CombiMatrix announced that the DoD has awarded a one-year, $2.2 mln contract to CombiMatrix for further development of its microarray technologies for a multipathogen- and chemical-detection system.
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,” commentsgeneticist 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.
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.”
Filed under: bioinformatics blog, DNA, gene expression, genetic medicine, microaray blog, microarray, microarray business, microarray cost, microarray industry, microarray price, Next Generation of DNA and RNA Microarrays | 1 Comment »
Personalized Medicine in 60 Seconds
Bioinformatics was a BOOM its was predicted to be next big thing, yet the industry which had hundereds of fragmented mom and pop kind small companies are now under mergers and acquisitions, Does everyone got their money back.
Bioinformatics is yet to become the big Billion billion Dollar, and on the door step the next big thing is ready for its journey
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
Filed under: Affymetrix, bioinformatics blog, DNA medicine, gene expression, genetics, Genomics, microarray blog, microarray for clinical diagnostics, personalized medicine, Pharmacogenomics, Theranostics | 2 Comments »
Does eating a lotf of spicy curry eliminates the chances of geting cancer and diseases like Alzheimer’s thats a yummy proposition, I wish it was that easy, but apparently the Indian curry cuisines has the capacity to prevent the onset or delay the disease, but dont reach out for the qwik e mart yet. The curry doesnt do the job all by itself ,one of the key spices used ‘the Turmeric’ does that work, Ayurvedic medicine practioners has known the value of turmeric for a very long time, the stuff even finds its ways into soaps and cosmetics
Scientists have for the first time isolated bisdemethoxycurcumin, the active ingredient of curcuminoids, a natural substance found in turmeric root that stimulates the immune system to destroy brain-clogging proteins that cause Alzheimer’s.
Researchers found that bisdemethoxycurcumin boosted immune cells called macrophages to clear amyloid beta. Amyloid beta is a peptide that forms the plaques found in Alzheimer’s disease.
Amyloid plaques are found outside the neurons. Two major pathways are involved in breakdown of APP (amyloid precursor protein) which makes the protein called B-amyloid protein. responsible for plaques .One pathway is normal and causes no problem. The second results in the changes seen in Alzheimer’s and in some of the other dementias.
Collaborative Drug Discovery Releases Next Generation Database for Both Private Collaborations and Public Open Access
Collaborative Drug Discovery enables scientists to archive, mine, and collaborate to more effectively develop new drug candidates for commercial and humanitarian markets.
The technology enables novel community-based research efforts that become more and more useful as additional participants contribute data. Publicly available data sets currently in the system include the FDA orphan and approved drugs and small molecule drug discovery data dating back over half a century. These data sets pertain to a diverse group of neglected diseases, including malaria, tuberculosis, African Sleeping Sickness, Chagas Disease and Leishmania.
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.