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NIH, Invitrogen, Applied Biosystems, DNAStar, US General Services Administration, USDA, Microchip Biotechnologies, US Army, Perlegen, NHGRI

NIH to Study Ethics and Implications of Human Microbiome Studies
Looking to address the ethical, legal, and social implications of the Human Microbiome Project in a similar way as it did the Human Genome Project, the National Institutes of Health last week said that it will fund roughly three awards with up to $250,000 per year over three years for human microbiome ELSI studies.
NIH expects that the studies, which it will fund under its Roadmap Program, will identify and begin to address the complex issues that the microbiome project may generate as researchers continue to conduct metagenomic analysis on the various microbes that inhabit human bodies.
Applicants may apply for a maximum of $750,000 over the three-year project period, and NIH expects that the sizes and duration of the awards will vary.
NIH said in a request for applications that there are a number of questions about human microbiome research that the scientists could aim to investigate, including questions about informed consent, privacy concerns, potential clinical applications of human microbiome research, and strategies for educating the public about the findings of human microbiome research.
More information about the program is available here.

Invitrogen, ABI Combo to Have Four Core Divisions
As the acquisition of Applied Biosystems by Invitrogen draws closer, the firms announced last week that the newly merged firm would operate under four core divisions: molecular biology systems, genetic systems, cell systems, and mass spectrometry systems.
They also announced the management team that will oversee these four divisions and other functions (see Paired Ends, this issue).
The molecular biology systems division will comprise ABI's molecular and cell biology function analysis division and Invitrogen's molecular biology business and will include systems and reagents for gene expression analysis, genotyping, gene regulation, and proteomics.
The genetic systems division will include ABI’s capillary electrophoresis and SOLiD sequencing systems and its applied markets business, as well as Invitrogen’s clinical applications business and third-generation sequencing development program.
The cell systems division will consist of Invitrogen’s cell analysis, bead-based separations, cell culture, bioproduction, and stem cell systems operations business units and ABI’s Poros and Tropix business lines. The mass spectrometry division will house ABI’s mass spec business.
Invitrogen said separately that it expects to complete a $2.65 billion bank facility this week to partially fund its roughly $6.7 billion acquisition of ABI. Invitrogen said that the facility, which is being underwritten by Bank of America, UBS, and Morgan Stanley, is “substantially oversubscribed.”
The Carlsbad, Calif.-based firm also said that it is currently engaged with the European Commission regarding European approval of the deal. The acquisition cleared the US antitrust waiting period in late July.
Invitrogen and ABI sent out a joint proxy statement/prospectus regarding the acquisition to shareholders earlier this month. The shareholders of both firms will vote on the deal next month, with closure of the transaction expected in the fourth quarter of this year.

GSA Buys DNAStar's Sequence Analysis Software
Bioinformatics company DNAStar will supply the US General Services Administration with its sequence analysis software under a new five-year agreement, the company said last week.
GSA provides products and services to a number of government agencies. Under the terms of the agreement, scientists who are allowed to buy through GSA can expedite the purchase of certain Lasergene sequence analysis software configurations under “favorable” terms.
The Lasergene software suite is primarily used to assemble and analyze DNA and protein sequences.

USDA to Provide $9.4M for Specialty Crop Genomics
Nine universities will use $9.4 million in funds from the US Department of Agriculture to conduct genomic studies to improve the quality, yield, and traits of certain specialty crops, the USDA said last week.
The funding, which comes through the Cooperative State Research, Education, and Extension Service, will support research into the genomics of sunflower, black cherry, peach, strawberry, apple, lettuce, potato, and tomato.
Under USDA’s National Research Initiative Plant Genome Program, scientists at the universities will use the money to study these crops in a program that augments the Specialty Crop Research Initiative started by the 2008 Farm Bill.
The aim of the plant program is to generate knowledge about the structure, function, and organization of plant genomes in order to improve crop sustainability, efficiency, and breeding, USDA said. The agency also expects this research to create new “educational, training, and extension avenues for students and the public in the area of fruit and vegetable crop sciences,” Buchanan said.
Under the program, the University of Arizona will receive a $319,000 grant; the University of California-Davis will receive a $362,500 grant and a $400,000 grant; the University of Georgia will receive two $400,000 grants; Michigan State University will receive a $5.4 million grant and a $400,000 grant; the University of New Hampshire will receive $383,000 in funding; Pennsylvania State University will receive $362,500; Virginia Tech will receive $400,000; and Washington State University will receive grants of $400,000 and $150,000.
MSU’s grant of $5.4 million is a Coordinated Agricultural Project award for studying specialty potatoes and tomatoes.
More information may be found here.

