Behind the Genes

Ellen Thomas: Genomics 101 - What is genetic or genomic testing?

In this explainer episode, we’ve asked Ellen Thomas, Interim Chief Medical Officer at Genomics England, to explain what genetic and genomic tests are, why someone might do a test, and how they are performed, in less than 10 minutes.

You can also find a series of short videos explaining some of the common terms you might encounter about genomics on our YouTube channel.

If you’ve got any questions, or have any other topics you’d like us to explain, feel free to contact us on info@genomicsengland.co.uk.

You can download the transcript or read it below.

Naimah: What is genetic or genomic testing? Today, I’m joined by Ellen Thomas, interim chief medical officer for Genomics England, who’s going to explain more. So, first of all Ellen, what is a genetic test?  

Ellen: Well, genetic tests examine a person’s genes to see if they have any changes in their DNA which might explain their symptoms. We all have DNA in most of the cells of our bodies, we inherit it from our parents and pass it on to our children. DNA provides the blueprint for our genes, and the proteins which build and run our bodies. Nearly all of our DNA is exactly the same across all of us, but around 5 million out of our 3 billion DNA letters are different, and each of these we call a genetic variant. The pattern of genetic variants that we all carry helps to make us who we are, and genetic testing is designed to examine some of these variants to help inform our healthcare.  

Naimah: So, why are they sometimes called genetic tests and sometimes called genomic tests?  

Ellen: Well, the words genetic and genomic are often used in exactly the same way, but broadly, genetic tests are usually used to look at just one or a small number of a patient’s genes, while a genomic test will look at hundreds or even thousands of genes at the same time. In general, it’s fine to use either.  

Naimah: If you want to hear more about the difference between genetics and genomics, you can find another explainer episode with Rich Scott on our website, which goes into more detail.  

Okay, so coming back to you, Ellen, what are the reasons we might do a genomic test?  

Ellen: Some rare health conditions are caused by DNA variants in our genes, conditions such as cystic fibrosis, Huntington’s disease or sickle cell disease. In these 3 conditions, there is usually just one gene that is responsible, the same gene for all patients. That means that you can often find the DNA variant which has caused a patient’s symptoms by doing a test which looks just at that gene, or even sometimes just at a part of the gene. But for other genetic conditions, a variant could be found in any of dozens or even hundreds of genes, which could cause the same condition or a group of conditions, and examples of that include familial forms of epilepsy or developmental disorders in children.  

For these conditions, to find an answer you often need to do a broader genomic test, looking at many genes at the same time, and also sometimes in between the genes. Finding the variant in a patient’s DNA which has caused the condition is useful, because it helps understand how the condition is passing down in the family, and whether it could affect anyone else in the family in the future. It is also increasingly used to work out which treatment an individual patient might respond to best.  

Genomic tests are also used to help diagnose and treat cancer. A tumour develops and spreads because new variants in the DNA build up inside the tumour, which are not present in the patient’s healthy cells. By testing the DNA of the tumour, you can sometimes understand more about why it happened and what treatment might be most effective.  

Naimah: So, can you tell me a bit about what sort of questions you can and can’t address with genomic testing, and how has this changed over time?  

Ellen: Well, at the most basic level, if a condition is not caused by DNA variants, then a genomic test will not provide any useful information. So, doctors use genomic tests when they suspect that a patient might have an explanation of their symptoms in their genes, but we don’t always find an answer. Sometimes patients with a genomic cause and those with a different cause may have very similar symptoms.  

We do constantly learn more about the ways in which genetic variants cause disease through research. Patients may have a gene variant causing their condition, but it’s so rare that it hasn’t yet been discovered, or so complex that it can’t be seen in the test analysis, so the test won’t identify the cause. Sometimes new understanding through research can then find the answer, which can be many years after the patient first developed symptoms.  

Naimah: And how are these tests performed? For example, are they a blood sample?  

Ellen: Yes, for most rare conditions, the tests use a blood sample. In cancers, a sample of the tumour needs to be tested after it’s removed by surgery or biopsy. The blood or the tumour is then processed to extract the DNA, and then there’s a range of different tests which can be used to read the DNA sequence. Expert scientists in the NHS then review variants in the DNA to make sense of the results and provide information to clinicians and patients about what it means for their diagnosis or treatment.  

Naimah: And why are there lots of different genomic tests which can be used in healthcare?  

Ellen: There are different types of genetic variants, and there are tests available that are specialised for these different types of genetic variant. Some tests look at a single gene, some tests look at many genes, often known as a panel of genes. Some also compare genomic information from a patient and their parents to understand which DNA variants are likely to be important. The tests will be selected to match what is understood about the patient’s symptoms and their likely cause, and to provide the best chance of finding information which will be useful for their care.  

Naimah: That was Ellen Thomas explaining genetic and genomic testing. If you’d like to hear more explainer episodes like this, you can find them on our website at www.genomicsengland.co.uk. Thank you for listening. 

Shaun Pye, Sarah Crawford, Sarah Wynn and Naimah Callachand: Shining a light on rare conditions

Joey was diagnosed with DYRK1A syndrome at the age of 13, through the 100,000 Genomes Project. DYRK1A syndrome is a rare chromosomal disorder, caused by changes in the DYRK1A gene which causes a degree of developmental delay or learning difficulty.

In today's episode, Naimah Callachand, Head of Product Engagement and Growth at Genomics England, speaks to Joey's parents, Shaun Pye and Sarah Crawford, and Sarah Wynn, CEO of Unique, as they discuss Joey's story and how her diagnosis enabled them to connect with other parents of children with similar conditions through the charity Unique. Shaun and Sarah also discuss their role in writing the BBC television comedy drama series 'There She Goes' and how this has helped to shine a light on the rare condition community.

Unique provides support, information and networking to families affected by rare chromosome and gene disorders. For more information and support visit Unique's website.

You can read more about Joey's story on Genomics England's website.

 

"Although we’re a group supporting families and patients, actually a big part of what we’re doing is around translating those complicated genetics terms, and trying to explain them to families, so they can understand the testing they’ve been offered, the results of testing, and really what the benefits and limitations of testing are...just knowing why it’s happened, being able to connect with others, being able to meet others, but actually often it doesn’t necessarily change treatment."

 

You can download the transcript or read it below.

Naimah: Welcome to the G Word.

[Music]

Sarah Crawford: But I would also say it’s okay to grieve the child that you didn’t have that you thought you were going to have. I just think that’s so important. And I think for me, the most difficult thing in the early couple of years was feeling like I couldn’t do that because nobody appreciated that I’d actually lost anything.

[Music]

Naimah: My name is Naimah Callachand and I’m head of product engagement and growth at Genomics England. On today’s episode, I’m joined by Shaun Pye and Sarah Crawford, who are parents of Joey, who was diagnosed with DYRK1A syndrome at the age of 13, and Sarah Wynn, CEO of Unique, a charity which provides support, information and networking to families affected by rare chromosome and gene disorders. Today, Shaun and Sarah are going to share Joey’s story, and discuss how their role in writing the BBC comedy drama There She Goes has helped to raise awareness of people with rare conditions in mainstream culture. If you enjoy today’s episode, we’d love your support. Please like, share and rate us on wherever you listen to your podcasts.

So first of all, Shaun and Sarah, I wonder if you could tell us a bit about Joey and what she’s like.

Shaun Pye: Yes. So, the medical stuff is that she’s got DYRK1A syndrome, which was diagnosed a few years ago, which means that she’s extremely learning disabled, nonverbal.

Sarah Crawford: Yeah, autistic traits.

Shaun Pye: Eating disorder, very challenging behaviour. She can be quite violent. She can be quite unpredictable. Doubly incontinent, let’s throw that in. She’s 17 but she obviously has a sort of childlike persona, I would say, you know. She sort of likes things that toddlers like, like toys and that sort of thing. But that’s the medical thing. What’s she like, she’s a vast mixture of different things. She can be infuriating, she can be obsessive, but she can be adorable. Occasionally, she can be very loving, especially to her mum.

Sarah Crawford: She’s very strong willed, you know. Once she knows she wants something, it’s impossible to shift her, isn’t it? So, she’s got a lot of self-determination [laughter].

Shaun Pye: So, her obsession at the minute, or it’s fading slightly, which is quite funny, is that she’s become obsessed by – there’s a toy called a Whoozit that she loves, but she became obsessed by the idea of – she was typing buggy baby Whoozit into her iPad, so that’s how she communicates. She’s got quite good literacy skills.

Sarah Crawford: Yeah.

Shaun Pye: And we figured out eventually that what she wanted was she wanted her mum to take her to the park to find a buggy with a baby in it that also had a Whoozit in it that she could steal, and when Sarah explained to her at some length that it was not yours, she would say, “It’s not yours,” that drove her insane with excitement, at the idea that she could steal another child’s toy. So, it’s a good example of her because it’s funny, and, you know, it is funny, and she’s so cheeky about it and she flaps her hands, she’s very hand flappy, and she sort of giggles and she gets really excited, but, you know, the 2,000 time she asked to do that, and we have to walk to Mortlake Green near our house, and to the point where – again, it’s funny when it happens, but you get to the green and she doesn’t even look for the buggies anymore. So, that’s an example.

But she’s a lot of different things, you know, and I suppose the thing that is dawning on us at the minute is that she’s 17, she’s going to be 18 very soon, and, you know, the list of presents that she gets on her birthday is always the same, ‘cos she’s autistic. So, at Christmas, she always gets the same presents. But the idea that, for her 18th birthday, we’re going to have to buy her children’s toys and – you know –

Sarah Crawford: Toddlers’ toys.

Shaun Pye: Toddlers’ toys and everything, it’s sort of hitting home, but that’s something – a bridge we’re going to cross on July 27th [laughter].

Naimah: Yeah, I can imagine that’s quite a difficult bridge to cross, but it sounds like, you know, Joey’s got lots of personality and you have lots of, you know, lovely times with her as well. I wanted to go back a bit before the diagnosis. So, you mentioned Joey’s been diagnosed with DYRK1A syndrome, but can you tell me what it was like before you both – and a bit about your journey, and when you suspected maybe something might be wrong and what you did first of all.

Sarah Crawford: I mean, there were hints that things might be wrong before she was born. The measurements were such that they thought there might be intrauterine growth restriction, because basically my belly wasn’t as big as it should be for dates, and that was obviously the working hypothesis. And they actually did a scan, an ultrasound quite late on in the pregnancy, which I picked up when I looked at the report was showing a small head measurement. And I remember querying it with the consultant, who said it was probably measurement artefact and nothing to worry about. But after she was born, she wouldn’t latch on, you know. We had to switch to bottle feeding straight away. She was small, and the head measurement actually was small. You know, you could see on the very early one, they must have taken it kind of three times to try and get it bigger, probably angling the tape measure, and it had been crossed out and rewritten. That was the pattern. So, her head simply did not grow in those early days in the way that you would expect.

So, I was wildly anxious about this right from the get-go, and very adamant very early on that I thought that, you know, she was learning disabled. And to be fair, you know, the GP took that seriously. You know, at the six-week check-up, things weren’t quite how they should be. We got in the system very early on, saw a paediatrician really quite early. So, I was, you know, fairly convinced very early. I mean, I’m a clinical psychologist, I’ve got training in learning disability, a bit more clued into these sorts of things I guess than the general public on the whole, and I think the bigger challenge for us wasn’t so much the attitude of, you know, the healthcare system. It was more trying to debate this with family, who were very much of the, “There’s nothing wrong with her,” kind of mantra.

Shaun Pye: She wasn’t our first child, so we had experience – and all children are different, but because we had that comparison – all children are different. Obviously, there’s not a set thing. But we had a benchmark in our own minds and hearts sort of, to know that she was missing things that he’d hit, and something wasn’t right. And the parental thing – basically, we’re talking about grandparents – it was sort of – there were two approaches that they took, one of which was to tell us nothing was wrong, because they couldn’t bear the idea that me and Sarah were in pain or unhappy. It was just out of pure love. It’s just a natural human reaction to say, “I’m sure everything’s going to be alright.” They were just trying to be supportive because that’s, you know, what they thought they should say.

And then the other approach from other members of the family was again from just a supportive, loving aspect, but it was a sort of, “They just need a bit of tough love, pull your socks up. Lots of children are different and you just need to learn ways of dealing with it.” And the way I describe it nowadays is that they’d mistaken Joey for someone on the far end of a spectrum of abilities or behaviours, whereas she wasn’t really on that spectrum at all. She was on a different spectrum [laughter]. She wasn’t a difficult child. She wasn’t a naughty child, was she?

Sarah Crawford: No, no, she was a child whose brain hadn’t developed.

Shaun Pye: She was a very, very different child. So, all of that has gone on over the years. And genetics wise, we had early genetics testing. Kingston Hospital took quite a lot of interest early on, and then they sort of didn’t take any interest [laughter].

Sarah Crawford: No, it’s more that they ran out of technology, so they couldn’t pinpoint the diagnosis with the technology they had. I mean, the geneticist was excellent, wasn’t he? We really loved him.

Shaun Pye: Yeah, Sarah’s going to like this, ‘cos I’m about to say I love geneticists ‘cos they’re – on the spectrum of doctors, I love them, ‘cos one of the guys we saw just looked at it like a puzzle and he was sort of excited to solve it, and he really wanted to work out – and in a way, you could have walked away from that thinking, “We wanted the bedside manner and we wanted the, “Oh, that’s terrible,”” whereas he really was just a sort of – he was terribly excited about the whole thing, and he wanted to solve a Sudoku, basically, yeah. But me and Sarah walked away from that just thrilled, ‘cos we’re the same [laughter]. There’s not a Sudoku or a crossword that we don’t love finishing. So, we walked away thinking, “These are exactly the people we want involved.”

And so when I say they gave up, that’s not fair. They just ran out of – you know, they can’t spend increasing amounts of NHS money. So, they tried – you know, different genes were mentioned.

Sarah Crawford: Yeah, they tested for a whole load. I mean, his attitude was right from the get-go, you know, based on the history, everything else that had been ruled out, dysmorphic features, those kinds of things – I don’t know if that’s the terminology they would use now – but that this was going to be a chromosomal disorder, and that they would do the tests that were available, but that it was possible that those wouldn’t pinpoint in, but that the technology was changing all the time, and that if they didn’t find it now, they would in the future. And that was how it played out.

Shaun Pye: There was one meeting that I did get a little bit – having said that, I got slightly – but you didn’t – about one of the geneticists, who sat there and said, “We’ll do this test and this test, and if they come back with any interesting things then we can get really excited.” And he used the word excited, and I was sort of a bit, “I’m not that excited by all of this.” But actually I calmed down quite quickly, and in hindsight I really wanted someone to get excited by the idea of working out – but then a long time went past. I wouldn’t say that we lost interest in finding out what her genetic condition was, we didn’t. It’s just it’s something that became less and less – it wasn’t like a holy grail for us. But then the opportunity came along with 100,000 Genomes, and we signed up immediately, and then they did that and it was a few years before that went through the system.

And then out of the blue really, we were asked to go and see a geneticist, and we had no idea that this is what it was. I honestly thought it was just a routine sort of, “We’ve got a few more theories,” or something, and she just said, “We’ve found out what it is.” And that moment is – well, we tried to describe it in the TV programme, but it’s quite hard to describe what goes through your mind when, after 13 and a half years, somebody suddenly says, “Oh, by the way, that thing that happened with your daughter, we’ve worked out what it is.”

[Music]

Naimah: I wonder if you could talk a bit about what the diagnosis meant for you both.

Shaun Pye: It was sort of different for both of us, wasn’t it? I was a bit more excited, Sarah was a bit more…

Sarah Crawford: My attitude early on was that, while the label would be nice to have, it wouldn’t make any material difference to anything to do – I mean, it was never going to be precise enough that it would give a map out of what we’d expect for her as an individual, and it wasn’t going to change the fact that there was a severe learning disability. It wasn’t going to change the challenges that we would have over things like schooling, therapies, you know, what the future holds for her. It is useful to have it, but it doesn’t really change the day to day.

Shaun Pye: But what it did change, and this is where Unique is so brilliant and important, is that it puts you in touch with people who have children with a similar condition. That’s the main takeaway from getting the diagnosis. ‘Cos Unique is great, and obviously in a broad sense it’s great, but to actually meet people and be in touch with people whose children have DRYK1A – so, I’ve met quite a lot of them now and I’ve met quite a few of the children. There was a meetup last year, and you just walk in and you just go, “Oh my god, oh my god” [laughter]. Literally girls running around, just the same as Joey, just the same, and the different ages as well. So, there were some in their twenties and there were some just starting out on their – who’d only, you know, very young, been diagnosed. But just to see your life just in front of you [laughter] is very useful. So, that’s the basic takeaway, I would say, from the diagnosis.

Naimah: Yeah. It must have been really nice to be connected with those other parents and to kind of share experiences as well.

Shaun Pye: It was, it was. And this applies to most – well, every family from Unique that I’ve ever encountered actually. Nearly all of the DYRK1A – ‘cos it’s spread around the world as well, so, you know, there’s slight cultural differences, but just to see that they are all of a very similar mindset is comforting, ‘cos it sort of makes you think, “Actually, we haven’t been doing this wrong.” It’s a sense of humour thing. It’s an attitude to the world. It’s the way they see their children. It’s the way they see the outside world. I’m not saying we’re all uniform, of course we’re not, but you can see it. When you talk to them, you can just see that they have the same sensibilities as you about the whole thing, and it’s sort of quite reassuring really that, you know, we’re not outliers.

Naimah: I just wanted to go back to, you know, when you were talking about the bit before the diagnosis, and I wanted to come to you, Sarah, to ask, you know, Shaun and Sarah both described their journey with a lot of uncertainty, but I wondered, could you tell me a bit more about the role Unique plays in this part of the journey for parents?

Sarah Wynn: Yes. Well, actually I think Shaun’s done such a good job of summing up why Unique exists already, thank you, Shaun. But I think really what we’re aiming to do is to try to alleviate that sense of helplessness and being overwhelmed, and isolation that often families feel when they have a child that’s got additional needs. I think our experience with our Unique community is very similar to that that Shaun and Sarah have described. So, many parents know that there is something – that their child isn’t developing as they would expect. And we hear lots and lots of stories of families going to healthcare professionals and actually not being taken seriously, or like Shaun and Sarah were saying, you know, everybody saying, “No, they’re just a bit delayed, it will all be fine.” And so I think that’s a common experience of many families, that the parents inherently understand and know their child better than everyone else, and it’s very common that families have to wait quite a long time to get to that point where they get to a diagnosis.

And often I think the uncertainty continues after you get that diagnosis, because as Shaun and Sarah said, you get a diagnosis of a rare condition and actually there just isn’t that much information available. So at Unique, we try to help in various ways. One is by connecting families with other families, and that might be other families who’ve got the same condition, but it might also be families who are just going through the same experiences as you are, so you’ve got someone to share your journey with. And the other thing we try to do is to help families understand the kinds of genetic testing they’ve been offered, and a bit about the results of genetic testing. Because of course genetics is something that lots of people haven’t thought about since school, and actually quite often hoped they never had to think about again.

Although we’re a group supporting families and patients, actually a big part of what we’re doing is around translating those complicated genetics terms, and trying to explain them to families, so they can understand the testing they’ve been offered, the results of testing, and really what the benefits and limitations of testing are. Sarah said, often you get a result and a diagnosis from genetic testing, but that doesn’t give you a magic treatment that’s going to cure your child. It’s really important, for all the reasons Shaun and Sarah have already said, just knowing why it’s happened, being able to connect with others, being able to meet others, but actually often it doesn’t necessarily change treatment.

Shaun Pye: I guess one thing I would say, just ‘cos it was important to us, and it’s de novo in our case, but that’s comforting to know. We always suspected it was and we were always told it was, but to have that confirmed means – I mean, we’re not going to have anymore children, but it’s more to do with our son and whether there’s something inherent that could be passed on.

Sarah Wynn: Yeah, it gives you information that you can use for either your own family planning or other family members.

Naimah: You mentioned that Joey received her diagnosis via the 100,000 Genomes Project. How did that come about?

Sarah Crawford: I think it was offered, as in the 100,000 Genomes Project was the only way that that was potentially available at the time, that this was effectively a project that was going on to try to answer those unanswerable questions with the technology they had at the time. I mean, it was years between us enrolling in it and getting the answer.

Shaun Pye: It’s so important to me in hindsight the diagnosis, just for all the reasons that we’ve been discussing, but without doing down the role of genetics, there was a period of Joey’s life when we thought we’d run out of road with the testing, and it wasn’t something that really I was obsessed with or occupied my mind massively. It wasn’t like me and Sarah were saying, “We must get back to Kingston Hospital. We must get back to the geneticists. We must write to the NHS. We must insist that they do this.” We’d sort of resigned ourselves to the fact that they’d done all that they could and they hadn’t found it, and that’s what it was going to be. Having said that, when 100,000 came along, we obviously jumped at the chance. We had no misgivings about it whatsoever, ‘cos I think we’d resigned ourselves to the fact that we might never know.

Sarah Crawford: I think I thought that at some point we would, because the technology, the methodology that they’re using obviously was changing all the time, but it didn’t preoccupy me because I didn’t think it would make a massive amount of difference. It probably made a bit more difference than I thought it would, for the reasons that Shaun and Sarah have said, about, you know, particularly the sort of connecting with others, you know, just realising how useful it is to be able to hear about the similarities and differences that other families experience.

Shaun Pye: I think a key point for us, and I’m sure this is true for the vast majority of Unique families, that we never thought that there was a cure. We never ever, ever, ever, ever, ever thought there was. And nobody in our family did. It’s not like anyone was saying, “Oh, with this treatment or that treatment…” Once you know that it’s DYRK1A, there’s obviously things that you can tailor towards her in terms of therapy, you know, there are things that you can do, but we were never under the illusion that if we found out what it was, she could go on and some sort of drug would suddenly make it better.

Sarah Crawford: Yeah, we’re not queuing up for experimental stem cell treatment [laughter] in weird and wonderful parts of the world, you know. What’s happened has happened. Her brain didn’t develop properly in utero and beyond. There is no changing that.

Naimah: But I guess with diagnosis, and like you said, if you can get some relief from some of those other symptoms that are caused by it, then, you know, that’s some sort of relief for Joey and a bit of help.

