Marienne Hibbert

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Marienne Hibbert
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BioGrid - Human Variome

• Overview of BioGrid
• Privacy protection and issues
• Biospecimen collection and analysis
• Requirements?
• Models of data availability and flow

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Funding

• Phase 1 funded by Victorian Government (A1.7
  M) 2003 2005
• Phase 2 funded by Australian Government (A4.4
  M) 2005 2007
• Phase 3 ACG funded by Victorian Government
  (A11.0 M) 2006 - 2009

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Privacy and Ethics

• MMIM infrastructure processes Ethically
  approved (all sites)
• One patient Unique Subject Index allocated
• Data available in de-identified (codified) form
  only
• Health data separate from identifying data
• Log-ons and passwords
• Virtual Private Networks for transmission of data
• Secure Internet access
• Access provided to specific tables on
  application research/purpose must be described
• Access approved by data custodians and management
  committee
• Confidentiality undertakings and deeds
• Linkage maintenance separate from health data

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Access to de-identified data

• User specifies databases and tables
• User specifies purpose the science
• Each database custodian approves
• Management committees approves
• Log-ons and password allocated
• Tracking of all queries
• Project IP protected

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Who ?
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What ?
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Genome Phenotype? Translational research

• Same cancer - different molecular makeup
• Different natural history
• Different response to treatment
• Need at the individual level

analysed bio-specman Pathology and clinical
outcome
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Human Variome Mission

• The Human Variome Project will achieve improved
  health outcomes by facilitating the unification
  of human genetic variation and its impact on
  human health.
• It will support the use of human variation
  information in clinical and research environments
  across the world by developing the resources
  required to undertake the .. (10 objectives).

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1. Capture all human gene variation

• Biospecimen samples VCB
• Consent and collection
• Expensive to maintain Biobanks
• ? Incorporate into clinical care
• Sample analysis
• Expensive
• How much can be made routine?
• Clinical outcome data
• BioGrid increasingly collating

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2. Data standards

• gene nomenclature
• reference sequences
• Start with current accepted
• What is the minimum data set?
• Pilot

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Other missions 3 - 7

• Curation
• IT architecture and software
• System that clinicians can use
• Support for laboratories
• Open access and logging IP
• Open access to data

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Missions 8 - 10

• Support for developing countries
• Communication and education
• Research

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2. For countries wanting simpler IT
1. For countries with sophisticated IT.
Clinical Data Genotype Phenotype Eg. Fam Bis
Surveillance in Australia
Clinical Data Genotype Phenotype Eg European
Databases
Clinical Data Stored Web Server
Clinical Data view for Doctors
Local Research Repository Europe
Local Research Repository Melbourne Health
Federated Data Integrator
De-identified Data Feed for each mutation
Collation of data from source
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Collation of data (2) and access
Human Variome Project Up to 20,000 mutations
specific current databases with International
locations
Federated Data Integrators
De-identified Data Feed for each mutation
Central Store of all data (mirrored)
InSiGHT MMR Gene Missense info Phenotype Virtual
Histology Others Interpretation
Locus Specific Databases
Text mining of public data (for data extraction
and validation) eg PubMed
NCBI / EBI
InSiGHT Portal
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Issues

• Open access ?
• Consent and privacy - patients
• Data custodians to consent IP
• Public acceptance
• Minimum data set? Have we enough now?
• Allele - sequence ssID, state
• Phenotype status - Have we enough now?
• Need an IT architecture - IT enabling the
  business
• Resources

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The BioGrid Team

• Business and admin
• Robert Merriel (Chair of Committee)
• Marienne Hibbert (Project Director)
• Richard Tate
• Vicki Vlekkert

• Cancer
• Peter Gibbs (CSO)
• Jayesh Desai
• Suzy Kosmider
• Kathryn Field
• Julie Johns
• Ngio Murigu
• Sandy Dupuis
• Daniel Compston

• Technical
• Naomi Rafael
• Kee Ming Kong
• Pranabh Jain
• Xiaobin Shen
• Nelson Wu
• Jana Graenz

• Life Sciences
• Henry Gasko
• Diana Salim

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Bio21 MMIM
www.biogrid.org.au