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Molecular Dx, World Health Organization, GTL, PerkinElmer, GMU, NHGRI, NIH, GAIN, GeneCare, Agendia, MMRC, PamGene, Innogenetics, BG Medicine, Mitsubishi, Solexa, Roche, Epigenomics

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Will Molecular Dx Shops Benefit If WHO Releases H5N1 Sequences?

Will companies developing molecular diagnostics against the H5N1 flu virus benefit if the World Health Organization makes public the roughly 2,300 viral sequences it maintains for a handful of exclusive labs?

The WHO, bending under mounting pressure from several international scientists asking it to release its avian flu database, said it plans to ask its member states to sign a pledge to share virus data.

For some researchers developing molecular diagnostics for the virus, gaining access to the WHO's H5N1 database might help their efforts. "Microarrays can gather so much information; it's important that we gather the right information and not the spurious information," said David Danley, director of homeland defense programs at CombiMatrix. "That's what [the WHO's] databases offer."

CombiMatrix has developed an H5N1 test that identifies pathogenicity by typing hemagglutin and neuraminidase genes. "We would like to have on our product those genetic markers that reflect pathogenicity in humans," he said.

But determining what those markers are is not possible without more data linking the strains of avian and human H5N1. Specifically, while data on H5N1 strains that have surfaced in humans in Vietnam and Thailand are now in the public domain, more recent information on human cases in Indonesia and Europe is not. Those and other data are maintained by WHO reference labs.

"The human data [for these cases] is really missing," said Henry Niman, a biologist with Recombinomics who is studying the H5N1 virus for recombinant strains. Earlier this month, his company publicly asked the WHO to release its H5N1 database.

Niman said that it is not countries but individual labs, designated as WHO reference labs, that are holding back data, and they are doing so for competitive academic reasons. The UK-based Veterinary Laboratories Agency in Weybridge "is holding onto most of the sequences in Europe, including the Iraqi (human) sample," he said. "And Hong Kong is holding onto all the human sequences from Indonesia."

Meanwhile, the WHO claims that a mixture of countries and labs have requested that the sequence data remain private. There are eight reference labs working on avian flu sequencing, and many are working with samples from countries that have refused to allow the data to be publicized.

"We're not the supervisors [of the reference labs]," WHO spokesperson Daniel Epstein told GenomeWeb News this week. "They serve us but they are independent. In a sense they are doing us a favor."

Christine McNab, another agency spokesperson, said the purpose of secrecy is "not to keep the virus sequences to ourselves ... [but] to give incentive to countries to share these."

A spokesperson for the UK's Department for Environment, Food and Rural Affairs said that Weybridge would be issuing more information on sequencing "soon," but could not specify when. As for the lab's past practices, he said that "top-line data was made available to the states involved in the outbreak and to the international authorities like the WHO [as soon as possible]."

China, too, is getting ready to release viral samples that have been held for over six months, the Wall Street Journal reported last week.

Both Niman and Steven Salzberg of the University of Maryland consider the pending sequences to be "fundamental" and said they could be released to GenBank immediately if WHO or other funders apply adequate pressure.

But Richard Janeczko, chief science officer of Tm Biosciences, suggested that these data are from first-pass sequences and thus not validated — and therefore not "fundamental" — and that the WHO has no business rushing its reference labs to release them.

"I don't want crap data," he said. "I want good data. Sequencing is not error-free. It's surprisingly error-prone. First-pass sequencing gives you something like 85-percent accuracy. I don't think anything is being held back. I think its being validated."

In January, Janeczko's company began marketing its new ID-Tag RVP (Respiratory Viral Panel) test under the Investigational Device Exemption rules as it prepares to file with the agency. The diagnostic is intended to distinguish between 21 respiratory viruses, including respiratory syncitial virus, SARS, parainfluenza, and various influenza viruses.

Janeczko said his company is satisfied with the data currently available. Moreover, he noted that while a new flood of sequences might allow Tm to make its ID-Tag panel "more reliable and up-to-date" — assuming the company or others validate them — it could also be something of a set-back for the product's FDA approval. "It's a balancing act between freedom of access and highly regulated safety standards."

But most researchers agreed that, regardless of the commercial implications, putting sequencing data in the public domain is a priority. "The flu community needs to move into the model that the genomics community moved into some years ago of releasing data quickly," said Salzberg. "Releasing the data quickly gives immediate benefits to people doing basic research on the flu, not just pathogenicists but also people doing epidemiological studies."

