Nicole Chai: How does X-linked inheritance work?

As 2024 comes to a close, we take a moment to reflect on what has been a busy year at Genomics England and in the wider genomics community. Throughout the year, guests have joined us to discuss groundbreaking research discoveries, important ethical considerations, and share their personal stories. It was also a year of transformation: we rebranded our podcast as Behind the Genes, welcomed Dr Rich Scott as our new Chief Executive Officer, and launched the Generation Study, in partnership with NHS England. The Participant Panel also saw changes, with Kirsty Irvine stepping into the role of Chair and Adam Clatworthy and Helen White becoming Vice Chairs. In this special end of year episode, Adam Clatworthy, Vice-Chair of the Participant Panel, sits down with Dr. Rich Scott, CEO of Genomics England, to look back on the highlights of 2024. Together, they revisit key podcast moments, reflect on research discoveries, and share insights into the evolving world of genomics. Below are the links to the podcasts mentioned in this episode, in order of appearance: Celebrating genomic breakthroughs - Insights from the Festival of Genomics Shining a light on rare conditions How has a groundbreaking genomic discovery impacted thousands worldwide? How can we work in partnership towards a new era of genomic medicine and research? How has design research shaped the Generation Study? How can we bridge the gap between diverse communities? Can Artificial Intelligence accelerate the impact of genomics? "It's really important that we just continue to bring that patient and participant community on that journey, just to ensure that they really understand the full benefits. And we've talked about that on the episode today. I know that the panel has always encouraged the Genomics England team to look at its boots while shooting for the moon. I really like that phrase just to make sure, look, we can't forget where we've come from to make sure we're taking people on that journey" You can download the transcript or read it below. Adam: Welcome to Behind the Genes.  Rich: Our vision at Genomics England is a world where everyone can benefit from genomic healthcare, thinking about how we ensure the lessons we’ve learnt through our diverse data programme is embedded across all of our work.  So that word “everyone” applies to people in lots of different ways, different communities people come from, different socioeconomic backgrounds, making sure that equity is baked into all of our work.  And there’s real opportunity for genomics to play a broader role than in rare conditions and in cancer, we’re proud of the impact we’re already having there, and we should really look to the future.  Adam: My name is Adam Clatworthy, and I’m the Vice-Chair for rare conditions on the Participant Panel at Genomics England.  On today’s episode, I’m going to be joined by Rich Scott, CEO of Genomics England.  We’re going to be taking a look back at the key milestones from 2024 for Genomics England, and really discussing our hopes and aspirations for the year ahead.  During this episode we’ll also hear from some of our guests we’ve had on the show this year, who have helped shape our discussions and shared some of their most impactful moments and insights.  And if you’d like to listen to more like this, then please subscribe to Behind the Genes on your favourite podcast app.  So, with that, thanks for joining me, Rich, how are you doing?  Rich: I’m great, thanks for hosting today, I’m really excited about it.    Adam: So, Rich, it’s been a pretty exciting year for you, you’ve taken on the CEO role at Genomics England full-time, so why don’t you just start by telling us about how those first few months have been for you?  Rich: It’s been a really exciting year, I think for us overall at Genomics England, and obviously personally taking on the CEO role, which is an enormous privilege.  I’ve been at Genomics England nine years, and I think both a privilege and a real responsibility to take on the role.  To think both about how we continue to honour the commitments we’ve given our participants and those we work with, and to think about the future, where we might go together, what evidence we need to generate, what our systems need to support.  So it’s been great taking on the role, and thinking about that, both the present and the future, and there’s been lots, as we’ll talk about, there’s been lots going on.  Adam: No, that’s great.  And I must say for myself as well, I started the Vice-Chair role at a very similar time to you early in the year.  When I started, we were in the process of looking for our next Chair.  Obviously, we had Jillian and Rebecca, both standing down, after many years in the role.  They’ve been there from the start, really guiding the Panel through this amazingly successful period.  But for me, I’ve really enjoyed working in partnership with Helen, who is our Vice-Chair for cancer.  It’s been a real partnership, in terms of filling in for that interim leadership role.  And we wanted to make sure that we weren’t just caretakers, we were really continuing to be actively involved in a lot of the discussions that are happening with your colleagues across Genomics England.  Very much leading the Panel, and starting to have those important discussions around, where does the Panel go next?  And what’s our strategy for the next two to three years?  What are the key areas that we can drive real value and impact, in line with your own milestones at Genomics England?    And, of course, I’ve just loved getting stuck into chairing the Panel meetings as well, for me, that’s the best part, is really bringing together these amazingly diverse and passionate people.  With so many different personalities, lived experiences, and a combined passion for just taking this forward together, and making sure that the benefits of genomics really impact, and that’s felt by the wider community itself.  So there’s been lots of highlights to recognise this year, a real stand-out for me has to be the Genomics England Research Summit, from what I understand it was the most attended event to date.  And it was just so good to see that a lot of the Panel were front and centre across that event, sharing their stories, having a really active role, whether introducing speakers, or telling their own journeys as part of the Q&A sessions.   I myself was really privileged to be on stage with Baroness Nicola Blackwood, literally nine days after I officially started the role.  So it was great to just dive in at the deep end, get in front of an incredible audience, and just see that the broader Panel was front and centre of the event itself.  And it was just great to see how popular the event was, many more people coming to have a chat to us on the stand than would have found us before, so, all in all, a really big highlight for myself.  So, for you, Rich, are there any other highlights that you want to call out for this year?  Rich: And first to say, absolutely agree with the Research Summit being, you know, a highlight.  The diversity of the discussions that we had, it’s one of the things we enjoy most about thinking about creating the summit, as you say, involving the participants very much at the centre.  Like, physically at the centre of the room, for people to come and talk to participants and hearing stories.  And then really seeing how over the years we can see the impact growing, and having talks, whether it’s about individual findings, or big research studies.  So the final talk of the day was from Charlie Swanton.  He was talking about some really exciting work that his team have done in our National Genomics Research Library, making a really important discovery about extra chromosomal DNA in cancer, and that’s now been published in Nature.  And then right next to him, we were having a policy talk from Sam, who’s the CEO of NICE.  And you can see the range of things, the sorts of evidence, sorts of conversation, we need to have, so that was really fantastic.  I’d call out one discovery this year that maybe we’ll come back to, and one other big highlight.  So I think the big discovery this year was the discovery of this piece of non-coding sequence in the genome called RNU4-2, which turns out to be pretty much the most common cause of developmental disorders that’s been discovered.  And it’s just so exciting to see that having been discovered in the National Genomics Research Library.  And then the news, the knowledge spread, across the world, and family support groups coming together to understand and learn more about what that means for them.  So that was, I think, the discovery over the years at Genomics England that’s touched me most, seeing that story.  And I’d say for us, organisationally, another big highlight has been the launch of our newborns programme, the Generation Study.  So as lots of people listening will know, we’ve been actually thinking about what the questions underlying this study are for a good number of years, doing a lot of preparatory work.  Actually, before we even started, setting up public dialogue jointly with the National Screening Committee about what the public were keen to understand and the appetite for research in this area.  And then we’ve been spending several years designing the study, working with the NHS how to design, safely launch it, National Screening Committee involved all along, and working with patients and the public to design it.  And this year now launching the study at a public launch, just a couple of months ago, by the time people are listening to this, and at the time of recording, more than 2,000 families have joined the programme.    So really exciting, us exploring a really big question for genomics, about the use of whole genome sequencing in newborn babies.  Whether that should be offered to every baby at birth, primarily driven by that desire to do better for those children born with treatable conditions, where genetics, genomics, can be a way in to finding them, but doing that at the right pace, and very much in a research setting.  That’s been a real, a moment, I think there’s been so much work on the path to it, but it’s right to sort of celebrate these staging posts on the way.  We’re early in the programme, there’s lots to do, lots to work through, lots of evidence that we’ll accrue, but it’s really exciting to be at that staging post.  Adam: No, absolutely, and from my side, I think seeing all of the media pick up for the Generation Study launch, you could really see the excitement in the wider kind of community.  Seeing it shared on social media, obviously those part of the 100,000 Genomes Project, seeing things like this.  It’s like they can see the tangible outcomes of all the work that they’ve done as part of that initial project, and seeing how those learnings are then taken onto this new study.  So we’ll now hear a clip from earlier in the year from Louise Fish, who is the former CEO of Genetic Alliance UK, who shares her thoughts on the potential of the Generation Study.  Louise: The Generation Study is 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 the natural history of the condition really early, and understanding how a family can be helped, through all aspects of the condition, which is giving people most excitement I think, alongside the potential to develop treatments.  Adam: So now, let’s look back at the priorities for Genomics England for 2025.  Now, Rich, would you like to just take us through some of the things you’ll be focusing on next year?  Rich: Yes, one of the things that we’ve been doing this year, but also actually in the year before, is really looking to the future.  And saying, where might we be in terms of genomics really living up to the impact it could have, if we collectively, in the UK and working with international partners, sort of get things right?  And that’s very much about balancing the realism of where we are, and the impact we’re already having, and being proud of that, and then getting that same sort of ambition and realism casting to the future.  And I’d say, I think there are two really broad themes.  I think the first thing is, we’re enormously proud of the impact we’ve had already for families with rare conditions, and people with cancer, and that impact will continue to grow in the coming years, in those areas.  And in the next few years, that’s where the biggest impact of genomics will continue, and the rare disease programme we have thinking increasingly about how we support the generation of evidence and pathways that lead to rare therapies.    So building, getting better all the time at finding diagnoses, which is still a long journey we’re on, and continuing that work.  Increasingly thinking about how we can support therapies, and in cancer, again, playing a better role in cancer, both by driving efficiency in diagnostics, and efficiency in identifying where therapies enabled by genomics can be targeted.  And we see lots of different examples of that, clinical trials is a big area where we hope to have more impact in the future, but also thinking about some of the novel therapies that are there, both for rare conditions, but also, for example, the cancer vaccines.  And I think we’re uniquely placed in the UK, because of our partnership at Genomics England with the NHS, and the broader science ecosystem, to have that impact.  So that’s the sort of like continuing very much where we are, but really pushing those boundaries.  And then also, if we look to the future, to say, what role could genomics play?  And we, as you know, our vision at Genomics England is a world that everyone can benefit from genomic healthcare, and I think that plays out in a couple of ways.  Firstly, thinking about how we ensure the lessons we’ve learnt through our diverse data programme is embedded across all of our work, so that word “everyone” applies to people in lots of different ways, different communities people come from, different socioeconomic backgrounds, making sure that equity is based into all of our work.  And then also, to say there’s real opportunity for genomics to play a broader role than in rare conditions and in cancer, we’re proud of the impact we’re already having there, and we should really look to the future.  And as we set out where we think what evidence is needed and where we need to learn what the digital infrastructure that we build and others build, need to build that to support that, we look across a few different areas.  But really you can see genomics playing a role across the lifetime, in different places in different roles.   To pick one really powerful example is something people often refer to as pharmacogenomics.  Which is a medical term for what boils down to look at a person’s DNA sequence, that’s the genomics bit, and making decisions based on what drug to give them, what drugs to avoid, or perhaps what dose to drug to give them.  Based on, for example, the desire to avoid adverse drug reactions that people might be at high risk of, and you can identify that risk looking at the DNA.  That is one example of genomics playing a role in being increasingly sort of preventive, getting away from disease, getting upstream of disease arising, or harm arising.  And there are other opportunities in common disease as well, sort of casting forward to what that impact might be, and we feel that genomics could play a role, really broadly, across healthcare, in probably as many as half of all healthcare encounters.    But what we need to do over the coming years for that to potentially be the case is we need to build out the evidence, and we also need to understand what digital infrastructure we need, to make that a possibility.  So that the information is there in simple format, for patients and the public, for their GPs, for their pharmacist, for people in any speciality in hospital, not just sort of rare disease clinics or in cancer, as we are at the moment.  And so very much we’re thinking about the programmes that we and others could run to ask some of those questions, to think about what we need to build out.  We feel that the UK’s uniquely placed to develop that evidence, so that we can make the choices about how genomics is used, and so we can be ready to embed it.    And it really aligns with that shift that we see and we hear, for example, in government being talked about, when we’re looking about sort of the shifts that the NHS sees as essential.  You know, increasingly preventive, increasingly digital, increasingly in the community, and that point of sort of getting upstream.  And genomics is going to be an important part of that.  And we at Genomics England are really excited about the role that we can play, whether it’s through the digital infrastructure we build, whether it’s the programmes that we run to develop the evidence.  Or whether it’s through the ethics and the engagement work, the work with the Panel, and the work with the wider public, to understand how we might develop this evidence, what people are comfortable with, what the expectations are.  And I think that, pulling that together is complex, it’s really exciting to think about how we do it.  I think we in the UK are uniquely placed to take advantage of that.  Adam: That’s great, and I think the pharmacogenomics piece is fascinating.  I mean, you hear many stories of people having adverse reactions to certain medications, and you wouldn’t even think it’s something that may be linked to their genetic makeup.  It’s so important that we take people along that journey, around what the benefits are, the ethics, to make sure that people really understand the journey that we’re making and what the potential impact could be.  Whilst there’s lots of amazing new areas to develop into, a key focus for us on the Panel is really continuing to demonstrate how the 100,000 Genomes Project participants continue to have an impact, and they’re helping shape a lot of these developments.  So they generously donated their data, it not only helps Genomics England develop the systems and services that now benefit many families, but it also continues to drive that scientific and technological enhancement.  So it wasn’t just about reaching that 100,000 genomes, that project was really the starting point, as it were, it’s not the finish line, it laid the groundwork for a lot of these developments.  So it’s about how do we focus on maximising the benefit for those participants over their lifetime, not just at that one point in time.    We know genomics is evolving so rapidly, what you can glean from a genome today is far more than what was possible in 2013.  And we know the Diagnostic Discovery team is continuing to analyse the data for participants in the project based on these new advances, the team led by Suzi (Walker), who’s doing some amazing work there.  Using all the latest tools and enhancements, just to make sure that those participants are really benefiting from that learning.  