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’.

Gene Logic sells in genomics division

It hardly a week I have wrote about acquisition and mergers , it seems the rain is noit going to stop any time soon, the latest one , to give away the home plate is Genelogic agreeing to sell its genomics division to India HQ Ocimum Biosolutions subject to the authorization of the transaction at a special meeting of shareholders of Gene Logic.

This is a transforming event of significant strategic proportion,” said Charles L. Dimmler, III, President and Chief Executive Officer of Gene Logic.

Genelogic bought its preclinical division from TherImmune, a Gaithersburg company, in April 2003 for $51 million which was sold to Bridge Pharmaceuticals for $15 Million,

Gene Logic Inc said it agreed to sell its Genomics assets to Ocimum Biosolutions Ltd for $10 million in cash. Under the terms of the Ocimum sale agreement, Gene Logic retains full rights in perpetuity to utilize the existing information data bases of its former Genomics business as key elements in building its emerging drug repositioning and development business. Furthermore, the Company will retain specified assets related to molecular diagnostics and will continue to explore strategic alternatives for these assets

The sale is part of the Genelogic new strategy to focus on to build drug repositioning and development business which was decided last year.

Ocium will assume certain liabilities associated with the Genomics assets and business and will pay Gene Logic $7 million at closing and $3 million payable in a promissory note due 18 months from closing.

The purchase includes Gene Logic’s Knowledge Products business including the The BioExpress® System a continually growing genomic database of gene expression data and associated clinical information from over 18,000 human and animal tissues and cell line samples. ToxExpress® a toxicogenomics reference database.

Ocimum will continue to operate the business out of the current state-of-the-art laboratory facility of Gene Logic in Gaithersburg, Maryland.

Mergers Acquisitions Consolidation-Microarray Industry bubble in making- The days are numbered

Bioinformatics promise has already had its brush with plenty of resistance, not it seems the time for microarray industry with consolidation and acqusitions and megers announced almost every week. The slow adoption and too many fragmented with disparate standards has made the industry a victim of its own success.

the new kid on the block to unload its microarray and genomics business include Nanogen with its plans to unload its loss making microarray business, While the most of the biotech IPO featured in the market in the last 6 month in US have failed to generate expected results.

But pharmaceutical firms are racing to buy up biotech firms Roche has acquired 454 Life science,and Nimblegen and now Bristol-Myers Squibb is buying Adnexus Therapeutics for $430 million. Wyeth has bought Haptogen Ltd, which emerged from Aberdeen University five years ago, pharmaceutical firm Wyeth is the fourth largest biotechnology company in the world. PerkinElmer is planning to buy the cord blood banking firm Viacell Inc

On the the report of Bradstreet Israel warning on Sunday that majority of Israel’s publicly-traded biotechnology companies will be forced to halt their research and development activities in as little as two-and-a-half years if they do not alter their business strategies immediately, research company Dun & In many cases, biotech companies are not doing sales, but only conducting research programs,” said Reuven Kuvent, director-general of D&B Israel. “They don’t focus enough on raising capital or attracting investor things they must do if they intend to continue to be operational over the next few years.”

While Asian genomics and biotech companies like Biocon which recently sold its enzu=yem business to NovoZyme and Strand Genomics which was selected as TECHNOLOGY PIONEERS 2007 by World Ecconomic Forum and smaller startups like Ocimum Biosolutions which are now pumping vast amount of funds into acquiring genomics business across US and Europe are waiting inthe wings to take off . Still there are others racing to create the cheapest microarray and sequencing methods only time will tell theeir fate,

Is the SBIR grant program is unfairly towards small biotech companies

28 patient organizations joined BIO in asking Congress to restore eligibility to venture-backed biotech companies to “help innovative research move forward in order to foster breakthrough cures.”

Under the SBA’s new rules, companies with more than 50 percent of their backing from venture capital can’t compete for grants

 Biotech industry calls on Congress to change grant program

IS Microarray facing the DOOM….Invading microarray turf……….

ChIP-sequencing (ChIPSeq) – a combination of chromatin immunoprecipitation and next-generation, or parallel, sequencing. The feat was performed “with a speed and precision that goes beyond what has been achieved with previous technologies,” comments University of Washington geneticist Stanley Fields, in an accompanying essay in Science.

hIP is a well-established lab technique to identify those specific sites where proteins latch onto the DNA. Cells are treated with a chemical to fossilize the links between DNA and protein, the chromatin is then isolated, the DNA broken up, and the attached proteins immunoprecipitated. Finally, the DNA stuck to the protein can be released and analyzed. Until now, the most high-throughput application of this technique involved using microarrays containing thousands of gene spots able to identify binding sites for transcription factors and the like.

Next-Generation Sequencing Invades Microarray Turf By Kevin Davies June 14, 2007 | Two new papers unveil a new dimension to commercial next-generation sequencing applications – one that could potentiallypose a threat to more-established microarray technologies. Using theGenome Analyzer from Illumina/Solexa, two groups working independentlyhave been able to map the locations across the genome where a specific
DNA-binding protein latches onto the DNA.

