UCSD uses RainDance technology for solid-tumor detection
February 2012

LEXINGTON, Mass.óUniversity of California, San Diego (UCSD) recently announced that it has published data that validates RainDance Technology Inc.'s approach for detecting low-prevalence somatic mutations in heterogeneous tumor samples.  
The publication, "Detection of Low Prevalence Somatic Mutations in Solid Tumors with Ultra-Deep Targeted Sequencing," was published online by Genome Biology on Dec. 20. To fully examine the low-prevalence somatic mutations in breast, colon and ovarian tumors, the team at UCSD 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, UCSD 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 system for ultra-deep tumor sequencing.  
According to the university, the ultra-deep targeted sequencing assay used in the study enabled the detection of low prevalence mutations at more than 70,000 positions in the mutational hotspots of 42 cancer genes.  
"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 Dr. Olivier Harismendy, assistant professor of pediatrics at the UCSD 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, making the majority of clinical samples amenable for DNA profiling, according to a news release issued by the parties. In this study, the researchers achieved true sensitivity and specificity (greater than 94 and 99 percent, 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, says RainDance.
"The ultra-deep targeted sequencing assay outlined in this publication forms the foundation of our DeepSeq 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," stated Dr. Darren Link, vice president of research and development at the company, 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.

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