So, we just need to make sure we stay close to that wider community, and just ensure they’re not forgotten, that’s really a key north star for us as the Panel.  And something that we’ve been pushing is better ways that we can help to communicate the ways that you're celebrating these successes, providing regular updates on research progress, offering personalised reports based on the latest findings.  And it’s all about providing them with that hope.  Some people may never get a diagnosis, but it’s about giving the hope that one day they might get that phone call out of the blue, so it’s about giving the hope that those possibilities are out there for others.    So we’re now going to shift gear onto hearing from Shaun Pye, who is the father of Joey.  She was diagnosed with DYRK1A syndrome, which is a rare chromosomal disorder, which causes a degree of developmental delay or learning difficulty, at the age of just thirteen.  In this podcast episode, Shaun and his wife Sarah told us of their journey to Joey’s diagnosis, and how their role in writing the BBC television comedy drama series, There She Goes, has helped to shine a light on the rare condition community.  Shaun: Then the opportunity came along with 100,000 Genomes, and we signed up immediately.  And then that, they did that, and it was a few years before that went through the system, and then we had, 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 it’s like, that moment is, well, we tried to describe it in the TV programme, but it is quite hard to describe what goes through your mind, when after thirteen 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.”  Adam: So here, Rich, did you want to provide some updates around future progress, particularly in diagnostic discovery and expanding the research?  Rich: When we’re looking to the future, we’re looking sort of in two areas.  How we can build the impact we’re having today for families with rare conditions and cancer, and that very much includes the participants in our programmes, 100,000 Genomes, those through the NHS Genomic Medicine Service, who joined the National Genomic Research Library.  And we’ve seen, I think the number that I’m most proud of at Genomics England is that number of diagnostic discoveries returned to the NHS, which has just hit the 4,000 mark.  And for those less familiar with the terminology, essentially what that means is where either researchers or the internal team at Genomics England have identified changes in the genome data, that with new knowledge, often with a fine tooth comb, it’s considered likely that that is the answer to the cause of the rare condition in that person in the programme.  So that’s 4,000 of those returned to the NHS.    And that tells you a lot about where we are for families with rare conditions, and I think there’s two points here.  The first one is, we’ve got a long way still to go to do what we want to for families with rare conditions.  I’m a doctor and still see families in my clinic once a month at Great Ormond Street, even with the incredible advances we’ve had over the last particularly 10or 15 years, with the changes in sequencing and analysis, we still find an answer for the minority of families.  So that number is growing, and we’re really proud of how much better we’ve done, and there’s a long way left to go.  And the really critical thing is designing a system which we’re so lucky with in the UK here, where we can continue to learn.  And that’s not just for learning for the knowledge of people who might encounter the health system in the future.  It’s to learn for those people who’ve joined the National Genomics Research Library, who’ve already trusted us to be the custodians of their data, and to do better in the future.  And that’s what our diagnostic discovery work really aims to do.  And sometimes that’s about new gene discoveries.  So all the time new things are being discovered each year.  And if you look at the DNA code, if you like, boil it down very simply.  99% of it is what we call non-coding DNA, I’ll come back to that, about 1% is the genes, which if you like are sort of the books in the library of the DNA, overall DNA code, that we understand relatively well how they’re read by the body.  The bits in between, it’s a bit of a funny, well-spaced out library this one, that’s the 99%, actually we’ve had very little understanding of most of that code in between.  But we’re beginning, and particularly this year, to gain an understanding of how we might interrogate some of those pieces.  And not all of the answers lie in that non-coding DNA, there’s lots of answers still left in genes that we don’t understand well.    But one of the examples I mentioned earlier, and in fact the thing, the single discovery I guess which I’m most proud of having happened in the National Genomic Research Library is this discovery of this non-coding region called RNU4-2.  Which is a funny, like technical series of letters and numbers, but basically it’s a very small patch of the whole DNA code.  Where this year, scientists discovered actually about 60 patients in the families in the National Genomic Research Library where that was the cause of their child’s developmental disorder.  Actually, that knowledge has really rapidly spread across the world.  So I actually saw on social media at the weekend, from one of the scientists involved in the discovery, that the family support group that’s been set up for what they’re calling ReNu syndrome, which I think is a lovely name in itself, speaks to that word hope that you mentioned, Adam.  There are now 248 members of that group, and that’s how fast that knowledge spreads across the world.  And what we’re doing is thinking how we can support those discoveries more broadly, and non-coding DNA is one of those areas where that growth is, but it’s not the only one where we’re looking to support things.  But it’s so exciting, and I think it gives you a sense of the scale of progress that is left to make.  And I think a really important point is that remains a really important area of our focus, it’s not about moving on and looking just to the future, but we need to keep working for the families who are already part of our programmes.    Adam: That’s incredible, that 248 members in such a short space of time.  And I love the ReNu name for that, I agree, I think that’s a fantastic way of positioning it.  Earlier this year, we heard from Lindsay Pearse, whose son Lars received a diagnosis through that groundbreaking discovery of the genetic change in the RNU4-2, or ReNu gene, which was made possible by whole genome sequencing.  She told us what the diagnosis meant for their family.  Lindsay: This feeling that, like, we’ve been on this deserted island for eight years, and now all of a sudden, you're sort of like looking around through the branches of the trees, and it’s like, wait a minute, there are other people on this island.  And in this case, actually there’s a lot more people on this island.  Yes, it’s very exciting, it’s validating, it gives us a lot of hope and, you know, it has been quite emotional too (laughter).  And also, a bit of an identity shift, because I spoke earlier about how being undiagnosed had become quite a big part of our identity, and so now that’s kind of shifting a little bit, that we have this new diagnosis, and are part of a new community.  Adam: You talked about it there, Rich, I mean, it’s been really seen as a success story for the whole genomics ecosystem, especially the speed at which it all came together.  From the conversations I had with some of the individuals that were involved in the study, from the date of seeing the first findings in the lab meeting to a polished pre-print going live, was exactly 47 days, which in science terms is less than a second.  So that’s how they positioned it to me, incredible.  And you’ve just said there, they set up this support group earlier this year, and already got 248 members, which is incredible.  The impact on families is significant, the mother touched upon it there.  I mean, for many parents there is that relief that it wasn’t something they did during pregnancy, but instead, it is a chance occurrence.  For some, this knowledge means that they can make important decisions, choosing to grow their family, for example.  And it really ends that diagnostic odyssey that many families face, providing answers and potentially ending unnecessary testing that their child is going through.  But I think, and I can talk from personal experience here, that the largest impact is really being able to connect with other families and building that community, you cannot really understate that.  If I look at our own experience of getting a CRELD1 diagnosis for our children, the first time we didn’t feel alone was when we could find that community.  We can support each other, we can learn from each other’s experiences, and really also drive forward further research into that condition through advocacy.  So, I remember seeing that post on the Facebook page, about that RNU4-2 discovery, and this was before I’d even started in the role at Genomics England on the Panel, but you could really feel that excitement and the relief that they had.  And they mentioned that the official paper only had 36 other people worldwide, they found this little Facebook group that they created with five families in, and in the space of, what, 6, 7 months, they’re already at 248.  That’s all people that understand what they’re going through.  And it’s really hard to describe, it’s like finding your family that you’ve never met, people that understand, and they really get what you're going through.  And being able to share tips, advice, learnings, and things that everyone’s going through at different stages in their child’s life.  So, I really don’t think you can talk highly enough of that, that community aspect, and that’s just been amazing to see.  And, look, this new era of research into the role of non-coding RNA genes, it really may open more opportunities for diagnoses for patients, participants potentially leading to hopefully more breakthroughs in the year ahead.  So now we’re going to move on to why it’s so important to engage patients and participants in the genomics world.  So, we’ll now hear a clip from Helen White, who is the Vice-Chair for cancer on the Participant Panel.  Now Helen and I have been working really closely together as Vice-Chairs in this interim leadership role, to really ensure that we continue advancing the Panel’s strategic initiatives while we recruit that new Chair.  So it’s been amazing learning and working with Helen.  In this clip, she discussed an important topic that’s been very much top of mind of the Panel, which is the importance of involving the patients and public in genomics research.  Helen: I think, you know, as patients, members of the public, we’re eager to get on and for change to happen and things to be better, but it’s, yes, a big, big process.  But also, good to hear that you talk about it being a collaborative approach, it’s not just Genomics England, it’s the NHS, it’s members of the public and patient voices, it’s other organisations working in partnership.  Adam: Now I think we all recognise the importance of engaging patients and public to ensure diverse communities understand the benefits of genomics, and actively involving patients and participants in the research, to make sure that they’re including the perspective of what matters most to them.   Rich: I mean, it goes back to the thing that we really see as central to the value that we at Genomics England can provide.  So we increasingly think of ourselves as a data and evidence engine for national scale genomics, and I think a really important to call out there is that evidence is broad.  And part of that evidence is about public expectations, public preferences, and patient preferences.  And if you think about the big things that we do and where we bring that value, and bring that data and evidence engine role, is, you know, firstly in the digital infrastructure that we build and the data that we hold and present to our various users.  Secondly, it’s in the evidence that we distil from that, and very much thinking about part of that being evidence in and around, including that piece on what people expect, this isn't just about hard science and health economics, this is an equally if not more important part of that.  And then thirdly, it is the third area of our focus is on that engagement piece, because that’s so fundamental.  And I think you and Helen called that out absolutely right, about that being, that’s integral to the whole process, and it’s the beginning of any programme you need to start with understanding what the big drivers are, what the expectations are, and doing this very much together.  That’s one of the reasons we’re so fortunate to have the Participant Panel we do, in our Newborns Programme the Panel have been an important part of that design from the outset.  It’s also about broader engagement with different communities, people who currently don’t engage with genomics, because they’ve had no need to, sort of understanding that piece.  And I think we’ve definitely seen over time in health data research, but also research more broadly, where it’s quite easy for these things to be disconnected.  And that results in two things.  It results in research happening about interesting esoteric stuff, but not on the stuff that makes a difference for families.  And I think that’s really important, because researchers need to be directed in the resource limited world towards the things that really make a difference.  So that’s the first thing.  And the second thing is, it’s very easy, with the best will in the world, for people to make wrong judgements about what people are or aren’t content with, and you need therefore to be absolutely transparent about what the research is.  Be really clear about what those questions are, and let people challenge you, right from the outset, so that we can design research studies, but also, the system as a whole, together in a way that everyone has a say.  Not everyone has the same view, but how we can develop a system that takes into account those things and gets that balance right.  This is about making a difference to people’s health outcomes, thinking about how we achieve that, while also balancing off all of the different views there are, is really important.  And that’s at the heart of it.  And it can be scary, because it’s right that there is that challenge out there.  And it’s one of the things that I think we’ve learnt at Genomics England, how important it is to be really open to that challenge, and to do that piece really early in all of our work, and have it there baked into our governance as well, for example, the Participant Panel.  Adam: Absolutely, and I think you’ve summarised all the key areas there really well, in terms of the importance of that engagement.  And one other area I’d just like to pick up on is the impact it can have on the patients or the participants, simply by having that connection with the researcher, that’s doing all of the amazing stuff that for some of us, it’s really hard to comprehend.  But having that interaction and collaboration with them, it’s so important in terms of, again, I go back to giving you that hope.  And a real highlight for me at the Genomics England Research Summit was when Hannah, one of the members of our Panel, she came running over to us and she was just beaming.  And she said, “Guys, you’ll never guess what, I’ve just met the scientist who discovered my daughter’s diagnosis in the NGRL.”  And you could see that she was so excited, you cannot understate the impacts that can have on them as a family.  Like having that interaction and that personal connection with the person that really in some ways kind of changed their lives, in terms of understanding more about what that could mean for their daughter growing up, and how they’re managing the condition.  So, it’s amazing when you can see those highlights and hopefully we’ll see more of those.  And it’s also really important that we get that diversity I think, as well, in that collaborative approach, just to make sure that it is equitable for all.  And that really brings us on nicely to the next topic, which is about how do we bridge the gap between those diverse communities, and make sure that we’re reaching everyone as best as possible?  So we’re now going to hear a clip from Sandra Igwe.  Sandra is a CEO and founder of the Motherhood Group, speaking about the Generation Study.  Now, Sandra spoke about the importance of building trust, and how it is vital to engage with a diverse group of communities in the design of research studies.  Sandra: Every community’s different, and every patient is different as well.  And so that may require different focuses or different formats or different messengers for different groups.  And so we like to have people with lived experience from the community representing that, and also driving the uptake of consent as well.  But failing to engage diverse voices can lead to perpetuating inequalities in access and uptake.  So it’s really important to have representation, because the lack of it in research can overlook communities’ specific concerns and needs.  Adam: So, Rich, did you want to talk about why it’s so important to have that diversity?  Rich: Yes, I mean, it’s critical.  One, I mentioned earlier, our vision as an organisation is a world where everyone benefits from genomic healthcare, and that word “everyone” really resonates.  I think Sandra has been really an important part of the work that we’ve done over the last couple of years, particularly through our Diverse Data programme.  But I think one of the real challenges for us is how we make sure that that is something which is embedded across all of our work.  And that’s something that we’re really focused on at the moment, how we embed the learnings that we’ve had through that standalone Diverse Data programme into everything we do.  Because we’re absolutely committed to that, and I think that is engagement with the diversity of different groups relevant to each programme.  I think one of the real important things is that transparency piece about actually that it’s hard to achieve equity in healthcare, full stop, because of historical underinvestment in some of these areas.  And I think being clear with people about that is a really important step, and then talking really practically about why it really makes sense to take different approaches.  And so one thing about our programmes and how we think about the future overall, if genomics is going to make a difference to more than half of healthcare encounters, it needs to be something that across all communities, and across the large majority of people in each of those, that this is something that they want to be part of.  Because it’s going to make a difference for them or their families or something they really buy into.  