Round 1

Capability Building Workstreams


Genomic Information Management

The information management workstream will develop an architecture for Queensland genomics information management and the standards, policies and procedures to support a common infrastructure for the management and use of genomic data.

The workstream will develop a prototype system to trial these standards for the capture and use of clinical and genomics data for clinical and research use.

Deliverables

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 demonstration projects and other Workstreams, 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:

  • Qld Genomics Data Repository will be installed at QCIF. This 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 demonstration projects can be uploaded and accessed appropriately.

Register of Queensland bioinformatics pipelines:

  • Using the AGHA pipeline registration guidelines, develop a register of bioinformatics pipelines being used by the QGHA Demonstration projects and other Qld 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 QGHA members. 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 GTI capability workstream and the 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. The artefacts will include the information models and terminology sets required for Demonstration projects.

Guidelines for germline variant sharing:

  • Undertake stakeholder engagement to understand the current practices of access to germline variant information, sharing and reporting. Develop guidelines for the sharing of germline variants within the Qld Genomics Health Alliance.

Guidelines for somatic variant sharing:

  • Undertake stakeholder engagement to understand the current practices of access to somatic variant information, sharing and reporting. Develop guidelines for the sharing of somatic variants within the Qld Genomics Health Alliance.

Trial of potential solutions for variant sharing:

  • Identify and trial potential solutions for a Variant Database for the sharing of clinical variant information across Queensland which will also contribute to any Australian solution.

Identifying data sharing requirements:

  • Identify the requirements across the Demonstration projects of data that needs to be shared and current sharing tools from initiatives such as the Global Alliance for Genomics

Usage of data sharing tools:

  • Provide data sharing tools as available to meet requirements of the Clinical Demonstration projects and capability workstreams. Report on the usage of these tools.

Usage data sharing requirements:

  • Identify the clinical systems that genomics 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 Activity 1 and Activity 2, we will develop a plan that will drive the implementation of the final version of GIM Architecture through the second and third funding phases.

Project Investigators

  • Lead - Dr David Hansen, Australian e-Health Research Centre, CSIRO

  • Lead - John Pearson, QIMR Berghofer Medical Research Institute

  • 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 & University of Queensland

  • Professor Naomi Wray, Institute for Molecular Bioscience & Queensland Brain Institute, 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

Genomic Information Management Factsheet [pdf]