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Genome Institute of Singapore, Expression Analysis, Broad Institute, Isilon Systems, University of Otago, Ontario Genomics Institute, National Institutes of Health, National Science Foundation, US Department of Energy, X Prize Foundation, Invitrogen, Appl

Genome Institute of Singapore Buys Three SOLiD Systems
Applied Biosystems said this week that the Genome Institute of Singapore has acquired three SOLiD DNA sequencing systems for use in studying the genetic underpinnings of cancer and other diseases.
GIS already had one SOLiD system on site, according to ABI. Researchers at the institute are studying how structural variants, such as copy number variations, single-base duplications, inversions, translocations, insertions, and deletions, contribute to the development of cancer.
"We evaluated several technologies for this kind of research, and concluded that the SOLiD System fits very well with our paired-end di-tag technology and will provide us with a platform that enables rapid, accurate, and cost-effective study of a variety of types of genetic variants present in cancer genomes," Yijun Ruan, associate director for genomic technologies at GIS, said in a statement.

Expression Analysis Offers Free GWAS Data Analysis, Resequencing on Helicos Platform Through Grant Program
Expression Analysis said this week that it has launched a grant program that will award researchers free data analysis for genome-wide association studies as well as follow-up resequencing services on the Helicos platform.
The Genome Wide Association Study Data Analysis and Resequencing Grant will offer GWAS data analysis, including identification of genes or regions of interest, using a "proprietary tool that simultaneously analyzes allelic and copy number variations, accomplishing in days what typically takes months."
Further, it will provide up to 10 gigabases of sequence data for genes or regions of interest, generated by Helicos BioSciences’ True Single Molecule Sequencing technology. Expression Analysis installed the Helicos system in March.
Durham, NC-based Expression Analysis said that the grant program is looking for projects that “show promise of identifying genetic element(s) that are important to human health and disease.”
Researchers or institutes can apply for the grant on Expression Analysis’ website. The firm is accepting applications for the grant through Dec. 15.
The company plans to fund up to three projects with a minimum of 1,000 samples, though it may consider smaller studies. It plans to make the awards on Feb. 15, 2009. The projects are scheduled to be completed by the end of 2009.

Broad Using Isilon's Clustered Storage for Genomics Data
The Broad Institute of MIT and Harvard is using Isilon Systems’ clustered storage system to handle and manage data from DNA sequencing projects, the company said this week.
The Isilon IQ system will allow the Broad to support a “five-fold increase in the volume of genomic data” that is analyzed and stored, the company said. The system will help the institute streamline data access for its next-generation DNA sequencing program, which generates several terabytes of genomic data per day.
The IQ system runs on the company’s OneFS operating system software and allows scientists to share their genomic data in a single scalable pool, Isilon said.

New Zealand Pledges $26M for Genomics Research Consortium
New Zealand will give the nation’s genomics research infrastructure a “shot in the arm” with funding of NZ$40 million (US$26.3 million) for a genomics consortium led by the University of Otago.
The nation’s Research Science and Technology Ministry has pledged the funding to the New Zealand Genomics Limited consortium, which includes the University of Otago, Massey University, the University of Auckland, and AgResearch. The venture is wholly owned by the University of Otago and will support all privately and publicly funded genomics research in the country.
RS&T Minister Pete Hodgson said that the funding, which will be spread out over nine years, will “provide a significant and much needed step-up in genomic research.”
The new funds will go to support new gene sequencing and bioinformatics tools, as well as recruiting new staff. The genomics programs will include research in medicine and health, agriculture, and environmental protection.

Ontario Genomics Institute Invests in DNA Barcode Research Project
The Ontario Genomics Institute said last week that it is investing in a Canadian public and private effort to develop a DNA barcode-based point-of-contact test that would recognize different groups of animal species in random plant and animal food samples.
OGI said it is investing in the effort, which includes the Biodiversity Institute of Ontario and the company Safeguard Biosystems, through its Pre-commercialization Business Development Fund. The institute did not say how much funding it is providing to the project, but the Biodiversity Institute receives its funding from Genome Canada through OGI, the National Sciences and Engineering Research Council of Canada, and Ontario’s Ministry of Research and Innovation, as well as from private and public funders.
The research will be led by the Canadian Centre for DNA Barcoding’s Associate Director Mehrdad Hajibabaei, and will involve Biodiversity Institute Director Paul Hebert and other international collaborators.
The barcoding tests will be based on Safeguard’s 3D Sensor Array technology, OGI said.
Safeguard CEO Richard Strafehl said in a statement that DNA barcoding is “a key discovery that will lead to the development of a series of products applicable to various areas including agriculture, forensics, and public health and safety.”