Microchip Biotechnologies Gets Army Contract for Sample Prep System
Microchip Biotechnologies has been awarded a $625,000 grant from the US Army to develop a universal sample preparation module for automatically purifying DNA from pathogen targets.
The grant was awarded from the Army’s inaugural Commercialization Pilot Program, which is intended to assist firms that are working on Phase II Small Business Innovation Research projects that meet high priority Army requirements in transitioning to commercial products.
MBI’s sample prep module will be designed to purify DNA from pathogen targets in complex matrices to provide samples for various downstream DoD-sponsored analytical platforms. The module, which will incorporate MBI’s Microscale On-chip Valves, will be used as a front end for a molecular diagnostics system aimed at detecting biological threat agents.

Perlegen to Study Rare Variants Linked to Breast Cancer by Resequencing Approach
Perlegen said last week that it is using a proprietary targeted resequencing approach to discover rare variants that influence the risk of women who have received hormone replacement therapy to develop breast cancer.
The company's sequencing approach targets the exome. It uses a new sample preparation method, automated processing on an unspecified next-generation sequencing discovery platform, and advanced data analysis methods.
The study builds on Perlegen's earlier work on common variants for breast cancer. The data for the study comes from the Women's Health Initiative, a long-term national project that began in 1993 and that focuses on strategies for preventing heart disease, breast and colorectal cancer, and fracture in postmenopausal women.
Perlegen said it expects to complete its study in early 2009 and plans to apply its sequencing approach in other disease areas to identify markers that help to guide healthcare decisions.

Researchers Merge Sequencing, Proteomics to Analyze Nitrogen-Fixing Cyanobacterium
A newly available genome sequence is revealing the unexpected genomic structure of a nitrogen-fixing cyanobacterium, or blue-green algae — and providing clues about how the organism temporally separates its functions.
A team of American researchers combined sequencing and proteomics approaches to begin characterizing the genome of a marine cyanobacterial species called Cyanothece sp. 51142, an organism that photosynthesizes by day and fixes nitrogen by night. The results, which were scheduled to appear online last week in the Proceedings of the National Academy of Sciences but were not yet online at press time, reveal key Cyanothece 51142 genetic pathways and uncover a genomic first for cyanobacteria — a linear chromosome.
Cyanobacteria are single-celled organisms that share features with both plants and microbes. For example, Cyanothece 51142 produces sugars via photosynthesis during the day. At night, it expresses genes involved in metabolism and respiration, as well as those needed for nitrogen fixation, the process of converting atmospheric nitrogen to a biologically accessible form.
Because it can produce ethanol and hydrogen, Cyanothece 51142 is also of interest for those researching alternative fuel sources.
For this paper, researchers at the Washington University Genome Sequencing Center used an Applied Biosystems 3730 capillary sequencer to sequence the roughly 5.5 million base pair Cyanothece 51142 genome.
They found that the genome is comprised of six parts: a circular chromosome of about 4.9 million bases, four circular plasmids ranging from about ten to 40 thousand bases, and — unexpectedly — a 429,701 base pair linear chromosome.
By coupling their sequencing efforts with proteomics analysis, the researchers were able to not only identify new genes but also get a much clearer picture of which genes are expressed by Cyanothece 51142. The team identified 2,735 protein-coding genes, plus another 506 protein-coding genes originally classified as hypothetical genes. They also picked out highly conserved gene clusters involved in nitrogen fixation and glucose metabolism and fingered the genes and pathways used for fermentation and metabolic storage.
Analyzing the linear chromosome was similarly informative. The chromosome contained a cluster of nine genes coding for enzymes involved in lactate fermentation — including the lone copy of the gene for the enzyme lactate dehydrogenase.
Together, these findings provide new insights into Cyanothece 51142 genome organization, providing a peak into the strategies that the cyanobacterium uses to fix nitrogen, separate its dark and light activities, and produce energy and fermentation products such as ethanol, lactate, acetate, and hydrogen.
In an effort to gain a more comprehensive understanding of Cyanothece functions — and particularly hydrogen production — the team is currently sequencing six additional Cyanothece strains isolated from the deep ocean and from rice paddies in Taiwan and India.

