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Short Reads: Mar 17, 2009

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University of Illinois Lands $1.3M for Agriculture Genomics

The University of Illinois at Urbana-Champaign will use $1.3 million from the US Department of Agriculture — through funding from the recently-signed Fiscal Year 2009 budget — for agriculture genomics projects, according to Senator Richard Durbin (D - Ill.).

Under the grants, provided through the Cooperative State Research, Education, and Extension Service, the university will use $745,000 to study soybean genomics and $564,000 for livestock genome sequencing projects, Durbin said in a press statement last week.

The soybean project will use genomics and genetic engineering in studies of drought resistance, disease tolerance, and resistance to soybean cyst nematode and soybean rust.

The livestock genome sequencing project will aim to identify every gene of the cattle and swine species, and establish a database to identify the functions of their genes.


23andMe-Led Team Offers Program to Enroll Parkinson's Patients

Direct-to-consumer genomics service firm 23andMe, the Michael J. Fox Foundation for Parkinson's Research, and the Parkinson's Institute and Clinical Center said last week that they are enrolling 10,000 people for a new Parkinson's disease community. The project aims to establish a resource for future genome-wide association studies and other research initiatives.

In an effort to entice individuals with Parkinson's disease to participate, 23andMe is slashing the price of its service from $399 to $25 for a limited time, for up to 10,000 individuals with Parkinson's disease who sign up through the Parkinson's Institute or the Michael J. Fox Foundation. Google co-founder Sergey Brin, who is married to 23andMe co-founder Ann Wojcicki, will ante up an undisclosed amount of cash to subsidize the genotyping costs.

To be eligible, individuals must have physician-diagnosed Parkinson's disease, agree to provide saliva samples, and fill out online surveys about their condition. Members of the Parkinson's community will also have access to the complete 23andMe Personal Genome Service. Current 23andMe customers who do not have the disease can participate as healthy controls in the project, by voluntarily filling out the company's Parkinson's disease survey.

The latest research project is distinct from a collaboration between the same organizations announced last spring, Rachel Cohen, manager of communications at 23andMe, told In Sequence's sister publication GenomeWeb Daily News. Cohen said that effort was specifically aimed at developing web-based diagnostic tools for Parkinson's disease, whereas the latest project is aimed at enrolling individuals with Parkinson's disease for research efforts.

The discounted rate will only be available for a few more weeks. There will likely be more enrollment efforts down the road, Cohen said, adding: "This is really wave one of enrollment."

Holly Barkhymer, associate director of communications at the Michael J. Fox Foundation, and Brian Fiske, an associate director and team leader of research programs at the Michael J. Fox Foundation, told GenomeWeb Daily News that the new project is aimed at building a community of individuals with Parkinson's disease for future genetic research studies. The idea is that these patients agree to participate in research studies as the tools become available, they explained.

According to a news release issued by the Michael J. Fox Foundation last week, the Foundation "has been funding a partnership between 23andMe and the Parkinson's Institute and Clinical Center to develop web-based tools and surveys to gather information from a community of [Parkinson's disease] patients in a scientifically meaningful way."

Although the Foundation provided funding for that project, which remains ongoing, Barkhymer explained, it has a non-funding role in the new project. Instead, it is tapping into its constituency of Parkinson's patients, spreading the word about the research, and distributing discount codes for eligible individuals.

Eventually, those involved hope to learn more about genetic variants related to disease onset, treatment response, and more. "We anticipate that we'll be able to do multiple studies," 23andMe's Cohen said.

"We are very excited by the approach," Fiske said, explaining that it is a good way to start collecting large amounts of data. "The projects kind of go hand in hand."

By Andrea Anderson; originally published on GenomeWeb Daily News


SeqWright Starts Offering Roche NimbleGen Sequence Capture Service

Sequencing service company SeqWright of Houston has started offering sequence capture services using Roche NimbleGen's capture arrays through a partnership between the companies, Roche NimbleGen said last week.

SeqWright is providing targeted resequencing services that couple the capture array technology with SeqWright’s existing 454 sequencing services on the Genome Sequencer FLX. SeqWright is offering its customers to use NimbleGen 2.1M Human Exome arrays, or to target regions of the human genome of their choice, ranging from 100 kilobases up to 30 megabases.

“As a CLIA certified facility, providing this service will enable applications of targeted resequencing and whole-exome sequencing from disease pathway studies to cancer research and much more,” said Fei Lu, CEO of SeqWright, in a statement.


