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Bottom-up ‘omics integration
December 2012
by Ilene Schneider  |  Email the author


TARRAGONA, Spain—In what Agilent Technologies Inc. Biological Systems Division Vice President/General Manager Gustavo Salem calls "a very strategic association between two organizations with similar goals," Agilent and Spain's Centre for Omic Sciences (COS) are collaborating on mass spectrometry and NMR-based metabolomics and automation applied to research in integrated systems biology.  
Agilent is well known as a measurement company specializing in chemical analysis, life sciences, diagnostics, electronics and communications.  
COS, established by Spain's Rovira i Virgili University in collaboration with the Technological Centre of Nutrition and Health, opened in September. It is equipped with Agilent instrumentation, including the 6550 iFunnel Quadrupole Time-of-Flight LC/MS, 7200 Quadrupole Time-of-Flight GC/MS, 6490 iFunnel Triple Quadrupole LC/MS, Bravo automated liquid handling systems and the SureScan DNA microarray scanner, software, consumables and services.
Founded in 1991, Rovira i Virgili University is a 15,000-student, publicly funded university that is attempting to become an international benchmark in the areas of chemistry, energy, nutrition and health, among other disciplines.  
While the collaboration came about because of the purchase, "we were not interested in just purchasing mass spectrometers, but in a long-term relationship with a technological partner," explains Dr. Oscar Yanes, principal investigator at COS and assistant professor at the university. "We recognized Agilent Technologies as an excellent fit for our approach to integrating data from different 'omics techniques."  
COS will host training sessions for Agilent's European metabolomics customers needing formal training, and the two groups will jointly work on developing GC/QTOF MS/MS libraries with the company's 7200 GC/Q-TOF instrument, according to Steve Fischer, Agilent's marketing manager for metabolomics and proteomics. Agilent will provide beta-test equipment and software and demonstrate integrated biology workflows to customers in such disciplines as genomics, proteomics, transcriptomics, lipidomics and metabolomics in search of biological breakthroughs. Together, the collaborators seek to create a center of excellence, Fischer explains.
"Both groups want to expand the use of metabolomics as a research tool," he adds. "If the relationship is successful, there will be more labs using metabolomics as a tool in their research. The opportunity to offer metabolomics training by the Centre for Omic Sciences to Agilent's European metabolomics customers will be a large benefit to the European metabolomics research community. The development of GC/QTOF MS/MS libraries should benefit researchers worldwide."  
COS's main collaborators are groups at the Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM). The organization also has established additional collaborations with Drs. Shabaz Mohammed and Albert Heck at Utrecht University in the Netherlands and Dr. Rafael Simó at the Vall d'Hebron Research Institute in Barcelona.
"The integration of various 'omics technologies will be at the computational level," Yanes says. "This integration will be made possible by improving experimental design that should take into account particular methodological issues in metabolomics, proteomics and genomics simultaneously. We believe it is critical to create an environment in which our technical staff responsible for the different 'omics technologies can meet and discuss concrete experimental designs in order to facilitate further data integration."  
Yanes believes that the ultimate goal of COS research is to achieve a "bottom-up 'omics integration," particularly between metabolomics and the other 'omics. 
"At the COS, we will interrogate the biochemical basis of disease, starting with a non-hypothesis-driven approach using metabolomics technologies," he explains. "The comprehensive characterization of the lowest level of the cellular information flow—that is, metabolites altered by disease—can facilitate the biochemical interpretation and therefore subsequent generation of novel hypotheses."  
Key areas of research will be diabetic retinopathy, lipoproteins and cardiovascular risk.  COS is also very interested in the field of microbiota and its impact on obesity and insulin resistance, according to Yanes.  
He adds, "In the near term, I anticipate new methodological advances in the field of metabolomics. These include new software for metabolite identification, optimized sample preparation and new lipoprotein measurement in serum. This will result in a more comprehensive interrogation of biological samples that, in turn, will increase our understanding of the mechanisms leading to neurodegeneration in diabetic retinopathy and the cardiovascular risk in obese and diabetic people." 

Agilent and Roche to provide continued support to Roche NimbleGen microarray customers  
SANTA CLARA, Calif.—In early November, Agilent Technologies Inc. and Roche signed an exclusive agreement to provide continued service to NimbleGen microarray customers as Roche phases out its NimbleGen array production and services.  
Researchers using NimbleGen microarrays for all applications, including comparative genomic hybridization, chromatin immunoprecipitation-on-chip, DNA methylation and gene expression can transition to Agilent arrays effective immediately, with minimal disruption. The similarities of the technologies and products from both companies provide an optimal transition path and the ability to run Agilent microarrays on the NimbleGen MS 200 Microarray Scanner.  
"This global collaboration provides our customers with a confident and straightforward solution to move from NimbleGen to Agilent microarrays," said Dan Zabrowski, head of Roche Applied Science, in a statement. "With Agilent as a leading global supplier of microarray technology, we are convinced researchers will be provided with the highest compatibility to NimbleGen products and services, and believe that they will continue to receive the exceptional service and support they have come to expect." 

Code: E121212



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