Linking Genomic and Clinical Data: The HVPA-BioGrid Experience
26
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 5 th Biennial Meeting 19-23 May 2014 UNESCO, Paris
-
Upload
human-variome-project -
Category
Science
-
view
282 -
download
0
description
The Australian node of the Human Variome Project (HVPA) has established systems and processes for capturing, curating, interpreting and sharing genetic variant information for diagnostic, treatment and research purposes. To support the accurate interpretation of variant information, linkage to clinical treatment and outcomes data from relevant health service providers is required. Unfortunately, the required clinical data is not collected systematically within the Australian healthcare system and linkage of such data is beyond the scope and resources currently available to HVPA. HVPA has partnered with BioGrid Australia, an independent not-for-profit organisation that provides a framework and infrastructure for data linkage and sharing that addresses patient privacy, data security, ethical issues and intellectual property concerns. Importantly, BioGrid’s vision and mission closely align with that of the Human Variome Project. Furthermore, BioGrid has existing relationships with, and linkages to clinical data from, numerous healthcare service providers, research institutes and universities around Australia. While BioGrid’s governance and legal framework, coupled with its existing infrastructure, provides the requisite platform to achieving national linkage of clinical data with the HVPA collected variant data, this requires time and significant stakeholder engagement to achieve. However, within the existing network of HVPA and BioGrid collaborators, we are currently undertaking a project to demonstrate the real potential value of data linkages for clinical and research purposes. A number of clinicians treating colorectal cancer at The Royal Melbourne Hospital are existing collaborators of both HVPA and BioGrid, providing an excellent opportunity to examine the potential benefits of data linkage. The pilot project is seeking to link deidentified, patient record level data from a range of sources with the goal of determining the depth and breadth of clinical data available for patients with specified variants at The Royal Melbourne Hospital. The secondary goal of this project is to determine whether, on review by subject matter experts, this clinical information can be used to support the determination of the pathogenicity of identified variants. We will discuss progress towards the first goal, however a detailed discussion of the second goal is beyond the scope of this abstract. By using existing clinical datasets and BioGrid’s data linkage platform to integrate de-identified, patient record level clinical and genetic data, HVPA can efficiently build a national capability to capture, curate and interpret genetic variant information. Further leveraging BioGrid’s online data access application system that incorporates scientific review with ethics committee oversight, HVPA can also ensure that data is shared with authorised users for approved diagnostic, treatment and research purposes.
Transcript of Linking Genomic and Clinical Data: The HVPA-BioGrid Experience
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
+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
