Megan Fealey, NovaSeq Implementation Lead, and Joseph Halstead, Bioinformatician, from All Wales Medical Genomics Service (AWMGS) joined us to discuss the important work being done at AWMGS. AWMGS is a national specialist genetic service for individuals and families concerned about rare genetic conditions. During the interview, Megan and Joseph spoke about the recent launch of WINGS (Wales Infants’ and Children’s Genome Service), the new service that provides rapid diagnostic testing for critically ill babies and children with unexplained rare disorders. Although their work does not always get the recognition it deserves, AWMGS are clearly leading the way in diagnostics by being the first UK NHS service to offer whole-genome sequencing to critically ill children.
Please can you tell me a little about yourselves, your roles in the All Wales Medical Genomics Service and the types of challenges you face in your jobs?
Joseph Halstead: I am a bioinformatician. I write software to analyse the data that we produce in the lab. My job is quite varied. Sometimes I might be doing data analysis; other times I could be writing bioinformatics pipelines that take the raw data and translate that into variant calls and other times I may be building databases or web applications to try and make things in the lab work a little smoother, for example, automating processes. I am mainly focused on germline stuff at the moment.
Megan Fealey: I am the NovaSeq Implementation Lead, I am a lead genetic technologist registered with the AHCS. Initially, my role started once the NovaSeq was purchased, and my job was to get it up and running and get people trained on it and make sure that our research partners could access it as well as us. At the moment, my job is quite focused on general service improvements; focussing on any service that could go onto the NovaSeq. The lab is organised into cancer work and constitutional work, so I do a little of both, I do a lot of quality improvement work. In terms of the challenges that we face, genomics is a very fast-moving field, particularly diagnostic genomics. There’s a lot of momentum at the moment to drive that into routine service and to make it part of routine patient care. Our biggest challenge at the moment is keeping up with it and making sure that we are providing the best for our patients with the technology that is available to us and the technology that is available generally on the market.
Can you tell me more about the All Wales Medical Genomics Service and what it does?
Megan Fealey: AWMGS is a NHS Wales tertiary service, we are a national service providing clinical and laboratory diagnostic genomics and genetics to the whole of Wales – a population of about 3.5 million people. The service is split into the lab and the clinic. The lab is organised by cancer work and constitutional work. The clinic then houses specialist clinicians; we have consultant geneticists and genomic counsellors and trainees in both. The whole department is made up of a really diverse group of staff. We have lots of admin staff, a business team, directors, managers, scientists, technologists and bioinformaticians. Services for Welsh patients are commissioned through something called WHSSC (Welsh Health Specialised Services Committee), which is a specialist service commissioning group. Due to our expertise in certain specialist areas, laboratories from across the UK, and around the world also send us samples for testing, improving our service further. For example, we often perform testing on samples which are sent to us from countries such as Finland and Italy.
Can you tell me about how AWMGS operates and how it is different from Genomics England?
Megan Fealey: We are a little different in the way that we are set up here. I think the main difference between us and the hubs that are within NHS England and Genomics England is that we are offering a national service rather than a regional service. So AWMGS delivers services to all of the health boards across Wales rather than to one region. And as we just mentioned, we are not just the lab; we are the lab and a clinical service. I think those are the main distinctions and because we’re a national service we do offer everything; everything is under one roof rather than in specialist centres.
Joseph Halstead: We have less competing interests as we are a national service, meaning we can often move a little faster. So, for example, we can talk to the Welsh Government directly to get grants and money; we can just introduce a new service and we can actually move that much faster than a lot of other labs can which is a bonus.
How do you think more awareness could be raised about the great work you’re doing at the All Wales Medical Genomics Service?
Joseph Halstead: If we introduce new services and manage to publicise these services and the fact that we’re actually helping patients in Wales, the word will spread and people will realise that there is this great lab in Wales that is doing great work. This is what happened with WINGS. Us publishing papers and attending events will also help and hopefully everyone will start to see the cool science we are doing here that has actually helped a lot of people in Wales.
You mentioned WINGS are you able to tell us more about what WINGS is?
Joseph Halstead: We first started doing literature reviews and realised there’s a lot of studies out there describing how doing these kind of first line tests on critically ill children – whole-genome sequencing – had a high diagnostic rate and could therefore really help. Consequently, we decided that this was something that Welsh patients would really benefit from. We eventually managed to get the funding to start implementing it here and the technology to do it affordably wasn’t available until recently. So that’s why it happened now rather than a few years ago.
