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here to printUCSD uses RainDance technology for solid-tumor detection
February 2012
SHARING OPTIONS:
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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