Podcasts about oxford nanopore

If science and innovation hold the keys to tomorrow's kingdoms, then their successful discovery, nurturing, and commercialisation will give advantage to the nations where they are found and built and in turn, offer the potential for significant investment opportunities. Greg Smith, is CEO of IP Group, one of the UK's very few specialised, publicly listed, investors in science and innovation. In this episode, Greg explains IP's business and opportunity set. He discusses UK innovation and where and why it is world class. He explains sourcing opportunities, the investment process, and why he is so excited about their portfolio (covering firms such as Oxford Nanopore, Istesso, Pulmocide, Oxa & Hysata).  He continues with discussing the hurdles in the UK to commercialising and retaining more of the great innovations found here, and assesses their early mover position.  Finally he discusses the share price's discount to NAV, and what may lie ahead. Sign up to our Newsletter | Follow us on LinkedIn | Watch on YouTube | Contact IP Group 

In this podcast we speak to experts from Lonza and Oxford Nanopore about their collaboration to bring direct mRNA sequencing (including N1-Methyl-pseudouridine) to a regulated environment and establish the new gold standard in sequencing technology. We discuss how nanopore sequencing will be used to perform unbiased identity testing while enabling the simultaneous analyses of multiple critical quality attributes such as integrity (mRNA length and poly-A tail length) and capping.

Oxford Nanopore y UK Biobank desarrollan el mayor mapa epigenético para combatir cáncer y demencia  Oxford Nanopore Technologies y UK Biobank están creando el mapa epigenético más completo del mundo. Este mapa va a registrar cómo factores externos, como el estilo de vida y el ambiente, modifican el ADN humano sin alterar su estructura.Déjanos tu comentario y escucha más en Flash Diario en Spotify.La epigenética, clave en este proyecto, estudia estos cambios y su impacto en enfermedades como el cáncer y la demencia. Utilizando tecnología de vanguardia, analizarán 50.000 muestras para identificar hasta el 98 % de los marcadores epigenéticos. Este conocimiento permitirá comprender mejor cómo se desarrollan estas enfermedades y diseñar tratamientos más precisos y personalizados. ¿Qué implica este avance para el futuro de la medicina y nuestra salud?  Este mapa puede redefinir el diagnóstico y tratamiento de enfermedades  Un mapa epigenético es una representación detallada de los cambios químicos que afectan cómo se expresan los genes, sin modificar el ADN. En este caso, el proyecto analizará cómo los estilos de vida, como la dieta o el tabaquismo, influyen en la activación o desactivación de ciertos genes. Oxford Nanopore, con su tecnología avanzada, permitirá mapear el 98 % de estas modificaciones, un salto gigantesco frente al 3 % que los métodos actuales lograban. Este análisis detallado se combinará con información genética, imágenes y datos médicos de los participantes para ofrecer una visión completa de cómo se desarrollan enfermedades en la mediana y tercera edad.  El cáncer y la demencia afectan a millones de personas cada año, y aunque los avances genéticos han ayudado, no siempre explican por qué surgen estas enfermedades. Ahí es donde entra la epigenética, que estudia los factores externos que alteran cómo funcionan los genes. Sin embargo, los datos disponibles hasta ahora han sido limitados y fragmentados. Esto ha dificultado la creación de herramientas efectivas para diagnóstico temprano o tratamiento personalizado. El nuevo proyecto promete resolver este problema al ofrecer un nivel de detalle sin precedentes, permitiendo identificar patrones de riesgo y comprender mejor la resistencia de tumores a los tratamientos actuales.  El impacto de este mapa epigenético puede ser transformador. Por un lado, permitirá a los médicos diseñar tratamientos personalizados basados en el perfil epigenético de cada paciente, lo que mejorará la eficacia de los tratamientos y reducirá efectos secundarios. Además, podría usarse para diagnosticar enfermedades como el cáncer o la demencia en sus primeras etapas, mucho antes de que aparezcan síntomas evidentes. Este proyecto también refuerza el liderazgo del Reino Unido en ciencias de la vida, posicionando al país como un referente en investigación y tecnología de vanguardia. Al integrar los hallazgos epigenéticos con datos genéticos y médicos, este avance representa un paso gigante hacia una medicina más preventiva y personalizada.  La epigenética permite entender por qué, a pesar de tener el mismo ADN, algunas personas desarrollan enfermedades y otras no. Este mapa, creado con muestras de participantes predominantemente sanos, servirá como referencia para identificar los primeros signos de enfermedades relacionadas con la edad. Además, las herramientas desarrolladas con este proyecto podrían usarse globalmente para mejorar la atención médica y reducir costos. Gordon Sanghera, CEO de Oxford Nanopore, destacó que el objetivo final es traducir estos avances científicos en beneficios reales para los pacientes.  El mapa epigenético que desarrollan Oxford Nanopore y UK Biobank promete revolucionar la medicina al ofrecer un análisis detallado de cómo el ambiente y el estilo de vida influyen en el desarrollo de enfermedades como el cáncer y la demencia. Este proyecto no solo avanza hacia la medicina personalizada, sino también hacia la prevención. ¿Qué opinas sobre este tipo de avances? Déjanos tu comentario y escucha más en Flash Diario en Spotify.Bibliografía:technologynetworks.comdevdiscourse.comindiatoday.inConviértete en un seguidor de este podcast: https://www.spreaker.com/podcast/flash-diario-de-el-siglo-21-es-hoy--5835407/support.

TWiM focuses on recent foodborne outbreaks of bacterial infections, and how nanopore sequencing technology can be used to identify pathogenic microbes and antimicrobial resistance genes in food products. Hosts: Vincent Racaniello, Michael Schmidt, Petra Levin and Michele Swanson. Become a patron of TWiM. Links for this episode Foodborne outbreaks (CDC) Race to nourish a warming world (Gates Foundation) Nanopore sequencing of foods (Food Microbiol) How is Oxford Nanopore used? (YouTube) Introduction to Nanopore sequencing (YouTube) Methods for detecting foodborne pathogens (Appl Micro Biotech) Take the TWiM Listener survey! Send your microbiology questions and comments (email or recorded audio) to twim@microbe.tv

In this episode of Oxford+, host Susannah de Jager is joined by Dave Norwood, founder of IP Group PLC and Oxford Science Innovation as they discuss his experiences and insights into the potential of Oxford as a hub for innovation, particularly in AI and quantum computing. The conversation also delves into the unique ecosystem of Oxford and the challenges and successes faced by entrepreneurs and innovators in the city, as well as the need for ambition, dreaming big, and collaboration within the Oxford community. (0:12) Introduction(1:15) How snake bites led to investment insights(11:15) Foreign investment(14:57) Government support and domestic capital(27:30) Cross-pollination and the Ellison Institute for Technology(36:18) Breaking away from mythsAbout the guest:Dave Norwood is the founder of IP Group PLC and Oxford Science Innovation, now Oxford Science Enterprises, the largest university venture fund globally, which has brought in over 1.5 billion of investment into Oxford since its inception in 2015. He has also founded and been a director of numerous UK technology companies including Oxford Nanopore, Proxy Imogen, Synergen, 4D Pharma, Index IT, Evolution Group and Aura Capital. Dave is also a grandmaster in chess and has represented both England and Andorra internationally. Without Dave, much of the investment landscape of Oxford would not look how it does todayAbout the host:Susannah de Jager is a seasoned professional with over 15 years of experience in UK asset management. She has worked closely with industry experts, entrepreneurs, and government officials to shape the conversation around domestic scale-up capital.Connect with Susannah on LinkedInVisit our website to learn more and subscribe to our newsletter - oxfordplus.co.ukIf you have a question for Susannah, please get in touch - oxfordplus.co.uk/contactOxford+ is hosted by Susannah de Jager, supported by Mischon de Reya and produced and edited by Story Ninety-Four in Oxford.

Today, we have Julia Hawkins with us. Julia is a General Partner at Phoenix Court, a $1.5bn AUM EMEA multi-stage tech investor, backing the most ambitious founders on their journey from seed through to public markets and beyond over the last two decades.LocalGlobe is the pre-seed and seed fund investing out of Phoenix Court's Fund 12 with an established portfolio of over 200 companies with notable investments including At-Bay, Motorway, Zego and Improbable. At Phoenix Court, Julia focuses on health and hard tech and led investments into AccuRx, Oxford Nanopore, Vaccitech, and more recently Spore Bio and Early Health.Go to eu.vc for our core learnings and the full video interview

George is a General Partner at Phoenix Court Group, the group of funds home to LocalGlobe in Somers Town, London, building global businesses based on innovative science and technology to have the maximum positive impact on society.LocalGlobe is investing out of their fifth institutional fund, of approx. 150M pounds, with a total AUM of over 1b pounds. Local Globe has an established portfolio of +60 companies and notable investments, including Melio, TravelPerk, Tide, Hibob, Motorway, Wise and Oxford Nanopore, AvantArte, and Sorare.At LocalGlobe, George focuses on Marketplaces, E-commerce 2.0, and SaaS with a particular focus on SMEs across New Palo Alto, a region that encompasses a market of 40 million people and is roughly 4 hours train ride from Phoenix Court's home next to St Pancras, London. George led the investments into Travelperk, Rekki, Taster, and Qogita.Go to eu.vc for our core learnings and the full video interview

