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DataSHaPER Workshop Data Pooling for Real

DataSHaPER Workshop Data Pooling for Real. Isabel Fortier Director of Research and Development P3G Consortium Paul Burton Professor of Genetic Epidemiology University of Leicester. Workshop plan. Acknowledgments Objectives Structure History to date. Thanks to our hosts and sponsors.

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DataSHaPER Workshop Data Pooling for Real

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  1. DataSHaPER WorkshopData Pooling for Real Isabel Fortier Director of Research and Development P3G Consortium Paul Burton Professor of Genetic Epidemiology University of Leicester

  2. Workshop plan • Acknowledgments • Objectives • Structure • History to date

  3. Thanks to our hosts and sponsors • Generation Scotland • P3G (Genome Canada and Genome Quebec) • PHOEBE (European Union, FP6) • Canadian Partnership Against Cancer

  4. Objectives of the workshop • Our definition of “harmonization” • Review history and progress of the DataSHaPER project • Share details of the science and structure of the DataSHaPER as it now stands • Discuss proposals for ongoing development • Extending the DataSHaPER and its component elements • Applied projects based on using the DataSHaPER • Papers • Development of a firm action plan (who, what, when?)

  5. Structure of the workshop • What is “harmonization”? • History and progress of the DataSHaPER project • A brief history of the DataSHaPER • A scientific context to our discussions • Structure and science of the DataSHaPER • Ongoing development and research opportunities • Creating new DataSHaPERs • Creating new DataSHaPER modules • Extending pre-existing modules • Applied projects based on using the DataSHaPER • Papers

  6. Structure of the workshop • Milestone: select extension to focus on in the future • Work program split: (i) in workshop; (ii) after workshop • In workshop: discuss and construct a draft DataSchema to reflect chosen focus. Discussion to be structured around modules: • Questionnaires • Physical and cognitive measures • Biochemical measures • Registries

  7. Structure of the workshop • After workshop: develop and finalize an action plan for the ongoing work program after the workshop • What – scientific focus, nature (e.g. DataSchema, Harmonization Platform, Quality Control issues), format (e.g. papers, full grants or work packages in grants), priorities • Who – which biobanks and which people want to be involved and at what level of commitment? Identify leaders for specific elements of the work? • When – time lines for production of work and meetings

  8. What is harmonization?

  9. Biobank harmonization • “A set of procedures that promote, both now and in the future, the effective interchange of valid information and samples between a number of studies or biobanks, accepting that there may be important differences between those studies” “I understand” “I understand” “I comprehend” X “Je comprends” “vx jhmkaiwb”

  10. Whatisharmonization? Identify subjects with a doctor diagnosis of diabetes for an aetiological study Assess smoker versus non-smoker as a confounder Measure FEV1 for genetics of lung function Perfect standardisation Ad hoc methods

  11. A brief history of the DataSHaPER

  12. A Brief History • Series of consensus workshops with experts from more than 25 large population-based biobanks (including EPIC, UK Biobank, etc.) • Development based on: • Expertise and comparison of current practice of 15 studies (NHANES, EPIC, UK Biobank, Cancer Prevention Study (USA), KadoorieStudy of Chronic Disease in China, National DNA Bank (Spain), CONOR (Norway), etc.) • Iterative discussion between workshops

  13. A Brief History • Montreal, September 2006 – preliminary planning • Edinburgh, November 2006 – first draft of “Generic Data Set” • Good agreement on domains, and the basic information to be collected, but empirically the way specific questions are constructed leads to significant heterogeneity. Emphasises need for prospective harmonization and shows that retrospective harmonization is difficult but important • P3G meeting, Montreal, May 2007

  14. A Brief History • Focus on harmonizing variables (the primary units of analysis) rather than the specific information items in individual studies • York, September 2007 – Workshop 2, fundamental restructuring • P3G meetings • San Diego, October 2007 • Barcelona, May 2008 • Philadelphia, November 2008 • Brussels, March 2009 Definitive concept of DataSHaPER Structure and contents developed Collaboration with CPAC and PhenX

  15. The scientific context

  16. The scientific context • Backdrop of Calibration Workshop • Excellent potential for calibration work • Methods development • Active harmonization • Focus on nutrition

  17. The scientific context • Other biobank harmonization organisations • BBMRI, ISBER • Sister project • PhenX (US) • Harmonization for real • Canadian Partnership for Tomorrow • GeneCure • ENGAGE • Multimorbidity Cohort • BBMRI and UK Obesity Projects • Ontologies

  18. How to take things forward? Isabel Fortier Director of Research and Development P3G Consortium Paul Burton Professor of Genetic Epidemiology University of Leicester

