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Human Cancer Genome Project, Structural Genomics Database, Invitrogen, Spotfire, ACD/Labs, Genedata, Sage-N Research, Eidogen-Sertanty, Biomax

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NCI, NHGRI Kick off Human Cancer Genome Project

Last week, the National Cancer Institute and the National Human Genome Research Institute launched a $100 million pilot project to determine the feasibility of mapping the genomic changes involved in all types of human cancer — a project that NCI and NHGRI have dubbed the Cancer Genome Atlas.

The project will develop and test the science and technology framework to systematically identify and characterize the genetic mutations and other genomic changes associated with cancer, NHGRI director Francis Collins said during a press conference in Washington, DC, to announce the effort on Dec. 13.

NCI and NHGRI have each committed $50 million to the three-year TCGA Pilot Project.

The pilot will focus on a few types of cancer and tumors, which have yet to be chosen. NCI deputy director Anna Barker said the tumors would be selected after evaluating existing repositories to identify those that exist in enough large quantities and are "reasonably" homogenous, with little contamination.

A Human Cancer Biospecimen Core Resource will help collect, process, and distribute cancerous and control tissue samples to Cancer Genome Characterization Centers and Genome Sequencing Centers, she said. These centers will be selected in 2006.

According to the TCGA website, the project also has a Data Management, Bioinformatics, and Computational Analysis component, which will help develop methods for handling the "unprecedented amount of information on human clinical biospecimens" generated by the project.

Informatics challenges for the project that are outlined on the site include: "development of data standards and controlled vocabularies for each new technology, establishment of an informatics pipeline for data to flow from production centers to a central repository, creation of portals for basic and clinical researchers to easily access the TCGA data, and encouragement of new computational approaches to analyze the data."

The NCI's Cancer Biomedical Informatics Grid project has developed a number of methods that will be used in the pilot project, including common data elements, metadata, and middleware to enable interactions among distributed databases, NCI said.

Each component of the pilot project will have clear milestones and goals. The success of the pilot will determine whether the project will be expanded to explore genomic changes involved in all 200 types of cancer to develop a complete atlas of the cancer genome, Collins said.


NIGMS Earmarks $2.5M for Structural Genomics Database

The National Institutes of Health's National Institute of General Medical Sciences has issued a request for applications for a project entitled, "Structural Genomics Knowledgebase."

According to the RFA, available at http://grants.nih.gov/grants/guide/rfa-files/RFA-GM-06-004.html, one grant of up to $2.5 million will be awarded to build a database to hold data from the NIGMS Protein Structure Initiative, which was initially launched in 2000 and entered its second phase this summer.

The RFA acknowledges that "a number of large databases already exist to serve the needs of the structural biology field," including NCBI and the PDB. "The Knowledgebase should not duplicate what has already been created in these existing databases," the RFA states, but is rather "expected to complement the functions of these resources and make seamless connections to them. The development of the Knowledgebase is intended to better coordinate the PSI projects, to make PSI products more easily accessible, and to communicate with the scientific community in order to better serve their needs."

Letters of intent are due Jan. 24 and applications are due Feb. 23.


Invitrogen Partners with Wiley to Bolster E-Commerce Resources

Invitrogen said last week that it has partnered with scientific publisher John Wiley & Sons to develop iProtocol, a free online version of Wiley's Current Protocols lab research manuals.

Invitrogen said that iProtocol adds to its online "eScience" initiative, which also includes several free bioinformatics resources, such as the iPath pathway database and Vector NTI Advance 10 [BioInform 9-19-05].

Invitrogen said that iProtocol will include "selected content" from Current Protocols titles covering methods for molecular biology, cell biology, immunology, and neuroscience. The content will be linked directly to reagents and other products in Invitrogen's online catalog.


FDA Approves Siga's INDA for Computationally Designed Smallpox Drug

Siga Technologies said last week that the US Food and Drug Administration has accepted its investigational new drug application to begin Phase I clinical trials of SIGA-246, a smallpox drug that the company designed using a computational approach. [BioInform 10-03-05]

The company said that it will begin Phase I clinical trials to evaluate SIGA-246 in healthy volunteers at the Biodefense Clinical Research Branch of the National Institute of Allergy and Infectious Diseases.