Shaun Pye: Yeah, there are absolutely concrete things that you can learn that will – Joey will never be better, but talking to the other families – eating disorder, that’s one of them. Constipation, that’s another thing. But hearing their experiences, hearing the roads they’ve gone down, finding out that there’s, you know, a unit somewhere in the country that specialises in this, that or the other, these are concrete things. It’s not just about emotional support. It’s absolutely about practical support. But there’s no magic wand, but there are things that, you know, we’ve learnt that can help.

Naimah: And then Sarah, to come to you then, do you find that families find it difficult to seek out help from Unique once they’ve received a diagnosis, or are they likely to come quite quickly to you? What’s your experience?

Sarah Wynn: It’s a really good question, and of course we don’t know the ones that never find their way to us. But what we try to do at Unique is to be sort of warm and friendly and welcoming, so that it’s not too daunting. ‘Cos I think all of these things are an extra thing for parents who are already busy and dealing with lots of medical appointments and therapies, so we try to make it as easy as possible to join us. Many, many families do join us at that point of diagnosis, because that’s when they’re looking for more information. Actually, you can get in touch with Unique and if you decided you didn’t want to join us, that’s also fine. So, we have a helpline that you can call. And for some people, joining a support group just isn’t their cup of tea, and that’s really fine. Other people find us a little bit later on, you know, perhaps when their child starts school or, you know, there’s sorts of crunch points where people are looking for extra information or support that they tend to find their way to us.

But one of the things we try really hard to do is to get the word out that organisations like ours exist, so that we can be contacted if people want to. And lots of our families come, like Shaun and Sarah, after the geneticist has told them that we’re there. So, that’s a really important thing for us is that everybody knows we’re there. You can join us and involve yourself as much or as little as you want. So, as we’ve already talked about, one of the things we do is put families in touch with each other, but not all families want that. So, you know, you can join and remain no contact, and stay quietly under the radar if you’d like to. But those people often want their child to be sort of counted in the system, you know. When you say how x number of people have DYRK1A, they want their child to be in that number even if they don’t want to go to the meetups, or they’re not quite ready to do that. And of course people change. So, some people join us and think, “We’re just going to quietly sit here for a bit,” and then change their mind a bit further down the line.

I think, although There She Goes, and what Sarah and Shaun have said about their journey is really similar to many people’s journeys, of course everyone is a bit different, and so people want different things at different times. And what we try to do at Unique is to be those things for whenever families need us.

Naimah: Yeah, that must be really reassuring for families, knowing that they can come to you whenever they feel ready to more than anything.

Shaun Pye: Just to jump in quickly as a sort of user of Unique, from the sort of different perspective from Sarah, that is literally how the service presents. That’s not an ideal that they aspire to. That’s what it’s like. So, I can confirm that – I mean, people think different things, and within our DYRK1A group, for example, you know, there’s a broad range of people who think various things, but the one thing about it and Unique is it’s very well self-policed, so people know how to behave. You won’t be subjected to ill informed sort of medical nonsense. It’s very well self-policed, but it’s also very, very occasionally – I’m speaking for the DYRK1A group – the example they gave me was around covid and vaccinations, and, you know, people have very strong views about it, and these forums aren’t the places to be having that sort of discussion.

Sarah Wynn: I think that’s exactly it. One of the ways families can connect with each other is via an online forum, and generally we take quite a light touch in moderating it, because the forum is for the families, and we want them to feel ownership and that it’s their safe space. But yeah, ever so occasionally, it needs just a tiny little bit of input. But yeah, I think Shaun’s right, everybody’s there for the same reason, and that’s to kind of share experiences, sometimes vent about the world, ask questions, and actually celebrate things that other people might not see as such a celebration. You know, lots of our families, their children might be late to walk, and it’s a place where you can celebrate all of those sorts of things as well.

[Music]

Naimah: So, next I want to move on to talk about 'There She Goes'. So, you mentioned it briefly there, Sarah. So, this is the BBC Two comedy drama, for which Shaun and Sarah were both writers on, and it really draws upon your real-life experiences of caring for Joey. And although the series is posed as a gentle comedy, it also displays really frank and honest emotions experienced by Emily and Simon, who are the parents of Rosie in the programme. Let’s listen to the poignant clip from the series by Jessica Hynes, who plays the mother, Emily.

Emily: You know, when you’re younger and daydream about what family you might have – so, I was the girl who thought Claire always got away with murder. Or when we found out Ben was going to be a boy, if it would be like you and Soph, you know, dorky older brother, biffy outdoor sister who everyone liked, you know. But in none of my dreams was there a girl who… Yeah, who was like Rosie. Yeah… No one ever dreams of a child like Rosie… You know, and I… I love Rosie, but why do I have to be defined by her? You know, for a long time, I felt cheated by her, because she wasn’t the girl that I dreamt about, you know. She’d taken her place. And then as she got older and I accepted her more, you know, what if it wasn’t that she’d taken her place, what if she just pushed in the queue and then if we started again, then if I had, you know, a normal girl, and then I wouldn’t have to… I wouldn’t have to resent Rosie anymore because I’d have the family that I’d always wanted, and I’d have – I’d have Rosie as well, yeah. [Sobbing] Just after all these years, haven’t I earnt that?

[Music]

Naimah: Off the back of that, I wondered if you could both tell me a bit more about what it meant for you being able to write for the programme and, you know, what it’s meant in the aftermath as well.

Shaun Pye: So, it came about - I basically am a TV writer and Sarah’s a psychologist, but it came about primarily because I was trying to think of something to write about and we realised that Joey’s just an incredible character. Those sort of children aren’t featured on mainstream television really at all, I would say. And so we thought it would be an interesting thing to do. But from that sort of slightly selfish motive, I wrote an episode, and Sarah read it and said, “You’re not doing that, it’s not honest enough” [laughter]. So, Sarah came on board as a writer with me and we cowrote it. The whole thing’s cowritten. And it’s the most important piece of work I’ve ever done, I ever will do, and it became far more than just a TV programme.

The first series went out and we had a screening, and Unique came to the screening, along with some of the other charities, and we were so terrified of what the response would be. And the fact that the response was what it was, which was overwhelmingly, “It’s like looking at our own lives on television,” it was recognition. It was nothing to do with whether the stupid jokes were funny or anything [laughter]. It was purely whether – if anyone had turned round and said, “This has got nothing to do with what it’s like bringing up our child,” or our brother or sister or whatever, that would have been quite bad for us, but it wasn’t, and that’s been the overwhelming response since. It’s, “Thank you for putting our life on television, ‘cos it’s not normally on television.”

So, it became that, and so the second series was even more about that, and then the special that we did was almost totally aimed at, we need to tell these stories because there are so many people in this country who this story isn’t being told for them. And it so happened that Joey hit puberty and had some very, very, very problematic behaviours, sort of self-harming behaviours, it happened quite close to her being diagnosed, so we thought this story is just written for us. Joey’s written it for us. So, we just sort of wrote down what happened. That was sort of what it was. And then obviously the response to that was very good. So yeah, and we wanted to feature Unique ‘cos that was such an important part of what we’d been through.

So yeah, it went from me wanting to further my career to that having nothing to do with it, and me wanting to [laughter] tell the story of children with rare chromosomal disorders and learning disability, and that’s what it became.

Naimah: I’m sure it must have been almost quite cathartic, I imagine, in a way, to share your story that way, and also, you know, give you a real sense of accomplishment to be able to kind of share your story on that platform. Like you said, like it’s never been done before in such a way, and to get that kind of response from other families, it must have really just helped you both in your journey as well, I can imagine.

Shaun Pye: For me, because it’s what I do for a living, it still retained a certain sense of my job. And, you know, emotionally, obviously, entirely committed to it. All the bits that make you sort of cry, or all the bits that are like, oh my god, Sarah wrote – I wrote all the stupid bits that David Tennant says [laughter]. So, I think it was more cathartic for you. You really had to dig deep into some quite unpleasant memories [laughter].

Sarah Crawford: Yeah, it wasn’t always the most comfortable process, you know. We’d sort of agree – I mean, particularly in the earlier process, we’d sort of have a little think about what we wanted to talk about, and then I’d go off and like kind of delve deep into memory, and just type a stream of consciousness, and I’d be sitting there sobbing [laughter], you know, with tears rolling down my face, you know, just reliving these really awful experiences. But yeah, I think the end process ended up being cathartic, and a lot of that was stuff that I would never have imagined sharing with anybody [laughter], let alone, you know, this huge audience of people, which – yeah, strange how things evolve.

Shaun Pye: Yeah, I think possibly if we hadn’t done this then we might have just tried to not think about these things and not bring them back, and I think we probably wouldn’t have spoken to each other – we may have, I don’t know. I don’t know what would have happened. But I don’t think these things would have come out into the open. And very interestingly, another side aspect of it in the catharsis way is the effect the programme had on the wider family. There were certain members of the family who were really shaken by that programme, really shaken, because they had a set view. Even as Joey got older, they had a set view of the history and what had happened, and they were really shaken by the idea that their – out of love again, there’s nothing bad here, but they were really shaken by the idea that their actions had a detrimental effect on us when Joey was born.

You know, there were people saying, “Well, I didn’t say that there was nothing wrong with her,” and, “I didn’t say this or that,” but actually when you see it presented in the programme then there was a lot of re-evaluation that went on, in a good way, in a positive way and it’s all good.

Sarah Crawford: I think there’s something about seeing it, you know, and especially given, you know, we were so fortunate with the cast because they’re so good at portraying it. And I think there’s a power in seeing things played out rather than just hearing about them in the abstract.

Naimah: Yeah, definitely. I definitely had moments of crying and laughing, and a range of emotions while I was watching it, so yeah, definitely very powerful. And I guess it’s really great for other families going through similar circumstances, for their families to see what’s happening and, you know, there’s a lot that can be learned from the programme as well. So, you know, it’s, yeah, really a powerful piece that you put together.

Sarah Wynn: I would really like to echo that. I think Shaun and Sarah have said before that they didn’t do it to represent everybody’s experience, but actually that is exactly what it has provided. I would say that huge numbers of people are really grateful that that portrayal is there, so that they can be seen and heard and understood so brilliantly. But it has provided other families with the opportunity to show it to their friends and family, so that they understand their life as well. And so I think it’s had a hugely positive reaction from our Unique community. And I think it’s not always an easy watch, I think lots of families would say it’s challenging to see it up close in front of you, but I think it’s really cathartic and has been just incredibly powerful at showing these sorts of stories, which, as you said, just don’t get shown very often.

And I think particularly when we think that rare conditions, although they’re individually rare, if you put all of the rare chromosome conditions together, they’re not actually that rare, so these are stories that are going on up and down the country and all over the world.

Shaun Pye: Just to follow up on something Sarah said earlier on about, you can take as much or little as you like from Unique, it’s the same with the show. I’ve had lots of people get in touch with me or talk to me in person and say, “I’m really sorry, I tried to watch ‘There She Goes’ and I can’t watch it,” and I have to say, “Don’t apologise, you have nothing to apologise for. You take what you need from it. If you can’t watch it then don’t watch it. If you can watch it then do. There is literally no right or wrong way of doing this. There really isn’t.” But having said that, the nicest comment – well, one of the nicest comments I’ve seen was on the DYRK1A forum. It was someone who casually referred to it as “our show,” as in the DYRK1A community, it belongs to them, and that – yeah, a little tear, a little tear went down my face [laughter].

Naimah: Yeah, that must have been a lovely thing for you to read. That’s really nice.

Sarah Wynn: Also from the Unique and general people who have rare conditions community, it’s been so fantastic for raising awareness about genetic testing and rare conditions in general, and, you know, there just isn’t – because these stories don’t get talked about or shown about very often, it’s been really great from that point of view as well.

Naimah: And hopefully this will be the catalyst for similar programmes and, you know, more things in the mainstream media as well. And you did touch on it briefly there, Sarah, about, you know, what the programme’s meant for Unique, you know, and the Unique community being very supportive, but have more people reached out to Unique since the programme?

Sarah Wynn: I think the main takeaway is that being heard, “Our family’s being heard and represented,” which I think is really important. But yes, we’ve got lots and lots of new families that have come to us through watching There She Goes. And it was really fortuitous that when the special aired last spring/summer, it was the evening before our awareness day, which I think was a complete coincidence but actually turned out to be really great timing. So, we got lots and lots of new families get in touch with us, many of whom then went on to join us. But actually what it also did was get lots of members who’d been members for a long time but perhaps had been a bit quiet, or hadn’t been in touch, so it sort of also reinvigorated that engagement from other members who we might not have heard about for ages, and who might have got older children and had been in touch at the point when they were diagnosed, and then hadn’t been.

So, it has just been such a brilliant, brilliant experience to have Unique as part of it. And I think that’s really important. At Unique, we have members from 120 different countries, and the reason is that when you have these rare conditions, you’re really unlikely to find someone in the same town as you, possibly not even the same country with some rare conditions, and so the idea that you can connect with people all over the world I think is really important, particularly in rare conditions.

Naimah: Yeah, that’s great, and hopefully, you know, it just continues to increase support with Unique and, you know, families know they can still come to you as a resource and as that continues. So, I just wanted to kind of wrap up here and come to the final question. So, you know, your story highlights a lot of challenges, a lot of difficulties, a lot of ups and downs, but I just wondered, Shaun and Sarah, if you had any advice for other parents going through similar circumstances.

Shaun Pye: Yeah, I think one of the things is what I just said, which is I would tell people there’s no right or wrong way of doing this. I would say, from my experience, don’t be hard on yourself, and you’re going to think that you wish it never happened to you and that’s fine. That is absolutely fine. That’s normal. We’ve all thought that. It doesn’t make you a bad parent. It makes you a normal human being. I would say to get in touch with Unique. I shied away a little bit from help and charities, ‘cos I think it was a sort of pride. I think I had a preconception that it would be glass half full, put on a happy smile, best foot forward, blitz spirit sort of. We have encountered it a little bit over the years, not very much, but we’ve encountered a little bit of, you know, “As long as you love them, that’s the most important thing,” and, you know, which is fine and that is an okay perspective to have, but there are times when it’s just not what you want to hear. I want to be allowed to feel the feelings that I’m having without feeling guilty.

So, I would encourage people to seek support from Unique or from wherever. But, you know, generally, the thing I’ve learnt about people is that the vast, vast majority of people are nice and kind and understanding about this. Not everyone, but most people are good people and, you know, people should remember that, I think.

Sarah Crawford: Yeah. I mean, the first thing I was going to say in terms of advice to other people was something Shaun said already, which is the don’t be harsh on yourself, because, you know, you’re allowed to find it difficult. But I would also say it’s okay to grieve the child that you didn’t have that you thought you were going to have. I just think that’s so important. And I think for me, the most difficult thing in the early couple of years was feeling like I couldn’t do that because nobody appreciated that I’d actually lost anything. The world seems to use the word difference a lot at the minute, you know, “These children are different, they’re differently abled,” but actually it is disability [laughter], and it is more difficult, you know.

There are rewards, there are positives, but, you know, she’s 17 and a half now, our daughter. When our son was 17 and a half, you know, the challenges were different, but they were also nowhere near as big [laughter], and I don’t think that should get lost. Because I think parents need to feel it’s okay to get the help they need and to push for the help they need, and not feel like they’ve just got to kind of put on a brave face and, you know, as Shaun was saying, the attitude sometimes of, “Well, you’ve just got to get on with it.” Because while you do, actually, you know, you do need help to do that. It is difficult.

Shaun Pye: The only other thing I’d say is, just ‘cos Sarah just mentioned it and it gets forgotten, is the siblings thing. The families with Unique will have all manner of different configurations. I can only speak from our own experience, but Joey has an elder brother, Frank, who is, well, in my opinion, the best human being in the world [laughter], and I’m sure in his mother’s opinion as well, but my experience, never forget about the toll it takes on siblings. ‘Cos Frank is a very, very loving brother. Only last night, Joey was typing, “Frank book.” ‘Cos he’s gone to university, she likes looking at pictures of him in the photo albums. She likes looking at pictures of old toys mainly.

Sarah Crawford: Yeah, yeah, she likes looking at her as a baby and the toys they had.

Shaun Pye: Yeah, but it’s not really advice, it’s just, you know, there’s a danger that Joey could have taken over our entire family life, and especially Sarah made sure that didn’t happen and that, you know, we were a unit and he was – but, you know, it is possible that it can swallow up your entire life.

[Music]

Naimah: Okay, so we’ll wrap the interview up there. Thank you so much to our guests, Shaun Pye, Sarah Crawford and Sarah Wynn for joining us today as we discussed Shaun and Sarah’s journey to Joey’s diagnosis, and how charities like Unique can support families of those living with rare conditions. If you’d like to hear more like this, please subscribe to the G Word on your favourite podcast app. Thank you for listening. I’ve been your host and producer, Naimah Callachand, and this podcast was edited by Bill Griffin at Ventoux Digital.

Clare Kennedy: Genomics 101 - What is the difference between DNA and RNA?

In this explainer episode, we’ve asked Clare Kennedy, Clinical Bioinformatician at Genomics England, to explain what the difference is between DNA and RNA, in less than 10 minutes.

You can also find a series of short videos explaining some of the common terms you might encounter about genomics on our YouTube channel.

If you’ve got any questions, or have any other topics you’d like us to explain, feel free to contact us on info@genomicsengland.co.uk.

Want to find out more? Check out the blog 'Genomics 101: RNA vs DNA, what's the difference?'

You can download the transcript or read it below.

Naimah: What is the difference between DNA and RNA? Today, I’m joined by Clare Kennedy, who’s a Clinical Bioinformatician here at Genomics England, who’s going to tell us more.

So first of all, Clare, what is DNA?

Clare: So, DNA stands for deoxyribonucleic acid, and although this is quite a mouthful, DNA is essentially an instruction manual for our body on how to function, and a copy of this manual is stored within almost every cell of the body in a structure called the nucleus. So, our DNA essentially comprises all of the genetic information we inherit from our parents, and this information is contained within two long strands of code, and we inherit one strand of code from our mother and one from our father, and both strands combine and they form a twisted ladder like structure that we call the DNA double helix. So, each strand is made up of small units called nucleotides, and these nucleotides, they differ based on their chemical composition. They can either contain a molecule of adenine, guanine, cytosine or thiamine, and this is why we often see our DNA sequence represented by the letters A, G, C or T. And in total, our entire DNA sequence consists of three billion of these nucleotides.

So, as this DNA instruction manual is quite long, it needs to be broken up into smaller sections that the body can read, and that’s where genes come in. So, a gene is a segment of the DNA and it contains a particular set of instructions, normally on how to make a protein. So, proteins are essential for life and they’re involved in almost every process within our body, and that is why we have around 20,000 protein coding genes in our DNA.

Naimah: So then can you tell me, what is RNA and how does this differ from DNA?

Clare: So, like DNA, RNA, which stands for ribonucleic acid, is an incredibly important molecule that encodes genetic information, and it’s found in all cells of the body. So, RNA consists of only a single strand of nucleotide units, and just like DNA, RNA can be represented by four letters that reflect the chemical composition of each nucleotide. These four letters do differ slightly though, because RNA contains uracil instead of thiamine, so you can distinguish a DNA sequence from an RNA sequence by the presence of the letter U and the absence of the letter T. So, while we think of the DNA as the instruction manual for the body that contains all of our genetic code, RNA is the reader of this instruction manual, and it helps the cell to carry out these instructions, so the proteins can be made.

Naimah: So, can you tell me a bit more about this protein production, and how are DNA and RNA involved?

Clare: So, protein production all starts in the nucleus with the DNA. So, if we want to make protein, we must first read the portion of the DNA or the gene that contains the instructions to make this protein. So, because DNA is so long, it’s really tightly packed into our nucleus, and the

region we’re interested in might not be accessible, so we first need to open this region out. So, molecules and enzymes help us open this region of the DNA, and once the gene is accessible, they start to read it, and they start to transcribe the instructions that are encoded within the gene into a type of RNA called messenger RNA. So, as the name suggests, messenger RNA is the communicator of the instructions contained within our DNA, and this process is called transcription.

So, the messenger RNA then leaves the nucleus and enters the main body of our cell, which is called the cytoplasm, and messenger RNA is transported to the ribosome. Now, the ribosome is a piece of machinery which will build the protein, and it’ll use the instructions that are encoded by the messenger RNA. But we need materials to build the protein, and that’s where a type of RNA called transfer RNA comes in. So, transfer RNA is instructed to hunt down the building blocks or the amino acids that we need to build the protein, and it brings these back to the ribosome. And then we have a third type of RNA that gets involved called ribosomal RNA. So, ribosomal RNA helps the ribosome assemble these amino acids into proteins in a process known as translation.

So, it really is a group effort between the messenger RNA, the transfer RNA and the ribosomal RNA. And once the protein has been assembled, it might go through some more processing steps, and it’s eventually exported by the cell to where it’s needed.

Naimah: Okay, so apart from their roles, are there other key differences between DNA and RNA?

Clare: So, as we touched on earlier, the main difference between DNA and RNA is in their structure. So, we have, DNA is in a double stranded helical structure, whereas RNA is single stranded. And because of DNA having this double standard helical structure, it’s actually much more stable than RNA, which is more susceptible to degradation by enzymes and other molecules. As DNA contains our genetic code, it’s much longer than RNA, and you can only find DNA in the nucleus of the cell as it’s much too large to leave the nucleus, whereas you can see RNA in the nucleus and in the cytoplasm. RNA and DNA also differ in the type of code or the lettering they use, so they both use the A, G and C letters in their code, while DNA’s is the T lettering and RNA’s is the U lettering, and this is due to the differences in the chemical compositions of the nucleotides that make up DNA and RNA.

And the nucleotides in DNA also contain different types of sugars from the nucleotides used in RNAs. So, in DNAs, you would have a deoxyribose sugar, whereas an RNA uses a ribose sugar. That’s where we get the deoxyribonucleic acid and the ribonucleic acid.

Naimah: So Clare, we’ve talked about the difference between DNA and RNA, but why are these important in clinical care?

Clare: So, we can use DNA and RNA to diagnose illness and to also develop therapies against these illnesses.

Naimah: Can you give me some examples of where DNA and RNA are used for diagnosing conditions?

Clare: Absolutely, so an excellent example is in the diagnosis of cancer. So, the majority of cancers are caused by mistakes in the genetic information encoded within our DNA, and result in the production of malformed proteins. So, we can normally look at the DNA and we can identify certain genetic mutations that cause the cancer. So, examples are breast cancer, ovarian cancers, lung cancers, essentially all types of cancers that you can think of will have genetic mutations associated with them. But then there are cases where no problem with the DNA can be identified, but then when we look at the RNA, we do see a problem. So, a particular example was recently shown in breast and ovarian cancer, where a gene that encodes for a protein called BRCA1 was not shown to have any genetic mutations, however when we looked at the RNA produced from that gene, we could see there are problems with that RNA and essentially identify a genetic cause for that cancer.

