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NIH, FDA, Rosetta, Perlegen, 454 Life Sciences, Taiwan Regulators, GE Healthcare, Eli Lilly, Abbott, Epigenomics, Lab21, Monogram Biosciences

NIH Releases Genetic and Clinical Data from 60-year Framingham Heart Study
The National Institutes of Health announced this week that it is releasing a large collection of genetic and clinical data from the Framingham Heart Study for free to qualified investigators.
Calling the program “one of the most extensive collections of clinical and genetic data ever made freely available to researchers worldwide,” the NIH said the data will allow researchers to study the genetic, clinical, and lab results from as many as 9,300 participants.
The data set, called the SNP Health Association Resource, or SHARe, can be accessed through the National Center for Biotechnology Information’s Database of Genotypes and Phenotypes, which NCBI launched in December 2006.
NIH said the Framingham SHARe data set includes data on more than 9,300 individuals spanning three generations of more than 900 families, and more than 550,000 SNPs.
The Framingham Heart Study began in 1948 and originally included more than 5,200 participants. Another 5,000 spouses and children were added to the study in 1971 and another 4,000 were enrolled in 2002, the NIH said. As the study is ongoing, more data will continue to be added to the database in the future.
Genotyping for the study was conducted by Affymetrix under a contract with the National Heart, Lung, and Blood Institute. Along with NHLBI, the Framingham study is being conducted under collaborations with Boston University’s School of Medicine and School of Public Health.
"The widespread availability of Framingham Heart Study data provides unprecedented opportunities to investigate the connections between genes and disease," said Health and Human Services Secretary Michael Leavitt.
He added that SHARe is a “major milestone” in personalized healthcare.
His comments follow last month’s release of "Personalized Health Care: Opportunities, Pathways, Resources," an HHS report in which Leavitt called for a stronger focus on personalized medicine under HHS.
"As one of the most comprehensive studies ever undertaken, the Framingham Heart Study will play a vital role in laying the foundation for this vast dataset to help researchers link genes and disease," added Elizabeth Nabels, who directs NHLBI.
Application information for the SHARe date can be found here.

FDA To Use Rosetta's Syllego to Analyze Genotyping Data in VXDS Program
Rosetta Biosoftware said this week that the US Food and Drug Administration will use its Syllego software to manage and analyze genotyping data used from genome-wide association studies that are submitted under the FDA’s Voluntary eXploratory Data Submission program.
Feeling more at ease with analyzing genomic data through its Voluntary Genomic Data Submissions program, the agency last year expanded VGDS to VXDS, allowing sponsors to submit “exploratory” biomarkers such as proteomics, metabolomics, and imaging data.
"There are a growing number of genome-wide association study data submissions to the FDA through VXDS," said Weida Tong, director of the Center for Toxicoinformatics at the FDA’s National Center for Toxicological Research.
Tong added that Syllego “allows us to effectively manage genotyping data submissions and also carry out analyses to understand why the sponsor might have used a particular method to arrive at a specific outcome.”
The NCTR will also “explore the possibility” of integrating Syllego system with its own ArrayTrack software.
The FDA’s Center for Drug Evaluation and Research is already using the company’s Rosetta Resolver software for gene expression data management and analysis under the VXDS program.

Perlegen, 454 Partner in Drug Response Re-sequencing Study
Perlegen and 454 Life Sciences will collaborate on a project to re-sequence “hundreds” of human DNA samples with the goal of developing a test to predict how patients will respond to a certain class of drug.
Perlegen said it has collected samples from individuals with specific responses to a “widely prescribed” class of drug. The partners intend to identify and validate genetic variations that could be developed into a clinical test that would predict response to the drug family.
Under the agreement, the companies will re-sequence portions of genomes from the samples using 454 sequencing and Perlegen's sample-prep and amplification technologies.
The companies' data analysis groups will work together to determine to what extent genetic variations influence patient response to this class of drugs.
Perlegen did not divulge the name of the drug class involved in the study, but said the research "holds the promise to improve therapeutic outcomes for a vast number of patients."
The Mountain View, Calif.-based company announced in June that it has collected more than 3,000 DNA samples from diabetic patients treated with two popular insulin-sensitizing thiazolidinediones, GlaxoSmithKline’s Avandia and Takeda’s Actos, to analyze the genetic variability associated with adverse events tied to this class of medications. At the time, Perlegen Chief Corporate Development Officer Rob Middlebrook revealed to Pharmacogenomics Reporter that the goal of the study is to ultimately develop a diagnostic that can aid physicians with treatment protocols for type 2 diabetes.
Financial terms of the agreement between Perlegen and 454 Life Sciences were not released.