Megan Fealey: Yes I agree. We had an increase in our funding a few years ago following the Welsh Government announcing the Genomics for Precision Medicine Strategy in 2017. We were advised to invest in NovaSeq and extra staff and resources to allow us to expand the service a little more and introducing rapid whole-genome sequencing was a big part of that. The Precision Medicine Strategy was a real driver behind all of that investment.
What sort of ethical issues do you think could arise from this?
Megan Fealey: I think the main one that comes to the front of everybody’s mind is probably the risk of incidental findings. With any kind of large-scale genomic test, there is a risk, especially as we are running patients as trios (so the baby and the parents), that we will find something that we were not necessarily looking for that maybe doesn’t explain a patient’s phenotype. We can support the patients through consent processes, explaining to them before they sign up to the test that there is a risk that we could find something. At the moment, it’s being dealt with on a case-by-case basis, depending on what the patient needs.
What are the future plans for WINGS and All Wales Medical Genomics Service?
Joseph Halstead: I guess technical improvements, so ways that we’re going to try and boost the diagnostic yield. At the moment, we’re looking at the small variants such as SNPS and indels whilst also looking at the larger scale ones through a conventional array-based platform. In the future, we’re hoping to validate CNV calling and structural variant calling and also move to a PCR free kit which allows us to call repeat expansions. So, expanding it to analyse all the data we are getting from the NGS rather than just a small subset as we are at the moment. We are also looking at other improvements to the pipeline, for example, using prediction tools to try and find very rare splice variants to boost the diagnostic yield further. As well as those technical improvements; we’re also hoping to expand it to more patients so the underlying technology and pipeline and assay can be expanded not just to critically ill children but to any people with genetic diseases where we have a trio.
Changing the subject now completely has All Wales Medical Genomics Service’s work been affected by COVID? If so how?
Megan Fealey: I think it has. I don’t think it’s probably any different to how it has affected everyone else. We have continued to provide a service throughout the entire pandemic; we’ve just had to adjust to new ways of working. We are sort of fortunate in a way that we’re spread between a couple of locations within the hospital so that has made social distancing a little easier. The Trust has been really supportive with allowing people or enabling people to work from home a little more. I think the team here have just worked together really well just to make it work. You know everything is still getting out of the door; all of the patients are still getting their results that’s the main thing. The clinical teams have also started rolling out something called “Attend Anywhere” which enables patients to attend the clinic virtually. It’s very new and it facilitates patients being able to access their appointments from wherever they are.
You attended the UK’s largest Genomics event, The Festival of Genomics in January, how did you find it?
Megan Fealey: I really enjoyed it; it was really good! This was the first year I’ve been to it and we exhibited there. We had a nice stand and it was great. We had loads of traffic at our booth; we were right by one of the open lecture theatres where everyone was listening to the talks with their headsets on. It was a really diverse crowd. There were people there from everywhere. There were people from pharma, people from other diagnostic labs and lots of commercial representation which was good because it’s always good for us to talk to industry.
Do you think that the Festival of Genomics helped you gain more exposure?
Megan Fealey: Yes. There is an awful lot going on here and I think the Festival helped us highlight that. When we were at the Festival we had people approaching us saying that they didn’t know that there was a NHS Wales and a NHS England or they were asking us what genomic hub we were part of. It’s good to be able to explain to people ‘no actually something different is happening in Wales.’ There’s a lot happening in Wales and we’re delivering loads of services.
Were there any talks that you remember finding particularly good or interesting in January?
Megan Fealey: The keynote talks were all really interesting. The CEO of Genomics England Chris Wigley was really interesting and there was a lecture by Lamia Mestek-Boukhibar from UCL about rapid paediatric whole-genome sequencing of critically ill children, that was really good as well. To be honest the exhibition booth was so busy, we didn’t get to go to half as many of the talks we wanted to! We did go to a Google seminar that was really interesting as well. The talks were really diverse and there was something there for everybody.
The Festival is going to be a digital event in January 2021. Are you planning to attend?
Megan Fealey: Yes, I think the virtual format will be really useful, especially for people who can’t be out of the lab for a few consecutive days. If people could attend from their desks, lots of additional people will be able to attend. I think you’ll get lots of extra traffic with the digital event format. We have a booth and we’re also giving a talk in January. We’re excited about returning!