Naimah: Could you also give me any examples of where RNA or DNA are being used in therapies?

Clare: So, absolutely. So, most of us will have heard of RNA vaccines in recent times, such as those that were generated against COVID-19. And essentially how these vaccines work is they deliver small messenger RNA from the virus into the body. The body can then make a protein from this messenger RNA, and the immune system recognises this as an invader and destroys it. So, this low level of viral exposure essentially trains your immune system to respond in the event of an infection, and really the success of the MRNA vaccines against covid has really paved the way for the use of MRNA vaccines against cancer. So, it’s believed that we can stimulate an immune response that would destroy a cancer cell using MRNA vaccines, and there are now some studies that are looking at developing messenger RNA vaccines against cervical cancer in particular.

So, DNA therapies can actually target genetic mutations and correct them to prevent illness, and one such example is a gene editing treatment that has been developed for the treatment of blood disorders, such as sickle cell anaemia.

Naimah: That was Clare Kennedy explaining the difference between DNA and RNA. If you’d like to hear more explainer episodes like this, you can find them on our website at www.genomicsengland.co.uk. Thank you for listening.

Lisa Beaton, Dr Celine Lewis, Jana Gurasashvili and Louise Fish: Hope for those with "no primary findings"

There are a range of outcomes from a genomic test. The results might provide a diagnosis, there may be a variant of uncertain significance, where a genetic variant is likely the cause of the condition, or there might be no particular gene found that is linked to the phenotype or clinical condition - also known as a "no primary finding" result. In this episode, our guests explore the impact of a "no primary finding" result on families, discussing the common experiences and expectations of parents and patients who undergo that genetic testing, and the role that hope plays in the experiences of children with rare and undiagnosed conditions.

Today's host, Lisa Beaton, member of the Participant Panel at Genomics England is joined by Dr Celine Lewis, Principal Research Fellow in Genomics at UCL, Great Ormond Street Institute of Child Health, Jana Gurasashvili, a Genetic Counsellor, and Louise Fish, CEO of Genetic Alliance.

 

"I think it’s also really important to add that hope isn’t necessarily lost when you don’t get a diagnostic result. And in a sense, what can be really helpful is for genetic counsellors to reframe that hope...sort of giving it a different context."

 

• For more information on the SWAN UK project which supports families with children that have been through genetic testing but have not found a result following that genetic testing, visit SWAN's website.
• Read more about the study by Jana Gurasashvili and Dr Celine Lewis: The disequilibrium of hope: a grounded theory analysis of parents' experiences of receiving a "no primary finding" result from genome sequencing.

 

You can download the transcript or read it below.

 

Lisa: Hello, welcome to the G Word. 

Lisa: I think in the back of my mind, subconsciously, I had hoped that when we eventually got a diagnosis, it would – I don’t know, bells and whistles, balloons going off, fireworks, etc. And then the experience of a letter thumping on the doormat, and I recognised the postmark quite quickly, and it was at that moment I suddenly thought, “Oh gosh, I haven’t buried all these feelings of hope.” Because I opened that letter with quite trembly hands, and then this diagnosis or lack of diagnosis, you know, nothing had been found, and it was a bit… I don’t know if it’s been described as like a nail in the coffin experience, because I really hadn’t realised I was still clinging to this hope all that time, and then again it was, you know, another, “No, nothing’s there.

Lisa: My name is Lisa Beaton and I’m a member of the participant panel at Genomics England. On today’s episode, I’m joined by Dr Celine Lewis, the principal research fellow in Genomics at UCL, Great Ormond Street Institute of Child Health, Jana Gurasashvili, a genetic counsellor, and Louise Fish, the CEO of Genetic Alliance. Today we’ll be discussing the impact on parents with children with rare conditions, who received a no primary findings result after diagnostic whole genome sequencing. If you enjoy today’s episode, we’d love your support. Please like, share and rate us on wherever you listen to your podcasts.

Can I ask all of us here present to introduce themselves, please?

Celine: Hi everyone, I’m Celine, I’m a behavioural scientist in genomics at UCL Institute of Child Health, and I currently hold an NAHR advanced fellowship to look at the implementation of WGS, or whole genome sequencing, in the NHS.

Jana: I’m Jana Gurasashvili and I’m a genetic counsellor at Northwest Thames Regional Genetic Service, and prior to that I was at Great Ormond Street, involved with consenting families to the 100,000 Genomes Project, and I also have an ongoing interest in the lived experience of patients and parents of genetic counselling and rare disease.

Louise: Hi, I’m Louise Fish, I’m the chief executive of Genetic Alliance UK, and we are an alliance of around 230 charities and support groups that work with patients and families who have particular rare conditions. We also run a really longstanding project called SWAN UK, and SWAN stands for syndromes without a name. And the SWAN UK project supports families with children that have been through genetic testing but have not found a result following that genetic testing. So, it’s clear they have a genetic condition, but science hasn’t quite advanced far enough yet to tell us what that means and what that will mean for their child, and what that will mean for their family over the coming years.

Lisa: And I personally can attest to the wonderful support that SWAN UK can offer because, as the parent of a still undiagnosed child, I have been involved myself with SWAN UK since my daughter was around the age of three to four years old. It’s brilliant being a part of my big SWAN UK family. We first realised that there were some – I suppose something wrong with our daughter when she was around two weeks of age, but it wasn’t something I could specifically put my finger on. I couldn’t at that point have taken her to a doctor and said, “I don’t know what’s wrong but there’s something wrong.” I just knew in my heart of hearts, probably because I have three elder children, that there were issues, and things weren’t developing as they should. She cried a lot, she screamed a lot, she never seemed to be comfortable in any position when you held her, when she was asleep, when she was upright. It didn’t seem to matter what you did, she was just a rigid, stuck child, for want of a better word. And all my mum senses were screaming, but it completely sounded ridiculous to take her to a doctor saying, “She feels wrong.”

And I think that’s quite a SWAN UK experience, from chatting to other families with similar situations. The parents just know that there’s something not right, but it can be very isolating not to be able to identify kind of where that starts and what it is. In our case, it wasn’t until our daughter was nine weeks old that things became much more obvious, that there were developmental concerns physically and medically, and at that point we went from my sort of mutterings that there was something wrong but I wasn’t sure what it was, to a sudden hospital admission with quite a shocking turn of events. From something that had started out quite normally, as a routine visit to the baby clinic, to suddenly being seen by a troop of different paediatricians, and doctors coming in and out constantly, asking different questions, and sending us off all over the building for different tests and x-rays and imaging. And being given a partial diagnosis that our daughter had a condition called arthrogryposis, but it was clear that there was much more going on than that, and we would need referring to many more different fields. And that day really our diagnostic odyssey, for want of a better word, began.

So actually, in terms of that diagnostic odyssey, many parents of children with rare undiagnosed conditions experience this, and when we agree to have genetic testing, we feel that we are going to get these answers straight away, and that every appointment that you go along to is going to be the one that brings you the answers. But certainly in our experience kind of 15 years on, that’s not been the story at all. Celine, can I ask you to explain what the words no primary findings actually mean when a parent receives that regarding their child?

Celine: So, there’s a range of different possible outcomes from a genomic test. So, the results might provide a diagnosis to that patient and family, or other situations, there might be a variant of uncertain significance, so we don’t necessarily know if the gene that we found, a genetic variant is the likely cause of the condition, or we might find no particular gene at all that we think is linked to the child’s phenotype or clinical condition. So, that’s what we mean really when we’re sort of saying no primary finding.

Lisa: Louise, would you be kind enough to explain what you think the impact of no primary findings means to families like my own, parents who don’t have a genetic likelihood cause, just a gene thrown up to diagnose their child?

Louise: Yeah, I think it’s a huge challenge for families, and you’ll obviously know that from your own experience. People go to have genetic testing hoping it will give them some answers, first and foremost, just to kind of understand, you know, what condition their child has and what the likely impact that’s going to be on their child and on the child’s life, and on the family’s wider life. And I think one of the things that we really ask genetic counsellors and geneticists to do is help people understand before the genetic testing takes place that there may be nothing found from it, so that that kind of expectation is built in. Because people hope that they will get a diagnosis that will give them answers about what the impact of the condition will be on their lives. In a best-case scenario, access to a particular treatment that might be a huge help for their child, but at the very least, access to a range of services and support for their child. So, that kind of diagnosis is often seen by families as the key to unlocking a range of services and support that will help them and their families at what is the beginning of a lifelong journey.

And I think when families get no diagnosis, there’s a real concern on behalf of families, a, that they don’t understand how their child’s going to be affected by the condition. What we’re really careful to say to families is, “Just ‘cos you don’t have a diagnosis with a name, your child is still the same person they were before. They still have exactly the same bundle of needs as they had before, and you will still need to work with the NHS and with wider services to make sure that they can access speech and language therapy, and physiotherapy, and all of the services that they are going to need and you are going to need to help them live their lives to the full.” But I think that moment of not getting a diagnosis is when people feel I think real – the uncertainty continues, and uncertainty, we know, is a really hard thing to live with, and the lack of clarity about which services you’ll be able to access. So, I think psychologically it’s a massive impact on the family not to have the answers that they were looking for, or the key to the services that they were hoping would be there.

Lisa: Thank you, Louise, yeah, I would definitely agree with that. We had a no primary findings result in I think it was 2019. It was a really bittersweet moment because my daughter’s list of various different conditions kind of – by this point, named parts of difficulties for her spans over sort of two pages of A4, and yet on the letter back from the genomics service, it just says that, you know, nothing causative has been found. And so part of you is left wondering, well, how can there be all these different conditions or difficulties, and yet there’s still nothing there? And I know personally, I had comments when she was much younger, every time a test came back, where people would say things like, “Oh well, that’s great news,” and to some extent it was great news that something hadn’t been found, but also if that hadn’t been found, what was still out there? And that fear of kind of the unknown was extremely difficult.

And also paradoxically, there was a sense of some very well meaning people saying things like, “Oh well, if they haven’t found anything then there can’t be too much wrong.” But yeah, I have a child who is tube fed and on multiple different medications, and cared for basically for 24 hours a day, so that doesn’t really fit in with the picture of there not being very much wrong from a personal perspective. And I think it can make you as a parent/carer feel perhaps there’s a tendency to downplay that there is an issue and that perhaps, you know, you’re making it up, for want of a better word, and that sense of isolation around that can certainly be problematic. Celine, if I can come to you, that diagnostic odyssey, what are the common experiences and expectations of parents and patients who undergo that genetic testing from your perspective?

Celine: Well, I think sort of parents go into genetics testing for a whole range of reasons really, and Louise has already alluded to many of these. Ones that I’ve come across in my own work include wanting to know why their child has a particular health problem, so that that child can access the most suitable treatments or therapies, or even access clinical trials. Even relief from guilt for many parents, a validation that the parents hadn’t done anything wrong during their pregnancy to cause the child’s condition, and that’s hugely important really, to try and get that relief from guilt. Also to know whether future children might be affected by the same condition, and then more social reasons really, for example, making contact with other parents through support groups, or access to social and educational support.

And I think there’s also a drive from many parents to feel that they’re doing everything absolutely possible for their child. I mean, particularly with something like the 100,000 Genomes Project, it was really a sort of first of its kind project, where patients were on a significant scale able to access this new whole genome sequencing technology. So, many of the parents taking part in that project felt like pioneers, and there was really a lot of expectations around whole genome sequencing in delivering a diagnosis for those parents who’d previously not been able to get hold of one.

Lisa: Yes, I strongly can resonate with a number of the points you made there, particularly the feelings of guilt. I must have asked myself a thousand times whether, you know, something I did do, something I didn’t do, something I thought of, something I hadn’t thought of [laughter], all those questions that swirl around, particularly in the small hours of the night when you feel particularly alone. And yes, I can completely relate to that. And also although SWAN UK is primarily for children and parent/carers whose children don’t have a diagnosis, actually a number of the parent/carers on there will have children with diagnoses that are so very rare that absolutely, you know, very, very little is known. They might be the only parent – the diagnosis, for want of a better word, they may have received may just be a series of kind of numbers and genetic dot-dashes, forgive my layman’s terms there, but it may not actually help them any further along in terms of feeling that they know anything further or the direction of, you know, where that will lead their children, and that can feel very, very isolating, I’m sure, probably just as much for those of us who don’t have that diagnosis.

Louise: Yeah, just to add to that, I think that’s absolutely right, Lisa, and I just want to give a shoutout – at SWAN UK, we tend to support families who don’t have a diagnosis at all, or, as you say, a small number of families who do but have been part of the SWAN UK family for so long that we’re very happy to keep them because of the support they’re finding from other parents. We work really closely with another of our members, Unique, who are a charity that support parents in exactly the situation you’ve talked about, where people have finally got a diagnosis and it’s that kind of relief of having a name, but it’s a super long name, and you find out you’re one of only three families in the world with that diagnosis. And so although there’s a real I think comfort for people, perhaps if you have a five year old and you’re meeting a family who have a 13 year old and a family of a 19 year old, then you start to see a little bit about how your child might develop, but there’s not enough kids affected that you can be really certain about that.

So, it gives you a little bit more information, but not the kind of wealth of information you were hoping for about how your child’s going to be impacted by a particular condition, and what the future might hold for you and for them. So, SWAN UK and Unique very much work alongside each other to kind of support families on whichever part of that journey they’re on, because there’s still a huge amount of uncertainty for families with those super rare conditions, as you say.

Lisa: Definitely, and I’m sure you’ll be familiar, Louise, yourself if you get time to go on the online communities and seeing the question that pops up quite regularly when somebody has received a diagnosis of, “Can we still remain part of the SWAN UK family?” And they very much use that word, family, because I think they do feel that, although all our children are different, there are children with physical, medical, cognitive, a combination of all the above syndromes, conditions, etc, they feel that kind of embrace of all being in a collective club of rare and unique and undiagnosed, and that’s very comforting to the members.

Louise: Absolutely, yeah, I think that sense of belonging and being able to reach out to other families that you’ve been on that journey with for many, many years. You know, many of our families join when their children are like one or two, and they’re still with us when, you know, their children are 26, 27 [laughter], and that sense of having that community and that family and that belonging is really, really important to people, I agree. It makes a big difference psychologically to be part of a community you can reach out to and ask the questions that perhaps you can’t ask to other people.

Lisa: Celine, can I ask you how many patients for the 100,000 Genome Project have had a no primary findings diagnosis back?

Celine: Well, back in 2021, there was a paper published in the New England Journal of Medicine, which reported that, in the initial pilot for the 100K, a diagnosis was found for around 25 percent of rare disease participants, and other studies looking at the diagnostic yield of whole genome sequencing have put the number anywhere between 25 percent to 55 percent, depending on the clinical indication. And we know that even already from the 100,000 Genomes Project, this pioneering project has led to more than 6,000 diagnoses being identified, and that number will obviously continue to go up as they explore the data and gather new insights. However, that still obviously leaves a significant number that won’t get a result from whole genome sequencing, as many as half of those rare disease patients, and that was really the basis of the study that Jana and I worked on.

So, we felt that there had been so much research really looking at the experience of parents who do receive a genetic diagnosis, and that a lot of attention rightfully does focus on the amazing successes of the 100,000 Genomes Project and genomic medicine more broadly, but actually that there is a considerable number of patients and parents and families who don’t get a result, and we felt that it was important that we also focus on those parents and patients, and try and understand their experiences.

Lisa: Yes, you can feel, if your child, for example, is under multiple different care specialists, that it can be quite hard, when you’ve just got this list of different names of things that are wrong, that you feel very much still out on the limb and forgotten about. But it’s clear that, from your work, you’re identifying that and pointing that back to the specialists, the consultants, to remind them that these parents and these children are still finding their ways through. Can I ask you, Jana, the study that was conducted, what would you say the main things from that study told us? Can you describe some of the emotions experienced by the parents, and what challenges that they have faced along that receiving the no primary findings diagnosis?

Jana: Yes. So, many participants really felt very strong disappointment and sadness on receiving that no result, and for many, it kind of reflected the feelings they had had when they first realised they had a child and there was no diagnosis for their condition. And as Celine said, this was such a new technology that people had invested a lot of hope in, and so many felt that it had been their last chance of finding a reason for their child’s condition, and that they’d come to the end of the road with that no primary finding result. And, well, one person described it as another door shut. And people talked about the actual toll taken, the emotional and physical toll, and one person described feeling low for several weeks following the result. And some talked about the timing of the result. Somebody got it as a letter just before Christmas, and so their whole family holiday that they’d prepared was marred by getting that news just before Christmas.

And it often seemed to leave parents feeling isolated and unable to contribute to normal parental roles, such as going to parent groups, etc, because they felt that other mothers particularly - as it’s mothers we were speaking to, other mothers, their experience of motherhood was so incredibly different to their own, and they felt a lack of support. And one parent actually talked about wanting to lock everyone in the house just to escape the feeling of judgement and pity from outside the front door. And some parents talked about finding it hard when other people would post on support groups that they had got results from the 100,000 Genomes Project, which was very difficult. And some talked about hope as finding it hard to keep hopeful but needing to keep hopeful. So, they talked of hanging onto a little bit of hope, as though that was quite an intense thing, which I think, Celine, you’ll agree, that made us able to kind of identify that hope was really part of a coping mechanism for this whole process of going through this diagnostic odyssey.

Celine: Yeah, people sort of talked about not wanting to let go of hope and the importance of hope, and that without hope, there was no sense of wanting to continue this journey of trying to find a diagnosis, and that it was still very important to people. And I think that parents did understand that, even though a no primary findings result now, that doesn’t necessarily mean that they won’t get a diagnosis at some point in the future. So, there’s obviously the opportunity to do future reanalysis of the genome, particularly as we understand more about the function of different genes, and as new genes are added to many of the panels that we’re using in whole genome sequencing. So, I don’t think not finding a result means that there is no hope in these circumstances, but for many parents, they did talk about hope being too painful, and not wanting to be let down again, and really preferred to focus on the here and the now rather than necessarily focus on the future.

Lisa: Yes, I can only speak from my own experience here, but I think I primed myself to actually forget about going on the 100,000 genomes sequencing because, having undergone genetic testing for certain conditions that they were quite convinced my daughter had from around the age of four months through to around the age of three years, I’d gone to so many appointments and thought, “Oh, this’ll be the time that I turn up and somebody will tell me this is what is the diagnosis.” And when I then joined the 100,000 Genomes Project in 2015 with my husband and my daughter, the genetic experience, the discussions that we had at the time were very helpful in that it was made quite clear to me that potentially we wouldn’t get a finding, and actually that any information that did come forward was perhaps unlikely to be hugely beneficial to our family at that point. So, I was quite clear what potential finding would mean to us.

But I think in the back of my mind, subconsciously, I had hoped that, when we eventually got a diagnosis, it would – I don’t know, bells, whistles, balloons going up, fireworks, etc. And then the experience of a letter thumping on the doormat, and I recognised the postmark quite quickly, and it was at that moment I suddenly thought, “Oh gosh, I haven’t buried all these feelings of hope.” Because I opened that letter with quite trembly hands, and then this diagnosis or lack of diagnosis, you know, nothing had been found, and it was a bit… I don’t know if it’s been described as like a nail in the coffin experience, because I really hadn’t realised I was still clinging to this hope all that time, and then again it was, you know, another, “No, nothing’s there.”

And I think because of the work I’ve undertaken with SWAN UK as a volunteer, and being quite involved in wanting to sort of educate myself and learn more, I did understand that, even though we had no primary findings, it didn’t mean that the study, everything was closed to us. It didn’t mean, you know, that things won’t still be looked for. But equally, at the same time, it just meant that we had nothing yet to pin anything on at that point. And I think it’s quite hard to pick yourself up and dust yourself off again, to be like, “Okay, we’re still here, we’re still circling that drain,” as it were.

I think actually that takes us on quite nicely really, about what role hope has in the experiences of a child with rare and undiagnosed conditions. And again if I can just say that there’s hope and there’s realism, and somewhere along the way, if you’ve been on the journey for quite a long period of time like ourselves, you have to try and find a way of living with that hope and realism all at the same time. So, we’re still hopeful that one day we might get some answers, but we’re realistic that day to day we need to focus on the difficulties or the experiences that my daughter has, so that we can manage to give her the skills to live her life to the very best of her abilities. Certainly, that’s our experience. And also I think if I’d let myself dwell forever on not having a diagnosis or a pathway specifically for that, it would have been quite difficult to carry on, pick ourselves up every day. What would you think about the role of hope there, Louise? What would you say your experience is from chatting to fellow parent/carers?

Louise: Yeah, I think you’ve described it really eloquently and better than I’ll be able to do, but when we talk to people, the phrase I always have in my head is kind of hope for tomorrow and help for today are the two things that people are looking for. So, making sure that that hope for tomorrow’s still there both in terms of, you know, the NHS being really clear that it will provide support for individuals without a diagnosis, and there may be opportunities for reanalysis in the future as science makes future progress. And, you know, there is progress being made so fast at the moment in genomics and that’s really welcome. So, making sure that people who’ve already had whole genome sequencing but not found anything continue to have access to that potential reanalysis I think is really important.

As you’ve rightly said, Lisa, as well, thinking through in terms of hope for tomorrow, the opportunity to take part in clinical trials and to make that as easy as possible where treatments are being delivered, to have the opportunities to take part in trials for non-condition specific treatments, whether that’s for epilepsy, which affects people across a whole range of conditions, or sleeplessness, which affects people across a whole range of genetic conditions. You know, there are both trials that only people who have a particular condition can take part in, and trials that are open more broadly, so making sure those opportunities are available as well, so that people have that kind of hope for the future.

But alongside that, I think it’s really important for the NHS to be clear with people about what help for today will continue to be available, and so we are working really hard with the NHS to emphasise the fact that when no diagnosis is possible, the NHS still needs to be clear to people about how they will be supported, whether that’s through the genetics team or a particular discipline, perhaps the one that is the closest fit for their child’s biggest need, whatever that may be, that they can still access more joined up care. So, you know, who is the person in the NHS, if you don’t have a diagnosis, who’s going to help you secure referrals to speech and language therapy, to physiotherapy, to learning disability nurses, and to the package of care that your child may need.

