Affymetrix and Illumina in war path again as fresh patent litigation on microarray patents

Illumina and Affymetrix have been in a patent battle since 2004. In its second wave of patent infringement litigation cas against illumina filed in UK, Germany and US, Affymetrix has targeted technology offered by Solexa, the company acquired by Illumina in January 2007, as well as all of Illumina’s BeadArray(TM) products.

The new case is for patents 5,902,723, 6,403,320, 6,420,169, 6,576,42, 7,056,666, 0834575, 0853679, 0799897

Affymetrix previously sued Illumina for patent infringement in 2004 in the United States District Court for the District of Delaware. In March 2007, the jury returned a verdict in favor of Affymetrix.

Affymetrix has developed one of the industry’s strongest patent portfolios, featuring more than 400 patents granted in the U.S. and more than 40 patents granted in Europe.

More details on the case is available at Affymetrix Investor Website

Things have improved for Affymetrix this year, The company has aposted Q3 profits with the company’s revenues for the quarter increasing 12 per cent to $94.9m compared with $84.7m during the same period last year.

The results of these lawsuits could dramatically change the face of the DNA microarray market that has seen such growth due to the application of genetic information to drug discovery and ‘personalised medicine’.

 

Affymetrix launches Affymetrix University an education effort

Affymetrix  launched Affymetrix University, a series of courses that will be held throughout Europe and North America.

from Affy website

Santa Clara-based Affymetrix  said the courses give biologists a better understanding of how to design their microarray experiments successfully with appropriate quality control, and how to apply statistical methods to interpret biological results more effectively.

for more details check the Affymetrix website  

Affymetrix expands into personalized medicine The next big thing

Affymetrix expands into personalized medicine! Why because The next big thing in health care? is You the individual

personalized medicine is the place step every one wants to be. Roche recently went after Nimblegen for a small foothold in this developing ssicne field, Now its the turn of Affymetrix the leader in microarray DNA chips.

The company is trying to get ahead of the market curve by partnering with drug companies that are making precisely targeted medicines, tailored for patients who have specific gene variations

the company opened the Affymetrix Clinical Services Laboratory to analyze the genes in blood and saliva samples for pharmaceutical companies, diagnostic laboratory businesses and hospitals

Genetically Guided Treatment For Cancer

Two critical characteristics of breast cancer that are important to treatment can be identified by measuring gene expression in the tumor, a research team led by scientists at The University of Texas M. D. Anderson Cancer Center reports in Lancet Oncology online.

Researchers developed and validated a new genomic microarray test that identifies whether a tumor’s growth is fueled by the female hormone estrogen and the role of a growth factor receptor known as HER-2 that makes a tumor vulnerable to a specific drug.

“This is one important step towards personalized diagnosis and treatment planning based on an integrated genomic test of an individual tumor,” said senior author W. Fraser Symmans, M.D., associate professor in the M. D. Anderson Department of Pathology.

The Lancet Oncology paper results are the latest in an effort by the research team to develop a single test to quickly and efficiently determine the characteristics and vulnerabilities of a patient’s breast cancer and ultimately to guide treatment.

About 70 percent of breast cancers are estrogen-receptor positive and another 15 to 25 percent are human epidermal growth factor receptor-2 (HER-2) positive. Each receptor status requires different types of treatment.

“This moves us closer to developing an integrated single genomic test that could estimate the risk of cancer relapse after surgery, determine the ER and HER2 receptor status, and also gauge the sensitivity of the tumor to hormone therapy and chemotherapy,” says Lajos Pusztai, M.D., Ph.D., associate professor in the M. D. Anderson Department of Breast Medical Oncology, and team leader with Symmans.

Last fall, the group published a study showing that a genomic microarray test can also predict a patient’s response to chemotherapy. They also presented a paper in December showing that another genomic index predicts how an ER-positive patient will respond to hormonal therapy.

The study was funded by the National Cancer Institute, the Breast Cancer Research Foundation and the Goodwin Foundation.

Co-authors with Symmans and Pusztai are: first author Yun Gong, M.D., and Nour Sneige, M.D., of the M. D. Anderson Department of Pathology; Kai Yan, Keith Anderson, and Kenneth Hess, of the M. D. Anderson Department of Biostatistics; Feng Lin, M.D., Vicente Valero, M.D., Daniel Booser, M.D., Jaime Mejia, M.D., and Gabriel Hortobagyi, M.D., of the M. D. Anderson Department of Breast Medical Oncology; Christos Sotiriou, M.D., Ph.D., Institut Jules Bordet, Brussels, Belgium; Fabrice Andre, M.D., of Institut Gustave Roussy, Villejuif, France; Frankie Holmes, M.D., John Pippen Jr., M.D., and Svetislava Vukelja, M.D., of U.S. Oncology-Texas Oncology; Henry Gomez, M.D., of the Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru; and Luis Barajas, M.D., Departmento de Ginecologia Oncologica, Instituto Mexicano del Seguro Social, Guadalajara, Mexico.