NIH, NSF, DOE to Back Biodiversity Studies With $2.5M In ‘09
The National Institutes of Health, the National Science Foundation, and the US Department of Energy will use $2.5 million in 2009 to support interdisciplinary biodiversity research partnerships that will include genomic and metagenomic microbial studies.
The three agencies will fund between two and three competitive grants for up to five years with a total of around $600,000 per year to form the International Cooperative Biodiversity Groups program. These groups will explore the interdependence of biodiversity, with an eye on how that diversity may be harnessed for applications in health or energy, according to an NIH request for applications.
On the energy side of the programs, DNA sequencing of isolated microbial communities will be a “significant component” of the research, and resources for the sequencing will be provided through DOE’s Joint Genome Institute, NIH said.
The funding agencies are particularly interested in studies of novel microorganisms that could help to degrade cellulosic materials, assimilate carbon dioxide, or generate new biofuels. The agencies also are interested in microorganisms from environments with high carbon turnover or the capabilities to degrade cellulose, hemicellulose, or lignins from tropical forest soils or from sea floors.
These groups also could support research and training on HIV/AIDS, parasitic diseases, cardiovascular diseases, mental disorders, obesity, and diabetes. Any therapeutic research would be focused mainly on finding and developing bioactive small molecules and peptides, but could include ethno-medical botanicals and botanical drugs that are significant to public health.
Proposed bioassays and development strategies should include “state of the art molecular, genetic, and biochemical approaches,” NIH said, and investigators are encouraged to use diverse biological screens to provide information about mammalian and microbial cells.
More information about the program may be found here.

X Prize Foundation Moves to Playa Vista
The X Prize Foundation said last week that it is moving its headquarters from Santa Monica to Playa Vista, both in California, effective Oct. 1.
The organization will lease nearly 18,000 square feet in an office building.
In 2006, the foundation launched the $10 million Archon X Prize for Genomics, which challenges research teams to sequence 100 human genomes in 10 days for $1 million or less.
It has since launched the $30 million Google Lunar X Prize and the $10 million Progressive Insurance Automotive X Prize, and is currently creating other prizes in exploration of space and oceans, life sciences, energy and environment, education, and global development.

Invitrogen, ABI Mails Merger Prospectus to Shareholders
Invitrogen and Applied Biosystems said last week that the registration statement for their proposed $6.7 billion merger has become effective, and that the firms would mail a joint proxy statement/prospectus to their respective shareholders that week.
Each firm will hold a special meeting of shareholders on Oct. 16 to vote on the proposed deal. ABI and Invitorgen shareholders of record as of the close of business on Sept. 5 are entitled to vote at the meetings.

Illumina Shareholders OK Share Increase for Stock Split
Illumina’s shareholders last week approved an increase in the number of authorized shares of the firm’s stock to 320 million from 120 million, clearing the way for a proposed 2-for-1 stock split.
Illumina had announced the proposed stock split in July. Sept. 10 was the date of record for the split, and Sept. 22 is the date on which additional shares will be distributed to shareholders.
“We believe that the stock split, if effected, may place the market price of our common stock in a range that is more attractive to investors, particularly individuals, which may result in a broader market for our stock,” the firm said in a statement at the time.

Netherlands University Licenses DNAStar Software for Plant Programs
Wageningen University and Research Center in the Netherlands has licensed DNAStar’s sequence analysis software, DNAStar said last week.
Under the site license agreement, Wageningen scientists at the Department of Plant Science and at Plant Research International — both part of the university — will use the software in their sequence analysis projects, the company said.
The Madison, Wis.-based company said the Lasergene software is used in assembly, visualization, and analysis operations on data generated through Sanger sequencing and next generation platforms from Roche’s 454 and Illumina.

Genomics Needs Informed Consent Overhaul, European Researchers Say
Genomic research presents a range of issues that challenge the effectiveness of existing informed consent guidelines, a new paper argues.
In an essay appearing online this week in PLoS Medicine, European researchers from a variety of disciplines voiced their concerns over informed consent in genomics research. They argued that such research requires a new way of thinking about consent and suggested that genomics studies need ongoing informed consent protocols to ensure that participants understand how their genetic information is used and to minimize their risk.
“Genetic information may hold a lot of unexpected things,” senior author Matthias Wjst, a researcher affiliated with the German Research Center for Environmental Health and the EURAC’s Institute of Genetic Medicine in Italy, told In Sequence’s sister publication GenomeWeb Daily News. “It may really influence your life and this is a completely different kind of risk” than typical clinical trials, he said.
Under traditional informed consent protocols, researchers must provide participating individuals or communities with clear information about research protocol, goals, and outcomes, along with the potential risks and benefits associated with the research. This is intended to maintain consent cornerstones such as patient/participant autonomy, beneficence, and non-malfeasance.
But while these guidelines may be adequate for most clinical trials, they may not realistically address issues related to genomic studies, Wjst said. Since frozen DNA samples or data can be accessed to generate new data — or new interpretations of the data — for years after a sample is taken, it is sometimes difficult to determine how a sample will be used at the outset of a genomics study.
Rather than using “broad consent,” the authors proposed a “circular process of information exchange” involving public presentations, feedback from research subjects, and information being provided by researchers to subjects, if desired.
Although Wjst conceded that such steps will inevitably add expense to already costly genomics studies, he noted new electronic technology that could help bridge the gap between researchers and their research subjects.
— Abridged version of an article by Andrea Anderson, originally published on GenomeWeb Daily News