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Neurome, Illumina, Wellcome Trust, Perlegen, Siemens, Biomax, Expression Analysis, Sequenom, Partek, Ribomed, Transgenomic, Auvation, Lynx, GenData, Battelle, GE Healthcare, Jubilant Biosys


Neurome purchases assets of Digital Gene

Neurome has purchased “substantially all” the assets owned by Digital Gene Technologies, including its gene expression assays and gene expression analysis platform called TOGA, the companies announced recently.

The Total Gene Expression Analysis platform is neither a chip nor array technology. “TOGA is an open profiling system,” Najla Aftahi, Neurome’s director of business development and corporate communications, told BioArray News. “You have the ability to discover novel genes that have not yet been characterized.”

According to Aftahi, the technology is also more sensitive than array technology. “TOGA is as sensitive as one copy in every 10 cells. That’s a couple orders of magnitude more sensitive,” than what microarrays offer, she said.

Neurome, which develops databases that depict and integrate gene-expression patterns of the brain, will also acquire DGT’s entire patent estate. This includes data and discoveries generated in commercial and academic research programs.

DGT had collaborations with a few pharmaceutical firms, including Italy’s Recordati, Ireland’s Elan, and Immunex, which is now part of Amgen. It also had nearly 30 academic collaborations with researchers around the world.

“So, it was very widely received and got a lot of really positive feedback. Our decision to acquire that technology was in part based on the fact that this is something that people are extremely excited to use and has a lot of application to gene research,” Aftahi said.

Neurome plans to use the TOGA technology in-house and in commercial collaborations, as well in select academic partnerships. Through the collaborations, the technology also will supply Neurome with near-term revenue growth.

The partners, which are both based in La Jolla, Calif., did not disclose terms of the purchase, but Aftahi said that it was made through the issuance of stock in the privately held firm.

Illumina Settles Litigation with Applera

Illumina will pay Applera $8.5 million in a settlement of litigation relating to a 1999 joint development agreement, Illumina said. This settlement ends all outstanding lawsuits between the company and Applera’s Applied Biosystems.

An Applied Biosystems spokesperson confirmed that the settlement had been reached.

Illumina claimed in its suit, filed in December 2002, that ABI was in breach of the 1999 joint development deal to commercialize a genotyping system. At about the same time, ABI sued Illumina in Federal court for patent infringement related to the oligo ligation assay.

Under the settlement, the companies will exchange royalty-free cross licenses to unspecified intellectual property rights for their technologies.

The payment to Applera comes out of $10 million in R&D funding that Applera provided to Illumina in November 1999 as part of the joint development agreement, Illumina said. This payment was repayable to Applera from the profits of any products to emerge from the collaboration, and had been recorded as a liability on Illumina’s balance sheet. As a result of the settlement, Illumina said it will remove the liability from its balance sheet and record a one-time gain of $1.5 million.

In a separate announcement, Illumina said it had completed the previously announced sale of its San Diego facilities for $42 million, and had entered into a 10-year lease of these facilities. The sale and leaseback agreement will net the company over $15 million.

Illumina to Perform Mouse Genotyping Study for Wellcome Trust, Inks Pact with Galileo

Illumina has signed an agreement to perform a large-scale mouse genotyping study for the Wellcome Trust Centre for Human Genetics at Oxford University.

Under the fast-track services pact, Illumina will generate over 25 million mouse genotypes for Wellcome Trust researchers, who will use SNP variants to search for quantitative trait loci. Since specific genes and gene order are highly conserved between mouse and human species, the partners believe that the information yielded from this study should promote a more rapid identification of disease genes and genetic functions in humans.

The Wellcome Trust will provide Illumina with SNP loci and samples from inbred mouse crosses. San Diego-based Illumina will develop the assays for high-multiplex genotyping using its GoldenGate protocol.

The alliance follows a pilot study the firm completed in 2003 for Oxford and the Genomics Institute of the Novartis Research Foundation and is expected to result in Illumina marketing a standard mouse panel for generating genotypes with predictive value for behavioral disorders.

The Wellcome Trust plans to publish the genotyping results and make the information available freely to other researchers and the general public.

In addition, Galileo Genomics has purchased two of Illumina’s BeadStation 500GX genotyping systems for its disease gene discovery programs in an agreement that could be worth $1.5 million.

Under the agreement, Galileo will use the genotyping systems in five disease gene association studies that use DNA samples from the Quebec Founder population, a pool of 6 million individuals of French descent in Quebec. Illumina will receive rights to diagnostics that could be developed from biomarkers discovered in the program, as well as from Galileo’s existing gene discovery program for osteoarthritis.

The first disease that Galileo is studying under this program is the chronic gastrointestinal disorder Crohn’s disease. The company has already conducted genome-wide scans of 1,500 individuals within the Quebec Founder population to identify candidate regions associated with the disease and will now analyze SNPs within that region, the companies said. The companies did not specify the four other diseases to be studied under the program.

Perlegen Gets NIMH Grant to Study Autism Genetics

Perlegen has won a grant from the National Institute of Mental Health to study the genetics of autism, the company recently announced.

