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AviaraDx, Transgenomic, CombiMatrix, Prisma Biotech, Agilent, GeneSpring, Ingenuity, Decode, ChondroGene, Kaiser Permanente, Biotage, Applera, Beckman Coulter, ABI

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AviaraDx to Launch Breast Cancer Prognostic Testing Service in 2006

AviaraDx, which was formerly known as Arcturus Bioscience, said last week in a statement that it intends to begin a prognostic testing service for breast cancer patients with partners in the wake of a study supporting its two-gene profile.

AviaraDx is "expecting our diagnostic licensing partners to launch a testing service based on both biomarkers in 2006" Toni Schuh, the company's CEO, said in a statement.

The company demonstrated the clinical utility of a two-gene expression prognostic profile for breast cancer in studies with the Mayo Clinic published in the April issue of Clinical Cancer Research.

The profile employs the genes HOXB13 and IL17BR, according to the company. The research used paraffin-embedded tumor tissue derived from postmenopausal women with early-stage, estrogen positive breast cancer.

The two-gene expression ratio was an independent marker of early breast cancer relapse and overall survival in lymph node negative breast cancer patients, but not lymph node positive tumors, the company said.


Transgenomic's Q1 Loss Narrows 89 Percent Despite 6-Percent Revenue Decline

Transgenomic this week reported a steep cut in net losses despite posting a minor decline in revenues during the first quarter.

Transgenomic's reported revenues of $6.5 million for the quarter ended March 31, down 6 percent from the $6.9 million year over year. Interim CEO Mike Summers in a statement attributed the decrease in revenues to foreign currency fluctuations.

Transgenomic said that it spent $604,000 on R&D expenses for the first quarter, roughly even with the $606,000 it spent for the same period last year.

Net loss for the period narrowed 89 percent to $318,000 from $2.9 million in the year-ago period.

As of March 31, Transgenomic had $6.6 million in cash and cash equivalents.


CombiMatrix to Test Speed of Bird Flu Monitor …

CombiMatrix and Washington State's Animal Disease Diagnostic Laboratory will test the company's Influenza Surveillance Technology to see if it can identify avian flu quickly in birds, Combi's parent, Acacia, said this week.

The current validated protocol for verifying a pathogenic influenza strain requires performing PCR to determine the existence of matrix protein gene. If matrix protein exists, researchers perform a successive PCR for hemagglutinin to determine if the H5 gene is also present.

Verification and further typing after a positive result requires the sample to be cultured and sequenced, which can take roughly on week or more, Combi said. The company said its monitoring system has shown "in laboratory tests" that it can confirm and type the infection in four hours.

"Our goal in this study is to demonstrate that our system produces quick virus typing results in the diagnostic laboratory environment that correlate to the standard protocol," Combi said in a statement.


… and Taps Prisma Biotech to Market, Sell CustomArrays in Taiwan, China

CombiMatrix last week said that Prisma Biotech will promote and sell its products in Taiwan, China, and "various" other countries.

The Acacia unit also said that Prisma "has the ability to synthesize content onto CombiMatrix CustomArrays and to sell those arrays to end customers."

Financial terms of the agreement were not disclosed.

CombiMatrix is currently establishing manufacturing and distribution relationships with regional companies to "enable them to manufacture arrays onsite for their local markets," the company said. "Such relationships benefit CombiMatrix by expanding the commercial market for its products without having to build additional infrastructure."

Besides selling its synthesizers to these partners, CombiMatrix said it "will continue to sell blank CustomArrays, reagents, additional synthesizers, and equipment to the partner for its local customers."


Agilent to Integrate GeneSpring Platform With Ingenuity's Pathways Analysis Tech

Agilent Technologies will integrate its GeneSpring software platform with Ingenuity's Pathways Analysis technology, Ingenuity said this week.

The integration is aimed at enabling researchers to analyze high-volume gene expression data and perform biological pathway analysis.

Financial terms of the agreement were not disclosed.


Decode's Q1 Revenues Rise 6 Percent As Losses Swell 20 Percent

Decode Genetics this week reported an approximately 6-percent increase in first-quarter revenues despite escalating losses.

Decode's revenues for the quarter ended March 31 rose to $10.1 million from $9.5 million year over year.

Decode said that R&D expenses for the first quarter swelled to $14.9 million from $8.3 million year over year.

The company's net loss swelled 20 percent to $20.3 million from $16.9 million in the year-ago period. Decode attributed the increase to higher R&D costs related to clinical trials and preclinical development work in the company's lead drug-development programs.

As of March 31, Decode had $140 million in cash and cash investments.


ChondroGene, Kaiser Permanente to Conduct Clinical Study for Colon Cancer Dx

ChondroGene said last week that it will partner with Kaiser Permanente of Northern California on a prospective clinical study to evaluate its molecular diagnostic test for colon cancer.

The study will compare the results of the company's ColonSentry blood-based colon cancer test to colonoscopy findings in a group of 600 patients from at-risk and confirmed cancer populations.