NHGRI Seeks Feedback on ENCODE Data-Release Policy with Nine-Month Publication Moratorium
The National Human Genome Research Institute is soliciting comments from the research community on an updated data release and publication policy for the Encyclopedia of DNA Elements, or ENCODE, project.
The draft policy, available here, calls for ENCODE data producers to release their data in a “timely” manner, but protects their interests by providing a nine-month period in which users of that information may not publish the results of any research based on the public data without prior consent.
“This will provide time for the resource producers to have a protected opportunity to publish initial analyses of the data they have generated,” NHGRI said in the draft policy.
NHGRI said in a notice on its website that the updated policy “provides more specificity” than its previous guidelines, which were based on the so-called “Fort Lauderdale agreement,” a general policy drafted in 2003 that called for the rapid release of data produced by “community resource projects.”
The updated policy would apply to all data generated under the ENCODE project, a large-scale effort to identify all functional elements in the human genome that began its second phase last year following a four-year pilot project. The policy also covers data from the modENCODE project, which is focused on the Drosophila melanogaster and Caenorhabditis elegans genomes.
According to the revised policy, “ENCODE/modENCODE resource producers will release data, as soon as they have been verified and prior to publication, to public databases.” Prior to publication of the data in a peer-reviewed journal, “NHGRI asks resource users to consider them to be unpublished and to follow standard scientific etiquette regarding the use of unpublished data.”
In order to enable the “compromise between unrestricted use of the data and unavailability of the data until publication,” NHGRI recommends a nine-month period during which researchers can freely use the ENCODE and modENCODE data as part of their research, but cannot submit for publication the results of any studies using unpublished ENCODE or modENCODE data without prior consent.
NHGRI said that this “publication moratorium” by resource users “ends either at the expiration of the nine-month protected period or when the data have been published, whichever is shorter.”
In addition to issues surrounding data release and publication for ENCODE data, the draft policy also addresses intellectual property.
Unlike the Human Genome Project and the International HapMap project, which generated raw data that did not have “utility,” from a patenting perspective, “the purpose of the ENCODE and modENCODE Projects is to generate data that identify or define genomic DNA sequence elements that have biological function, and therefore might be considered to have utility and be able to be patented,” the policy states. “Therefore, the use of patents in ways that might restrict access to large amounts or broad categories of data, e.g., all transcription factor binding sites, is an issue that needs to be addressed.”
As a result, NHGRI “encourages all ENCODE/modENCODE resource producers to consider placing all information generated from their project-related efforts in the public domain.”
In cases where consortium members decide to exercise their IP rights, NHGRI said it “encourages consideration of maximal use of non-exclusive licensing of patents to allow for broad access and stimulate the development of multiple products.” NHGRI’s recommendations for licensing genomic inventions are available here.
NHGRI added that it also encourages users of the ENCODE data to “act responsibly.” As an example, the policy states, “if a data user were to incorporate ENCODE/modENCODE data into an invention, the subsequent license should not restrict the access of others to the ENCODE/modENCODE data.”
NHGRI said that it is seeking comments on the proposal from the research community before finalizing the policy. Comments should be sent to [email protected] by Oct. 15.

Additional information about the ENCODE data-release policy is available here.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.