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FDA, CDC, Affymetrix, Pfizer Pharmaceuticals, Ingenuity Systems, Wellcome Trust Case Control Consortium, Celera, Merck

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FDA Releases Guidance Document to Harmonize PGx Research Terms
 
Seeking to provide internationally harmonious regulatory foundations for personalized medicine studies, the US Food and Drug Administration this week issued a guidance document covering definitions for pharmacogenomics and pharmacogenetics. 
 
The FDA said that this glossary of definitions will be in harmony with that of the European Union and Japan, and that it is “intended to facilitate the integration of the discipline of pharmacogenomics and pharmacogenetics into global drug development and approval processes.”
 
As part of its efforts to regulate drugs and drug research, the FDA said, “it is important to ensure that consistent definitions of terminology are being applied across all constituents of the International Conference on Harmonization.”
 
The FDA said in the guidance document that it defines pharmacogenomics as simply “the study of variations of DNA and RNA characteristics as related to drug response.”
 
Pharmacogenetics, the agency said, is “the study of variations in DNA sequence as related to drug response.”
 
The guideline also offers harmonized definitions for four general coding categories of biological samples used to generate data in pharmacogenomics and pharmacogenetic studies including identified, coded, anonymized, and anonymous.
 
Researchers should consider the implications of using such specific data and sample coding categories when they design their pharmacogenomics and pharmacogenetic studies, the FDA advised.
 
A genomic biomarker is defined by the guidance as a “measurable DNA or RNA characteristic that is an indicator of normal biologic, pathogenic processes, and/or a response to therapeutic or other interventions,” the FDA said. A biomarker could be a measurement of the expression of a gene, the function of a gene, or the regulation of a gene, the agency said.
 
DNA characteristics could include, but are not limited to: single nucleotide polymorphisms; variability of short sequence repeats; haplotypes; DNA modifications such as methylation; deletions or insertions of single nucleotides; copy number variations; and cytogenetic rearrangements, such as translocations, duplications, deletions, or inversions.
 
Similarly, RNA characteristics include, but are not limited to: RNA sequences; RNA expression levels; RNA processing, such as splicing and editing; and microRNA levels.
 
Under the new guidance, a genomic biomarker is not limited to human samples, and includes samples from viruses, infectious agents, and animal samples. The FDA does not consider a genomic biomarker to include the measurement and characterization of proteins or low-molecular-weight metabolites.
 
The definitions were issued by the FDA’s Center for Drug Evaluation and Research and the Center for Biologics Evaluation and Research.
 
In the guidance document, entitled “E15 Definitions for Genomic Biomarkers, Pharmacogenomics, Pharmacogenetics, Genomic Data and Sample Coding Categories,” the FDA also laid the framework intended to harmonize four general coding categories of biological samples that are used to generate data in pharmacogenomic and pharmacogenetic research.
 
The agency said it expects it may review and expand this guidance as the disciplines of pharmacogenomics and pharmacogenetics advance. The guidance was developed within the International Conference on Harmonization’s Technical Requirements for Registration of Pharmaceuticals for Human Use working group.
 

 
CDC's Genomics Office to Grant Around $3.6M to Translate Genomics to Practice
 
The US Centers for Disease Control and Prevention will spend $1.2 million per year over the next three years to fund research aimed at finding ways to translate genomics research advances into medical practice.
 
The CDC’s National Office on Public Health Genomics said in a funding announcement that it will offer a total of $3.6 million over the three years of the program, and will fund between four and eight grants with up to $350,000 for the first year of the proposed research.
 
The CDC said the program’s goal is to move human genome applications, including family history applications, into health practice in effective ways, and to support programs in policy, surveillance, or education related to genomic tests, family history, and other genomic interventions. These programs should focus on preventing disease in large, well-defined populations in the US, the CDC said.
 
The NOPHG is promoting this research in a context in which there is “much skepticism on the validity and/or utility of many genomic tests,” due to a “lack of scientific evidence.”
 
The CDC also has been working with the Agency for Healthcare Research and Quality to develop evidence reviews of the analytical and clinical validity and utility of family history and family risk assessment genomic tests for chronic diseases such as coronary heart disease, stroke, diabetes, breast and ovarian cancer, and colorectal cancer.
 
Education programs eligible for funding could include those that increase awareness about the validity and utility of certain tests, or those that increase education to the public and providers for BRCA1 & BRCA2 testing.
 
The CDC said applications are due June 6. More information may be found here.
 

 
Affymetrix Extends Cancer Research Program to North America; Inks 25 Partners
 
Affymetrix said this week that it has extended its Collaborations in Cancer Research Program to North America and has signed alliances with 25 cancer researchers on the continent.
 
