What do you actually do!? Episode 36: John Filby, Clinical Scientist

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John is a clinical scientist at Congenica, a digital health company specialising in genomic medicine. Before that he worked in the genomics service in the NHS and completed the NHS Scientist Training Programme. He graduated from York in 2012. In this episode, John and Kate talk about the opportunities in clinical sciences, his tips for current students, and how the pandemic has changed his working day.

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Kate  0:02  

You’re listening to the What Do You Actually Do!? podcast. Each week we want to bring you an inspiring interview, a useful tip or encouraging message to help you find your place in the professional world. 

Kate  0:13  

Hello and welcome to this episode of What Do You Actually Do!?. My name is Kate Morris, and I’ll be your host today. In today’s episode we’ll be talking about working in clinical science. Today we’re joined via Skype by John Filby who is a clinical scientist with digital health company Congenica. So John, what do you actually do? 

John  0:31  

Hi Kate, thanks for having me. So I’m a clinical scientist, and the specialism I work in is molecular pathology and medical genomics, and I’ve drawn experience over the NHS and in industry now.


So you’ve just changed jobs recently, haven’t you? You were with the NHS for quite a few years, and now you’ve joined Congenica?


Yes, I did my three year training programme to train to be a scientist in the NHS. I think that’s one of the only places that you can do training programmes. And then I worked for a year and a bit in the same laboratory that I’ve trained in, which is fantastic. And then I’ve just moved into industry, because I just wanted to see what the other side of the coin was like.


Oh, interesting. So sort of in a couple of years time you’ll have done, seen the whole spectrum kind of thing.


Probably not seen the whole spectrum. Clinical science is quite a vast sort of sea of areas you can go into. So some people go into academic research, some people go into quality management. There’s lots of areas that people can go into. So I’ve seen the clinical side, but I’ve still got many other areas of clinical science still to explore.


So can you do that? If you wanted to go down more the academic route in the future? Can you explore those other routes, or do you kind of pick a lane and stay with that? 


Yes, absolutely. So if you train as a clinical scientist, your bread and butter will be diagnostic, prognostic and treatment work. But like with any career, the more experience you gain, the more you can sort of push your career in one direction or other. So I know some clinical scientists who have moved completely into academic research, some who traverse that fence between research and clinical work, some who have gone into management, some who sit on boards of hospitals. There are lots of areas you can go into, and you can very much be in control of that. Especially in the NHS they very much support you taking your career in multiple directions, and bringing your expertise from one area into other areas.


That’s really interesting. So there’s sort of getting the foundational knowledge, you can then go into, you’ve got a lot of different options to progress your career in lots of different ways.


Yeah, absolutely. It’s fantastic really, because a lot of the management staff do have a background in clinical science, and that means that they speak the same language of the staff that they’re managing, and the strategies that they’re controlling. So having that background, and having that mutual understanding of the field that you’re working on, or the field that you’re managing, or the field that you’re moving away from, if there’s still some relevancy, it’s really good.


So what are the key elements of your role then? Are you kind of in a lab, are you working with other clinicians? Are you seeing patients? What’s it sort of like?


So, this is a tough question because there are over 30 specialisms in clinical science, and they span the array of sciences. So if you’re looking at sort of… You can be a pharmaceutical clinical scientist, where you are involved in software development and drug manufacture. Or you can be involved in neurophysiology. So that might include something like critical care, or cardiac science, or gastroenterology. You can also be a life scientist. So within the life scientist cohort you’ve got people like myself, who are geneticists, you’ve got the embryologist, the biochemists, and so on and so forth. And then you’ve got engineering. So you might be a rehabilitation engineer, or reconstructive engineer. And then you also have the physicists who might be dealing with medical devices or ionizing radiation. And because it spans so many different specialisms, there’s always a specialism for a person, no matter what you’re interested in, or what you want to do. In each specialism, there will be different things on a day to day basis. So I can only really speak from the perspective of a geneticist. But essentially to say that clinical scientists essentially sits between clinical medicine, biomedical science, and academic or applied research – is sort of where their position is, and translating between those three groups of people to make sure that science is working for the benefit of patients. In my particular field, in genomics. I spent a huge amount of my workload doing diagnostic work. So in genetics, there are around 7000 to 8000 rare diseases, many of which have a genomic component. They’re often quite hard to diagnose, and patients will have some time spent, you know, decades being bounced around different clinicians to try and find the diagnosis, and never really get an answer. And they always end up coming to genetics, that kind of weird and wonderful cases end up coming to genetics, and they are quite hard to solve. And so we will sort of liaise with the clinicians and MDTs, who will get the [inaudible] information from a patient from an assessment, and then they’ll send that information to us. And we’ll get the genotypic information, which is the DNA, and then we’ll look for mutations – or we tend to use the term variants now, because mutations can be seen as a bit of an  offensive term. So we look for variants compared to a standard healthy genome, and we see if those variants could potentially be causing the disease. And we do that by looking at lots of different evidence screens, so case control data, functional data, in silico data, and so on and so forth. So we assess lots of different evidence types to paint a picture of what this variant is doing to the patient. And then we might go back to our clinicians, say we need some more information from the patient, or we need you to do an extra study here, or you need to send another sample elsewhere, or you need to get some more family members in. And then once we’ve got a diagnosis, we’ll write a report for the clinician, which will explain our findings, and that will then allow the clinician to go and get further samples from potentially at risk relatives. So people who could be a carrier for a recessive disease, or alternatively, people who could be predicted to be impacted by the disease in the future. So for example, a lady might be sent to us who has breast cancer, and we might find a mutation in the BRCA gene. That might result in cascade testing of their family members, and we might find that other family members such as daughters, or nieces, or aunts, or whoever might also carry the same variant, and they might be at an increased risk of having cancer themselves. So they might be put on some kind of prophylactic treatment programme or monitoring programme.