As we approach the conclusion of 2023, we reflect on a year that not only signifies our 10-year anniversary but also marks another chapter of The G Word. Throughout the year, guests have joined us fortnightly to share their research, stories, and aspirations for the future of genomic healthcare.  In this special end-of-year episode, Naimah Callachand sits down with Dr Rich Scott, Interim Chief Executive Officer at Genomics England, to look back on the last decade of Genomics England. Tune in as we revisit memorable moments from the 2023 podcast episodes through key quotes, reflecting on the transformative journey of Genomics England. Join us for this insightful recap and a glimpse into the exciting future ahead!  Below are the links to the podcasts mentioned in this episode, in order of appearance:  Adam Rutherford, Laurence Hurst, Cristina Fonseca and Vivienne Parry: Public views on genetics - what have we learnt?  Dr Jack Bartram: Can genomics improve our understanding of childhood cancers?  Helen Webb, Lizzie Mordey, Kirsty Russell and Prabs Arumugam: How can advances in genome sequencing support patients through their sarcoma journey? Vivienne Parry and David Bick: Which conditions will we look for initially in the Generation Study?   Dr Nicola Byrne: What are the challenges of data governance in the digital age?  Chris Wigley: The journey to the Human Genome Project and beyond with Dr Francis Collins   “We're also looking to the future where, as I say, we're proud of the impact that there already has been, and the NHS Genomic Medicine Service is the first national healthcare system to offer whole genome sequencing and that is extraordinary. Thinking about how we can broaden our impact is a really important part of that, and that's thinking about how we can be supportive of genomic technologies broader than just whole genome.”    You can read the transcript below or download it here: Reflecting-on-2023-transcript.docx   Naimah: Welcome to the G Word. Rich: We're in an extraordinary time. The power to analyse genomic data has changed enormously. These are big changes in terms of the, sort of, analytics that AI could bring and the potential to work not just within the UK but with other countries and other big initiatives to make sure that we're answering the questions as best we can. Naimah: I'm your host Naimah Callachand and today we'll be hearing from Rich Scott, Interim CEO for Genomics England. He'll be sharing insights with us from the last year, and we'll be revisiting key moments from earlier podcasts in the year featuring some of the voices that have shaped our discussions. If you enjoyed today's episode we would love your support, please like, share and rate us on wherever you listen to your podcasts. Now let's get into the interview. So, this year we celebrated our ten-year anniversary and as 2023 comes to a close we want to reflect on our achievements not just in the last year but over the last ten. So, Rich first of all can you talk us through where we started in 2013 and where we are now? Rich: It's amazing really to think about how much things have changed in terms of genomics in clinic and in hospitals and then for us as Genomics England over the last ten years. So, actually thinking back ten years ago was only ten years after the Human Genome Project was completed, and when one thinks about what one could do in clinic and those questions you could answer using genomics in clinic. We could see what was coming, we could see these new technologies, next generation sequence in coming, but it was much more dependent on very targeted testing. And now with, you know, our founding project, the 100,000 Genomes Project that Genomics England was founded to deliver in partnership with the NHS we asked the first big question if you like which was how can whole genome sequencing play a role in routine clinical care. And that's now played out where evidence from the project, what we've learnt, the infrastructure we've built, and also evidence from around the world that through the NHS Genomics Medicine Service has now put that into practice and we're working in partnership to help them deliver it. So, it has gone from an idea where we could see this new technology, this potential, to a position where now patients in the NHS with cancer or with rare conditions have whole genome sequencing as a routine part of their clinical care where that's in that national genomic test directory that NHS England have set up. Naimah: Earlier in the year we heard from Dr Adam Rutherford, geneticist, author and broadcaster who commented on how the public perception of genetics and science has evolved over the last few decades. “I've been doing this a long time and I think that when it comes down to it, genetics which is a relatively young science and really in a sophisticated way, you know, a mere few decades old, but what is it at its absolute core, it's thinking about families, it's thinking about inheritance and it's thinking about sex. And these have been the major preoccupations of humans for thousands of years, and it's only really in the last century, really only in the last 30 years or so, that we've had a sophisticated understanding of how these things work, if indeed we have had at all.” Naimah: Let's get back to Rich. Rich, I've already touched briefly on it, but can we dive a bit deeper into the 100,000 Genomes Project and can you tell me a bit more about how it started. Rich: Yes, so the 100,000 Genomes Project as I said was there to ask what role can whole genome sequencing play in understanding medical conditions, you know, is it ready for clinical prime time. And also how can we link routine clinical care to research so that we're not just asking questions with today's knowledge, but we can continue to build that knowledge for the future. So, the 100,000 Genomes Project was driven by that idea that people realising, the government realising and the NHS forming a partnership with us Genomics England to explore that question in real depth. And it's not just about the clinical aspects and the scientific questions, it has also been working with participants and the public to understand how we could do that. And through the 100,000 Genomes Project we worked particularly with patients with cancer and rare conditions to see how we could help make diagnosis and improve care. And also with their consent make their data available in our secure, trusted research environment so that researchers could continue to look for answers that we couldn't answer today, and we continue to do that work for those participants now. Naimah: Next we're going to hear from an interview with Dr Jack Bartram, a Consultant Paediatric Haematologist at Great Ormond Street Hospital for Children. He spoke about the significance and impact of integrating genomics into routine clinical care in diagnosing cancer in children. “If I look back and if I reflect on the last three years, you know, we could probably accurately say at least a quarter of patients it has given us additional information which is either aided in diagnosis or like I had said help risk stratify a patient or potentially reveal a target for a therapy that we didn't know of before. And what this has led to and what we've seen over the last three years or so is that we have actually changed management of patients based on this. So, definitely we've got examples where we scan clarify the diagnosis, we've changed the risk category, or we've identified for example that an unexpected cancer predisposition in a family which has then led onto screening for the family which can then give the family the knowledge to try and do things to either modify the risk of cancer in the family or at least screen for it so they can detect things early to prevent things presenting too late.” Naimah: Okay, now let's talk a little bit about some of the initiatives at Genomics England. Can we talk about how they've progressed and what they might look like in the future. Rich: Yeah, so we really are on a journey both as an organisation but with all of those partners that we work with across the UK system. And one of the great things I think about genomics and genomics in the UK is that the ecosystem that we're in and the strong partnerships that we can form to ask these really big questions. So, if you like when we formed as an organisation we had the questions that we're asking around diagnostic use of whole genome sequencing in the 100,000 Genomes Project. And if you like in our second chapter as we've moved on to support the NHS in delivery of life clinical care we also have been thinking about the other big questions that we need to address. And those have played out and we've been really fortunate to gain the funding and to work in partnership with the NHS and others on these big questions. So, firstly our newborn genomes programme, secondly our diverse data programme and then our cancer 2.0 initiative. And each of them have big questions behind them so that we're saying, you know, where could genomics better support healthcare and move forward and improve care for everyone. Our vision at Genomics England is a world where everyone can benefit from genomic healthcare and each of them is pushing those boundaries, asking those questions in different ways. For the newborns programme the big question is should every newborn baby be offered whole genome sequencing driven particularly by that potential to identify more treatable severe genetic conditions at birth, and if so how should we do that. Again, developing evidence in and around really broadly across the clinical and scientific aspects, but also engaging and understanding public attitudes how we might do that. And really understanding how that might impact on the healthcare system, how it might be delivered in clinical care. For the diverse data initiative we recognise the challenges historically that there have been because of the inequity in terms of the communities who have been engaged with and included in genomic research. And the diverse data initiative aims to both understand where we are today but also to make sure for example the national genomic research library is at least representative of the UK population so that we can work towards again that word that's in our vision, everyone, a world where everyone can benefit from genomic healthcare. And in the cancer 2.0 initiative we've been exploring two really promising areas in terms of cancer genomics. Firstly, exploring different sequencing technologies and in this case partnering with the NHS to work on the Oxford Nanopore technology which we think is really promising in terms of use in diagnostics to speed up and better diagnose and treat cancers. And also looking in our multimodal element of our cancer 2.0 initiative at bringing in a broader range of data alongside the genomic and clinical data that participants in our programme consent to us holding in our trusted research environments. And bringing in image data, images of their tumours on the histopathology slides that are looked at traditionally down a microscope but scanning those at very high resolution and with uniformity between participants working with NPIC to do that. And also bringing in imaging, so radiology type imaging, of tumours so that that data is there to drive new discovery. And working in partnership with academics and with industry for example insitro to understand how we can both bring that data together usefully, put the right tools next to it and then allow that discovery so that our participants know that we're looking not just on what we know today but to improve things for the future. Naimah: Rich mentioned some of our initiatives here at Genomics England. And now we're going to hear from some G Word guests on how these programmes can make a difference for those with a genetic diagnosis. We spoke to Lizzy Mordey, a clinical trials co-ordinator, whose husband Steve sadly passed away last year after receiving a sarcoma diagnosis. Lizzy commented on the pivotal role whole genome sequencing can play in receiving a quicker diagnosis on the identification of suitable treatments for patients with sarcoma. “Personally, I would hope for quicker diagnosis, and I know that's super hard to do and I think as we've discussed before on this call it's such a rare thing and it, kind of, often doesn't fit the standard clinical pathway and that's one of the reasons why it's so frustrating. So, anything that we can do on that front that I think would be hugely valuable to anyone experiencing a journey like what me and Steve went through, and yes advances like genome sequencing are really amazing in supporting that. Yes, as I mentioned as well any information about types of treatment, you know, the diagnosis is important but then the other aspect of getting a diagnosis and a specific diagnosis is understanding what's most likely to help.” Naimah: Next we're going to hear from David Bick who is a principal clinician for the Newborn Genomes Programme at Genomics England. He spoke about the generation study which is being delivered in partnership with the NHS. “I'm doing this because I imagine a day when all over the world we will find and treat children before they get ill. This is one of the most wonderful programmes to be involved with because I can see that future. I want there to be a healthcare system. I really want to help children stay healthy and really live their best lives, that's what's so exciting for me.” Naimah: Now let's get back to the interview with Rich. You mentioned all of the partnerships there and also one important one is with the NHS. As you know the NHS also celebrated its 75th anniversary year as well as our tenth anniversary. And I wondered if you could tell me a bit more about that relationship with Genomics England and the NHS and how we're working together.  Rich: Our relationship with the NHS is absolutely critical. So, as we're thinking about what we can do to enable better genomic healthcare we're so fortunate in this country to have a national healthcare system. And for us and for our work at Genomics England it's absolutely critical to work hand in hand with NHS England both in supporting their live clinical services so we enable their national whole genome sequencing service through the Genomic Medicine Service and also as we work through all of our patient facing research. So, as we did for the 100,000 Genomes Project, as we are for our Newborn Genomes Programme and so forth co-designing these programmes so that the evidence that we're able to generate is relevant in the UK for our healthcare system but also that national scale is just so extraordinarily powerful. And I think we're really lucky for many reasons, the UK genomics ecosystem, it's richness, the investment that has come from government and from the NHS in genomics and the recognition of its importance and from funders, and then that ability to ask questions at national scale. And when you look internationally I think that's the piece that people are often most jealous of in terms of the power of the questions that we can ask together with the NHS so that we can do exactly what we want to do which is transform care so that it's better in the future. Naimah: Rich highlighted the importance of our relationship with the NHS in transforming patient care. Louise Fish, CEO of Genetic Alliance UK commented on the importance of joined up care following diagnosis to support them throughout their lives. “So, there is a lot more we need to do to work with the NHS to make sure that the care from the health service is joined up and co-ordinated for people. And then beyond that how does the co-ordination reach out to education, to housing, to benefits, to social care. The bit that almost should be simplest is if the NHS has someone who understands your child's condition. But it should be possible for their school to be in touch and to find out how that condition is going to affect them and what support the school might need to put in place through an education health and care plan, but those links out to the other services aren't there either. So, for us there is a lot of work to do that's not just around the diagnosis but it's about ensuring that lifelong care and support is delivered in a co-ordinated way. And as more people are getting genetic diagnosis through this amazing, kind of, clinical advances how do we make sure there is also investment into the clinical services that are going to support people throughout their lives.” Naimah: One of the key factors in supporting Genomics England to deliver this important work and all of our initiatives is the participants and the trust that they have in us. I wondered if you could share a bit more on this, so how Genomics England works with their participant panel. Rich: Yes, so I think one of the things I'm proudest about at Genomics England and it was established about the time I was arriving at the organisation is the participant panel who are a group of our participants who represent a broader participant across the national genomic research library. And they're a part of our governance, which governance sounds like a boring word, our relationship with the participant panel and their role in our governance is absolutely critical. They are the people whose data we are the custodians of, and we have a responsibility to them to live up to their expectations and also to make sure that they're driving the decisions that we're making. An example is how we setup the access to data for researchers. So, I mentioned that the way the national genomic research library works and a model that we developed through engagement with the public and with the input of our participants is that people can visit the de-identified data in our trusted research environment, but they can't take it away. They come and look at the data, they carry out their research which is on approved projects that is exploring healthcare questions. Those researchers have to go through an access process overseen by an independent access review committee that has our participants on it. So, they are making the decisions about the sort of research that they are comfortable with and that they want to be done on their data, and I think that's really critical. It has also been a real pleasure to work with our participants as we design future programmes either on for example finding further answers or looking for better treatments for people who are already in the national genomic research library, already a part of our participants or to help us design future programmes, for example our Newborn Genomes Programme. Our participants as well as engagement with potential future participants and the public more broadly has been absolutely critical in guiding us on how we do that. It's a team sport what we're doing in many different ways. That's with our broader ecosystem, it's with our participants, and that means this isn't about some people going away and sort of thinking up what sounds like the right programme and using all of their knowledge and expertise and producing something which is set in stone. This is about dialogue and engagement and using that to understand the right way of us approaching the questions we are and responding to what we hear. And our participant panel are absolutely critical in that. Naimah: And maybe it would be good now to discuss a bit about the new challenges that we're currently facing such as AI and issues with data sharing and data protection. Can you comment a bit on that. Rich: Yeah, so genomics is a fast moving area. We're really proud of the impact that we've had already, but we also recognise that at the moment we can only use genomics in a particular number of clinical situations. And even within those we can only help a certain proportion of patients. And what our participants say to us is that we need to be restless if you like and not accept where we are today. I think it's quite easy to merely celebrate progress but it's really important to also then ask where we need to be going next. I'm always guided by our participants thinking about what the new technologies are and what the different ways of approaching these scientific questions is critical. We're in an extraordinary time, genomic technology has changed enormously. The power to analyse genomic data has changed enormously. These are big changes in terms of the sorts of analytics that AI could bring and the potential to work not just within the UK but with other countries and other big initiatives to make sure that we're answering the questions as best we can. That brings with it as with all of these areas questions about how you best do things and how you balance the importance of privacy, data privacy, with the benefits of being able to look across larger number of research participants to find answers that you just wouldn't otherwise. Likewise with AI there is the potential for us to both speed up current processes but also ask broader questions that we can't yet using some of these technologies. Doing that in conversation with our participants and the public to understand how to best balance the different benefits and also clarify where there are, sort of, very clear expectations that we shouldn't exceed is really important. And I think that's one of the things that puts us in such a strong position is that confidence that our participants are guiding us and often, and speaking as a doctor myself, it's interesting the medical community is often quite paternalistic, quite cautious and quite narrow in what they might think their participants would want. What we like to do is be driven by what our participants want and expect, and I think that has been really important for us in our history up to now as an organisation and increasingly in the future. Naimah: Yeah, and I think you've really highlighted how Genomics England were trying to keep the participants at the heart of everything that we do. Dr Nicola Byrne, the National Data Guardian for health and adult social care in England spoke about challenges with sharing health data and the importance of transparency and accountability in how data is used to support better outcomes from health and care services. “So, it's absolutely important that people feel that they can share that information and then feel confident that any information they do share is going to be used in ways that are safe, appropriate and ethical. Whether that's for their own care or thinking about the benefit of other people in future through research, innovation and planning.” Naimah: Well, let's get back to the interview for some final reflections with Rich. So, we've been looking back at our achievements over the last ten years, and I'll be keen for us to look at what's next. So, we've touched on it, but let's take some time to reflect on the research that has taken place across the global genomic landscape for example and, you know, what we've done here at Genomics England. Rich: The world has changed a lot in ten years. We've learnt a lot ourselves as an organisation and the researchers that work with our participants data and the national genomic research library have done extraordinary work. So, to give you a flavour of the sorts of things that I guess have changed in terms of what we can enable them doing in terms of research and research work. When participants data enters the research library they're consenting to their genomic data sitting there alongside deidentified clinical data from their longitudinal health records. As I said through our multimodal cancer initiative we're also now able to bring in image data for our cancer participants. And increasingly, and this is something that Matt Brown, our chief scientist, was talking a lot about at our research summit in September, was bringing in additional modalities of data alongside that. So, for example, in our rare disease participants bringing in proteomic, transcriptomic and long read data alongside the current sets of data. It means that that resource becomes even more powerful and able to answer a broader set of questions and able to ask questions across a broader set of data in terms of what might be useful for improving the understanding of medical conditions and improving clinical care. So, for example, there has been amazing work over the last few years on cancer and the mutational signatures that are there in tumours. For example, Serena Nik-Zainal's group understanding the patterns of mutation that are there in tumours driven by the underlying biology, not just because it helps us understand how things have happened, but also because it helps us understand about prognosis and how to treat conditions. We've got really exciting early insights from the work on the image data, that multimodal data, working as I said with academia and also looking at the work that insitro are doing. Recognising patterns between you can see down the microscope of a tumour and the genomics. To understand some of those processes that we've just not been in a position to explore before. And I think one of the really powerful pieces of work that is ongoing and will continue to is the ability for researchers and teams within Genomics England to continue to look for answers as our knowledge improves. So, some of the research work that we're doing is discovering some new fields if you like of understanding. We also know that each year literally hundreds of new genes linked to rare conditions are identified. So, enabling research that allows us to go back and look in our existing participants data to see if that new knowledge, that new knowledge about gene to condition links or better understanding of genomic variation means that we can keep looking for and finding things relevant to people who at the moment are research studies, 100,000 Genomes Project, or the Genomic Medicine Service initial testing with today's knowledge or the knowledge of today or whenever their test was couldn't identify because of the limitations of knowledge. Now we can go back and identify through by sharing likely insights of clinical importance with NHS laboratories. We can then pass those findings back to participants and that has been the case in more than 2,000 of our 100,000 Genomes participants already and it's enormously powerful. I think as we think about the direction of travel in the future, I think thinking about how we make sure that the breadth of questions that can be addressed for our participants in the national genomic research library is even broader, is really important. And that's, as I say, something that's particularly bringing in other types of data alongside has been a really important part of. We're also looking to the future where as I say we're proud of the impact that there already has been, and the NHS Genomic Medicine Service is the first national healthcare system to offer whole genome sequencing and that is extraordinary. Thinking about how we can broaden our impact is a really important part of that, and that's thinking about how we can be supportive of genomic technologies broader than just whole genome. So, for example,  panel and exome data and thinking about some of those other modalities of data like transcriptomes is really important as well for us. And that's something that we're exploring at the moment how we best do that, how we might do that. Also thinking about the range of settings that genomics is currently playing a role and we can see a future in five to ten years' time where rather than genomics being something where it plays a role in a small proportion of healthcare encounters where it could be impactful, over a much larger proportion, perhaps even up to a half of all healthcare encounters through, for example, pharmacogenomics potentially. And our Newborn Genome Programme is developing evidence that will help us understand whether that whole genome sequencing should be offered to all newborns. Potentially in research studies like Our Future Health are asking questions around the value of integrated or polygenic risk scores. Through those sorts of elements we can see genomics playing a role much more broadly both in terms of the number, proportion of clinical settings where it's relevant, much more towards it being a routine part of healthcare, but also across the lifetime at different stages and thinking about the value of genomic data if you like through the life course as something that can be looked at repeatedly increasingly without requiring specialist knowledge from the clinical teams so that it can have the impact it can. And thinking about how we might play a role in developing that evidence but also supporting the infrastructure through our expert knowledge in the management of coherent national genomic data sets. And also having that dialogue in public about how genomic data might be used and working out how we generate evidence that can drive policy change. I think there is enormous potential in the future and we in the UK I think remain uniquely placed to explore those sorts of questions. Naimah: So, we'll wrap up there and that brings us to the end of our podcast for 2023. Thanks to Rich Scott for sharing his reflections on the last ten years of Genomics England and his aspirations for the future. Moving into the new year we'll leave you with a powerful quote from our podcast with Dr Francis Collins who is renowned for his landmark discoveries and leadership in the Human Genome Project.  “My dream Chris is that we come up with in the next decade a scalable approach to every genetic disease where you know the mutation.” You can find all of the podcast episodes mentioned in this podcast plus many more on our website www.genomicsengland.co.uk or on your favourite podcast app. We look forward to bringing you some new episodes with more exciting guests in the New Year but do get in touch if you have any topics you would like us to cover. I've been your host Naimah Callachand, and this episode was edited by Mark Kendrick at Ventoux Digital. Thank you for listening.  