— Elizabeth Kiem, a GenomeWeb News staff reporter


Following Review, GTL Revises Goals, Scraps Funding Opportunities

The Department of Energy's Office of Science has restructured the facilities plan for its Genomics: Genomes to Life program in response to a review by the National Research Council of the National Academies.

The DOE said that rather than creating four separate facilities devoted specifically to protein production, biomolecular imaging, proteomics, and systems biology, as it had earlier planned, GTL now envisions "one or two vertically integrated centers with a focus on bioenergy research." However, it said that it would consider building centers for systems biology research into carbon sequestration and bioremediation in future years.

Additionally, the DOE said that it has cancelled its funding opportunity announcement for a planned GTL facility for the production and characterization of proteins and molecular tags, issued in early January. DOE said it plans to issue a new solicitation in the coming months for one or more centers for bioenergy research, and that bioenergy research has become an increasing priority for GTL.

DOE said that the new R&D plan "should be able to accomplish the GTL program's objectives more rapidly and at reduced cost."

The NRC recently recommended in a non-binding review that GTL uproot its R&D plan of creating four separate facilities devoted to specific genomic-related technologies in favor of building four vertically integrated facilities in which the four original disciplines would look for applications for tasks already identified as GTL targets.


PerkinElmer, GMU Form Proteomic-Based Cancer Biomarker Alliance

PerkinElmer and George Mason University will begin a five-year research collaboration to develop proteomic technologies and cancer biomarkers, the partners said this week.

As first reported last week in Pharmacogenomics Reporter sister publication ProteoMonitor, scientists from both organizations will work together to design new proteomic platforms for biomarker discovery.

The new technologies will operate on a "new concept ... that requires both the precise mass and the amino acid sequence of the candidate biomarker," said Emanuel Petricoin of George Mason.

The researchers will use PerkinElmer's Bioxpression platform for biomarker candidates and will be validated in clinical trials.

Financial details were not provided.

The research will focus on stage one lung, ovarian, and breast cancer.


NHGRI Adds IP-Management Guidelines to Genome Sequencing Center RFA

The National Human Genome Research Institute has amended a large-scale sequencing RFA that it issued in December to include guidelines for intellectual property related to the initiative.

In a notice issued last week, NHGRI updated its previous "Genome Sequencing Centers" request for applications to include the stipulation that awardees manage IP and data in a way that will "maximize the public benefit of the data produced."

As a result, "applicants should develop a comprehensive IP and data management strategy that is consistent with the NIH Research Tools Policy," NIH said.

"Applicants should submit an IP Management Plan that assures that data is rapidly released according to approved criteria, that licensing and sharing practices ensure the availability of data and research resources for future use by the scientific community, and that research collaboration or sponsorship agreements are consistent with the requirements of the TCGA [The Cancer Genome Atlas] and the NHGRI medical sequencing program," NIH said in the notice.

Further details are available here.


NIH Seeks Genotyping Samples for GAIN Initiative

The National Institutes of Health is soliciting samples from genotyping studies for the Genetic Association Information Network that it launched last month.

GAIN will genotype samples from existing case-control studies of common diseases to provide data for whole-genome association studies. According to a notice the NIH issued Friday, the samples for this study have not been identified yet, so investigators are encouraged to nominate "appropriate sets of samples, and the associated phenotype and exposure data, from existing studies."

GAIN will fund the genotyping, so there will be no cost to those investigators who contribute samples, NIH said.

Further information is available here.


GeneCare to Distribute Agendia Products in South Africa

GeneCare will distribute Agendia's MammaPrint and CupPrint tests in South Africa, Agendia said this week.

No other details were released.

Agendia, based in Amsterdam, develops gene expression-profiling diagnostics. GeneCare is a diagnostic company based in South Africa that focuses on early detection and disease prevention.


MMRC Launches Genomics Initiative for Myeloma Research

The Multiple Myeloma Research Consortium announced this week the launch of a multi-million dollar research program called the Multiple Myeloma Genomic Initiative.

The mapping program is a collaboration between MMRC, The Translational Genomics Research Institute and the Broad Institute of MIT and Harvard.

The initiative will draw on the resources of the MMRC tissue bank, which houses bone marrow aspirates and blood samples accrued under GLP standards, according to a statement.


