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Febit, Prognosys Biosciences, NIH, NCRR, OPX Biotechnologies

Febit and Prognosys Partner for Microbial Sequencing and Array Services
Febit and Prognosys Biosciences have teamed up to offer microbial genome sequencing and microarray services, the companies said this week.
Prognosys, based in La Jolla, Calif., will offer genome sequencing of microbial organisms using next-generation sequencing. As In Sequence’s sister publication BioArray News reported earlier this year (BAN 9/25/2007), Prognosys owns an Illumina Genome Analyzer.
Febit’s Geniom technology will be used to enrich sample DNA and to support the assembly process following sequencing. The company also offers a service to design microarrays on its Geniom One instrument, based on the sequence data. Alternatively, customers who own a Geniom One can produce and analyze their own arrays.

NIH Offering $28M Over Four Years for Human Microbiome Demonstration Projects
The National Institutes of Health has set aside $28 million over four years to fund demonstration projects “that will examine, through molecular approaches, the relationship between changes in the human microbiome and human health and disease.”
In a request for applications issued last week, the NIH said that it plans to fund up to 10 early-phase and five later-phase studies of the human microbiome under the program, which is part of the NIH Roadmap Initiative’s Human Microbiome Project.
The NIH will allot $4 million in total costs for fiscal year 2009 for early-phase projects, and $24.3 million for fiscal years 2010 through 2012 for scaled-up projects. The expected amount of each early-stage award is between $300,000 and $700,000, while the amount for later-phase awards is between $1 million and $4 million. 
Applicants should address a number of goals, NIH said, including identifying “an important biological system” that could “demonstrate the relationship between the human microbiome and health or disease;” the use of high-throughput, cost-effective technologies to produce a data set that can be used to study the human microbiome in selected body regions under specified conditions;” and the design or adaptation of analytical tools “that will allow conclusions to be drawn about the relationship of the human microbiota to health and disease.”
Technologies “should include16S rRNA gene sequencing and metagenomic shotgun sequencing,” but applicants can also propose expression analysis by high throughput methods, proteomic analysis, or other approaches “if appropriate.”
“If large-scale sequencing is to be used, either with existing Sanger sequencing methods or utilizing new sequencing technologies, the applicant must provide evidence that the sequencing facility is capable of the throughput, quality and cost needed for the project,” the RFA states.  
Funding for the later-phase studies will decrease by 10 percent each year, “because NIH expects that the cost of data production will drop by at least that much per year.” Applicants are asked to address how they want to reduce production cost by at least that factor. “If new technologies, particularly sequencing technologies, are to be utilized, the applicant’s track record in using the technologies must be provided; this will be an important review criterion,” according to the RFA. 
Applications are due May 22, 2008. The anticipated start date of the pilot phase is April 2009. More information is available here.

NIH to Grant $43M in FY 2009 Under Shared Instruments Program
The National Institutes of Health’s National Center for Research Resources plans to grant around $43 million in fiscal year 2009 to fund the purchase of expensive biomedical instruments.
According to a program announcement released last week, the NCRR’s Shared Instrument Grant program is seeking applications from groups of NIH-supported researchers looking to buy or upgrade equipment that costs between $100,000 and $500,000.
NIH said it expects to hand out approximately 125 awards, but the number may vary, depending on the size of the awards and the total funds available to the program.
The tools investigators may purchase under the funding would be shared with other NIH researchers, and could include DNA sequencers, biosensors, biomedical imagers, mass spectrometers, biomedical imagers, confocal and electron microscopes, cell sorters, X-ray diffraction systems, and NMR spectrometers, among others.
Applications are due March 24, 2008. More information is available here

OPX Lands $3.6M in Venture Financing to Support Biofuel Genomics
OPX Biotechnologies has received $3.6 million in its second round of venture financing, which was led by Mohr Davidow Ventures.
Other investors in the round included X/Seed Capital, which provided OPX’s seed financing in June 2007, and Robert Chess, who has been named OPX CEO and chairman.
Boulder, Colo.-based OPX is developing genomics technologies designed for microbial biofuel development.
OPX’s set of tools and intellectual property, called SCALEs, enable massively parallel full genome search, identification of specific causative genes, and rapid genetic modification and testing, the company said. These tools are used to design new microbes that would improve tolerance, productivity, and specificity for fuel and chemicals production.
Chess said the SCALEs technology can “identify the role of each gene and how to modify it to achieve the characteristics needed for specific fuel and chemical products 1,000 to 5,000 times faster than conventional methods.”

The Scan

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.

New Insights Into TP53-Driven Cancer

Researchers examine in Nature how TP53 mutations arise and spark tumor development.

Mapping Single-Cell Genomic, Transcriptomic Landscapes of Colorectal Cancer

In Genome Medicine, researchers present a map of single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer.

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.