And that’s why this isn't just about thinking only about specific programmes where this is a question, it’s about making sure that we’re designing a system, developing the evidence that is really broadly applicable, and continues to learn.  Because we know that what we learn today is hopefully an improvement on where we are, but we continue to learn and learn and learn.  And it’s about creating a system that does that, and does that equitably, or as equitably as we can.  Adam: So we’re now going to hear from Moestak Hussein, who works to build and embed cohesion, inclusion, and social justice, in her role at Bristol City Council, in public health and communities.  Moestak talks about the value of co-production, and how this can help to build trust with communities who have historically been underserved or mistreated.  Moestak: If we talk about co-production, true co-production is really creating a power balance where there’s no hierarchy, it’s an empowering model.  It empowers both the researchers or the person that comes in, but also the communities that participate, and you all start on the same level, on the same outcomes and the same goals and aims that you want to achieve.  Adam: So, if I look at that from our perspective on the Panel, I think co-production in genomics research, so using participant data in the NGRL, is certainly what we’d like to see much more of.  To ensure that research is not only relevant to its intended audience, but also aligns with broader democratic principles of citizenship, accountability, and that transparency as well.  But look, we have to be realistic.  Some genomics research projects are not going to lend themselves to meaningful patient and public involvement in the early stages, but it’s really important later on in the research pathway, if the findings identify a patient population who might benefit from that research.  At the moment, involvement of patients and participants, carers in research, is really not great, in terms of the researchers using the NGRL.  So, in conversations what we’re hearing is they’re saying, “Well, we don’t know how to do it, we don’t know what steps we should take.”  Or “We don’t think it’s relevant because we do this particular research.”    But really, our view is that some PPIE, or patient and public involvement engagement is better than none.  Some may not be relevant for all stages of the research pathway, we’re not really seeing enough of that happening at the moment, and some papers are even being published without any context of the participants’ lived experience at all.  Which can actually be quite frustrating, if you're that patient or parent, and you see a paper published, and you think, well, actually, why didn’t they reach out to us?  Just to understand a bit about the symptoms that we’re experiencing, what are the challenges that we’re facing, just to really add that important context.  So, I think there’s certainly an opportunity for us on the Panel, certainly for Genomics England, to be that kind of guiding light for those researchers.  Whether it’s providing them with researchers, research papers, or a hub of patient advocacy organisations that are already connecting those patients with researchers.  It’s all about signposting them the relevant information, so I think there’s certainly things we can do there.  And it really fits in with the bigger engagement piece.  So, whether there’s a landing page or a dedicated website that shows them, where do they go, what are the steps that they can take, what’s the best practice, what’s worked well for another researcher, and how did that lead to really great outcomes for the families involved?  That’s where I think we can all play a part in guiding them on that journey, rather than it just being a case of, they’re not doing that patient and participant engagement very well, and kind of criticising it.  Let’s reach out to them and say, “Look, we can help you and guide you on that journey.”  Rich: I really agree with the need to make those connections happen.  One of the things I think that is often missing is just a confidence just to crack on and do some of this stuff.  And I think, actually, looking at the ReNu syndrome experience, that was work that was swiftly done.  Scientific at the beginning, the initial publication put out there so that people could understand, and was quite medical by necessity, in terms of the speed of getting information out there.  And then very quickly, and quite organically, patient support groups have formed, and also, the scientists are working with that group.  I had a really interesting conversation with Sarah Wynn, who’s the CEO of the Unique last week, about how some of that has played out, how the role they’ve played in facilitating some of that.  And some of it just comes down to sort of really simple things, and working through how you can set up Zoom or whatever meeting, for people to learn about the condition.  And how you preserve anonymity, where that’s appropriate, but also allow people to have discussions about their loved ones where they want to, etc.  So it’s partly just about giving people the space and the confidence to get on with some of these things.  And as you say our, one of the things we at Genomics England are quite thoughtful about, and I think it’s a really good topic to continue talking to the Panel about, is how we get that balance right.  Where, actually, us being a connector and, as you say, signposting useful resources or ways of doing these things, just to break down some of those barriers.  Because almost always the research groups, when they discover something new, this is really new territory for them, and they’re often nervous about doing the wrong thing.  And so it’s about breaking down some of that anxiety actually I think.  Adam: Yes, absolutely.  In our case, with our condition that we’re advocating for our son, we’ve been working with a researcher.  And it’s almost on us as well just to kind of share our story with them, and making them feel more comfortable to ask us questions and be very open and transparent about the more we can share, the more that can hopefully benefit their research moving forward.  It’s very much a two-way thing as well, but I like what you said there about having the confidence just to kind of reach out and start those conversations, and have that starting point.  Next topic, we’re going to look at some of the innovations that are on the horizon, that we’re seeing in the world of genomics.  So, Rich, do you want to take us through what are the most exciting things that you're exploring at the moment?  I know we hear a lot about AI and the technological aspect, so why don’t you take us through some of those?  Rich: Yes, so I guess this comes back to that question where we’ve been looking forward, you know, where might genomics be impactful and making a real difference to people’s lives, to helping us have a more efficient healthcare system in the future?  And I think part of that is about this general shift.  You know, genomics technology, we just take for granted now how much it’s shifted, how it’s within the means of the healthcare system to generate genomic data.  And we’re really fortunate in this country because of the digital infrastructure that we’ve been able to build together with the NHS, that opens up a lot of these questions.  And it’s just extraordinary the time we’re at in genomics, so almost take those two things for granted, which we should never do.  The change in genomic testing technology, which continues to advance, and secondly, thinking about the digital infrastructure, like the nuts and bolts of what we’ve got, and the ability to safely store and reuse and analyse some of that data at scale.  And point at two big things.  Firstly, genomics enabled therapies are changing a lot.  So, our understanding, our ability to make a diagnosis, or understand what’s different about a cancer, for example, mean that in various ways it’s becoming feasible to do more tailored therapies.  Where knowing that, the genomics nitty-gritty of that condition, helps you tailor that, or create sometimes even a bespoke personalised, truly for that one individual, therapy.  And in rare conditions we see that with the so-called N=1 therapies, but also with gene therapies and so forth.  And in cancer we see that with the cancer vaccines, for example.  So that’s an enormous area of change, and one of our responsibilities is to support that sort of research, to help identify people who might be eligible for trials or treatments.  But it’s also to work with the ecosystem to think about how we can help support the generation of evidence that means that those therapies can be affordable and so forth, on a scalable basis.  So that’s one really big area of excitement.  And we see our Rare Therapies Launch Pad being part of that, the National Cancer Vaccine Launch Pad, being part of that.  So that’s thing one.  Thing two is AI and machine learning, and I think sat on alongside the sort of broader picture of saying, there’s a lot left to learn, there’s enormous potential in genomics in terms of playing a role in many different situations, not just in rare conditions, in cancer.  And we know doing that well, but also scaling it, making it really efficient, so that we can do that in a context of a really busy health service, one of the answers is making sure that we’re leveraging everything we can about the potential of AI.  And there’s lots of different ways in which that can be supportive, I won't list lots of them.  But one of the things that we’re doing at Genomics England and working with the NHS is thinking about the most promising areas.  And some of those are quite, like, down and dirty, if you like, so sort of saying, which jobs are there that we can use AI, if you like, as a co-pilot, alongside experienced scientists, to speed up their work?  And we’re really excited about the role we can play in a few ways actually.  So the first one, back to that sort of data and evidence engine point, is helping organisations who have a tool, help validate it for use in the NHS, and say, “Does it perform to this standard?  What do we want to say about how it performs from an equity point of view?  And from a clinical safety point of view?” etc.  And making that leap from stuff that makes a Nature paper to stuff that lands in clinic is surprisingly challenging, and that’s one of our roles.  And we really enjoyed working with various companies and academics over the last few years on that.  We did some work recently with Google DeepMind, on their AlphaMissense tool, thinking about how we can think about that role that might play, for example, in speeding up the interpretation of rare variants that might cause rare conditions.  And there’s enormous potential in all sorts of different parts of the sort of end to end of genomics playing a role in healthcare.  And then I’d also say one of the really important things is because genomics in many ways just needs to be part of healthcare and not be treated differently, we also need to recognise where there are questions we need to work through really thoroughly that are a bit more bespoke.  And one of the things that we’re really committed to doing, as we look to the future, is making sure that we can support on some of those questions that we really need to be clear on.  I’ll go back to that point on, what do we mean about making sure we understand how a tool is working, and whether it’s producing results in an equitable way for all different communities?  How do we understand that?  How do we explain what we understand about the performance of a tool?  How do we make sure that patient identifiable data remains non-identifiable if a tool’s been built, trained on data?  Working through some of those questions.  But they’re really important for us to do, and we’re enormously excited about the potential, and we’re really committed to working through in detail how we can make that path to adoption safely and in the way that everyone would expect and desire as rapid as possible.  We’re just one step in that process.  But we really see a sort of important role for helping people who are producing various tools or various use cases, helping them prove them, helping them validate them, and making the system more efficient overall, but in ways that we really understand.  Adam: That’s fantastic.  Look, not that I'm biased at all, but I can tell you that the AlphaMissense innovations that are being developed are shared a lot internally at Google, it has been seen as an amazing success case.  So hopefully we’ll see more on that moving forward.  But in the next clip, we’re going to hear from Francisco.  So Francisco is the Director of Bioinformatics at Genomics England, who tells us more about the application of AI and its benefits in genomics in healthcare.  Francisco: 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, for the 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.  Adam: While all of these innovations sound really exciting, it’s really important that we just continue to bring that patient and participant community on that journey, just to ensure that they really understand the full benefits, and we talked about that on the episode today.  I know that the panel has always encouraged Genomics England team to look at its boots while shooting for the moon.  I really like that phrase, just to make sure, look, we can’t forget where we’ve come from to make sure we’re taking people on that journey.  So, we’re going to wrap up there.  Thank you to Rich Scott for joining me today, as we reflected on key milestones for 2024, and looked at the year ahead for both Genomics England and the wider genomic ecosystem.  If you enjoyed today’s episode, we’d love your support.  Please like, share and rate us on wherever you listen to your podcasts.  I’ve been your host, Adam Clatworthy, this podcast was edited by Bill Griffin at Ventoux Digital and produced by Naimah Callachand.  Thank you everyone for listening. 

In this explainer episode, we’ve asked Katrina Stone, Clinical Genetics Doctor, and Clinical Fellow at Genomics England, to explain what happens when you go for whole genome sequencing for a rare condition. 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 [email protected]. You can download the transcript or read it below. Florence: What happens when I go for whole genome sequencing? I'm joined by Katrina Stone, Clinical Genetics Doctor, to find out more. So, Katrina, first things first. What is the purpose of whole genome sequencing?   Katrina: The purpose of whole genome sequencing is to try to make a precise genetic diagnosis for someone with a suspected or confirmed genetic condition.  Florence: And why might someone get whole genome sequencing?   Katrina: They might get whole genome sequencing because they are known to have a condition which is likely to be genetic, but the medical team wants to find out what the exact genetic cause is. In other cases, the diagnosis might not be known, and the reason for doing whole genome sequencing is to find out whether there is a genetic condition present.  Some of the benefits of having the test is that. If a condition is identified, this can provide an explanation for the family about what's been going on, and it can also bring to an end further unnecessary investigations. Also, if a genetic diagnosis is confirmed, this can sometimes point towards other things which might need to be kept an eye on for the individual.  In addition, once a diagnosis is confirmed, a doctor can advise the family on the likelihood of other members of the family or future children being affected with the same condition, and they can use this information to help with future family planning.  Florence: So, then what happens when a person physically goes to get the test?   Katrina: In most cases, an individual will see a specialist doctor. This might be a genetics doctor, but it could be a doctor specialising in another body system. They'll do a full assessment of the individual, including finding out lots of information about them and their family, and also examining them to look for any clues that might point towards a specific genetic diagnosis.  Once the family have decided to go ahead with the test, their consent will be taken, where the test will be explained in more detail, including the pros and cons of going ahead with the test and after that samples can be taken. Usually this is a blood sample, but occasionally a saliva sample or cheek swab could be taken.  The best way to perform whole genome sequencing is with a sample from the person being tested along with both of their parents. And the reason for this is that it makes it easier to separate out genetic changes that are more likely to be significant from those that just represent harmless genetic variation what makes us all unique.  Florence: What happens to this sample after the test has taken place?   Katrina: So, the blood samples will go to a genetics lab where the genetic material known as DNA is extracted. The DNA is then sequenced, so we get an electronic file of all their genetic information. This is then analysed firstly by a computer which picks out changes or variants in their DNA, which are more likely to be significant.  After this, a trained clinical scientist analyses the data in detail. Sometimes there isn't a clear-cut result, and the scientists might need help from others and interpreting the result, but if there is, they can create a report which details the likely diagnosis.  Florence: And finally, how will the patient get the result from their whole genome sequencing test?  Katrina: Usually, the result is fed back to the patient and their family by the clinician who arranged their testing or one of their close colleagues. It's important to note that not everyone will get a genetic diagnosis from the test. This doesn't necessarily mean there isn't a genetic diagnosis present.  There are several reasons why tests might be negative. One is that no test is perfect and something important might have been missed because of the way the test works. Or it may be that the person being tested has a change in a gene that hasn't been described as causing a disease before, so we wouldn't even know to look for it.  There's also a possibility that there isn't a single genetic cause for their symptoms. Rather, lots of minor genetic factors are causing their condition. We're not very good at testing for these yet. Finally, there could be a non-genetic cause that just hasn't been identified yet.  One of the benefits of having a whole genome sequencing test is that the data can be stored and looked at again in the future, either in light of new evidence or once our knowledge of genetics has improved.  Florence: That was Katrina Stone explaining what happens when you get whole genome sequencing. 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.

