, treatment and cure of cancer. For more information, visit .

About Prognosys Biosciences, Inc.

Prognosys Biosciences is focused on the development of novel genomic and proteomic technologies to enable research discoveries and clinical applications. The company offers Next Gen Sequencing services through its Sequensys(R) division and high quality data analysis through its Voila!(TM) cloud-based computing platform. In addition, Prognosys provides Rivia(R) Target Enrichment kits for custom regions of the human, mouse, and rat genomes. For more information, please visit .

About RainDance Technologies

RainDance Technologies is pioneering the use of high-throughput microdroplet-based analysis in human health and life science research. The company's core RainStorm(TM) technology generates millions of discrete droplets that can encapsulate a single molecule, cell or reaction and be digitally analyzed and sorted one at a time. The power, precision and simplicity of microdroplets enable researchers to answer complex questions with unprecedented sensitivity and quantitation. The complete RainDance solution includes automated instrumentation, customizable bioinformatics and high-value consumables and reagents for applications including targeted next-generation DNA sequencing, methylation, digital PCR and single cell analysis. Based in Lexington, Massachusetts, the company supports scientists around the world through its international sales and support operations and a global network of distributors and service providers. For more information, please visit .

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RainDance Technologies, the RainDance Technologies logo, RainStorm, ThunderStorm, Digital Biology, DeepSeq and MethylSeq are trademarks of RainDance Technologies, Inc. All other brands may be trademarks of their respective holders.