Linking Genomic and Clinical Data: The HVPA-BioGrid Experience

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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.

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Linking Genomic and Clinical Data: The HVPA-BioGrid Experience

  1. 1. 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
  2. 2.  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
  3. 3. 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
  4. 4.  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
  5. 5.  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
  6. 6.  Established 2003 via Bio21 Cluster Victoria to address difficulties of conducting patient-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
  7. 7.  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
  8. 8. BioGrid Members and Collaborators
  9. 9.  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
  10. 10.  Streamlined process, single online application - Science - Data requested - Ethical considerations - People involved  Agree to BioGrid Collaboration Terms and Conditions re 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
  11. 11. Royal Melbourne Hospital Canberra Hospital Royal Hobart Hospital Royal Adelaide Hospital
  12. 12. Royal Melbourne Hospital Canberra Hospital Royal Hobart Hospital Royal Adelaide Hospital
  13. 13. Royal Melbourne Hospital Canberra Hospital Royal Hobart Hospital Royal Adelaide Hospital
  14. 14. Royal Melbourne Hospital Canberra Hospital Royal Hobart Hospital Royal Adelaide Hospital
  15. 15. Royal Melbourne Hospital Royal Adelaide Hospital Canberra Hospital Royal Hobart Hospital
  16. 16.  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
  17. 17. BioGrid Australia Reports include relevant genetic variant & clinical information HVP Australia Node Genetic Variant Data Patient ID #278 Pathology Lab 1 Genetic Variant Data Pathology Lab 2 Genetic Variant Data Patient ID #278 Familial Cancer Clinic Patient ID #278 Patient Administration Patient ID #278 Genetic Testing Patient ID #278 BioGrid Application, Review & Approval Process Health Service A (e.g. Hospital) Familial Cancer Clinic Hospital Administration Patient ID #278 Clinical Treatment & Outcomes Patient ID #278 Health Service B (e.g. Genetics Service) HVPA-BioGrid (NeCTAR Project)
  18. 18. HVP Australia Node Record Count Genetic Variant 50K Health Service A Record Count Patient Admin. 1.2M Familial Cancer Clinics 10,000 Treatment & Outcomes 5,000 Health Service B Record Count Patient Admin. 100K Familial Cancer Clinics 5,000 Genetic Testing 75,000 BioGrid Australia Records in Common HVPA-BioGrid (NeCTAR Project)
  19. 19. HVP Australia Variant Path Service A Variant Path Service B Variant
  20. 20. PAS Path. FAMBIZ Health Service Chemo. Service PAS Tx Pharm Dx. Admit. Mortality Cancer Registry HVP Australia Variant
  21. 21. PAS Path. FAMBIZ Health Service Chemo. Service PAS Tx Pharm Dx. Admit. Mortality Cancer Registry HVP Australia Variant
  22. 22.  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
  23. 23. 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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