Transposon insertion site profiling chip (TIP-chip)

Transposon insertion site profiling chip (TIP-chip) was invented by Researchers at the Johns Hopkins’ High Throughput Biology Center. Tip-chip can be used to help identify otherwise elusive disease-causing mutations in the 97 percent of the genome long believed to be “junk.”

TIP-chip (transposable element insertion point) can locate in the genome where so-called jumping genes have landed and disrupted normal gene function. This chip is described n the Proceedings of the National Academy of Sciences. the article titled Eukaryotic Transposable Elements and Genome Evolution Special Feature: Transposon insertion site profiling chip (TIP-chip

The most commonly used gene chips are glass slides that have arrayed on them neat grids of tiny dots containing small sequences of only hand-selected non-junk DNA. TIP-chips contains all DNA sequences. Because each chip can hold thousands of these dots – even a whole genome’s worth of information – scientists in the future may be able to rapidly and efficiently identify, by comparing a DNA sample from a patient with the DNA on the chip, exactly where mutations lie.

Jef Boeke, Ph.D., Sc.D, professor of molecular biology and genetics and director of the HiT (High Throughput Biology Center), who spearheaded both studies at the Institute of Basic Biomedical Sciences at Hopkins, and his team have focused particularly on transposable elements, segments of DNA that hop around from chromosome to chromosome.

These elements can, depending on where they land, wrongly turn on or off nearby genes, interrupt a gene by lodging in the middle of it, or cause chromosomes to break. Transposable elements long have been suspected of playing a role vital to disease-causing mutations in people. Boeke hopes that the TIP-chip eventually can be used to look for such mutations in people.

The new TIP-chip contains evenly sized fragments of the yeast genome arrayed in dots left to right in the same order as they appear on the chromosome. Boeke’s team used the one-celled yeast genome as starting material because, unlike the human genome, which contains hundreds of thousands of transposable elements of which perhaps a few hundred are actively moving around, the yeast genome contains only a few dozen copies.

Like a word-find puzzle, where words are hidden in a jumbled grid of letters, the TIP-chip highlights exactly where along the DNA sequence these elements have landed. By chopping up the DNA, amplifying the DNA next to the transposable elements and then applying these amplified copies to the TIP chip, the researchers were able to map more than 94 percent of the transposable elements to their exact chromosome locations.

double-tiled DNA chip 

Standard chips contain one layer of DNA dots that read from left to right, like the across section of a crossword puzzle. Boeke’s new double-capacity chips hold two layers of dots, a bottom layer that reads across and a top layer that reads down, again using the crossword analogy. So if their experiment lights up a horizontal row of dots, the researchers learn that the data maps to the region of the genome contained in the bottom layer; likewise, if the experiment highlights a vertical row, the data correspond to the top layer.

Says Boeke, “It’s so easy to differentiate the top and bottom layers. Next we’re going to try adding another layer reading diagonally” to triple the amount of genomic information packed onto the tiny chips.

Authors of the TIP-chip and double-tiled DNA chip papers are Sarah Wheelan, a new faculty member in the Department of Oncology, Lisa Scheifele, Francisco Martinez-Murillo, Rafael Irizarry and Boeke, all of Hopkins.

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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’.

 

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.

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 

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