BioSystems International to Use Spotfire DecisionSite for Biomarker Discovery

Spotfire said last week that BioSystems International has purchased its DecisionSite software for use in its clinical biomarker discovery program.

BSI is using DecisionSite to investigate several classes of biomarkers, including stratification markers that predict the likelihood of a drug response, efficacy biomarkers that predict a clinical outcome, screening markers for the early detection of diseases, and prognostic markers to predict the likely course of the disease.

Financial terms of the agreement were not provided.


Bayer CropScience Expands Deployment of ACD/Labs' NMR Software

Advanced Chemistry Development said last week that Bayer CropScience has extended its installation of the company's NMR processing and data-management tools across all of its European research centers in Monheim, Frankfurt, and Lyon.

The software was previously deployed at a single site within Bayer CropScience.

"We decided to extend the installation of ACD/Labs' NMR solutions to ensure that our NMR knowledge is retained and accessible from different sites," said Winfried Etzel, head of NMR and HTA at Bayer CropScience, Germany, in a statement.


TransTech Pharma To Use Genedata's Screener Software

TransTech Pharma has signed a multi-year license for Genedata's Screener high-throughput screening software, Genedata said last week.

Screener has been integrated with TransTech Pharma's IT and screening infrastructure, and it will be used to automate data-quality evaluation and standardize the analysis of compound bioactivity, the company said.


Sage-N Research to Open R&D Center in China

Sage-N Research said last week that it will open a research and development center in the New Science Park in Shanghai, China, in "early 2006."

Sage-N, a developer of accelerated proteomics informatics tools, said that the Shanghai center will expand its software-development capabilities. The company's headquarters will remain in San Jose, Calif., and will focus on marketing, sales, and administration.

Sage-N has developed an accelerated analysis appliance called Sorcerer, as well as the the Sequest Sorcerer system marketed by Thermo Electron. The company's flagship product, Sorcerer Proteomics Edition, is a high-throughput proteomics analysis system.

The company said that the Shanghai center will "work closely with leading proteomics scientists to quickly and cost-effectively incorporate new technologies and applications into the Sorcerer appliance in the form of plug-in modules."

The first modules are expected to eliminate false positive results, provide multiple peptide scoring functions, and offer "extensive" post-translational modification searches, the company said.


Eidogen-Sertanty Enters Discovery Collaboration with Kalypsys …

Eidogen-Sertanty said last week that it will collaborate with Kalypsys on a project to discover small molecules for anti-inflammatory indications.

Eidogen-Sertanty said it will use its DirectDesign computational drug discovery platform to design a library of novel, synthetically tractable, and drug-like compounds with predicted activity against a target of interest to Kalypsys.

Kalypsys' is already of customer of Eidogen-Sertanty's Target Informatics Platform, a protein structure informatics system.

Financial terms of the agreement were not provided.


… as it Licenses Target Informatics Platform to AstraZeneca

Separately, Eidogen-Sertanty said last week that AstraZeneca has licensed its Target Informatics Platform (TIP).

Under the terms of the agreement, scientists at AstraZeneca's R&D center in Boston will use the TIP and the company's EVE comparative visualization software within their cancer and anti-infective therapeutic programs.

Financial terms were not disclosed.


Korean Livestock Institute Licenses Biomax BioRS System

Biomax Informatics said last week that the National Livestock Research Institute in Suwon, Korea, has licensing its BioRS Integration and Retrieval System.

The agreement adds to the institute's existing license for the Biomax Pedant-Pro Sequence Analysis Suite, which it is using to support the Cow EST Project and the International Pig Genome Project.

Financial terms of the agreement were not provided.

Filed under

The Scan

Panel Votes for COVID-19 Pill

A US Food and Drug Administration panel has voted to support the emergency use authorization of an antiviral pill for COVID-19 from Merck and Ridgeback Biotherapeutics, CNN says.

But Not Harm

New Scientist reports that UK bioethicists say that though gene editing may improve food production, it should not harm livestock welfare.

Effectiveness Drop Anticipated

Moderna's Stéphane Bancel predicts that that current SARS-CoV-2 vaccines may be less effective against the Omicron variant, the Financial Times reports.

Cell Studies of Human Chromatin Accessibility, SARS-CoV-2 Variants, Cell Signaling Networks

In Cell this week: chromatin accessibility maps of adult human tissues, modeling to track SARS-CoV-2 variants of concern, and more.