In this episode, we explore the importance of patient involvement in shaping rare condition research initiatives. Our guests discuss why it’s crucial to involve individuals with lived experiences, including patients and caregivers, in setting research agendas. In doing so, this approach ensures research can be more inclusive, efficient, and impactful, addressing the issues that matter most to those affected. Mel Dixon, Founder Cure DHDDS and member of Genomics England Participant Panel is joined by Jo Balfour, Founder of CamRARE and Dr Rona Smith, Senior Research Associate at the University of Cambridge and Honorary Consultant in Nephrology and Vasculitis. Find out more about the Cambridge Rare Disease Research Network, discussed in the episode, which aims to support the rare condition community in building an online network of partnerships and resources to facilitate new patient-centred research opportunities. "We’re really turning research on its head, moving away from it being a researcher-led activity where they decide on the idea and the research concept and bring patients in at different points along that research journey and instead starting with the patient’s idea in the first place.  It can only be a better system for all because it improves efficiency, it improves potentially the long term outputs and, most importantly, outcomes for patients." You can download the transcript or read it below. Mel: Welcome to Behind the Genes. Rona: I think it really means that we measure what matters to patients and individuals that are affected.  Often, it’s really difficult to capture kind of the real impact of disease and there’s a tendency for researchers to measure things that are easy to measure and are reproducible, which of course is important but what’s most important is actually being able to truly capture the impact of an intervention on an individual’s condition.  So, I think that’s another key aspect of having people with lived experience involved right from the start. Mel: My name is Mel Dixon and I’m a member of the Participant Panel at Genomics England and founder of Cure DHDDS, a charity set up to raise awareness, support families and help drive research into the ultra-rare DHDDS gene variant.  On today’s episode I’m joined by Jo Balfour, Managing Director of CamRARE, which is the Cambridge Rare Disease Network.  This network unites patients, advocates, experts and leaders to address the challenges faced by people affected by rare conditions.  I’m also joined by Rona Smith, Associate Professor at the University of Cambridge and honorary consultant in nephrology and vasculitis.  Today we’ll be discussing the role of patients in setting research agendas and how their involvement can lead to more impactful and patient-centred research.  If you enjoy today’s episode we’d love your support.  Please like, share and rate us on wherever you listen to your podcasts. Before we begin the interview I’d like to share a little bit of my story.  In November 2022, following whole genome sequencing, we received the news that two of our three children carried a neurodevelopmental and neurodegenerative DHDDS genetic variant.  At the time of our children’s diagnosis there was very little information on our gene, minimal research happening into it and no treatment pathway.  Through our charity, Cure DHDDS, we have worked tirelessly to instigate research and create a collaborative scientific research community.  I am a huge advocate for patient-led research and have witnessed first-hand the positive impact it can have on patient lives.  Thanks to the work of the many scientists that we have had the honour of collaborating with, within two years of our children’s diagnosis we have a disease-modifying therapy in our sight and an ASO (Antisense oligonucleotides) therapy in development.  We are incredibly grateful for the opportunities genetic testing has given us but I also appreciate how overwhelming a genetic diagnosis can be and how challenging it can be for families to initiate research projects with little to no resources, and that’s why initiatives such as CamRARE that we’ll be discussing today are so important.   On that note, let’s get back to our podcast guests.  I wonder before we dive into today’s topic if you could both give a brief introduction, and, Rona, if you could also give the less scientifically-minded of us an explanation about what nephrology is. Rona: Thank you for inviting me today.  So I’m Rona Smith, I work in Cambridge and I’m a nephrologist and that means somebody that looks after individuals who have diseases that affect their kidneys.  My specialist interest is in something called vasculitis which is a rare autoimmune disease that affects all organs in the body but kidneys as well.  Mel: Thank you.  And Jo?  Jo: Hi Mel.  I’m Jo Balfour, the Managing Director and one of the founding members of Cambridge Rare Disease Network, or CamRARE for short.  I think we’re often described as the ‘Chief Everything Officers’.  I manage the charity and all of our operations and our wonderful team.    Mel: Lovely.  Thank you very much.  Rona, I wonder also if you could explain to our listeners what is a research agenda?  Rona: So in brief a research agenda is really a strategy that outlines key questions or topics that a research community, and that might be investigators, clinicians, scientists, patients, industry,  and they are the priorities that they want to explore and address over a period of time.  So it’s really a direction of travel and identification of areas of importance and where there are gaps in knowledge so that it then leads to the opportunity to form specific research questions that you can then go on and address.  Mel: Why do you both think it’s important to involve patients in setting these research agendas?  Jo: Well I think critically one of the things that I’ve learnt over my time working, not just in the rare disease sector but also earlier in social care and education, is that we should as professionals never assume anything; you know, we have not lived in their shoes and we don’t know what the daily life of people living with rare conditions is like.  So gathering that day to day lived experience is really crucial.  And I have a unique opportunity to see into that daily life with our local community of rare disease families who have a range of different rare conditions.  I’m party to their conversations, to their daily trials and tribulations, the things that are difficult, the things that they find joy in but I still will always go back to them and ask their opinion.  I see myself as a spokesperson for them as we’re an umbrella organisation but I certainly never really know what it’s like to live with their conditions.  I think they bring with them diverse experiences which we really need and value in setting research priorities, they have unique knowledge of their own conditions.  They ethically have a right to be involved from the start and to set that priority and agenda but, equally, it’s valuable for us as researchers because if we can involve people early we have definitely more chance of good engagement and later success, better outcomes for everyone.  Mel: Couldn’t agree more.  And, Rona, is there anything you’d like to add to that? Rona: I think it really means that we measure what matters to patients and individuals that are affected.  Often it’s really difficult to capture kind of the real impact of disease and there’s a tendency for researchers to measure things that are easy to measure and are reproducible, which of course is important but what’s most important is actually being able to truly capture the impact of an intervention on an individual’s condition.  So I think that’s another key aspect of having people with lived experience involved right from the start.  Jo: Another thing that’s actually quite interesting that I’m going to mention here is that I think when you live day in, day out with a condition your perception of things like pain is different from your average person’s so you become almost accepting of your daily norm, and I think that’s really critical to understand as well.  And it’s only by getting to really know patients and understand. When we say, “What’s your pain like on a scale of 1 to 10?” you know, something that I feel as pain because I get it rarely I probably am going to put it at a higher score than somebody who has that every day.  So I think there’s subtleties and nuances like that as well which are really critical to get across by conversation with patients.  Mel: That makes absolute sense.  And I see that from the patient perspective myself.  I was out with my friends the other day and they said, “Oh my goodness, you’re constantly taking your children to sports activities.”  Because of their physical needs we’re constantly,  they go to Pilates, they go to swimming, they go to gym class – we try to keep them fit and healthy – and we, even though they’re older, have to take them there and back and that’s become our norm but when you’re speaking to families whose children don’t have those difficulties they have no idea how much time that actually takes up.  And I had no idea how much like time it takes up compared to what other people are doing because that is our norm, that’s what we’ve accepted as the norm.  Patients and patient groups are incredibly driven and invested in their rare disease as well so they make really good rare disease research partners.     And, moving on, what do you see as the challenges and barriers to patient involvement and how do we overcome these? Rona: I think probably the biggest barrier is time.  So, the most important thing is investing time to build relationships, to really understand in-depth perspectives both from the patient’s side but also the researcher’s side. And, inevitably, we always want to do things faster and actually this is one really, really critical aspect is investing time.  Funding is also a challenge.  Often you have to do a lot of upstream work before you have got funding for a project and that takes time from individuals and that’s another challenge.  And I think the third thing for me is individuals that are patient partners in research, they’re not just patients, they’re people - they have lives, they have work, they have families, they have everything else that goes on in life - and so actually fitting this all in is really challenging.  Mel: Jo, is there anything you’d like to add there?  Jo: Yeah, I think just a word about diversity really and, you know, how do we uncover those hidden families and patients who currently don’t really have a voice.  I think we’d all acknowledge that there are key voices within the rare disease community who will share the views of their community and they’ve become well-oiled machines almost at being great advocates but, as I mentioned earlier, even though I’m perhaps one of those people, you know, I speak for a community, I would never assume anything.  So, I still need to uncover the thoughts and the feelings and the emotions and the needs and the what matters from those people, and, as Rona mentioned, that takes time and it takes building relationships and trust with people.  So, we have a wonderful community in the Eastern region of England which is made up of families affected by all different rare diseases, and undiagnosed.  And some are babies and have been lucky enough to get a very early diagnosis and others are young adults but what we’re finding through that is that experience is diverse and experience changes over time as families go through transition periods or they meet a roadblock and they’re having to navigate things differently.  So, it’s about building those relationships.  That takes times, it takes resources, it takes sometimes a reset in the way that we think things need to be done.  So instead of asking questions all the time and putting surveys out and trying to get response that way it takes a bit of thinking about how do we listen better and how do we give those people who don’t have a voice, who are non-verbal or perhaps have a learning disability, how do we ensure that we’re capturing their views as well.    And we did a really lovely project actually last year, it was something funded by the NHS called My Story, My Way, where we actually spent three months with our young adults working out what it was they wanted from our community next, how did they want us to follow them into adulthood.  And we knew that there were a number of young people in that group who were non-verbal and had some learning differences and we knew that we couldn’t just do it in the normal format, we couldn’t just do a focus group and ask their opinion, so we actually did it through photography.  So each of the familiess well, the young person themself was given a simple camera.  They basically had thirty-six shots.  You got thirty-six clicks to capture the things, the people, the places that you love and then to share them with us as a community.  And then we all discuss, you know, how these things might be something we can build into our future plans for them.  And it was such a wonderful activity.  We gave them plenty of time, plenty of opportunities to ask questions.  If the young person themself couldn’t physically click the camera their sibling got to help them.  And their sibling or their parent was given another camera in black and white so we had distinctive pictures, pictures that the kid themself had taken, pictures that the family had taken, but all together, you know, it gave this lovely kind of medley, this beautiful visual representations of what mattered to them.  And I think it’s about taking the time to be creative with people like that and really get to the bottom of “How do we find out what matters to you?” Mel: Although it takes time to think about those ideas.  That could be translatable across the board really, couldn’t it, throughout various conditions.  I think that’s fantastic.  Rona, I wonder if you can tell us how has the work that’s already been done through the patient-led research hub facilitated addressing research priorities.  Rona: So just a tiny bit about the patient-led research hub.  So, this has been now running for nearly ten years through Cambridge.  It’s a partnership between the Cambridge Biomedical Research Campus and we’re based within the university and the Trust.  And in essence it kind of was set up because of really a mismatch between what many patients wanted from research and what investigators’ views were.  And so really the premise is that we welcome patients to come to us with an idea, a problem, an unmet need in their disease area – and we do focus on rare disease – and we work with them to see “Well actually what do we already know about that?” and then if there is a gap in knowledge we then move to kind of trying to work and develop a question that we can then address.  And that might be a question that’s addressed through generating more information through surveys or it may actually be a question of an intervention that we can test.  So, we’ve had lots of projects come through and we, just an example of a project was from a group of patients with a rare kidney condition called autosomal dominant polycystic kidney disease, and that is a condition where over time you accumulate cysts in your kidneys and the kidneys become large, they become very painful and eventually they can fail.  And a question that the patient group had was about whether drinking more water could impact the rate of growth of these cysts, and there’s a strong hypothesis behind that that drinking lots of water reduces down the level of a particular hormone.  And we actually worked with the charity behind this group, the Polycystic Kidney Disease Charity, and designed a study to test a very high water intake to a normal water intake to see whether it was possible over a period of eight weeks for patients to actually stick to this.  It’s quite difficult to do.  And they recorded how much water they’d drunk, they tested their own urine and actually it showed that this was feasible to do this kind of work.  So, I think the patient-led research hub is kind of taking the research priorities that are important to patients but working in a patient-led way to come right through to a project.  Mel: That sounds great.  And if the patients are engaged from the start of the project and it’s led by them they’re obviously going to be much more driven to take part in the actual research and see the research through themselves.    So, Jo, I’m very excited to hear about the launch of the Rare Disease Research Network.  Can you please tell me what the research network is and what you hope to achieve with it?  Jo: So the Rare Disease Research Network is first of all a bit of a mouthful so we’re going to try and encourage people to call it the RDRN.  It’s a co-created project which really the patient-led research hub in Cambridge approached us about in 2022, I think, we started talking about this, approached CamRARE as a partner to apply for an NIHR partnership grant, and we were successful with that to really take the model that the patient-led research hub had already developed and found was successful, and perhaps too successful for its own good – they were receiving more applications and more ideas than they could manage – and to develop that into an online platform.  So taking the same model, making it more accessible to a wider group of people, potentially worldwide, and providing the hand-holding that the patient-led research hub has always done, helping patients really consider their question, formulate that into a research idea, then do the literature search to find out “Is this question already answered, and if it is, great, can we provide that information to our community?  If it’s not, how do we then build a team?  Who needs to be in my research team?  How do we then get funding together to take this idea forward?”  So, it’s really taking the model, taking the good practice that already existed and creating an online platform to really attempt to replicate that as best we can. So the platform will launch on 23rd November (2024) at CamRARE’s Rarefest which is a lovely in-person activity that’s going on in Cambridge, and that platform will be open to anyone who has an interest in rare disease research.  But I think, critically, what’s different about this is that, you know, we’ve talked about setting research agendas and we’ve talked about patients contributing to that, contributing to setting the priorities, what’s different here is that the patients decide on the questions; it’s what matters to the patients coming from them and their community.  And it’s an opportunity for them to showcase those questions and those idea on a platform and almost to have a call to action, “Is there anyone else on this platform who has similar research interests to me?”  The platform will matchmake them together through a series of choosing tags, choosing tags about particular disease areas -  It’s linked to the Orphanet database - choosing tags about the type of research that you’re interested in.  That matchmaking process will happen, which at the moment is a very serendipitous process but we hope to take it a little bit further on from that.  It’s still going to be a little bit of potluck who’s on the platform at the time who’s got similar interests as you but hopefully it will improve that serendipitous system.  And it will allow them to access resources on the platform, which is the kind of hand-holding bit, and also, critically, some mentoring.  So, there’s a real sort of opportunity here for professionals – researchers, industry partners, healthcare professionals – who have particular skills in research to be able to say, “Well I can help.  I might not be able to be part of your team at this point but if you need half an hour on a Zoom call with me to think about your research question I can offer to mentor you on that.”  But, likewise, I think there’s going to be lovely opportunities here for patient groups to support each other too because what we’ve always realised is that patient groups are at different points of their research journey.  You know, we see some organisations that are really well-funded now who are in partnership with industry, you know, they have a group of pharma companies that are supporting the development of treatments and they’ve kind of reached that point where they’re very highly skilled and very well experienced.  And then there’s others who are mum and dad who’ve just had a recent diagnosis for their child, they’ve gone searching on the internet, they can’t find information, they don’t have a patient organisation to rely on so they’re going to make one themselves.  This happens all the time in the rare disease field.  There are 11,000 different rare conditions and there’s not a group for all of them so mum and dad will often start something themselves and then in lots of cases want to do some research, they want to answer some of these questions.  So, you know, they’re really starting from a very different beginning stage here where they’ve going to need some help, and sometimes the best help comes from their peers, it comes from other patient groups.  So that’s in a nutshell what it’s about; it’s about providing opportunity for patient groups to showcase their great ideas, build partnerships and take research forward.   Rona: The only thing just to add there is I think, although rare diseases are individually rare, collectively, as Jo said, they’re quite common, there’s 11,000 rare diseases, and often, although they all have distinct features, there are common threads through rare diseases in terms of maybe symptoms that patients experience or challenges that their rare disease brings.  So, for example, you may have symptoms of pain or seizures that are common across many conditions, there may be educational needs that are threads going through.   And groups could work together maybe to answer a question that’s relevant to a number of conditions and so bringing people together for that.  