So are you always trying to identify a known variant? Or are you, do you sometimes come across new diseases or new variations that then kind of people understand: ‘Oh, wow, there’s this other condition we didn’t know about.


Yes – is a short answer to that question. So many of the variants that we see have never ever been seen before. So I might be the first person to see a mutation that’s not in any kind of literature or any kind of record. And as you can imagine, that’s a bit of a nightmare, because it’s often very little data. If it’s really rare, and it’s co-occurring with a disease in a family, for example, we call that segregation. That could… It points to a sort of a suspicion, but it doesn’t ever really reach an evidence threshold. So it can be quite hard when you see those kinds of variants, but that’s our job. And like I mentioned before, there’s between 7000 and 8000 rare diseases, of which a huge number of those are either caused by or, or have a genetic contribution. So oftentimes we’re expected to become an expert in a disease in the timeframe of a few hours. Sometimes I can find myself googling a new disease I’ve never heard of before, and then trying to wrap my head around it. So it’s good, it’s interesting because you see so much stuff and you get huge exposure to a huge number of diseases. But it’s also that level of responsibility can be a bit daunting sometimes, because there’s always that question in the back your mind – have I read everything about this disease to make sure I’m fully informed about this before I’ve made any decisions about what the variant is doing to the patient, and whether or not it’s actually causal.


Has the pandemic sort of changed how your day works at all? I’m assuming you can’t do all this genetic testing from your living room. So are you sort of still able to go to work as normal? Is anything different?


I am doing all the genetic analysis from home.


No way! You’ve got petri dishes on your, like, side table…


No, definitely not. I am very, very dangerous in a laboratory, you can ask some of my old supervisors. Ehm, a lot of the – we call that wet work – a lot of the laboratory work is done centralised, and it’s not, it tends not to be the remit of a clinical scientist in genetics to do the laboratory work. It’s usually a biomedical scientist who will do that kind of work. And then they generate the data, and then they send the data to us. Our job is more about clinical interpretation. So our job is translating between that biomedical science and clinical medicine, and taking that data, and then also taking the clinical information we have on the patient that the medic, or the counselor, or the nurse has got, and marrying them together, and looking for evidence [inaudible] on this diagnostic, prognostic or treatment based report. So all of that stuff can be done online, it’s all data driven. Some clinical scientists in genetics will end up going into the lab. So in previous experiences, sometimes clinical scientists go into the lab to troubleshoot, or to do procedures if there’re staff shortages, or to do particularly delicate procedures, so for example to identify fetal paths if you’ve got a fetal sample in.


There was like a few years between you graduating from your undergrad degree and doing your masters in clinical science. How did this time out after your original degree impact on your career plans and where did the interest in genomics come from?


The STP – which doesn’t stand for sticky toffee pudding, which is what a lot of people think it does – is a scientist training programme, which is the programme you need to do to get registration to practice as a clinical scientist in the UK. So when I left university I was a bit aimless, I travelled a bit. And then I came back from America and I was looking for a job. And I was really lucky, I just managed to [inaudible] got a job at a really great medical device company called Rocket Medical. And that was a fantastic experience, I really enjoyed it. But what that experience did do is introduce me to some of the clinical scientists, and specifically some of the embryologists. And I found myself becoming quite envious of their job; every time I’d go and visit them I’d just be thinking – ‘I’m at the wrong end of the sale here’, because obviously I was selling devices to them. And that was when I started looking into retraining as a clinical scientist. I always enjoyed genetics and genomics; I actually applied for both embryology and genomics as my specialisms. And then when it came to crunch time to decide, there was so much going on in genetics and genomics, that I felt that it had more appeal to me for progression in the future.


