Microarrays in Personalized Medicine- $200M-US Aided Personalized Medicine Program

I have written quiet often about this subject and companies that promises solution for personalized medicine. especially the use of genomics information in organ transplant patients and cancer treatment. XDx and Genomic Health are two such companies . XDX has applied microarray, to monitor the immune system, with the help of Gene expression to address the challenge of balancing the risk of acute cellular rejection against the known adverse effects of immunosuppressants; especially inexpression testing for patients with heart transplants. Genomic Health provides individualized genomic profiling of tumor tissue may help improve cancer management.

personalized medicine is still dismissed of by many as the cost are still high, and there are very few trained physicians who can use this extra information for better clinical outcome.

US institutes Biodesign Institute at Arizona State University, Fred Hutchinson Cancer Center Translational Genomics Research Institute (TGen), the Institute for Systems Biology, and the Partnership for Personalized Medicine will help the government of Luxembourg start a three-pronged, $200 million-plus biomedical initiative focused on harnessing genomics technologies to study human health problems.

For those who wants to cry foul that genomic information can lead to discrimination against individuals by insurance companies or others can take solace on GINA . In may 21.2008 President  George Bush has signed into law the Genetic Information Nondiscrimination Act (GINA) that will protect Americans against discrimination based on their genetic information when it comes to health insurance and employment.

The most immediate benefit of GINA is to remove barriers to identifying individuals at high risk for diseases due to genetic mutations before the onset of the disease

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.

DNA test results in three days, or Money Back

IDENTIGENE Becomes First DNA Testing Lab to Promise Fast Results with a Money-Back Guarantee . The company now Now Offers the Industry’s First Money-Back Guarantee, together with a Three-Day Turnaround on Results

the website says IDENTIGENE is the only DNA testing lab with a money-back guarantee

 

 

 

 

 

Transplant Patients Could Live Free of Anti-Rejection Drugs

Scientists from the Lucile Packard Childrens Hospital and the Stanford University School of Medicine have identified a pattern of gene expression shared by a small group of patients who beat the odds and remained healthy for years without medication, after undergoing Organ transplant.

The findings made by Minnie Sarwal, MD, PhD, a pediatric nephrologist at Packard Children’s is a major advantage in organ transplantation treatment. Transplant recipients who share the same pattern of genes but are still on conventional medication may be able to reduce or eliminate their lifelong dependence on immunosuppressive drugs. The study may also help physicians determine how best to induce acceptance, or tolerance, of donor organs in all transplant patients, regardless of their gene expression profiles.

Although the anti-rejection medications, known as immunosuppressants, tamp down the immune system enough to permit lifesaving organ transplants, their benefits come at a price. They also quash the bodys natural response to dangerous invaders, such as bacteria and viruses, and to rogue cancer cells. Transplant physicians prescribing immunosuppressants to their patients walk a fine line between avoiding organ rejection and increasing the risk of infection and cancer

The researchers used microarray, or gene chip, technology to compare gene expression patterns in blood samples from 16 healthy volunteers with those from three groups of adult kidney transplant recipients from the United States, Canada and France

The IBM Clinical Genomics for targeted clinical research

THe Haifa Lab of IBM provides the Technlogy for Clinicalgenomics and leads the research in lifesciences fieds.

The Clinica, Genomics division plans to provide technology to integrate clinial genomics data and HL7 and other complaince protocls followed in clinical research and clinia, trial and integrate them to provide better and focused clinical trials

Clinical genomics for biopharmaceuticals from IBM

the main advatages as per IBM website is that

  • Encapsulate raw genomic data into an HL7 Clinical Genomics message, including transformation services of proprietary data formats to standardized formats like MAGE and BSML
  • Access patient’s clinical history stored in an enterprise EHR system
  • Access all major ontologies that provide genotype-phenotype relationships like OMIM, PharmGKB, etc.
  • Parse the encapsulated raw genomic data and bubble-up selected genomic data items based on ontological knowledge as well as the patient clinical data
  • Compare two Genotypes (the data model at the heart of the HL7 specs) in order to provide case-based reasoning services to decision support application that will use CGL7 as a specialized clinical genomics middleware
  • Find a similar pedigree in case base of pedigrees in order to support risk assessment applications that base their assessment on family history

Pharmacogenomics has started

IT been a long time since my last post, So I thought of catching up with other blogger before going to do anything myslef. So here is what got my attention from Alla Katsnelson blog on the scientist magazine  that  USFDA approved updated labeling for the widely used blood-thinning drug, Coumadin, to explain that people’s genetic makeup may influence how they respond to the drug.

so whats going to be good for common man, the next time (not very soon) you are going to be under treatment of a controversial drug you might get to know how your genetics makeup can affect the treatment, thats going to be a good relief especially cancer patients and those who undergo HRT

while Frost&Sullivan reports in its latest industry update that  genomics platforms that are too inefficient and expensive for ultra-high throughput comprehensive genome-wide analysis are hindering the realization of personal genomics.

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.”

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