Day Zero Diagnostics and Oxford Nanopore today announced a collaboration to develop a solution for diagnosing bloodstream infections. Fast Five hosts Jim Hammerand and Sean Whooley dive into the details of the partnership. Asensus Surgical inked a manufacturing deal with Flex for services around its next-generation surgical robot platform. Listen for the details of the partnership and some other news about Asensus' other surgical robotic offerings. Johnson & Johnson MedTech followed up its Ottava news from last week with a regulatory win for a different surgical robot in China. The hosts unpack what the company's Monarch robot does and why its latest milestone is significant. The FDA says the recall of stolen, defective Medtronic laryngoscopes is Class I, the most serious kind. Hear all the details of this recall, including how third parties are attempting to profit from these stolen devices. Vicarious Surgical is cutting its headcount again as it pushed back the development timeline for its surgical robotic platform. The hosts break down the updated timeline, the ramifications of the layoffs and what analysts have to say on the matter. Check out the show notes at MassDevice.com/podcast.

This week's episode begins with a discussion of housebuilder Barratt Developments' results. What makes Barratt different from other housebuilders? And what can it tell us about the housing market as a whole? Next on the roster is a dive into UK economics. The ONS has released the latest GDP figures, but what can they tell us about the country's position amongst other G7 nations? And what upcoming data can we expect in the weeks ahead?Last up is genome sequencing company Oxford Nanopore. The team discusses the headwinds facing the company and considers the drivers to profitability it will need to harness in the coming years.Dan Jones is joined by Mitchell Labiak, Alex Newman, Hermione Taylor and Jennifer Johnson Hosted on Acast. See acast.com/privacy for more information.

Oxford Nanopore Technologies is one of the most promising and exciting companies operating in the UK today. Its handheld devices read genomes and mark a new era for how easily and quickly DNA can be sequenced, which should have significant benefits for health and fitness. In this episode of Business Studies we speak to Gordon Sanghera, the chief executive and co-founder, about how the company was built, how it was inspired by the Arctic Monkeys, Brian Clough and Rinus Michels, and why he is unlike most other FTSE bosses… This is a public episode. If you would like to discuss this with other subscribers or get access to bonus episodes, visit offtolunch.substack.com

L'essor du numérique a entraîné l'apparition d'une nouvelle génération d'entreprises à la croisée du médical et de la technologie, que les anglo-saxons, avec leur pragmatisme habituel, ont tôt fait de baptiser "medtechs". Une fois n'est pas coutume, ce mot- valise fonctionne aussi en français. Oxford Nanopore Technologies est donc une medtech créée par des chercheurs qui ont inventé une nouvelle méthode de séquençage de l'ADN. Schématiquement, ils sont capables de séquencer l'ADN en mesurant les changements de courant électrique produits par le passage d'une molécule à travers des nanopores, c'est-à-dire de tous, tous petit trous.

When scientists want to know about genes, chances are they use instruments called sequencers. Some of them can generate long-reads, which helps with analyzing genomes. The method of the year according to Nature Methods is: long read-sequencing. For a story I chatted with scientists at companies and in academia about long-read sequencing and did some podcasts, too. This episode is with Dr. Gordon Sanghera, CEO of Oxford Nanopore Technologies. (Art: J. Jackson).The following music was used for this media project: Winnie The Moog, Funky Energetic Intro and Acid Trumpet by Kevin MacLeod Free download: https://filmmusic.io/song/3340-acid-trumpet License (CC BY 4.0): https://filmmusic.io/standard-license

Bill Chater, investment specialist for the Baillie Gifford Global Discovery fund, gives us an in-depth perspective on the fund's investment style and why the long-term approach delivers results. He comments on the core fundamentals the team looks for in its stock picks, touches on the current market conditions and the impact on the fund, and why the potential within healthcare is so exciting, with names like Alnylam and Oxford Nanopore. He finishes by offering more details on Ocado's big deal in the US and on the automation technology that makes it a compelling addition to the fund's basket.More about this episode:Current market conditions and the impact on the fundThe fund's core mission Micro-economic vs macro-economic factorsHow individual company analysis is more appropriate to the team than sector or geographical considerationsBuilding resilience into the portfolioThe Chinese holdings in the fundThe potential for healthcare technologyOcado's potential in the US, with the move towards increased automationMore about the fund:Renowned for the quality of its in-house research, Baillie Gifford brought its smaller companies' teams together in 2011 to form the Global Discovery team. This fund consists of what the team believe to be the most innovative and fast-growing smaller companies in the world. It has a strong growth bias and is aggressive in nature.Learn more on fundcalibre.comPlease remember, we've been discussing individual companies to bring investing to life for you. It's not a recommendation to buy or sell. The fund may or may not still hold these companies at the time of listening. Elite Ratings are based on FundCalibre's research methodology and are the opinion of FundCalibre's research team only.

