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News Briefs from the Bio-IT World Conference Floor, Boston March 30-April 1, 2004


IBM and Affy to Co-Develop Clinical Genomics Standards

IBM and Affymetrix have entered into a partnership to develop standards for integrating clinical information with genomics data. The initiative falls under IBM’s new information-based medicine business segment, and is aimed toward establishing experimental protocols and data standards that will “leverage clinical data sets in coordination with high-throughput research data,” said Kareem Saad, worldwide executive director of clinical genomics for IBM Healthcare and Life Sciences.

This level of integration is a crucial component in Affymetrix’s vision of moving its GeneChip technology into the clinic, Steve Lombardi, vice president of corporate development for Affymetrix, told BioInform. Lombardi said that the biopharmaceutical industry’s nascent interest in pharmacogenomics is set to grow rapidly. He estimated that there are around 50 microarray-based clinical trials underway now as “one-off” proof-of concept demonstrations — a number that is likely to grow, he added, but only if drug companies are provided with the means of integrating high-throughput genomic data with “traditional” clinical trials information.

The partnership is “very much around standards,” Lombardi said — including standards for experimental design, data collection protocols, and data formats. Acknowledging that standardization efforts currently exist for microarray experiments, Lombardi noted that in the clinical world, “the rigor has to be a step higher” than it does in the research realm.

Saad said the companies are looking into accepted standards for both the genomics and the clinical domains — such as CDISC, HL7, MAGE-ML, and BioSML — as a starting point for the initiative.

Paracel Targets Diagnostic Labs with Agent Genotyping Software

Paracel launched an upgraded version of its Agent automated genotyping software that is geared toward large diagnostic labs, the company said.

The first version of the software was launched just under a year ago, and still represents a “small fraction” of the company’s business, Michael Curtin, vice president of engineering for the Celera Genomics subsidiary, told BioInform. Nevertheless, the genotyping tool does broaden the user base for the company’s software. Curtin said that so far, most sales for Agent have been to customers that don’t already use the company’s more well-known GeneMatcher and BlastMachine hardware systems.

Agent 2.0 is based on the company’s TraceTuner base-calling software, and offers a multiple patient alignment feature that places genotyping data within the context of a reference genome. The software is built on a client/server architecture, and can be pre-configured to run on the company’s Cyclone Linux server.

Fujitsu Eyes US for Bioinformatics Business

Fujitsu has established a US-based sales team to extend its reach into the North American bioinformatics market, Michael McManus, vice president of Fujitsu America’s Bio-IT group, told BioInform.

The company has a healthy bioinformatics business in Japan, McManus said, with around 200 software engineers working on life science applications. Now, Fujitsu is building a sales force to extend its reach into the US market, he said.

Currently, the company’s CAChE molecular simulation software is the only product available in the US, but McManus said that Fujitsu is currently preparing several tools for US distribution, including a new parallel supercomputer optimized for life science applications.

Sun Debuts Customer-Ready Bioinformatics Cluster

Loralyn Mears, Sun Microsystems’s segment manager for life sciences market development, told BioInform that the interest level for the company’s new pre-configured bioinformatics cluster has been high, and that the company has already taken several orders for the system, which was introduced on Monday.

There was no floor model of the system at the conference, but photos offered a glimpse of the knee-high “box on wheels” bioinformatics cluster. The Sun Fire Starter Cluster for Bioinformatics is a four-node x86 cluster of Sun Fire V60x and V65x servers that comes pre-loaded with Message Parsing Interface (MPI), N1 Grid Engine resource management, and Incogen’s VIBE (Visual Integrated Bioinformatics Environment) workflow software. Initially available for the Linux operating system on the Intel Xeon architecture, the cluster will be available on the Opteron platform for both Linux and Solaris this summer. A CD of public bioinformatics algorithms, called BioBox, optimized for Solaris and Linux, will ship with the bundle at that time.

Mears said the company sees the low-priced (under $22,000) cluster as an opportunity to introduce new users to Sun technology. The market is “switching more and more to commodity systems” she noted, but “many people don’t even know that we offer x86.” The company expects the ready-made bioinformatics cluster to serve as a stepping-stone to larger infrastructure deals for life science research groups. “We don’t want to just be a box vendor,” Mears said.

NetGenics Founder Launches Lucidyx

Manuel Glynias, who founded NetGenics in 1996 and sold the company to Lion Biosciences in 2002, has resurfaced (after waiting out a non-compete agreement with Lion). Glynias has founded a new company, called Lucidyx, that made its debut at the conference.

The company’s name is derived from its mission to “illuminate the genome,” Glynias said. Lucidyx’s flagship product, called Lucidyx Searcher, allows users to query across multiple publicly available databases at once and then view their results in a genome browser interface. Search results can be combined in a common view with search results from PubMed or Google, and the product can also automatically annotate Affymetrix datasets.

The software was developed for researchers at the Cleveland Clinic, Glynias said, and is geared toward biology research groups that may not have access to a bioinformaticist. Researchers in fields like neurology and immunology “have to be genome-aware” today, Glynias said, “but most of them don’t even know what Blast is.”

The system is sold under a perpetual license, for unlimited users, at a commercial rate of $50,000 and an academic rate of $30,000. Glynias said that Lucidyx will provide source code for the software under a license that permits internal modification, but not redistribution.

CareGroup Opts for 40-TB EMC Multi-Tier Storage System

CareGroup, a healthcare network of four Boston-area hospitals affiliated with Harvard Medical School, has turned to EMC to create a 40-terabyte “multi-tiered” storage system that spans high-end, mid-tier, disk archive, and mass storage.

The hybrid system falls into what Roberta Katz, EMCs’s director of global life sciences, called the company’s “key strategy” of information life cycle management — a solutions-based approach that assesses the types of data a customer needs to store within the context of long-term business goals, research demands, and regulatory requirements to provide the proper storage option for each type of data.

CareGroup, for example, plans to keep patient information on high-performance, highly available storage for real-time access, while its less-critical data will be stored on a lower-cost mid-tier system. EMC is also providing a Celerra network-attached storage system connected to a 50-node cluster of HP-UX servers to store research data, including human genome sequence data, protein folding information, and drug modeling information.

HP to Collaborate with TCAG on Predictive Medicine R&D

Hewlett-Packard and the Center for the Advancement of Genomics (TCAG) have entered into a research collaboration to develop software-based tools that will use genomic data to evaluate the probability that an individual will develop a serious illness, and to recommend lifestyle changes or medical treatment to prevent the predicted disease.

TCAG, which is affiliated with the J. Craig Venter Science Foundation, will serve as a “test and development environment” for tools, systems, and technologies developed as part of the project.

The collaboration will focus on several projects, including the creation of an optimized genome-sequencing pipeline, and the development of open standards for data and tools related to the initiative.

Genomics Collaborative and Celestar Build LiSH Gene Expression Database

Genomics Collaborative and Celestar-Lexico Sciences plan to work together to build a database of genes expressed in human breast cancer using Celestar’s LiSH (Large-scale in situ Hybridization) technology and Genomics Collaborative’s Global Repository of human biological samples.

Celestar said the project is the first to use LisH with human tissue samples.

The companies will first conduct a pilot study to identify expression differences in normal and cancerous tissue samples for a “modest set” of target genes. If the pilot is successful, the companies said they would scale up the project and market the database to pharmaceutical firms.

Filed under

The Scan

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Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.