Or there may be another group that’s already tried to answer that question in their condition and you can learn what worked, what didn’t work.  I think that’s the other thing, is there will be common threads that come through, and I think that would be a real strength of the network to draw those people together. Jo: I think as well, Mel, if we take this back to what we said right at the outset about optimising success for patients by bringing them into the conversation early, I think this platform provides the perfect opportunity to do that.  So we’re moving away from, we’re really turning research on its head, moving away from it being a researcher-led activity where they decide on the idea and the research concept and bring patients in at different points along that research journey and instead starting with the patient’s idea in the first place.  It can only be a better system for all because it improves efficiency, it improves potentially the long-term outputs and, most importantly, outcomes for patients.  Mel: We were that family, that mum and dad setting up the charity a year and a half ago for the ultra-rare disease that our children had.  I think, you know, the match-making opportunities that are here are fantastic because finding yourself in that position is incredibly isolating.  And not only the matchmaking opportunities with the researchers but, as you were saying, Rona, as well with similar diseases; there’s so much to learn from other diseases that may have, I don’t know, a similar phenotype in the cells or similar symptoms.  That’s what we found from connecting with these other rare conditions.  So, for us it’s lysosomal storage diseases, we’ve now got the opportunity potentially to piggyback on drugs better used for their diseases for our own ultra rare condition, you know, where for us to run a full-on clinical trial by ourselves with a new drug, I mean, we just wouldn’t have,  there’s no funding, there’s not enough interest.  So, I think the opportunities that lie in this network are really, really exciting.  Jo, can you tell me a bit more about who can join the research network?  Jo: So anyone with a rare disease research interest. That’s everybody from individuals affected themselves, their family members, their caregivers, the patient organisations, that support them, and then, you know, all sorts of rare disease professional researchers.  So, we’re looking for PhD students who are looking for their first exciting project to undertake, have they taken a look at the Rare Disease Research Network to see if there’s any ideas that might pique their interest.  We’re looking for established researchers, medical professionals who are undertaking clinical research but also I think, importantly, companies.   You know, we hear more and more about concepts like drug repurposing for rare diseases where we’re looking at the opportunities for taking drugs that already exist and have been proven safe to be redeployed to other rare diseases. It’s quicker, it’s more efficient, it’s cheaper, so does it open up opportunities for companies that are using that technique to get involved.  And also pharma companies.  This platform is not all going to be about finding cures and treatments but it certainly will be a priority for some groups.  So we really are welcoming everyone with an interest in rare disease research to get involved, be part of the network, collaborate, help where you can. Rona: And also, as we’ve said before, once you’ve got that level of engagement and the patients leading these initiatives we’ve found, certainly with our group, the patients are much more willing to, say, find the MRI scans for the scientists, to have a blood sample done, to have skin fibroblasts taken.  If they know and they understand and they’re driven and, as you said, the research idea has come from them as a patient group it certainly increases the chance of them being fully involved in the project from the start to the finish.  And all these things are imperative to understanding rare conditions because without researchers having the opportunity to look at these various samples you’re not going to stand much of a chance of finding a treatment.  Jo: And we want the opportunity to upskill patients as well.  I think there are many people out there with great ideas who haven’t yet found the confidence to promote those ideas because they’re not quite sure of what the research journey looks like or what it might entail or whether they’ve got the right skills.  But I think by joining the platform and almost kind of watching how other people are managing these things and utilising the resources and the mentoring I do really hope that will build that confidence and those skills sets in people so that they can engage.  Rona: Yeah, just to add to that, I don’t think it’s just upskilling patients and patient groups, I think it’s upskilling everybody involved in rare disease research.  This is quite a different way of approaching research, it’s something that maybe academics may feel a little bit uncomfortable with, it’s not how it’s normally done, so I think there’s a whole learning process.  And the aim is that this RDR network will evolve and will develop and the direction it goes will be driven by the community that are engaging with it.  So I think it’s a really exciting time just as we’re coming up to launch to see where this goes.  Jo: Mel, you’ve been involved in this project, it would be really interesting actually to hear from you. I was just thinking, as part of the co-creation community we had 25 individuals from the rare disease community who built this platform from scratch with us; Rona and I might have set out all the vision for how we wanted the platform to be or what we thought might be a good idea but ultimately it was the community who decided and they literally have fact-checked and cross-referenced every word that’s gone on the platform. What has that experience been like for you as a patient representative?  Mel: I think it’s been really welcome to see a network that is truly putting patients at the centre of everything.  So, from the very beginning foundations you have the rare disease community involved which is exactly what you’re trying to create through your network.  So, I think it’s been very welcome to be involved in the project and I also think that hopefully it will sort of be self-perpetuating that this will start to press a reset button on how we think about rare conditions and how it needs to be a more equitable field with patients.  Because I think, as you’ve both alluded to, while some clinicians and researchers are very onboard with this, for others it’s a new concept that they still need to potentially adjust to or get their head round because it is a different way of thinking.  But in rare disease, well, in any condition really but particularly rare disease because there’s so few experiences to draw on, I think that patients are vital to moving forward and to making that change so that diseases and conditions that have previously had no treatment, like, hopefully this way of thinking can expedite those treatments because, well, as a rare disease representative myself for our community that’s one of our biggest drivers.  We’re dealing with a condition that’s progressive that affects most of our community’s children; that is what we want, we want treatment, we want something that can stabilise the conditions.  You know, you can have researchers doing random projects that would make no difference to the final outcome of patients but if researchers know it’s a priority of this particular group, hopefully that can channel in their focus and get the outcomes that the patients want in a more timely collaborative way.  So, I am a huge advocate for what you’re doing, I think it’s an incredible initiative.  Is there anything either of you would like to add to that? Rona: Rare disease disproportionately affects children and young people.  So, 7 out of 10 rare diseases develop in childhood and at the moment the Rare Disease Research Network hasn’t really got a forum for including children and young people, and really that’s partly because, and Jo can speak much more eloquently to this with her experience.  Actually, we didn’t do that at the start because we feel that this is actually a discreet piece of work that really needs to be done in collaboration with children and young people to make sure that it’s done well so that they can engage in the platform. So, Jo, I don’t know if you want to talk about how we’re hoping to take this forward.  Jo: Yeah, so we’re busy developing a project plan at the moment which we’re hoping to get funding for to work over eighteen months with a team of young adults with rare conditions, probably from our Unique Feet community and keep it local because we already have a good relationship with them and they have our trust.  But the idea would be to work with lots of other young people’s forums.  So there’s already ones established in and around our area, such as Pedal, which works with really small children, and there’s also groups that are set up for young people with cancer.  So we’ve already had lots of great conversations with them about how we can work with them, how they can help us sense-check our project, and then in return we can help them better understand research and their ability to be involved in that.  But ultimately by the end we want to run focus groups, we want to develop some peer mentors within our community, so young adults who’ve, you know, perhaps come out the other end of a period of transition into adulthood who can support other young people with rare diseases to also become researchers, to come up with their own ideas and their own questions, and to sense-check projects that come through the platform.  So it’s a really exciting opportunity to truly involve the people who are affected most by rare conditions but we know through our My Story, My Way project that this has to be done gently, carefully, given time and done really thoughtfully.  So that’s our next step and we hope to be able to share those learnings with people so that it can be done elsewhere.  Mel: And do you see the network also working with children with learning differences? Jo: Absolutely.  We’ll invest a lot of time and energy in ensuring that materials are accessible, inclusive and suitable for the community that we’re working with.  Mel: So looking to the future, how do you think, Rona, can patient-led research help to shape the future landscape?  Rona: So I think, Jo used the term earlier, kind of this is really turning research on its head, so it’s really putting patients right at the centre of research, so it just makes sure that it’s absolutely driven by what matters to them to get the outcomes that matter.  And, again, it’s just got all that benefit of efficiency and really answering those questions that matter.  Mel: And, Jo, do you think this could lead to more collaborative partnership, for example, between industry and academia, potentially leading to quicker clinical advancement? Jo: I would absolutely like to think so.  You know, as CamRARE we run a companies forum which is a roundtable meeting for pharma and biotech companies and other organisations like Genomics England who are involved in the rare disease therapeutic space and diagnostics, and I think one thing that I find really heart-warming about those meetings is that, you know, different companies are able to sit around a table as competitors but with a very open mind to addressing the barriers and the bottlenecks that prevent them from getting drugs to patients.  Because of course it’s not just the research journey that’s a challenge, it’s the regulatory side of things at the end of that journey; just because you’ve created a great drug it doesn’t matter in the end if it doesn’t get to the patient.  So, you know, access is critical and involving patients at the earliest possible moment to ensure that that treatment gets through to the regulators and gets access to patients is the only way forward.  We had a recent companies forum meeting where we were exploring health-related patient reported outcome measures, or PROMs, and we had a speaker from NICE who’s the regulatory body, we had a speaker from Sheffield University who was talking as an academic about developing PROMs for industry and for patient groups and we had Emily Reuben, the CEO of Duchenne UK, and we had an amazing discussion about the importance of involving the patient community from the outset.  And the academic explained that developing a PROM for Duchenne UK had taken them two years and it had taken them that length of time because they’d followed this careful thoughtful pathway of making sure that they didn’t assume anything about what matters to patients.  But that of course, as we said earlier, involves time, it involves financial commitment, it involves resources and the right attitude, but I do think that a platform like the Rare Disease Research Network can really try to harness all of those things by bringing the right people together – industry, academia and patients – to work together equitably. Mel: And with the network do you think you’ll be getting the regulators in at that initial stage as well so that, like you said, the patients can gain access while we’re dealing with their priorities, the regulators are informed at the very earliest stages so that we know the process that’s being followed will ultimately lead to patients gaining access to the relevant therapies?  Jo: Yes, I think this is really important, and there’s actually, we’ve got a section on the new platform which really talks to each of the different stakeholders.  ‘What’s in this for me?’  ‘Why is it important for you to be here and to join?’  And one part of that is funders and that includes the regulatory bodies.  And at the next companies forum meeting we’re actually going to be bringing the Rare Disease Research Network Platform and its potential to the companies forum meeting and we’ll have regulators involved in that.  So, you know, we are constantly talking to people about why it’s important for them all to be involved and all to see what matters. I think I’d like to advocate for an extra letter at the end of PPIEP - if we could squeeze a D in there at the end too.  So over time that terminology has expanded to be Public Patient Involvement Engagement and Participation, which was added I think this year, but it would be lovely to have the D on the end and to include ‘Driven’ because I think what’s really important about this platform is that it’s not just engagement and involvement, it’s not just participation, it’s initiated by and driven by patients. Mel: So I think we’ll wrap here.  Thank you to our guests, Jo Balfour and Dr Rona Smith, for joining me today as we discuss the role of patients in setting research agendas.  If you’d like to hear more like this, please subscribe to Behind the Genes on your favourite podcast app.  Thank you for listening.  I’ve been your host, Mel Dixon, and this podcast was edited by Bill Griffin at Ventoux Digital and produced by Naimah Callachand. 

In this explainer episode, we’ve asked Meriel McEntagart, Clinical Geneticist in the NHS and Clinical Lead for Rare Disease Technologies at Genomics England, to explain how genetic conditions can be inherited, and other ways they may arise. 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 [email protected]. To learn more about X-linked inheritance, as mentioned in the episode, tune in to our explainer episode, how does X-linked inheritance work? You can download the transcript or read it below. Florence: Are genetic conditions always inherited from parents? I'm joined by Meriel McEntagart, clinical geneticist for the NHS to find out more. So, Meriel, first things first. How can a genetic change cause a condition?   Meriel: We have about 20,000 genes. That's the estimate and they are the code or blueprint for how to grow and develop a human being. And, if you think about a code, you can have a mistake in a code or a variant in a code. And if that happens, such as one genetic letter being changed for another, the result can be that the code doesn't give the correct instructions about how to grow and develop that human being. There are lots of different ways in which those changes can happen.  Florence: And how can we inherit conditions from our parents?   Meriel: Well, for the most part, like I mentioned, we've got 20,000 pairs of genes and we get one of each pair from our mother and our father. And so, for lots of genetic conditions, they follow a pattern of inheritance where one copy of that pair of genes has got the variant or spelling mistake in it, which causes the condition.  So just having a single mistake in that pair of genes is enough to cause you to develop the symptoms of the condition. Other conditions show where you only develop the condition if both copies of the pair, the one you get from your mother and the one you get from your father have got a variant or a spelling mistake in the gene.  So, you actually don't have a working copy of that gene. There are other patterns of inheritance as well. And so, we talk about X-linked inheritance. That can arise because women have what we call two X chromosomes; men only have one X chromosome.  Florence: If you want to learn more about X-linked Inheritance, you can check out our previous podcast. How does X-linked inheritance work? So then do parents who have a condition always pass it on to their children?  Meriel: So, this is again, where we think about some of those patterns of inheritance that I've just mentioned. If somebody has a condition, for example, a dominant condition, they will have that variant or genetic change that's causing their condition in one of their pair of genes. So then it's 50:50 when they have a child, whether they pass on the gene that's carrying that variant or not, because the child will be getting the other copy of that pair from their partner.  If they do inherit that copy with the variant in it, then they will develop the symptoms of the condition in most cases. In some situations, however, a parent can have a genetic condition. So, they develop symptoms of the condition, and as I've mentioned, it's 50:50, whether it gets passed onto the child, so the child could actually inherit that genetic variant, but potentially not show signs of the condition. And this is what we call ‘reduced penetrance’. This means you can carry a genetic variant and probably some other event has to take place to cause you to develop symptoms.  So that might be that there's other genetic factors that you inherit that trigger you to develop symptoms or there might be an illness or something that you experience that brings out the expression of that gene. So that's quite an important, consideration when we're looking at genetic variants and whether somebody will develop symptoms.  Florence: And finally, how do we develop conditions that don't come from our parents?  Meriel: Well, I suppose the main explanation for that is what we call a de novo genetic event. So that can arise when we are conceived. So for example, genes get copied to be put into the sperm or our genes get copied to be put into the egg. And in that process of making the sperm and the egg, a spelling mistake or mutation can arise in the DNA and then that sperm or that egg, whichever one has it, takes that forward into making the baby. And then the baby from that point will have that genetic variant in every single cell in their body. So it hasn’t come from the parents, so it’s not inherited but it still is a genetic condition. This is something that now that we're able to do whole genome sequencing, we are finding is a more common explanation for developmental disorders or conditions in children than we previously appreciated. And quite a lot of conditions where the child has congenital abnormalities when they're born, like a congenital heart problem with some global development delay or difficulties or some other sort of problem, when we do their whole genome sequencing, we find that they have a de novo mutation in an important developmental gene.  There are also some more unusual ways in which a genetic condition can arise for the first time in the family. The first example I might give is, the condition, Huntington's disease. Huntington's disease is a neurodegenerative condition that causes a movement disorder, often starting in adult life. And sometimes people will know that it's in their family. However, sometimes it can arise in somebody and there's no history of it in the family at all.  Huntington's disease is what we call a triplet repeat condition. This is where, in our DNA sometimes we have little strings of letters that are repeating after each other. So, usually we'd have 25 repeats or less. This can slip up on transmission from a parent to the child, so it can increase in size and if it slips up into the range of 40 repeats or more, then that person will develop symptoms of the condition.  Another example I thought that might be worth mentioning is what we call imprinting. When we inherit our genes from our parents, for some genes, it actually matters whether the gene copy has come from your mum or from your dad, and it will have an imprint or a mark on it that says, this is the maternal copy, this is the paternal copy.  The reason that imprint is there is that it may potentially switch off that gene and say, this shouldn't be expressed in the baby. And if this doesn't work properly, you can get some conditions like for example, Prader-Willi Syndrome. This is where a child has developmental delay and maybe a very increased appetite. And it's because the differential gene expression hasn't worked. Florence: That was Meriel McEntagart, explaining whether genetic conditions are always inherited. If you would like to hear more explainer episodes like this, you can find them on our website at www.genomicsengland.co.uk. Thank you for listening.