PamGene Says Innogenetics to Introduce HLA Typing on its Array Platform This Year

Innogenetics, a Belgian diagnostics company, will begin offering human leukocyte antigen typing on PamGene's microarray platform later this year, according to a PamGene scientific advisory board member.

Bertrand Jordan, who sits on PamGene's SAB, told Pharmacogenomics Reporter sister publication BioArray News at the World Microarray Congress last week that Innogenetics is using a system specifically designed for its use called the PamStation 12 to introduce the HLA typing.

The companies began collaborating on the development of the PamStation 12 in May 2004.

Jordan said that Innogenetics plans to introduce additional tests for the PamStation platform, including tests for cystic fibrosis and the mannose-binding lectin 2 (MBL2) gene in 2007, and for infectious disease, neurodegeneration, oncology, and immunuological diseases in 2008.

Jordan said the deal is significant for PamGene, and that Innogenetics may use as many as 130 of the PS-12 stations as it adds tests to its menu. PamGene has historically sold systems that run experiments on four arrays or 96 arrays, dubbed the PamStation 4 and PamStation 96, respectively, but Jordan said that the company, which contracts out its manufacturing, was able to design throughput levels to meet the needs of its clients.

Innogenetics does not have exclusive rights to the PS-12, however. "PamGene will be able to sell PS-12 outside of Innogenetics," Jordan said.

Jordan said that the deal with Innogenetics is significant for PamGene's three-dimensional array technology in the diagnostic arena.

"Array diagnostics still have some difficulty getting into the marketplace due to a lot of competition from RT-PCR," he said. He added that PamGene's 3D array technology is not yet "mainstream" due to "a lack of high-profile collaborations and papers."

— Justin Petrone, BioArray News editor


BG Medicine, Mitsubishi Pharma Partner on Biomarker Discovery for Muscle Toxicity

BG Medicine said this week that it has signed a collaborative research agreement with Mitsubishi Pharma of Osaka, Japan, to discover biomarkers associated with muscle toxicity in lipid-lowering compounds.

BG Medicine said it will use proteomics, metabolomics, and computational analyses to study the molecular effects of selected lipid-lowering agents on skeletal muscle and to identify specific plasma biomarkers of these effects.

Mitsubishi Pharma will contribute transcript, clinical chemistry, and histopathology data to the project.

BG Medicine said that it will jointly own "certain rights" to the project data and biomarkers with Mitsubishi Pharma, but additional terms of the agreement were not disclosed.


Solexa Reports Wider Q4 Loss and Greater Revenue; Plans to Begin Hiring for Sequencer Launch

Solexa this week reported widened net loss for the fourth quarter of 2005 despite solid revenue growth.

Solexa also said it plans to add staff to sales, marketing, and manufacturing staff "to support broad commercial release" of its Genome Analysis System to academic and government core labs, commercial sequencing companies, and pharmaceutical and biotech companies.

Solexa has said in the past it will initially target large genome centers and other prospective customers in an early access release. The company reiterated its plan to begin reporting sales of the sequencer during the second quarter, which begins April 1.

Revenue for the three months ended Dec. 31, 2005, meantime, surged to $1.3 million from $23,000 in the prior-year quarter, mostly from service fees generated from its genomic services business.

Research and development expenses increased to $4.9 million from $2.3 million year over year, Solexa reported.

According to Solexa, the net loss attributable to common shareholders for the quarter widened 73 percent to $3.7 million from $2.2 million in the year-ago quarter.

The company stated that cash and cash equivalents as of Dec. 31, 2005, stood at $38.4 million.


Roche Extends Cancer Screening Project with Epigenomics

Epigenomics and Roche Molecular Diagnostics have extended by 18 months their collaboration on cancer screening products, the companies said last week in a statement.

Roche has agreed to extend a license it took from Epigenomics in December on a panel of markers for colorectal cancer screening, and it will continue working on the validation of breast and prostate screening products, the companies said.

Under the terms of the agreement, Epigenomics will take over sensitivity validation for its screening tests for colorectal, prostate, and breast cancer, the companies said.

The colorectal cancer screening project is scheduled to continue until the end of the year, the prostate cancer screening project is scheduled to last until at least Oct. 15, and the breast cancer screening project is scheduled to last until at least March 30, 2007, the companies said.

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