California Startup Publishes Data on Circulating Nucleic Acids; Seeks Partners

Chronix Biomedical said last week that its scientists have published a study in the current issue of Clinical Chemistry, which it said provides proof-of-concept for the diagnostic and prognostic utility of circulating nucleic acids.

The San Jose, Calif.-based startup has developed data analysis tools to characterize and categorize circulating nucleic acids. The study, it says, confirms its previous research showing that CNAs can identify the presence of certain diseases in blood samples months to years before clinical symptoms appear.

In the study, Chronix's scientists sequenced CNAs in several allegedly healthy individuals using the 454 Genome Sequencer FLX platform. The company believes that databases of CNAs associated with specific disease states can be used to identify people with undiagnosed disease, and could also potentially be used to track changes in disease status.

The recent study follows company research published in January in Nucleic Acids Research, which showed that a blood test based on circulating DNA sequences could identify bovine spongiform encephalopathy and chronic wasting disease in live animals before symptoms were evident.

The firm has also recently published an abstract in the journal Blood demonstrating the potential utility of CNAs in the management of cancer.

"Even in these experiments we found unexpected results — undiagnosed hepatitis in one patient and a secondary cancer in another — confirming the utility of CNAs in finding unsuspected disease," Chronix Biomedical CEO Howard Urnovitz said in a statement. "With these multiple proof-of-concept experiments now completed, we are embarking on the studies needed to further confirm and commercialize this powerful new approach with important applications in personalized medicine and human health."

Chronix is currently seeking industry partners to help further develop and commercialize the CNA profiling approach, which it says is platform-independent, for diagnostic and prognostic applications. It also said that it is discussing use of the technology with potential pharmaceutical partners, who could use it in drug development studies.


Canada Gives Genome Atlantic $2.3M Grant for Atlantic Cod Studies

The Canadian government has given C$3 million ($2.3 million) to Genome Atlantic to conduct genomics studies of the Atlantic cod in order to understand what causes a developmental problem in the fish.

Genome Atlantic, a non-profit research entity based in Halifax, Nova Scotia that is focused on genomic studies of sea life, said recently that it has received the funds from the Atlantic Canada Opportunities Agency's Atlantic Innovation Fund in order to support the project.

The study's goal is to solve the "challenge of early maturation in cod, which can account for significant financial losses due to increased production time and decreased quality," Genome Atlantic said.

The Comparative Assessment of Diploid & Polyploid Physiology & Production Traits (C-ADAP3T) project will use genomics and selective breeding to develop sterile production fish that can overcome the early maturation barrier, Genome Atlantic President and CEO Steve Armstrong said in a statement.

Genome Atlantic is leading and will manage the project, which will include regional researchers and companies including Fisheries and Oceans Canada's St. Andrews Biological Station, Memorial University's Ocean Sciences Centre, Cooke Aquaculture, the Huntsman Marine Science Centre, the University of New Brunswick, and the University of Guelph.

Genome Atlantic estimated that the cod-farming industry in the Atlantic region could potentially be worth as much as C$545 million.


Agilent to Shift Life Science Focus from R&D to Profits

Agilent Technologies is looking to generate a greater return on its R&D investments in the life science space, according to a company official.

While the firm will continue to invest in developing new technologies for the life science market, R&D spending as a percentage of revenues will shrink from a current level of around 12 percent to the single-digit range, Nick Roelofs, vice president and general manager of Agilent's Life Sciences Solutions unit, told In Sequence's sister publication ProteoMonitor at a conference last week.

Roelofs said that after several years of building up its presence in the life-science space with new technology development, the firm now needs to create "a long-term sustainable model" for the business.

For the past several years, Agilent has expanded its presence in the life-science market amid a shift from the semiconductor business. That strategy originally meant building up its strengths in four areas: proteomics, DNA microarrays, informatics, and diagnostics.

With that has come relatively high R&D spending in order to create the necessary products to bring to market. According to Roelofs, 12 percent of Agilent's top line in its life-science business has been reinvested back into R&D, while its competitors' R&D spending as a percentage of revenues has been typically in the single digits.

"In order to fund that kind of investment, we have to have the rest of the corporation much more profitable to fund the high level of investment in a single sector," Roelofs said. And to take on such an investment strategy, "we have to have a light at the end of the tunnel where we say, 'OK, we will move the life science business toward the industry average.'"

