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

microarray-based Clinical diagnostic tests

 Pathwork Diagnostics, and the Virginia Commonwealth University School of Medicine has initiated an investigational study Genomics-Based diagnostic Test to determine a tumor’s origin so that tissue-specific management can begin.

The test uses microarrays from Affymetrix

More news on Pathworks website 

A new strain of virus named after Washington University

A new strain of virus has been identified by the medical school and named the “WU” virus after Washington University.

The virus, a type known as a polyomavirus, is closely related to two others, JC and BK, which attack the nervous system of HIV patients and cause kidney transplants to fail, respectively.

The virus has been reported in such geographically disparate countries as the United States, Australia, Germany and Korea, according to Gardner.

In fact, the first samples of the then-unknown WU virus came from the University of Queensland in Australia.

The samples were sent to the University because the school has ViroChip, a sophisticated pan-viral DNA microarray. This tool allows scientists to quickly screen viral samples and compare their structure to more than 22,000 known viruses. It was instrumental in distinguishing SARS from known viruses during the 2003 outbreak

David Wang, a University professor who leads the research team, states that the WU virus has unique properties unlike either of the others and he questions if it even is a human pathogen.

The scientific article is published at PLOS Identification of a Novel Polyomavirus from Patients with Acute Respiratory Tract Infections

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

Microarray to detect mutations in largest Human Gene

The average human gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases. Residing at Chromosome 4 it has long been of interest to the medical community because its the gene responsible for huntington’s disease, polycystic kidney disease, a form of muscular dystrophy and a variety of other inherited disorders. Chromosome 2 is noteworthy for being the second largest human chromosome, trailing only chromosome 1 in size. It is also home to the gene with the longest known, protein-coding sequence – a 280,000 base pair gene that codes for a muscle protein, called titin, which is 33,000 amino acids long.

Now reseacrhers at Emory university has developed a microarray based test to chek for mutations in this gene. The current test do not detect all types of mutation that affects 1 in 3500 males according to the university wesbite.

Mutations in the dystrophin such as point mutations in a sequence of DNA can result in mistakes in gene  expression and nonfunctional proteins that causes Duchenne muscular dystrophy (DMD).

A detailed presentation of the advantages of the test is available at the Emory Genetics Testing website. The test offeredon the Nimblegen CGH array platform gains more prominance as the company is now being acquired by Roche who has plans to dominate the clinical microarray market with its products in genetics testing space

The emory university Genetics testing lab offers numerous other genetic tests

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.

Microarray based DRUG DISCOVERY and CLINICAL DIAGNOSIS and biosensor designed to identify viruses

 Prof. David Dandy of Colorado State University chemical and biological engineering has proven that called microarray assays can be used for biomedical disease and drug screening assays could rapidly increase drug discovery,

Although not ready for hospital or office use, microarrays represent a novel miniaturized multi-spot diagnostic format that has huge potential for patient diagnosis if found reliable and approved.

Smaller is often better, according to a new scientific study that appears this week in the Proceedings of the National Academy of Sciences by Professor David Dandy, Dr. David Dandyhead of the Department of Chemical and Biological Engineering at Colorado State. Dandy co-wrote the paper with David Grainger, a former chemistry professor at Colorado State who now is chair of the Department of Pharmaceutics & Pharmaceutical Chemistry at the University of Utah.

The study was funded by a multi-year, $2.5 million grant from the National Institutes of Health.

“This work is extremely useful from an industrial perspective,” said Michael Lochhead, chief scientist at Accelr8 Technology Corp., a Denver-based developer of innovative materials and instrumentation for advanced applications in medical instrumentation, basic research, drug discovery, and bio-detection.

The critical importance of this work is illustrated by the fact that, to date, a single microarray-based test has been approved by the FDA for clinical use.

According to Roche, the manufacturer of this diagnostic microarray, “This test analyzes a patient’s Cytochrome P450 2D6 and 2C19 genotypes from genomic DNA extracted from a blood sample. Test results will allow physicians to consider unique genetic information from patients in selecting medications and doses of medications for a wide variety of common conditions such as cardiac diseases, pain and cancer.”

 

 

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