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Posted: Feb 02, 2011
RainDance Launches DeepSeq FFPE Solution for Discovery of Rare Cancer Mutations
(Nanowerk News) RainDance Technologies, Inc., the leading provider of microdroplet-based single molecule and single cell analysis solutions, today announced the availability of the DeepSeq™ FFPE Solution, an end-to-end workflow for the ultra-deep targeted sequencing of Formalin-Fixed Paraffin-Embedded (FFPE) and fresh frozen tissue samples. The company is launching the DeepSeq Solution this week at the 12th annual Advances in Genome Biology and Technology (AGBT) meeting in Marco Island, Florida.
DeepSeq FFPE Solution
RainDance's DeepSeq FFPE Solution enables researchers to discover common and rare cancer mutations that represent as little as one percent of a heterogeneous tumor. For the first time, researchers can analyze as many as 500 genomic targets at up to 50,000-fold coverage per loci to discover rare cancers and other disease-specific mutations from heterogeneous samples. Based on the proven RainStorm™ microdroplet-based single molecule PCR technology, the DeepSeq Solution delivers high specificity, accurate quantitation and unbiased allelic representation. The ultra-deep resolution of genomic targets represents a significant enhancement over the 10-30 percent allelic sensitivity achievable with current next-generation sequencing, target capture / hybridization, or microarray methods.
The DeepSeq FFPE Solution is optimized for both fresh frozen and FFPE tissue, which are the standard archival methods for nearly all solid tumors. Historically, researchers have been limited in applying next-generation sequencing to FFPE samples due to challenges with low yield, degraded DNA, and sample extraction. With an estimated 400 million FFPE samples stored in tissue banks worldwide1, cancer researchers and oncologists can now detect specific novel and causative mutations that drive drug resistance, metastasis and progression of different forms of the disease.
"In order to achieve the promise of targeted therapy cocktails optimized for the individual patient, we need cost-effective tools that address the heterogeneous nature of cancers," said Kelly A. Frazer, Ph.D., Founding Chief of the Division of Genome Information Sciences for the Department of Pediatrics at the UCSD School of Medicine. "Technologies, such as those offered by RainDance, will help us identify rare mutations present in as little as one percent of a tumor biopsy."
The DeepSeq FFPE Solution runs on the RDT 1000, an automated instrument that produces two million single molecule microdroplet-PCR reactions per sample in a single tube in less than one hour. The solution also introduces a number of innovative enhancements to simplify customer workflow and lower sequencing costs, including:
Custom Primer Libraries – Proprietary, automated design pipeline to generate unique primers for targeting customer-defined genomic regions up to 100 kilobases
Tailed Primers to Eliminate Library Generation – Integrated next-generation sequencing adapters to produce sequence-ready targets without any library generation
Multi-Sample Indexing – Integrated sequencing platform-specific bar codes in RainDance primers to improve sequencing capacity and efficiency with indexing of 12 samples per sequencer lane
"The DeepSeq FFPE Solution provides cancer researchers with the key to unlock their vast biobanks of FFPE samples and enables them to accelerate the discovery of rare mutations using the latest advances in sequencing technologies," said Roopom Banerjee, President and CEO of RainDance Technologies. "This launch expands our growing portfolio of targeted sequencing solutions for cancer, which already includes an Oncology Gene Network panel for studying major cancer pathways associated with druggable targets and MethylSeq™, the only single-base resolution application for the investigation of methylation status in bisulfite-treated DNA."
To further enhance the DeepSeq FFPE Solution, RainDance is collaborating with NuGEN Technologies, Inc. to develop a complementary fast and simple Whole Genome Amplification (WGA) FFPE sample preparation kit. NuGEN's Ovation® WGA FFPE product delivers accurate and unbiased genomic representation and generates microgram amounts of DNA from 100 nanograms of starting FFPE DNA samples.
"FFPE samples represent a huge repository of clinical information that has remained virtually untapped by next-generation sequencing due to the lack of available high-performance sample preparation technologies," said Elizabeth Hutt, CEO of NuGEN. "In this collaboration with RainDance, we will provide cancer researchers with a new, powerful and cost-effective solution to generate high quality next-generation sequencing data."
RainDance at AGBT
RainDance's microdroplet-based technology will be the focus of three AGBT presentations:
Olivier Harismendy, Ph.D., Assistant Project Scientist in the Kelly Laboratory at UCSD will present findings from a study using the DeepSeq FFPE Solution to analyze chromosomal 'hot spots' in tumors using next-generation sequencing on Thursday, February 3 at 7:30 p.m. ET.
Researchers from the University of Pennsylvania will present a poster on the preparation of HIV samples using RainDance's RainStorm technology and Pacific Biosciences' SMRTbell™ template preparation method for sequencing of the virus on the PacBio RS third-generation sequencing platform on February 3, between 1:00 p.m.-2:30 p.m. ET.
Roopom Banerjee will discuss the DeepSeq and MethylSeq capabilities during the RainDance-sponsored workshop series at 2:00 p.m. ET on Friday, February 4, between 2:00-4:00 p.m. ET.
RainDance will also be showcasing its technology throughout AGBT in its hospitality suite (Lanai #287).
For more information about the DeepSeq FFPE Solution, please visit the product website at www.RainDanceTech.com/DeepSeq.
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™ 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, simplicity and precision of microdroplets enable researchers to answer complex questions with unprecedented sensitivity and quantification. 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 www.RainDanceTech.com.