LEXINGTON, Mass.—University of California, San Diego (UCSD)recently announced that it has published data that validates RainDanceTechnology Inc.'s approach for detecting low-prevalence somatic mutations inheterogeneous tumor samples.
The publication, "Detection of Low Prevalence SomaticMutations in Solid Tumors with Ultra-Deep Targeted Sequencing," was publishedonline by Genome Biology on Dec. 20.
To fully examine the low-prevalence somatic mutations inbreast, colon and ovarian tumors, the team at UCSD School of Medicine used asolution, which included RainDance's automated RDT 1000 system and cancerhotspot panel, as well as an ultra-deep targeted sequencing assay (UDT-Seq) andprotocol that were co-developed by researchers from RainDance, UCSD andPrognosys Biosciences. Using this method, researchers were able to create ahigh-performing streamlined workflow using Illumina's Genome Analyzer systemand, as part of a performance comparison, generate the first peer-reviewedpublication featuring the combination of the RainDance platform with theIllumina MiSeq system for ultra-deep tumor sequencing.
According to the university, the ultra-deep targetedsequencing assay used in the study enabled the detection of low prevalencemutations at more than 70,000 positions in the mutational hotspots of 42 cancergenes.
"Clinical samples collected from surgery or biopsies areoften contaminated with normal tissue or infiltrated with immune cells. Tumorscan also be heterogeneous, and it is not clear how the different subclonesaffect tumor progression or response to drugs," said Dr. Olivier Harismendy,assistant professor of pediatrics at the UCSD Moores Cancer Center and lead authorof the paper. "The approach outlined in the publication provides the necessarycoverage, breadth and depth to allow for the more accurate selection ofpatients for targeted treatments or clinical trials, testing novel targetedtherapies or repurposing of approved drugs."
The limit of detection achieved with this assay is muchlower than current methods of similar or higher breadth, making the majority ofclinical samples amenable for DNA profiling, according to a news release issuedby the parties. In this study, the researchers achieved true sensitivity andspecificity (greater than 94 and 99 percent, respectively) for low-prevalencemutations as measured from blends of known DNA. The team was able to detectmany mutations at a frequency as low as one percent of a heterogeneous sample.Such an assay will open up many research opportunities aimed at guidingclinical decisions and studying clonal selection in vivo, says RainDance.
"The ultra-deep targeted sequencing assay outlined in thispublication forms the foundation of our DeepSeq FFPE Solution, which offers therequired sensitivity to interrogate regions of the cancer genome at aresolution that cannot be achieved with next-generation sequencing alone,"stated Dr. Darren Link, vice president of research and development at thecompany, and a co-author on the paper. "In the near future, customers will beable to add more power to these types of cancer research projects by combiningour innovative digital PCR solution for downstream validation and characterizationof mutations discovered by next-generation sequencing."
RainDance offers a complete portfolio of innovativemicrodroplet-based cancer research solutions that capture, interrogate andquantitate biological information.