Who is the clinician, if you don’t have a clear diagnosis, who’s going to be the person with the authority and the confidence to lead the multidisciplinary team, maybe up to 30 healthcare professionals who are going to support your child. You know, who is going to be the lead clinician that’s going to pull that multidisciplinary team together and make sure that your child’s not being prescribed stuff that’s contraindicated, or that’s going to help one element of their condition but make another element worse. So, we are really trying to work with the NHS to make sure they’re thinking through, where will that support be for the family in terms of their healthcare.

And alongside that, you know, many wider services like schools or social care or employers welcome the chance to talk to a geneticist or a genetic counsellor or nurse to understand what adjustments they might need to make for someone who clearly has a genetic condition but doesn’t have a clear diagnosis. And so we’re trying to kind of make sure the NHS is both focused on the kind of science side and making sure that the hope for future findings is there, but also the help side, and making sure that the right package of care is still available for families who clearly have a genetic condition.

Lisa: Actually Louise, yeah, you’ve really summed it up excellently there, and whilst I am hugely grateful to the NHS and the various services, I can say, hand on my heart, my daughter has a huge number of professionals involved, both from the health side of things and social care side of things, and actually the person that kind of holds all that together is myself. And because we’re under multiple different teams, every time a new medication, for example, is prescribed, I need to go back to our lead team, which in this case happens to be neuromuscular, and check that, for example, if gastroenterology have prescribed a medication, that it’s not contraindicated from a neuromuscular side of things and so forth.

It’s all a bit like having sort of interlocking parts of a jigsaw, but perhaps no picture to follow [laughter], and that can be quite an isolating experience. And certainly, having chatted to fellow parent/carers, I know that’s their experience as well. And I imagine, Celine and Jana, you found sort of similar experiences when conducting the research.

Celine: Yeah, so my PhD actually was focusing on the sort of journey for parents as they go through the diagnostic process, and one of the things that came out really strongly from that body of work was how the parents were really carving their own care pathway, how they had to sort of push and fight to access services, but at the same time were the gatekeepers for their child’s health. Having to make sure all the various teams and clinicians were kept up to date with all the different tests that they had and all the results. And, you know, at times, this could be really frustrating for a lot of parents, ‘cos they had to keep repeating their story over and over again, particularly ‘cos they didn’t have a diagnosis. So, these parents really were having a very different parental experience to many of their friends and family, because their experience of being a parent to a child with an undiagnosed condition was really sort of as being a patient advocate, and as having to push and fight to access services.

Lisa: Yeah, it’s quite a unique experience. You are the specialist for your own child in that sense, I think would be the way I’d describe it. And I suppose over the years, I’ve got so used to sort of trotting out different medical explanations in terms that you can almost sound like you know what you’re doing [laughter]. And a few times when I’ve been at medical appointments, and perhaps we’ve met a new specialist or consultant, they’ve said, “Oh, what’s your field? What’s your area of expertise?” And actually you just think, “No, I’m just a specialist in my own child” [laughter]. But that’s quite an empowering feeling actually, so I guess that plays back into the feelings around hope and expectation, even with having an undiagnosed child.

Lisa:    When I was recruited to the 100,000 Genome Programme, we didn’t actually as a family receive genetic counselling specifically, and I know that this is something that is incredibly important to many families, and how that can support you sort of going forward. We were quite lucky in our experience in that we knew that our daughter was definitely going to be our last child, so we didn’t have the thoughts and insecurities around potentially what it might mean for any future children that we had. But certainly as my daughter has got older and she’s asking her own questions, and our older children are at a stage in life where they’re looking at potentially having families in the future, I know that those things have come up, and we’re just still exploring what that will mean in the bigger picture. But can you tell us, Jana, really what can genetic counsellors do to help parents feel less isolated and better to cope with the uncertainty surrounding their child’s condition?

Jana: Yes, well, I’m sorry to hear you didn’t have any genetic counselling prior to going on the 100,000 Genomes Project, because that consent conversation right at the beginning, before the whole genome sequencing, is really important. It’s important to know what the range of outcomes may be, so that it may be that you might get a result, you might get a variant of uncertain significance, or you might get no result. And parents in our study did suggest that their sense of isolation when they got a no primary finding result would have been alleviated if they’d known how many were not getting results. So I think in the longer run, it’s 40 percent perhaps received a result, so that’s 60 percent that didn’t receive a result, so those parents were not alone, but they felt very alone. And some suggested if they’d just had a leaflet really explaining that, and explaining that they’d still contributed to research and that that had been, you know, a good outcome in a sense, then they would have felt better about it.

So, a lot of work can be done before the testing really, to explore how you might feel on that range of results, and then that way sort of prepare parents for how they’re going to feel, and perhaps that helps them to have things in place, to know that it might be a vulnerable time with that letter, although that was particular for the 100,000 Genomes Project, to get the result in a letter in that way, and as you described, after such a long time, that you’d been able to forget that you’d been on the project. But to actually be a little bit prepared that it make take its toll on you might actually help with preparing oneself. It also might be helpful to include ways of promoting ways to enhance health and wellbeing for parents in terms of practical support, such as those things that you’re already attempting to access, like the respite services, school support, support groups, and thinking about psychological wellbeing and ways of managing stress, psychological support for parents, and possibly spirituality based resources as well.

And focusing maybe on what is known about the child’s condition even without a diagnosis, so what’s likely to be beneficial, and support parents in actively coping, such as what research they might be able to access, and continued medical support. And also actually having a named person within the genetics service, so they have someone to go to for any follow-up that has a name, and so they don’t feel isolated from the genetic service. And signposting to those external resources, such as SWAN UK, can be very important as well, of course.

Celine: I think it’s also really important to add that hope isn’t necessarily lost when you don’t get a diagnostic result. And in a sense, what can be really helpful is for genetic counsellors to reframe that hope, if you like. So, one thing that we talk about in our paper is that it might be useful for health professionals to ask a question such as, “In light of the new information that we now have from the whole genome sequencing result, what are you hoping for now?” So in a way, it’s sort of reframing that hope, sort of giving it a different context.

Lisa: Definitely, and I think one of the things as well is that, because potentially for when parents were first recruited to a study such as the 100,000 Genome specifically in this case, that it might be quite a length of time between that initial recruitment and when the actual result comes out. And of course, in that time, with the advances in genetics, it’s sort of somewhat of a Pandora’s box really, isn’t it, in that we’re almost kind of finding the information out quicker than we actually know how to process it and what it potentially means. So actually if there’s a genetic counsellor available to speak to those parents, or for those parents to be signposted to somebody who can say, “Well look, since you were recruited, actually this is happening, that’s happening,” or, “These research projects are happening,” personally, I can say that is going to be really helpful and handy, and would have been really useful. I just know that for myself anyway and my family, that if there was a leaflet or something that had given me a way of knowing how I could contact somebody in the future, that would be really helpful.

What ways do genetic counsellors use in maintaining a delicate balance between not creating false hope but also providing meaningful support to parents? What would you say around that, Jana?

Jana: I think as we’ve already touched on, it’s that managing expectations from the outset when the test is offered. So, not generating too much hype or excitement, but setting those expectations, giving that information about the diagnostic yield. Also, informing parents that what people do experience has been described as a rollercoaster of emotions. It’s normal. You might also want to explore people, not only what they’re hoping for, but also the outcomes that they might be fearing, and giving them a chance to voice those, because they can be very powerful things as well. A diagnosis might not be what you want to hear, so there can be a lot of ambivalence around wanting a diagnosis when it might actually be a life limiting condition, that you didn’t really want that certainty.

And also helping parents to explore how not receiving a result might feel, so that they’ve actually rehearsed it a little bit, and where they might go to when they need a bit of extra support. So, they already know, “I go and talk to my friends, that’s where I get my support from,” so that they’re kind of ready for it, and that might help them with that sense of isolation, but also validating these feelings. So, it’s okay, it’s okay to have that dip, it’s okay to feel, that it’s something that many people experience. And creating a safe space for people to feel that, so if they want to talk to a professional or a friend, that those feelings are validated.

And in that way, kind of with that pre-counselling really, helping parents to develop their own set of resources, so they’ve got those to draw on. And as you’ve mentioned, Lisa, it’s like having your own resources also helps generate that feeling of empowerment and control. And as Celine has said, it’s really facilitating parents through that passage of reframing what you’re hoping for, reframing what the future looks like, if you had one picture of a future. You need to become comfortable with the future you’re now looking at.

Lisa: Thank you, Jana. Louise, if I can ask you really, we’ve already touched on the role that SWAN UK can play for parents dealing with undiagnosed rare conditions, but perhaps if you could home in on that and explain in more detail the main focus of SWAN UK, and what that can do for parent/carers.

Louise: So, what SWAN UK primarily does is bring together parents who are in a similar situation. So, we have a team of amazing parent representatives, who Lisa is one, who help us shape the support that SWAN UK can provide, and really make sure that it’s based on a really strong understanding of what it’s like to be a parent of a child with an undiagnosed genetic condition, and an understanding of that kind of expertise that parents who have been on that journey themselves will bring. So, we have a series of Facebook groups. Some of them are for different regions, so people come into contact with other parents in their area who are going through similar circumstances. Some of them are more around age. So, you know, we have Facebook groups for parents who are waiting for a diagnosis or have got a new diagnosis, and then we have a group called SWAN Graduates, which is for children who are older and over 18, so their parents can come together and share their experiences.

So, it’s really to help parents be able to talk to one another, to share their experiences, to support one another, and often to ask for advice. They’re often kind of practical questions about, you know, “My child needs this kind of wheelchair, has anybody been able to source that from somewhere?” “My child’s having real difficulties eating at the moment, can anyone give some advice on this particular challenge?” “This thing someone else has faced, how did you approach it? Where did you reach out for support?” So, that peer to peer advice and support is really at the heart of SWAN UK.

And then what we try and provide around that is access sometimes to information events, where there’s particular issues that are affecting a lot of SWAN families. So, we hope over the coming year to have a series of information events targeted at families with children who don’t have a diagnosis, and some of it is just trying to have social events and bring people together again. We’ve had, for example, an active dads group in Wales, who’ve been bowling and wanted to go axe throwing, and really they just want to come together with other dads who are in the same situation, and being able to talk to one another and provide emotional support to one another.

So, that’s kind of the nub of SWAN UK and what we do, and then alongside that, that kind of fits in with Genetic Alliance’s wider goal, which is much more around campaigning for improved services. So for example, the Genetic Alliance UK team has worked really closely with commissioners in Wales, who actually commissioned the first SWAN clinic, which is in Cardiff. That was a two year pilot, to see what support could be provided both to help SWAN families get a diagnosis, but far beyond that, to make sure that the care for families who don’t have a diagnosis is better joined up. And that we feel has been a real success. Again, there hasn’t been a really high diagnostic yield, there have been very few new diagnoses, but the support provided to the families who are in contact with that clinic, in terms of helping them access better joined up care both from the NHS and from services more widely, has been brilliant. And we’re currently working with NHS England in the UK, who are exploring an opportunity to commission two SWAN clinics in England.

So, that trying to kind of improve services, and then the third aspect of that is just working generally with the new genomic medicine service alliances as they emerge across England, to try and make sure they are thinking through what support they will need to continue providing to families who’ve gone for whole genome sequencing in future, not through a research project like 100,000 Genomes, but just through routine clinical practice and routine clinical diagnostics, what support will they need to provide for families who go through that process and don’t get an answer. And that won’t change the support they will need from the NHS. It will just mean that perhaps that clinic needs to play a more active role in helping them access those services. So, all of that kind of campaigning to have better services for family who have an undiagnosed genetic condition continues as well.

Lisa: So, I think one of the things really just to finish off today, is of course looking at the future. Considering advancements in technology, would you say that future reanalysis of the 100,000 Genome Project is going to yield additional insights? Celine, can I ask you to comment on that?

Celine: Yes, absolutely. As we understand more about the role and function of different genes, and as new genes are added to the panels, we will definitely be able to provide a diagnosis for more parents and more families. But I think we don’t yet necessarily know exactly what that reanalysis will look like, and it’s not really clear yet how this will work in practice.

Lisa: And Louise, would you have anything else to add to that at all really?

Louise: No, I think it is just that hope for the future and kind of help for today. I think the NHS needs to be equally clear about, you know, there’s some amazing investment by the UK government in genomic research, and that’s brilliant and we want that to continue, but equally we want the investment to be taking place into routine clinical services and diagnostic services, so that we can talk to people both about the hope of potentially getting a diagnosis in future, but making sure that the help continues to be available for as long as they don’t have a diagnosis, and that help for families who don’t have a diagnosis is going to be just as important. And what we try to ask for is both real clarity around what the NHS can provide, and really clear signposting to organisations like SWAN for families that continue to not have a diagnosis. And again, just to give an equal shout out to Unique, who are able to support families who have an ultrarare diagnosis, where perhaps they’re the only person in the country with that particular diagnosis, or one of a handful of families around the world. Signposting to that peer to peer support will continue to be a really important part of the process as well, so that families can help one another, learn from one another, and just give each other support that they are kind of sharing that same journey and walking alongside one another on that journey as it continues.

Lisa: And bringing this podcast to a close, can I just ask you really, any final thoughts, anything that you would sum up from your experience of researching the no primary findings and where we now are today?

Celine: I think the main thing for me is just to sort of make it clear to parents that a diagnosis isn’t necessarily a magic wand, even though it is obviously very important to a lot of parents. But that even without a diagnosis, we still have the opportunity to manage patients’ symptoms, and often a diagnosis doesn’t make a substantial difference, because parents are sometimes left with a lot of uncertainties and a lot of unanswered questions. So I think, and as Louise and Jana have said before, it’s really sort of on focusing what we do know, and thinking about what we can offer and what support we can provide to parents and families even without a diagnosis.

Lisa: Thank you very much to our guests today, Jana Gurasashvili, Celine Lewis and Louise Fish, for joining me as we discussed the impact of a no primary findings result. If you’d like to hear more like this then please subscribe to the G Word on your favourite podcast app. Thank you for listening. I’ve been your host, Lisa Beaton. This podcast was edited by Mark Kendrick at Ventoux Digital, and produced by Naimah Callachand.

 

 

Helen Brittain: Genomics 101 - What is a variant of uncertain significance?

In this explainer episode, we’ve asked Helen Brittain, Clinical Lead for Rare Disease Diagnostics at Genomics England, to explain what a variant of uncertain significance is, in less than 10 minutes.

You can also find a series of short videos explaining some of the common terms you might encounter about genomics on our YouTube channel.

If you’ve got any questions, or have any other topics you’d like us to explain, feel free to contact us on info@genomicsengland.co.uk.

You can download the transcript or read it below.

Naimah: What is a variant of uncertain significance? Today I’m joined by Helen Brittain, who’s the clinical lead for rare disease diagnostics at Genomics England, to find out more. So first of all, Helen, before we dive into the topic, I’d like to go one step further back and ask you to explain what is a gene? 

Helen: A gene is effectively a section of our DNA, which is our genetic code, and it contains an instruction, something important about how we grow, how we develop, how we function as a human. Humans in total have around 20,000 genes, which is our complete set of instructions, to tell us everything we need to know about ourselves. 

Naimah: So, what are gene variants then, and do they all have an effect? 

Helen: Variants are effectively differences within genes. So genes, like I said, are instructions, and they have a particular way that they’re spelled out and structured, so that the body can understand them and make sense of that instruction. A variant is where there’s something different about the way that that gene is spelled out or structured that could affect how it works, and basically a variant is a difference to what we expect to see. 

Naimah: And do all of these have an effect? 

Helen: So no, not all of them will have an effect. Some differences or variants within a gene may not affect the way it works at all, whereas others might alter that gene so significantly that it can’t do its job anymore, and could be very significant for that person’s health. 

Naimah: And how do we find these gene variants? 

Helen: Gene variants are exactly what we’re looking for when we’re trying to find a diagnosis for somebody. So, somebody with a rare condition is likely to have an underlying difference within their genes that would be the explanation for it. We’re finding these through doing genetic testing or genomic testing, so looking at an individual gene, a series of genes, or even across someone’s entire genetic code, through whole genome sequencing, and we find these variants through doing that testing. 

Naimah: And this might be a good opportunity to mention our other Genomics 101 episode on genetic testing, if you’d like to find out some more information on that as well. So, moving on with the next question, how is a variant’s significance determined? 

Helen: Variants, as we say, come from the genetic tests we undertake, and there are a team of people who look at and try to determine what effect that variant might have on that person. This is the majority of the time the work done within the laboratory teams, through the clinical scientists, who have expertise in understanding the impact of variants within a gene, and they work together with other clinical representatives, like the clinician looking after the patient, to understand that patient’s disease in as much detail as they can, to try to pull all of the information together and determine whether that variant is making a difference or not.  

They would look at a lot of different pieces of information to try to work out, could this be the reason behind that person’s genetic disorder? And that might be things like have we seen it before, can we predict the effect of that variant on the gene? And we have to understand how variants within that gene cause a condition to be able to match up against the variant that’s seen, as to whether that would make sense for that individual. So, it’s a lengthy process but an important one, to make sure that we’ve got the most accurate information about that variant, and the understanding about that in that person’s health and development. 

Naimah: So then, what would be a variant of uncertain significance? 

Helen: So, the output of that clinical scientist’s work looking at whether a variant is significant or not comes out into five categories, but three main groupings. What we’re looking for obviously through doing genetic testing is to try to find a diagnosis for somebody, and a diagnosis would be a place where we are confident that that variant impacts on that gene and leads to the condition that that person is presenting with. So, that would be a diagnosis on one end of the spectrum of what we might find.  

On the very other end of the spectrum are variants that don’t make an effect on the gene, that would be benign. We would call those harmless variants, things that don’t change the gene and wouldn’t be expected to be associated with a condition.  

And then, in life there’s always a grey area, and the part in the middle, between being confident about a diagnosis on one end or being confident that that variant really doesn’t impact the gene and is harmless. We have variants that we find that we do not yet understand, and that’s basically because our knowledge as of when the variant is looked at is good, but it’s not perfect. There could be more to learn about particular variants or particular conditions, but at the moment we just don’t have enough information to be sure one way or the other. And that’s really important, we’ve got to get it right, so we do have this grey area in the middle, which are the variants, differences in the gene, where the significance of them on that person is uncertain. 

Naimah: How often do we find these variants of uncertain significance when we’re trying to genetically diagnose patients?  

Helen: They are relatively common for us to encounter, and that’s for a number of reasons, I would say. I think that we know a lot about our genes, and our knowledge has come on leaps and bounds, and it’s still improving at a rapid rate, but we don’t know everything yet, so there will be areas where we haven’t met a particular variant before, or we can’t predict how it might affect that gene, or there’s some uncertainty about it because we don’t have full knowledge yet. So, it does happen relatively commonly, and it probably happens more commonly the more genes or the more information we’re looking at. So a test looking across someone’s genome, like whole genome sequencing, we’re more likely to come across these things than if we’re doing a very targeted test looking at one specific gene that we understand very well, for example. 

Naimah: And how can knowing the significance of a gene variant be impactful for clinicians and the patient? 

Helen: This is really important, knowing the significance of a variant is key. It’s fundamental to genetic testing, because we are trying to make a confident diagnosis for somebody, and we have to get that right, because if we make a diagnosis in somebody there are lots of knock-on implications of how that information is used to inform the healthcare of the individual who has the condition, or maybe even to inform their family members, who could be at risk of the same condition. Obviously, we share our genetic information amongst our families, and so a genetic test might be used for a family member as a result of a diagnosis in one individual within their family.  

And of course, in some situations, that might lead them into either needing screening for a particular condition that could happen, or being removed from screening if they don’t have the genetic cause within their family. Equally, people might make choices surrounding whether to extend a family or reproductive choices around the knowledge of a genetic condition within a family. So you can see, the implications are huge. It’s really important this is correct.  

Naimah: And finally, I just wanted to ask, can we reclassify variants of uncertain significance? 

Helen: Yes, there’s real need to do this because people are wanting genetic diagnosis answers for understanding, and for all of the implications we just mentioned about why are diagnoses important. So yes, we can reclassify variants of uncertain significance, and that can happen in different ways. It’s not always possible straight away, unfortunately. So, what we often need is time, and that is time to understand that variant a bit better, and that might be through seeing it again in other people, maybe who have the same pattern of health problems or same picture in terms of their rare disease, and we start to understand, okay, that might actually add up to suggest that that variant is affecting the way that gene is working. Or equally, we might see it in other people who don’t have the same rare disorder, so we’re starting to see, well actually, maybe it’s harmless and it’s just part of the natural genetic differences we all have. 

The other way that we can understand variants of uncertain significance better would be through research, so for example researchers looking at designing studies to try to see if they can make a model, for example, with an animal who might have the same type of variant, and see if that causes an effect on their health, so learning specifically about that variant through research could also help. And there are things that clinicians also actively try to do, and this is why we work together with the clinical scientists is to understand, are there other people within the family with the same rare condition, and would it help to test them to see if they also share the same rare variant. And sometimes that can help, not always. So yes, we really want to try to reclassify variants of uncertain significance, and as far as possible, we will, but sometimes they do just need that time for us to build that bigger picture. 

Naimah: That was Helen Brittain explaining variants of uncertain significant. I’ve been your host, Naimah Callachand, and if you’d like to hear more explainer podcasts like this, you can find them on our website at www.genomicsengland.co.uk. Thank you for listening. 

Julia Vitarello, Rich Scott and Ana Lisa Tavares: Treating Mila - Lessons for those living with rare conditions

29 February marks Rare Disease Day. This day is an opportunity for the rare community to come together to raise awareness of the common issues affecting those living with rare conditions. A rare condition is a condition that affects less than one in 2,000 in the population, and although rare conditions are individually rare they are collectively common. It is estimated that there are over 7,000 rare conditions. Around 80% of rare conditions have an identified genetic origin.

In this episode of the G Word, our host Julia Vitarello, Founder and CEO of Mila’s Miracle Foundation, is joined by Rich Scott, Interim CEO for Genomics England, and Ana Lisa Tavares, Clinical Lead for Rare Disease Research at Genomics England, as they discuss challenges for those living with a rare condition and the work being carried out across the genomics ecosystem to support them.

Julia is the mother of Mila, a young girl who was diagnosed with a rare genetic condition called Batten Disease, and in this episode Julia takes us through Mila's story, and how she hopes to help many more families access treatments for their children.

 

"So when parents, children, are diagnosed whether it’s a fatal or life-longing debilitating or difficult disease, if you know that what’s being learned from your child both from just the genomics to the potential treatments that’s helping the next child, that helps parents like me be able to continue living."

