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FDA, LabCorp, MDS, Proteome Systems, Bristol-Myers Squibb, Ingenuity Systems, Invitrogen, ABI, AnaSpec, University of Washington, NYU, Natural History Museum

FDA Questions Validation of LabCorp’s OvaSure Dx
The US Food and Drug Administration is dissatisfied with how the Laboratory Corporation of America clinically validated its homebrew OvaSure ovarian cancer test, which the agency considers a “high-risk” product, according to a warning letter sent to the company early last month.
The FDA Office of In Vitro Device Evaluation and Safety has asked LabCorp to discuss with the agency the utility of its OvaSure test after it learned that the performance characteristics of the test were based on research that is not representative of the intended pool of patients.
LabCorp launched OvaSure, a six-biomarker assay developed in collaboration with Yale University School of Medicine, in June as a laboratory-developed test under the Clinical Laboratories Improvement Act [see PM 06/26/08]. 
The company decided to begin offering the test after its Yale collaborators published a Phase II study that indicated the test had 95.3 percent sensitivity and 99.4 percent specificity. The Yale researchers are currently conducting a Phase III trial for the test and expect to publish their results by the end of the year.
LabCorp officials told ProteoMonitor in June that they believed the test was accurate enough to begin offering it to physicians. “Although the data from the Phase III trial has not been published, our internal data that we’ve generated to date at LabCorp on OvaSure has been validated with 99-percent correlation to the performance characteristics in the Phase II trial,” Myla Lai-Goldman, executive vice president and chief medical officer of LabCorp, said at the time.
But in a letter to LabCorp dated Aug. 7, OIVD Director Steve Gutman wrote that the Phase II was not sufficient to validate the test. 
“We note that this research was carried out, and performance derived, on two populations that are strongly clinically biased for being healthy and normal, and for having already experienced ovarian cancer,” the later stated. “Based on the available information, we do not believe the scientific community would consider the reported study sufficient to establish performance characteristics of a test in ‘high risk women who might have ovarian cancer’, i.e., in a clinical setting, as claimed in your intended use and promotional materials.”
Gutman told LabCorp that OIVD would like to talk to the company about offering the test, and any other strategies the company may have for validating the test.
LabCorp said in statement that it “shares the FDA’s determination to help assure that patients are protected without … imposing unnecessary regulatory burdens on new critically needed tests” and that it “looks forward to working with the agency to review the clinical data related to this important test.”
FDA also is looking again into whether or not to regulate an ovarian cancer test made by Correlogic Systems, a company that in 2004 saw its OvaCheck test halted by the agency.
According to Correlogic’s website, it is currently involved in discussions with FDA to determine the scope of the review that will be required to commercially offer the OvaCheck test.
“FDA’s position has been that it has regulatory authority over OvaCheck and other tests of this nature — and that approval therefore is required,” Annette Fribourg, Correlogic’s VP of Government and Public Relations, told ProteoMonitor sister publication GenomeWeb Daily News in an e-mail this week.
“As a result,” Fribourg continued, “Correlogic has conducted extensive clinical trials on the test and we expect to make our submission to FDA shortly.”

MDS' Q3 Revenues Drop 4 Percent as Mass Spec Shipments Decline
MDS this week reported that its third-quarter revenues fell 4 percent year over year and the firm swung to a loss from a profit on restructuring charges.
The Toronto-based firm brought in total revenues of $321 million for the three-month period ended July 31, compared to revenues of $333 million in the comparable period of 2007.
Sales for the firm’s MDS Analytical Technologies segment declined 9 percent to $104 million from $114 million due to lower shipments of mass spectrometers to its joint venture partner, Applied Biosystems. MDS said that despite this decrease in shipments, end-user revenue from mass specs grew 5 percent.
The MDS Pharma Services segment had 1 percent revenue growth to $145 million from $143 million year over year. Foreign exchange rates contributed $6 million to that segment’s revenue. MDS is in the process of restructuring the Pharma Services segment, which includes reducing headcount and closing several offices. As part of that effort, the unit took $8 million in restructuring charges during the quarter, and MDS anticipates a further $6 million to $8 million of such charges during the fourth quarter.
MDS said in July that it planned to lay off 210 employees in a restructuring effort aimed at improving profitability in its MDS Pharma Services and MDS Analytical Technologies business units.
MDS Nordion’s revenue fell 5 percent to $72 million from $76 million.
MDS reported a net loss of $10 million, or $.08 per share, for the third quarter, compared to a profit of $7 million, or $.05 per share, for Q3 of 2007. This year’s results include an $11 million asset impairment charge and a $10 million restructuring charge. Last year’s results included a restructuring charge of $3 million.
The firm’s R&D expenses declined 5 percent to $19 million from $20 million year over year, and its SG&A costs also fell 5 percent to $63 million from $66 million.
MDS finished the quarter with $130 million in cash and cash equivalents.
MDS said that as a result of “slower than expected ramp up of revenue at MDS Pharma Services, related to the delay in the start of certain customer studies,” it has lowered its 2008 revenue guidance to a range of between $1.33 billion and $1.35 billion compared to its earlier forecast of between $1.35 billion and $1.4 billion.

