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Affymetrix, Luminex, MIT, Tri-Conference, Nanogen, Epoch, LabCorp, Yale, Third Wave, Chiron, Bayer, Bayer Healthcare, Transgenomic, Nasdaq, CombiMatrix, US Air Force, Tepnel, BSI, AstraZeneca


Affymetrix Warns of Slowdown in 500K Array Market

The market for whole genome mapping products has "temporarily slowed," Affymetrix said in an SEC filing this week.

The company noted that "since many customers complete projects before reordering, this may affect the timing of the 500K product reorders" and that these "factors ... may increase the risk around our expected revenue targets for the Mapping 500K Array Set."

Affymetrix did not announce a revenue target for the 500K, and has not in the past.

In the filing, Affymetrix also announced the opening of a new probe array manufacturing facility in Singapore, and reported that recent production yields on its Mapping 500K array set "consistently exceed 75 percent" in its Sacramento,Calif., facility.Affy also said it expected to meet customer demand for the product in 2006.

Luminex Licenses miRNA IP from MIT to Develop and Sell Assays

Luminex has taken a non-exclusive license from the Massachusetts Institute of Technology to develop and commercialize miRNA assays, the company said this week.

The deal applies to intellectual property developed by MIT, Howard Hughes Medical Institute, Dana-Farber Cancer Institute, and other members of the Broad Institute.

Additional details were not released.

State of Molecular Dx 'Embarrassingly Bad,' Say Tri-Conference Speakers

Despite recent advancements in molecular diagnostics, insiders from industry and academia sounded a cautious note when describing the state of the industry during Cambridge Healthtech's Molecular Medicine Tri-Conference, held in San Francisco last week.

Jorge Leon, the acting chief scientific officer of Orion Genomics, said during a presentation that, in particular, "the cancer diagnostic market is really pathetic."

"There is a great need for breast and ovarian cancer screening diagnostics," said Leon. Orion, based in St. Louis, has been working on screening tests for ovarian, colorectal, and breast cancers, he said.

Leon's words were echoed by John Ioannidis, a professor at the University of Ioannina School of Medicine in Greece, who said during his presentation on Friday that "diagnostics in the 20th century [were] embarrassingly bad."

"I think the tests we have available show poor performance; they don't provide useful information in the clinical setting," Ioannidis told Pharmacogenomics Reporter sister publication GenomeWeb News after his talk. "For most diseases we are almost at a loss."

According to David Ransohoff, an epidemiologist at the University of North Carolina, Chapel Hill, a central dilemma that molecular diagnostics faces is that the "field is dominated by small groups looking to hit a home run."

He said that many companies are led into thinking that discovery is easy, and that many studies that result in diagnostic efforts "don't give reproducible results."

"The field has got to organize itself more in a way parallel to how drugs are developed," Ransohoff said. "We need to design studies that are reliable and we can build on. If the units of knowledge in the field are not strong then the field cannot solve these problems."

Ultimately, though, Ransohoff said he thinks "people are going to look back on this as a naïve and inefficient time."

"People will look back at this time and say that the mistakes that we have made could have been predicted," he said.

However, Ransohoff and others pointed out that there is some good work being done. He said that the success of Genomic Health in developing the OncotypeDx test for breast cancer recurrence has "outlined a kind of model that the field can learn from."

Ioannidis added that "progress in the field will be incremental."

"[Our] faith stems from the fact that we can measure a lot of things," he said. "But the answer is buried somewhere in the data. Finding the answer is the problem."

Nanogen's Q4 Revenues Triple as Net Loss Balloons Due to Epoch Charge

Nanogen reported last week that its 2005 fourth quarter revenues more than tripled to $3.1 million from $1.0 million in the year-ago quarter.

Product sales grew to $1.2 million in the quarter ended Dec. 31, 2005, from $410,000 in the prior-year period, while license fees and royalty income grew to $1.5 million from $276,000 in the fourth quarter of 2004.

Nanogen's net loss for the quarter widened drastically, however, to $69.7 million, or $1.27 per share, from $11.2 million, or $0.31 per share during the same period in 2004.

The net loss for the current quarter included a previously disclosed goodwill impairment charge of $59 million attributable to Nanogen's 2004 purchase of Epoch Biosciences.

The impairment is a non-cash charge "related to the original value assigned to goodwill recorded on our balance sheet at the time of the Epoch acquisition," said Robert Saltmarsh, Nanogen's chief financial officer, in a statement. He added that the charge "does not reflect the performance of Epoch," but rather "reflects an adjustment to the estimated fair value of this goodwill asset based on current valuation methodologies."

Nanogen's R&D spending rose to $6.4 million in the fourth quarter of 2005 from $5.2 million in the year-ago period.