You’ve mentioned that there’s a lot of different roles that you can pursue, and different specialisms you can pursue, following this clinical science training. What personal strengths or qualities would you say you need to have to be happy and successful working in clinical science?


I think that there’s probably a preconception about scientists that we are all sort of maybe a bit nerdy, and we don’t like interacting with people. But I think certainly one of the things I’ve found in clinical science is that your ability to communicate with people, and manage yourself, and manage your time, and interact with people is really key. That’s probably true for most jobs though. Obviously you need scientific literacy, technical expertise in the area you’re going into. And I think probably a bit of a dark sense of humor as well, it probably helps.


Well yeah, I can imagine, because it must be quite harrowing sometimes, the research that you’re doing and you know the impact it’s going to have on, not necessarily just one person’s life, but their family’s life, and the implications of that. So I can imagine you do have to find a way to cope with that sort of responsibility and knowledge.


Definitely. So sometimes, I mean, I’d say the majority of the time, your case is sort of, because the patient’s not sat in front of you, they do sometimes sort of become numbers. And it’s quite easy to dissociate the case from the patient, and that’s good in a way. As a clinical scientist, obviously, you need to maintain objectivity. In that sense – it’s good. Sometimes though you do get cases which kind of pull at your heartstrings. So often when there’s children involved, and they usually are in a lot of the general cases, or when the disease, there’s no treatment for it. So you’re writing a diagnostic report, and you know that the prognosis is ‘a few years left’, sometimes brings it home a bit about the kind of work that you’re doing, and why it’s important. Because laying down this diagnostic bed is really important for developing management therapies. A lot of these diseases that we are diagnosing at the moment, they might not necessarily have a cure or a treatment, but we’re on that journey now, because we’re developing these diagnoses, that those diseases can be studied for treatment and for management. It’s a kind of a two-sided coin; it can be quite difficult sometimes, but then at the same time you know that the work that you’re doing is really important to helping people in the future. So yeah, it kind of compensates.


What do you sort of personally enjoy the most? What’s the sort of best aspect of the role for you?


I think I’m really proud of the work that I do. I’ve got friends who work in lots of different fields – corporate field, charitable field, all kinds of things. And I think that the one thing that I feel the most proud about coming back into my work is that it’s really meaningful. I’m not making money for someone, I’m not, you know, pushing numbers around or anything like that, not to say that… That’s actually incredibly important for the economy and other businesses. But my interest is in people and in health, so for me, finishing the working day and knowing that I’ve got a diagnosis for someone, that will allow them to get the right treatment, is very rewarding. It’s meaningful work.


Yeah, I can see how that would feel like that, and obviously it is. Is there anything that you feel – ‘Ugh, don’t like doing this aspect’, or where you have to sort of push yourself to do it, because it’s the least enjoyable aspect of the role.


Sometimes you get variants, which are really really difficult. And they will be… We have this five point classification scale. So definitely pathogenic, three to unknown significance, and then definitely benign. And sometimes, well quite often, you get variants that hover in this unknown significance area. And they are really challenging, because you can spend a huge amount of time trying to update it, to push them one way or the other, or to find evidence that they’re not important or important for the patient. And then sometimes you never reach a threshold, so you just feel like you’ve wasted time. And then other times, they’ll be really suspicious, but you still want to have enough evidence to push it up or down. So you sort of end up parking it in the unknown significance category, which means really nothing to a patient other than giving them anxiety really. But you might feel that in a few years time, there might be a bit more data that comes out, that will change it for the patient. So that could be frustrating. Sometimes getting to grips with a completely new disease, especially diseases that are really complex. There’s a lot of genomic phenomena that we have to sort of tackle within our interpretations. And sometimes you get a really complex disease with a really complex constellation of symptoms, and the gene doesn’t behave in the way that we expect it to, nor does the inheritance. And then there’s lots of [inaudible] you have to deal with, such as reduced penetrance, or variable expressivity, and you can spend hours trying to figure out what’s going on, and still be none the wiser after you’ve spent so long reading up about it. That can sometimes be challenging, but also is quite interesting as well, because that’s when you do most of the learning, because that’s when you’re really focused on really trying to get to the bottom of something. But if you get a few of those variants on the same day, it’s – can’t wait for 5 o’clock.


Just tell me the answer…. 




So what do you think the key challenges will be for the healthcare sector over the next few years? I know we were chatting before and saying that there’s just so much, there’s so much going on in the world right now. But for your sector, what do you think is useful to have a heads up about, and for students to be sort of trying to research and consider a bit more.


