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Lynx Therapeutics Targets a Normal Mouse Tissue Sample Database for NIH


Lynx Therapeutics has won a contract to create a baseline database of certain normal-state mouse tissues for the US National Institutes of Health.

Last week, the Hayward, Calif.-based company said it had signed an agreement to characterize gene-expression patterns in a large number of common laboratory mouse tissue samples for a consortium of researchers from 11 of the 27 institutes within NIH.


“The deal sprang out of the fact that there has been a lot of interest in [massively parallel signature sequencing] around the NIH,” said Thomas Vasicek, vice president of business development at Lynx. “A wide variety of scientists from various institutes were generating samples and wanted a normal reference in order to compare. In the past, they have had to generate the normal counterpart for the tissues, pathological samples, or developmental states they were studying and that required significant additional expense.”

This news came just as the company announced last week the resignation of its chief financial officer, Ed Albini, who is leaving to pursue an undisclosed opportunity.” It is a sad loss,” Vasiceck told BioArray News. “He is a great friend.”

Susan Berland, most recently the chief financial officer at now-defunct DNA Sciences and a consultant for Lynx, will step into that role as the company seeks a permanent replacement.

Albini’s decision was not a sudden thing, said Vasicek. “There was a transition and we had plenty of time to plan for it,” he said.

Meantime, the 12-year-old company is gearing up to apply its MPSS technology to build this database for the research consortium.

“We expect this project will create a lot of interest because it basically creates a reference for [the] normal [state of gene expression],” Vasicek said. “We are building the baseline, and facilitating a lot of these other studies that have been ongoing at NIH for several years now where people are looking at their own favorite pathological situation or developmental biology situation.”

The company is not disclosing financial details of the agree-ment. The deal comes at a time when Lynx, with a market capitalization of $34 million as of Friday, is in the midst of a financial rebound with its stock price up some 50 percent since September. In November the company, which has operated at a loss since its inception in 1992, announced a net income of $1.8 million for its third quarter, an event coming between successful private placements of $3 million in September and another $4 million in December.

Lynx operates around its flagship MPSS system, the brainchild of Nobel laureate Sidney Brenner, which consists of tags that attach to the ends of DNA fragments in the sample to be studied, and complementary antitags that are added to microbeads.

The tagged fragments hybridize to the antitags, and the beads are directed into a flow cell, where the fragments are sequenced using Lynx’s instruments. The sequenced fragments are counted to see how much of a certain transcript is present in each sample — an absolutely quantitative type of readout, in contrast to current mainstream microarray analysis, which provides a representation of relative expression between two samples.

Lynx’s technology is sold on a services basis and is regarded as producing high-quality data at a much higher degree of resolution than other methods.

The company’s current collaborators, customers, and licensees for MPSS include Takara Bio, DuPont, BASF, Bayer CropScience, and Geron. Additionally, the company has recently added a number of new customers for its services including: Pfizer, Millennium Pharmaceuticals, the Institute for Systems Biology, the National Institute on Aging, the Genome Institute of Singapore, the University of Delaware, Northeastern University, and the International Livestock Research Institute.

Lynx will seek future private infusions of cash to fuel growth, said Vasicek.

“We will continue on that trend for the near future,” he said. “We are interested in increasing our war chest, rather than growing organically, to really launch this [technology] as quickly as possible.”

The contract and the delivery of services will be managed by SAIC-Frederick, a subsidiary of SAIC, which is the operations and tech-nical support contractor for the National Cancer Institute.

Vasicek said he expects Lynx to deliver data from its analysis by mid-summer.

“We are receiving samples as quickly as they can dissect them,” he said.

Lynx is scaling its production and is running two shifts of workers at times to handle this and other large projects it is conducting.

The deal took some 10 months to complete, largely due to the need to establish procedures for generating the samples to be analyzed.

Lynx Sees Advantages in MPSS

While Lynx does not conduct its analysis services on a microarray platform, it claims its technology — which does compete against Affymetrix, Agilent, and others who provide microarray-based, gene-expression profiling services and technologies — provides quantitative answers to the same questions.

“With a microarray, you are querying what you can interrogate with the microarray, those features represented on the microarray and those which can provide meaningful response in a hybridization assay,” Vasicek said. “That is highly limited while MPSS data provide a quantitative readout that is precise, accurate, and permanent. We count the molecules that are in the cell. We actually know how many are there.”

With access to the database of information coming from MPSS analysis, researchers will save time and costs, said Vasicek, who has deep experience in microarray technology. With a Harvard Medical School PhD in genetics and immunology, he has cycled through thousands of microarrays in previous career stops that saw him manage Millennium Pharmaceuticals’ microarray technologies, followed by a stint as director of commercial technology for Corning’s short-lived microarray manufacturing effort, and a position as a visiting scientist at the Whitehead Institute, where he evaluated genomic technologies.

“This [data] will be a great facilitator,” he said. “When you want to study something in skin, you already have that in the database and it’s not like a microarray where you have to do the normal right alongside the abnormal.”

Toward Mapping Every Cell

Give Lynx enough funding, and samples, and the company could produce a reference database on human tissues in about a month, said Vasicek, in response to a question on other potential projects on which the MPSS technology could be deployed.

“Sidney Brenner’s goal in inventing this technology was to identify all the molecules of every cell in the body,” he said. “And that is what we continue to drive for — to create the complete map of every molecule and every cell in the body at every time in development, and every pathological state.”

For now, however, the company is focusing on this admittedly small set of samples and the five months it will take to complete the database.



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