Nature Methods Wants Your Data, Raw
The journal Nature Methods is asking proteomics researchers to deposit their raw data in advance of submitting their final manuscripts.
In an editorial in the current edition of the journal, editors said they have begun their new policy of “strongly” recommending researchers deposit their data in any of a number of public repositories in order to allow others in the field to evaluate their studies, or even reproduce their results.
In doing so, Nature Methods joins other publications, including sister publication Nature Biotechnology, that are pushing for greater access to the raw data from researchers’ experiments. In addition, funding agencies such as the National Institutes of Health and the National Cancer Institute are asking researchers to share their data.
In the editorial, the authors say that in many fields, including genome sequencing, microarrays, and protein structures, raw data is routinely deposited into a community-endorsed public repository by their authors when they submit an article for publication. But in proteomics “there is no such habit.”
In particular, they write, mass spectrometry results are reported “haphazardly … often in formats [that make] their re-analysis impossible. Even worse, the sheer volume of data associated with many proteomics papers exceeds the supplementary information capacity of most journals.”
Without such data, reviewers cannot comprehensively access a study’s findings, and the findings cannot be reproduced by other researchers. Also software developers miss the chance to test evaluate datasets, hindering tool development, the authors say.
The lack of data-reporting is as much the result of a shortage of “appropriate repositories and the large variety of formats,” as the unwillingness of scientists, the authors say. With the creation of PRIDE, Peptide Atlas, Global Proteome Machine Database, the Tranche project, and Human Proteinpedia, that has changed, however.
While the process to deposit data still isn’t seamless, database administrators have shown a willingness to address issues raised by researchers.
“We hope that the dialogue between database administrators and data producers will solve the problems to a point where data deposition cannot be considered an undue burden on investigators and can be mandated as part of manuscript submission,” the editors say.
Vermillion Posts $3.3M Q4 Loss, Signs Dx Deal with Stanford, Implements Reverse Stock Split
In the midst of reporting a $3.3 million loss for its fourth quarter, Vermillion this week said it will collaborate with Stanford University to develop and commercialize a diagnostic test for peripheral artery disease, and implemented its reverse stock split.
For the three months ended Dec. 31, 2007, the company once called Ciphergen recorded revenues of $23,000, compared to $1.2 million during the fourth quarter of 2006. Because of the sale of its SELDI platform to Bio-Rad Laboratories in November 2006, Vermillion repeated it anticipates no major revenue pending commercialization of its diagnostic tests under development.
Its $3.3 million loss for the quarter compares to a loss of $1.9 million in the year-ago period.
For full-year 2007, the company reported a loss of $21.3 million on revenues of $44,000. In 2006, it posted a loss of $22.1 million on revenues of $18.2 million. Vermillion said it had cash, and short- and long-term investments of $20.4 million as of Dec. 31.
The company also said it has entered into a deal with Stanford to commercialize a biomarker panel to assess a patient's risk of developing peripheral artery disease, which is estimated to affect 12 million Americans.
Under the terms of the deal, Vermillion will have exclusive rights to the panel and will develop and commercialize it into a blood-based test. No other financial terms were disclosed.
The company and Stanford recently completed a 540-patient clinical study evaluating the ability of the panel to classify patients as being at high risk or low risk of developing PAD. The results are expected to be published in the coming months, the company said in a statement. Vermillion is also creating a steering committee to help design a clinical trial in support of submitting the test to the US Food and Drug Administration for approval.
Vermillion also said this week that its 1-for-10 reverse stock split took effect on March 3. Its shares began trading on the Nasdaq Capital Market under the symbol "VRMLD" on March 4 and will continue to do so for 20 trading days to designate that it is being traded on a post-reverse split basis. After the 20-day period, its shares will trade under the symbol "VRML" again.
As a result of the split, the number of shares outstanding has been reduced from about 63.8 million to 6.4 million. Last week, the company said that the Nasdaq had sent it a letter warning it was not in compliance with listing rules and in danger of being delisted.
Applera Files Divorce Papers for Celera
Applera last week said it has filed with the US Securities and Exchange Commission for the separation of Celera from the Applera Group, which also includes Applied Biosystems.
