SNOMED International, working with CSIRO, Australia’s national science agency and a national partner agency of the Australian Genomics Health Alliance, recently completed an Australian Genomics Cardiovascular Flagship pilot project. The project is aimed at using SNOMED CT to capture detailed patient phenotype information and providing recommendations to improve SNOMED CT.

Australian Genomics is a national initiative building evidence and developing a framework to support the implementation of genomics medicine in the Australian healthcare system.

Owned and maintained by SNOMED International, SNOMED CT is the world’s largest clinical terminology, representing a collection of more than 350,000+ clinical concepts and built upon ontological principles. SNOMED CT’s primary purpose is to support all healthcare professionals in their recording and sharing of detailed patient information within Electronic Health Records (EHRs) and across healthcare communities globally. Its ontological foundation allows SNOMED CT data to drive detailed data analytics to meet a variety of use cases from local requirements to population-based analytics.

As part of its 2020-2025 strategic plan, SNOMED International is committed to leveraging emerging technologies such as genomics to deliver value for stakeholders and drive efficiencies in the provision of patient care across all stakeholder groups.

The pilot concluded that SNOMED CT is suitable to do deep phenotyping in cardiovascular genetic disorders, since only a small number of missing concepts and modelling issues were identified, mostly in the congenital heart disease space. Recommendations have been made to include missing synonyms and concepts, and to review some of the current modelling. This pilot follows two smaller pilots that SNOMED International conducted in 2019, looking at integrating genomic medicine into care for those with inherited kidney diseases.

Funded by the Australian Genomics Health Alliance Program and SNOMED International, the project had two main goals: to assess the suitability of SNOMED CT to do deep phenotyping in this specific clinical domain, and to provide recommendations on how to improve SNOMED CT where gaps were found. 

As part of the pilot, CSIRO’s Australian e-Health Research Centre analysed data collected between April 2019 and June 2020.

"This pilot was a great opportunity to design the data collection instruments for the Cardiovascular Flagship from the ground up using standardised terminology, to ensure high-quality clinical data is collected alongside the genomic data,” said Dr Alejandro Metke, Senior Research Scientist at CSIRO’s Australian e-Health Research Centre.

 “Our analysis found the majority of the concepts that clinicians wanted to capture were already in SNOMED CT and therefore it is a suitable choice for this clinical area."

Ian Green, SNOMED International’s Customer Relations Lead, Europe, and Clinical Engagement Business Manager,  added that the pilot project has supplied a greater understanding and evidence of the use of SNOMED CT in the realm of genomics. “The work has provided insight into the future development of SNOMED CT and the requirement for detailed documentation in the form of guidance and documented exemplar use cases,” he said. “SNOMED International is committed to further developing SNOMED CT to support the important work within genomics globally, and the pilot has provided essential practical understanding to inform future developments.”

The pilot project was to design in consultation with flagship clinicians a Research Electronic Data Capture (REDCap) form that could capture the detailed clinical data required for deep phenotyping for those capturing that information – typically genetic counselors with limited time for the task. 

The form that was designed uses a pattern that allows the entry of free text descriptions whenever a SNOMED CT concept is not found. These free text descriptions were used to find gaps in SNOMED CT based on data for 276 patients. The pilot also included the development of value sets to constrain the search space of autocomplete widgets used in the forms.

One challenge was that REDCap forms are not integrated with any other systems, making pre-population of any fields impossible.

Other issues directly related to SNOMED CT that were identified and corrected as part of the project included missing synonyms, missing concepts and incorrect modelling. Issues identified in the value sets that were defined to bind some of the autocomplete fields in the REDCap form were also corrected

The pilot found that SNOMED CT’s comprehensive coverage, particularly its phenotype and procedure-related content, strongly position the terminology for these types of clinical applications.

“We are proud to have demonstrated SNOMED CT’s ability to enhance genomics terminology to support improved treatment and better outcomes for patients with genetic heart conditions,” said SNOMED International CEO Don Sweete. “Working with CSIRO, we were able to further improve the product, thus maximizing its value in future deep phenotyping initiatives.”