SCIEX and Illumina expand genomics and proteomics project

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  • Published: Mar 18, 2015
  • Author: Jon Evans
  • Source: SCIEX
  • Suppliers: AB SCIEX
  • Channels: Laboratory Informatics / HPLC / Base Peak / Chemometrics & Informatics

Three US organizations have all recently unveiled novel ways for analyzing and comparing proteomics and genomics data as part of the OneOmics project, an exclusive partnership between Illumina and SCIEX.

The OneOmics project develops ways to integrate SCIEX’s SWATH Acquisition-based next-generation proteomics (NGP) and next-generation sequencing (NGS) data on Illumina’s BaseSpace cloud computing environment, with the aim of eliminating the informatics barriers that exist between different omics disciplines. As part of that effort, Advaita Bioinformatics, the Institute for Systems Biology (ISB) and researchers at Yale University have each now developed cloud-based applications and libraries that utilize SWATH proteomics data in novel ways.

Rob Moritz, associate professor at the ISB, led a team that developed the SWATHAtlas Ion Library Generator Application, which provides fast and simplified access to ISB libraries for use in NGP experiments with SWATH Acquisition. Currently, ISB hosts ion libraries for the human, yeast and Mycobacterium tuberculosis proteomes. ‘We are delighted to be part of this project with SCIEX and Illumina,’ said Moritz. ‘Collectively, our tools developed at ISB and in the wider academic community will provide a powerful solution that will impact the way that proteomics research and systems biology will be conducted in the future.’

Advaita Bioinformatics has developed the iPathwayGuide app for the BaseSpace platform. The app performs biochemical pathway analysis, gene ontology analysis, miRNA prediction, and drug and disease analyses of SWATH proteomics and Illumina RNASeq data. It simplifies the process of finding real biological insights from integrated proteomics and transcriptomics data sets, and will help to advance biomarker discovery and disease research.

Chris Colangelo and Rob Kitchen at Yale University worked together to develop the RNASeq Translator Application for the BaseSpace platform. This application translates the output from an Illumina RNASeq experiment into a protein database that can be used to create ion libraries to mine SCIEX SWATHTM Acquisition data. As such, it allows a more targeted approach to proteomics analysis within the context of identifying splice variants, which can be critically important to researchers seeking to understand the genetics of a particular disease. This serial workflow is a common requirement for systems biology research, but until now has required complex bioinformatics protocols that are beyond the reach of all but a few specialized laboratories.

‘SWATHTM Acquisition enables researchers to accurately and reproducibly quantify several thousand proteins across hundreds of samples, leading to meaningful conclusions about how the proteome changes in response to perturbation,’ said Aaron Hudson, senior director of academic and clinical research business at SCIEX. ‘The next logical step is to integrate those proteomic conclusions with other omics results, such as genomics and transcriptomics. Our collaborators at ISB, Yale University and Advaita Bioinformatics have all launched complimentary applications that expand the workflow and provide general access and standardization of data analysis across two of the largest fields in life science.’

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