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Gene Express, Tecan, Invitrogen, Iconix, Illumina, ExonHit, Sequenom, Ariadne, GeneGo, InPharmatica, Molecular Connections, Chromosome 5, Maize Genome


Gene Express Extends Patent Protection Internationally

Gene Express of Toledo, Ohio, said this week that it has received 11 international patents for its gene expression analysis technology.

The patents, granted in the European Union, Japan, and Russia, extend the protection of three US patents the company licensed from the Medical College of Ohio and the University of Rochester.

Gene Express said it holds exclusive worldwide rights on each of the patents and “has been working to extend the US patents internationally since 1997.”

The US patents — 5,643,765; 5,639,606; and 5,876,978 — are all entitled, “Method for quantitative measurement of gene expression using multiplex competitive reverse transcriptase-polymerase chain reaction.” They protect technology invented by James Willey, Gene Express’s chief scientific and medical consultant, while he was at the Medical College of Ohio and the University of Rochester.

The ‘978 patent from MCO has received patents in Russia and the European Union, while the two patents based on Willey’s work at the University of Rochester (‘765 and ‘606) received a combined patent in Japan.

The company said that additional international patents covering the MCO and University of Rochester technology and patents for molecular diagnostics for lung cancer are pending in several countries.

Tecan, Invitrogen Link Research Kits and Automation

Tecan and Invitrogen last week announced a non-exclusive collaboration to create products for use in sample preparation, microarrays, and cell-based assays.

New product combinations will link Invitrogen’s research kits with Tecan’s laboratory automation products, multimode detection devices, and microarray systems that both companies will market.

Financial details were not disclosed.

Iconix to Collaborate on CNS Gene Expression Study

Iconix has signed an agreement with Roderick Jensen, acting director of the biotechnology center and laboratory for functional genomics at the Brigham and Women’s Hospital/Harvard Medical School, to study and validate gene expression patterns in patients with neurological diseases.

Jensen’s team will validate gene expression changes in human peripheral blood for diagnostics, prognostics, and drug response. His lab has devised a high-throughput validation strategy using multiple gene expression platforms to assay tissue samples. According to the partners, the study will test the high-throughput validation strategy with samples from patients with Parkinson’s disease.

Iconix has a collection of drug signature genomic biomarkers used for research and validation on multiple array platforms.

Illumina in Genotyping Study Pact

Illumina signed an agreement to collaborate on a rheumatoid arthritis genotyping study with the North American Rheumatoid Arthritis Consortium, the company announced last week.

The study involves the analysis of 3,125 samples using Illumina’s Linkage IV SNP panel with its BeadArray platform. NARAC researchers will analyze the data in hopes of identifying genes associated with rheumatoid arthritis, Illumina said.

The effort is led by Peter Gregersen, director of the Robert S. Boas Center for Genomics and Human Genetics at the Institute for Medical Research in Manhasset, NY. Gregersen is also the principal investigator of the Multiple Autoimmune Disease Genetics Consortium, an effort by the US National Institutes of Health effort to identify genes linked to autoimmune diseases.

The company declined to disclose financial details of the deal.

ExonHit Licenses Toxicity Evaluation System to Mitsubishi Pharma

ExonHit Therapeutics has licensed its microarray-based toxicity evaluation system, Safe-Hit, to Mitsubishi Pharma, the Paris-based company said last week.

Safe-Hit allows users to evaluate and rank compounds according to their toxicity. The content of the microarray is based on a library of RNA splicing events specific to toxicity that ExonHit developed using a model of cellular stress.

Mitsubishi evaluated the system for one year using its own compounds.

Sequenom sells MassArray system to Australian Institute

Sequenom has sold one of its MassArray Compact systems to the Garvan Institute of Medical Research in Sydney, Australia.

The institute intends to perform SNP discovery, SNP-genotyping, and gene-expression studies on the system, Sequenom said. Specifically, researchers at the center plan to use the MassArray instrument to help them develop new genetic markers for cancer risk, diagnosis, disease progression, and therapeutic responsiveness.

Financial terms of the sale were not disclosed.

Sequenom began selling the desktop MassArray one year ago, according to Pharmacogenomics Reporter, GenomeWeb News’ sister publication. The product, which is 73 percent smaller than the full-size system and costs around $285,000, takes 45 minutes to run a single plate, according to a company spokesperson. The standard MassArray platform takes around 25 minutes and costs around $500,000.

Ariadne, GeneGo in Text-Mining Alliance

Ariadne Genomics of Rockville, Md., and GeneGo of St. Joseph, Mich., will integrate and co-market two of their software products for the analysis of high-throughput experimental data, the companies announced.

Under the agreement, Ariadne’s MedScan TextMiner automated text-mining software will be integrated with GeneGo’s MetaCore molecular interaction analysis software.

MedScan uses a natural language processing engine to mine the scientific literature for molecular interactions. MetaCore builds networks of molecular interactions, using manually curated databases, and allows users to import data from a variety of platforms.

InPharmatica Licenses Protein Database to Chugai

Inpharmatica, through its partner PharmaDesign, has licensed its Biopendium database to Chugai Pharmaceutical of Japan, the company said this week.

Chugai decided to take an online subscription to Biopendium, the protein annotation component of Inpharmatica’s PharmaCarta platform. Biopendium provides sequence annotations for over 150 organisms.

Chugai is the fourth Japanese subscriber to Biopendium, according to London-based Inpharmatica.

Molecular Connections, Protana Expand Curation Pact

Molecular Connections said that Protana, formerly MDS Proteomics, has renewed and expanded the companies’ literature curation and annotation services collaboration.

According to Bangalore, India-based Molecular Connections, its literature mining and annotation services are used by Protana to summarize scientific knowledge about proteins in order to help its scientific teams make appropriate research and development decisions.

“We have established a very productive relationship with Molecular Connections,” Thodoros Topaloglou, senior vice president and head of bioinformatics at Protana, said in a statement. “More importantly, Molecular Connections has the ... capability to scale up. Expansion of the collaboration is a logical move.”

Additional terms of the arrangement were not disclosed.

JGI Completes Sequence Analysis of Human Chromosome 5

The US Department of Energy’s Joint Genome Institute has finished analyzing the sequence of human chromosome 5. It is the 12th fully analyzed chromosome and the second chromosome completed by the Institute and the Stanford Human Genome Center, said JGI.

The final analysis was published in the Sept. 16 issue of Nature.

Chromosome 5 is the largest yet completed, with 180.9 million bases and 923 genes, including 66 known disease genes. Another 14 diseases are linked to chromosome 5.

One duplicated region on chromosome 5 could eventually help explain how spinal muscular dystrophy is inherited. The region contains many duplications and other rearrangements that vary between individuals, leading to a possible explanation of differences in the disease’s severity.

US Agencies to Collaborate on Maize Genome Sequencing Project

The US National Science Foundation, the US Department of Energy, and the US Department of Agriculture last week announced their joint support of a Maize Genome Sequencing Project.

The total estimated amount of project funding is $30 million, available in two awards over the course of three years, “depending on the quality of proposals and availability of funds,” the agencies said in a program solicitation.

NSF will provide funding in the form of a cooperative agreement, while the DOE and the USDA will supply grants or contracts.

The deadline for full proposals is Feb. 18, 2005.

The project, which involves the sequencing of 2.5 gigabases of the maize B73 strain, represents one of the goals of the National Plant Genome Initiative’s five-year plan.

The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.