ChIPSeq is a cost-effective alternative to microarray methods, with a significant upside. “Other ultrahigh-throughput sequencing platforms, such as the one from 454 LifeSciences, could also be used to assay ChIP products, but whatever sequencing platform is used, our results indicate that read numbercapacity and input ChIP DNA size are key parameters,” Johnson et al. writes.ChIPSeq might be an order of magnitude cheaper than microarray alternatives, with the eight flow cell lanes in theGenome Analyzer offering excellent design flexibility. Fewer materialsare required, and the method can be applied to any organism – it is not restricted to available gene arrays.

Changing ChIPs
The advantages of ChIPSeq over ChIP-chip include the ability to interrogate the entire genome rather than just the genesrepresented on a microarray. (For example, Johnson et al. point out thata similar experiment using Affymetrix-style microarrays would requireroughly 1 billion features per array.) There is also the benefit of
sidestepping known hybridization complications with microarrayplatforms. “Perhaps most usefully,” writes Fields, “ChIPSeq canimmediately be applied to any of those [available] genomes, rather thanonly those for which microarrays are available.”

Hocus Locus Spins out of University of Albany

Hocus Locus, a bioinformatics company which is part of the $225 million Gen*NY*Sis   Programe (Generating Employment through New York State Science) is located at the Center for Excellence in Cancer Genomics in University of Albany, it makes products to help small drug discovery companies speed up development of new drugs.

New horizons ahead

Its been two years since I have been with Ocimum Biosolutions ,the India HQ company serving bioinformatics and microarray market in US with office in Indianapolis and another lab in netherlands, I have been working in the business development of the company’s microarray arm in US which was acquired from MWG biotech, we had tasted success,

I have been busy lately as I have resigned from the company now that explains the absence of any new posts for few weeks now. Ocimum is one of the unique bioinformatics oraganization to make its mark in this industry, because unlike many new companies .  it was started by people with no biological background but has been selected as one of fastest growing life science company in India and Asia many times by Deloitte ranking and many other independent agencies. apart from winning awards from government and even a funding fro world bank. So what makes them so sucessful

Ocimum offers services in bioinformatics oligo microarray and R&D but its the presence of its labs near to its customers and the company’s software development division housed at Hyderabad India that makes the difference. Coupled with India’s cost efficiency, it has many advantages

Bioinformatics industry is going through a face of consolidation, marketed in India in its infancy as a glamorous field to work many who jumped into the fray has burned their hands. and industry analysis in 2000 predicted the industry to become a 100 billion worth by 2004, yet even in 2007, majority of the biologists are yet to warm upto the industry in a way predicted by the software pundits

Research and Markets (http://www.researchandmarkets.com/reports/c59429) has announced the addition of “Biomed Outsourcing Report: An Overview of the Life Sciences and Outsourcing Landscape in India: Spotlight on Bangalore” to their offering.

Genetics and Business

I have been busy lately but found some time to go through an interesting story and a good article published in scientist magazine

1. Father-in-law of now-infamous extensively drug-resistant TB patient studies tuberculosis at the CDC, and is now under review by the agency
2. Genotyping with PCR -How to choose the right approach

I am working on an article about consolidation in Microarray and Bioinformatics industry so interesting to know about GenoLogics Announces Bioinformatics Partnership with Illumina  so is the  news of Roche acquiring Nimblgen and the end of patent wars with Affymetrix, Roche has also acquired 454 life sciences, It seems Roche plans to get inot clinical genomcis and theranostics application industry, the company already has FDA approved amplichip CYP450 arrays for clinical diagnostics

With many other acquisitions in the last one year  and many more in the pipeline it seems paydays for early starters.

Future of High Throughput Genome Sequencing

In Bangalore Bio 2007 LabIndia has introduced  SOLiD: Sequencing by Oligonucleotide Ligation and Detection which is the Future of High Throughput Sequencing.

“This is useful for those who want to do full genome sequencing. Whole genome projects will be more cost effective with this new instrument than they are today,” said Dr. Anupama Gaur, Team Leader Application Support, Labindia Instruments, Pvt. Ltd.

HistoGenetics has come up with Sequence Based Typing which has many advantages such as identifying many rare and new alleles. “Nearly 2000 alleles have been identified so far and it has been launched in the US and UK as of now” said Dr. Cereb Nezih, M.D., President and co-founder, Histogenetics, Inc.

Stein GAVE Bioinformatics Ten Years to Live

Its an old story but looking at whats happening in bioinformatics industry now i think this topics some what relevant. The industry has seen an unprecedented number of mergers and collaboration something unthinkable at the early stages of bioinformatics era.

Lincoln Stein’s keynote at the O’Reilly Bioinformatics Technology Conference was provocatively titled “Bioinformatics: Gone in 2012. it was proved to some level that all the compaies that sproute up are not going to be around for a long time. but it seems 2012 is defenitely not going to be the end of bioinformatics. personalized medicine, functional genomics and theranostics have given it a new lease of life and lot of steam to speed ahead

the old article is present at oreilynetwork