In many regions of the world, HPV and its association with cervical cancer is a well-known but rarely considered issue, after the rollout of the HPV vaccine in the late 2000s. However, while this rollout significantly impacted cervical cancer rates where it was implemented, it was not universal and in many areas of the world HPV induced cervical cancer remains a critical issue. Cervical cancer is the leading cause of death for people with a cervix living in poverty in low-resource regions and on the continent of Africa, it is estimated that in 2020 as many people with a cervix died of cervical cancer as COVID-19. In this episode of Talking techniques, supported by Oxford Nanopore, Senior Investigator Michael Dean and Post-baccalaureate Fellow Nicole Rossi, from the NIH's National Cancer Institute (MD, USA), discuss their research into the relationship between HPV and cervical cancer. Expounding on the points mentioned above, they reveal the tremendous insights into cancer and immunology still to be gained, document the key tools used in their studies and explain how their work can be translated into more effective immunotherapies and treatments for cervical cancer. ContentsIntroduction: 00:00-01:40How big an issue does HPV present to the world? 01:40-03:30HPV's association with cancer: 03:30-05:15Why does HPV target DNA repair mechanisms? 05:15-06:00Key goals of research into HPV: 06:00-07:15Challenges of HPV research: 07:15- 08:20Solutions available to deal with these challenges: 08:20-09:30The most exciting discoveries in HPV using long-read sequencing: 09:30-11:00HPV16- the most oncogenic variant: 11:00-11:40Translating research into clinical results for HPV: 11:40-12:45How effective is the current HPV vaccine? 12:45-13:30What would you ask for to improve research into HPV and cancer? 13:30-14:30How big an issue is vaccine rejection? 14:30-15:40Final thoughts: 15:40-17:00

In many regions of the world, HPV and its association with cervical cancer is a well-known but rarely considered issue, after the rollout of the HPV vaccine in the late 2000s. However, while this rollout significantly impacted cervical cancer rates where it was implemented, it was not universal and in many areas of the world HPV induced cervical cancer remains a critical issue.Cervical cancer is the leading cause of death for people with a cervix living in poverty in low-resource regions and on the continent of Africa, it is estimated that in 2020 as many people with a cervix died of cervical cancer as COVID-19.In this episode of Talking techniques, supported by Oxford Nanopore, Senior Investigator Michael Dean and Post-baccalaureate Fellow Nicole Rossi, from the NIH's National Cancer Institute (MD, USA), discuss their research into the relationship between HPV and cervical cancer. Expounding on the points mentioned above, they reveal the tremendous insights into cancer and immunology still to be gained, document the key tools used in their studies and explain how their work can be translated into more effective immunotherapies and treatments for cervical cancer. ContentsIntroduction: 00:00-01:40How big an issue does HPV present to the world? 01:40-03:30HPV's association with cancer: 03:30-05:15Why does HPV target DNA repair mechanisms? 05:15-06:00Key goals of research into HPV: 06:00-07:15Challenges of HPV research: 07:15- 08:20Solutions available to deal with these challenges: 08:20-09:30The most exciting discoveries in HPV using long-read sequencing: 09:30-11:00HPV16- the most oncogenic variant: 11:00-11:40Translating research into clinical results for HPV: 11:40-12:45How effective is the current HPV vaccine? 12:45-13:30What would you ask for to improve research into HPV and cancer? 13:30-14:30How big an issue is vaccine rejection? 14:30-15:40Final thoughts: 15:40-17:00 See acast.com/privacy for privacy and opt-out information.

