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DataSHaPER WorkshopDataSHaPER WorkshopData Pooling for RealData Pooling for Real

Isabel FortierDirector of Research and DevelopmentP3G Consortium

Paul BurtonProfessor of Genetic EpidemiologyUniversity of Leicester

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Workshop planWorkshop plan

Acknowledgments Objectives Structure History to date

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Thanks to our hosts and sponsorsThanks to our hosts and sponsors

Generation Scotland P3G (Genome Canada and Genome Quebec) PHOEBE (European Union, FP6) Canadian Partnership Against Cancer

Objectives of the workshopObjectives 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?)

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Structure of the workshopStructure 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

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Structure of the workshopStructure 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

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Structure of the workshopStructure 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

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What is harmonization?What is harmonization?

Biobank harmonizationBiobank 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”

“vx jhmkaiwb”

“I understand”

“I understand”

“Je comprends” X

“I comprehend”

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Perfectstandardisation

Ad hocmethods

Measure FEV1

for genetics oflung function

Assess smoker versus non-smoker as a confounder

Identify subjects with a doctordiagnosis of diabetes for an aetiological study

What is harmonization?

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A brief history of the A brief history of the DataSHaPERDataSHaPER

A Brief HistoryA 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), Kadoorie Study of Chronic Disease in China, National DNA Bank (Spain), CONOR (Norway), etc.)

• Iterative discussion between workshops12

A Brief HistoryA Brief History Montreal, September 2006 – preliminary planning Edinburgh, November 2006 – first draft of “Generic Data Set”

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• 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

A Brief HistoryA Brief History York, September 2007 – Workshop 2, fundamental

restructuring

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• Focus on harmonizing variables (the primary units of analysis) rather than the specific information items in individual studies

P3G meetings• San Diego, October 2007• Barcelona, May 2008• Philadelphia, November 2008• Brussels, March 2009

Definitive concept of DataSHaPERStructure and contents developedCollaboration with CPAC and PhenX

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The scientific contextThe scientific context

The scientific contextThe scientific context Backdrop of Calibration Workshop

• Excellent potential for calibration work Methods development Active harmonization

• Focus on nutrition

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The scientific contextThe 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

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How to take things forward?How to take things forward?

Isabel FortierDirector of Research and DevelopmentP3G Consortium

Paul BurtonProfessor of Genetic EpidemiologyUniversity of Leicester

Issues to considerIssues 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)

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Issues to considerIssues 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)

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Issues to considerIssues 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

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Guidance for discussionGuidance 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?

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A proposedA proposedUK Obesity ProjectUK Obesity Project

Paul BurtonProfessor of Genetic EpidemiologyUniversity of LeicesterChair: Wellcome Trust SDEG

UK: The strategic contextUK: 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?

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Obesity-related researchObesity-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

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http://www.foresight.gov.uk/OurWork/http://www.foresight.gov.uk/OurWork/ActiveProjects/Obesity/KeyInfo/Index.aspActiveProjects/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).

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Three key meetingsThree 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!

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Strategic opportunitiesStrategic opportunities

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UK Cohorts

Pre-existing Data Collections

New Data Collection

New sweep(s) in pre-existing cohort(s)

New cohort(s)SCIENTIFIC TARGETSNew phenotyping standardsRetrospective + prospective harmonizationNew sets of information constructed and made availableNew data generationNew discoveries based on an enhanced platform

Topics of interest to fundersTopics 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

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Stated infrastructural requirementsStated 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*

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UK Obesity ProjectUK 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

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Why an obesity Data SHaPER?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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