Taiwan Regulators Plan Genetic Testing for Dangerous Side Effects of Anticonvulsant
Taiwan’s Department of Health said this week that it has updated the label for the anticonvulsant drug carbamazapine to warn patients of a genetic link to potentially serious side effects, and said that it plans to test patients for adverse reactions to the drug.
According to Taiwan’s National Reporting System of Adverse Drug Reactions, carbamazepine — a mood-stabilizing drug used for epilepsy and bipolar disorder — is responsible for severe adverse drug reactions such as Stevens-Johnson syndrome and Toxic Epidermal Necrolysis, also called SJS/TEN. There is a high incidence of carbamazapine-induced SJS/TEN in Taiwan compared to other countries, the DOH said.
A series of retrospective studies has shown that the human leukocyte antigen HLA-B*1502 marker — which is present in about 5 percent of the Taiwanese population — “has a very strong association” with these serious ADRs, the DOH said, prompting the label change for carbamazapine.
The updated label notes this risk and warns that “a patient who carries the HLA-B*1502 gene will have at least 193 times higher risk of developing ADR than a patient who is not a HLA-B*1502 carrier. Approximately 5% of the Taiwan population carry the HLA-B*1502 gene."
This data connecting the drug to the biomarker was drawn from retrospective studies conducted by Yuan-Tsong Chen, director of the Institute of Biomedical Sciences in Taiwan and a professor of Pediatrics and Genetics at Duke University Medical Center.
The DOH said in a statement that due to the retrospective study design, “the clinical application of the results is somewhat limited,” so it is planning to conduct a series of preventive prospective studies between 2008 and 2012 “to assess the clinical applications of the risk genes” and to determine if genetic screening “can effectively reduce the incidence of ADR.”
Chen told Pharmacogenomics Reporter sister publication GenomeWeb Daily News in an e-mail that he has been invited to present the data from the biomarker studies to the US Food and Drug Administration.

GE Healthcare, Lilly to Co-develop IVDs to Predict Efficacy of Cancer Drugs
Eli Lilly has signed a three-year collaboration with GE Healthcare and GE Global Research to develop in vitro diagnostics to predict the response of patients to targeted cancer therapies, the companies said this week.
The collaboration covers targeted cancer therapeutics under development at Lilly and GE’s multiplexed tissue-based assays and image analysis tools.
The partners plan to discover protein and gene signatures that will predict the likelihood that a given therapy will be effective in treating certain cancers. These signatures could then be used to pre-select patients who are good candidates for the targeted therapy, the companies said.
The collaboration “complements Lilly's research and development strategy of tailored therapeutics, or in other words, finding the right dose of the right medication at the right time for patients,” said Richard Gaynor, vice president of cancer research and global oncology for Eli Lilly.
Gaynor said that Lilly is hoping to identify biomarkers for two of its targeted cancer therapeutic agents “by examining patient tissues in order to determine which patients are most likely to respond to the medications and, just as importantly, which are not."
Under the terms of the agreement, GE will have access to clinical tissue samples from unidentified patients enrolled in Lilly's clinical trials and Lilly will have access to GE's tissue-based image analysis technology and molecular reagents.
Further terms of the agreement were not disclosed.

Abbott Licenses Epigenomics' Methylation Biomarker IP for Cancer IVD
Abbott and Epigenomics have penned a non-exclusive license and collaboration agreement to develop a colorectal cancer diagnostic based on Epigenomics' intellectual property, Epigenomics said last week.
Under the terms of the agreement, Abbott has licensed worldwide rights to Epigenomics’ DNA methylation biomarker Septin 9, which the companies plan to develop into an in vitro diagnostic blood test for early detection of colorectal cancer.
The companies plan to launch a CE-marked test in Europe in 2009, and plan to file for approval with the US Food and Drug Administration in 2010.
Under the deal, Abbott will give Epigenomics an up-front fee, milestone payments, and royalties from sales of the test. A side provision in the agreement allows Abbott to evaluate Epigenomics' "other proprietary biomarkers for additional cancer indications."
Epigenomics said this test will be the first cancer diagnostic to run on Abbott's m2000 platform.

Lab21, Monogram Biosciences Secure Deal to Provide Trofile Assay in UK, Ireland
UK-based Lab21 penned an exclusive partnership with Monogram Biosciences this week to provide access to the HIV Trofile assay in the UK. 
Under the terms of the agreement, Lab21 will provide operations and logistical services for the tropism assay, which is a companion diagnostic used in the patient selection process for Pfizer’s CCR5-antagonist Selzentry.
Pfizer and Monogram in May 2006 announced a non-exclusive collaboration to make Monogram’s Trofile assay available for patients worldwide.
Monogram will use Lab21’s logistics and operations capabilities to “ensure that samples are properly collected and rapidly transported to Monogram’s laboratory in South San Francisco where they will be tested,” Lab21 said in a release. Lab21 will also handle reporting results to the clinic and will be responsible for ensuring that Trofile is available for patients across the UK and Ireland.

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