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Oct 7, 2010

GeneGo and GenomeQuest Combine Tools for Analyzing NGS Data in Terms of Pathways

  • GeneGo and GenomeQuest announced the integration of the latter’s Sequence Data Management (SDM) platform with GeneGo’s MetaCore™ and MetaDrug™ tools. The SDM platform is designed to allow researchers to manage and share sequence data, and access a collection of reference databases from a web-browser and personalized “dashboard”.

    GeneGo’s flagship MetaCore product is an integrated knowledge database and software suite for pathway analysis of experimental data and gene lists. The firm claims the tool supports data types including microarray and sequence-based gene expression, SNPs and CGH arrays, proteomics, metabolomics, Co-IP pull-out, and other custom interactions.

    MetaDrug is a systems pharmacology platform designed for evaluating the biological effects of small molecule compounds on the human body with pathway analysis and other bioinformatics applications from toxicogenomics to translational medicine. The tool is ideal for use in solving a drug’s mechanism of action, toxicity and off-target effects deduced from the structure and any kind of supplementary toxicogenomics data, GeneGo claims.

    “This integration will allow our joint customers to seamlessly work with next-generation sequencing data in the context of pathways,” explains Julie Bryant, vp of business development at GeneGo. “The integrated workflows will lead our users from raw sequence runs to functional hypothesis generation of drug targets and biomarkers.”

    “The ability to analyze hundreds of datasets, reducing millions of reads down to a short list of particular genes of interest, and then being able to visualize where those genes are active in specific (potentially disease-related) pathways, is a significant accomplishment in the integration of omics software,” adds Don Gregory, Ph.D., GenomeQuest’s director of field application scientists. “Scientists will be able to quickly focus on their scientific questions, rather than manipulating large read datasets and lists of thousands of genes.”

    The agreement between GenomeQuest and GeneGo comes just a week or so after the latter announced a deal with Omicsoft to integrate Omicsoft‘s Array Studio next-generation sequencing tools with GeneGo‘s MetaCore data-mining suite. Also during September GeneGo was awarded a National Institute on Drug Abuse SBIR grant to develop an integrated systems biology platform for research into the causes and treatment of tobacco dependence, nicotine addiction, smoking cessation, and tobacco/nicotine withdrawal.

    The funding will be used to develop a database and systems biology tool-set specifically designed for study of the pathways involved in nicotine addiction and withdrawal, mutations, and sequence heterogeneity in human genes and their controlling regions that affect these responses, and the evaluation of new targets, therapeutic strategies, and biomarkers for treatment of nicotine addiction.

    In August GenomeQuest and SGI announced the launch of what they claim is the world’s first whole-genome analysis (WGA) services for researchers. The new offering is designed to give companies, laboratories, government agencies, and clinics direct access to whole-genome processing capabilities that could previously only be accessed through dedicated genome centers. GenomeQuest and SGI co-developed a software and hardware architecture they say is optimized for next-generation sequencing, and enables whole-genome scale and performance. Based on this architecture the WGA services are available through the recently upgraded GenomeQuest data center or can be deployed directly into a customer data center.


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