Perlegen will assay DNA samples collected by the Autism Genetic Resource Exchange for single nucleotide polymorphisms from its collection of validated SNPs. The company aims to identify genetic variants that, in combination, contribute to the inheritability of autism.

MountainView, Calif.-based Perlegen is a spin-off from Affymetrix.

Siemens, Biomax in Gene Expression Collaboration

German companies Siemens and Biomax Informatics announced that they will collaborate in the area of gene expression modeling and simulation.

Under the terms of the agreement, Siemens will use its BioSim gene expression simulator to uncover specific interdependencies in gene expression data, while Biomax will use its BioXM gene expression tool to place the correlations “in a relevant functional and biological context,” the companies said in statement.

Financial terms of the deal were not disclosed.

Expression Analysis to Provide Emory with Gene Expression Services

Expression Analysis has signed a multi-year agreement with Emory University to provide the school with gene expression services using Affymetrix’s platform.

In June, Durham, NC-based EA renewed and extended a similar agreement forged in 2001 with Duke University Medical Center.

Kim Gernert, current director of Emory’s Biomolecular Computing Resource, will serve as the gene expression analysis core facility program director, EA said.

Sequenom Signs On University of Tuebingen Institute as MassArray User

Sequenom has signed on the University of Tuebingen in Germany as a user of its MassArray gene expression platform.

Under the agreement, the Institute of Medical Genetics and the microarray facility at the university will use the MassArray Quantitative Gene Expression application to validate existing microarray data and for additional research in Parkinson’s disease, Huntington’s disease, and certain cancers.

The institute will also be a reference site for the system, Sequenom said.

The parties did not disclose the financial terms of the agreement.

Partek Licenses Gene Expression Software to Canadian Researchers

Partek has licensed its Partek Pro software for the statistical and visual analysis of gene expression data to the DNA Core Facility at the Canadian Science Centre for Human and Animal Health.

The St. Louis, Mo.-based firm recently licensed the software to Yale University, where researchers in the chemistry department intend to use it for pattern recognition of interactions between proteins and synthetic receptors.

Ribomed Awarded $1M to Develop Molecular Biowarfare Detection System

Ribomed Biotechnologies has been awarded a $1 million contract from the US Homeland Security Advanced Research Projects Agency to develop a sensor for DNA, RNA, and proteins in biowarfare agents.

The company, based in Phoenix, Ariz., said it received the contract in July under HSARPA’s Bioagent Autonomous Network Detector, or BAND, program. It funds the 18-month initial phase of what the company said it expects to be a four-year project.

The contract involves developing a system that will sample the air every three hours then analyze for at least 20 agents, including anthrax and smallpox. The company will adapt for this purpose its RiboMaker dectection system, which uses an isothermal abscription, or abortive transcription process for detection of target nucleic acids or proteins.

In the initial phase, the company will focus on optimizing abscription for mass spectrometry-based detection of RNA viruses and protein toxins.

The company said that Northrop-Grumman will build the device and will utilize sample collection technologies developed by MicroET, as well as DNA amplification technologies developed by Ionian Technologies, and RNA and protein detection technologies developed by Ribomed.

Transgenomic Posts Slight Increase in Revenues, Widening Losses for Q2

Transgenomic reported increased revenues and widening losses for the second quarter of 2004.

The company booked $9 million in revenues for the quarter, up from $8.5 million during the same quarter last year.

R&D costs decreased to $1.7 million, down from $2.4 million during the same period a year ago.

Transgenomic’s net loss for the quarter amounted to $15.1 million, or $.52 per share, up from $4.7 million, or $.20 per share, during the second quarter a year ago. The 2004 second-quarter loss included a $12 million non-cash impairment charge related to the company’s nucleic acids operating segment.

Auvation, ExpressOn Biosystems to Collab-orate in Developing Anti-Cancer Targets

Auvation, a Scottish company that focuses on developing biomarkers for tumors, and ExpressOn Biosystems, another Scottish company that focuses on the development of antisense RNA interference, have forged an agreement to collaborate in developing targets for cancer therapy, Auvation officials recently announced.

According to the agreement, Auvation will provide up to 20 targets from its cancer marker portfolio, and ExpressOn will use its ACCESSarray technology to determine regions on the corresponding RNA molecules that are optimally accessible to silencing reagents, which shut off the production of a target protein.

Auvation officials said their company will make upfront payments in return for access to ExpressOn’s ACCESSarray technology.

Financial terms of the deal were not disclosed.

Amidst Continued Losses, Lynx Takes Steps to Merge with Solexa

Lynx Therapeutics reported that it has signed a non-binding letter of intent to merge with privately held, UK-based company Solexa. As part of the deal, Solexa will provide Lynx with up to $2.5 million in loans to sustain Lynx’s operations.

Lynx announced the agreement as it reported revenues of $1.7 million for the second quarter of this year, down drastically from $4.6 million for the second quarter of 2003.

Lynx’s losses widened this year, with the company suffering a net loss of $3.6 million, or $.48 per share, for the quarter that ended June 30, 2004. Last year, the company posted a net loss of $2.9 million, or $.61 per share, during the second quarter.