In this episode, we explore findings from a groundbreaking study recently published in Nature which revealed potential targets for bowel cancer prevention and treatment. The study provides the most detailed understanding yet of bowel cancer’s genetic makeup. The research, which used data from the 100,000 Genomes Project identified over 250 genes that play a crucial role in the condition, driver genes and potential drug targets. Our guests discuss the potential impact of these findings on patient outcomes, screening for bowel cancer, and future prevention strategies. Helen White, Participant Panel Vice-Chair for Cancer at Genomics England is joined by Professor Ian Tomlinson, Professor of Cancer Genetics at the University of Oxford, Claire Coughlan, Clinical Lead for Bowel Cancer UK and consultant nurse in colorectal cancer, and Dr David Church, a clinical scientist fellow and a medical doctor specialising in oncology at Oxford University. "The people that were kind enough to donate samples to the 100,000 Genomes Project, they did so knowing that they almost certainly wouldn’t benefit personally from their donation from their gift and that any benefits would be some way down the line and hopefully benefit others which is what we’re seeking to realise now. But, you know, it’s not a given when we treat people in the clinic so we’re very, very grateful to those individuals." You can read more about the study in our colorectal cancer blog and our study findings news story. You can download the transcript or read it below. Helen: Welcome to Behind the Genes. Ian: One of the great hopes is that some of these new genes that we’ve found could be useful in preventing cancer and it doesn’t necessarily matter that they’re rare, even if they’re only 1% of cancers, by using those and changing those in the normal individual before they have had cancer then we may be able to reduce that risk. So, there are lots of potential new targets for prevention that are coming through.  My name is Helen White and I’m the Participant Panel Vice-Chair for Cancer at Genomics England. Today I’m delighted to be joined by Professor Ian Tomlinson, Professor of Cancer Genetics at the University of Oxford, Claire Coughlan, Clinical Lead for Bowel Cancer UK and consultant nurse in colorectal cancer, and Dr David Church, a clinical scientist fellow and a medical doctor specialising in oncology at Oxford University.   Today we will be discussing a pioneering colorectal cancer study which using data from the 100,000 Genomes Project has uncovered new insights that could transform diagnosis and treatment for patients with bowel cancer. If you enjoyed today’s episode we would love your support, please like, share and rate us on wherever you listen to your podcast.  Thank you for joining me today. We’re going to be discussing the findings from a landmark study that has been published in nature. This study used data generously donated by people with bowel cancer who took part in the 100,000 Genomes Project giving us the most detailed look yet at the genetic makeup of colorectal cancer better known as bowel cancer. But before we get into that let’s start by hearing from my guests. Could each of you please introduce yourselves.  Ian: I’m Ian Tomlinson, I work at the University of Oxford and most of my work is research into bowel cancer, it’s genetic causes, the genes that are involved in actually causing the cancer to grow which may be different from genetic causes and also the use of that data to help patients whether guiding future treatments or potentially helping to prevent bowel cancer which would obviously be our optimum strategy to have the biggest impact on the disease and its incidents.   Claire: So, I’m Claire Coughlan, I’m the clinical lead for Bowel Cancer UK and my remit at the charity is to ensure that everything we do is clinically relevant and that we’re providing services that meet the needs of those affected by bowel cancer and the educational needs of those health professionals that work with people affected by bowel cancer. I’m also a nurse consultant in colorectal cancer at Lewisham and Greenwich NHS Trust and I lead an urgent referral service there and also work with patients with late effects of bowel cancer.  David: I’m David Church, I’m a medical oncologist and Cancer Research UK advanced clinician scientist at the University of Oxford. I treat bowel cancer clinically and do research on bowel cancer and womb cancer including a lot of research using samples and data from Genomics England data service we’re discussing today of course.  Helen: Great, thank you. Now let’s turn to Claire to learn more about bowel cancer. Claire, can you share with us how common it is, how treatable it is and if there are any trends in terms of which groups of people are affected?  Claire: Of course, bowel cancer is a relatively common cancer, there are about 46,000 people each year in the UK diagnosed with bowel cancer so that is quite a large number. The thing that really drives us forward in bowel cancer is that the earlier stage you’re diagnosed at the greater chance of survival. So, the figures for that are quite stark, we stage bowel cancer through stage one to 4 with one being the earliest stage and 4 being the most advanced.   If you are diagnosed with bowel cancer at stage one you have a 9 in 10 chance of being alive and well 5 years after your diagnosis of bowel cancer. And if you’re diagnosed at the other end of the spectrum at stage 4 that drops to a 1 in 10 and should people survive after a diagnosis of stage 4, which more people than before do they will have had a lot of treatment for their bowel cancer so the burden of the treatment will also be with them after that. So, it’s really important that we diagnose at the earliest possible stage which is why studies such as the one we’re going to talk about today are so important.   We have noticed that there has been a slight increase in being diagnosed at a younger age. That said the latest statistic is 2,600 people were diagnosed under the age 50 in the UK last year so it’s still a disease of older people, you still have a greater chance of getting bowel cancer as you get older but it’s really, really important that we’re aware that you can still get bowel cancer as a younger person.   Probably one of the most exciting things that has happened for bowel cancer of recent years is our bowel cancer screening programme and the age for that now has been brought down to 50, we’re not quite there all over the country, but in the UK that is the aim that everyone will be screened for bowel cancer at the age of 50. So, yes it’s a common disease and staging an early detection is vital. Helen: That’s lovely Claire, thank you very much for that. David, turning to you could you please explain to us how bowel cancer typically develops? David: Yes, so we know compared with many cancer types quite a lot about how bowel cancer develops because the bowel is accessible to collect samples by a technique called endoscopy which is putting a camera into the bowel from which you can sample tumours or lumps. And so from genetic research done in the last 10 years we know that, or we’ve known for many years actually, for much longer, that cancer is a genetic disease, it’s a disease caused by alterations in genes and particularly genes that control whether the cells in our bowel grow normally and die normally as they should do. And collectively when there are alterations in genes that regulate those processes you can have a cell or collection of cells which are able to grow without restraint and don’t die when they should do which are some of the hallmarks of a cancer and they also require the ability to spread elsewhere in the body which is what kills people with cancer including bowel cancer. We know from research done in the last 10 to 15 years that some of the alterations in genes that can cause bowel cancer in combination occur very early in our life, even in the first and second decade of life, but don’t cause cancer. The earliest detectable abnormality is typically a polyp which is a tumour, a lump within the bowel which is detectable and if removed is almost certainly cured by removal alone but if it’s not detected then as that grows and acquires more alterations in genes then it can become a cancer and cancers develop the ability to invade the bowel wall, to spread to what we call lymph nodes or glands nearby and also to spread further afield, most commonly to the liver or to the lungs.   And for most people whom bowel cancer has spread to the liver or to the lungs or elsewhere unfortunately we’re not able to cure their disease which as Claire has said is why there is such an importance in detecting cancers and pre-cancers as we call them so that the tumours are not actually cancerous but come before bowel cancer as early as possible.  Helen: Thank you David. Moving on to the study, Ian perhaps you can take this, in the study that you carried out my understanding is that the whole genome sequencing was used to investigate the genetic changes that lead to the development and growth of bowel cancer. And for this participants with bowel cancer in the 100,000 Genomes Project donated both a blood sample and a tumour sample while those with rare conditions only provided a blood sample, can you explain why that is?  Ian: As you said the study really looked at 2 quite separate arms albeit with a little bit of overlap as we’ll see. So, one very important aim was to look at individuals, both children and adults, who had medical problems or other conditions that were unexplained but which had some features that suggested that they weren’t necessarily inherited but there may be some variation in their genes that had caused them, and roughly half of the programme was dedicated to that.   Within that there was a small number of people who had a strong family history of bowel cancer or who had large numbers of polyps in the bowel and they were analysed in a separate part of the project from what we’re mostly discussing. Within the cancer arm there was a collection really throughout England of patients who had most of the common types of cancer and a few with less common cancers.   And because when we’re looking at genetic and related changes in cancers we need to make sure that those changes have actually occurred in the cancer as it started growing from its earliest stages with a small number of cells in the body that were slightly abnormal and then progressing. We need to look at what genetic variation the patient has in all the cells of their body. We don’t want to look at patients and say that looks an interesting change, we may be able to use that if it’s present in all of the normal cells in that patient’s system.   We want to make sure the change is specific to the cancer itself and therefore we have to sequence both a sample probably taken from blood and a sample taken from the actual cancer. And in a way we subtract out the changes in the blood to identify the changes that have actually occurred in the cancer itself.  Helen: That’s a very helpful explanation. Does this research show that there is a role for whole genome sequencing in clinical care?  Ian: I think my own view is it is all a question of cost. I think the advantages it provides it can assess multiple types of genetic change at once. It is relatively consistent across each cancer’s genome between cancers, even between centres mean that it is the method of choice. There are undoubtedly developments that will happen in the future, maybe being able to sequence longer stretches of DNA in one go that will help the analysis.   And some of the computational methods are likely to develop to identify some of the slightly difficult to identify genetic changes but it ought to be the standard of choice. There are issues and potential difficulties in collecting the high-quality samples that have been needed from pathology laboratory and that will be difficult going forward with current budges and there are lots of challenges but ultimately it in some form has to be the method of choice. What wasn’t done is to look at other molecule tests or essays, looking at RNA wasn’t really done on a big scale as well as DNA and other changes to DNA apart from the genetic changes were not looked at.   So, there are certainly ways it could be improved if you had limitless money but I think the project, 100,000 Genomes has shown the whole genomes are. They have a lot of advantages and ultimately probably will be adopted by the NHS and similar organisations.  Helen: David, could you now tell us about the findings of this pioneering study and what impact these findings might have on people with bowel cancer in the future?  David: So, this is the largest study to date to analyse the entire genome of bowel cancer by some margin and the fact that we’ve done whole genome sequencing and in so many people it has really given us an unprecedented ability to identify the genetic alterations that drive bowel cancer. And within bowel cancer we’ve known for some time it is not a homogeneous entity that bowel cancer is not all created equal, that there are sub-groups of bowel cancer and we have been able to refine those over previous efforts. And I guess if you were to ask what the biggest take home for me from the study is it’s just the complexity of the disease.   So, as we’ve mentioned we know that cancer is a genetic disease, that it’s driven by genetic alterations, alterations in genes which regulate the growth of cells or the death of cells or the spread of cells. And we’ve known for many years that there is a modest number of genes which are commonly malfunctioning in bowel cancer and they would be in the tens to dozens really. But with this work we’ve hugely extended our understanding of the genes that drive bowel cancer and in fact we’ve discovered nearly 250 genes which are altered in bowel cancer and appear to drive the growth of the cancer.   Now we know that not all of those will be validated and by that I mean that there are associations that we find at the moment, not all of which will be biologically relevant but interpreted in the data we know a large number that are previously undiscovered are or we can be fairly confident of that. And one of the take homes from that is that many of these are only altered in a small fraction of bowel cancers.   So, rather than being perhaps half of bowel cancers or a third of bowel cancers there are a good number of genes, a very substantial number of genes, which are altered in say 3 to even 1% of bowel cancers. And if we think about how we go about targeting those and perhaps we’ll come onto treatment later that poses really challenges for how we work and we would think about treating patients with bowel cancer who have those particular alterations in their cancers.  Helen: Thank you David, yes we’ll come onto treatment shortly, but I think Claire has a question for you.   Claire: Yes, thank you. For me as somebody who works in this every day this is such an exciting and interesting study, particularly in light of what we said earlier about early detection and how critically important that is for improving outcomes in people with bowel cancer. So, in your view do you think this research could help shape future screening programmes or prevention strategies?  David: That’s a great question, I suppose in terms of screening at the moment the majority of screening is done in the UK at least by testing for blood in the stool which is relatively non-specific so I’m not sure that that would be directly impacted by this research. But one area of early cancer detection that is perhaps more relevant is quite a lot of work including from Oxford actually in recent years looking at blood tests. So, testing blood samples for early detection of cancer whereby you can test for genetic alterations, fragments of DNA that have alterations from the bowel cancer or any cancer that circulates in the blood and that tends to rely on a small number of common alterations.   And with this data I could see that we might be able to refine those tests and in so doing improve our early detection of cancer but that would need quite some work before we could actually say look that had real potential I think. And in terms of prevention there are, I think Ian may want to come in on this, one or 2 sub-groups which you might think that you could try to prevent but of course that needs a lot of extra work really.   But I think we have some clues of the biology of bowel cancer and particularly some of the sub-groups where you might think well this drug would work better in terms of preventing that sub-group or that sub-group but that will need to be the subject of future study.  Helen: Ian, did you want to come in on that at all?  Ian: So, at the moment prevention is a fairly new way of helping to reduce the number of people with bowel cancer at the level of the whole population which is what we have in the UK above a certain age group as we heard from Claire earlier. The methods used, again as we heard, are screening for occult blood in the stool and then colonoscopy to identify either hopefully early cancers or polyps and remove those. But when we think about the methods that we use for preventing other diseases then normally where they’re successful using a more easily delivered and I have to say less expensive method.   So, high blood pressure is treated to reduce the risk of cardiovascular disease and there are other diseases where those what you might call molecularly-based prevented strategies are coming in. We really lack that for bowel cancer in particular, it does happen for some other cancers, but one of the great hopes is that some of these new genes that we’ve found could be useful in preventing cancer. And it doesn’t necessarily matter that they’re rare, even if there are only 1% of cancers, by using those and changing those in a normal individual before they have had cancer then we may be able to reduce that risk.   So, there are lots of potential new targets for prevention that are coming through and as David said it is going to take a lot of work to work out which of those are deliverable and who will benefit. But we have quite a lot of opportunities in that space and although that may not be us that takes that forward, it may be, but it may not be. We think it is a lot of material for those interested in chemo prevention using drugs of cancer that they can work on and with luck deliver some new ways of preventing cancer that may be simply popping a pill every morning to take your risk right down to as close as zero as we can.  Helen: Thank you Ian. David, I think you had something to add here.  David: Thanks Helen. One area of prevention that we’re really interested in Oxford and many others are is using the genetic alterations that we find in bowel cancers and other cancers as targets for vaccination. Now we know that gene alterations will cause abnormal proteins which while they might drive the cancer, make it grow or not die, can also be recognised by the immune system so the abnormal proteins can be recognised by the immune system as being foreign and as foreign they can be targeted by the immune system so the immune system will try and kill the cells carrying those alterations. And we know for some sub-sets of bowel cancers those alterations can be relatively predictable actually, they occur in quite a sizeable fraction of some sub-groups of bowel cancers.   And one area that we’re particularly interested in at the moment and actively pursuing is using those targets where you need some additional work to demonstrate when they are particularly recognisable by the immune system. But to use these genetic alterations is potential targets for vaccination with the intention ultimately of preventing bowel cancer in at risk individuals or ideally in the full-term time the whole population. And we’ve received some funding from Cancer Research UK to pursue this line of research and we have a group working on this in Oxford and as I say many others do elsewhere.  Helen: Thank you David, yes I have a vested interest in this because my understanding is this work is aimed primarily at people with a genetic condition called lynch syndrome which predisposes the people who have inherited this gene change alteration to bowel cancer, womb cancer and other cancer. And I had womb cancer, as I think David you know, a few years back and discovered it was due to lynch syndrome and so it’s really exciting that you’re now looking at vaccinating preventing because yes I take aspirin every day, I have my colonoscopy every 2 years which have some effect on preventing these cancers but it’s not 100% guaranteed. And I don’t suppose it ever will be but having the vaccination in that armoury would be fantastic I think for future generations, it’s very exciting and we look forward to hearing more about it.   Thank you Ian and David. I mean we’ve heard a lot there about preventing bowel cancer but I think moving back now to potential treatments, you know, we’ve heard from David how this study has shown a number of actionable findings but what are the next steps towards treatment? How can these findings be turned into real actions that will benefit those people diagnosed with bowel cancer in the future? Ian, perhaps you would like to pick up on this to start.  Ian: That step is one, you know, in which I’m not personally an expert but a lot of the newer treatments are based on the finding of so called driving mutations which are simply genetic changes that occur as the cancer grows and contribute to that growth and ultimately if it’s not treated to the spread and dissemination of a cancer. And the fact that we have reported 250 which need validation but of which a large proportion are likely to be true drivers means that anyone of those can be a potential new target.   The criteria to be used for which of those mutations to pursue, which of those driver genes to chase up are quite complicated normally, depend on many things such as the interest of research groups and small and larger drug companies. And the similarity of those genes to other genes that have evolved and the processes that they make to go slightly wrong in the cancer.   So, there is also the issue that because these are uncommon, everybody talks a lot about personalised medicine or precision medicine, this would be truly precision or personalised medicine because a genetic change that was driving the cancer in only 1% of patients is obviously not a huge number of patients although bowel cancer is a common cancer so it’s not a tiny number either. But it would mean investment at that level to benefit let’s say 1 to 2% potentially of all patients with bowel cancer but I think that’s a nettle we have to grasp. And I think our results are showing that most of the really common drug changes either have not yet been successfully targeted in treatment or are too difficult to target.   So, we’re going to have to start looking at these less common genetic drivers and design strategies, inhibitors, you know, again that can be delivered to patients relatively straightforwardly in order to see whether they benefit the patients concerned. But there is this problem of getting enough patients enrolled in clinical trials where a change is only present in a relatively small proportion of all the patients with that cancer type.   Helen: Thank you Ian. Presumably if there is a relatively small number of patients the people who are looking at running these trials might be looking at perhaps international trials, would that be one way to go?  Ian: So, I think David can speak with more personal knowledge but there are international trial networks and there are collaborations along these lines already under way. I would hope that those could be made use of even more than they are already. There is, you know, a financial consideration for those developing new anticancer treatments which are, you know, high risk work and also the costs of setting up trials and enrolling people is not a trivial thing. So, I think those are hurdles that can be overcome but it would need a concerted effort to do that. Patients will play a major role in that and patient organisations as well as 100,00 Genomes and other similar projects.  Helen: Yes, thank you, David I don’t know if you want to come in on that.  David: Yes, the challenge of testing therapies in small groups is a very real one and there is lots of interest at the moment in exploring alternatives to conventional clinical trials. And as we use more electronic patient records and we have pharmacy records so there is the potential to get those data from routine clinical practice and there is lots of investments and attention on that at the moment so called real world data which is always an interesting term as if patients in clinical trials aren’t in the real world which of course they are.   