Nanogen had $6.2 million in cash and cash equivalents and $32.4 million in cash, cash equivalents, and short term investments as of Dec. 31, 2005.

LabCorp Exclusively Licenses Yale's Blood Test for Epithelial Ovarian Cancer

Laboratory Corporation of America announced last week that it has entered into an exclusive licensing agreement with Yale University to commercialize the university's new blood testing technology for epithelial ovarian cancer.

Under terms of the agreement, Yale will receive signing, milestone and royalty fees.

The new epithelial ovarian cancer test is based on a collection of serum proteins associated with cancer biology. Each protein marker is analyzed using an ELISA assay, and a statistical analysis is then performed to score the combined results.

Third Wave Moves to Dismiss Its HCV Lawsuit Against Chiron, Bayer, Bayer Healthcare

Third Wave Technologies hopes to dismiss its lawsuit against Chiron, Bayer, and Bayer HealthCare for allegedly infringing its hepatitis C virus diagnostic patents, the company said last week.

The companies said no payments were made and no licenses were granted or taken.

Third Wave filed the lawsuit on Oct. 11, 2005, in federal court in Madison, Wis., seeking a ruling supporting its right to sell HCV diagnostics. John Puisis, then the company's CEO, said in a statement at the time that the firm wanted to "clear any remaining ambiguities about the company's freedom to operate in valuable markets like those for HCV and HPV."

Chiron owns "several patents" relating to HCV and Bayer has licensed those patents for clinical diagnostics, said Third Wave in October.

Earlier this month, Third Wave took a license to Innogenetics' HCV patent in order to settle its lawsuit against that company, and in January, the company settled its suit against Digene concerning human papilloma virus patents, which it had originally filed on the same day as its suit against Chiron, Bayer, and Bayer Healthcare.

Third Wave said it had now resolved all of its patent-related lawsuits, with the exception of its suit against Stratagene. In September, a federal jury found Stratagene infringed two Third Wave patents related to that company's Invader platform, and in December, a federal judge overseeing the suit tripled the damages awarded to Third Wave to $15.9 million.

Stratagene posted a $21-million bond in January to secure the damages awarded to Third Wave.

Stratagene said in January that it plans to appeal the District Court's decision in the Court of Appeals for the Federal Circuit in Washington, D.C., once a final judgement has been entered by the District Court. In addition, Stratagene said it will seek to have the damages amount reduced or eliminated.

Transgenomic Receives Warning from Nasdaq for Failing to Maintain Minimum Share Bid Price

Transgenomic has received a letter from the Nasdaq exchange indicating that the company does not comply with the $1 minimum bid price requirement, the company announced last week.

According to the letter, which was received Feb. 15, Transgenomic has until Aug. 14 to regain compliance. The share price must close at or above $1 for 10 consecutive days, though Nasdaq may require the company to maintain that closing price for a longer period before determining compliance.

CombiMatrix Inks New Air Force Deal for Biomarkers

CombiMatrix and the US Air Force have agreed to cooperate to develop a "personal health monitoring system," CombiMatrix said last week.

Under the agreement, the applied biotechnology branch of the US Air Force research laboratory's human effectiveness directorate, biosciences and protection division, will use CombiMatrix's CustomArray technology to develop a biomonitor device capable of analyzing multiple DNA or protein biomarkers to "aid the US Department of Defense in its mission to effectively monitor the health status of military service personnel before, during and after deployment, where untoward exposures may impact on their performance or health," according to a statement.

The program is in addition to a previous agreement with the Air Force to develop pathogen-detecting microarrays and is the product of a "Presidential directive," said CombiMatrix.

Financial details were not provided.

Tepnel Plans New Facility in Scotland to Flesh Out PGx Play

Tepnel Life Sciences last week announced it has bought 1.7 acres in Livingston, Scotland, to construct a dedicated pharmaceutical, protein, and genomic facility.

The facility will allow the company to expand its pharmacogenomics capabilities to include high-throughput genotyping and other genomic techniques, said Tepnel in a statement.

Tepnel is a UK-based molecular diagnostics company with laboratories in the US, UK, and France.

BSI, AstraZeneca Ink Osteoarthritis Biomarker Deal

BioSystems International and AstraZeneca will collaborate to discover biomarkers for the treatment of osteoarthritis, BioSystems International announced last week.

Under the agreement, AstraZeneca will provide samples and funding for the research done by BSI, which will retain rights and income from diagnostic applications.

AstraZeneca receives a non-exclusive license to use the results for internal R&D activities, including exclusive rights to any new targets. The drug maker will also have a worldwide license to cite or recommend the use of the products developed by BSI as part of the collaboration.

Financial details were not released.

Filed under

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.