Bottom-up ‘omics integration

Agilent, Spain’s Centre for Omic Sciences in systems biology collaboration

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TARRAGONA, Spain—In what Agilent Technologies Inc. BiologicalSystems Division Vice President/General Manager Gustavo Salem calls "a verystrategic association between two organizations with similar goals," Agilentand Spain's Centre for Omic Sciences (COS) are collaborating on massspectrometry and NMR-based metabolomics and automation applied to research inintegrated systems biology.
Agilent is well known as a measurement company specializingin chemical analysis, life sciences, diagnostics, electronics andcommunications.
COS, established by Spain's Rovira i Virgili University incollaboration with the Technological Centre of Nutrition and Health, opened inSeptember. It is equipped with Agilent instrumentation, including the 6550iFunnel Quadrupole Time-of-Flight LC/MS, 7200 Quadrupole Time-of-Flight GC/MS, 6490iFunnel Triple Quadrupole LC/MS, Bravo automated liquid handling systems andthe SureScan DNA microarray scanner, software, consumables and services.
Founded in 1991, Rovira i Virgili University is a15,000-student, publicly funded university that is attempting to become aninternational benchmark in the areas of chemistry, energy, nutrition andhealth, among other disciplines.
While the collaboration came about because of the purchase,"we were not interested in just purchasing mass spectrometers, but in along-term relationship with a technological partner," explains Dr. Oscar Yanes,principal investigator at COS and assistant professor at the university. "Werecognized Agilent Technologies as an excellent fit for our approach tointegrating data from different 'omics techniques."
COS will host training sessions for Agilent's Europeanmetabolomics customers needing formal training, and the two groups will jointlywork on developing GC/QTOF MS/MS libraries with the company's 7200 GC/Q-TOFinstrument, according to Steve Fischer, Agilent's marketing manager formetabolomics and proteomics. Agilent will provide beta-test equipment andsoftware and demonstrate integrated biology workflows to customers in suchdisciplines as genomics, proteomics, transcriptomics, lipidomics andmetabolomics in search of biological breakthroughs. Together, the collaboratorsseek to create a center of excellence, Fischer explains.
"Both groups want to expand the use of metabolomics as aresearch tool," he adds. "If the relationship is successful, there will be morelabs using metabolomics as a tool in their research. The opportunity to offermetabolomics training by the Centre for Omic Sciences to Agilent's Europeanmetabolomics customers will be a large benefit to the European metabolomicsresearch community. The development of GC/QTOF MS/MS libraries should benefitresearchers worldwide."
COS's main collaborators are groups at the SpanishBiomedical Research Centre in Diabetes and Associated Metabolic Disorders(CIBERDEM). The organization also has established additional collaborationswith Drs. Shabaz Mohammed and Albert Heck at Utrecht University in theNetherlands and Dr. Rafael Simó at the Vall d'Hebron Research Institute inBarcelona.
"The integration of various 'omics technologies will be atthe computational level," Yanes says. "This integration will be made possibleby improving experimental design that should take into account particularmethodological issues in metabolomics, proteomics and genomics simultaneously.We believe it is critical to create an environment in which our technical staffresponsible for the different 'omics technologies can meet and discuss concreteexperimental designs in order to facilitate further data integration."
Yanes believes that the ultimate goal of COS research is toachieve a "bottom-up 'omics integration," particularly between metabolomics andthe other 'omics. 
"At the COS, we will interrogate the biochemical basis ofdisease, starting with a non-hypothesis-driven approach using metabolomicstechnologies," he explains. "The comprehensive characterization of the lowestlevel of the cellular information flow—that is, metabolites altered bydisease—can facilitate the biochemical interpretation and therefore subsequentgeneration 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 onobesity and insulin resistance, according to Yanes.
He adds, "In the near term, I anticipate new methodologicaladvances in the field of metabolomics. These include new software formetabolite identification, optimized sample preparation and new lipoproteinmeasurement in serum. This will result in a more comprehensive interrogation ofbiological samples that, in turn, will increase our understanding of themechanisms leading to neurodegeneration in diabetic retinopathy and thecardiovascular risk in obese and diabetic people." 

Agilent and Roche toprovide continued support to Roche NimbleGen microarray customers
SANTA CLARA, Calif.—In early November, Agilent TechnologiesInc. and Roche signed an exclusive agreement to provide continued service toNimbleGen microarray customers as Roche phases out its NimbleGen arrayproduction and services.
Researchers using NimbleGen microarrays for allapplications, including comparative genomic hybridization, chromatinimmunoprecipitation-on-chip, DNA methylation and gene expression can transitionto Agilent arrays effective immediately, with minimal disruption. Thesimilarities of the technologies and products from both companies provide anoptimal transition path and the ability to run Agilent microarrays on theNimbleGen MS 200 Microarray Scanner.
"This global collaboration provides our customers with aconfident and straightforward solution to move from NimbleGen to Agilentmicroarrays," said Dan Zabrowski, head of Roche Applied Science, in astatement. "With Agilent as a leading global supplier of microarray technology,we are convinced researchers will be provided with the highest compatibility toNimbleGen products and services, and believe that they will continue to receivethe exceptional service and support they have come to expect." 

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