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Serving it up rare
LEXINGTON, Mass.—RainDance Technologies announced April 20 a strategic collaboration with genomic services company Expression Analysis that takes a path of focusing on rare gene variants instead of common ones as a way to accelerate research into complex diseases. According to the two companies, the collaboration "will help characterize rare mutations that would otherwise prove difficult or impossible to identify using alternative methods."
As part of the collaboration, the companies are sponsoring a program to work directly with leading cancer researchers to define a panel of high-priority genomic targets that would facilitate large-scale targeted resequencing studies of cancer samples.
"There has been a hypothesis in a lot of research that there are common gene variances that are related to common diseases," says Stephen E. Becker, vice president, commercial operations for RainDance Technologies. "But there's a growing thought that it's really the rare variances that are truly causative of disease, so the ability to detect rare variants across populations—with hundreds or thousands of patients screened in the process—is becoming one of the true enabling factors in research."
While next-generation sequencing is "a fabulous enabling tool," he says, the ability to analyze DNA sequences to the necessary degree to identify rare variants is still far too costly.
"As the research community moves from a common variant for common disease hypothesis to a rare variant hypothesis, the screening of samples using the next-generation sequencing technologies will become more prevalent. Only by the sequencing of target regions associated with disease or drug response to indentify the presence of these rare variants can researchers begin to better understand the mechanisms of the underlying disease and treatment," he says.
Advances in DNA sequencing technologies have provided enormous advantages in sequencing capacity for researchers, notes Steve McPhail, president and CEO of Expression Analysis.
"However, in order to leverage the benefits there remains a need to analyze genomic loci, at high resolution, across large numbers of samples," McPhail says. "Our collaboration with RainDance Technologies will enable us to provide targeted resequencing for areas of the genome thought to be involved in disease processes, thereby providing the research community with tools to accelerate the pace of cancer research."
Becker says that RainDance considers Expression Analysis to be one of the leaders in the field for genomic analysis, noting that they have extended their business from traditional array analysis to now include next-gen sequencing, "and we expect that they will provide the same, if not higher, levels of service in this new market area. For our part, we can provide high-quality enrichment of those specific portions of the genome to really improve sequencing efficiency."
At some point, RainDance will probably pursue similar programs with Expression Analysis or other companies in other disease areas like autoimmune disease, neurological disorders and cardiovascular conditions. But for now, Becker says, RainDance wants to bring together a community of cancer researchers who can help develop a library that can map back to specific areas on the genome that would give researchers the information they need about important rare gene variants, and make that library readily available to the research community.
"Eight researchers will be chosen to work with our companies," he says. "Genomic discoveries are paramount to ultimately uncovering underlying mechanisms of cancer development and we believe this collaboration will work to further quicken the progress of those discoveries."
The program is expected to provide: PCR primer design for genes and loci specified by study participants using the RainDance primer library design service; enrichment of target loci performed on the RainDance RDT 1000 by Expression Analysis as well as sequencing of the enriched loci also by Expression Analysis on the Illumina Genome Analyzer; and data analysis, including mapping and SNP detection.