In clinical science, and in genomics specifically, there is a huge amount of data that’s coming back towards us, this huge wave of clinical data and scientific data. And that’s been developed from research laboratories and academic laboratories on a massive scale. And it’s a job for clinical scientists, like I said, to translate into, bring that science and make that science work for patients in the NHS, or in the private industries. There’s just not enough of us, there’s not enough clinical scientists, there’s not enough time in the day, to manage all of your priorities, and make sense of all that information. And prioritising, choosing which bits are the ones that you want to focus on is going to be really hard, specifically in genomics. To give an example, there’s a 100,000 Genomes Project, and that’s created a massive wave of genomic data. And the bottleneck in the system isn’t the generation of that data, that’s comparatively simple – you put onto a sequencer, and you get the data back. The challenge is the interpretation. So that’s getting enough people on the ground to look at these variants, and dig around for the data, and make sense of what these variants mean for patients. And then once we do start to make sense of that data, it’s going to be translating that data into workflows, and to restructure clinical workflows to make sure that that data can be used for the patient. So it’s not just about saying – ‘Okay, great, we’ve got your diagnosis’, it’s about making sure that the clinical end of our work reflects that, and they can say – ‘Well, what can we then do with this diagnosis? Is there a trial that we can put you on? Or is there any management for this disease? Or is there a cohort of patients, or a patient advocacy group that we can put you in contact with?’. So I think that’s the challenge that genomics faces.


So is that about just more people need to go into the sector, and have the knowledge to do it? Or is there, is it sort of…. Was it a 100,000 Genome Project, did you say? 




So is that throwing up the need for new skills? You mentioned digital quite a few times. Is there something extra that people need to be gaining now because of these new developments? Or is it kind of, we just need more people to do the normal work.


Both. We definitely need more people. But I think that there are certain areas of – I can’t speak for other areas of clinical science, but I can speak for genomics. Bioinformatics is an area where there’s a lot of skill shortage. So we need a lot of bioinformaticians, and people who can manage data really well and apply that data in a relevant way, and in a clinical context. People who have those skills will be really sought after. It will be a useful thing to have, and to be able to talk about that, and to be able to understand that kind of data. It’s not something that I was trained in, and now it’s really quite frustrating, because there’s often new concepts now coming out of bioinformatics, which are allowing us to introduce, for example, artificial intelligence machine learning to our career, and it’s something that I feel a bit excluded from, because I just don’t have that experience or that knowledge. So it’s something that other people I would say – get, definitely get to grips with that. Because computing power is massive, obviously going to be really… really assist with managing large amounts of data, which is, especially in genomics, what we’re dealing with now.


That’s really interesting how the sort of the data, it’s… Data capturing, data analysis, and AI is affecting so many different industries in loads of different ways now.


Yeah, it’s quite scary, because you just think, how long is it going to be until I’m replaced by a computer? So I’d rather be on the other side learning bioinformatics and writing that code myself. 


Yeah, and only you know the answer to the code, and you can control it. Any other sort of advice for students thinking about working in clinical sciences? Are there any sort of particular type of work experience you think it’s useful to try and get? I appreciate we’ve just been talking about some of the skills around data and interpersonal skills, because you’re working with people. Is there anything else that you sort of think, if you want to get a taster of it, or want to make yourself more employable, or to get on to one of the NHS schemes, that’d be useful to do?


I did a lot of clinical experience, work experience. I think that a lot of applicants sometimes ask maybe what’s lacking. That clinical focus of, it’s great talking about the research skills and research projects that they’ve been involved with, but obviously there are two elements to this job. There’s a science element and there’s a clinical element as well. So demonstrating that motivation, and interest, and commitment to patients and to clinical work is important. One way that you can demonstrate that is by attending, there’s lots of open days for the training programmes, the clinical science STP. For example, that is one at Leeds, they have clinical scientists and biomedical scientists from all the different specialisms come and present, and that is one way to demonstrate your commitment, and one way to kind of have a bit of a taster into what it will involve. But yeah, I guess when – if you’re really interested in career in clinical science – when you’re thinking about your research project, it might be worth thinking about if there are any relationships, for example, with the hospital or with clinical groups, that you could do a project that’s focused on that kind of work, because that would demonstrate motivation, interest and capacity for that kind of work.


Brilliant! Well, for more info about the career areas we’ve mentioned today, I’m going to add some relevant links to the episode description, and a link to the full transcript of today’s show. But I just want to say thank you so much John, that’s been really really interesting. And thank you for giving up your time away from all your research on your sofa today to do this. 


That’s brilliant! Thank you very much.


Thanks for joining us this week on What Do You Actually Do!? This episode was hosted by myself Kate Morris, edited by Stephen Furlong, and produced by both of us. If you love this podcast, spread the word and subscribe. Are you eager to get more tips? Follow University of York Careers and Placements on YouTube, Twitter, Facebook and Instagram. All useful links are in this episode description. This has been produced at the University of York Careers and Placements. For more information visit york.ac.uk/careers