The Australian Genomics Health Alliance is a national collaboration of researchers and clinicians working together to provide effective and sustainable delivery of genomic medicine in healthcare. The alliance is comprised of four programs: 1) A National Diagnostic and Research Network, 2) A National Approach to Data Federation and Analysis, 3) Evaluation, Policy and Ethics, and 4) Workforce and Education. The Phenotype Capture project is part of Program 2 and is looking specifically at standardising phenotypic data for different clinical areas.
In this implementation guide we focus on the minimum clinical data set that is being collected for the Acute Care Flagship, which provides rapid genomic testing for babies and children in intensive care units, with the aim to provide diagnostic certainty and guide acute care management.
The clinical data is currently collected using REDCap, but it is not standardised. Also, some key fields, such as the patient phenotype, are captured using free text. The form is currently being migrated to replace some of these free text fields with a REDCap FHIR Ontology plugin configured to access HPO terms, but the information model is still non-standard.
A REDCap to FHIR transformation engine, FHIRCap, has been developed as part of the Phenotype Capture group and it can be used to tranform data in REDCap into FHIR resources. However, the tool is generic and does not provide guidance around which resources to use. The main goal of this implementation guide is to specify the minimum clinical data set that needs to be captured for this clinical area.
This implementation guide is meant to support secondary use, that is, it will define the characteristics of data that will be submitted to a FHIR repository that will be used for research. This means that the data will need to be de-identified. The main source of data at the moment is REDCap, so these restrictions will be implemented in FHIRCap, but if other sources are be added in the future, such as electronic medical records, a transformation to comply with the implementation guide might be necessary.