Introducing GLIMS Genomics Clinical

Last year, CliniSys | MIPS brought its genomics LIMS to the UK, following a successful phase of development and deployment on the continent. Now, it has launched a clinical counterpart to the system. Stéphane Decap and Emma Huntridge outline the benefits of GLIMS Genomics Clinical to clinicians, laboratories, patients and their families.

Let’s start with a quick reminder: what is GLIMS Genomics?

Emma Huntridge, Genomics Business Development Director, CliniSys | MIPS: GLIMS Genomics is a laboratory information management system built to meet the requirements of genomic laboratories. It was launched in the UK in November 2020,  following a successful first deployment at Poitiers University Hospital in France.

Since then, it has gone live at 2 additional laboratories in France, a further 5 across Europe are in the preparatory stages for implementation with the first NHS Trust site in the UK due to go live in 2022. It is also attracting a lot of interest in the rest of the UK, as genomic testing is evolving and becoming an established diagnostic tool for an increasing number of patients.

Genomics laboratories need to move away from receiving orders on paper and managing samples on spreadsheets. They require an automated, streamlined approach that can increase sample throughput, standardise workflows, and improve efficiency to deliver results back to clinicians rapidly along with the information required for result interpretation.

In short, genomic laboratories need a modern, dedicated laboratory information management system, and that is what GLIMS Genomics delivers.

So, what is GLIMS Genomics Clinical?

Emma: Until now, GLIMS Genomics has been a laboratory system, used by laboratory staff. Now, we are opening it up to clinicians working with patients and families. GLIMS Genomics Clinical helps clinicians run their clinics, order tests electronically, and manage their patients’ genomic records. It also integrates with hospital electronic patient record systems, using a HL7 interface.

Why do clinicians need GLIMS Genomics Clinical?

Stéphane Decap, Genetics Product Manager, CliniSys | MIPS: Genomic testing is complex. Two or three decades ago, it was exciting just to be able to sequence genetic material, but the arrival of next generation sequencing technologies has led to an explosion of discoveries of novel mutations or variants. That presents a challenge to clinical geneticists, clinical oncologists, and other clinical specialists who need to know what tests to order and how to accurately interpret the results to maximise the benefits for their patients.

To do that, they need to consider numerous types of information, such as a patient’s family history, their medical record, their phenotype, genotype-phenotype relationships, the possibilities that personalised medicine can offer, and importantly the patient’s wishes. All this information can help a clinician to decide whether it is appropriate to consider a genomic test for their patient, and which test(s) to offer.

GLIMS Genomics Clinical is built around forms that clinicians can use to collect this information in order to come to an informed decision on the next step. If a genetic test is indicated, then GLIMS Genomics Clinical is fully embedded within the laboratory element of GLIMS Genomics to enable efficient and seamless ordering of that test, followed by receipt of the report as soon as it is issued by the laboratory.

How does GLIMS Genomics Clinical help clinicians and laboratories provide a high quality service?

Stéphane: Historically, clinical laboratory scientists have always worked very closely with their clinical colleagues in order to provide first class services for their patients. Recently in the UK, separate LIMS and electronic patient health records (EPR) have been introduced which are highly complex and offer sophisticated and capable IT solutions. However, having two different systems makes data access less efficient than having everything available in a single application.

This is where GLIMS Genomics Clinical can help elevate the quality of a service, by bringing scientists and clinicians together to enable the seamless sharing of each other’s data. GLIMS Genomics Clinical can interface with the EPR, so clinicians and scientists each still have their own systems and all the benefits they bring, with GLIMS Genomics Clinical sitting in the middle acting as a specialist extension to the EPR and shared with GLIMS Genomics.

What sort of information needs to be shared between clinicians and laboratories that GLIMS Genomics Clinical can help with?

Emma: A key requirement for determining which diagnostic tests to do and subsequently interpreting the results, is to have accurate information about a patient’s clinical phenotype. A worldwide initiative and key project of the Global Alliance for Genomics and Health is to standardise the terms used to describe clinical phenotypes, using the Human Phenotype Ontology (HPO). The HPO contains more than 13,000 standardised terms which describe clinical abnormalities, along with over 156,000 links to genetic diseases and their causative genes. The information in HPO is constantly being updated as we discover new variants or find out more about the impact of known variants on specific conditions. Thanks to the link between GLIMS Genomics Clinical and the HPO, clinicians will always have access to this latest information and will be able to readily import and record relevant HPO terms into their patients’ records in GLIMS Genomics Clinical. The laboratory will have seamless access to this data to help them manage individual tests and results.

How does GLIMS Genomics Clinical support patient management?

Emma: Many hospitals manage their appointments through their electronic patient record. So, the interface between the EPR and GLIMS Genomics Clinical will enable clinical geneticists to pull appointments into clinic lists.

A really useful feature of the system is that it enables clinicians to track the progress of a test. This is important information to feedback to patients and to help inform them when to expect their results. This facility should reduce the number of calls clinicians have to put into a laboratory to find out where tests have got to, which is inefficient use of both the clinician’s and laboratory’s time.

Clinicians can create or update a family tree to identify family members who may need counselling and testing. Or they can add flags to their clinical notes for review and follow-up. Some patients with genetic conditions may not develop symptoms of their disease for many years, so it’s important to be able to monitor their progress over time.

The HL7 interface also allows information to be sent back into the EPR; but for a sensitive condition with life-changing impacts, like Huntington disease, we would expect all the consultation and testing data to be securely maintained on the GLIMS database.

Have CliniSys | MIPS and CliniSys | MIPS worked with clinical partners to develop this solution?

Stéphane: We have worked with two partners: Poitiers University Hospital and ULB ERASME Bruxelle, which have comprehensive genomic departments that incorporate both counselling and laboratory testing. There is a very close relationship between the two, so these hospitals are well-placed to advise on what is required. The model is the same as found in Clinical Genomic centres in the UK, where clinical, laboratory and often academic groups work closely together.

One of the features of GLIMS Genomics is that it is very configurable, so we can easily configure the system for different centres in the UK.

What is the big picture: how will this support the development of personalised medicine?

Emma: Personalised, or precision medicine, involves tailoring the treatment and predicting and preventing disease for individuals, based on information about a person’s genetic makeup. This means selecting treatments that reduce the likelihood of adverse effects and are most effective for the patient, and highlighting future risks of disease so that preventative measures can be recommended, like changes to lifestyle and diet.

At the moment there are relatively few diseases that benefit from this approach, but the number is increasing as more data is generated from large scale sequencing projects like the UK 100,000 Genome Project, and as whole genome sequencing becomes routine for some diseases.

In order to identify what personalised medicines are applicable for an individual patient, the DNA sequence and all the clinical details of the patient need to be readily accessible to upload into bioinformatic programs that interpret the data. This is where GLIMS Genomics Clinical supports personalised medicine, by collating all the clinical data in a standardised way using HPO terms, and making that data accessible along with the patient’s genetic test results stored in GLIMS Genomics.

By interfacing GLIMS Genomics Clinical with a hospital’s EPR, the outcomes of genomic tests can be exported into the EPR for all healthcare professionals managing a patient to act on. As the applications of personalised medicine increase, the need for good informatic systems to convey information will become even more important to ensure clinicians can manage their patients effectively and safely. 

A second area where GLIMS Genomics Clinical can support personalised medicine is research, as all the relevant clinical and genomic data will be standardised, readily accessible and searchable for research initiatives looking at personalised medicine.