Inclusion of individual's genetic variation data (e.g. specific genetic test results, SNPs, whole genome sequencing) in the EHR is becoming increasingly important for Personalised/Precision Medicine.
While it is possible to save such data using existing openEHR data structures and types, given the fact that the Bioinformatics domain has been enjoying good standardisation in terms of terminology, data, meta-data and protocols long before health informatics, an opportunity exists to more appropriately represent such data natively by possibly extending RM (or even creating a new Genomic RM!) and also by creating new family of archetypes to represent clinical genetics concepts. Thus we have decided to establish an authoritative group to further investigate and advise.
During 2018, a clinical modelling group was consisting of members from the CRS4 research institute in Sardinia, Italy; the HiGHmed project in Germany; the CINTESIS group in Porto, Portugal; the BigMed project in Norway, and the international openEHR clinical modelling programme. The objective of the group was to consolidate, enhance, review and publish a set of archetypes about genetic variants as lab results.
Initial Interest Group
Clinical modelling group
- Cecilia Mascia (CRS4)
- Paolo Uva (CRS4)
- Francesca Frexia (CRS4)
- Gideon Giacomelli (HiGHmed)
- Christina Jaeger-Schmidt (HiGHmed)
- Simon Schumacher (HiGHmed)
- Florian Kärcher (HiGHmed)
- Priscila Maranhão (CINTESIS)
- Gustavo Bacelar-Silva (CINTESIS)
- Duarte Gonçalves-Ferreira (CINTESIS)
- Ricardo Correia (CINTESIS)
- Sjur Gjerald (BigMed)
- Bjørn Næss (BigMed/DIPS)
- Anca Heyd (DIPS)
- Heather Leslie (openEHR clinical program)
- Vebjørn Arntzen (openEHR clinical program)
- John Tore Valand (openEHR clinical program)
- Silje Ljosland Bakke (openEHR clinical program)
- Liv Laugen (openEHR clinical program)
Clinical modelling history
Both the CRS4 and the CINTESIS teams had developed a set of archetypes, both based on the same premise that they should be used within a modified version of the Laboratory test result OBSERVATION archetype. These archetypes were uploaded to the international openEHR CKM Genomics project, and a comparison mindmap was created to identify the differences between them. A Slack channel was initiated to support informal communication within the group.
The Genetic variant CLUSTER archetype was sent out for its initial review round on April 26 2019.
How to participate
To make sure you get invited to reviews of the genomics archetypes, adopt the archetypes in the international openEHR Genomics project.
Overview of the proposed archetype structure
Alterovitz G, Warner J, Zhang P, Chen Y, Ullman-Cullere M, Kreda D, et al. SMART on FHIR Genomics: Facilitating standardized clinico-genomic apps. Journal of the American Medical Informatics Association. 2015 Jul 21;ocv045.
C. Mascia, P. Uva, S. Leo, G. Zanetti, OpenEHR modeling for genomics in clinical practice, Int. J. Med. Inform. (2018). doi: 10.1016/j.ijmedinf.2018.10.007
- Genetic testing information standardization in HL7 CDA and ISO13606. https://www.ncbi.nlm.nih.gov/pubmed/23920572