The new agreements expand the CCRP, which was launched a year ago and initially included collaborations with 15 researchers throughout Europe.
 
Affymetrix said the collaborators are using integrated genomics products from the firm including its SNP 6.0 array and Human Exon 1.0 ST array to research more than 10 types of cancer. The Santa Clara, Calif.-based microarray firm said that it expects initial data from the studies to be released in the next three to six months.
 
One of the researchers involved in the program, Tak Mak Wah, a professor in the department of medical biophysics at the University of Toronto, said that he is using the SNP 6.0 arrays to obtain a comprehensive profile of genetic abnormalities for discovering novel molecular targets. “The ability to integrate the exon and SNP array data will help us identify candidate driver genes underlying these genomic abnormalities and speed up their validation,” he said in a statement.
 
Affymetrix is partially funding selected research projects that demonstrate clinical utility, helping participants obtain tools and training, and providing forums where investigators can share knowledge and best practices.
 
In addition to Wah, the firm is collaborating with researchers from the University of Michigan, the Broad Institute, Memorial Sloan-Kettering Cancer Institute, and Oregon Health and Science University, among others.
 
Affymetrix expects to expand the CCRP to the Asia-Pacific region later this year.
 

 
Pfizer to Use Ingenuity Systems' Software in Rx Programs
 
Pfizer Pharmaceuticals will use Ingenuity Systems’ bioinformatics software under a multi-year agreement, Ingenuity said this week.
 
Under the agreement, Pfizer will integrate the Ingenuity Pathway Analysis software and related content from Ingenuity’s biological and chemical knowledgebase with other informatics solutions that Pfizer uses throughout its organization, Ingenuity said.
 
Ingenuity CEO Jake Leschly said that the company also has tailored “a suite of powerful capabilities” specifically for Pfizer.
 
The IPA software enables scientists to model and analyze biological and chemical systems, and its search functions give users access to information about genes, drugs, chemicals, protein families, cellular and disease processes, and signaling and metabolic pathways.
 
Financial terms of the agreement were not released.
 

 
Wellcome Trust Expanding Genomic Disease Studies
 
A new series of genome-wide association studies driven by the Wellcome Trust and involving up to 60 international institutes will analyze DNA from around 120,000 people, the Wellcome Trust said this week in a statement.
 
The Wellcome Trust Case Control Consortium is using £30 million ($59.5 million) to study genomic contributions to 25 diseases, as well as studying the genetics of learning in children and individuals’ response to statins, the Wellcome Trust said.
 
"Breakthroughs in our understanding of the human genome and rapid advances in sequencing technology mean that we are able to do very powerful analysis much faster and on a vastly bigger scale than ever before," said University of Oxford Professor Peter Donnelly, who will chair the consortium.
 
The Wellcome Trust Sanger Institute at Hinxton, Cambridge, will “devote a large part of its high-throughput genotyping pipeline” to perform DNA testing, and most of the data analysis will be performed by the Wellcome Trust Center for Human Genetics at the University of Oxford.
 
During the two-year project, the Wellcome Trust and its collaborators will analyze as many as 120 billion pieces of genetic data in the hunt for genes that could be linked to various diseases, including multiple sclerosis, schizophrenia, asthma, and others. The researchers will study between 500,000 and 1 million SNPs per sample and “a comprehensive set of copy number variants,” the Wellcome Trust said.
 
In February, the Wellcome Trust made public its plan to massively increase spending on biomedical research, saying that it expects to lay out around £4 billion over the next five years to respond to medical needs and to pursue scientific opportunities.
 
Last year, the Wellcome Trust Case Control Consortium published data from its £9 million study of genetics and disease that involved 17,000 people across the UK.
 

 
Celera Licenses Oncology Targets to Merck; Retains Theranostics Rights
 
Celera said last week that it has signed an exclusive, two-year licensing deal with Merck, under which the pharmaceutical giant will have access to up to 10 cancer targets discovered by Celera using its proteomics discovery platform.
 
The Alameda, Calif.-based subsidiary of Applera said that Merck would use the targets to develop RNAi-based therapeutics.
 
Celera retains rights under the pact to develop and commercialize related companion diagnostics that are specific to Merck’s therapeutic candidates. Financial terms of the alliance were not disclosed, but Celera said that Merck would pay it a license fee, milestone payments based on development and commercialization goals, and royalties on selected targets.
 
Merck acquired RNAi drug developer Sirna Therapeutics for roughly $1.1 billion in cash at the end of 2006. Just a couple of months before that deal, it also licensed rights to ExonHit Therapeutics’ RNA splicing microarray patent

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