What is SNOMED CT and why are we using it?
What is SNOMED CT?
SNOMED CT is a standardised health care vocabulary and we are adopting it within the development of the UKCRC Tissue Directory. Every project involving data will have some form of data standard, whether it is formalised to the level of SNOMED CT or whether it is just an informal understanding.
Much of the work we have undertaken to date was based on the excellent work of the Confederation of Cancer Biobanks (CCB) and their data standard. The CCB data standard as drafted, however, did not define the terms to be used and this is why we have turned to SNOMED CT.
The we use SNOMED CT is linked heavily to the decision to use it within all health care environments within the UK. The hope is that by adopting SNOMED CT, and by building this into our systems (and therefore into how sample resources describe themselves), we will help sample resource be prepared for handling SNOMED CT terms from other healthcare systems.
In 2012, the then Prime Minister David Cameron announced funding for the 100,000 Genomes Project, to be organised by Genomics England (GE), a private company formed by the Department of Health in 2013. Through this project, GE works in partnership with NHS England (itself a non-departmental public body of the Department of Health) to integrate WGS into the NHS. The 100,000 Genomes Project aims to sequence 100,000 genomes from NHS patients with cancer and rare diseases. Data collected from the 100,000 Genomes Project can inform research on rare diseases, or benefit patient care potentially by streamlining the diagnostic process and tailoring care to the individual.
The project has strict inclusion criteria, to ensure data of clinical and research benefit is gathered. For over 300 rare diseases, specific criteria[1] are applied to maximise chance of recruiting individuals whose disease may have a Mendelian basis. The project also requires submission of phenotypic data using SNOMED[2] (standardised healthcare terminology used for electronic health records and coding in over fifty countries https://www.snomed.org/snomed-ct/what-is-snomed-ct) terms, and evidence of previous genetic testing (to screen out previously known mutations). A patient’s whole blood samples must pass quality assurance and quality control tests. When relevant, close relatives (usually the parents) of the patient also undergo WGS. In the case of autosomal dominant conditions all affected members may be sequenced.
As a result of historic investment and forward-planning for developments in informatics, the Salford Royal Foundation Trust is currently in an enviable position as one of the most digitally mature NHS Trusts in England.
The Trust’s EPR system was implemented in 1999 and now holds 1.3 million patient records, with millions of documents, diagnoses and diagnostic results.
This wealth of clinical data has proved to be a powerful research resource, with a number of successful studies carried out by partner organisation North West Ehealth.
Additionally, SRFT has been chosen as one of the twelve organisations to take part in the Global Digital Excellence programme. It will be funded to accelerate them towards achieving Healthcare Information Management Systems Society (HIMSS) level 6 and 7 status.
There will be a strong emphasis on standardisation of systems (Snomed CT, GS1 and FHIR) and these technologies will form the basis of a powerful interoperability platform, providing a much improved research resource.