But it’s perhaps a little more cost effective sometimes in clinical trials, of course it does pose its own challenges in how you disentangle true treatment effect from other factors because there are many factors impacting on how long people with cancer live. But there is a lot of investment and effort going into that at the moment and it will be interesting to see how that develops over the coming years.  Helen: Turning to you Claire based on your experience how well do you think people with bowel cancer understand how genomes can help with their care and what support is currently available to them in this area?  Claire: I think the answer, as it is so often is, it’s dependent on individuals and not just one individual. So, I think some patients are very motivated to know as much about this as possible and to understand and to know what the next steps may be in their own treatment that may be helped by this. Others don’t want to have the same knowledge and want to be guided very much by their medical teams but I think oncologists obviously are at the forefront of this and we see at the charity … we have services at the charity that supports patients and we see lots of queries into our ask the nurse service where people have been given variable information about I suppose personalised medicine as Ian alluded to and how their very specific bowel cancer may be treated, so I think it varies from patient to patient.   There is support available so we have the ask the nurse service I alluded to. We have a brilliant patient forum actually and everybody in clinical practice will have seen this, patients often become more expert than anybody and they share advice and they’re moderated forums that are a very safe place for people to ask questions where there is a moderator to ensure that it is made really clear that circumstances are individual.   And the same with the ask the nurse service because you don’t have all the clinical information so it is about empowering people, so there is support available. I think the other thing that is really important is equipping specialist nurses with the knowledge that they need to support their patients. This is a really exciting area of evolution for bowel cancer particularly I think in all cancers at the moment but for bowel cancer I think things have changed fairly rapidly in recent years and specialist nurses really need support in knowing that they have up-to-date information to give their patients.   So, that’s another challenge for us and any specialist nurses that might be listening to this podcast we have online education on genomics for specialist nurses. Just while we’re talking about that and you mentioned lynch syndrome earlier, so there has been a lynch syndrome project as I’m sure you’re aware where we’re trying to get testing for lynch syndrome brought into local hospitals.   So, there was some funding via NHS England so that the testing be done at time of diagnosis, so a pre-test and then a final test if that’s appropriate, for everybody diagnosed with bowel cancer to see if they have lynch syndrome. And in some trusts that has been done and in others it hasn’t yet and the funding hasn’t quite followed in the way that we need it to enable that to happen. It’s vitally important, we think there are about 175,000 people in the UK with lynch syndrome and we only know about 5% of them. And this is a gene change that is an inherited gene change so we can do what we call cascade testing where we test family members and we can then employ preventative strategies to prevent people from developing bowel cancer.   So, it’s a really important project, so I think as well as supporting patients with the information around the changes that are happening in this area we also need to ensure that we support the workforce and have investment there to enable the support of all the changes and the genomic landscape.  Helen: Absolutely Claire and so much resonates there with what you’ve said. Having myself had cancer discovered that was due to lynch syndrome, cascade testing offered to my family members so valuable. It turns out I inherited my change from my mum who is 83, has never had cancer, so I think that’s a very good example of, you know, it doesn’t necessarily mean that you will get cancer but actually on that point that you made about empowering patients I always have a right smile because there is my mum going off to all her other medical appointments because at 83 she sees quite a few people and she is always the one telling them about lynch syndrome and educating them because most of them haven’t heard of it, so yes it’s really, really important.   And that patient forum, you’re probably aware of Lynch Syndrome UK, I don’t have any involvement in that other than being a member but that is so valuable for people with a particular condition to go somewhere where they can talk to or listen to other people with a similar condition, really, really valuable.   Right, well I think circling back really to the 100,000 Genomes Project I think you touched on this earlier David but reflecting on what you and Ian have told us about your study what is it about the 100,000 Genomes Project bowel cancer dataset that made this work possible?  David: There are a few things, one of which and not least of which is the sheer size of the effort. So, to have whole genome sequencing for more than 2,000 individuals is previously unprecedented and we’ll be seeing more of this now as we scale up our research efforts but at the inception of the project it was very, very ambitious and to be able to deliver that is a huge achievement. And the quality and breadth of the analysis is very strong as well.   And ultimately, you know, the former gives thanks to the people that were kind enough to donate samples to the 100,000 Genomes Project, they did so knowing that they almost certainly wouldn’t benefit personally from their donation from their gift and that any benefits would be some way down the line and hopefully benefit others which is what we’re seeking to realise now. But, you know, it’s not a given when we treat people in the clinic so we’re very, very grateful to those individuals.   And I think also to the scientists who worked incredibly hard over the last 5 years to deliver this work actually. So, having been part of the team and being lucky enough to be part of the team along with Ian we’ve had hugely motivated individuals that really have dedicated a large fraction of their working lives to delivering this project which I think is a fantastic achievement as well.  Helen: Thank you, thank you to all those participants who at a time when their lives probably were turned completely upside down by a cancer diagnosis were offered the chance to join the 100,000 Genomes Project and said yes. As you say most of them will have known that it won’t have helped them but by donating their data, you know, it has allowed this work to happen and potentially it could change lots of people’s lives in the future, so thank you to them.  Ian: Could I also just emphasise and agree with what David has said, I won’t go through all the individuals by name, but if anybody wants to read the published report of the work there are several people on there, Alex Cornish is the first author, but many colleagues from an institute of Cancer Research, The University of Manchester, Birmingham, Leeds, other universities in London that all contributed, but also colleagues in the NHS and/or universities who recruited patients, collected samples, processed them etc and of course the people who did the preparation of the samples in genetics laboratories and actually did the sequencing and basic analysis too.   So, it is a truly huge effort across particularly all the cancer types which is particularly a complex collection given the fact the tumour is needed and a blood sample. It’s quite difficult in a way to find a formal way of thanking them for all of this but without them it wouldn’t have happened.  Helen: On that note I think we’ll wrap up there. A huge thank you to our guests, Professor Ian Tomlinson, Clare Coughlan and Dr David Church for an enlightening discussion on the groundbreaking study published in nature. This research is set to reshape our understanding of colorectal cancer and pave the way for new possibilities in treatment and patient care.   If you would like to hear more like this please subscribe to Behind the Genes on your favourite podcast app. Thank you for listening. I have been your host, Helen White. This podcast was edited by Bill Griffin at Ventoux Digital and produced by Naimah Callachand. 

In this explainer episode, we’ve asked Adrianto Wirawan, Director of Bioinformatics Engineering at Genomics England, to explain what the term 'no primary findings' means. 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 [email protected]. You can download the transcript or read it below. Florence: What does ‘no primary findings’ mean? I'm joined by Adrianto Wirawan, Director of Bioinformatics Engineering for Genomics England, to find out more. So firstly, Adrianto, when we speak about findings from genomic tests, what does this mean? What are we looking for when we do a genomic test?  Adrianto: Our DNA is made up of a long sequence of letters that act like instructions for your body.  Genomic testing analyses these letters to see if there are any unusual patterns or changes that might change your health. You can imagine your DNA as a book full of recipes for your body. Every recipe tells your body how to make proteins that keep you healthy, and sometimes there might be a typo in the recipe, like missing an ingredient or mixing up the steps. This could result in a health problem, just like how a changed recipe can lead to a bad dish.  On average, we would expect about 5 million out of our 3 billion DNA letters to be different. And each of these, we call them a genetic variant. Genomic testing is designed to examine some of these variants to help inform our healthcare. So, for example, in understanding why certain health problems happen and in choosing the best treatment based on our unique genetic makeup.  Florence: And what do we mean by primary findings?  Adrianto: Primary findings mean that in a patient's genomic testing, we identified a set of variants that is linked to the patient's condition. The variants that we have makes us who we are. However, not all of them cause a disease or contribute to a health problem. our bioinformatics pipelines will automatically prioritise variants of potential relevance to the patient's conditions. Using this data, the NHS clinical scientists will then determine whether any of these prioritised variants are linked to the patient's condition and whether a genetic diagnosis has been identified, which would explain why certain health problems happen.  Florence: So, then what happens when there are no primary findings?   Adrianto: When no primary findings are found, that means that no genetic diagnosis has been identified. As developments are made and our knowledge of the variance improves over time, additional findings might be identified in the future.  The clinical team responsible for a patient's care may request reanalysis of data according to the national guidance, following a change in the patient's clinical status to inform reproductive decisions, or after significant new disease gene associations have emerged.  In addition, Genomics England also provides the diagnostic discovery pathway where we focus on uncovering new diagnosis, where the participants of the 100,000 Genomes Project, as well as the patient's sequenced through the NHS Genomic Medicine Service   This is meant to be more equitable as we don't rely on the clinical teams to raise individual separate requests.  Florence: And finally, what do we mean by secondary findings?   Adrianto: Secondary findings are additional findings not related to the conditions in which the patient was recruited for. For example, if a patient was recruited for one type of cancer, but perhaps we found variants linked to a different condition. We explored secondary findings for the 100,000 Genomes Project but we do not do secondary findings for the Genomic Medicine Service.   Florence: That was Adrianto Wirawan explaining what we mean by ‘no primary findings’. 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. 

In this explainer episode, we’ve asked Mathilde Leblond, Senior Design Researcher for the Generation Study at Genomics England, to answer some frequently asked questions that we received from parents who we engaged with for the design of the study. You can hear more information about Generation Study via the study's official website and in our previous podcast episodes: How has design research shaped the Generation Study? Which conditions will we look for initially in the Generation 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 [email protected]. You can download the transcript or read it below. Naimah: You may have heard about the Generation Study. This research study led by Genomics England in partnership with NHS England will sequence the whole genomes of a hundred thousand newborn babies and will look for more than 200 rare conditions that could be treated in the NHS in early childhood.  The study seeks to improve how we diagnose and treat rare genetic conditions to enable babies and families to have better outcomes. Today I'm joined by Mathilde Leblond, who leads design research for the Generation Study, and will be answering some of the frequently asked questions that we receive from parents who we engaged with for the design of the study — the same questions that expectant parents at participating hospitals might have before deciding if they want to take part.  So first of all, Mathilde, can you tell me a little bit more about your role?  Mathilde: Hello. So, I'm a design researcher. My role is to support my colleagues, understand our users deeply so that we can create experiences that are as positive and seamless as possible.  So today we'll talk about the parents who are the ones invited to take part in the Generation Study, but our users also include the midwives who are approaching them and taking blood samples. The clinical scientists who are interpreting the results and the specialist paediatricians will be contacting the parents if a condition is suspected, and even many more users actually.  So, we did a lot of research prior to launching to shape the Generation Study, and now that we're live, we continue doing more to keep improving the experience.  Naimah: Okay, so can you give us a bit of background? How did you engage with parents in this study?  Mathilde: Yeah, so today we've involved over 150 pregnant and recent parents in our co-design sessions.  And these sessions were slightly different each time with different topics and exercises, but generally we spend around 90 minutes with one parent. And we asked them to bring someone who helped them make decisions about their baby during their pregnancy. So that meant that we had their mums, their sisters, their husbands, their wives and friends as well, taking part and discussing the Generation Study with us.  During that time with them, we would test our materials. We listened out to what's important to them and what they asked about, and we got them to show us what would work better for them so that we could then shape the materials around that.   Naimah: So you can find out a bit more about why it's important to involve users in co-design in our podcast ‘How has design research helped shape the Generation Study?’, which is available on our website.   So, we have a list of frequently asked questions from some of the parents, and I wanted to post some of them to you today, Mathilde. So first of all, one of the questions was, why should my baby take part in this study?  Mathilde: Yeah, I mean, that's really the key questions that all parents are asking themselves before they even spend any time finding out more about the Generation Study. And our materials do reflect that. So what tends to matter most to the parents we spoke to, is that there's a small chance that their baby may benefit directly from taking part because if a condition is suspected, they'll be invited for further specialised tests within the NHS, and they could receive treatment much sooner than if we had waited for the symptoms to develop and for a diagnosis to come, which can sometimes take years for some rare conditions. But for a large majority of the babies, 99%, they will have no condition suspected and so their involvement really is more altruistic. Taking part means that their parents agree to share the baby's healthcare records on an ongoing basis and their genome with researchers who can then look at this together with information from thousands of other babies and patients to help improve our understanding of genes and health.  So taking part in the Generation Study also means that you might help uncover some life-changing early treatments for babies in the future. And finally, something that's super important to us is that people from Black, Asian and other minority ethnic communities have historically been underrepresented in this type of research. So, we're working hard to make the Generation Study as inclusive as possible to help genetic testing and treatments be improved for everybody in the future. So, there's many reasons to take part in the Generation Study.   Naimah: You mentioned the word altruistic there. Can you tell me what that means?   Mathilde: Yeah, so that's really to help society. They may not get benefits within their own lives or within their own family, but somebody somewhere will benefit from it in the future. And that's what altruistic means.   Naimah: Thank you. So, some parents might also ask, will this test tell me every illness that my baby might have now and in the future?  Mathilde: No. So first of all, we're still learning a lot about how genes work, how the environment affects them, and there's also many conditions that we still don't understand very well. So those are not in. Of the conditions that we do understand quite well. We did a big piece of public engagement in 2022 to try and decide which ones to include as part of the screening.  And while some parents told us that they would want to know every single thing in advance, a lot of parents were worried about how much it would raise their anxiety to find out about a potentially incurable condition at such a fragile and beautiful moment when you have a new baby. So, for this reason and many other reasons, we've decided to proceed really cautiously so that the conditions that we'll be testing for have been chosen to reflect 4 key principles. And you can find them on the website. But the main gist is that we'll only be looking for conditions that normally start in childhood, first few years of life. So, nothing around Alzheimer’s, nothing around breast cancer, for instance. And another principle is that there's has to be already existing pathways within the NHS so that the babies can be seen and treated quickly. So, we're only including those conditions that start in childhood, and something can be done about them early on.  Naimah: You can also listen to our podcast on our website 'Which conditions will we look for initially in the Generation study?’ to find out more about the list of 200 conditions, which we'll look for in the study and how this may change over the course of time as new evidence emerges.  So, another common theme with the parents was that they are aware that the NHS is already under a lot of pressure, and they asked if my baby is flagged for more testing, will I really be able to get the support I need from the NHS in time?   Mathilde: Yeah, that's a question that we've heard a lot actually, and it really makes sense considering the media coverage that's coming out daily, and that's been really in the papers for months now about how stretched the NHS is.  We've worked really closely with the NHS to ensure that all the babies that have a condition suspected as part of the Generation Study can be seen as soon as possible. So, our team has been in touch with specialists from across the country to understand how ready they are to take in those babies, to run confirmatory tests and potentially start treating them sooner.  So, it's been really key for us to make sure that we're not flagging up a baby for more testing and they just have to wait for months before they can get extra tests and attention. And that's so important for us to get right. In the long term, we hope that screening could actually relieve some pressure from the NHS if we can get babies to the correct doctor earlier on while their health is still good.  Naimah: Some parents might also ask, this research sounds very new. Is my baby going to be a Guinea pig?   Mathilde: Those two words, Guinea pig, came up again and again in almost every single session that I've had with parents, it was almost a freaky coincidence. I find that most parents use this wording to mean, will we inject anything into their baby or give them any medication that has not been tested and approved?  And the answer to this is no. What does happen is that when a baby's born after the birth, we need to take a few drops of blood so that we can create their genome, their DNA, and normally we'll take a bit from their umbilical cords, and that is happening in most of the birth at the moment of the participants.  But if for any reason we couldn't take that, maybe it was a complex labour, there was some emergency. The parents are asked a bit later if they would allow for a bit of blood to be collected using the heel prick methods. And that's a method that's been used in the babies in the UK within 5 days of birth for many, many years. And it looks for 9 conditions, as a current NHS test. So that's definitely safe. And usually when parents find out that that's all there is to it, they feel a lot more comfortable. A little disclaimer here because we mentioned the 5-day heel prick, while we use a similar method to get the blood, if we couldn't get blood from the umbilical cords, it's important to see that this is a different test, it's a proven test within the NHS which says many lives. So, parents who choose to take part in the Generation Study are very much encouraged to also agree to the day 5 newborn screen screening.   With all of that being said, this is a new research study and there are some uncertainties. Most of them revolve around how quickly we can process the results, how will parents and the NHS react to receiving these results so early, but also will this be inclusive for everybody? And might we inadvertently create more inequities? We're actively listening to sites now that we have opened and we have a survey that our participants can fill out, and we're working with UCL to help evaluate the impact of the Generation Study in an unbiased way.  Naimah: Okay. And another frequently asked question, if you have my baby's DNA, does that mean that you can clone them?   Mathilde: Cloning comes up regularly in our interviews with parents, though sometimes I found that people can feel a little bit silly asking about it, but actually it's a quite big topic that's top of mind when we talk about DNA and genomes.  Not least because of how much it comes up in sci-fi, it's just everywhere. So first of all, about cloning, it's important to remember that it's completely illegal, but it also has a whole host of other ethical concerns, which we don't take lightly at all here at Genomics England. So, the research that our study will support will be firmly within the bands of law and ethics and will only focus on discovering answers to questions that could help the health and wellbeing of babies, and really all of us in the future. No cloning involved.  Naimah: Okay. And then the final question, how can I take part in the study?  Mathilde: We've already opened in over 10 hospitals in England, which we are very excited about and we're actively working on opening more. You can visit our website, www.generationstudy.co.uk, to see an up-to-date list of hospitals which are currently taking part, and to read more about what taking part entails. Then you can contact your local research team to log your interest if you're planning on giving birth in one of our partner hospitals, and they'll be in touch to let you know about the next steps.  Naimah: That was Mathilde Leblond answering some of the frequently asked questions from parents that we have engaged with for this study. If you've got any questions or you'd like to hear more, please contact us at [email protected], or you could find out more on the Generation Study website www.generationstudy.co.uk.  Thank you for listening.