 

You can find out more about Mila's story in our previous podcast episode with Rich Scott, Julia Vitarello and Dr Tim Yu.

 

You can download the transcript or read it below.

Julia: Welcome to the G Word

So my life at that point seemed to just disappear in that moment, all the things that had mattered to me were gone; I knew there was something wrong with my daughter but I had absolutely no idea that a typical child who was outgoing and active and verbal and had friends could suddenly lose all of her abilities and die.

My name is Julia Vitarello, and I’m your host for today’s episode. Today joining me in conversation is Rich Scott, Interim CEO for Genomics England, and Ana Lisa Tavares, Clinical Lead for Rare Disease Research, also at Genomics England. Today we’ll be discussing challenges for those living with a rare condition and the work being carried out across the genomics ecosystem to support them. If you enjoy today’s episode, please like, share and rate the G Word on wherever you listen to your podcasts.

The 29^th of February marks rare disease day. This day is an opportunity for the rare community to come together to raise awareness of the common issues affecting those living with rare conditions. A rare condition is a condition that affects less than one in 2,000 in the population, and although rare conditions are individually rare they are collectively common. It is estimated that there are over 7,000 rare conditions. Around 80% of rare conditions have an identified genetic origin.

Before I get into speaking with Rich and Ana Lisa, I wanted to share my story and my daughter, Mila’s, story. My life as a mother started really like anyone else’s, my daughter was perfectly healthy, her name is Mila. For the first three or four years of her life she was like any other kid. I live in Colorado in the United States, my daughter was a skier, she was a hiker, she was rock climbing, she was incredibly active and singing songs and swimming and riding bikes. But around four years’ old she started tripping and falling, she started pulling books and toys up closely to her face; she started being covered in bruises, getting stuck on words and repeating her sentences and I brought her to about 100 different doctors and therapists around the United States to try to figure out what was going on with her.

Around four years’ old I started speaking with orthopaedic surgeons, with ophthalmologists, with neurologists, with speech therapists and each one of them, you know, told me pretty much that I was a crazy mom and that my daughter was typical and normal and that she would grow out of these sort of strange symptoms that she was having.     

By the time that she was six years’ old, I had had enough and I was crying on a regular basis, no doctor could help me and I was tired of lugging my daughter, who was now covered in bruises and tripping and falling and stuttering, together with my newborn son at the time, kind of around the country only to be told that I was crazy. And at that point at six years’ old I brought her into the emergency room in the Children’s Hospital Colorado, near where I live. She was in there for about a week and underwent a battery of tests and at the end of that week I was told that my daughter had a rare genetic condition called Batten Disease and that she would lose all of her abilities and die in the next few years. So my life at that point, first four years of my life seemed to just disappear in that moment, all the things that had mattered to me were gone. I knew there was something wrong with my daughter but I had absolutely no idea that a typical child who was outgoing and active and verbal and had friends could suddenly lose all of her abilities and die.

After crying on my closet floor pretty much most of the day for a few weeks I picked myself up. I started to read white papers, I started to go online and learn about other rare conditions. I started to speak with parents that had fought for their children with physicians, with researchers, and did everything I could to kind of figure out if there was even a glimmer of hope. And what I was told at the time at the end of 2016 was that there is almost nothing that could be done and very little was known about my daughter’s form of Batten Disease. But that there was a tiny glimmer of hope that we could maybe stop genetic disease, and that’s all I needed. I started Mila’s Miracle Foundation, which is a non-profit organization. I started telling Mila’s story and taking care of my kids by day and trying to fight and learn and raise money by night and I started a gene replacement therapy because it was the only option that I could take on as we didn’t know much at all about the disease, and by replacing it, it was kind of the only thing that I could do, but it was going to take many years and millions and millions of dollars and I knew that it wouldn’t be in time for my daughter.

Along the way, there was something a little bit unusual which was that my daughter had an auto recessive disease which meant that she needed to have a mutation in the same Batten causing gene from her mom, myself, and her father, and they could only find one of these two. That led me to learn about whole genome sequencing, which was kind of the most extensive way of looking at Mila’s genome to figure out where this missing mutation was. And in that search I crossed paths with a Dr Timothy Yu at Boston Children’s Hospital, and he volunteered with his lab to help me find this missing mutation that no other lab could possibly find. And within a few months and a lot of work, a lot of late nights and weekends and staring at screens, through whole genome sequencing, the team was able to find Mila’s missing mutation and finally diagnose her fully with this rare form of an already rare Batten disease.

That is where Mila’s story changed and turned direction. At that point, a recently approved drug for spinal muscular atrophy was on all neurologists’ minds at that moment because it had just been approved in the US by the FDA and in other countries, and it was a game changer, these children were dying and on respirators and in wheelchairs you know at the age of two and with this new drug they were actually living, many of them were living long lives and were active and happy and healthy and going to school. And Mila looking her whole genome sequence was able to kind of fit that same criteria, and so the doctors, including Dr Yu said, “What if we did the same thing for these children? What if we made a drug like this for Mila?” This drug called Antisense Oligonucleotides, or ASO seemed to be a good fit for Mila’s mutation. And so a drug was made for Mila and named after her called Milasen and it was a race against time for an entire a year with a team of honestly hundreds of people across academics and industry, I was fighting to try to raise the money and awareness and working with a scientific team. And one year after Mila was diagnosed when she turned seven years’ old, we moved to Boston and Mila began receiving Milasen, which was named after her, and only in that moment in time did I realise not only what a big deal this was for me as her mother, but what a big deal this was for science.

She was the first person in the world to receive a medicine that was tailored just to one person and it was named after her because there was no-one else in the world they could find that shared that same mutation.

When Mila began this, you know, I didn’t know what to expect but I knew that she was going to lose all her abilities and die if she didn’t receive this. And so once she started receiving this within just a few months, her 30 seizures a day went down to nothing; she had occasional small tiny seizures that were barely visible but her quality of life was incredibly you know improved, not to mention our family’s because she was no longer thrashing and smashing her arms and legs up against walls and tables.

She had been slumped and could no longer sit up. She could no longer hold her body up and take steps with my support from behind and after Milasen she started being able to do that even walk up the stairs with alternating feet with me supporting her from behind. She also had received a G-tube and was receiving all of her nutrition through the G-tube and after Milasen she started eating by mouth, it wasn’t perfect, but she was eating pureed foods, and being able to swallow better and probably most importantly she was able to smile and laugh at the funny parts in the books and the stories that I had been reading and singing to her and that she had kind of really not been responding to as much before Milasen and some of that came back.

So, a year into this everyone was quite shocked that Mila had done so incredibly well in this first year despite how progressed she was, progressed her condition was. Unfortunately in the second year it was during COVID and it was unclear whether or not Mila’s disease had kind of stopped or whether it was slowly progressing and in the third year Mila started having problems associated with her rare condition and I was faced as a mother with the most horrible decisions anyone should ever, never, never, never have to face to decide what Mila would want if she were able to talk and tell me whether or not this was a life that she felt like she would want to live. And after three years on Milasen, which was three years ago almost this week, Mila died and in many ways my life as I knew it was kind of over. I’m a very positive happy person and I have a son and I continue getting up every day and pushing through the day but I’m not sure how any parent makes it through days, weeks, months and their whole life without their child physically there with them.

Ana Lisa: We can really hear the perseverance that you had to get a diagnosis through whole genome sequencing eventually for Mila. Can you tell us a little bit more about that process and what that diagnosis, what did it mean for Mila and for your family?

Julia: When Mila was first diagnosed with Batten Disease, one of the missing mutations could not be found by any lab. I did research and found out that whole genome sequencing which at the time was very, very hard to find a lab that would do it or anyone that would do it in the United States, I did learn that that was really what was needed in order to try to really get down to find the underlying genetic cause of Mila’s disease and give her a full diagnosis. So once we managed to have Dr Yu’s lab at Boston Children's Hospital carry out the whole genome sequence, obviously we were able to then find exactly where the broken, underlying broken kind of genetic mutation was and why that was important was for two reasons: 1) was so that we could actually have a diagnosis and even though it was the worst diagnosis we could have ever asked for, at least there was an answer and for so many years I didn’t have an answer and there is nothing worse than seeing your child, you know, having all of these different symptoms and problems and having you know tens, if not hundreds, of different doctors and therapists tell you that they don’t know and maybe you’re just a little bit over-worked and over-worried about things, and having no answer and no idea what’s wrong is like living in this limbo that’s just terrible.

And so whole genome sequencing allowed for us to have a full diagnosis for Mila, and it also allowed us to use that data since it was truly the precise place where, you know, we could find the precise plan where her gene was broken. It allowed the researchers to then also think about what could be done about it as well, which is the second thing a parent thinks about after they have the kind of relief in some ways, which is a strange word to use but it’s true, of knowing what is wrong and then thinking, “What could I do about it now?” And so for me I would say that’s how, Ana Lisa, that’s how I reacted to that, is there was enormous relief initially, which is just the weirdest word ever to use for that but at least I felt like I wasn’t crazy and that there was an actual reason and that it allowed us, allowed me and others to think what kind of action can we take now.

Rich: One of the things that often strikes me, I’m a clinical geneticist by background, just like Ana Lisa, is how often particularly several years ago when we were in a different situation, it depended on families and parents pushing and pushing and pushing and asking, that’s something I think in the UK we’re really lucky that there have been changes in terms of availability of testing. Julia, as you know, we were set up ten years ago initially to run a project, a research project in partnership with the NHS called ‘The 100,000 Genome Project’ asking the question about whether whole genome sequencing could be used in a diagnostic setting. Whole genome sequencing had just emerged as a thing that could even be conceived of as affordable in a healthcare system back then, and we worked with the NHS and tens of thousands of families with rare conditions and people with cancer to ask that question and again, we’re really proud of what that work and our partnership with the NHS has led to, which is now in the UK.

There is the availability nationally of whole genome sequencing to test in certain settings including in rare conditions that are hard to solve in this sort of way and it’s one of the things which has really changed the way we can go about this, but we also know that there’s still, it’s still hard often to identify who should be seen by a specialist who might do a test and so on. But it has really changed things and I think it’s hearing from families like yours about how challenging it is and thinking about how we turn, looking across all of the story that you told us of everything you went through, how we can make that be something where we can make it be more systematically available and work for many more people, and I know your phrase from Mila to millions really strikes a chord with me, and I know with the NHS mind-set here in the UK where it’s about equity of access and I think that mind-set that you bring is so important.

Julia: Yes, Rich, I think it’s a really good point you know, because a lot of parents like myself, we’re talking about probably millions around the world and tens of thousands just in the UK alone, spend so much time going from one physician to another and to a therapist and it takes an enormous amount of energy and time in a family that’s already dealing with pain and confusion and not understanding what’s going on, not to mention usually that child, in my case, Mila, is having problems that it’s not easy to leave the house and get in the car and go to all these appointments. And the more we can push towards whole genome sequencing as one of the first places to go, if not the first place to go, the more it’s going to cut that sort of diagnostic odyssey down to the very bare minimal.

And so of course a dream would be is that any child that has, I like to think of it as soon as you kind of have more than one symptom that shouldn’t normally go together, that sort of has a little red flag that goes off and in most parts of the world right now no physician wants to scare a parent like me, it’s happened a number of times to me where a physician has said, “Well, you know, there is this rare condition but I’m not going to bring that up because it’s so rare that the likelihood that your daughter has that, I wouldn’t want to scare you.” But the more we can move towards whole genome sequencing right away to help with that answer that could cut months and very often years from that odyssey, and that is where we need to be, we can’t have the tapping on the knee and stacking up blocks and running down the hall for months and years just to figure out what’s going on.

Ana Lisa: And I think Rich also there said a power of having a national healthcare service where patients who are having whole genome sequencing can also decide whether they wish to consent to be part of research and combining that with a national genomic research library and then the ability to work so closely with the NHS and go back to patients if there is a new diagnosis that could benefit them is really powerful I think, and that’s definitely one thing that we’ve also learnt from these big whole genome sequencing efforts is that our knowledge is continuing to develop and some people will get a diagnosis from that immediately and we’ve got amazing colleagues working on diagnostic discovery looking at whole cohorts of patients now who are having whole genome sequencing and that’s also been really informative and allowed a lot of new diagnoses identified also through research and through these efforts to be found.

Julia: Absolutely and I think that the UK is incredibly well suited to have such widespread sort of country-wide whole genome sequencing project like what Genomics England has done because you have one system where all of the clinical and genetic data can all come in and kind of be analysed both for like you said diagnostics but also it could be, if families and patients are interested, right, in contributing to the research which then comes full circle and helps the entire system benefit from better treatments you know and better understanding of diseases.

Rich: And that point of sort of thinking about how to move things forward, so the NHS has a service based in Exeter which is addressing the question where children are on intensive care, where often intervention is needed really rapidly to make a difference, so that’s one of the examples where sort of thinking about making sure that service is available early and rapidly is being set up and that’s been really successful and identifying a cause where that really changes the care of that child on intensive care.

The other area where we’re working really closely with the NHS at the moment, as you know, Julia, and in fact I think this was probably one of the reasons we first came to talk to you was thinking about our newborn genomes programme where if you like, the big question there is saying we know that there are a few hundred conditions that are within that longer list of rare conditions where there is a treatment available routinely if the diagnosis is made, and saying could we use whole genome sequencing alongside existing newborn heel prick testing which in the UK currently looks for nine, shortly to be ten, conditions. So we’re just about to launch that programme and that will sequence the genomes of 100,000 babies born at maternity hospitals, not selected for children where there’s something, a concern, raised, but any baby at that hospital would be eligible for the family to choose to join that research programme and really to ask that question about whether this is something that we should offer to all babies developing the scientific evidence around it, learning about how you might implement it in practice, and also having conversations about how one might do that, what public attitudes are to it and so forth, developing evidence that can move us forward in that area too.

And back to Ana Lisa’s point about improving knowledge, we know that today there are a certain number of conditions that one might think are comparable to those nine that are currently looked for in the UK on the heel prick that we could use genetics as a way in. We also know that through the sort of innovation and the new knowledge that you mentioned that was relevant to Mila, that list might grow quite considerably in the coming years, so it’s thinking about how we set ourselves up to make sure that we’re able to take advantage of that to its full.

Julia: Yeah, and I think it’s a great, I’m glad you brought this up Rich because the UK really is leading the world in this, there is no-one else that is doing whole genome sequencing at birth, and ultimately, that’s where we need to be. You know it’s not going to happen overnight and like you said, the purpose of this is really to learn a lot about how and if to roll this out maybe in a larger scale way across the UK. But ultimately, you know, as Mila’s mom, I think all the time about you know how incredible what I saw at a very progressed state for Mila with this treatment and the only way to actually really truly help Mila and other Milas is to get to these children early enough so that they’re diagnosed before they have symptoms and they’re treated before they have symptoms. And the way to move towards that is to at least have efforts like the project, you know, the newborn screening project so that we can get to children, find them before they have symptoms, treat them before that and from what I saw from Mila I feel pretty strongly that if Mila had received Milasen at birth she might never know the effects of Batten Disease, and we as a family might never know what it’s like living with a rare condition, and this is a step in that direction to help.

Effie Parks: Hi there, I’m Effie Parks, mom to Ford, who lives with a rare neurodevelopmental disorder called CTNNB1 and the host of the Once Upon a Gene podcast. Our show connects families facing rare diseases, offering stories from parents, insights from experts and discussions on everything from navigating grief to exploring genetic advances. It’s a space for understanding, connection and empowerment. For support and inspiration on your rare disease journey, subscribe to the Once Upon a Gene podcast on your favourite podcast app and let’s navigate this path together.

Ana Lisa: Julia, I’m interested to hear what you think the development of individualised medicines like the N1 treatment Mila had what that means for the sort of collaboration that’s required across the genomics ecosystem to achieve that.

Julia: Yeah, that’s a really good question. It’s been seven years that I’ve been thinking about this kind of individualised medicine concept, you know, as Mila kind of became the pioneer in this field and I’m not a scientist, I’m not a physician, but I’ve learned a lot because I’ve been fortunate enough to be part of thousands and thousands of conversations, including with all of you and others, Genomics England, and around the world and I think what I learned and what I’ve learned so far is that when you have a genetic condition most genetic conditions are individually rare and unfortunately that doesn’t make them very suited to have anyone go after a treatment for them because really the only way to connect a patient, a child like Mila, to a science or technology is if they’re lucky enough, and I hate to use the word ‘lucky’ but they’re lucky enough to be part of a large kind of cohort of people, and that allows them to be, you know, commercially viable, so a company will be maybe develop if they’re lucky, a treatment for that, for those people.

The only other option is this sort of like Herculean effort of which myself and Dr Yu and others went through, we had to raise millions of dollars and get hundreds of people to get on board and develop a novel medicine for one person – now how scalable is that? How many times can we do that, right? And so the only people that really have access to medicines today with genetic conditions are those that are fortunate to be part of one of these two groups, but what about everyone else which is 95% of the people?

And so I think what the field is learning is that we kind of have the patients and we’re finding them, especially thanks to Genomics England and others, we’re starting to find them more rapidly earlier, more of them, and we have these technologies to be able to not only find them but to also treat them but we just do not have the infrastructure and the processes to connect them, we have clinical trials and we have these sort of named patient route but we don’t have anything else. And so I think the genomics community, especially in the UK because it’s so well suited with all the efforts that we’ve just brought up, is really well suited to kind of try to work together to allow for access kind of no matter how many people could benefit, it’s not only one, it could be six or 20, or 200 or 500. Right now there is no access for them. So I think that the UK is really well suited, starting with whole genome sequencing, that’s where it begins, it begins by identifying patients early enough and getting the data that’s needed in order to diagnose them and also to help with the treatment you know, and so this is how I think the UK is really leading the world right now, including in the recent announcement of the rare therapies launch pad, which Genomics England is part of, I am part of, others are part of, Oxford Harrington Rare Disease Centre, the MHRA, others are all part of really trying to be dedicated to building the infrastructure and resources and processes that are needed to connect the patients to these technologies that exist today.

Rich: I’ve been really inspired by the conversations and the drive that you, Julia, personally have given to those conversations. And I think what’s really interesting and I think it’s relevant more broadly than just in rare therapies particularly, but I think that challenge of recognising the need for the system to change to be able to respond to evidence and make the response proportionate to the expectations of various people, the patients or the families who are receiving it, the system as a whole, these sorts of therapies and rare conditions as well, are just not the shape that works well with existing paradigms, but I think it’s relevant you know, in other settings as well.

I’m really interested in some of the conversations that I’ve had with you before about balancing risk and understanding how to get that right and the fact that that really needs an open discussion in public to also understand the journey and the situation that families find themselves in. I wonder if you could tell us a bit about your perspective on getting that risk balance right?

Julia: Thanks for bringing that up, Rich. I think it’s really, really important because to me the way we think of risk and benefit and the risk tolerance maybe is a better way to put it is the foundation of the house that we’re building. So, you know, the regulatory process and everything behind that are built on top of how we think about risk. And one of the things that I regularly think about is children that have end stage cancer, and that we as a society have accepted an enormous amount of risk for a child at end-stage cancer that has no other options that’s going to die no matter what, probably very rapidly and that if they don’t respond to kind of some of the main line treatments then to turn to an experimental cancer treatment which carries a very high risk is considered very acceptable by our society and that everyone, the clinicians, the families, the regulators, everyone is willing to take that risk for that child because they’re going to die otherwise. And they’re willing to spend money and they’re willing to take the risk and often perhaps to buy that child maybe three or six months of life.

So then if you look at Mila and if I tell you that instead of having a rare condition that she has an end-stage genetic disease, and I use the words from cancer, from oncology, is now suddenly the discussion changes a little bit, so Mila’s going to die no matter what, no child has ever lived with her form of Batten Disease and she’s going to lose all of her ability, so we know the risk of not treating Mila. The risk of treating Mila in this case was an antisense oligonucleotide, which is a modality that’s been around for 30+ years, tested in animals and more frequently in numerous humans across different sort of trials. And the labs that worked on Mila’s medicine felt that it was safe enough and hopefully efficacious enough. And at that point why is the hurdle so exponentially higher than what it would be for a child with end-stage cancer? The way that we are thinking about these children with end-stage genetic disease and end-stage cancer, is drastically different, so we need to first, to your point Rich, we need to start realising we’ve already set that precedent, we don’t need to be having this discussion again. We know the risk we’re willing to take for a dying child when there’s no other therapeutic, no other option and they’re going to die no matter what. So the risk of treating Mila, versus the risk of not treating Mila is black and white and we need to do our best and then we need to not only treat Mila but we need to learn from the treatment of Mila. We need to collect those learnings, they must be iterative learnings so that the next child that’s treated with an individualised different ASO or different medicine that they don’t happen in silos, but that all of this knowledge comes together so that the second and the third and the fourth and the tenth and the twentieth, the process gets better and faster and eventually cheaper so that it’s accessible.

Rich: Yes, and that’s very much back to Ana Lisa’s point on the link and for diagnostics too on continuing to learn and creating a system that recognises that that’s crucial to offering the best care today but also in the future and being able to make proactive decisions more confidently if you’re a policymaker, knowing that you’ll continue to learn, you don’t have to pretend you know everything today.

Julia: It’s very meaningful for parents. So when parents, children, are diagnosed whether it’s a fatal or life-longing debilitating or difficult disease, if you know that what’s being learned from your child both from just the genomics to the potential treatments that that’s helping the next child, that helps parents like me be able to continue living. And so you know, research is this kind of generic word, I wish there were a better word for it. Really what it is, is it’s learnings and it’s what can be learned from my child that can help the next child?

Ana Lisa: And then that learning requires a lot of collaboration, which is the super important part I think of your story.

Julia: Yes, it does, it requires a lot of people starting with those diagnosing the children with whole genome sequencing all the way through just to the clinicians who are in the NHS, not to mention the researchers who are then looking at the data and bettering their understanding.

Ana Lisa: I think there are also, maybe one can extend some of those parallels as well, in that I think currently we sometimes think of an individualised therapy of NF1 as being something that takes a lot of time and benefits an individual, and actually if we can really collaborate we can really set up processes that work across the ecosystem and keep learning, then I’d love to dream that actually this could help many, many different patients, with many, many different types of rare conditions because actually we’ve learnt how to target a little bit more at source, perhaps a particular type of genetic variant, and so a bit like cancer, we’re not thinking about breast cancer, we’re thinking about what sub-type, what genetic causes there are and targeting those, and if we can apply that one day more broadly across rare conditions then it might be that actually once you’ve learnt a certain amount, that you could scale up and treat many, many different conditions, not dependent on their frequency in the population.