Roelofs emphasized that the company is not backing off new product development, but will grow R&D spending at a slower pace compared to revenue growth — eventually bringing it into the high single digits as a percentage of revenues.

The company's life-science business is only now able to move in that direction because only now has that business achieved the level of "competency" to do so, he said.

Getting to that point involved honing its market focus as well as ramping up its technology. The life sciences is such a "broad and diffuse field of interest" that it's tempting for a large firm to chase all applications at once, he said.

As an example, Roelofs cited Agilent's microarray business, noting that for a decade, the firm was "very enamored" with the technology's "broad range of interesting applications" — to the point that it was chasing after its competitors, especially Affymetrix, in supporting new applications for the technology.

But in doing so, that part of Agilent's business spread itself too thin. Today, the company is more focused on which applications are best suited for its microarrays — such as array-CGH, ChIP-chip, and microRNA analysis — "and that's burst that business into profitability because the ratio at what we're looking at to what the top line can afford has gotten much, much better," Roelofs said. Agilent recently a solution-based genome selection technology for sequencing that is based on its arrays and plans to launch a capture array product later this year.

Indeed, Agilent cited microarrays as one of its strongest growth areas in its most recent financial statements. For its first fiscal quarter of 2009, the company reported double-digit growth in its array business, and for the fourth fiscal quarter of 2008, it posted 40 percent growth in arrays.

Beyond arrays, Roelofs said that all of Agilent's life science businesses have seen a turnaround during the past two years. In 2007, the company had five businesses in life sciences. Of that, only one, liquid chromatography, turned a profit. Today, Agilent has seven businesses in the segment, including the purchases of Stratagene and Velocity 11, and all are profitable, Roelofs said.

Between 2007 and 2009, the goal was to move all the businesses "out of the red ink," he said. Moving forward, by 2012, the goal will be to grow all the businesses within life sciences by double digits.

Roelofs also reiterated the company's goal of expanding its presence in the academic and government markets. That has, so far, entailed retraining and redeploying sales staff to specifically address the needs of researchers in those markets. Unlike industrial customers who are more "routine driven," academic/government scientists need platforms that will help them answer more pure research questions, he said.

Despite the company's ongoing restructuring, which involves the layoff of at least 1,100 staffers, Agilent is actually hiring life science sales staff, Roelofs said.

— By Tony Fong, originally published on GenomeWeb Daily News


BioNanomatrix Gets $2.1M Grant to Develop Single Molecule Analyzer

BioNanomatrix this week said it has received a Phase II grant in the amount of nearly $2.1 million from the National Human Genome Research Institute to support further development of the firm's single-molecule nanoscale whole-genome analyzer.

The 30-month Small Business Innovation Research award was made under the BioEngineering Nanotechnology Initiative, which is intended to support the development of nanotechnologies for biomedicine applications. The newest grant follows completion of a similar Phase I grant for initial development of the technology.

"BioNanomatrix's nanoscale technology is intended to allow researchers to directly image and analyze very long, individual intact strands of DNA at the single-molecule level with very high resolution, yielding a great deal of genomic information that is not currently accessible," said BioNanomatrix President and CEO Michael Boyce-Jacino in a statement.

"We believe our technology has the potential to increase the utility of whole-genome imaging and analysis for a wide range of research and diagnostic applications, and we are delighted at NHGRI's renewed vote of confidence in the potential of our program," he said.

Philadelphia-based BioNanomatrix also is working with Complete Genomics on a DNA sequencer that they hope will achieve the "$100 genome." The firms received $8.8 million in funding from the National Institute of Standards and Technology in October 2007 to support efforts to combine BioNanomatrix’s nanofluidic DNA imaging device and Complete Genomics’ sequencing chemistry.

The Scan

Call to Look Again

More than a dozen researchers penned a letter in Science saying a previous investigation into the origin of SARS-CoV-2 did not give theories equal consideration.

Not Always Trusted

In a new poll, slightly more than half of US adults have a great deal or quite a lot of trust in the Centers for Disease Control and Prevention, the Hill reports.

Identified Decades Later

A genetic genealogy approach has identified "Christy Crystal Creek," the New York Times reports.

Science Papers Report on Splicing Enhancer, Point of Care Test for Sexual Transmitted Disease

In Science this week: a novel RNA structural element that acts as a splicing enhancer, and more.