For people with common health problems like diabetes or high blood pressure or high cholesterol, progress in pharmaceuticals has worked wonders and extended lifespans enormously. But there's another category of people who tend to get overlooked by the drug industry: patients with rare genetic disorders that affect only one in a thousand or one in two thousand people. If you add up all the different rare genetic disorders known to medicine, it's a very large number; Harry's guest this week, Charlene Son Rigby, says there may be as many as 10,000 separate genetic disorders affecting as many as 30 million people in the United States and 350 million people worldwide. That's a lot of people who are being underserved by the medical establishment.Rigby is the head of a new non-profit organization called Rare-X that's trying to tackle a systematic problem that affects everyone with a rare disease: Data. In the rare disease world, Rigby says, data collection is so inconsistent that each effort to understand and treat a specific disease feels like reinventing the wheel. For longtime listeners of the show, that's a familiar story. Time and again, Harry has talked with people who point out the harms of storing patient data in separate formats in separate silos, and who have new ideas for ways to break down the walls between these silos. Rare-X is trying to do exactly that for the rare disease world, by building what Rigby calls a federated, cloud-based, cross-disorder data sharing platform. The basic idea is to take the burden of data management off of rare disease patients and their families and create a single central repository that can help accelerate drug development.Harry talked with Rigby about the challenges involved in that work, how it gets funded, how soon it might start to benefit patients, and what it might mean in a near-future world where every child's genome is screened at birth for potential mutations that could lead to the discovery of rare medical disorders.Please rate and review The Harry Glorikian Show on Apple Podcasts! Here's how to do that from an iPhone, iPad, or iPod touch:1. Open the Podcasts app on your iPhone, iPad, or Mac. 2. Navigate to The Harry Glorikian Show podcast. You can find it by searching for it or selecting it from your library. Just note that you'll have to go to the series page which shows all the episodes, not just the page for a single episode.3. Scroll down to find the subhead titled "Ratings & Reviews."4. Under one of the highlighted reviews, select "Write a Review."5. Next, select a star rating at the top — you have the option of choosing between one and five stars. 6. Using the text box at the top, write a title for your review. Then, in the lower text box, write your review. Your review can be up to 300 words long.7. Once you've finished, select "Send" or "Save" in the top-right corner. 8. If you've never left a podcast review before, enter a nickname. Your nickname will be displayed next to any reviews you leave from here on out. 9. After selecting a nickname, tap OK. Your review may not be immediately visible.That's it! Thanks so much.TranscriptHarry Glorikian: Hello. I'm Harry Glorikian, and this is The Harry Glorikian Show, where we explore how technology is changing everything we know about healthcare.For people with common health problems like diabetes or high blood pressure or high cholesterol, pharmaceuticals has worked wonders and extended lifespans enormously.But there's another category of people who tend to get overlooked by the drug industry.And that's patients with rare genetic disorders.By definition, rare diseases are rare, meaning they might only affect one in a thousand or one in two thousand people. But here's the thing. If you add up all the different rare genetic disorders known to medicine, it's a very large number.My guest today, Charlene Son Rigby, says there may be as many as 10,000 separate disorders affecting small populations.And if you count everyone who has these conditions, it may add up to as many as 30 million people in the United States and 350 million people worldwide.That's a lot of people who are being underserved by the medical establishment.And Rigby is the head of a new non-profit organization called Rare-X that's trying to fix that.Now, there are a lot of rare disease organizations that are looking for a cure for a specific condition.Rigby actually came to Rare-X from one of those, the STXBP1 Foundation, which is searching for a treatment for a rare neurological condition that affects Rigby's own daughter Juno.But Rare-X is a little different. It's trying to tackle a systematic problem that affects everyone with a rare disease. The problem is data.Rigby says that in the rare disease world, data collection is so inconsistent that each effort to understand and treat a specific disease feels like reinventing the wheel. For longtime listeners, that'll be a very familiar story.Time and again I've talked with people who point out the harms of storing patient data in separate formats in separate silos, and who have new ideas for ways to break down the walls between these silos. Rare-X is trying to do exactly that for the rare disease world, by building what Rigby calls a federated, cloud-based, cross-disorder data sharing platform.The basic idea is to take the burden of data management off of rare disease patients and their families and create a single central repository that can help accelerate drug development.I talked with Rigby about the challenges involved in that work, how it gets funded, how soon it might start to benefit patients, and what it might mean in a near-future world where every child's genome is screened at birth for potential mutations that could lead to the discovery of rare medical disorders.Here's our full conversation.Harry Glorikian: Charlene, welcome to the show.Charlene Son Rigby: Thanks. Nice to be here, Harry.Harry Glorikian: So I've been reading about what you guys are doing. I mean, all of it sounds super exciting. I'm, you know, been looking into this space for a long time from a rare disease, but many different angles of it. But can you just start off, tell us a little bit about yourself and how you got active in this world of rare disease research?Charlene Son Rigby: Yeah, thanks for that question. So I've spent most of my career building scalable software solutions for analyzing big data, and that's been both in health care as well as enterprise software. And so I'm now the CEO at Rare-X where we're building a platform to analyze rare disease data cross-disorder. And prior to being at Rare-X, I was the chief business officer at a company called Fabric Genomics, where we developed artificial intelligence approaches to speed diagnosis of patients through genomics. We had a considerable focus on rare disease and contributed to projects like the 100,000 Genomes Project and also the work that Stephen Kingsmore is doing at Rady Children's with diagnosing critically ill newborns in the NICU. And so when I started at Fabric, my daughter Juno was ten weeks old. She's my second child. And it was kind of a fortuitous timing, in some ways kismet, because at when I started at Fabric, I didn't know that she was going to start experiencing issues with her development. But at around four months she started missing milestones. And that started us on a three and a half year journey to find an answer to what was going on with her. And so during that time, we went through many, many tests, including genetic tests, MRIs, all kinds of all kinds of things, and everything kept coming back as negative or inconclusive. And so I was working at a genomics company, and so I kept pushing for whole exome testing, which at that time was still not, not readily available clinically and by insurance was still considered experimental. So we were denied three times, until we finally were able to get authorization in 2015. And so in early 2016, we got my daughter's diagnosis and she has a mutation in a gene that's involved in communication between neurons and the genes called STXBP1.Charlene Son Rigby: And so it's very rare. Thirteen kids born a day somewhere in the world. So thinking about Juno and thinking about this from a science standpoint, that it was pretty interesting that when she was diagnosed because she didn't have a classic phenotype for STXBP1. So most kids, 90% of the kids have seizures. And she has more of the symptoms around developmental delay, low muscle tone, cognitive issues and delayed walking and motor issues. And, you know, this this kind of challenge around these atypical phenotypes, I think, is actually becoming much more common in disease generally, so in rare disease and also more broadly in more common conditions as we're really starting to understand kind of the true breadth of patients. So in terms of your original question about my journey through rare disease, so I went on to co-found the STXBP1 Foundation to accelerate the development of therapies for kids like my daughter. And then coming to Rare-X was really a kind of joining of my software background with my passion for rare disease and really wanting to do something more broadly for the rare disease community.Harry Glorikian: I have to tell you, like what you said, three and a half years, I'm like, oh, my God. Like, I would be I have so many stories. And like when I was at Applied Biosystems and, you know, we're doing all this work. It just boggles the mind that some of these things are not really readily available to help get over that diagnostic odyssey for especially parents, because you're going to do anything to help your child. I'm glad it's actually moving theoretically faster these days. I'm not sure if insurance has actually kept up, but we're, on the technology side, I know we're everybody's pushing the envelope now. But when we talk about rare disease and you did some of the numbers but we hear about these rare diseases, I think a lot of people think of like there's an n of 1, right? They assume that this disease only affects a tiny number of people. Right. Maybe just one or a handful worldwide. But I mean, the fact is, if you add up all these different rare genetic diseases that exist in the human population, the number of people is actually pretty big. I mean, can you sort of. Put that into some sort of scale for us in what you've seen.Charlene Son Rigby: Yeah, you're absolutely right. You know, rare disease is by definition rare. And so it's easy in some ways to be dismissive of a rare disease because, oh, it's only affecting a few people. And it's true that a single rare disease can affect a very small number of people, even down to the n of 1 case that you talked about. From a definition standpoint, so, in the US, rare disease is defined as a disease affecting fewer than 200,000 Americans. And in Europe, in the EU, it's defined as affecting no more than one in 2,000 people. So we even though for ultra rare or n of 1 diseases, we can be talking about a small number of people, or like in my daughter's disorder, we can be talking about low thousands, there are still thousands of rare diseases and the traditional number that we hear a lot is 7,000. So 7,000 rare diseases. Rare-X is about to come out with some research that indicates that there are over 10,000 individual rare diseases, and this is really due to our growing understanding of genetics. So previously we might have grouped together a set of disorders based on what the symptoms were like. But now we understand that those actually are due to a different genetic etiology or different cause at a genetic level. And so if you aggregate all of those people up, across those 10,000 rare diseases, you know, what we're looking at is one in ten, potentially one in ten people in the world. And so in the US that's about 30 million people and in total 350 million people worldwide. So it's really a huge number of people. And from an impact standpoint, it's staggering when you look at the impact from a health care standpoint and from an economic standpoint.Harry Glorikian: Yeah, I mean, if you can diagnose, I mean, if there is a way to treat someone, then you get to it faster. And the economic impact is huge and unfortunately, if there isn't, maybe it spurs a pharmaceutical company to, you know, start working on it or figure out a way to treat that patient better. But at least you, I always tell people, the better the diagnosis, the better the next step. I see people sometimes, it seems like they're throwing a dart, you know, and they're it's an educated guess, but it's not, you know, the accurate diagnosis that you'd like to have. So. But how and where, when was sort of Rare-X born and what are you trying to do with the organization? What do you want to fix?Charlene Son Rigby: Yeah. So Rare-X was a pandemic baby. The organization was started in early 2020 and I just joined the organization last year. But, you know, it's really been quite a journey being able to have the, launch the platform during COVID. And I know we can talk about that in a little bit, but the unsolved problem that we are working to address is really around collecting data for rare disease. And one might ask, well, why is this an issue? I'll give an example. From the early days of the STXBP1 Foundation. W e assembled our scientific advisory board and we got together for our first scientific meeting. And we were going to develop our roadmap so that that would guide our priorities in terms of scientific development. And we were all very focused on therapies. So my expectation going into the meeting was we were going to talk about all the mice models we were going to build. What did we need to do in the lab? How are we going to get to that first therapeutic candidate? And the number one priority that came out of that meeting was to build a prospective regulatory-compliant natural history study. And so it was a huge learning for me because if you look at the kind of canonical steps in terms of drug development, it's always preclinical and then you move into clinical. And what I think that kind of simple model misses is this foundational layer around the data that you need and the real kind of understanding of the symptoms and the disease progression that is critical to building effective therapies, developing effective therapies.Charlene Son Rigby: And so that's really what Rare-X was started to do, was to enable the gathering of this data, the structuring of this data and enable it to be shared and to do this at scale. So, cross-disorder. And there are several problems today that that make this challenging. And so maybe I can talk a little bit about that. There are three or four of these significant challenges. So today some of this data does exist, but it's often kind of trapped in data silos. So it was generated in an individual project that might have happened in academia or industry. And then the data is often really only accessible to the group that collected it. And in rare disease where we don't have that many patients, it really makes it challenging to create a kind of more comprehensive understanding and picture of the patients if that data is trapped in these individual silos. Charlene Son Rigby: Another challenge that that we've seen is the lack of usable data. So individual studies may not include the key data that's needed to drive drug development forward. So some of these data repositories, they might either be a symptom specific. So they're looking at a specific organ system that might have been of interest to that researcher. So they're an incomplete picture. Or some of these repositories or these registries were started by passionate parents. You talked about that, the urgency that one feels as a parent, that I feel as a parent. And the registry may have been structured or the questions may have been structured in a way that isn't necessarily immediately usable by researchers because of the fact that it was started by a parent who, like you, you might not have had a statistical analysis background, you might not have had a survey methodology background. And we so those can be challenges in terms of having the data be robust and usable later. Charlene Son Rigby: And then the other thing that can be challenging and probably is often the most challenging is, is especially in these very, very new diseases, there's no data, and it takes quite a bit of funding to start data collection. Often, often passionate parents are going around trying to get researchers interested in their disorder. But it's often that you have to have a little bit of data to get a researcher interested. And so this is a huge challenge in terms of implementing data collection. And the other thing that kind of underlies this is that patients often are not empowered in this process. And so that was a fundamental piece of the way that we've structured Rare-X and the way that we collect data and the way that we enable patients to participate in the process to power data collection.Harry Glorikian: Yeah. I mean, it's, you know, they make movies out of this, right? People trying to push this boulder up a hill. So, what are the new ideas that say Rare-X is bringing to the table? I mean, your organization has called for like, you know, the largest data collection and federated data system and analysis platform in rare disease. So, I think unpacking that statement because it's a big statement, right, of, you know, what are you doing to improve data collection? What do you mean by federated, for those people that are listening? And why is it important? A  nd how will the platform enable better analysis of this rare disease data?Charlene Son Rigby: Yeah. Great question. From a design perspective, the one of the things that we wanted to do was make sure that the platform was cross-disorder. So a lot of registries are started for an individual disorder. And what we really wanted to be able to do was given that number of 10,000 diseases, how do we scale to support so many disorders to accelerate therapies? And so a fundamental design principle was to do that cross- disorder. The other piece of this is that we are focused on patient-reported data. So typically a participant will join the research program, create an account on the platform and they are either a patient or a caregiver of a patient and providing information on their symptoms. There is a lot of other data out there in the ecosystem that could come from other related registries, or it could come from clinical data, it could come from many different types of studies. And so we really want to enable the aggregation of or federation of that data. So you asked me to define that term. It really means bringing together multiple different data sets in a way that enables those data sets to be analyzed together. And I think, again, going back to this theme that for any individual rare disorder, there aren't that many patients. And so analyzing that data, kind of individually, we are really missing the opportunity to maximally use the data that's been contributed by rare disease patients. And I would even argue that it's a moral imperative for us to do that as a rare disease community, because we urgently need to move these understanding of these disorders forward in development of therapies as well.Harry Glorikian: I almost wish I could take all the companies I know doing this and put them there so the n goes up for everybody. But I know that there's all sorts of reasons that that doesn't happen. But, you know, when you were saying we're pulling in patient-reported data, you know, the first thing, and we talk a lot about this from different groups on the show is, you know, would a wearable or one of these other devices that are now available give you more granular, real- time information that might be valuable to this sort of study. And have you guys considered things like that?Charlene Son Rigby: T he short answer is yes, because the our desire is to really continue to expand the types of data that are collected. And the I think that the nice thing about mobile, mobile devices, wearables, is that it makes it very easy to collect that data. And so we have a partnership with Huma. They do work in the mobile space. And we're definitely continuing to evaluate where we can develop partnerships there. I mean, our goal overall is to de- burden patients and so that the, if we can do that in a way that additive to an overall body of research, then we're huge proponents of it. And I think that it's also important that we're really trying to create an open system. So our partnership model is a very, very open partnership model in terms of who we can work with.Harry Glorikian: Yeah, I had a really extensive conversation with the head of data sciences at WHOOP yesterday and you know, they're pulling in somewhere between 50 and 100 megabytes of data per patient per day. I shouldn't say patient -- per individual per day. Right. I was like, that's a lot of data. And she was, you know, the kid in a candy store because they're she's like, we can really see what's happening with people. And you can ask questions at a scale that you couldn't ask before. Like she was saying, you know, the last one of the things that we're working on publishing is 300,000 people. You couldn't imagine that in the world of, say, a clinical trial of 300,000 people are just going to, you know, and you have all the data, almost 24/7 on this person that's delivered by this device, which is sort of interesting, you know, place to be. So, you know, I know that you don't have 300,000 people in one in one area, but it'd be interesting to have that sort of 24/7 data available from these kids if you could, you know, get a device that would lend itself to that. But what stage is the company at in building the platform and you know, I guess the killer question is, when will drug developers or other researchers be able to start using it? If they already are, do you have any early success stories you can share?Charlene Son Rigby: Yeah, yeah. It's really a very exciting time at Rare-X. So the platform launched last summer and we have over 25 communities on the platform. And those encompass several hundred participants already. So we're really starting to see some exciting numbers in terms of in terms of participants. So we are launching our researcher portal at the end of Q2. So very soon. And at that point, any researcher, so academic researchers, pharma researchers, will be able to access the data and be able to utilize analytical tools to really interrogate the data. I'm excited that we also have launched our first sponsored program, and that's with Travere. They're supporting the homocystinuria community to start data collection, to start a registry. And we just launched that at the end of February.Harry Glorikian: So I want to. Jump back, like just talking through some of the biggest technical challenges along the way. I mean I know one of your goals is like interconnecting all these disparate data sources. But one of the issues that always comes up is how do you clean up that that existing data so that you can store it all the same way. And then obviously that enables somebody to then do the analytics right after that. But the biggest issue that I hear from a lot of people is, man, it takes a lot of effort to make sure that that data is cleaned up and put in the right place.Charlene Son Rigby: Yes, the data munging. Yeah. I mean, I think that that is really the, a significant challenge, because creating research-ready data and then harmonizing data sets is a huge amount of upfront work that has to happen before you can actually do any of the analysis and the data mining. So what we have done with the core data that's being generated within Rare-X is that we have mapped it to data standards. So we utilize standards like the human phenotype ontology, OMIM, HL7, so that the data that we're producing already is mapped to all of these generally utilized standards. And then we would if we were working on a federation project, the same thing would need to happen with these other data sets to really enable that type of integrated that type of integrated analysis. And you're right, it's it can be a very brute force effort in terms of doing it accurately. And that's why I think that it's really important from a from an industry perspective to really start adopting these standards and putting them into the base model, you know, for assuming just making the assumption up front that the data is going to be federated and utilized downstream. I think that kind of traditional studies, a lot of the scope was more really looked at in terms of what are we doing with the data today? And we need to be really thinking about from a lifetime perspective, how is this data going to be used?