Julia: Yeah, that’s a great dream, I share that dream. Rich, what is your, you’ve been in this for many years, what’s your dream for the next five, ten years?

Rich: I guess I have, I think there’s two aspects to it. I think there’s two, I think there’s a lot of distance left to run for us improving on the diagnostics and I think thinking back to your conceptualisation of it Julia, of sort of thinking about how we can bring that earlier, whether that is that for example we’re able to sort of more proactively flag when children have you know, more than one visit to a particular type of doctor or something that makes that happen much earlier in the process. So the tooling that we now know works whether it’s whole genome sequencing or something more targeted can be used earlier in the process, or whether for example in our newborn genomes programme we get that evidence that we can look for a broader range of conditions in a screening context right at the beginning of life.

And I think in five to ten years we should be in a substantially different place, we’ll know whether or not we think whole genome sequencing should be there but offered for every baby at birth, and we can be much more proactive also when symptoms arise. I would also hope that on the side of therapies and intervention, we’re in a substantially different position and I think, I’ve been amazed the last five years how my level of hope has increased. I believe we should now be in a position in five to ten years where those with a therapy that is potentially there to benefit them, should at least be able to be aware of it and there will be a clear pathway by which either that is available if it’s proven, or there’s a pathway that we all understand about how that can be trialled. And I think we’re at the beginning of that journey and I now feel it’s a responsibility of ours to work through how we can bring the right pieces into place, we can’t prejudge the science, but we can set up the system that makes us be able to respond to it.

Julia: Yeah, I remember Rich when you and I were speaking a number of months ago and maybe you could share the story because you talked about your hope kind of changing over time as a clinician I thought that was really powerful to me.

Rich: Yeah, I remember it’s probably now maybe 15 years ago being asked by a family about what my advice would be to them on the likelihood of there being a treatment for their child’s particular condition being available and in fact they asked me to do it in a way that I sort of provided a formal written report to them that I spent a lot of time thinking about and agonising over and was very honestly you know saying it was highly unlikely that something would become available. If I had to write that same report today it would be very different.

Julia: That’s so promising to hear that. I don’t know, Ana Lisa, have you had any experiences like that in the past that you feel differently now of how you would approach a family like mine?

Ana Lisa: I think it’s a real balance between having that hope ourselves, sharing that hope with other people and not giving false hope and it’s such a balance when right now more than 95% of rare diseases don’t have a treatment and I think that’s such a difficult position to be in right now. And everything we’ve been talking about gives me massive hope for the future and a lot of what we’re pouring our energy and efforts into is both the diagnostics so that we’re not trying to make a puzzle with missing pieces in the dark and that’s mission-critical, and then the real hope that actually this will drive therapies, which is what we really want for everybody who needs a therapy to have a therapy that’s effective, whether they’ve got a common condition, a rare condition and that’s our driving ideal.

So I think I’m full of hope and optimism and I hope that it will accelerate, that’s what I really hope, the momentum will build and we’ll get to a certain level of knowledge, we’re learning the processes, we’re learning the evidence, we’re learning the collaborative models that are needed to really suddenly explode our ability to treat rare conditions.

Julia: Yeah, you know when Mila was, I guess when I look at newborn screening in the United States and Batten CLN7, which is Mila’s kind of sub-type of her condition is not on newborn screening tests because there is no treatment for it, but the whole genome sequencing that was done for Mila was the data that we got from that was what was needed to create a treatment for her and so it’s an unusual case where she was sequenced and a child and a baby, a newborn in the UK could be sequenced and not only told that they have a disease, so they have time to kind of understand the disease more but also potentially kind of prepare for a treatment that might be in the pipeline, but that data is also going to help scientists and researchers create new treatments that may not be available when that child is born but that’s the data that’s needed to create the treatment.

Right now you guys are you’re really at the forefront of solving both halves of the what I consider like a rare condition, you know, global health crisis with tens and hundreds of millions of people that have you know families like mine, like my story sounds unique, it sounds impossible but there are tens of millions of other people like me, like my story sounds unique, it sounds impossible but there is tens of millions of other people like me and so to have the UK kind of leading this effort to solve both halves of the problem, the diagnostic half, you know, what disease does a child have and find it in time and also kind of the treatments, here’s where we’re headed, and if we don’t solve both of those problems then there is no such as access, you know to a better life, so I’m really grateful for the fact that you’ve set a precedent for other countries because now finally there are other countries that are looking towards you and kind of really trying to do the same thing that you’re doing.

Rich: Yeah, well I think we feel we’re uniquely placed; the NHS in the UK and for Genomics England our partnership with the NHS, together with a number of other factors and I think the recognition from government as well as the NHS over a long period that the importance and the power of genomics and the importance of for example, making changes to regulation to get it right mean that it’s something that I think we feel really privileged to be in the position to even be able to ask these big questions.

Julia: yeah, I think the UK is really uniquely suited to have hung their hat on genomics so that the topics you’re taking on are very central, they’re not kind of on the sideline, they seem whenever I’m in the UK they say that what Genomics England is doing is at the forefront and in the middle of all the discussions with academics and companies and regulators and government. What do both of you think are the, what are the biggest kind of hurdles we have coming a few years in the newborn programme or you know, any of your other initiatives?

Rich: I guess all of these are big questions and I think we need, it’s back to that sort of point from Ana Lisa sort of balancing the hope and expectation, I think we’re uniquely placed to develop the evidence really clearly and one of the things that we again think is so important is having this conversation in the public about it and developing a shared view, almost you know, it drives policy but it’s also something which I think the whole of society needs to sort of think about how we address and what we want to do collectively. I wouldn’t place it as a barrier but I would highlight it as a strength that we’ve had and I think we’re hopeful that we’ll continue is that long-term commitment in terms of government and the NHS and I think that’s really powerful in this space to maintain the UK’s position as being able to ask these questions and to show that leadership.

Ana Lisa: And to bring together, we need to work really closely across the ecosystem. So in my mind one of the challenges is if one part is missing then that person is not going to get the treatment and how we keep joining up these really important dots across the whole ecosystem to make sure that most people will one day be able to get a treatment.

Julia: And all those dots honestly, those dots can never even start unless you have a diagnosis and it’s in time. And so there are so many people around the world working on each of those dots that connect a child or a patient to a treatment, but if you can’t even be diagnosed or if you’re diagnosed too late, which is what the reality is in the world of rare conditions right, then you know, then it’s a little bit futile to race to a treatment or even think if that’s possible. So I think the very, very first thing is: can we find children and patients, like can we find children like Mila in time? And I love hearing the word ‘hope’ that’s the word that keeps me going and doing what I’m doing because if there isn’t any hope it’s pretty hard to keep fighting, so I’m really glad, thank you both for having hope.

Okay, we’ll wrap up here. Thank you to Ana Lisa and to Rich for joining me in this conversation today as we shed some light on the challenges you know that those with rare conditions are facing. We touched on the work being carried out across the Genomics ecosystem in the UK to support those living with rare conditions. If you’d like to hear more of this, please subscribe to the G Word on your favourite podcast app. And thank you so much for listening. I’ve been your host, Julia Vitarello. This podcast was edited by Mark Kendrick at Ventoux Digital, and produced by Naimah Callachand.

 

David Bick: Genomics 101 - What is the Generation Study?

In this explainer episode, we’ve asked David Bick, Principal Clinician for the Newborn Genomes Programme at Genomics England, to explain more about the Generation Study, in less than 10 minutes.

For more information you can listen to our podcast episode where David discusses the conditions that we will initially look for in the study.

You can also find a series of short videos explaining some of the common terms you might encounter about genomics on our YouTube channel.

If you’ve got any questions, or have any other topics you’d like us to explain, feel free to contact us on info@genomicsengland.co.uk.

Want to find out more? Check out the blog 'Genomics 101: What is the Generation Study?'

You can download the transcript or read it below.

Naimah: What is the Generation Study? I'm Naimah Callachand, and today I'm joined by David Bick, the principal clinician for the Newborn Genomes Program at Genomics England, and he's going to explain more.

Okay, so first of all, David, please, can you tell me what is the generation study?

David: The Generation Study is a research study organised by Genomics England in partnership with the NHS. So what is the study exactly? We know that children are born every day with treatable genetic conditions. What we want to do in this study is we want to find those children and treat them before they become sick. We know that if we can find these children early in life, we can keep them healthy.

Naimah: Can you tell me a bit about how the study was designed?

David: Yes, this study was designed to look for genetic conditions that are treatable, and we went about looking for which conditions to include through an extensive evaluation that involves specialists, laboratory specialists, the NHS and patients from different support groups. And through this process, we identified more than 200 conditions that are treatable, and we are including those in the study.

Naimah: And David, you mentioned the conditions list there. You can also find an additional podcast on our website where you go into more detail as to why the conditions on that list were chosen initially for the study.

Can you tell me how this fits in with the current newborn screening program?

David: The current newborn screening program looks for a smaller number of conditions, nine conditions. It has been extremely successful and is an extremely important program, and so we're looking to see how our program could be an adjunct to the current screening process.

Naimah: How would people take part in this study?

David: What we're going to do is we're going to ask couples in mid-trimester, in the middle of pregnancy to join in the study, we're going give them a number of opportunities to learn about the study and those that sign up. We plan to obtain cord blood from the placenta after birth. And as you may recall, the placenta is discarded and so this cord blood would normally simply be discarded, but we can take this umbilical cord blood and test it for genes. We expect it to expand to perhaps 40 trusts across the country.

Naimah: And David, the NHS is already under quite a lot of pressure at the minute. What will this study mean for the NHS? What impact will it have?

David: That has been one of the main concerns as we went forward with thinking about the study was to make sure that we did not add additional burden to the NHS. But it's important to realise that the children that we're looking for already have the condition, they're going to become ill.

And our plan is, our hope is that if we can find them before they become ill, we will actually relieve stress on the NHS system. Let me give an example. There is a condition called biotinidase deficiency. Here is a condition where the child who has it, is unable to recycle a vitamin called biotin. Well, biotin is something you can pick up at the health food store, and so these children.

Need to be given extra biotin every day. Very, very inexpensive, very, very safe. But if you don't find these children before they become ill, they can become quite seriously ill. So if we can find these children before they get sick, get them started on this very simple, very inexpensive, very safe medication vitamin. In fact, this will actually save money for the NHS, but also help the NHS function more effectively. And most importantly, to allow parents to have the knowledge that they have done something for their child, which will prevent their child from becoming ill. 

Naimah: Some parents might want to know if their child's data is being kept safe. What are you doing to ensure this?

David: Data safety is very important to us. We know that this information is extremely sensitive, and so our data protection is a very high priority. We're controlling very carefully who will have access to the data. There are groups that we do want to work with this data. We want researchers and the pharmaceutical industry to work with this data to improve treatments.

We know that there are many, many genetic conditions for which there is no treatment. Those conditions are not on our panel, and so we're hoping that the information that we learn from these genomes can be used to improve the care of conditions that exist, that are treatable, but most importantly, to find treatments for conditions that are currently not treatable.

And one way that we're doing this is we're going to ask families to stay with us for several years after the program starts. Once we have screened families, we're going to find some that are going to be screened positive, in which case we would look to see whether they have the condition or not, and then go ahead and start treatment.

We also, unfortunately, in a screening situation, we know that we're going to miss some cases, and so again, we want to stay in contact with families so we can know how to improve the testing, but most importantly, to understand how the test works, how screening works using genome and determine whether this makes sense to include all patients that are born in England going forward.

Naimah: And can you just finally tell me where you expect this study to go? In the coming months?

David: What we hope is that one day we'll reach a point where we can find and treat children who have treatable conditions before they get ill. this would really make our healthcare system a real healthcare system. We would find children before they get ill.

In this way we can keep children healthy and help them lead and live their best lives.

Naimah: So that was David Bick explaining ‘what is The Generation Study’. You can find out more about the study on our website and if you'd like to follow us on social media, you'll be able to keep up to date with any of the updates.

Thank you for listening.

Vivienne Parry, Louise Fish and Professor Matt Brown: Celebrating genomic breakthroughs - Insights from the Festival of Genomics

In January we saw experts from across the genomics ecosystem, including patients and those with an interest in genomics, gather at the Festival of Genomics - the UK's largest annual life sciences event.

In this episode, our host, Vivienne Parry, Head of Engagement at Genomics England, speaks to Louise Fish, CEO of Genetic Alliance UK, and Professor Matt Brown, Chief Scientific Officer at Genomics England, to discuss the event and emerging future trends in genomics. 

In this episode you'll also hear some exciting future advances in genomics research from some eminent speakers at the Festival:

• Harold Sneider, Professor of Genetic Epidemiology, University Medical Center Groningen sheds light on the "Identification of methylation markers for Type 2 diabetes up to 10 years before disease onset."
• Nagy Habib, Professor of Surgery, Imperial College London, delves into "The future of saRNA therapeutics and its potential for treatment". 
• Lennard Lee, National Clinical Advisor on innovation and cancer vaccines, presents his perspectives on "The Future of Cancer Vaccines," offering a glimpse into the promising advancements in this critical field.

"The scientific breakthroughs that are being made are absolutely incredible and they’re really exciting, but from the point of someone living with a genetic condition, what they want to see is those scientific breakthroughs making a real difference in the clinics...For some conditions, it’s about treatments, but it’s also about being able to get a diagnosis faster, to be able to understand what condition is impacting on you, how it might affect you over your lifetime and your wider family, and to be able to work with NHS services to understand and plan for the care and treatment that you’ll need throughout your lifetime."

 

You can download the transcript or read it below.

Vivienne Parry: Hello and welcome to the G Word.

The Festival of Genomics is the UK’s biggest genomics event, and it’s become an essential part of our year. It’s free for 90% of its delegates, it’s in person, and with more than 5,000 people expected, it’s now so big that it’s had to move to ExCel’s cavernous Dockland Halls. It’s the place to hear top science and to spot new trends, but actually for me the joy of the festival is the people you meet. Of course, it’s great to catch up with old friends, but it’s the new collaborations sparked by random encounters at the festival which I think are the lifeblood of the genomics ecosystem, and everyone with an interest in genomics is here, patients, clinicians from the NHS, researchers, industry, policymakers, and the G Word.

What we thought we’d do is bring you a flavour of this great event from the floor of the ExCel halls, and give you a quick soundbite from three of the speakers that we felt best exemplify the future of genomics. With me to discuss the event and future trends in genomics, Professor Matt Brown, Genomic England’s chief scientific officer, and Louise Fish, CEO of the Genetic Alliance UK, which as its name suggests, is an alliance of over 200 organisations reflecting the needs and concerns of those affected by genetic conditions. My name’s Vivienne Parry, I’m head of public engagement at Genomics England, and I’m delighted to be your host for today’s pod from the Festival of Genomics. Welcome to you both. So, let’s start with you, Matt. How important is the Festival of Genomics for genomics in the UK?

Matt Brown: Well, the Festival of Genomics has become a really key meeting for the genomics community in the UK, and I think increasingly in Europe as well. It’s a really large, high quality event that brings together commercial and academic and biotech companies in the one forum, and I think it’s a really exciting programme.

Vivienne Parry: And of course, Louise, it’s open to patients as well, which makes it an unusual event.

Louise Fish: Absolutely, and it’s brilliant to have patients and families here. So, people living with genetic conditions clearly need to be part of the debate when we’re talking about developing new services, and developing new treatments and diagnostics, so it’s absolutely fantastic to be able to come together in one room with people from the NHS and the broader sector.

Vivienne Parry: And it’s grown enormously, and I guess that reflects, as much as anything else, just how exciting genomics is. Matt, I’m going to pin you to the ground [laughter] and say, why is it so exciting in genomics at the moment?

Matt Brown: Look, the field’s really hitting its tracks. We’re seeing advances in technology, analytics, application in the clinical space, and of course booming commercial activity associated with that. But from a situation ten years ago, where we had research capability for using genomics to assist in diagnosis and cancer profiling, now we’re in a situation where we have multiple different approaches to assist with both of those things, transcriptomics, proteomics, spatial, single cell methods, optical mapping, a whole monopoly of different technologies that have developed out of the research world but are pretty close to being ready for clinical application. Of course, in analytics, the rise of AI and the potential that has for improving interpretation of genomes and improving personalised medicine prediction in cancers and in multivariant data, those are absolutely massive things. But aligned to that, there’s also, you know, the growing worldwide application of genomics in clinical spaces, of course led through the UK and the NHS Genomic Medical Service, which has really shown the way for the world about how this might make a difference.

Vivienne Parry: And Louise, that’s the really exciting thing is we’re now seeing not just talk about therapies, we are seeing the therapies for rare disease actually going into clinical trials and into services even.

Louise Fish: Yeah, absolutely, and that’s why people living with genetic conditions and their families want to see the change. The scientific breakthroughs that are being made are absolutely incredible and they’re really exciting, but from the point of someone living with a genetic condition, what they want to see is those scientific breakthroughs making a real difference in the clinics. And that’s sometimes about treatments, you know. For some conditions, it’s about treatments, but it’s also about being able to get a diagnosis faster, to be able to understand what condition is impacting on you, how it might affect you over your lifetime and your wider family, and to be able to work with NHS services to understand and plan for the care and treatment that you’ll need throughout your lifetime. So, treatment’s one part of it, but actually that ability to better understand what the future will hold for you, and to plan ahead for the care and support that you will need to live your life to the full is what really excites people living with genetic conditions and their families.

Vivienne Parry: Now, let’s hear the first of our three clips. The programme is absolutely vast, but these were three presentations that we just thought were terrific. Let’s hear the first one.

Nagy Habib: My name is Professor Nagy Habib. I’m a consultant surgeon at Hammersmith Hospital, Imperial College, London. We are going through a very exciting time, where we know what is the problem with the diseases, and so far we couldn’t do anything about it, but suddenly the door is opening and it all came with the RNA vaccine, because we had to go very fast to get a vaccine for covid, to protect the population, and that pushed the science to go very fast, and now we can apply it to other areas apart from covid, like cancer and rare genetic diseases. And these therapeutics are what you and I and everybody else have received during vaccination. There has been six billion injections around the world, so you can imagine that everybody had an RNA injection. And RNA is that molecule between our genome, the DNA, and the protein. For anything to happen in our body, it requires the protein, but there must be an RNA in between. In the past, it was all about DNA, but now it is RNA. Why can’t we get a vaccine against cancer?

And so now the field is growing very fast for a vaccine for cancer. Now, the way we think about it is that we can have an injection so that we don’t develop cancer of the prostate or cancer of the breast and so on, but in actual fact today what we can say is that if we take out a tumour with surgery, and we can take the RNA from the tumour and inject it in the patient, the early clinical trials tell us that this might work, and to stop the tumour coming back. It is very important to make sure that, once the tumour is out, it doesn’t come back. And I think there is hope that we can have RNA vaccines in cancer. Now, to treat cancer without surgery, still we have some way to go, but again, now we know that the problem with cancer is that some of our immune cells that are there to defend us from cancer, they change their mind and suddenly they collaborate with the enemy. So instead of helping us, they are destroying our immune system, and we are developing drugs that can stop that from happening to our immune systems.

Now, when you really think about what are the diseases that kill people, cancer is definitely very high up. The second one, not in a particular order, but cardiovascular system, we get heart attacks and we die from heart failure, or we get stroke and we die from stroke, and that’s because we eat too much. The food is very tasty [laughter]. So, now we have injections, and the injection can make us lose weight, and we lose weight very fast. The problem is again it’s very expensive. Who can afford £600 a week? And when you stop the injection, you put on weight again. So, now we are working again with RNA, and we have found a way where you inject only once every six months.

And then the final thing, which is really the dream of everybody, is to stop Alzheimer’s disease. So, Alzheimer’s disease, as we get old, there are toxic materials that are accumulating in our brain cells, and only this year we’ve got two drugs coming along that can help stopping Alzheimer’s disease at an early stage. Now, what we need to do is to bring that it works on all types, even the advance type of Alzheimer’s disease, and now there are [inaudible 0:09:26] where we can take it from the nose. So, you inhale it from the nose and it goes straight to the brain, because there is sort of a motorway that connects the roof of the nose with the base of the brain, which is very simple. It doesn’t even need an injection in the arm vein. So, it’s all very, very exciting.

Vivienne Parry: That is so fascinating. It’s real future casting. Matt, I mean, I say it’s future casting, but tell me a bit about the Rare Therapies Launchpad, because, you know, that picks up some of what Nagy has outlined.

Matt Brown: Yeah, so DNA and RNA therapeutics are absolutely booming, and that’s one of the big excitements is that we’re not only being able to diagnose people, but we’re coming up with new ways of actually providing treatments for patients with rare diseases and cancers through nucleic acid therapeutics. For rare diseases, the type of clinical trials that are involved are really quite different, and you can’t just basically translate what was used for common diseases into the rare disease space. It just doesn’t work, and that’s really held back the field a lot. So, to try and enable rare therapies to actually make that leap from a research setting into actual clinical practice, Genomics England, in partnership with the Medical Health Regulatory Authority and others, have set up a Rare Therapies Launchpad, to provide an end to end solution for people to be able to run clinical trials for rare and ultra rare diseases, particularly focusing on nucleic acid therapies, and linking that with both the regulatory authorities and health funding authorities so that we can get these ultimately into clinical practice. I think we need these sorts of initiatives so that we don’t continue to see rare therapies falling over because they’re being assessed and made to go through the hurdles that common therapies do nowadays.

Vivienne Parry: So Louise, we really are in the area of what people call N of 1 medicines.

Louise Fish: Yeah, absolutely. So, these are medicines that are made specifically for one person and will help that one person, and obviously that brings a whole heap of possibilities for people living with genetic conditions, but also a load of challenges that we understand for decision makers within the MHRA and NICE and the NHS. And so I think there are some real challenges that we’re really aware of from the decisions that are already being made by those decision making authorities about treatment. Obviously, putting it at the most basic level, you don’t have the same evidence base for treatment that’s just available for one person that you do from a clinical trial, where thousands of people will have taken part in a trial to understand how it affects a whole host of people.

So, we know that the decision making bodies are going to need to take a different approach to evidence, so are going to need to be willing to look at evidence that is just from a trial involving one person. They’re going to need to be able to extrapolate the benefits of that treatment across someone’s lifetime, and that can be challenging, and we’ve seen that before in rare disease medicines and the new treatments that have come along in recent years. So, there are definitely some challenges, and we’re really glad to see those challenges being acknowledged upfront by Genomics England, the MHRA and others, and being debated and discussed, and trying to find solution now rather than waiting for those treatments to come along later, and then trying to retrofit and decide how to manage them. So, it’s great to see this debate taking place early, and we’re really keen to make sure that the voices of people living with rare conditions and their families are part of that discussion.

