Delivering a Genomics Engine: GenOCEANIC
GenOCEANIC is a sustainable platform for managing genomics activity to improve understanding of rare diseases and power precision medicine.
In 2003, a ground-breaking study known as The Human Genome Project saw the full human genome published for the first time. Since then, genomics (the field of biology focused on genes) has accelerated rapidly. Genomic sequencing has become an incredibly valuable tool in the diagnosis of rare diseases, but many rare disease patients still experience a lengthy “diagnostic odyssey”; receiving the correct rare disease diagnosis still takes an average of 5.6 years, eight clinicians (including four specialists), and three misdiagnoses.
The more we learn about the genetic causes of rare diseases, the shorter this diagnostic odyssey can become.
In 2012, the 100,000 Genomes Project was created with the intention to sequence 100,000 complete human genomes to improve understanding of rare diseases and to power precision medicine. Though the project focused primarily on England, Northern Ireland and the other Devolved Nations subsequently joined the project.
Many diseases have a genomic basis, from rare single gene disorders such as cystic fibrosis to complex, polygenic disorders such as ischaemic heart disease. Looking for these used to be a complex and incredibly time-intensive task, but it’s now possible to sequence millions of fragments of DNA simultaneously – if you have the right tools.
Genetic sequencing not only improves diagnostics but also helps in the delivery of precision medicine. Precision medicine takes into account individual variability in genes, environment, and lifestyle for each person and is used to create personalised treatment plans, breaking away from the old one-size-fits-all approach to healthcare. Coupling genomic data with a patient’s clinical information enables a better understanding of their condition and what can be done to treat it.
In 2019, after the 100,000 Genomes Project’s completion, Genomics England announced that a number of the toolsets used to run the project were to be retired; this meant that the UK Genomic Medicine Centres needed to develop new informatics approaches in order to continue the important work of genomic diagnostics.
The Belfast Health and Social Care Trust (BHSCT) team, led by Principal Investigator Dr Shane McKee, Consultant Clinical Geneticist, saw that they needed a new solution that they could use to leverage the full benefit of genome sequencing going forwards. They sought something based on open standards so that they would never again lose access to such a vital system.
Created by BHSCT in collaboration with Cambio, GenOCEANIC (Genomics Open Core Engine Accelerating Northern Ireland Care) is based on an openEHR Clinical Data Repository (CDR) to provide a platform for managing genomics activity. GenOCEANIC was created as a means of evaluating technologies to provide a sustainable platform to support Northern Ireland’s adoption of precision medicine now and in the future. Funded by the Department of Health, this collaboration aims to make genomic medicine part of mainstream clinical care in Northern Ireland.
Although a full sequence contains an incredible amount of information, it does not give a full picture of a patient’s health when looked at in isolation. This is why the solution links a patient’s genomic results with their electronic health record (EHR), linking everything from patient-reported symptoms to phenotypic data. To help implement openEHR, Cambio brought in the expertise of Future Perfect who work to ‘deliver interoperable, real-time electronic care records patient-centred solutions, using an open standards clinical repository.’ Having previously worked with a number of English genomics centres, they are a valuable addition to the team.
A lot of medicine currently relies on the individual expertise of clinicians – and genetics is no exception. Reliance on personal expertise and understanding is a risky game, especially in something as complex and critical as rare disease genomics. Part of the GenOCEANIC solution will be Cambio’s Clinical Decision Support (CDS) module. Using the combined expertise of multiple experienced geneticists, including Dr Shane McKee, CDS will automatically use the patient data in the openEHR CDR to provide guidance to the clinicians on which investigations (gene panels) are most appropriate to run.
For patients and providers
GenOCEANIC can help drive personalised care and power earlier diagnosis, which in turn leads to more treatment choice and, in some cases, improved outcomes. A greater understanding of disease risk factors helps providers move from treatment to prevention, supporting better population health and reducing the burden on the healthcare system.
Not only does whole-genome sequencing enable the creation of personalised treatment plans, but it also has the ability to drive wider clinical research. An openEHR-compliant Clinical Data Repository (CDR) such as GenOCEANIC is a hugely powerful research tool that can have vast benefits for the entire population. De-identified data can be used to power research done by other genomic medical centres and approved academic institutions across the UK and beyond in a secure governance framework that complies with ethical and legislative frameworks such as GDPR. Standardised and linked data enables the creation of longitudinal data about rare diseases, which is an absolutely crucial asset in improving our understanding.
Another key goal of GenOCEANIC is to repatriate Northern Ireland patient data that was provided to Genomics England as part of the 100,000 Genomes Project. This can help populate the openEHR Clinical Data Repository as well as ensure that people in Northern Ireland benefit from research that has been carried out based on their data.
Delivering patient-focused care has been a long-term goal of the NHS for some time, but many tools rely on funding that is tied to a project to maintain them, frequently stalling progress when these projects come to an end. Based on open standards, GenOCEANIC seeks to dodge this pitfall as it fits in with the ‘once for NI’ principle wherein providers are not having to constantly reinvent the wheel every time a new system is created. The data is retained for use and re-use in the patient’s medical record and is not constrained to a “silo”. It is planned that this will connect with Northern Ireland’s new regional digital integrated care record system encompass (Epic) to ensure that data follows the patient, and to deliver maximum benefit throughout their health and care journey and over the course of their lifetime.