[musical interlude]Harry Glorikian: Let's pause the conversation for a minute to talk about one small but important thing you can do, to help keep the podcast going. And that's leave a rating and a review for the show on Apple Podcasts.All you have to do is open the Apple Podcasts app on your smartphone, search for The Harry Glorikian Show, and scroll down to the Ratings & Reviews section. Tap the stars to rate the show, and then tap the link that says Write a Review to leave your comments. It'll only take a minute, but you'll be doing a lot to help other listeners discover the show.And one more thing. If you like the interviews we do here on the show I know you'll like my new book, The Future You: How Artificial Intelligence Can Help You Get Healthier, Stress Less, and Live Longer.It's a friendly and accessible tour of all the ways today's information technologies are helping us diagnose diseases faster, treat them more precisely, and create personalized diet and exercise programs to prevent them in the first place.The book is now available in print and ebook formats. Just go to Amazon or Barnes & Noble and search for The Future You by Harry Glorikian.And now, back to the show.[musical interlude]Harry Glorikian: Now if we go one step before like getting that data, I mean. I have to imagine there's a huge political, bureaucratic or organizational challenge when it comes to who controls that data. And I think I have to assume,  part of your job is convincing them to share it, right, despite its potential as intellectual property. Right. So how do you get on the phone and say, “Why don't you press send and shoot that over to me and so that we can take the next steps with it?”Charlene Son Rigby: Yeah, well, this is a really significant challenge, and I think that we're in a time of change in terms of attitudes around this. And part of it is what's been happening in terms of national programs to collect data. And people are starting to see the benefit of being able to share and really utilize these larger data sets. But the reality today is that in terms of the status quo, researchers control the data, and that's because the data was generated in a specific project that might have happened in academia or in industry. And there's a challenge with alignment of incentives. So on the academic side, I think that if one were to ask a researcher, do they want to hoard data, they don't want to hoard data. But the reality is, is that we still have this challenge with academic tenure and needing to publish or perish in that environment. And so researchers are still rightly concerned because of that paradigm that they have to write their paper and get their paper in before they can feel comfortable with allowing others to access the data. And so something really needs to happen there to that incentive system. Charlene Son Rigby: And in pharma, interestingly, I think that that's also an area where there has been a feeling that data is almost akin to intellectual property. But I think that especially in rare disease, there has been a growing understanding that accessing natural history data is not going to, at the end of the day, enable pharma to win because they're going to win on the quality of their therapeutic pipeline and how quickly they can get those therapies through to a successful market approval. And so what we've been really working to do is position natural history data as pre-competitive and for rare disease, frankly, it's too expensive to build these data sets, you know, alone. They're, as we scale to all of these disorders it's going to become untenable to for each company to build their own data set. The thing that we need to do and what Rare-X has been working to do with our collaborators is to transform the way that research has been done and initiated and break down these barriers and just show that the model of building these pre-competitive collaborations can work, both from a how does the business model work and then how is the data shared? And so I think that Rare-X being a nonprofit and a kind of neutral third party is really additive in terms of building those relationships so that this, this kind of public-private partnership model can really serve as a way to drive this type of change.Harry Glorikian: Now. Okay. So we've talked about industry sharing data, but I always I mean, especially in the last maybe 5 to 10 years, I keep thinking about, you know, how much of this comes directly or will come directly from patients, right? If they have control or access to their data, they have the ability, theoretically, the ability to then share that data. Right. And it could be just for the research in general as opposed to, not specifically to find a cure for a specific disease. So how do you get that data or convince patients to share it?Charlene Son Rigby: Yeah, well, I think that in in rare disease patients are typically highly motivated. You know, there are many rare diseases that can be pretty devastating in terms of the symptoms and the disease progression. And so overall, there is a a good portion of the rare disease population that is motivated to provide their data. And so what we do there and I think that that your points about the paradigms and thinking about it, that the patients are sharing their data, is really important. Because I think that that gets lost a lot. You know, a patient, and we've all signed up for some research study in our lives. You go and you fill out a survey or you contribute a blood sample or something, but oftentimes the patient contributions get forgotten because it becomes part of the researcher's data set. And so the what we're really trying to do is turn around that kind of paradigm with a core principle that patients are the ones who own their data and they're contributing their data. And so we enable them to, through an innovative consent process, we enable them to basically say that, yes, they're willing to share their data for these types of projects, and they can change that at any time. And we really feel that that changes the paradigm and allows them to have a real seat at the table. And then I wanted to also talk about, because obviously not everyone is — there is this proportion of folks who are motivated and trust and that's part of the reason that they will be willing to share their data — but there is also a portion of the population that might not be as motivated. And so it's important for us to be able to reach those populations and to build trust in the approach that we're taking and the value of it in terms of really being able to drive research. And so patient education is an important component of our model patient education, patient engagement. So we work directly with patient advocacy organizations and patient advocates to educate their communities on the value of data collection, how it really spurs and supports research. I think that that's a critical component to this as well.Harry Glorikian: Well, hopefully people will listen to this podcast worldwide and me that may spur someone to search you guys up on the web. But I noticed that another principle of the company is you don't sell patient data, right? Does that mean you're giving it away? And if that is true, what's the criteria of doing that? And do your data partners that you're giving it to have to meet certain standards?Charlene Son Rigby: Yeah, this is a great question because monetization models around data are very, very common today. Some companies have built significant valuations around data monetization. And for from a Rare-X standpoint, and this is part of the reason why we were started, is that the question was asked like, is that the right thing to do, especially for diseases where we're in the very early stages of understanding a disorder, and so I talked about this a little bit earlier, that if you have no data, getting any researcher interested is already then a huge challenge. And so we're here really to break down barriers to advancing rare disease research and encourage that research. And so I say sometimes that it's really important that we free the data. So we don't sell data at Rare-X. And we have an open access model for researchers to access the data. Charlene Son Rigby: And so there it is not, “we open the doors and anybody can come, come and access the data.” It's done in a responsible way. So one of the key things is that the data is de-identified. And so it is it is critical to do that, because we want the data to be utilized for research. It doesn't need to have identifiable information in it to drive that research forward. You know, the second thing is, is that researchers need to submit information on their project, and then that's reviewed by a data access committee. And the idea behind this data access committee is not to slow down things. It's a streamlined and efficient process. But the idea is that there is a review process. The researchers need to specify whether there's an IRB with whether that protocol has gone through an institutional review board review, and patients can opt to only have their data. As an example, patients can opt to only have their data shared with projects that have gone through IRB review. So there's really kind of a, since this is in many ways a two sided platform, there's really a way that patients can actively engage in terms of who's accessing their data. And then the researchers also in terms of the types of projects that they're that they're going to put forward.Harry Glorikian: Okay. So now you're giving away the data. Remember, I'm a venture capitalist, so you're giving away the data, right? First question somebody like me asks is, how do you pay for the operations? I mean, you're building this fairly sophisticated system that is, you know, you've got to clean the data, you've got to make it available. You're trying to talk to all these people. I mean, are you funded by let's say, I mean the typical stuff, grants? Is it member donations? Is it major gifts from individuals? You know, those are all the questions that that would cross my mind.Charlene Son Rigby: Yeah, absolutely. So frankly, it took me some time to get my arms around this, because my whole career has been in tech and venture backed companies. And so so I took some time to really think about this and think about this scalable model from a scalability standpoint before joining. So we get our funding largely through pharma and industry, as well as some grants. And the way that that funding happens is, it's basically platform investment. And I think that this is a really key thing from my perspective of, of thinking about the, the platform as something that is, if you will, a social good. Because they're investing in expanding the platform. They might invest, like Travere did, additionally to help to onboard specific groups or expand our capabilities in terms of being able to gather data in a particular disease area. But the funding that they're providing is to make the platform and the research program more robust. The data at the back end will be open in the way that we've we have talked about it. We have a unique ability to do that and create that kind of model as a nonprofit. And you're right that what we're doing, we're kind of blending this health tech company with this this nonprofit  tmodel. But I think that there are some good examples out there of public private partnerships that have been very successful in the long term in doing this. And that's the model that we're really pursuing.Harry Glorikian: This area is small. I feel like I've been in and around it for a long time because of, you know, being in and around genomics. But there's a small but sort of growing infrastructure of support for rare disease, you know, patients in the world, sort of nonprofits, NGOs, patient advocacy group. Tthere's Global Genes, right? There's the Rare and Undiagnosed Network, RUN. There's the Undiagnosed Disease Network Foundation, and then there's the n-Lorem Foundation. And so many others that I don't want to leave out, right, the long list. But how does your, or, does your group overlap with these? I mean, I was reading a press release that this summer you guys will launch a collaboration with RUN and the Undiagnosed Disease Network Foundation to launch something called the Undiagnosed Data Collection Program. I mean, if you could sort of talk about what that project is about. Is your real ambition to be the data infrastructure sharing platform for the entire community of rare disease patients and families?Charlene Son Rigby: Yeah, well, I love that you call it infrastructure because I think this is critical from a concept standpoint. Rare disease should not be a model where each rare disease is doing it on its own. That was one thing that really struck me, thinking again about my daughter's disorder, where we were looking at ways to ladder up to that prospective natural history study. And we were trying to do something. I talked to a few other genetic neurodevelopmental conditions that were kind of our cohort, if you will, and we were all doing it in different ways. And it's such an opportunity cost to be figuring out the model new each time. And so these groups like Global Genes, amazing organization, actually, the Rare-X founder, Nicole Boyce, was also the founder of Global Genes. And we were, the STXBP1 Foundation used every single resource possible that came out of Global Genes. You know, that there's this broad this really broad education and enablement that needs to happen for people who want to become rare disease advocates. And that Global Genes has really done that in a tremendous way for so many organizations and so many individuals. And so we partner with them in terms of, and are very complementary, in terms of providing that infrastructure where Rare-X is focused on this area of how do you accelerate research through data collection, and then we use that.Charlene Son Rigby: It's great that you saw the announcement on the work that we're doing with RUN and the UDNF. I'm particularly excited about this because Rare-X, we talked earlier about ultra rare diseases, about n of 1 diseases. The reason why Rare-X is able to collect data across all of these disorders is that we have a fundamental assumption in the way that we collect data, which is that we don't assume that anybody does or does not have any symptoms. So we start out with a very high level, head to toe type of set of questions that if you say yes to any of them, it leads into a more detailed set of questions to collect data on particular symptoms. And so this is really ideally suited to situations where there isn't a lot of characterization around or understanding of the symptoms in a disorder and where you don't have a diagnosis. Because then what we're really enabling an individual to do is to gather robust data about their individual symptoms and disease progression that then can be utilized for research. And so we're very excited about being able to work with and support RUN and UDNF in in that effort. Charlene Son Rigby: And so do we have, you asked about ambition? You know, do we have a goal of being the only data sharing platform? I would say that our goal is to be an incredibly robust comprehensive cross- disorder platform. We believe that the way that we are approaching things really is enabling us to support all rare diseases. And we're really focused on de- burdening patients. So we're enabling patient communities to get started very quickly. And they don't have to become experts in protocol development, they don't have to become experts in creating clinical outcome assessments, etc. At the same time, the world is large and that they're going to be groups who decide that they need specific solutions. They may want to take on the role of being a principal investigator, as an example. And so I think that that's also the reason why federation is an important component of what we're really bringing forward as a as a way to bring all of that data together.Harry Glorikian: So again, you know, being on the venture side, right. You can lead a horse to water, but you can't make them drink, right? So you can do a lot. You can improve clinical trial readiness. You can make sure the data is better about rare disease patients, and that it's available. But you can't force the drug discovery companies or the drug makers to sort of develop a cure for a specific disease. Right. How do you think about that as part of a rare disease problem? Is that is that part of the work that Rare-X is,are you making it less risky so that they are willing to take that next leap?Charlene Son Rigby: You're right that pharma is going to be making, I would say, rational business decisions based on commercial drivers. And the challenge with a lot of rare diseases is that no one knows about that individual rare disease, and there isn't much data on it. And so anything that can be done to de-risk that process for a pharma company  is huge in terms of increasing their interest or generating interest for them and then increasing their interest. And those things can include knowing that there's an activated community, you know, because if you have a clinical trial and nobody wants to participate in the clinical trial, that's going to be a huge problem in terms of being able to get that drug through an approval process. And so Rare-X, by building a very robust data set, is able to de-risk that process in terms of that investment, of trying to understand what the disorder is and also trying rto understand disease progression. And going back to that point about activation of the community, we're also able to help to demonstrate the activation of the community because of the number of people participating in the in the data collection.Harry Glorikian: I know it's not science fiction. I think it's right around the corner, hopefully, but I think, isn't an ideal future where we do either whole-exome or preferably whole genome on every newborn and scan for these genetic changes that are associated with rare diseases. I mean, I'm assuming that would really push this area much farther along. And if that is true, if that statement is true, how long do you think it'll take for us to get there?Charlene Son Rigby: Wow. You're reminding me of the Gattaca movie, but hopefully that's not the real future for us, you know. Winding things back. So my daughter was born, my daughter Juno was born in 2013. So that's nine years ago. And it took three years for us to get a diagnosis. And, you know, that's like an entire other podcast. But I think that the really, if we fast forward to 2022, we have groups like Stephen Kingsmore's group at Rady Children's where they're diagnosing newborns who are in the NICU, in less than 24 hours. And even standard exome testing, which it took us three months to get our results, the standard exome testing results are now returned in less than two weeks. You can also get it faster if you have an urgent testing and we have the tech. Illumina has long been dominant and continues to be dominant in the clinical area. But you have these new entrants with Oxford Nanopore, Element, Singular, and there are others that are entering now. And so these costs are coming down and this is really going to be a transformative in terms of becoming, I do think that this is going to become standard of care and it's closer than we think. I think that it's probably going to be in the next ten years, less than ten years.Charlene Son Rigby: We already have some analogs to this in terms of or precursors, I should say, in terms of newborn screening. And so what I think is going to happen is that genomic sequencing is is going to become a core newborn screening tool. And the interesting thing is that there are applications, not just in rare disease, but also in common conditions and the value of genomic sequencing. So today, 5% of rare diseases have a therapy, but there are right now hundreds of gene therapies that are currently in preclinical and clinical pipeline. So this picture is going to change enormously in the next five years. And so because the value of is going to grow, because there are therapies, the other important thing is therapeutic windows. So therapeutic windows are when we can intervene to have the most impact on a disorder. And so that's often when someone's young before the symptoms present or start or very early in that process. And so I think that this is going to become a reality in the next decade. And frankly, I think it's a very exciting time. I have always been a big believer that knowledge is power. And this is this is one of those great situations where we have the ability to do something because we know.Harry Glorikian: Yeah, I talk about some of this in my book and there's some, you know, interesting stories and it's a fascinating time. And when I think back, you know, to when we first started sequencing and people would say, why would you want to sequence anything? And now it's the complete opposite. And the price is coming down. It's becoming easier and faster. And I mean, at some point, I think the price is going to be low enough between the actual sequencing and then the analysis, that as my friend says, it's going to be a nothingburger. I mean, it's just going to be like, yeah, we should just do that because it gives us the information we need for the next step, which is sort of going to be interesting.Charlene Son Rigby: Yeah, absolutely. I think that the that is the challenges that I talked about, cost of sequencing. But you're right that, you know, the analysis is still quite expensive today. And that's something that we're also going to need to need to improve. I mean, AI and the growing knowledge bases is really going to help to address that. Yeah. And but that's a huge component of it as well today. Absolutely.Harry Glorikian: Yeah. I'm looking at a company that in this particular area of oncology, they've gotten the whole genome analytics down to about $60. So it's, you know, it's coming to a point where you're like, why wouldn't you do that? Like, what's stopping you from doing that? So it's been great having you. Great conversation. I wish you guys incredible success. A nd I'd love to keep up on how things are going with the organization.Charlene Son Rigby: That'd be great, Harry. Really enjoyed it today. Thanks.Harry Glorikian: Thank you.Harry Glorikian: That's it for this week's episode. You can find a full transcript of this episode as well as the full archive of episodes of The Harry Glorikian Show and MoneyBall Medicine at our website. Just go to glorikian.com and click on the tab Podcasts.I'd like to thank our listeners for boosting The Harry Glorikian Show into the top three percent of global podcasts.If you want to be sure to get every new episode of the show automatically, be sure to open Apple Podcasts or your favorite podcast player and hit follow or subscribe.Don't forget to leave us a rating and review on Apple Podcasts. And we always love to hear from listeners on Twitter, where you can find me at hglorikian.Thanks for listening, stay healthy, and be sure to tune in two weeks from now for our next interview.