Proteome System Abandons Rx for Biomarker Dx
Proteome Systems said last month that it would shut down its drug-development business and focus solely on biomarker-based diagnostics operations.
The Sydney, Australia-based firm has been trying to develop a therapeutic compound portfolio since its merger with Eukarion in 2005. However, that portfolio “no longer fits with our corporate development strategy,” the company said.
Proteome said it will continue research via funding from the US government but will close its Boston office within the next three months. It said that it will retain the rights to a portfolio of assets covering antioxidant compounds for dermatological and neurological indications, and it will consider out-licensing opportunities.
The firm expects the closure of its US operations to save $550,000 per year starting in February 2009.
Proteome said it will focus on its near-term revenue-generating programs, particularly a collaboration with Bayer CropSciences for its WheatRite test for wheat quality and a partnership with Becton Dickinson for a tuberculosis test.
Separately, the company said it has closed a private placement of AUS$2.5 million (US$2.2 million), the company said today.
Proteome Systems will issue 23,809,524 shares at AUS$0.105 per share to participants in the funding including Oppenheimer Funds and other US and Australian investors.
The Sydney-based firm said it will use the money to maintain development timelines for its two lead programs including a rapid point-of-care test for tuberculosis and an on-site test used to determine the quality of wheat, which will be used to help determine pricing.
The placement is being arranged by Foster Stockbroking, and the new shares will be ranked equal to the company’s ordinary shares.

Bristol-Myers Squibb Licenses Ingenuity’s IPA Software
Bristol-Myers Squibb will use Ingenuity Systems’ Ingenuity Pathways Analysis software under a multi-year agreement announced this week.
Bristol-Myers will use the IPA software to interpret, model, and visualize proteomics and genomic data to identify “key biological insights to accelerate their drug discovery programs,” the company said in a statement.
The agreement gives Bristol-Myers research scientists enterprise-wide access to IPA. They will have access to the newest version of IPA, which supports Affymetrix GeneChip Exon arrays, supports many new species, and included enhancements such as the Path Designer publishing tool and capabilities for metabolomics, biomarker, and toxicology research.
No financial details of the agreement were disclosed.

Invitrogen, ABI Voters to Weigh in on Merger
Invitrogen and Applied Biosystems announced separately last month that they each will hold a special meeting of shareholders on Oct. 16 to vote on the proposed $6.7 billion merger of the two firms.
Invitrogen and ABI each said that shareholders of record as of the close of business on Sept. 5 are entitled to vote at the meetings. The firms will mail a proxy statement and relevant materials to shareholders the week of Sept. 8, they said.
Shareholders of both firms must approve the transaction, and the merger requires the approval of the European Commission.
Under terms of the deal, ABI shareholders will receive $38 for each share they own in the form of Invitrogen stock and cash, with cash accounting for 45 percent of the split. The purchase price represents a 12 percent premium to ABI’s average closing price for the previous 30 trading days.
Applied Biosystems also said last month that its board of directors declared a quarterly dividend of $.0425 per share of ABI common stock. The dividend is payable on Oct. 1 to shareholders of record as of the close of business on Sept. 2.

AnaSpec Licenses Protein Technology IP from UW
Proteomics products company AnaSpec has licensed intellectual property from the University of Washington’s technology transfer arm, the company announced last month.
AnaSpec has licensed the rights to make, use, and sell protein tyrosine phosphatase substrates covered under UW TechTransfer’s patent No. 5,739,278, entitled “Compositions for Protein Tyrosine Phosphatases.” The San Jose-based company, which sells peptides, detection reagents, and combinatorial chemistry products, said it plans to market the UW protein technology as part of its GO Peptides line.
UW TechTransfer manages over 2,000 issued and pending patents filed in the US and abroad, and since its founding in 1982 has been involved in the creation of over 235 companies. 
Financial terms of the agreement were not released.

NYU, Natural History Museum to Use $1.6M NSF Grant for Plant Proteome Bioinformatics Research
The National Science Foundation has given three scientists at New York University and at the American Museum of Natural History a $1.6 million grant to study the proteomes of two plants and to place their data in a public database, NYU said this week.
The investigators will use the three-year grant to study the structure, evolution, and function of the proteomes of the Arabidopsis thaliana, a small flowering plant that was the first plant to have its genome sequenced, and the rice plant Oryza sativa.
The studies will be conducted by two biologists at NYU’s Center for Genomics and Systems Biology, Richard Bonneau and Michael Purugganan, and by Rod DeSalle at the Sackler Institute for Comparative Genomics at AMNH.
The scientists will map information about the evolutionary importance of certain parts of genes and study how proteins are encoded into the genomes in order to find out what all the proteins are doing. The research will focus on using bioinformatics techniques and will be conducted using the World Community Grid, which is an IBM-supported computing platform that involves 400,000 volunteer computers worldwide.
NYU said that scientists at its Courant Institute of Mathematical Sciences, which is run by Bonneau, have already used the grid to develop structure predictions for more than 150 genomes.
These methods will be useful for annotating proteins that have unknown functions, and which currently have no detectable similarity to another protein with a known structure. Annotating these proteins means translating the gene sequence into predictions about how the gene functions, NYU said.
The project also will be linked to a continuing education program at NYU’s Steinhardt School for Culture, Education, and Human Development to train teachers how to use bioinformatics in high school science classes.

The Scan

Pig Organ Transplants Considered

The Wall Street Journal reports that the US Food and Drug Administration may soon allow clinical trials that involve transplanting pig organs into humans.

'Poo-Bank' Proposal

Harvard Medical School researchers suggest people should bank stool samples when they are young to transplant when they later develop age-related diseases.

Spurred to Develop Again

New Scientist reports that researchers may have uncovered why about 60 percent of in vitro fertilization embryos stop developing.

Science Papers Examine Breast Milk Cell Populations, Cerebral Cortex Cellular Diversity, Micronesia Population History

In Science this week: unique cell populations found within breast milk, 100 transcriptionally distinct cell populations uncovered in the cerebral cortex, and more.