  19. Issues to consider • Venue for work program • in workshop • after workshop • What can we do? • Create/extend a DataSchema (in) • Construct/develop elements of a harmonization platform (after) • Discuss and develop an approach to QA and QC for pooling (probably future)

  20. Issues to consider • Scientific focus of interest • Obesity (proposal to be justified) • Mental Health, Infections (designated research priorities) • Others • Population of special interest • Age group (e.g. newborn, elderly)

  21. Issues to consider • Outcome or exposure based focus • e.g. new disease-based Data SHaPER • e.g. nutrition, physical exercise, environmental exposures including pollution • Source of information • Questionnaire, physical/cognitive measures, biochemical measures, registries • Temporality • Base-line cross sectional, longitudinal reassessment, continuous longitudinal tracking

  22. Guidance for discussion • Proposed choices: • Topic: obesity – but for discussion after presentation • Task in: create DataSchema (Task after: for discussion) • Modules: (Q, P/CM,BM,R) – probably all? • Open questions: • Temporality • baseline, longitudinal reassess, longitudinal track? • Outcome phenotypes • Measures of obesity, measures of sequelae of obesity? • Exposures relevant to obesity • Nutrition, physical activity, etc? • Age group • Newborn, childhood, adult, middle-age, elderly?

  23. A proposedUK Obesity Project Paul Burton Professor of Genetic Epidemiology University of Leicester Chair: Wellcome Trust SDEG

  24. UK: The strategic context • Cohort platforms are expensive to create and maintain • Must think strategically as well as scientifically • But science is the ultimate goal • If we are to invest heavily in creating, developing and maintaining platforms, that must be with the intention of supporting research with a purpose • What potential purposes? • e.g.Obesity;immunity and infection; mental health? • Can we identify a good fit between infrastructural investment and development, and high quality science?

  25. Obesity-related research • Very strong in the UK (e.g. see MRC Nutrition report) • Highly relevant at many levels • Basic, clinical, social and public health science • Direct impact in many health related areas • Very topical • Concerns about “the obesity epidemic” • Widely recognised as a priority • Politically and publically as well as scientifically • Highly multi-disciplinary

  26. http://www.foresight.gov.uk/OurWork/ActiveProjects/Obesity/KeyInfo/Index.asphttp://www.foresight.gov.uk/OurWork/ActiveProjects/Obesity/KeyInfo/Index.asp • More research is needed that is aimed at understanding the emergence and evolution of this “epidemic”, at investigating its implications and in developing and evaluating effective approaches to managing obesity and its consequences at the level of the individual, the health system and across society as a whole (see Tackling Obesities: Future Choices, Foresight 2007).

  27. Three key meetings • October 2008 (ESRC/MRC/WT Cohorts meeting) • Where are we now and where might we go (strategically) with research based on the major UK cohorts and their development? • January 2009 (WT – brainstorm, obesity research) • What are the key scientific issues in the field of obesity-related research (in its broadest sense)? • March 2009 (WT/MRC – Obesity/Cohorts Workshop) • Is there a strategic fit that would favour targeted investment in/development of the platform provided by the major national cohorts as a springboard for a major multi-disciplinary program in obesity related research? YES!

  28. Strategic opportunities UK Cohorts Pre-existingData Collections New Data Collection New sweep(s) in pre-existing cohort(s) SCIENTIFIC TARGETS New phenotyping standards Retrospective + prospective harmonization New sets of information constructed and made available New data generation New discoveries based on an enhanced platform New cohort(s)

  29. Topics of interest to funders • Understanding the causes of the obesity epidemic • Understanding, evaluating and managing a response to the epidemic • Understanding the causal architectures of obesity, body weight, fat distribution, weight gain ... including the interaction between biology and the social environment and modulation of direct effects (e.g. FTO). • Understanding the causal pathways leading from obesity to its detrimental consequences • Understanding, evaluating and managing a response to obesity at a clinical, public health, social and/or political level

  30. Stated infrastructural requirements • Manage active interface between the cohorts • Manage active interface between cohorts and key elements of bioscience community • Provide relevant integrative information about the cohorts (web-based portal and catalogues) • Explore development of a common access system • Develop a targeted program in harmonization* • New DataSHaPERs (particularly Obesity-related)!! • Retrospective and prospective • Oversee active interface with international initiatives*

  31. UK Obesity Project • Funders (WT, MRC, ESRC) warmly supportive • Strategic bid being developed • An obesity Data SHaPER would be of immense value • Part of project could be used to extend such a Data SHaPER

  32. Why an obesity Data SHaPER? • Study of obesity very relevant scientifically and to public health • Seen as important across society • Obesity research will make extensive use of biobanks, and will demand effective pooling • Construction now would be very timely • An obesity Data SHaPER would have many other roles because obesity is related to so many key exposures and disease outcomes

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