The move follows comments from the management of both Applera and Celera that the board of directors of Applera favored separating the firms and is subject to a number of conditions. Applera must gain final board approval, SEC clearance of the registration statement, and receipt of an opinion of tax counsel as to the tax-free nature of the separation, before it closes the transaction. Applera shareholders are not required to approve the deal.
Under the terms of the separation, shareholders of the Applera Group-Celera Group tracking stock would receive one share of new Celera Corporation shares for each share of the tracking stock they currently own. Upon completion of the deal, Celera would become an independent, publicly traded company.
The firms expect Celera to trade on the Nasdaq under its current ticker symbol, CRA, while its current tracking stock would be delisted from the New York Stock Exchange. Celera President Kathy Ordoñez is expected to serve as CEO of the firm, which will be based in Alameda, Calif.
Applera-ABI common stock will continue to trade on the New York Stock Exchange.
Last August, Applera announced that it had hired investment bank Morgan Stanley to conduct a review and advise the company on its options for restructuring the business.
Bio-Rad Q4 Revs Rise 34 Percent as Profits Fall 25 Percent
Bio-Rad Laboratories last week reported a 34 percent increase in fourth-quarter revenues, helped by the acquisition of diagnostics firm Diamed, while its profit dipped 25.3 percent due to charges related to that acquisition.
Fourth-quarter 2007 revenues of $459.7 million compared to revenues of $343.1 million in the comparable period the year before. Though revenue growth was 34 percent, excluding the contribution from DiaMed, revenues increased 15.9 percent year over year, said Bio-Rad.
Its life science segment sales were $184.5 million, up 16.1 percent year over year, and clinical diagnostics segment sales were up 50.7 percent at $271.4 million. Excluding DiaMed’s contribution, sales for the segment were up 16.3 percent.
The firm’s net income dropped to $12.4 million, or $.45 per share, from $16.6 million, or $.61 per share. Bio-Rad recognized non-cash charges of $12.9 million in the quarter related to purchased in-process R&D and amortization of intangibles tied to the DiaMed acquisition.
Bio-Rad’s R&D costs climbed 19.8 percent to $39.9 million from $33.3 million year over year, while SG&A expenses increased 33.1 percent to $163 million from $122.5 million.
For full-year 2007, Bio-Rad reported revenues of $1.46 billion, up 14.7 percent from revenues of $1.27 billion in 2006. Sales for the life sciences segment grew 6.9 percent to $615.1 million, while clinical diagnostics sales increased 21.5 percent to $832.2 million.
The firm’s net income slipped 10 percent to $93 million, or $3.41 per share, from $103.3 million, or $3.83 per share. Last year’s results include $11.7 million in revenue from a legal settlement with bioMerieux.
Bio-Rad’s R&D expenses in 2007 increased 13.9 percent to $140.6 million from $123.4 million, while SG&A expenses were up 15.7 percent at $508 million versus $438.9 million the year before.
The firm finished the year with $161.8 million in cash and cash equivalents.
Waters, Hitachi to Develop Chromatography Software
Waters and Hitachi High-Technologies said this week that they have signed a development and distribution agreement related to Waters’ Empower 2 chromatography data software.
Under the terms of the agreement, HHT will develop an interface for Empower 2 so that it can be used with its own LaChrom Elite and Lachrom Ultra liquid chromatography systems.
In addition, HHT subsidiary Hitachi High Technologies America will sell Waters’ Empower products in combination with the LaChrom Elite and LaChrom Ultra LC systems.
Financial terms of the agreement were not provided.
Invitrogen to Validate Reagents with Tecan, BMG Labtech
Invitrogen said this week it has entered into two new agreements, one with Tecan and another with BMG Labtech, to study and validate its reagents with the companies’ microplate instruments.
Under the terms of both of the agreements, announced separately, Invitrogen will work with the companies to develop and promote joint applications to market to pharmaceutical companies.
In the agreement with Tecan, Invitrogen will validate the compatibility of its reagents with Tecan’s microplate detection tools.