Contact: Scott Merville
University of Texas M. D. Anderson Cancer Center

NYIT Professor Discovers Next Generation of DNA and RNA Microarrays brings hopes of personalized medicine

A novel invention developed by a scientist from New York Institute of Technology (NYIT) could revolutionize biological and clinical research and may lead to treatments for cancer, AIDS, Alzheimer’s, diabetes, and genetic and infectious diseases.

The invention allows the immobilisation of intact. double-stranded, multi-stranded or alternative DNA or RNA and has the potential to revolutionise biological and clinical research by allowing scientists to duplicate the cell environment and experiment with human, bacterial and viral genes.

Since the discovery of DNA, biologists have worked to unlock the secrets of the human cell.

Scientist Dr. Claude E. Gagna, Ph.D., an associate professor at NYIT’s School of Health Professions, Behavioral and Life Sciences, discovered how to immobilize intact double-stranded (ds-), multi-stranded or alternative DNA and RNA on one microarray. This immobilization allows scientists to duplicate the environment of a cell, and study, examine and experiment with human, bacterial and viral genes. This invention provides the methodology to analyze more than 150,000 non-denatured genes.

The “Gagna/NYIT Multi-Stranded and Alternative DNA, RNA and Plasmid Microarray,” has been patented (#6,936,461) in the United States and is pending in Europe and Asia. Gagna’s discovery will help scientists understand how transitions in DNA structure regulate gene expression (B-DNA to Z-DNA), and how DNA-protein, and DNA-drug interactions regulate genes. The breakthrough can aid in genetic screening, clinical diagnosis, forensics, DNA synthesis-sequencing and biodefense.

“This patent represents a leap forward from conventional DNA microarrays that use hybridisation,” said Dr Gagna, associate professor of the New York Institute of Technology.

This will help pharmaceutical companies produce new classes of drugs that target genes, with fewer side effects,” Dr Gagna continued.

“It will lower the cost and increase the speed of drug discovery, saving millions of dollars.”

Since the invention of the DNA microarray in 1991, the technology has become one of the most powerful research tools for drug discovery research allowing scientist to perform thousands of experiments with incredible accuracy and speed. According to MarketResearch.com sales of DNA microarrays are expected to be higher than $5.3bn (€ bn) by 2009.

The technology hinges around a novel surface that increases the adherence of DNA to the microarray so that any type of nucleic acid can be anchored, unlike conventional arrays that allow only single-stranded DNA to be immobilised.

Additionally, Gagna has developed a novel surface that increases the adherence of the DNA to the microarray so that any type of nucleic acid can be anchored. Unlike conventional microarrays, which immobilize single-stranded DNA, scientists will now be able to “secure intact, non-denatured, unaltered ds-DNA, triplex-, quadruplex-, or pentaplex DNA onto the microarray,” says Gagna. “With this technology, one day we will have tailor-made molecular medicine for patients.”

“With this technology, one day we will have tailor-made molecular medicine for patients,” said Dr Gagna.

and sure the news site are buzzing with the discovery

read more about the research and the original article details at

Dr Gagna, associate professor of the New York Institute of Technology. and also at www.nyit.edu/dnamicroarrays


Microarray test to anlyse the role of estrogen in breast cancer

Two critical characteristics of breast cancer that are important to treatment can be identified by measuring gene expression in the tumor, a research team led by scientists at The University of Texas M. D. Anderson Cancer Center reports in Lancet Oncology online.

Researchers developed and validated a new genomic microarray test that identifies whether a tumor’s growth is fueled by the female hormone estrogen and the role of a growth factor receptor known as HER-2 that makes a tumor vulnerable to a specific drug. The status of these factors is now determined by pathology tests.

About 70 percent of breast cancers are estrogen-receptor positive and another 15 to 25 percent are human epidermal growth factor receptor-2 (HER-2) positive. Each receptor status requires different types of treatment.

Read the complete article that talkes about the revolutionary test that promises to chage the way cancer is treated

http://www.huliq.com/11047/er-and-her-2-status-of-breast-tumors 

standardization in microarray analysis software industry

scouting for the right software for the microarray analysis software , kept me thinkng why despite these software being used by scores or scientists no one has come forward to create what can be called as a standard for such software, the confusion rains in this field as one company’s software data do not work with another one and vice versa, For an industry like biology and drug discovery  that is trying to benefit from the knowledge of mathematics statitics and chemistry physics inability to port data across platform is a serious roadblock. there are standards such as MIAMe and MAGE but these are just data standards, not for softwares, I believe ther should be  something similar to ISO standards, SEI CMI etc.

majority of the newsgroup and forums are used by graduate and at times senor researchers to find out which is the best software to be used, I thought of starting a wiki page where researchers can post their comments and rate the products and compare the features against each other,

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