Vivienne Parry: And the really cheering thing that we’re hearing from Professor Habib is that he thinks that the cost is going to be much less, because some of these things, you know, have million pound price tickets, so to have something that will be cheap is really going to be I think the gamechanger.  

Louise Fish: One of the challenges with that is understanding the lifetime costs of someone living with a genetic condition and all of the complexities that are involved, and not just the medical care that they need, but the social care and the wraparound care that they’ll need, the extra support from schools and colleges, the extra support from employers if they’re able to go in employment. So, I think we’re constantly trying to help the government and decision makers have a better understanding that those lifetime costs of living with a genetic condition are the things that should be taken into account when they’re making decisions about a new treatment that could be totally game changing for someone’s health and their future.

Vivienne Parry: Cheaper treatments on the way, Matt?

Matt Brown: So, I think we absolutely need to work on reducing the costs of these treatments, because at the moment the costs are so high that, were we to extrapolate that out to try and treat the thousands to tens of thousands of different rare diseases that there are out there, we couldn’t possibly afford it. I think it’s very promising that we will get cheaper treatments. This might come about through reducing the development costs, in particular reducing the clinical trial programmes, and the level of safety and efficacy evidence that you require before you can actually make these treatments available. I think that will make a massive difference, if we can simplify that.

And another thing is, by better collaboration between the different rare disease communities and genetic medical services around the world, to make sure that what might be an N equals 1 condition in the United Kingdom, when you consider it around the world, might actually be an N equals 100 people, and then basically the cost per patient drops substantially. To achieve that, we need much better coordination between the national genomic medical services.

Vivienne Parry: At the end there, you heard talk of using RNA therapies for obesity and Alzheimer’s, and we principally talk, particularly in Genomics England, not just about cancer and rare disease. But I wanted to present to you another presentation, which I just thought was extraordinary, which comes from the Netherlands, and it’s about picking up signs of diabetes using genomics ten years in advance. Just listen to this.

Harold Sneider: Hi, I’m Harold Sneider, I’m a genetic epidemiologist working at the University Medical Centre in Groningen in the Netherlands, and my focus is on cardiometabolic disease, and I have a great interest in hypertension, for example, obesity, but also type two diabetes. So, one of my major interests is to try and identify genes for common complex, mostly cardiometabolic diseases, so our approach is to do genome-wide association studies using genetics, but also epigenetics. And epigenetics can be screened for so-called methylation markers, and those methylation markers have an effect on expression of the genes, and we can look at this all over the genome. Then a very interesting question came up, whether these types of epigenetic signals or methylation markers could actually be used to predict disease in people that are still healthy.

So, the goal of this type of work always consists of two parts. First, it’s that we try to find out which genes are highlighted by these DNA methylation markers, because they are located at certain positions on the genome, so we know which genes are involved in those regions and we can learn more about the underlying biological mechanisms that play a role in the development of the disease. Because we found those signals up to ten years before the disease occurred, so that tells us something about changes that already happen at an early stage. It’s like an early detection mechanism. At the same time, a combination of these markers together lets you calculate what’s called a methylation score that can be used for the prediction of the disease, and the ultimate goal here is that even in healthy individuals, when you have those measurements, you can calculate such a score to improve the prediction and identify people with a higher probability to develop such a disease. I definitely think we can apply this general approach also to other – for example, cardiometabolic diseases, such as coronary artery disease or also hypertension.

Vivienne Parry: Harold Sneider there from Groningen. And extraordinary, the idea that you might be able to pick up not just diabetes perhaps ten years in advance, but also he was talking about potential for other lifestyle diseases, like cardiovascular disease, for instance. What are your thoughts about that, Matt?

Matt Brown: Look, I think it’s always been an aspiration of the clinical community to move treatments from treating patients with established disease to actually working in really early or preclinical spaces, where you’ve got a much better chance of preventing end organ damage, and secondly you’ve got a much better chance of actually inducing remissions or potentially actually curing diseases. And I think not just in diabetes, but also in a range of immune mediated diseases, there’s pretty good evidence now that you can, by intervening early, really make a massive difference to the natural history of diseases, and new methods are coming about to identify those patients, be it polygenic risk scores or other biomarkers, to enable us to sort of flip the approach of medicine from being reactive to pre-emptive.

Vivienne Parry: And rare conditions, as they do so often, Louise, are leading the way in understanding the issues, which will then spill out into a much wider area of the population.

Louise Fish: Yeah, absolutely, and rare conditions obviously is the space that we work in. So, Genetic Alliance UK, as you say, is an alliance of around 230 charities that support people largely with rare genetic conditions, and many of those charities are condition specific or look after groups of conditions, like metabolic rare diseases. So, that’s the kind of space that we come from, and obviously in our space, the excitement is around the work that we’re doing with Genomics England around the Generation Study, and trying to use that to understand whether it's possible to screen babies to understand whether they have a rare genetic condition, and if so to identify that condition and intervene early. And again, excitingly, that’s not just about treatment, it’s about whether there’s a way of helping that child and their family, if you can identify very early to help really improve their lifestyle choices. And one of the best examples we have is identifying children with brittle bone disease, where if you pick them up through screening, you’d be able to teach their parents to handle them safely, so they didn’t have breaks in their bones as babies, which is what we see now.

So from our perspective, it’s obviously different to the polygenic risk scoring, but again it’s that idea of using genomics as a way of identifying conditions very early, and intervening before signs and symptoms start, to try and improve the life chances of the person living with that condition, and help their wider family to help them, which is really exciting from our perspective.

Vivienne Parry: But the experience and knowledge that you’ve gained as rare disease organisations actually is enormously valuable to other people. I mean, rare has always been at the forefront. I mean, in cancer, for example, it was chronic myeloid leukaemia, which was a rare cancer, that kind of unlocked cancer targeted treatments for everybody else. And it always seems to me that rare is at the forefront. Although it’s often seen to be behind, it actually is the key to unlocking so many other things, and the experiences that you have all had are so valuable for much wider populations.

Louise Fish: Yeah, absolutely, and one of the reasons we run Genetic Alliance UK is so our member organisations can learn from one another, ‘cos there’s always one of the rare patient organisations which is surging ahead in a particular space, doing something really exciting, doing something really new, and we try and make sure that our members can learn from one another and don’t have to kind of reinvent that wheel. But I know that spills out into the wider cancer space and beyond, which is fantastic.

Vivienne Parry: And Louise, do you think there are particular conditions which, if I can put it like this, are on a roll at the moment, where genomics is really advancing fast for them?

Louise Fish: Oh goodness, that’s a really good question. There are lots of conditions where genomics is making a significant difference really quickly. For us, I think we go back to the Generation Study, and at the moment we only screen in this country for nine conditions, soon to be ten with the addition of a new condition, but the Generation Study’s looking at 200 conditions and whether it’s possible to screen for them. And for all of those 200 conditions, it’s a really exciting opportunity to see if we can learn more, both about the potential to understand and develop treatments early, but also just about the chance to understand the natural history of that condition so much earlier than we do at the moment. And I think that’s it, it’s that understanding of the natural history of the condition really early, and understanding how a family can be helped through all the aspects of the condition, which is giving people most excitement, I think, alongside the potential to develop treatments.

And I know we talk about treatments a lot, but at the moment only five percent of rare diseases have a condition specific treatment available, so we really try and balance, within Genetic Alliance UK, that hope for the small number of conditions that do have treatments, which is really exciting, or have treatments in development, and actually making sure that the scientific breakthroughs in genomics are something that all conditions can benefit from, whether there’s a treatment or not. The potential for early identification of people with a condition, understanding the natural history better, and wrapping a package of support and care around people that is not just about a drug itself, is really important to us and to all of our members.

Vivienne Parry: Matt, are you seeing any particular areas where there’s a really rapid success?

Matt Brown: Look, I think there have been some absolute standout successes in nucleic acid therapies in recent years. So, one is the treatment of familial hypercholesterolemia, with siRNAs for PCSK9, so the Inclisiran type approach, which has absolutely revolutionised management of that disease. In recent times, I’d highlight, for example, the treatment of sickle cell disease, an absolutely massive global problem, and now we’ve got a therapy which can really control sickling crisis and make a big difference to a disease which isn’t just a disease of developed countries, in fact it’s particularly a disease of Africa, of course. On a global level, that’s just going to have a huge effect.

But I think, yeah, I just would like to come back to that comment you made about things starting with rare diseases. So, in genomics, rare disease genomics has taught us a heck of a lot about what drives common diseases as well, and to my mind, gold dust for drug development companies is where you have genes that are associated with both rare and common forms of the same type of disease. And that tells you that basically you’re very likely, through your treatment, to be able to actually influence the disease, and that it will influence a large proportion of patients with the disease. So, I’m really enjoying seeing this division between rare diseases and common diseases broken down a little bit, and a lot more learning in therapies going from one to the other.

Vivienne Parry: Let’s move to a completely different area, one that’s very important to Genomics England and less important, Louise, at the Genetic Alliance UK, which is cancer. We’re going to hear from Lennard Lee about cancer vaccine.

Lennard Lee: I’m Dr Lennard Lee, I’m a medical oncologist, so I practice as an NHS doctor, treating cancer, and I’m an associate professor at the University of Oxford. We’ve come to a position whereby vaccines can be developed quicker than anyone thought. In the last few years, we’ve realised that the technology has moved on rapidly, MRNA technology, and you can make vaccines and update them really, really quickly. We’ve now come to a situation where vaccines can be made against cancer, and this is where genomics is really starting to supercharge this technology. If you can sequence a cancer then what we’re finding now is that the technology now exists for you to print off an MRNA vaccine for that patient, a truly personalised product. And it’s amazing because the genetic basis of the cancer, what the genomics sequencing shows then becomes a vaccine itself. The vaccine is designed based on that sequence, and that’s why genomics has really supercharged this field of vaccinations for cancer.

One of the possible things we just need to clarify and be aware of is that when people talk about cancer vaccines, they mean a number of things. Ultimately, what it involves is getting a new treatment for people with cancer, because it’s based on their genetic sequence, so it’s used to treat people with cancer. The future’s an exciting one, truly personalised medicine based on genomics. Genomics is going through so many different phases in the field of cancer. Firstly, we were starting to understand why cancer happened and what patients outcomes were. The second phase started to kick off where genomics would help patients select the right drugs at the right time for them, which is amazing. And now we’ve entered the final evolution of genomics, where it now becomes the actual drugs that we treat people with. And cancer vaccine is one of the first potential areas where genomics will start to form the basis of the treatments going ahead. In five years’ time, we’re going to know if it works or not, where an individual vaccine based on the genomic abnormality seen in that cancer is going to give better outcomes for patients than an off the shelf product.

We know that every cancer’s different, so genomics has showed us this, but all of a sudden that sequence could become that vaccine, which then primes that immune system, truly personalised therapy. And it is so exciting that we’re going to be talking about this in this festival, and it’s being driven as from the UK, which has got so much strength in terms of genomic capabilities as we’re developing vaccines.

Vivienne Parry: So Lennard Lee there, absolutely confident of the importance of cancer vaccines. Matt, what are your thoughts on that? 

Matt Brown: I think it’s a tremendously exciting field. The early data on cancer vaccines with melanoma, for example, showed that for a cancer which previously had been resistant to virtually all of our approaches, is actually quite responsive to novel cancer vaccine approaches. We are yet to see across what diversity of cancers this is actually going to work, so there’s clearly a huge clinical trial programme that’s going to be required to drive this, and the UK is playing a really central role through the Cancer Vaccines Launchpad that Lennard’s involved with running, in creating the evidence base about whether these are going to achieve the promise that they hold.

I also think that they’ve got a lot of possibility for inherited cancer types. For example, I think the programme’s looking at cancer vaccines for Lynch syndrome, to try and prevent colorectal cancer in that group of patients. So, I think they’ve got lots and lots of opportunities, and it’s nice to see something positive actually coming out of the pandemic like this, for what was a pretty bleak episode worldwide otherwise.

Vivienne Parry: They are a small part, I know, of your organisation, Louise, but in some ways, those people with inherited cancers in their families are seeing the benefits of genomics on both sides, both in that earlier diagnosis, picking up right from the very beginning, and of course in the promise of these new treatments.

Louise Fish: Yeah, absolutely, and you’re right, it’s a small part of our remit. We do have some organisations in our membership who specifically support people with rare inherited cancers, and we work very closely with an organisation called Cancer 52, who also represent organisations with rare cancers. I’ll just give them a quick shoutout in case anyone listening is not aware of them and their amazing work. But you’re right, I think there are a couple of things going on that are really exciting in the cancer space. It’s that ability to better understand why some people are likely to inherit cancers, how that pattern works within families, and to support those families and help them understand like the risk that they have, and to make informed decisions about their own treatment and care in the future. And also about whether they want to have children, and if they do want to have children, kind of how they want to approach that to try and reduce the risk of passing on that heritability. So, that’s a really important part for everybody. I think there’s also potential to develop new treatments, which is absolutely amazing and really exciting, and it is really exciting to hear about the potential for cancer vaccines.

The other area where I think people living with inherited cancers are interested to find out more is what impact it might have on better understanding which treatments will work for which people. And we know, for example, that there are some cancer treatments that only work for one in four people with that particular kind of cancer, but it’s been really hard to understand why that’s the case. And I think the potential for genomics to identify which people could benefit from a particular cancer treatment would have two huge benefits. A, cancer treatments, many of them are really horrible, you know. They’re horrible things to go through, and if you had a better confidence that a particular treatment was going to work for you because of your genetic makeup, that would make you a lot more confident about deciding to try that treatment, and taking on board the side effects of the treatment and how it’s going to impact on you.

That would also obviously massively impact on the cost effectiveness of that treatment. At the moment, we might give it to four people and only one of them would benefit, but you’re paying for the cost of giving it to all four people. If you could identify in advance which people were more likely to benefit then you’d give it to fewer people, they’d be more likely to benefit, and the cost would come down. So, I think that there is real potential in this field of genetics and genomics to help in all kinds of ways that people living with these conditions are really excited to see and explore.

Vivienne Parry: So Matt there, it’s not of course simply about identifying, you know, what the cancer is like and its genomic makeup, but actually it’s that wider field of pharmacogenomics, which is a big feature of the programme at the Festival of Genomics this year. And we’re very much involved in that, aren’t we?

Matt Brown: Yeah, we are. So, pharmacogenomics is one of those areas where genomics is about to make a big difference in clinical practice. What we’re hoping to get to is the point where we have people who are not yet treated with a medication actually already have the genetic profiling done, so that when they go to a general practitioner or a physician and be prescribed a medication, the data will already be there to say what the appropriate dose should be, and whether they’re at risk of getting adverse reactions to those medications, so we could avoid them or use alternate medications. So, that sort of pre-emptive pharmacogenomics is just over the horizon, and if we can achieve that, we’re going to significantly improve patient care and reduce the risk of adverse drug reactions, which are a major cause of morbidity and hospital admissions not just in the UK but worldwide.

Vivienne Parry: So Matt, perfect segue into our next question, which was, you’ve already identified one area which you think is going to be big in the next few years. You’re both absolutely in the centre of the genomics ecosystem. What do you think we’re going to be seeing at next year’s Festival of Genomics? What do you think is going to be the big thing that’s coming up on the inside rail?

Matt Brown: So look, I’d like to say what I think’s going to be in next year and what I think’s going to be in ten years. Next year, I think the big things are going to be advances in AI and genomic analytics. That’s really ramping up fast, and I think we’re going to see it in clinical implementation a lot more next year. I think the cancer therapy vaccines are going to be really big next year, as are nucleic acid therapies. Multiomics for rare disease diagnosis and cancer personalised medicine, I think is also ramping up very fast. In ten years’ time, the two areas that we’ve not discussed so far where I think genomics is going to make a big difference are going to be in infectious diseases and in pathology services. In infectious diseases, genomics I think has a fair chance of replacing to a large extent culture based practice, or serology based diagnosis of infectious diseases, which will be done by sequencing instead. And that will be a massive change to the practice there, because you’ll be able to rapidly work out, even if people have been treated with antibiotics already, what the infections are and what the likely treatment responses are going to be.

Louise Fish: So from my perspective, next year what I hope to see is people getting just as excited about the differences that some of the technology we hear about this year are actually making when they’re being applied in clinical practice. So I think from my perspective, it’s all about that move from being excited about the science to seeing people just as excited about the difference that science is actually making when it’s benefiting people living with rare conditions and their families through clinics across the UK and the NHS. Next year, I’d like to hear that excitement when people are talking about how it’s actually affecting real lives. In ten years’ time, I hope we’ll be talking about the massive difference that some of the amazing techniques we’ve heard about here this year have made to the lives of people living with genetic and rare conditions.

So, you know, in ten years’ time, I hope that some of the treatments and the opportunities and the tests we hear about today, we can see how they’ve affected the natural history of the condition across ten years of lives, and that we can really see that people are living their lives to the full as a result of the fantastic technological breakthroughs that we’re hearing about today.

Vivienne Parry: Fantastic. It’s been great to talk to you both, and it has been a fantastic festival.

Vivienne Parry: So, thank you to you again, and also thank you to Frontline Genomics, who organised the Festival of Genomics, because it really has been a wonderful, wonderful event. And if you’re interested in things genomic, you can subscribe to the G Word on your favourite podcast app, and if you’re new to our podcast, and we always welcome our new listeners, do check out our back catalogue. You’ll find it’s really extensive. There’s a wonderful set of genomic listening available to you, in which even spatial transcriptomics gets explained. I’ve been your host, Vivienne Parry. This podcast was edited by Mark Kendrick at Ventoux Digital, and produced by Naimah Callachand, and it's very good to have had you with us. Bye for now, and hope to see you at the Festival of Genomics next year.

Ana Lisa Tavares: Genomics 101 - What is a rare condition?

In this explainer episode, we’ve asked Ana Lisa Tavares, Clinical Lead for rare disease research at Genomics England, to explain what a rare condition is, in less than 10 minutes.

You can also find a series of short videos explaining some of the common terms you might encounter about genomics on our YouTube channel

If you’ve got any questions, or have any other topics you’d like us to explain, feel free to contact us on info@genomicsengland.co.uk.

Want to find out more? Check out the blog 'Genomics 101: What is a rare condition?'

You can download the transcript or read it below.

Naimah: What is a rare condition? Today I’m joined by Ana Lisa Tavares, Clinical Lead for rare disease research at Genomics England, and she’s going to explain more.

Ana Lisa: There are thousands of rare conditions. I hesitate to say a number as we’re learning all the time, so this keeps changing. There are estimated to be perhaps around 10,000 different rare conditions, as an order of magnitude. Many rare conditions start in childhood, 75% or three quarters affect children. A little over 10% affect adults, only adults, and some, around 20% can start in children or adults.

Naimah: So, what makes a condition rare?

Ana Lisa: A rare condition can be defined as affecting less than one in 2,000 people in the general population. This is a definition that’s used in Europe. Different parts of the world use slightly different numbers and definitions, so for example, the number of people with a rare condition living in that country, there isn’t one single universal definition.

The important part I think is that this is a practical way to help shine a spotlight on rare conditions, which collectively affect a lot of people, and the particular challenges in making diagnoses and finding treatments for rare conditions. So together, it’s estimated 7% of people are affected by a rare disease in their lifetime, or one in 17, so that means that there are 3 and a half million people in the UK affected by a rare disease, and in the world, probably somewhere between 250 to 450 million people, so perhaps 350 million people, a really huge number.

When you look into these numbers, there are rare conditions that are much more common than others. So, 80% of people with a rare condition have one of the 150 most commonly occurring rare conditions. Cystic fibrosis would be an example that many people will have heard of, and if you look at those numbers from a different angle, 85% of rare conditions affect less than one in a million people, so are very rare, and it’s important to bring together these different voices to solve some of the common challenges.

Naimah: Can you explain to me how these differ from more common conditions?

Ana Lisa: The simplest answer is that they are defined by the frequency, so how often they happen in the general population, and one reason for grouping together thousands of rare conditions is to highlight some of the particular challenges. This includes delays in getting a correct diagnosis that can often take years, an increased chance of a misdiagnosis before getting to an accurate diagnosis, and treatment challenges, as 95% of rare conditions don’t have a specific treatment. This is a very good question, and I would like to note that it’s also an artificial distinction to some extent. So, human conditions have a range of underlying causes that can be broadly grouped together, including genetic and environmental, such as a viral infection.

However, it gets complicated, for example, a proportion of common conditions that may have many different causes will have a genetic component, so for example causing an early onset familial form of a condition, such as diabetes. And in fact, genetic causes may give or can give the clue or the key that’s necessary to develop a new drug therapy that can then help many people with the condition, so those that may have a rare genetic cause and those that have a more common cause, such as for high cholesterol.

So, one other way that rare and common conditions can differ, not just based on frequency, is the causes of those rare conditions and common conditions. I’ll start by saying that there are lots of rare conditions that aren’t genetic, and there are common conditions that do have a genetic basis, so none of these observations are absolute, but there’s a spectrum of different causes for rare and common conditions. So, I would say there are more rare conditions that are caused by a single genetic cause, and there are more common conditions that might be caused by many very small genetic effects acting together, and also many different environmental causes.

Naimah: So, are rare conditions always genetic?

Ana Lisa: The short answer is no. Many rare conditions do have a genetic cause, perhaps 70 to 80% of rare conditions, so if you had 10 people with different rare conditions together in a room, the chances are that 8 of them will have a genetic component to their rare condition. And when we talk about genetic causes, these can of course be very varied, from a single letter change in the DNA code to an extra chromosome with several hundred genes. Rare conditions include ones without any known genetic cause, so for example some rare infectious diseases and some rare cancers. And I think it’s important to say that there’s a lot that we collectively don’t know yet about rare conditions, so our understanding is incomplete and imperfect, and there’s still a huge amount to understand.

Naimah: And it would be good to understand what challenges patients with rare conditions might face.

Ana Lisa: There are many challenges in achieving an accurate diagnosis, getting well organised, coordinated care, and the fact that 95% of rare conditions don’t have a specific treatment. There’s a big impact on emotional wellbeing for those with rare conditions and their parents and carers. Genomic Alliance did a survey showing that 88% of those with a rare condition felt emotionally exhausted from having their rare condition, and there are big impacts on other aspects, such as education, employment, etc. 

