Cancer
Genomic testing offers personalised treatment for patients with myeloid blood cancers
Genomic Information Management
This project will streamline the processing, management and exchange of genomic information in clinical settings and with researchers.
The genomic information management (GIM) workstream developed an architecture for Queensland genomic information management, and the standards, policies and procedures to support a common infrastructure for the management and use of genomic data.
The project team developed a prototype system to trial these standards for the capture and use of clinical and genomics data for clinical and research use.
Project Deliverables
To ensure Queensland is equipped to apply medical genomics to everyday healthcare, a number of capability building projects were funded in Round 1.
Establish the Information and Data Governance Framework
- Working closely with the Ethics, Legal and Social Implications Workstream, document the legal, regulatory and business (clinical/research) context within which genomic information and data are created, used and managed
Establish the Enterprise Architecture Principles
- In line with the Australian Government Enterprise Architecture Principles and with input from the other Round 1 projects, establish the business, technical, information principles of the GIM solution
Define the Enterprise Information Management Architecture
- Based on the above framework and principles, define the structure and operation for the GIM architecture
Qld Genomics Data Repository Installation
- A Qld Genomics Data Repository will be installed at QCIF. The repository will allow for a de-identified collection of genomes to be stored and shared according to appropriate ethics.
Qld Genomics Data Repository Ready for Use
- Appropriate guidelines on the use of the GRALFI database will be implemented so that the sequence data from Clinical Demonstration Projects can be uploaded and accessed appropriately
Register of Queensland bioinformatics pipelines
- Using the Australian Genomics Health Alliance bioinformatics pipeline registration guidelines, develop a register of bioinformatics pipelines being used by Queensland Genomics projects.
Availability of infrastructure for bioinformatics pipelines quality control
- At least one bioinformatics pipeline will be available from the QCIF infrastructure for the purpose of providing a test pipeline for use by Queensland Genomics projects. Additionally, standard data sets for validating and quality control of pipelines will be available along with guidelines for their use and expected results.
Requirements for genomic test ordering and reporting
- Identification of requirements for genomic test ordering and reporting from the Genomic Testing Innovation capability building workstream and the Round 1 Clinical Demonstration Projects.
Prototypes for genomic test ordering and reporting
- Prototype for the test ordering and reporting including the information required to order the test and the information returned. Artefacts will include the information models and terminology sets required for clinical demonstration projects.
Guidelines for germline variant sharing
- Engage with stakeholders to understand current practices of access to germline variant information, sharing and reporting. Develop guidelines for sharing germline variants within Queensland Genomics.
Guidelines for somatic variant sharing
- Engage with stakeholders to understand current practices of access to somatic variant information, sharing and reporting. Develop guidelines for sharing somatic variants within Queensland Genomics.
Trial of potential solutions for variant sharing
- Identify and trial potential solutions for a variant database for sharing clinical variant information across Queensland which will also contribute to an Australian solution.
Identifying data sharing requirements
- Identify the data sharing requirements for the Clinical Demonstration Projects, and current sharing tools from initiatives such as the Global Alliance for Genomics and Health (GA4GH)
Usage of data sharing tools
- Provide data sharing tools as available to meet requirements of the Clinical Demonstration Projects and Capability Building Workstreams. Report on the usage of these tools.
Usage data sharing requirements
- Identify the clinical systems that genomic tests and reports need to interact with, and emerging standards, such as SMART and FHIR, for interoperating with these systems.
Plan for implementation of a GIM System
- Based on the progress and outcomes of early deliverables, we will develop a plan to drive the implementation of the final version of GIM Architecture through the second and third funding phases.
Project Investigators
Project leaders engage with and draw upon the expertise of partners within universities, research institutes and hospital and health services around Queensland.
Dr David Hansen, Australian e-Health Research Centre, CSIRO (Co-lead)
John Pearson, QIMR Berghofer Medical Research Institute (Co-lead)
Dr Dominique Gorse, Queensland Cyber Infrastructure Foundation
Associate Professor Paul Leo, Queensland University of Technology
Associate Professor Pamela Pollock, Queensland University of Technology
Dr Nic Waddell, QIMR Berghofer Medical Research Institute
Dr Amanda Spurdle, QIMR Berghofer Medical Research Institute
Professor Sunil Lakhani, Pathology Queensland & The University of Queensland
Professor Naomi Wray, The University of Queensland
Dr Hugo Leroux, Australian e-Health Research Centre, CSIRO
Dr Alejandro Metke, Australian e-Health Research Centre, CSIRO
Ms Emma Tudini, QIMR Berghofer Medical Research Institute
Round 1 – Capability-building projects
