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Massachusetts Institute of Technology, E8 Pharmaceuticals, Affymetrix, Asuragen, GeneGo, Keck Microarray Center at Yale University, Applied Biosystems, Integromics, Antigen Discovery

MIT, E8 File Patent Infringement Suit Against Affymetrix
The Massachusetts Institute of Technology and E8 Pharmaceuticals have filed a suit against Affymetrix alleging that the firm is infringing their patent covering a genotyping method.
The suit, which was filed last week in the US District Court for the District of Massachusetts, claims that Affy’s use, manufacture, and sale of its GeneChip products for certain applications infringes US Patent No. 6,703,228. That patent was issued to MIT in March 2004 and was licensed to E8 Pharmaceuticals, a Cambridge, Mass.-based firm co-founded by MIT Professor David Housman, who is named as one of the inventors in the patent.
According to court documents, the ‘228 patent covers technology that “enables users to perform accurate, reproducible and cost-effective genetic analysis, using minute amounts of sample DNA and a small number of reactants to generate results that were previously impossible, even in specialized high-throughput centers using many thousands of different reactants.”
The dispute between Affy and MIT over the patent has been ongoing for a few years. Six months after MIT was granted the ‘228 patent, Affymetrix filed a patent application claiming priority to an earlier 1994 application, according to the suit filed this week. Then, in March 2005, Affy filed new claims with the US Patent and Trademark Office asserting the patentability and ownership of the method claims in the ‘228 patent.
Following a year of patent interference proceedings, the USPTO on May 2, 2007, ruled that Housman’s group at MIT “was the first to invent the claimed methods and was therefore entitled to the patent,” according to court documents.
MIT and E8 have asked the court to enter a judgment that Affy has infringed the ‘228 patent. They also are seeking triple damages because they believe that the alleged infringement has been willful. In addition, they have asked the court to award them ongoing royalties or issue a permanent injunction prohibiting Affy from “continued unlicensed infringement.”
In a filing with the US Securities and Exchange Commission last week, Affy said that it believes the plaintiffs' "claims are without merit and we will vigorously defend against the claims advanced in the complaint." 
An Affy spokesperson last week declined to comment further on the litigation. The attorney representing MIT and E8 did not return a call seeking comment by time of publication.

Affy to Distribute Asuragen's IVT Reagent Kits for Molecular Diagnostics
Affymetrix will market Asuragen’s in vitro transcription reagent kits for use with its diagnostic microarray platform, the companies said this week. 
Under the terms of the agreement, Asuragen will develop and manufacture IVT reagent kits configured for use with Affy’s GeneChip System 3000Dx, a diagnostic microarray platform that has gained 510(k) clearance from the US Food and Drug Administration and the CE mark from the European Union.
Kevin King, president of Affymetrix, said in a statement that the kit will “strengthen our growing diagnostic product portfolio."

Yale Keck Microarray Center Becomes a GeneGo Center of Excellence
GeneGo said this week that the Keck Microarray Center at Yale University has become a certified GeneGo Center of Excellence. Yale researchers will now have access to GeneGo's MetaCore analysis software, training, and advanced support.
GeneGo said that MetaCore is likely to be used at Yale to study basic and translational research; cancer biology; neuroscience research; and other clinical conditions. Overall, the COE will provide a pathway analysis environment and support for all the University's researchers and will also act as a training facility for GeneGo, the firm said.
"Neurosciences is one of the key [areas] we have chosen to focus on this year,” Julie Bryant, GeneGo’s vice president of business development, said in a statement. “Working with Yale is important to GeneGo as they are a leader in this field.”
Financial details were not discussed.

ABI, Integromics Integrate PCR Systems, Data Analysis Software in Biomarker Platform
Applied Biosystems and Integromics have worked together to integrate their data handling and PCR systems for biomarker analysis, drug development, and clinical studies, ABI said last week.
The companies have integrated ABI’s TaqMan arrays and real-time PCR systems with Integromics StatMiner software, which combines data visualization functions with statistical analysis and data mining tools, for use in analyzing real-time gene expression data from biomarker research.
ABI and Integromics began the development and co-marketing project, which included assistance from Novartis Pharma, in December 2007.  
ABI said Novartis is working to promote gene expression biomarkers in drug development studies, and recently used ABI’s TaqMan arrays in a large-scale pilot study.
The integrated products support “customers such as Novartis in their gene expression research, by enabling them to turn their data into meaningful information for use in a range of research projects including drug discovery and development,” Xavier Cristina, Applied Biosystems’ European manager for business development in functional analysis, said in a statement.

Antigen Discovery Nets $3M SBIR Grant
Antigen Discovery said last week that it has received a $3 million Phase II Small Business Innovation Research grant to fund further development of its protein microarray-based serodiagnostic platform.
The Irvine, Calif.-based firm said that the platform is being developed for biodefense and emerging infectious disease applications. It will collaborate on the development program with researchers at the proteomics core facility of the Pacific Southwest Regional Center of Excellence at the University of California, Irvine.
“By using our novel protein array systems and statistical algorithms, we can rapidly discover antigen sets that will provide serological tests that discriminate between different infections, or even between different stages of the same infection,” Huw Davies, principal investigator on the grant, said in a statement.
The SBIR grant was awarded by the National Institute of Allergy and Infectious Diseases and the National Center for Research Resources. 

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.