A Diagnostics & Imaging Week
Applied Biosystems (Foster City, California), a business of Applera, reported that the U.S. Department of Defense (DoD) has awarded it a $24.5 million contract to push the development of a prototype instrument system to improve the way infectious diseases are identified for epidemiological and biosecurity purposes.
The system will be designed to give reproducible results in less than one hour following sample processing via streamlined workflow and the ability to simultaneously analyze multiple pathogen targets in a single test.
Applied Bio said that last month it presented key components of the prototype to the U.S. Air Force, which will be responsible for validating the next-generation pathogen identification system.
By developing a system simplifying the processing and analysis of pathogen detection tests, Applied Bio said it expects to enable a new generation of decentralized molecular detection systems that can be deployed in diverse locations and operated by a broader range of public health and safety professionals. The new systems also will have a modular design enabling rapid customization of new test panels to detect emerging pathogens.
It said early prototypes have demonstrated the ability to identify up to 10 pathogens simultaneously on a credit card-sized test array and are expected to provide more detailed information about the nature of each sample.
In other grant news:
• Affymetrix (Santa Clara, California) reported that the Autism Consortium has selected its single Affymetrix GeneChip Human Mapping 500K Array for what it described as "the world's most comprehensive study" of the genes associated with autism, called the Autism Gene Discovery Project
The study will be conducted by scientists from the Autism Consortium and the Broad Institute of Massachusetts Institute of Technology (MIT; Cambridge, Massachusetts) and Harvard (also Cambridge). The researchers will use the 500K Array to perform whole-genome association studies across 3,700 samples collected from autistic subjects.
Autism is the fastest growing disability in the U.S., the company said.
According to the Autism Consortium, a clinical collaboration of 11 Boston-area institutions, a child is diagnosed with autism every 21 minutes and now affects one in every 166 children.
It said a number of recent research studies indicate that the underlying cause of this disease is strongly influenced by a person's genetics. However, definitive links to specific genes contributing to autism have not been fully elucidated, in part due to limitations of analytic technologies.
The Affymetrix 500K Array is designed to enable researchers to perform studies across thousands of samples to find genes with subtle effects in a complex disease like autism.
Affymetrix said its new single 500K Array further increases the power of association studies to quickly find disease-related genes. Researchers can analyze more samples because of the array's low cost and they can extract more information because each array has about twice the SNP content as the earlier version of the 500K. The single 500K Array is a direct result of an ongoing collaboration between Affymetrix and scientists at the Broad Institute of MIT and Harvard.
The Boston-based consortium is also collaborating with scientists at Johns Hopkins University (Baltimore), who are in the third year of an autism study using the 500K to scan 600 families. The two groups will be combining their data to avoid duplication of efforts and accelerate disease-gene discovery.
The Hopkins study is funded through the National Institute of Mental Health (NIMH) of the National Institutes of Health (NIH; both Bethesda, Maryland).
"One only has to look at how far genetic discoveries have gone in driving the development of promising new therapies for other inherited diseases, e.g. Alzheimer's disease, to see that we cannot afford to wait any longer to do the same for autism," said Rudy Tanzi, PhD, a member of the Autism Consortium and professor of neurology at Harvard Medical School. "We need to identify the genes underlying autism as soon as possible and then begin translating those findings into innovative treatments."
"It is critical to analyze thousands of samples in order to identify genetic variations associated with complex diseases such as autism," said Tom Willis, PhD, vice president, DNA Marketing at Affymetrix. "The Affymetrix 500K is making these studies possible today by enabling researchers to study both genotypes and copy number polymorphisms across this population, all at an affordable price."
Affymetrix says that its photolithographic manufacturing process provides the most information capacity available today on an array, enabling researchers to use a whole-genome approach to analyzing the relationship between genetics and health.
• GeneGo (St. Joseph, Michigan), a provider of databases, software and services in systems biology, reported receiving a $750,000 Phase II SBIR grant from the DoD to develop a systems biology suite for functional analysis of proteomics data. In Phase II, GeneGo will adapt its data-mining platform, MetaCore, for handling different types of proteomics data and implement new algorithms for reconstruction of protein-state-specific biological networks and pathways.
GeneGo will work with Professor Austin Yang's group from the University of Southern California (Los Angeles), Rosetta Biosystems (Seattle) and the Michigan Proteome Consortium (Ann Arbor).
GeneGo's first platform allows an integration and analysis of different kinds of experimental data (mRNA expression, proteomics, metabolites, phenotypic data) and active chemistry (metabolites, drugs, other xenobiotics) within the framework of biological pathways and networks. The company's first product, MetaCore, assists in target selection and validation, identification of biomarkers for disease states and toxicology.