Naimah: And what do you think the future looks like for the treatment of patients with rare conditions?

Ana Lisa: So, this is a huge question with many answers. I think key is coordinated care, and I’m personally really excited about the potential for new rare therapies to be made for particular types of genetic causes that perhaps one day could be modified to treat many different types of rare conditions. To me, this would be incredibly powerful and would be a dream to transform therapies for rare conditions.

Naimah: That was Ana Lisa Tavares explaining what a rare condition is. I’ve been your host, Naimah Callachand, and if you want to hear more explainer episodes like this, you can find them on our website at www.genomicsengland.co.uk. Thank you for listening.

Dr Natalie Banner, Ismael Kherroubi García and Francisco Azuaje: Can Artificial Intelligence accelerate the impact of genomics?

On this episode, we delve into the promising advances that artificial intelligence (AI) brings to the world of genomics, exploring its potential to revolutionise patient care. Our guests discuss public perspectives on AI in genomics and address the ethical complexities that arise in this rapidly evolving field. Gain valuable insights into the future landscape of genomics and AI, as our experts discuss what to expect on the horizon. 

Our host Dr Natalie Banner, Director of Ethics at Genomics England, is joined by Ismael Kherroubi García, member of the Participant Panel and Ethics Advisory Committee at Genomics England, and Francisco Azuaje, Director of Bioinformatics at Genomics England. 

 

“So, AI is already driving the development of personalised medicine for both research and healthcare purposes. [...] In the context of healthcare, we are talking about AI tools that can support the prioritisation, the ranking of genomic variants. To allow clinicians to make more accurate and faster diagnosis.” 

 

You can download the transcript or read it below.

Natalie Banner: Hello, and welcome to the G Word. In the past few years, artificial intelligence, or AI as a shorthand, has taken centre stage in the headlines. Sometimes for really exciting, positive reasons about the potential to drive improvements for society, and sometimes because of its potential risks and harms.  These discussions and stories can sometimes seem like they're straight out of science fiction. There are a lot of questions, excitement, concerns about the societal impact of AI, so not just looking at individual patients, but that broader what does this mean for society?  

Ismael Kherroubi García: My somewhat hot take is that AI only accelerates societal impacts that genomics research and healthcare can have. So the impacts, of course, will be diverse and complex and quite widespread, especially given the quite nuance and sometimes difficult to understand areas of genomics and artificial intelligence.  But the key takeaway from what I want to say is that it only accelerates the impacts of genomics and healthcare. So if we take genomics research to promote human flourishing, ideally, artificial intelligence will also only help further human flourishing.  Conversely, applying artificial intelligence tools to genomics research can help perpetuate certain stereotypes and related harms.  

Natalie Banner: My name is Natalie Banner, and I'm the Director of Ethics at Genomics England. On today's episode I'm joined by Ismael Kherroubi García, member of the Participant Panel, and Ethics Advisory Committee at Genomics England. And Francisco Azuaje, Director of Bioinformatics at Genomics England. In today's episode we aim to cut through the hype and hyperbole and explore the real possibilities for AI within the domain of genomics and healthcare. We'll look at how AI tools and techniques have been used to date, and what the future holds, considering both the benefits and challenges faced in the genomics ecosystem. If you enjoy today's episode, we'd love your support. Please like, share, and rate us on wherever you listen to your podcasts.  

AI is in the news an awful lot, and not always for good reasons. There are many big and small tech companies that are exploring the use of AI in all walks of life, from finance to retail, to healthcare. And it's not always clear what AI means in these contexts, where it actually has the potential to really help people, drive improvements to healthcare and society, for example.  But there are some exciting stories, so recently, Genomics England undertook a collaboration with DeepMind on their AlphaMissense tool, and that sought to classify the effects of 71 million missense mutations in the human genome. So it could process data at a scale and a speed far faster than any human has ever been able to before. So there's an awful lot of exciting work going on in AI, but we should emphasise that although some of this technology is really cutting edge, a lot of the techniques that are being used and talked about in AI, have actually been around for quite a long time. So Francisco, if I could start with you, can you help us understand what artificial intelligence, AI really is in the context of genomics? And maybe explain to us the difference between AI and machine learning, and how they relate to one another? 

Francisco Azuaje: Sure, Natalie. AI involves the creation of computer systems capable of performing tasks that typically require human intelligence, such as understanding natural language, recognising patterns in big data sets, and making decisions. Now, machine learning is the most successful technology within the field of AI, but machine learning focuses on the use of algorithms that allow computers to learn from the data and make predictions about the data without the need for explicit programming for each task or application. 

Natalie Banner: Ismael, perhaps I can turn to you. What do you see as the primary motivations or reasons for incorporating AI into genomics research and, indeed, into healthcare? 

Ismael Kherroubi García: So I think it's already been mentioned and focusing on genomics research because challenges, the enormous amounts of data that are required to shift through and analyse and get insights from.  So one number that's worth just mentioning is that the human genome is made up of 3.2 billion base pairs, As with the Ts and the Gs with the Cs in our DNA. And one way to put that 3.2 billion, with a B, in terms we might understand, is to say that to list all of those letters we would have to be typing 60 words a minute, eight hours a day for about 50 years, that's how enormous just one human's genome is.  And I kept looking for other ways of depicting just how enormous this data set is, and it turns out if you uncoil those strands that we usually see depicted when talking about DNA, if we uncoil them for one person, we would have a string about 67 billion, again with a B, miles long for each person, that's roughly 150,000 round trips to the moon.  So, again, this is just one person, those numbers are enormous.  

It's also worth considering the role technology has had to play in enabling genomic research. So if we look back at maybe a very significant catalyst for genomics research, the human genome project which started in 1990, they took 13 years to sequence one human genome. Now, what we're talking about is estimating that by 2025 genomic-related data will be up to 40 exabytes of data. Now I didn't even know what an exabyte even was before this podcast, so I did look it up, that's about a billion gigabytes, I definitely don't know how to even begin to imagine what 40 exabytes even means.  Bringing it a bit closer to home, I try to figure out how many copies of Doctor Who we would need to make 40 exabytes of data, I found that Doctor Who is roughly 850 gigabytes, I found this on Reddit, very scientific. And the number is then 40 exabytes over 850 gigabytes, that's roughly 47 million copies of all the decades of Doctor Who media is what's necessary to reach the amount of data we expect from genomic research within a couple of years. So we need a technology capable of analysing the equivalent of 47 million copies of the entirety of Doctor Who, and currently, as you've both mentioned, AI provides the best way we have to do this. 

Natalie Banner: Wow! So we are talking absolutely vast amounts of data.  And I do love the analogies there, it's very helpful to actually sort of bring it home and make it real.  So we're talking vast amounts of data and currently it feels as thought AI may be the best way to try to analyse and explore that scale of data.  So given that's what we're talking about in genomics, in what ways is AI currently being applied in the field of healthcare and genomics?  Francisco, I'm wondering, can you give us any examples of how Genomics England is integrating AI models and tools into its research efforts? And I know particularly we have a programme of work exploring multimodal data, can you tell us a little bit about that?  

Francisco Azuaje: Absolutely. But first of all, just to give you an overview of the type of applications in research and healthcare, right now AI offers opportunities to develop tools that are needed to support interpretation of genomic variants, and the relationship between those variants and medical conditions, drug responses.  AI is also a powerful approach to supporting the detection of diseases and some subtypes of these conditions, and matching those conditions to treatments, using different types of data, in the clinic this is happening already in the clinic, and examples of data include medical images, clinical report, electronic health records. So AI is already driving the development of personalised medicine for both research and healthcare purposes.   

Now, at Genomics England we are investigating the use of AI to support a number of tasks with potential impact in both research and healthcare.  In the context of healthcare, we are talking about AI tools that can support the prioritisation, the ranking of genomic variants to allow clinicians to make more accurate and faster diagnosis. You mentioned the multimodal programme at Genomics England, as part of our mission to enabling research, we are developing tools and applications to help researchers extract information from different modalities of data or data types. In this context, AI plays a crucial role to deal not only with the size and the volumes of this data, but also to allow the meaningful extraction of useful information with clinical value based on the combination of different data sets. And that's a complex challenge, that only AI can approach. Here, we're talking about large, diverse, and complex data sets coming from different types of clinical imaging modalities. We are talking of course about genomic data, clinical reports, and in general any information that is included in the patient's medical health record. 

Natalie Banner: Thanks, Francisco. And can you talk a little more about the specific tools or projects you're working on at the moment in multimodal? 

Francisco Azuaje: Absolutely. So, in the case of multimodality, we are talking about applications that aim to improve the way we connect any of these data sources, including imaging and genomics, with clinical outcomes. For example, how to improve the way we predict not only a diagnostic type, but also how that information can be correlated with the potential response of a patient to a particular therapy. Or a prediction of the potential evolution of that patient within a particular subtype of condition or phenotype. To do this we rely on a type of a machine learning technique called deep learning, just very briefly, deep learning models are again a branch of AI, so within machine learning, these models are very powerful tools that apply deep neural networks. These networks consist of multiple layers of mathematical transformations that are applied to the data. And these transformations allow them the automatic discovery of complex patterns in this data, including all these modalities that I mentioned before. So this is a key approach that we need to extract useful features with diagnostic or prognostic value from these different modalities of clinical information. 

Natalie Banner: So there's obviously a really clear focus there on the benefits to patient, the patient outcomes, really trying to ensure that we can create personalised medicine as far as possible.  That every patient can have an outcome that's kind of very much about their own particular circumstances and condition.  So not just looking at individual patients, but broader, what does this mean for society? Ismael, I wonder if you can tell us a little bit, your thoughts on the questions about societal impacts with the increasing use of AI, particularly in genomics and healthcare more widely? 

Ismael Kherroubi García: Yeah. So my somewhat hot take is that AI only accelerates societal impacts that genomics research and healthcare can have.  So the impacts, of course, will be diverse and complex and quite widespread, especially given the quite nuanced and sometimes difficult to understand areas of genomics and artificial intelligence.  But the key takeaway from what I want to say is that, it only accelerates the impacts of genomics and healthcare.  So if we take genomics research to promote human flourishing, ideally artificial intelligence will also only help further human flourishing.  Conversely, applying artificial intelligence tools to genomics research can help perpetuate certain stereotypes and related harms. Genomics England has diverse data initiative and they show that Europeans represent 78% of people in genome-wide association studies.   

The challenge here is that, if we train artificial intelligence tools on complex interrelations of mainly the genomes of people with European ancestry, then we are over-sampling people with European ancestry, and the findings will have very limited effectiveness on different populations, both around the UK and diverse populations around the world and within the UK. So whilst artificial intelligence will have societal impacts as a general sort of technology that can be applied to many different fields, in the context of genomics and healthcare, I think that the societal impacts we should really be focusing on relate with genomics and healthcare in particular.   

Francisco Azuaje: I agree with Ismael, that the real value of AI is not only in the acceleration of technological progress, but in the impact at different levels of society. Including the way we improve health in an ethical way, and also in the way we support people to develop tools that have an impact in the way we operate as societies and the way we relate to each other. So I totally agree, it's more than just technological acceleration.   

Natalie Banner: Absolutely, okay. So we've talked about the potential societal impacts, and I mentioned at the outset that there's a lot of hype and a lot of interesting narratives about AI in the public domain.  Things can feel very utopian or dystopian as an awful lot of marketing, but understandably as well a lot of fear coming from the public perspective, especially if you think that most people's understandings of terms like AI have come from science fiction, for example. So, Ismael, what concerns are there from a public perspective? Particularly for, you know, when patients faced with the increasing use of AI and machine learning in genomics and healthcare, and the idea that their care or their treatment could be informed by these tools and technologies. What kind of challenges might arise for patients in the future as these technologies continue to advance? And what are the perceptions like from that public and patient perspective? 

Ismael Kherroubi García: I think you got it entirely right. The biggest concern relates with the public perception of AI and that perception in turn is significantly impacted by what we see in mainstream media, be it in the news media, social media in adverts, and so on. And unfortunately, as artificial intelligence is usually depicted as this extremely technical field, the conversation, the narrative is more often than not steered by big tech, so organisations and people with very clear agendas.  The example I want to make this case with is this open letter, I think it was in March this year, which was put together by a series of company CEOs, a few researchers as well, and it's ultimately been signed by over 30,000 people. And this open letter called for a six-month pause on what they called 'giant AI experiments'. So this was an open letter and direct response to the launch of ChatGPT, which is an AI-based chatbot launched by Open AI in November 2022.   

The open letter suggests that we might, in quotes, that 'we might be developing non-human minds that might eventually out-number and out-smart us. And we're risking loss of control of our civilisation'. These are extremely serious fears, and I would be really afraid if I believed them.  So the concern here is that the fears aren't really grounded in reality, but in common fiction or narratives about AI.  And very quick way to see that there's a lot of fiction around AI, if you go online, go to your favourite images browser, and look for 'artificial intelligence', you're going to find a lot of images of blue, floating brains, a few versions of the terminator, robot shaking hands with people.

There's one great image of a robot using a laptop – which always makes me laugh. These are not informative depictions of artificial intelligence, let alone genomics. And the risk is ultimately that, if the general public has easy access to unhelpful fictions about AI, then there's a great possibility that genomics research, which is going to remain intricately linked with AI advancements, will be perceived negatively, so genomics services fuelled by AI will not be trusted. And ultimately, given my stance, and I think the shared stance that AI is necessary for genomics, who's going to pay? Well, that will be the patient.  

Natalie Banner: So we have quite a battle on our hands, in terms of trying to create space for those informative discussions, as you call them, Ismael, about the realities of what AI can and will be doing in genomics.  Francisco, how are we addressing those kind of questions and concerns in our work at Genomics England?  What steps do you think we can take at Genomics England to talk more openly about the work that we're doing involving AI to try and create space for those informative discussions that aren't led by the hype or the fears of AI? 

Francisco Azuaje: I agree that we have to ensure that we are not distracted from many discussions that emphasise potentially fictional or existential risk of AI.  I think there are valid concerns about existential risks that don't represent the AI fictional view of Hollywood, but that really affect the way we operate our societies. For example, existential risk for democracies, if you have monopolies of this technology. If we have less accountability, in terms of governance. If we have electoral systems that do not work. So if that doesn't work it's going to be very hard to benefit from AI within healthcare, so that's something to be considered as well.  But I agree that sometimes the discussion is driven by this interest in very long-term potential scenarios. I think the key is to achieve a balance between longer-term and near-term priorities. And in the case of healthcare, there are many challenges and issues that we should be discussing and addressing by now, including challenges regarding the privacy and the respect of rights of our patients and individuals. Concerns about the biases embedded in the data used to build the systems, biases actually embedded in the practices for building the systems. So these are real risks, that in the case of healthcare and research need to be addressed now.   

In the case of Genomics England, we are doing a lot of work that is laying the groundwork for safer, ethical uses of AI. So this means, for example, that we will continue doing what we do, inspire and driven by the need to respect our patients' our participants' privacy and rights and voices, so that's essential.  In practice, this means that we work closely with our Participant Panel and different committees responsible and accountable for protecting these views and rights. From a machine learning point of view, there are technologies and tools that are quickly emerging that we are using to ensure that our systems are properly designed with ethical considerations in mind.  

For example, we ensure that our data sets are of good quality, and good quality means not only the information that we want to use for a particular application, but also means that we identify and quickly mitigate potential biases embedded in the data. It also means that if we share a tool, for example, within our Research Environment, these tools have been properly tested. Not only for reliability but also for potential risks associated with privacy, with biases, etc., before these tools are deployed to a production environment or shared with the wider community. So these are basic steps, but I think they are essential, starting with the protection of our data and also by applying best practice in the way we build and evaluate these models carefully before they are deployed to a wider use.   

Ismael Kherroubi García: And that, to me, makes perfect sense, and it's always encouraging to hear the practices around AI and Genomics England. There is one challenge that came to mind that you mentioned, the impact of democratic values, on potentially artificial intelligence informing social media, that informs electoral processes. And there's another very real, tangible issue with artificial intelligence, which is the environmental impact. So what's really interesting, the challenge here is that artificial intelligence tools have significant environmental impacts.  You have enormous data centres that need to be submerged in water, maintained, kept cool, and we're developing enormous algorithms, ChatGPT, and so on, that require these huge amounts of data I mentioned earlier on. So there is this really tricky balance between health and the natural environment, which I don't have the capacity to even begin to think about.   

So, I sit on the Participant Panel at Genomics England, and the conversation often goes around how Genomics England use our data, how our privacy is preserved. But at the intersection of artificial intelligence in Genomics England, I might have slightly different concerns that don't relate directly with privacy. I usually think about three – scalability, automation bias and explainability. So I mentioned before that there's a risk of promoting issues that genomics research already faces, that over-sampling of certain populations. So if we take what genomics can teach us based on mostly European ancestry data, we end up imposing assumptions on populations across the globe.  The role of AI here is in scaling the impact of those assumptions, taking bias algorithmic models, and applying them to diverse communities within and beyond the UK, risks not identifying certain conditions, missing patterns, potentially informing poor medical practices, if we take these bias data samples and ultimately algorithms. So the issue here about scalability is that artificial intelligence promotes the limitations of genomics research.   

The second issues I mentioned on automation bias is about individuals, people potentially valuing the output of computational systems because they're mathematical and therefore might seem objective. And the challenge here is very real, if we have a clinician who is diagnosing someone and the clinician says no, there's no clear evidence for there being cancer. Following all the metrics that this clinician has learnt over the years of their work, and they're faced with an AI tool that says that this agrees that says actually there is a case for there being cancer or whatever the other option is.  So the automation bias there, if it were to kick in, would be for the clinician to raise their hands, give up and say, "Well, the machine says that there is..." or "there isn't cancer, so we'll just go with what it says."  The other option of is for the clinician to actually challenge what the AI tool says.  And the crucial difference here is that the rationale of the clinician can be described, it can be outlined, explained. And that's the third issue, that's the issue of explainability.  

So modern AI tools tend to use an enormous data set and neural networks or other machine learning technologies where outputs are produced with little or no explanation. The clinician can explain why they decided on one diagnosis or another, the AI tool cannot. Ideally, this is the really tricky bit, hospitals, Genomics England and others, would have the government structures in place to handle these discrepancies in outputs from clinicians who can explain what they have to say, and AI tools which are mathematically very sophisticated, they sound pretty cool, it's a challenge.  

Natalie Banner: It absolutely is a challenge, and very helpful to talk through some of those broader ethical issues and questions. Because they are, they're questions to what I understand, you know, the law and regulation hasn't caught up yet with these very, very rapidly advancing tools and technologies. And actually, if we are working at the frontier of some of these, then these ethical questions are precisely the ones that we need to work how to navigate through.  Not necessarily because of a regulatory structure, but just through bringing different voices, different perspectives to the table, trying to anticipate consequences, and thinking through where some of those questions, for example, as you raised on explainability, what could we do? Where could we address some of those challenges? 

Francisco Azuaje: Yes. The issue of transparency is crucial, not only to ensure that we have useful tools, but to ensure that we improve privacy, that we respect the uses of these technologies. At the same time regardless of the techniques that we use to make systems more explainable or interpretable, the idea behind transparency also means, let's ensure that if we say that something works well, indeed, we are providing evidence that that something is working well. That means that we ensure that first of all we have reliable and robust systems, and that by doing that we are also bringing actual benefits to patients and society. So I think that's a more fundamental question than discussing which techniques can make this model or that model more explainable, or the actual practices for making something more transparent. So in general this transparency is there because we want to ensure that we deploy ethical, robust and fair systems.  And that this starts by enhancing the quality and transparency of the development of the tool, but also the evaluation of those tools before their deployment, and even after these systems have been deployed to a research environment or to a clinical setting.  

Ismael Kherroubi García: It sounds like there's a need for continuous monitoring, right. Throughout the life cycle of developing an AI tool, but also once implemented how we get feedback, so that the tool can be improved, but also future and other tools can be improved. 

Natalie Banner: Thank you so much. So we have had a real whistle stop tour through the world of AI and genomics.  We've highlighted some real potential advances in exciting areas. We've cautioned about some of the risks and questions about how to tackle some of the ethical complexities that are emerging. So just to wrap us up, Francisco, can I turn to you first, could you tell us what you see as being the biggest or the most significant impacts in the world of AI and genomics in the next, say, three to give years? 

Francisco Azuaje: In the next three to five years, we should expect significant advances in genomics, AI genomics, beyond the focus individual genes or markers or actually the idea of gene panels.  So we should expect that the full patient genomic analysis will become more common to provide a more comprehensive view of genetic influences on health, and also the combination of genomic data with other types of health information will offer deeper insights for supporting more accurate, faster medical decision-making.

The challenge lies in connecting this data to clinical decisions moving beyond diagnosis to actually recommend personalised treatment options.  Matching patients with relevant clinical trials based on their genomic and other types of clinical information will also become more effective, more efficient. However, concerns about reliability, safety of these applications remain, and I think that in the next few years we will see an acceleration in the development of tools and applications. But also an improvement in the way we evaluate these tools before they are deployed to a real-world environment.  So this will be crucial in the next few years, and despite all these challenges, there is reason to be very optimistic about the future of AI in genomics and medicine for the benefit of patients.   

Natalie Banner: Thank you, Francisco. And Ismael, a last word to you, what's your key takeaway for those developing AI tools for use in genomics? 

Ismael Kherroubi García: For me the biggest challenge is that there must be multidisciplinary approaches, so those developing these tools need to speak with one another and be exposed to patients. So, on the one hand, AI tools for medical applications must involve multidisciplinary collaborations, critically including the voices of clinicians, and that point was raised by Francisco. And the COVID-19 pandemic, to work with something... work for an example, already showed us the value of behavioural and other social sciences in understanding the impacts of public health policies. So genomics and general genomics research must consider multidisciplinarity in a similar way and bring different disciplines together.

On the other hand, genomics data remain intricately linked with individuals. Research participants and patients must be kept abreast of developments in the complex space that is this interaction of AI and genomics to avoid the trust issues mentioned earlier on. Ultimately, those developing AI tools for use in genomics must follow inclusive practices. 

Natalie Banner: We'll wrap up there. Thank you to our guests, Ismael Kherroubi García and Francisco Azuaje for joining me today as we discussed the role of AI in genomics and healthcare, and the importance of having open, informative conversations about both the promises and the challenges in this exciting space. If you'd like to her more like this, please subscribe to the G Word on your favourite podcast app. Thank you for listening, I've been your host, Natalie Banner.