RNAi Global Initiative - Scottish Centre for Genomic Technology and Informatics

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The University of Edinburgh

Scottish Centre for Genomic Technology and Informatics (GTI)

	The Scottish Centre for Genomic Technology and Informatics (GTI) is a centre for world class post-genomic research located within the University of Edinburgh Medical School. Our goal is to harness the power of post-genomic science and technology to provide insights into human health & disease. GTI is conducting pioneering research programmes in: · Pathway Biology, developing a fundamental understanding of the complex molecular interactions in the human body. · Biochip Medicine, translating this research into clinical healthcare using intelligent biochips to measure these interactions.

	GTI has a unique and innovative approach. We believe that dramatic progress can be made from a collaborative, multidisciplinary style of research based on integrated teams working on common research goals. Our studies cross traditional boundaries combining science and technology, blue-sky and applied research, academic and business. GTI is one of the 10 founding members of the genome-wide RNAi Global Initiative. We are currently embarking on a full scale screen of the human genome with a full genome library from Dharmacon. This will be used to dissect and understand further the pathway by which human cytomegalovirus (CMV) infects and replicates with human cells. This information will be used to build a more detailed model of viral infection. This work fits well with our pioneering 'pathway biology' approach to biomedical research. Access to the genome-wide RNAi library will enable us to systematically and selectively explore the role of individual components within molecular networks. Informatics at GTI The GTI has an informatics team supporting the work of the experimentalists in the lab. We provide statistical expertise in the analysis of microarray experiments and develop software tools to manage the large amount of experimental data we generate. In particular we have developed laboratory information management systems (LIMS) to support the design and manufacture of custom microarrays and to keep an electronic record of the microarray experiments carried out at the GTI. This last system, GPX-Repository, conforms to the minimum information about a microarray experiment (MIAME) standards. It allows experimentalists to record their experimental design, protocols and results as the experiment progresses and it helps the GTI maintain a record of all out experimental work. GPX Repository supports multiple microarray platforms, from custom arrays through to Affymetrix, CodeLink and Agilent platforms. We also provide tools to analyse this data and provide a web based interface to the data GPX-Discovery. Published datasets are made generally available at the GPX website. A keen area of research at the GTI is Pathway Biology. In particular, we are interested in the elucidation and understanding of Interferon regulated pathways in the context of the macrophage. To support this work we are developing a database application to hold and analyse scientific and clinical pathway-related information. An important aspect of this work is the development of a graphical notation that can clearly represent the interactions occurring in the pathway. To this end we are founder members of the Systems Biology Graphical Notation consortium and have been actively involved in developing this standard. The GTI is also a member of the INFOBIOMED (www.infobiomed.org) network of excellence. This is an EU funded program which promotes collaborative research and a synergy between the fields of Bioinformatics and Medical Informatics throughout the EU. The GTI is leading a pilot project in this programme which aims to demonstrate the utility of pathway biology in a clinical context. Current work is focussed on the application of new predictive algorithms for biomarker identification and the integration of this data with patient and viral genotype information in order to develop new targets for therapeutic intervention. We are also a partner in the Edinburgh NTRAC centre. The aim of the NTRAC Centre is to set up an infrastructure to support translational research. More specifically, the GTI will bring its microarray expertise to the centre by running genomic microarray experiment on biological samples from the NTRAC patient cohort and by integrating the GPX-Repository containing these results to the NTRAC e-science infrastructure for further analysis and research. The informatics team is taking an active interest in RNAi work at the GTI and we are keen to apply expertise acquired in the development of microarray data collection standards to this evolving area. In particular, we feel our experience in the application of MIAME standards will prove very useful in the development of an equivalent set of guidelines for RNAi experiments. The immediate objective of this work is to agree the Minimum Information About an RNAi Experiment (MIARE) standard. The MIARE standard should contain enough information to unambiguously describe an RNAi experiment. MIARE would be similar to the MIAME standard employed by the microarray community (for more information see the MIAME website). The benefit of agreeing what information we require as a minimum is that is gives us a baseline to work from in the future development of data-exchange formats, database schemas and LIMS systems. As a roadmap to establishing the MIARE standard we have proposed the following steps: 1) Establish a core MIARE group, with 1 representative from each consortium member who will act as a main point of contact. 2) Draw up a requirements questionnaire with input from consortium members. 3) Get the questionnaires completed by RNAi "experts" from each member. 4) Run a requirements workshop (at the next consortium meeting?) using the questionnaire responses to drive the workshop. It is important that RNAi experts should also participate in this workshop. The aim would be to agree on an initial draft of the standard. 5) Publish the draft standard for comment and consultation. Contact Details Deborah Spencer, Business Development Manager Scottish Centre for Genomic Technology & Informatics University of Edinburgh Medical School Chancellor's Building Little France Crescent Edinburgh EH16 4SB T: +44 (0) 131 242 6281 F: +44 (0) 131 242 6244 Email deborah.spencer@ed.ac.uk For more information visit our website at www.gti.ed.ac.uk