linking genomic and clinical data: the hvpa-biogrid experience
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Maureen Turner, BioGrid Australia
Leon Heffer, BioGrid Australia
Alice Johnstone, BioGrid Australia
Timothy Smith, HVP Australia
John-Paul Plazzer, Royal Melbourne Hospital, Australia
Alan Lo, V3 Alliance, Australia
Finlay Macrae, Royal Melbourne Hospital, Australia
Linking Genomic and Clinical Data: The
HVPA-BioGrid Experience
The Human Variome Project 5th Biennial Meeting 19-23 May 2014 UNESCO, Paris
Data sharing considerations and challenges
Collaborative federation model
BioGrid – a grass roots solution
Data ethics, privacy, security for research
Dynamic data linkage – how BioGrid works
Data access management
HVPA-BioGrid: linking genomic & clinical data
Overview
Clinical- Colorectal Cancer
- Breast Cancer
- Diabetes
- Cardiac Surgery
Population Health- Cancer Registries
- Screening Registries
- Diabetes Registries
- Rare Diseases
Government- Death Dates/Cause
- Admitted Episodes
- Bureau Statistics
- Medicare PBS
Research- Biospecimens
- Clinical Trials
- Audit
- Quality of Life
Administration- Demographics
- Admissions
- Procedures
- Events
In-Hospital- Pharmacy
- Pathology
- Radiology
- Imaging
Maintaining patient privacy
Ethics approval for process and projects
Data governance framework
Secure data management
Authorised data access
Protection of intellectual property
Infrastructure capability
Data Sharing Considerations and Challenges
Collaboration governance
IP management (collaboration and project specific)
Framework for undertaking projects
Commercialisation of project IP
Data access and usage management
Terms for acknowledgement in presentations and publications etc. from use of data
BioGrid Collaboration Agreement
Established 2003 via Bio21 Cluster Victoria to address difficulties of conductingpatient-specific privacy-protected research across institutions and diseases
Created by clinical researchers to ethically access existing and incorporate new data sources for clinical research
Not-for-profit company limited by guarantee owned by 28 members (43 institutions)
Background
BioGrid specialises in linkage of clinical datasets that reside within hospitals and clinics
BioGrid operates in a virtual environment enabling data to be connected and linked across institutions, jurisdictions and diseases
BioGrid provides a centralised infrastructure and resource for the secure integration of data on behalf of its members and collaborators
BioGrid Expertise
BioGrid Members and Collaborators
Ethics approval at each participating institution for BioGrid linkage methodology and processes
Data access controlled and provided- ONLY to authorised users (Data Custodian, HREC)- ONLY in de-identified form- ONLY for ethically approved projects
Data governance and security- Unique subject identifier (linkage key) encrypted- Regular external security audits- All data queries monitored and logged
Data custodian retains FULL control over their data
Data Ethics, Privacy and Security
Streamlined process, single online application- Science - Data requested- Ethical considerations - People involved
Agree to BioGrid Collaboration Terms and Conditionsre data use/security, IP, privacy
Data custodian reviews application, access provided per project application ONLY when approved by data custodian
HREC (low-risk sub-committee) reviews application
Application to Access granted ~1 month (avg)
Applying for Access to Data
Royal Melbourne Hospital
Canberra Hospital
RoyalHobart
Hospital
Royal Adelaide Hospital
Royal Melbourne Hospital
Canberra Hospital
RoyalHobart
Hospital
Royal Adelaide Hospital
Royal Melbourne Hospital
Canberra Hospital
RoyalHobart
Hospital
Royal Adelaide Hospital
Royal Melbourne Hospital
Canberra Hospital
RoyalHobart
Hospital
Royal Adelaide Hospital
Royal Melbourne Hospital
Royal Adelaide Hospital
Canberra Hospital
RoyalHobart
Hospital
NeCTAR grant to improve HVPA data collection tools and to generate and capture data linkage keys for use on the BioGrid platform to enable molecular data to be linked to clinical data
HVPA-BioGrid (NeCTAR Project)
Grant Partners: University of Melbourne, V3 Alliance, University of South Australia, HVP International, InSiGHT, BioGrid Australia, Melbourne Health (Royal Melbourne Hospital)
Pilot linkage project with HVPA, InSiGHT and Melbourne Health relating to colorectal cancer
BioGrid Australia
Reports include relevant genetic variant & clinical
information
HVP Australia NodeGenetic Variant Data
Patient ID #278
Pathology Lab 1Genetic Variant Data
Pathology Lab 2Genetic Variant Data
Patient ID #278
Familial Cancer Clinic
Patient ID #278
Patient Administration Patient ID #278
Genetic TestingPatient ID #278
BioGrid Application, Review & Approval
Process
Health Service A (e.g. Hospital)
Familial Cancer Clinic
Hospital Administration Patient ID #278
Clinical Treatment &
OutcomesPatient ID #278
Health Service B (e.g. Genetics Service)
HVPA-BioGrid (NeCTAR Project)
HVP Australia Node
Record CountGenetic Variant 50K
Health Service A
Record CountPatient Admin. 1.2M
Familial Cancer Clinics 10,000Treatment & Outcomes 5,000
Health Service B
Record CountPatient Admin. 100K
Familial Cancer Clinics 5,000Genetic Testing 75,000
BioGrid AustraliaRecords in Common
HVPA-BioGrid (NeCTAR Project)
HVPAustralia
Variant
Path Service A
Variant
Path Service B
Variant
PAS
Path.
FAMBIZ
Health Service
Chemo.Service
PAS
Tx
Pharm
Dx.
Admit.
Mortality
Cancer Registry
HVPAustralia
Variant
PAS
Path.
FAMBIZ
Health Service
Chemo.Service
PAS
Tx
Pharm
Dx.
Admit.
Mortality
Cancer Registry
HVPAustralia
Variant
BioGrid is able to integrate de-identified, patient record level clinical and genetic data
Enables HVPA to build a national capability to capture, curate and interpret genetic variant information
HVPA can leverage BioGrid’s online data access application system to ensure data can be shared with authorised users for approved diagnostic, treatment and research purposes
Summary
Thank You
www.biogrid.org.au
enquiries@biogrid.org.au
+61 (0)3 9342 3167
BioGrid Australia acknowledges its supporters- BioGrid Australia Members and Collaborators
- National eResearch Collaboration Tools and Resources
- Victorian Cancer Agency, Victorian Department of Health
- Victorian Government Department of Business and Innovation
- Australian Government Department of Innovation, Industry, Science and Research
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