Specifically, the companies will validate Invitrogen’s drug discovery reagents on the Tecan Infinite series readers, and on assay systems for key target classes, including Invitrogen’s LanthaScreen TR-FRET for protein kinases, the GeneBLAzer reporter-gene technology for G protein-coupled receptors, and the Adapta assay system for lipid kinases.
Under the BMG Labtech agreement, Invitrogen will test its reagents with certain of the company’s readers, as well as its PHERAstar and Omega series instruments.
This collaboration will also focus on Invitrogen’s LanthaScreen TR-FRET, GeneBLAzer, and Adapta assays, as well as the PolarScreen FP technology for nuclear receptors.
Agilent Inks Software Deal with ACD
Agilent Technologies and Advanced Chemistry Development announced an agreement this week to co-market ACD/Labs’ AutoChrom method-development software with Agilent’s ChemStation instrument-control software for its HPLC, Rapid Resolution LC, and LC/MS systems.
AutoChrom can perform combinations of column, solvent, and buffer screening experiments, as well as automatic method optimization, the companies said. When experiments are complete, the data are automatically transferred from the ChemStation control software back to AutoChrom for processing and interpretation.
ACD/AutoChrom for ChemStation supports Agilent 1100, 1200, and 1200 SL Series liquid chromatographs; and model G1946 and G1956 mass spectrometers.
The companies said they expect support for Agilent 6100 Series mass spectrometers to be available in the fourth quarter of 2008.
Neurobiological Technologies Licenses Patent Rights From Buck Institute
Neurobiological Technologies will exclusively license certain patent rights to a naturally occurring protein that has been shown to reverse the symptoms of Alzheimer's disease, under an agreement reached with the Buck Institute, the company said this week.
Under the agreement, Neurobiological will fund a joint research collaboration with the institute related to the Alzheimer's drug development for up to three years. Research funding in the initial year will total $1.2 million. Neurobiological will pay upfront licensing fees of $175,000 during a three-year period.
Current studies at Buck Institute are focused on a protein to inhibit the production of amyloid-B peptide, which has been implicated in the development of Alzheimer's disease. One theory is that an overabundance of the peptide causes the disease, which afflicts an estimated 24 million people worldwide.
Genmab, Pepscan to ID Antibodies
Genmab and Pepscan this week said they will collaborate to identify fully human monoclonal antibodies against intractable disease targets. Such targets include "those that are difficult to address using commonly available technologies but are highly desirable for targeting with monoclonal antibodies," the companies said in a joint statement.
Pepscan will use its proprietary CLIPS technology to identify functional mimics of the essential parts of such targets. Genmab will then use these mimics to create and select therapeutic antibodies using its fully human monoclonal antibody technology.
Financial terms of the collaboration were not disclosed.
Proteomika Orders MorphoSys Customer Antibodies
MorphoSys this week said its AbD Serotec business unit has received a “multiple research antibody order” from Proteomika, a Spanish biomarker-discovery firm.
Proteomika has ordered HuCAL-based research antibodies against a broad range of target molecules, MorphoSys said in a statement. Proteomika was founded in 2002 as a subsidiary of genomics firm Progenika Biopharma to develop diagnostic and prognostic products based on biomarkers.
Financial details of the deal were not disclosed.
MDS' Fiscal Q1 Revenues Rise 23 Percent
MDS this week said that fiscal first-quarter revenues rose 23 percent as sales from Molecular Devices exceeded the firm’s expectations.
For the three-month period ended Jan. 31, MDS reported revenues of $296 million, up from $241 million in the first quarter of 2007.
Molecular Devices, which was acquired in the second quarter of 2007 and is part of the MDS Analytical Technologies unit, brought in first-quarter revenues of $56 million, according to MDS.
Overall, that unit had revenue of $116 million, up 119 percent year over year. Sciex contributed $60 million in revenue for the quarter.
Currency effects increased net revenue in the first quarter of 2008 compared to the first quarter of 2007 by approximately $25 million.
MDS posted a first-quarter profit of $17 million, or $.14 per share, compared to $16 million, or $.11 per share, in the first quarter of 2007.
R&D expenses rose 67 percent to $20 million from $12 million.
MDS finished the first quarter with $144 million in cash and cash equivalents.