Standardisation in clinical genomic testing

One of the major drivers for forming genomic laboratory hubs is to ensure quality at scale and equitable testing, by encouraging greater standardisation. However, CliniSys | MIPS genomics consultant Steve Abbs argues that hubs in themselves will struggle to achieve this, and other drivers and facilitators are needed – not least a single LIMS.

Genetic medicine has developed rapidly over the past thirty years, and the NHS is making increasing use of genomic testing to inform treatment decisions for cancer patients and those living with inherited diseases. To support these developments, NHS England has created a Genomic Medicine Service, with seven genomic laboratory hubs to deliver the National Genomic Test Directory.

Steve Abbs, genomics consultant to CliniSys | MIPS, says genomics labs are aiming to adopt standardised ways of working in order to maintain quality and improve efficiency as they start to deliver the much greater volume of testing that will be required to support the development of precision medicine.

In this blog, he considers some of the factors that drive and support standardisation, based on 25 years’ experience of running genetics labs in Cambridge and London, and CliniSys | MIPS unrivalled expertise in delivering LIMS to pathology networks.

What drives standardisation in clinical genomic testing laboratories?

Accreditation

There is a requirement to achieve laboratory accreditation to ISO 15189 Standards for Medical Laboratories. However, while the standards specify the generic aspects that medical laboratories should abide by through use of a quality management system, they do not specify how different tests should be performed.

External quality assessment

Achieving satisfactory performance in external quality assessment schemes is a requirement of ISO 15189. EQA assesses a laboratory’s ability to achieve a “consensus” outcome for a given test. Again, the process does not specify how the different tests should be performed in order to achieve this “consensus” outcome.

However, as a general rule, if a lab is applying the same testing methodology as all the others, it would expect to achieve the same results; so adopting “consensus” testing methodology helps a lab to achieve the “consensus” results it needs in EQA.

Inheritance

Clinical genetics laboratories are testing for genetic variants that are inherited within families, so it is essential that relatives with the same genetic variant receive the same information about that variant. This makes it particularly important for genetics labs to standardise their testing and reporting practise.

For example, if two siblings affected with the same inherited disorder are tested in different laboratories because they live in different parts of the country, an element of standardisation is required to make sure that they both receive the same quality of testing (sensitivity and specificity) so the causative genetic variant present is actually detected in both individuals.

At the same time, an element of standardisation is required to make sure that the genetic variant found in both siblings is interpreted in a consistent manner by the two reporting laboratories, both in terms of what that variant means (is it pathogenic or benign?) and what the implications are for those individuals and their clinical management.

Without standardisation, there is the possibility of two siblings with identical genetic variants being clinically managed very differently; this would likely come to light in time, and the two laboratories would need to review their results and reach a consensus. However, damage may have been done before the difference was realised.

What facilitates standardisation?

Professional best practice guidelines

Labs and clinicians working in them have access to disease specific guidelines (for DMD, Cystic Fibrosis, Huntington disease, and so on) and generic guidelines (for reporting, prenatal testing, variant classification, etc) and both types of guideline encourage a standardised approach.

Laboratories are likely to follow best practice guidelines or BPGs because they are developed using a consensus approach by the profession. Often, there is a workshop at which key experts will gather and reach a consensus on the best approaches, after which the guidelines undergo a formal review and consultation process, giving everybody in the profession the opportunity to contribute to and express their opinions.

This whole process is overseen by the Quality Sub-Committee of the Association for Clinical Genomic Science in the UK, and by the European Molecular Quality Network at a European level. These two organizations often “join forces” to share and endorse each other’s guidelines and avoid unnecessary duplication.

Often, the BPGs will form the basis for developing the marking criteria that are used in EQAs, and therefore it is in laboratories’ interests to follow the guidelines if they hope to achieve satisfactory EQA performance.

Networks

A key aim of the formation of laboratory networks is to enable economies of scale through the consolidation of testing into larger, higher throughput, highly efficient laboratories. The process of consolidating certain tests into a single laboratory obviously brings about standardisation for those tests and for the population covered by that network.

But it does not ensure standardisation between networks. Indeed, there is no guarantee that tests that are still performed in more than one lab within a given network will be standardised. They may be, but this will require co-ordination and instructions from the network management.

As a result, networks are a facilitator rather than a driver of standardisation. Not least because the journey towards standardisation can be lengthy and stressful, since there is little real incentive for those directly involved in the testing to move in this direction.

A single laboratory information management system (LIMS)

A LIMS can help to make the daily functions of a laboratory more efficient, through bringing together all the information that is needed to conduct a test, to interpret the results, and to generate a clinical report. All the data will be stored in the LIMS, making it readily accessible to managers, who can see at a glance the status of any operation.

That means they can spot bottlenecks immediately, before they generate large backlogs, and deploy resources to avoid such problems. That helps to ensure continual high efficiency.

At the same time, the experience of the development of pathology networks in England demonstrates that the introduction of a common LIMS across all laboratories within a network can act as a real catalyst towards standardisation in those labs.

That process of planning is an ideal opportunity to assess workflows for opportunities to improve efficiency. Then, once an optimal workflow has been established, only a single approach is required within the LIMS to manage it. The result: all laboratories undertaking that procedure end up with the same process – immediate standardisation!

Time for genomics labs to invest in a LIMS

The big take-away here is that while a LIMS will help primarily in making laboratory procedures more efficient, the process of planning for and then deploying a LIMS will additionally ensure common procedures in all labs adopting that LIMS.

Indeed, while there are many drivers and facilitators for standardisation, a common LIMS can act as its catalyst, by making sure that all labs in a network adopt best practice approaches and optimal workflows.