The results of the study will be used to advance development of the test, ChondroGene said, and will "allow Kaiser Permanente to evaluate the test in a patient population."

Compared to current stool-based or endoscopic-based screening approaches, "a blood-based test would be more convenient and would likely enhance patient compliance," said T. R. Levin, director of colorectal cancer screening for the Kaiser Permanente Medical Group.

The ColonSentry test is the first commercial diagnostic application of ChondroGene's Sentinel Principle molecular diagnostic technology.


Biotage Reports 68-Percent Rise in Q1 Sales as Per-Share Loss Climbs 14.2 Percent

Biotage last week said that first-quarter net sales increased 68 percent.

Net sales for the three months ended increased to 120.6 million SEK ($16.3 million) from 72 million SEK in the year-ago period.

The company said loss per share in the period increased to 0.24 SEK from 0.21 year over year.

Additional financials were not disclosed.


Applera, Beckman Coulter Disclose Terms of Settlement for CE, PCR Suit; Licenses Will Cost Applera $35M and Beckman $20M

ABI parent Applera and Beckman Coulter are trying to settle an ongoing patent dispute, and each company has agreed to pay the other royalty-bearing licenses for their respective technologies.

The settlement resolves "all outstanding legal disputes" regarding Beckman's capillary electrophoresis and PCR instrumentation technology and Applera's breach-of-contract allegations against Beckman.

Terms of the settlement call for Beckman to grant Applera licenses to its patents for replaceable gels for capillary electrophoresis instruments and DNA sequencers, and to its patent for a heated lid for thermal cyclers. As a result, ABI will pay Beckman $35 million to "release ... any and all claims of infringement relating to DNA sequencer and thermal cycler products."

Applera, meantime, will grant Beckman licenses to its patents for nucleic acid sequencing and real time PCR thermalcycling that the company will be able to use in the diagnostics market. Consequently, Beckman will pay Applera's Celera Genomic segment $20 million over 30 months for rights to use the technology in that market.

"Once executed, this agreement will provide both companies with access to important patents and technologies required for continued success in the rapidly growing field of nucleic acid sequencing and molecular diagnostic testing," Beckman President and CEO Scott Garrett said in a statement.

The settlement will enable Beckman Coulter to add DNA sequencing to the menu of molecular diagnostic tests available on its recently launched Vidiera NsD capillary electrophoresis systems and CEQ family of instruments.

"Access to real time thermalcycling provides a key technology needed for our plans to fully automate high value molecular diagnostic testing from sample preparation through final analysis," Garrett said.

The US District Court for the Central District of California has said it will stay its proceedings for 90 days pending completion of definitive agreements based on these terms.


ABI's Fiscal Q3 Revenue Grows 8 Percent as Sequencing Stumbles and RT-PCR Shines

Applied Biosystems last week reported that fiscal third-quarter sales increased 8 percent as R&D spending declined 6 percent and profits surged 121 percent.

Total revenues for the three months ended March 31 increased to $490.7 million from $454.8 million in the year-ago period. Revenue from the firm's DNA sequencing segment declined 4 percent to $136.5 million, while mass spec sales jumped 9 percent to $113.9 million, core PCR and DNA synthesis revenue increased 4 percent to $51.7 million, and "other" product lines inched up 1 percent to $26.4 million.

Revenue from the RT-PCR and applied genomics segment surged 23 percent year over year to $162.2 million, though the increase was buoyed by revenue generated by an Ambion business ABI acquired March 1.

ABI said the Ambion assets contributed 1 percent to total third-quarter revenue and unfavorable currency valuations shed around 2 percent from the company's top line. Receipts also included around $14 million in licensing fees and royalty payments related to ABI's settlement with Bio-Rad Laboratories and its MJ Research business.

ABI said fiscal third-quarter R&D spending declined to $48 million from $51 million year over year.

Profits, however, surged in the period to $124.4 million, or $.67 per basic share, from $55.5 million, or $.28 per basic share. For the quarter, certain items decreased profits by a total of $5.4 million, ABI said. These items included a pre-tax charge of $35 million ABI paid as part of an agreement with Beckman Coulter to settle certain patent infringement claims against ABI; $33.4 million related to the Bio-Rad settlement; a $3.4 million pre-tax charge to write off certain parts of the Ambion acquisition; and a $900,000 "favorable" pre-tax adjustment for a previously recorded asset impairment.

The fiscal third quarter also included $63.3 million in tax benefits related to a completed IRS exam, a state valuation allowance reversal, and research and development credits, ABI said.

ABI does not disclose its balance sheet.

Looking ahead, the company said expects revenue for the remainder of the fiscal year to grow in the mid-single-digit range. ABI said it expects revenue to continue to grow in its RT-PCR/applied genomics, mass spec, and core PCR and DNA synthesis product categories. The company also said it expects revenue to decline in DNA sequencing and "other" product lines.

Filed under

The Scan

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The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.