Why genomics labs need a modern laboratory information system
Steve Abbs is working as a
We have reached an interesting point in the development of genetic medicine in the UK. It is no longer the preserve of a few, small research groups. It is on the cusp of becoming a routine part of medical practice, and an established diagnostic tool for some cohorts of patients.
To support these developments,
Moving from lab to hub requires a LIMS
How have we got to this point? Genetics was originally two disciplines. Cytogenetics looks at genetic material under a microscope in order to identify chromosomal abnormalities. While molecular genetics looks at changes at a more detailed level of the DNA sequence within genes and the genome.
As a discipline, cytogenetics made big advances in the 1960s and 1970s, while molecular genetics came along in the 1980s. The first human gene to be sequenced was the gene for cystic fibrosis, in 1989. Since then, 20,000 genes have been sequenced, while the first whole genome, for Haemophilus influenza, was sequenced in 1995, and the first human genome followed in 2003.
So, there has been rapid and impressive progress in this area. On the lab front, the developments encouraged the NHS to set up labs to provide clinical genetic services. Most of them came out of a research setting and initially were very small. But to build on the 100,000 Genomes Project that ran from 2014-18, the NHS in England decided to establish a national
This is being delivered by seven
Historically, genetic and cancer tests have generally been provided in different laboratories, as molecular and cytogenetic tests have been. In theory, the GLHs are uniting the two disciplines of cyto and molecular genetics and testing for both cancer and inherited disorders.
However, in practice, we know that the degree of integration is variable, and any process that involves changing traditional practice is lengthy and difficult. This is one area where the deployment of a modern LIMS can help; as pathology networks have proved, using a common IT system encourages common working practices [a subject I’ve blogged about in more detail here].
Replacing risky, costly paper processes
One of the principal reasons for setting up
Sending samples around the system requires a considerable amount of administration and, at the moment, this is a very paper-based process. Many orders come into a lab on paper, they are sent on to other labs with accompanying paperwork, and if they are sent to the central lab for whole genome sequencing they have to be transcribed onto the new national
This is where a modern LIMS would really come into its own, because the whole purpose of a LIMS is to keep track of orders, samples and results. Similarly, when
Integrating the
Supporting the interpretation of complex data
These arguments in favour of a LIMS will be familiar to pathologists – who would probably find it hard to imagine running a modern path lab without one! But a genetics LIMS needs some specific features.
One is that it needs to be able to report results to clinicians in a way that is useful. The output from a genetic test is rarely a simple number. There tends to be a qualitative element that explains how the result was arrived at and what it is likely to mean for the clinician, their patient and their family.
That’s because for most of the inherited conditions that you might be running a test for there is no treatment available, currently. Instead, the test is initially a diagnostic test for the index case, and after that the results are available to be used in a predictive manner. For example, they may be used to advise a family on their chances of having another severely ill child, or to let relatives know that they are at greater risk of developing a condition later in life, like Huntington Disease.
A genetics LIMS will bring all that complex information together. The genetics LIMS that
A genetics LIMS will also give direct access to expert interpretive resources;
Integrating LIMS and EPR lays the foundation for precision medicine
What is the future for
This means that, if a patient is going to benefit, the causative variant needs to be recorded accurately in their medical history to enable clinicians to readily identify whether a patient is suitable for treatment, or could be added to a patient registry used to source patients who are eligible for clinical trials.
Another positive development is that whole genome sequencing is becoming more common. Although the primary indication for receiving whole genome sequencing is likely to be a diagnostic test, the fact that the
One important reason for doing this interrogation is to identify
These can affect the risk of a patient experiencing a severe or fatal side effect from the fluoropyrimidines that are commonly used to treat a number of cancers. The genotypes at these four loci are used to indicate the starting dose for treatment with fluoropyrimidines, or whether patients are given a completely different treatment, in order to minimise the risk of an adverse effect.
Adverse reactions to drugs are a huge and expensive problem in the NHS, as in all healthcare systems, so being able to avoid them like this is a major benefit for patients and for healthcare funding bodies. But to do that, the
These examples of precision medicine mean that a final – and very important – justification for
Making the right IT investments, now
These kinds of scenario are only going to become more common as more
Having direct connectivity to all the relevant information from the genetic LIMS via the EPR would greatly facilitate these meetings. But in the future, it may be possible for clinicians to enter a patient’s symptoms into a rules-engine within an EPR, pull up a standard genetics order set, and send off for the tests they need to get an answer.
There is no doubt that precision medicine is sending ripples of excitement through the clinical community and that it holds out enormous potential for delivering more accurate treatment and prevention strategies to patients. However, it can only happen if we have good integration between the systems that are used to order tests, to run
GLIMS Genetics is designed for clinical
GLIMS Genetics is a comprehensive, modern LIMS for state of the art