In this explainer episode, we’ve asked Callum Morris, Pharmaceutical Research and Development Insights Manager at Genomics England, to explain what happens in a clinical trial. 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 [email protected]. You can download the transcript or read it below. Florence: What happens in a clinical trial? I'm joined with Callum Morris, Pharmaceutical Research and Development Insights Manager for Genomics England, to find out more. So, Callum, first things first. What is a clinical trial?   Callum: So, a clinical trial is a study that looks to people to answer a specific medical research question.  So, this involves gathering a group of participants that are willing to participate in providing evidence on how to improve clinical care. And so, the main purpose for a clinical trial is to evaluate health related outcomes between different groups of participants. If it's an interventional clinical trial, you change clinical care for one group and not another.  And evaluate whether the change you made improved health outcomes for that group, or if it's an observational clinical trial, you might focus on different groups but not change anything about their clinical care and collect real world data to understand how outcomes differ across the groups.  Florence: Can you briefly explain what we mean by real world data?   Callum: Sure. So real world data relates to data collected routinely as part of standard clinical care. So, it could be collected from your electronic health records, data from product or disease registries, or data gathered from other sources such as digital health technologies.  And all of this can inform on particular groups from the population you're interested in.  Florence: And are there different types of clinical trials?   Callum: Yes. Clinical trials can take many forms depending on the medical research question you're trying to answer. They could be related to understanding the risk of disease. So, evaluating a potential risk factor that you may be concerned with. They might evaluate preventing disease. So, what different approaches can you take to people who have never had the disease, and does this prevent its occurrence? You can have a clinical trial that looks at screening for disease. For cancer, that's really important.  Does a new screening approach mean more people with cancer can be identified earlier? And importantly, does this lead to an improvement in survival? You can have clinical trials that evaluate the different approaches to diagnosing a disease and can you diagnose a patient earlier and better?  And then the classical clinical trial is revolving therapeutics or different treatments, and you can have treatments that are addressing the disease itself. Or you'd have treatments that are controlling the symptoms of side effects you might get from another treatment you might be taking.   So even within a specific medical research question, you can have different clinical trials depending on how much evidence you already have regarding that question. For clinical trials involving the assessment of new treatments and therapies, these are broken down into three stages and we call these phases.  So, you have phase one, phase 2, and phase 3.  Florence: Can you explain a bit more about these phases?   Callum: Sure. So, the overarching medical research question might be, what is the safety profile of this new therapy, and does it work improving on the current standard of care? So, you'll break this down depending on the phase, and with each phase you expand your clinical trial to a larger population.  Phase ones are typically on a small group of people around, let's say 20 to 50, and are designed to check the safety of a new drug that's being entered into humans for the first time. Sometimes, especially in early phase cancer trials, you're trying to find the right dose for your patients.  So, you might take a small group, test them on a low dose, and if there are no severe reactions to the new drug, you start incrementally increasing your dose a little bit more. And this gives you a really good idea of the safety profile of your drug as you try it for the first time in a human population.  Next, you'll move on to a phase 2. And these are typically larger than your phase one, around 50 to 200 people. And, usually you use the dose recommended by the phase one. So instead of slowly adjusting your dose and just focusing on the drug safety profile, the phase 2 will evaluate the safety of the medicine in a large population, but also have an additional focus on health-related outcomes.  Is the medicine causing the effect you want? Whether that's relief of symptoms or for cancer reduction in the size of your cancer. If the data is really promising from your phase two, it will move to a phase 3. And the idea is the same, increasing the size of the population. typically phase threes can be from 300 to 3000 participants.  And the key thing here is that you will evaluate the potential benefit of your new treatment against the current standard of care. Normally, meaning the treatments that are already available in the clinic. Health regulators will need to look at all the data collected from all the trials before they approve it for the general population.  And typically, they need a phase 3 to do this. They need a phase 3 to confirm that the benefit provided by the treatment outweighs the potential risks associated with it, across a fairly large cohort of participants. And this is to ensure the therapy is appropriate to be given to the general patient population.  But also, a phase 3 is needed to see that if the new treatment is moving clinical care forward in the right direction and in providing improvements for patients against what is already available in the clinic. And this is the process by which we call it evidence-based changes, to make improvements to clinical care.  Florence: So then how do people join clinical trials?  Callum: So firstly, it's about becoming aware of the clinical trial. You might be referred to a clinical trial by your doctor who's been aware of it and where it is. Or you might be able to find a clinical trial using clinical trial databases or finding about them through patient advocacy groups.  And they should be able to tell you which hospitals are taking part in the clinical trial. So, the next step might be your doctor can contact someone on the research team, and there is always a principal investigator per research site that is always a medical professional.  The study team at the site have all undergone training from the people organising the trial to run through the protocols necessary to keep the trial consistent in different sites.  Once they've been contacted, you'll undergo a screening process, and what they'll determine is your eligibility for the trial. They might assess medical history or your health status. And if you're eligible for the trial, the next step is to provide informed consent. The healthcare team should provide detailed information about the trial, its risks and benefits, the aim of the trial, and who's funding it.  And what are the treatment options for participating and not participating in the trial? How long is the follow-up in the clinical trial? And what will happen if you leave the clinical trial? And then also what are the safety concerns for the clinical trials and the possible side effects if it's something to do with a new treatment. Once you've been informed of all these details and you agree to be part of the clinical trial, you'll sign a consent form, and that means you're officially enrolled in the clinical trial.  Florence: And what happens once someone is enrolled in a clinical trial?   Callum: Once you are in the trial, you'll follow the procedures outlined in the trial protocol. This can take many forms, but normally it involves more regular follow-ups and check-ins with the clinical care team. And this is to establish safety concerns and to enable lots of data collection.  There also may be additional checks related to health outcomes during the trial, and so the study team may want to take additional samples to understand what is happening physiologically during the study. There also may be additional questionnaires for you to fill out, to capture patient reported health outcomes.  And this is to understand the patient's quality of life whilst they're on the trial. So, depending on the protocol, you may be followed up for a set period of time, and that may get less frequent as time goes on. And of course, you may pull out of the trial at any point after which the follow up will stop.  So, following data collection, there may be a while before you see anything, but results should be published following analysis of the data.   Florence: And finally, why might someone want to be involved in a clinical trial?   Callum: Clinical trials are all about providing evidence to improve clinical care. At any time we want to make a change to healthcare, we want it to be evidence-based. And so, this requires lots of people all contributing in a group effort to generate a data set large enough to determine how to change our approach to healthcare and move the field forward for improving people's lives.  Florence: That was Callum Morris explaining what happens in a clinical trial. If you'd like to hear more explainer episodes like this, you can find them on our website www.genomicsengland.co.uk. Thank you for listening. 

In this explainer episode, we’ve asked Nicole Chai, Research and Development Bioinformatician at Genomics England, to explain what X-linked inheritance is. 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 [email protected]. You can download the transcript or read it below. Florence: How does X-linked inheritance work? I'm joined by Nicole Chai, Research and Development Bioinformatician for Genomics England, to find out more. So firstly, Nicole, can you explain a bit about the X and Y chromosomes?   Nicole: Sure. So, the X and Y chromosomes are what we call sex chromosomes. And chromosomes are packages of DNA in our cells that are inherited from our parents, and they contain information about our physical and biological traits.  Some examples of traits that are determined by our chromosomes include what colour our hair is and what colour our eyes are. And each of these individual traits are determined by smaller sections on the chromosome called genes. Genes can also determine what medical conditions we may inherit from our parents.  As humans, we all typically have 23 pairs of chromosomes in each of our cells. One of these pairs consists of the sex chromosomes, and as their name suggests, sex chromosomes determine sex of an individual. And typically, females will have two X chromosomes and males will have one X and one Y chromosome.  Florence: So then, what do we mean by the term X-linked condition?  Nicole: So, an X-linked condition means that the condition is associated with genetic changes on the X chromosome. And what we mean when we say genetic changes are changes to the normal sequence of DNA on the gene. And this can sometimes lead to medical disorders.  Florence: Do you have a specific example of an X-linked condition?   Nicole: Sure. So, an example of an X-linked condition is Duchenne muscular dystrophy.  And with this condition you get a progressive loss of muscle due to the lack of a protein known as dystrophin. Another example of an X-linked condition is red-green colour blindness. And this is where people affected with the condition can't see shades of red and green the way most people see them.   Florence: Could you explain how X-linked conditions are inherited?   Nicole: Sure. So, for many conditions, there are two ways they can be inherited, either dominantly or recessively. Dominant inheritance is usually when you just need one copy of the gene to be affected by the condition, whereas recessive inheritance is when you need two copies of the gene to be affected by the condition.  However, this works slightly differently with X-linked conditions, and most X-linked conditions are inherited recessively.  Florence: So why does inheritance work differently for X-linked conditions?  Nicole: So the reason that inheritance works differently for X-linked conditions is down to the differences between sex chromosomes, between females and males. As females have two X chromosomes and males have X and Y, this means that for recessive excellent conditions, males only need one altered gene to have the condition.  So, because males only have one X chromosome, if they inherit a faulty copy of a recessive gene, they don't have another healthy copy to compensate.  On the other hand, as females have two X chromosomes, if they inherit just one faulty copy, they do have a healthy one that can compensate for that one. So as a result, what we tend to see is that males are more commonly affected by X-linked recessive conditions.  Florence: That was Nicole Chai explaining the term X-linked inheritance. If you'd like to hear more explainer episodes like this, you can find them on our website www.genomicsengland.co.uk. Thank you for listening. 

In this explainer episode, we’ve asked Arina Puzriakova, Scientific Curator at Genomics England, to explain what a polygenic disorder is. 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 [email protected]. You can download the transcript or read it below. Florence: What is a polygenic disorder? I'm joined by Arina Puzriakova, Scientific Curator for Genomics England to find out more. So, Arina, first things first. How can our genes affect our health?   Arina: So, genes are short sections of DNA that contain information that the cells in your body need in order to make proteins. Each gene carries the instructions for making a specific protein, and each protein performs a different task that allows the body to develop and function properly, depending on the genes that we inherit from our parents. Also determines our unique physical features such as our eye colour, hair colour, and height.  When a gene contains a change that disrupts the gene's instructions, also known as a gene variant, in some cases, this can lead to the production of a defective protein or prevents a protein from being made altogether. A missing protein or one that is not working properly can have a knock-on effect on how the body functions and this can result in health issues or the development of a genetic disorder.  Florence: So then how can a gene variant lead to a disorder?   Arina: So the genetics of each disorder are unique. In some cases, a change in a single gene is enough to cause a genetic disorder, and these are known as monogenic disorders. These conditions often occur in childhood and tend to cause severe illness. individually, they are more rare affecting a smaller number of people in the population, and usually they run in families as parents pass the damaging variance onto their children.  But these changes can also happen spontaneously without a known cause. An example of a monogenic disorder, which some may be familiar with, is cystic fibrosis. Cystic fibrosis affects one in every 2,500 babies born in the UK, meaning that there's about 11,000 people living with cystic fibrosis.  Florence: So, we've just talked through monogenic disorders. What do we mean by polygenic disorder?   Arina: So polygenic disorders are on the other end of the spectrum for disorders.  They are caused by the combined effects of multiple different genes. Individually, each gene has a very small effect on causing the disease, but many variations in different genes can act together to have a great impact on individual's susceptibility to that condition. Environmental and behavioural factors such as your lifestyle and diet also often have an effect.  Polygenic disorders are much more common, typically affecting millions of people in the population, and they're usually diagnosed in adulthood.   Florence: Could you give me an example of a polygenic disorder?   Arina: A common example of a polygenic disorder is type two diabetes. It affects almost 4 million people in the UK.  So this means that we know there are many genetic variants that could have made these individuals more susceptible to diabetes, but there are also other factors such as age or being overweight that could have increased their risk.  Florence: Are there specific challenges when it comes to diagnosing or treating polygenic disorders?  Arina: So, if I start with monogenic disorders, these are much easier to test for because we simply need to look for the presence or the absence of a faulty gene in order to determine whether someone is a carrier of a genetic disorder. On the other hand, testing for a polygenic disorder is a lot more complex as they are influenced by the combined effects of many genes.  Meaning there is no single genetic test or treatment that will work for all patients with the same condition. We need large and diverse groups of patients to study in order to accurately determine which genes are important and which ones are not.  And this can be challenging to obtain. Also accurately measuring and comparing lifetime environmental factors and exposures further complicates the assessment.  Another challenge with polygenic disorders is that even though they can cluster in families, the inheritance is not as clear cut or predictable as it is with monogenic disorders. Carrying a specific combination of genetic variants that are already known to be associated with polygenic disorder does not necessarily mean that you will definitely develop that disorder.  However, this information can be used to calculate something known as a polygenic risk score, and this provides an estimate for the risk of developing polygenic disease at some point in life based on individual's unique genetic profile.  Florence: And why can knowing apologetic risk score be helpful?  Arina: So, by being informed about the probability of developing a particular polygenic disease, an individual can make behaviour or lifestyles changes that could help reduce their risk. To go back to the previous example, somebody who is more likely to develop type two diabetes based on their genetic makeup can do things like maintain a healthy weight. And eat a healthy diet to help reduce their risk of developing type two diabetes in the future.  Florence: That was Arina Puzriakova explaining what we mean by polygenic disorder. 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.