Research and development expenses were down this year, with the company spending $2.6 million during the three months up to June 30, 2004. Last year, the company spent $3.2 million in R&D during the same period.

As of June 30, Lynx had cash, cash equivalents, and short-term investments of $2.4 million, including $400,000 million of restricted cash, and total current assets of $4.2 million.

Under preliminary, non-binding terms of the stock-for-stock merger with Solexa, the companies agreed that Solexa shareholders would hold a majority interest of the combined company. Lynx has received a first loan advance of $750,000 under a loan agreement between the two parties.

Lynx said the decision to pursue a merger with Solexa was based in part on the desire to have a combined company to pursue further development of the “cluster technology” assets that were acquired from Swiss-based Manteia by Lynx and Solexa jointly in March.

“We believe that a combination of [Solexa and Lynx’s] resources would allow for faster integration of the cluster technology, which in turn would enable us to expand our services offering and accelerate the development of MPSS [massively parallel signature sequencing]-based instrumentation,” said Kevin Corcoran, Lynx’s president and chief executive officer.

The companies are currently reviewing and discussing the proposed merger with the objective of concluding a definitive, binding merger agreement in September. Lynx has engaged Seven Hills Partners LLC as its financial advisor in merger discussions.

Due to lower than anticipated sample volume, Lynx revised its revenue guidance for the year to half of the net revenues of $16 million to $19 million it had predicted in March.

GenData and Battelle to Collaborate on Biomarkers for COPD

GenData Research Corporation and Batelle have entered into a collaboration to identify, develop, and commercialize biomarkers for chronic obstructive pulmonary disease, a lung disease that is the fourth leading cause of death in the United States and the cause of 2.9 million deaths worldwide every year.

Using mass spectrometry and nuclear magnetic resonance techniques, as well as phenotyping and genotyping techniques, the companies plan to do a comprehensive analysis of protein and metabolite markers taken from patients with COPD and matched control patients. The goal of the analysis is to be able to identify underlying factors associated with the disease, which the companies said could lead to better diagnostic and therapeutic treatments.

Headquartered in Salt Lake City, Utah, GenData collaborates with the University of Utah to do genetic studies on human populations. Batelle, headquartered in Columbus, Ohio, has collaborated with the US Food and Drug Administration in studying problems associated with smoke inhalation and in developing animal models for COPD.

GE Healthcare Creates Molecular Dx Unit, Moves Discovery Systems Research to NY

GE Healthcare announced it has established a Molecular Diagnostics business unit, based in Piscataway, NJ, and has appointed Trevor Hawkins as its president.

Separately, the Little Chalfont, UK, unit of General Electric said that it has moved research activities of its Discovery Systems business to the GE Global Research Center, in Niskayuna, New York. These moves come several months after GE’s acquisition of Amersham Bioscience in April, and its reorganization of GE Healthcare.

“Both of these moves underscore the strategic importance of functional biology and molecular diagnostics,” Peter Loescher, president and CEO of GE Healthcare said in a statement. “By transferring Discovery Systems’ research activities to GE Global Research, we benefit from unparalleled scientific and technological resources. Through the establishment of our Molecular Diagnostics business unit, we will accelerate the accuracy and speed of determining disease predisposition and diagnosis.”

Jubilant Maps Affy Probes Using Pathways Database

Jubilant Biosys of Bangalore, India, said that it has used PathArt, a database of over 900 signaling and metabolic pathways that are manually curated from literature, to map Affymetrix Probeset IDs.

“PathArt ... includes wide coverage on disease-specific pathways such as several cancers, arthritis, Alzheimer’s, asthma, multiple sclerosis, Parkinson’s, diabetes, and atherosclerosis,” Sreenivas Devidas, Jubilant’s vice president of business development and strategy, said in a statement. Researchers would be able to map the data generated from Affymetrix chips directly onto pathways.

Expression Analysis launches Affy-based Genotyping Services

Expression Analysis has added genotyping to its pharmacogenomics testing services. The Durham, N.C.-based firm will offer genotyping services utilizing the Affymetrix Centurion Array set and the GeneChip Mapping 10K 2.0 Arrays.

According to EA CEO Steve McPhail, the Centurion Array set enables researchers to evaluate more than 100,000 DNA polymorphisms using an assay that requires only 500 nanograms of DNA for each sample.



The Scan

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.

Study Points to Benefits of Local Consolidative Therapy, Targeted Treatments in Cancer Care

In JCO Precision Oncology, researchers report that local consolidative therapy combined with molecularly targeted treatments could improve survival for some lung cancer patients.

Genetic Variants That Lower LDL Cholesterol Linked to Reduced Heart Disease Risk

Rare variants in two genes that lower LDL cholesterol are also associated with a decreased risk of coronary heart disease, according to a new JAMA Cardiology study.

Study Links Evolution of Longevity, Social Organization in Mammals

With the help of comparative phylogenetics and transcriptomics, researchers in Nature Communications see ties between lifespan and social organization in mammals.