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8 January 2021

Why genomics labs should look for bespoke LIMS, and not fall back on the EPR

Steve Abbs


Steve Abbs is an experienced laboratory director, with more than 25 years’ experience of running NHS clinical diagnostics. He is the former director of the clinical molecular genetics laboratory at Guy’s Hospital and was director of the genetics laboratories at Cambridge University Hospitals NHS Foundation Trust until May 2020. He is currently working as a genomics consultant to CliniSys, which has just launched GLIMS Genomics in the UK.

CliniSys has brought GLIMS Genomics to the UK. In a launch webinar, experts explained how the new laboratory information system built for genomics labs can put them in charge of their IT, drive standardisation, and deliver reports that clinicians can use as they move into the exciting world of precision medicine. And Dr Fabienne Dufernez explained how these benefits are already being delivered in Poitiers University Hospital.

This summer, Steve Abbs pointed out that we have reached an interesting point in the development of genomic medicine in the UK. The experienced laboratory director, who is acting as a genomics consultant to CliniSys, blogged that genomic testing is no longer the preserve of few, small, research groups.

Instead, it is on the verge of becoming an established diagnostic tool for some cohorts of patients, and on the way towards becoming a routine part of precision medicine. In recognition of that, the NHS in England established a national Genomic Medicine Service, delivered by seven genomic laboratory hubs that will, between them, deliver the National Genomic Test Directory.

However, Abbs argued that if the GLHs are going to do what is hoped, they are going to need good IT; both to deliver an effective, standardised service, and to make sure results are accurately interpreted and linked back to patient histories.

Now, CliniSys has formally launched GLIMS Genomics in the UK; a laboratory information system built for genomics labs with these requirements in mind. It is already being successfully deployed at Poitiers University Hospital in south west France, and will soon be deployed in seven further genomics laboratories across Europe.

Why not just use the EPR?

Genomics labs do have other options, Abbs acknowledged on a launch webinar. For example, they could choose to use the electronic patient record of the trust hosting them. However, he argued that a LIMS and an EPR are fundamentally different creatures – “an EPR is based around patient encounters, while a LIMS is built around specimens” – and there are other factors to consider.

For instance, if the EPR ‘goes down’ then the laboratory will ‘go down’ with it and might not find itself at the front of the queue when it comes to getting up and running again. Or, if the lab needs a bug fix or new feature, it could find itself competing with other departments for the limited resources of the trust’s IT team.

With a “bespoke” LIMS, these issues don’t arise. Or, as Abbs put it: “You, as a lab, are in complete control of it, along with your supplier. With an EPR, your hospital is in control. Whereas, with a purpose built LIMS, you are in control.”

Built for the needs of genomics labs

Plus, there is that very important distinction that an EPR and a LIMS are built to do different things. Emma Huntridge, genomics business development director at CliniSys, told the webinar that GLIMS Genomics builds on the company’s extensive experience of working with laboratories to handle specimens in the most effective way possible.

“The CliniSys Group is based in the UK and Europe and has more than 30 years’ experience of delivering IT solutions,” she said. “We are now the largest European LIMS provider, while in the UK we predominantly work with trusts to implement pathology network solutions.

“Our new LIMS for genomics laboratories combines the strength of a mature LIMS for routine diagnostic laboratory areas with functionality to meet the special requirements of genomics.”

For example, Huntridge showed the webinar one of the graphical features of GLIMS Genomics, which enables labs to build simple or highly complex workflows, known as “approach plans”. These lay down the standard procedures for all workflows in the laboratory, including booking in samples, determining how their genetic material should be extracted, running tests, concluding this process, and reporting results.

The approach plans are visible at the bottom of the screens that laboratory technicians use at each step, so they can readily see what has been done and what should happen next. The approach plans and the screens themselves are highly configurable, so labs have flexibility about how much information is recorded throughout a procedure, and privacy controls ‘screen’ sensitive fields from users who do not need to see them.

Solving the IT puzzle at Poitiers University Hospital

Another graphical feature of GLIMS Genomics is the “pedigree tool” which enables the user to construct a family tree for a patient and to map their genetic inheritance onto it. Huntridge demonstrated how she could construct a family tree for pregnant ‘Anne Long’ showing that her parents were carriers of the cystic fibrosis gene and her brother died from a complication of the disease.

She also demonstrated how she could create a report for her clinicians that can include interpretive data from leading global databases and charts or tables from different systems.

Earlier in the webinar, Dr Fabienne Dufernez, senior cytogeneticist and quality manager at Poitiers University Hospital, was able to show a real (but, of course, anonymised) report from her hospital populated with data from GLIMS Genomics, which is just in the final stages of being deployed.

Dr Dufernez explained that all genetic testing is carried out in university hospitals in France because of its complexity. Her own hospital wanted to streamline its workflows and to standardise the approach taken to the different tests that it conducts.

“We needed a way to bring together different parts into one system,” she said, “because previously it looked like a puzzle [as] everybody used different tools to do the same work.” Now, she added, “GLIMS Genomics handles all the work, from reception, to extraction, to analysis, validation and reporting” and the hospital is seeing significant benefits as a result.

Supporting labs now, ready for the precision medicine future

One of those benefits is that the laboratory has access to dashboards that make it simple for managers to see, at a glance, how much work has been completed, and what tests are being run.

Additionally, Huntridge explained: “The system can generate a report on whatever data has been collected. So, if you have data that needs to go to NHS England/Improvement, for example, then it can be sent to them; or it can be analysed internally to drive efficiency and quality improvements.”

Still, that is hardly where the true potential of GLIMS Genomics lies. As Huntridge, who was formerly national genomics informatics lead for NHS England/Improvement pointed out, the system has been designed as “an optimised genomics LIMS that will meet current and future requirements.”

And, as such, it is: “Aligned with the strategy for greater inclusion of genomics in broader healthcare, and particularly the development of personalised patient care and precision medicine.”