Danny's Bio Danny Grannick is the CEO & Co-founder of Bristle, an oral microbiome testing company focused on helping people measure, understand and improve their oral health. Danny earned his BA in Biochemistry at the University of San Diego before moving into a variety of commercial roles in genomic sequencing, working at companies including Illumina and Oxford Nanopore. During his time, he worked with companies leveraging genomics across consumer health, oncology, and synthetic biology. Danny is located in San Diego, CA. Overview of Bristle Bristle is the first comprehensive at-home oral microbiome test to help people measure, understand, and improve their oral health. Our test identifies and quantifies all 100+ unique bacterial species in a saliva sample, both beneficial and pathogenic, and provides scores related to cavities, gum disease, halitosis, and gut inflammation. Based on test results, we provide prevention-focused diet, hygiene, and oral care ingredient & product recommendations to help users improve their health. Each user also receives a 1:1 coaching session with one of our oral health & hygiene experts to review their results. https://www.bmq30trk.com/3DCFHG/J8P3N/ Use code: TYGP15 to save 15% on your kit!

SHOW NOTESFor information on how to donate to the refugee crisis in Ukraine, please visit https://www.dec.org.uk/Check out Oxford Nanopore at https://nanoporetech.com/Check out OxSonics at https://oxsonics.com/sonotran-platform/Meet Barbara Souza https://granttree.co.uk/blog/granttree-news/specialist-spotlight-barbara-souza/Top six UK innovators in nanotechnology https://granttree.co.uk/blog/innovative/uk-innovators-nanotechnology/FIND US ONLINEAll previous episodes: granttree.co.uk/what-comes-next/Twitter: @wcnpodInstagram: @wcnpodGET IN TOUCHQuestions? Comments? Fiery opinions? We'd love to hear them! Drop us an email at wcn@granttree.co.uk.

Gordon Sanghera is the co-founder and CEO of Oxford Nanopore. With the help of some of the brightest minds around the globe Gordon, who has over 15 years experience in the design and development of biosensor devices, and his team have been able to develop revolutionary sensing technology that performs precise analysis of single molecules. Riding Unicorns invited Gordon on the show to explain in simple terms what the company does, the real world benefits to its products and how despite the difficulty they were able to find a commercial model that worked. We also delve into the rock n roll culture Gordon has helped implement at Oxford Nanopore, why he hires people with a diverse skill set and what the future looks like for him and the company Make sure to like and subscribe to the Riding Unicorns podcast to never miss an episode. Also don't forget to give Riding Unicorns a follow on Twitter and LinkedIn to keep on top of the latest developments.

Today we are talking about oral health. Why? Because our oral microbiome and oral health directly impacts what's going on in the rest of your body. We've always been so reactionary in the past with just trying to manage the symptoms and treat the symptoms, but not really understanding, why it's happening. It turns out that it has a lot more to do with the bacteria living in your mouth, and the westernized diet that we call the SAD diet, the Standard American Diet, which is very high in processed sugars, grains, and things like that. My Guest on Todays Episode is Danny Grannick Danny started an oral microbiome company called Bristle. They will test your oral microbiome and tell you if you have the wrong bacteria living in your mouth. I'm really excited about this because many of the patients that I see inevitably have gut issues. Oftentimes, what's living in our mouths is impacting our gut microbiome, which is impacting our health systemically. It's all connected.On this podcast, we are going to talk about...How your oral health is impacted by your oral microbiome.How your overall health is impacted by your oral microbiome.What is the actual cause of cavities?How our diets affect our oral health.One thing that you can do to improve your oral microbiome.Oral health during pregnancy and how it can impact our children's health later in life.About Danny GrannickDanny Grannick is the CEO and co-founder of Bristle. He received his BA in biochemistry from the University of San Diego. After receiving his degree, Danny moved into a variety of commercial roles at Illumina where he focused on bringing genomic tent technologies and applications to existing and emerging markets. Danny was then recruited by Oxford Nanopore to lead sales and business development for Northern Carroll, California in strategic accounts. His passion is in bridging the gap between innovation and implementation. He has really pivoted and is going in a new direction.Resources Mentioned:Bristle Oral Microbiome Test: https://www.bristlehealth.com/productWhere to connect with Danny & BristleLearn more about oral health on the Bristle Blog: https://www.bristlehealth.com/blogFollow Bristle on Instagram: https://www.instagram.com/bristlehealth/Follow Bristle on Facebook: https://www.facebook.com/bristlehealth/https://www.facebook.com/bristlehealth/Additional ResourcesBristle's Website: https://www.bristlehealth.com/Don't forget to sign up for my free resource! The Functional Gynecologist's Guide to Balancing your Hormones: https://lcvjtpc8.pages.infusionsoft.net/Dr. Tabatha's Website: https://www.drtabatha.com/Dr. Tabatha's Facebook: https://www.facebook.com/DrTabathaDr. Tabatha's IG: https://www.instagram.com/thegutsygynecologist/Dr. Tabatha's YouTube: https://www.youtube.com/c/TheFunctionalGynecologistRemember to Subscribe to this podcast wherever you listen so you don't miss an episode and take time to leave a review.

