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Fluidigm Licenses Stanford's Screening IP, As Various Projects Point Towards Dx Future

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Fluidigm last week said it has co-exclusively licensed from Stanford University a set of patents covering techniques, including a combination of digital PCR and high-throughput sequencing, for detecting fetal genetic characteristics in maternal plasma.
 
The patents cover a technique published by Stanford’s Stephen Quake and colleagues in October in the Proceedings of the National Academy of Sciences that uses high-throughput sequencing to detect trace amounts of fetal DNA in a pregnant woman's blood to determine whether any chromosomes are over-represented.
 
Quake is a co-founder of Fluidigm and the chair of its scientific advisory board. The licenses cover inventions that use digital analysis to noninvasively screen fetal DNA; second-generation sequencing to noninvasively diagnose fetal aneuploidy; and digital PCR to rapidly diagnose fetal aneuploidy.
 
The licenses cover inventions that use digital analysis to noninvasively screen fetal DNA; second-generation sequencing to noninvasively diagnose fetal aneuploidy; and digital PCR to rapidly diagnose fetal aneuploidy.
 
According to Fluidigm, the company sought the IP to enable its customers to pursue similar research, but also to have the option to develop and use a similar assay in the future.
 
In the study described in the PNAS paper, Quake and his team used Fluidigm’s digital PCR technology to count individual molecules and “set the exact parameters for sequencing steps that helped determine the amounts of critical fetal DNA,” Fluidigm said in a statement at the time.
 
This week, Fluidigm spokesperson Howard High said the company decided to license the Stanford patents for a number of reasons. "At the core, this important discovery was accomplished with the use of our technology," he told BioArray News. "Since we knew that Stanford was only going to license their discovery to a few [licensees], it seemed appropriate to secure access to that IP so our customers could pursue research in this area.
 
"The area of non-invasive, prenatal research is tending to be a popular and important area of research and discovery," High added. "We want to do all that we can to help researchers discover breakthroughs and approaches using our technology, and the Stanford IP provides one approach in non-invasive, prenatal discovery, and it seemed valuable to us to have IP rights to this work."
South San Francisco, Calif.-based Fluidigm, founded in 1999, sells three systems for genetic analysis and protein crystallization: the BioMark, which performs digital PCR on a 96-well by 96-assay consumable array that the firm refers to as an integrated fluidic circuit; the TOPAZ, which enables users to perform free interface diffusion in protein crystallization; and the EP1, launched last month, which enables both high-throughput mid-multiplex genotyping and end-point digital PCR. 
 
The methodology described in the Stanford patents uses the BioMark system and its SlingShot protocol to optimize sample concentrations for second-generation sequencing.
 
The IP "helps establish and confirm the value of SlingShot protocol from Fluidigm," High said.
 
SlingShot uses digital PCR assays to detect only amplifiable molecules within the sample mixture, according to the company. This measurement eliminates the need for mass-based calibrators or reference samples, and makes it possible for users to achieve quantitative results with minimal sample requirements, the firm claims.
 
Fluidigm sells SlingShot kits for use with Illumina's Genome Analyzer, Applied Biosystem's SOLiD sequencer, and Roche 454 Life Sciences' FLX instrument.
 
Diagnostic Developments
 
High said Stanford’s IP validates the utility of the SlingShot protocol and kit, but said that the firm is evaluating ways to take advantage of the test's opportunities.
 
"Specific product plans are still under consideration," High said. Global market estimates for non-invasive, prenatal diagnostics, which High said hovers around $6 billion, are similarly embryonic. High said. “I haven’t seen a breakout of that projected market size number in terms of geographic breakout, market projections by year, or comparisons with birth rates."
 

"It seemed appropriate to secure access to that IP so our customers could pursue research in this area without concern about the IP landscape."

So far, Fluidigm has catered strictly to the research market, but its customers are increasingly moving in the direction of clinical diagnostics. In October, CEO Gajus Worthington told BioArray News that several clients are developing panels on the BioMark system to that end.
 
One, Salt Lake City-based Myriad Genetics, has been developing a panel of markers to help stratify prostate cancer patients, and is "discovering gene expression profiles for prostate tumor samples that will inform whether this is a particular dangerous or less dangerous strain of the disease," Worthington said.
 
In their work, "they needed to be able to look at around 1,000 genes with exquisite performance," he said. "That was a perfect fit for us and we hope to be their platform when they run the diagnostic as well.“
 
In another project, researchers at Memorial Sloan-Kettering Cancer Center in New York developed a method for obtaining circulating tumor cells from a blood sample, and recently began looking to use the company’s BioMark platform to test individual circulating cancer cells, profile them for gene expression, and identify the pathway of the particular cell.
 
"They have been working on this for about a year and a half now, but they are already doing research work to prepare data for eventual regulatory submission," said Worthington. "This is part of a general theme. Worldwide, we are getting a lot of interest for single-cell gene expression for variety of applications," he added.
 
And in July, Fluidigm announced that researchers at the Fred Hutchinson Cancer Research Center have developed a method for the early detection of a common mechanism of resistance to drugs for chronic myeloid leukemia.
 
The Hutch scientists were able to detect a specific point mutation associated with acquired resistance to the targeted drugs Gleevec, Sprycel, and Tasigna as much as 100 days faster than standard tests used in clinical practice, Fluidigm said at the time.
 
High said that single-cell gene expression is becoming more attractive to users making "these types of discoveries," And stressed that the firm's BioMark and EP1 platforms were suitable for assays in development
 
High, asked whether Fluidigm might pursue licensing agreements with any of these users, said the company will "continue to develop and secure our own IP as we develop new products and technologies and uses of our discoveries." He added that the firm "will also continue to license IP that builds upon our products and technologies as it makes sense and where we can afford to do so."
 
"The BioMark system upgrade gives the researcher full flexibility to run sequencing, quality control, single-cell gene expression, real-time and digital PCR, high-resolution melting curve analysis," he said. "Given that many lab budgets might be under pressure next year, we have had several customers choose the BioMark solution so they can lock in the full flexibility and capabilities and can handle any demands that their research might bring them in the new year."

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