This week Harry is joined by Kevin Davies, author of the 2020 book Editing Humanity: The CRISPR Revolution and the New Era of Genome Editing. CRISPR—an acronym for Clustered Regularly Interspaced Short Palindromic Repeats—consists of DNA sequences that evolved to help bacteria recognize and defend against viral invaders, as a kind of primitive immune system. Thanks to its ability to precisely detect and cut other DNA sequences, CRISPR has spread to labs across the world in the nine years since Jennifer Doudna and Emmanuel Charpentier published a groundbreaking 2012 Science paper describing how the process works. The Nobel Prize committee recognized the two scientists for the achievement in 2020, one day after Davies' book came out. The book explains how CRISPR was discovered, how it was turned into an easily programmable tool for cutting and pasting stretches of DNA, how most of the early pioneers in the field have now formed competing biotech companies, and how the technology is being used to help patients today—and in at least one famous case, misused. Today's interview covers all of that ground and more.Davies is a PhD geneticist who has spent most of his career in life sciences publishing. After his postdoc with Harvey Lodish at the Whitehead Institute, Davies worked as an assistant editor at Nature, the founding editor of Nature Genetics (Nature's first spinoff journal), editor-in-chief at Cell Press, founding editor-in-chief of the Boston-based publication Bio-IT World, and publisher of Chemical & Engineering News. In 2018 he helped to launch The CRISPR Journal, where he is the executive editor. Davies' previous books include Breakthrough (1995) about the race to understand the BRCA1 breast cancer gene, Cracking the Genome (2001) about the Human Genome Project, The $1,000 Genome (2010) about next-generation sequencing companies, and DNA (2017), an updated version of James Watson's 2004 book, co-authored with Watson and Andrew Berry.Please rate and review MoneyBall Medicine on Apple Podcasts! Here's how to do that from an iPhone, iPad, or iPod touch:1. Open the Podcasts app on your iPhone, iPad, or Mac. 2. Navigate to the page of the MoneyBall Medicine podcast. You can find it by searching for it or selecting it from your library. 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Your review may not be immediately visible.Full TranscriptHarry Glorikian: I'm Harry Glorikian, and this is MoneyBall Medicine, the interview podcast where we meet researchers, entrepreneurs, and physicians who are using the power of data to improve patient health and make healthcare delivery more efficient. You can think of each episode as a new chapter in the never-ending audio version of my 2017 book, “MoneyBall Medicine: Thriving in the New Data-Driven Healthcare Market.” If you like the show, please do us a favor and leave a rating and review at Apple Podcasts.Harry Glorikian: We talk a lot on the show about how computation and data are changing the way we develop new medicines and the way we deliver healthcare. Some executives in the drug discovery business speak of the computing and software side of the business as the “dry lab” —to set it apart from the “wet labs” where scientists get their hands dirty working with actual cells, tissues, and reagents.But the thing is, recent progress on the wet lab side of biotech has been just as amazing as progress in areas like machine learning. And this week, my friend Kevin Davies is here to talk about the most powerful tool to come along in the last decade, namely, precise gene editing using CRISPR.Of course, CRISPR-based gene editing has been all over the news since Jennifer Doudna and Emmanuel Charpentier published a groundbreaking Science paper in 2012 describing how the process works in the lab. That work earned them a Nobel Prize in medicine just eight years later, in 2020.But what's not as well-known is the story of how CRISPR was discovered, how it was turned into an easily programmable tool for cutting and pasting stretches of DNA, how most of the early pioneers in the field have now formed competing biotech companies, and how the technology is being used to help patients today—and in at least one famous case, misused.Kevin put that whole fascinating story together in his 2020 book Editing Humanity. And as the executive editor of The CRISPR Journal, the former editor-in-chief of Bio-IT World, the founding editor at Nature Genetics, and the author of several other important books about genomics, Kevin is one of the best-placed people in the world to tell that story. Here's our conversation.Harry Glorikian: Kevin, welcome to the show. Kevin Davies: Great to see you again, Harry. Thanks for having me on.Harry Glorikian: Yeah, no, I mean, I seem to be saying this a lot lately, it's been such a long time since, because of this whole pandemic, nobody's really seeing anybody on a regular basis. I want to give everybody a chance to hear about, you had written this book called Editing Humanity, which is, you know, beautifully placed behind you for, for product placement here. But I want to hear, can you give everybody sort of an overview of the book and why you feel that this fairly technical laboratory tool called CRISPR is so important that you needed to write a book about it?Kevin Davies: Thank you. Yes. As you may know, from some of my previous “bestsellers” or not, I've written about big stories in genetics because that's the only thing I'm remotely qualified to write about. I trained as a human geneticist in London and came over to do actually a pair of post-docs in the Boston area before realizing my talents, whatever they might be, certainly weren't as a bench researcher. So I had to find another way to stay in science but get away from the bench and hang up the lab coats.So moving into science publishing and getting a job with Nature and then launching Nature Genetics was the route for me. And over the last 30 years, I've written four or five books that have all been about, a) something big happening in genomics, b) something really big that will have both medical and societal significance, like the mapping and discovery of the BRCA1 breast cancer gene in the mid-90s, the Human Genome Project at the turn of the century, and then the birth and the dawn of consumer genetics and personalized medicine with The $1,000 Genome. And the third ingredient I really look for if I'm trying to reach a moderately, significantly large audience is for the human elements. Who are they, the heroes and the anti heroes to propel the story? Where is the human drama? Because, you know, we all love a good juicy, gossipy piece of story and rating the good guys and the bad guys. And CRISPR, when it first really took off in 2012, 2013 as a gene editing tool a lot of scientists knew about this. I mean, these papers are being published in Science in particular, not exactly a specialized journal, but I was off doing other things and really missed the initial excitement, I'm embarrassed to say. It was only a couple of years later, working on a sequel to Jim Watson's DNA, where I was tasked with trying to find and summarize the big advances in genomic technology over the previous decade or whatever, that I thought, well, this CRISPR thing seems to be taking off and the Doudnas and the Charpentiers are, you know, winning Breakthrough Prizes and being feted by celebrities. And it's going on 60 Minutes. They're going to make a film with the Rock, Dwayne Johnson. What the heck is going on. And it took very little time after that, for me to think, you know, this is such an exciting, game-changing disruptive technology that I've got to do two things. I've gotta, a) write a book and b) launch a journal, and that's what I did. And started planning at any rate in sort of 2016 and 17. We launched the CRISPR Journal at the beginning of 2018. And the book Editing Humanity came out towards the end of 2020. So 2020, literally one day before the Nobel Prize—how about that for timing?—for Doudna and Charpentier for chemistry last year. Harry Glorikian: When I think about it, I remember working with different companies that had different types of gene editing technology you know, working with some particularly in the sort of agriculture space, cause it a little bit easier to run faster than in the human space. And you could see what was happening, but CRISPR now is still very new. But from the news and different advances that are happening, especially here in the Boston area, you know, it's having some real world impacts. If you had to point to the best or the most exciting example of CRISPR technology helping an actual patient, would you say, and I've heard you say it, Victoria Gray, I think, would be the person that comes to mind. I've even, I think in one of your last interviews, you said something about her being, you know, her name will go down in history. Can you explain the technology that is helping her and what some of the similar uses of CRISPR might be?Kevin Davies: So the first half of Editing Humanity is about the heroes of CRISPR, how we, how scientists turned it from this bizarre under-appreciated bacterial antiviral defense system and leveraged it and got to grips with it, and then figured out ways to turn it into a programmable gene editing technology. And within a year or two of that happening that the classic Doudna-Charpentier paper came out in the summer of 2012. Of course the first wave of biotech companies were launched by some of the big names, indeed most of the big names in CRISPR gene editing hierarchies. So Emmanuel Charpentier, Nobel Laureate, launched CRISPR Therapeutics, Jennifer Doudna co-founded Editas Medicine with several other luminaries. That didn't go well for, for reasons of intellectual property. So she withdrew from Editas and became a co-founder of Intellia Therapeutics as well as her own company, Caribou, which just went public, and Feng Zhang and others launched Editas Medicine. So we had this sort of three-way race, if you will, by three CRISPR empowered gene editing companies who all went public within the next two or three years and all set their sights on various different genetic Mendelian disorders with a view to trying to produce clinical success for this very powerful gene editing tool. And so, yes, Victoria Gray is the first patient, the first American patient with sickle cell anemia in a trial that is being run by CRISPR Therapeutics in close association with Vertex Pharmaceuticals. And that breakthrough paper, as I think many of your listeners will know, came out right at the end of 2020 published in the New England Journal of Medicine. Doesn't get much more prestigious than that. And in the first handful of patients that CRISPR Therapeutics have edited with a view to raising the levels of fetal hemoglobin, fetal globin, to compensate for the defective beta globin that these patients have inherited, the results were truly spectacular.And if we fast forward now to about two years after the initial administration, the initial procedures for Victoria Gray and some of her other volunteer patients, the results still look as spectacular. Earlier this year CRISPR Therapeutics put out of sort of an update where they are saying that the first 20 or 24 patients that they have dosed with sickle cell and beta thallasemia are all doing well. There've been little or no adverse events. And the idea of this being a once and done therapy appears very well founded. Now it's not a trivial therapy. This is ex-vivo gene editing as obviously rounds of chemotherapy to provide the room for the gene edited stem cells to be reimplanted into the patient. So this is not an easily scalable or affordable or ideal system, but when did we, when will we ever able to say we've pretty much got a cure for sickle cell disease? This is an absolutely spectacular moment, not just for CRISPR, but for medicine, I think, overall. And Victoria Gray, who's been brilliantly profiled in a long running series on National Public Radio, led by the science broadcaster Rob Stein, she is, you know, we, we can call her Queen Victoria, we can call it many things, but I really hope that ,it's not just my idea, that she will be one of those names like Louise Brown and other heroes of modern medicine, that we look and celebrate for decades to come.So the sickle cell results have been great, and then much more recently, also in the New England Journal, we have work led by Intellia Therapeutics, one of the other three companies that I named, where they've been also using CRISPR gene editing, but they've been looking at a rare liver disease, a form of amyloidosis where a toxic protein builds up and looking to find ways to knock out the production of that abnormal gene.And so they've been doing in vivo gene editing, really using CRISPR for the first time. It's been attempted using other gene editing platforms like zinc fingers, but this is the first time that I think we can really say and the New England Journal results prove it. In the first six patients that have been reported remarkable reductions in the level of this toxic protein far, not far better, but certainly better than any approved drugs that are currently on the market. So again, this is a very, very exciting proof of principle for in vivo gene editing, which is important, not just for patients with this rare liver disorder, but it really gives I think the whole field and the whole industry enormous confidence that CRISPR is safe and can be used for a growing list of Mendelian disorders, it's 6,000 or 7,000 diseases about which we know the root genetic cause, and we're not going to tackle all of them anytime soon, but there's a list of ones that now are within reach. And more and more companies are being launched all the time to try and get at some of these diseases.So as we stand here in the summer of 2021, it's a really exciting time. The future looks very bright, but there's so much more to be done. Harry Glorikian: No, we're just at the beginning. I mean, I remember when I first saw this, my first question was off target effects, right? How are we going to manage that? How are they going to get it to that place that they need to get it to, to have it to that cell at that time, in the right way to get it to do what it needs to do. And you know, all these sorts of technical questions, but at the same time, I remember I'm going to, trying to explain this to my friends. I'm like, “You don't understand, this can change everything.” And now a high school student, I say this to people and they look at me strangely, a high school student can order it and it shows up at your house.Kevin Davies: Yeah, well, this is why I think, and this is why one reason why CRISPR has become such an exciting story and receives the Nobel Prize eight years after the sort of launch publication or the first demonstration of it as a gene editing tool. It is so relatively easy to get to work. It's truly become a democratized or democratizing technology. You don't need a million-dollar Illumina sequencer or anything. And so labs literally all around the world can do basic CRISPR experiments. Not everyone is going to be able to launch a clinical trial. But the technology is so universally used, and that means that advances in our understanding of the mechanisms, new tools for the CRISPR toolbox new pathways, new targets, new oftware, new programs, they're all coming from all corners of the globe to help not just medicine, but many other applications of CRISPR as well.Harry Glorikian: Yeah. I always joke about like, there, there are things going on in high school biology classes now that weren't, available, when I was in college and even when we were in industry and now what used to take an entire room, you can do on a corner of a lab bench.Kevin Davies: Yeah. Yeah. As far as the industry goes we mentioned three companies. But you know, today there's probably a dozen or more CRISPR based or gene editing based biotech companies. More undoubtedly are going to be launched before the end of this year. I'm sure we'll spend a bit of time talking about CRISPR 2.0, it seems too soon to be even thinking about a new and improved version of CRISPR, but I think there's a lot of excitement around also two other Boston-based companies, Beam Therapeutics in Cambridge and Verve Therapeutics both of which are launching or commercializing base editing. So base editing is a tool developed from the lab of David Lu of the Broad Institute [of MIT and Harvard]. And the early signs, again, this technology is only five or six years old, but the early signs of this are incredibly promising. David's team, academic team, had a paper in Nature earlier this year, really reporting successful base editing treatment of sickle cell disease in an animal model, not by raising the fetal globin levels, which was sort of a more indirect method that is working very well in the clinic, but by going right at the point mutation that results in sickle cell disease and using given the chemical repertoire of base editing.Base editing is able to make specific single base changes. It can't do the full repertoire of single base changes. So there are some limitations on researchers' flexibility. So they were unable to flip the sickle cell variant back to the quote unquote wild type variants, but the change they were able to make is one that they can live with, we can live with because it's a known benign variant, a very rare variant that has been observed in other, in rare people around the world. So that's completely fine. It's the next best thing. And so that looks very promising. Beam Therapeutics, which is the company that David founded or co-founded is trying a related approach, also going right at the sickle cell mutation. And there are other companies, including one that Matthew Porteus has recently founded and has gone public called Graphite Bio.So this is an exciting time for a disease sickle cell disease that has been woefully neglected, I think you would agree, both in terms of basic research, funding, medical prioritization, and medical education. Now we have many, many shots on goal and it doesn't really, it's not a matter of one's going to win and the others are going to fall by the wayside. Just like we have many COVID vaccines. We'll hopefully have many strategies for tackling sickle cell disease, but they are going to be expensive. And I think you know the economics better than I do. But I think that is the worry, that by analogy with gene therapies that have been recently approved, it's all, it's really exciting that we can now see the first quote, unquote cures in the clinic. That's amazingly exciting. But if the price tag is going to be $1 million or $2 million when these things are finally approved, if and when, that's going to be a rather deflating moment. But given the extraordinary research resources that the CRISPRs and Intellias and Beams and Graphites are pouring into this research, obviously they've got to get some return back on their investment so that they can plow it back into the company to develop the next wave of of gene editing therapies. So you know, it's a predicament Harry Glorikian: One of these days maybe I have to have a show based on the financial parts of it. Because there's a number of different ways to look at it. But just for the benefit of the listeners, right, who may not be experts, how would you explain CRISPR is different from say traditional gene therapies. And is CRISPR going to replace older methods of, of gene therapy or, or will they both have their place? Kevin Davies: No, I think they'll both have their place. CRISPR and, and these newer gene editing tools, base editing and another one called prime editing, which has a company behind it now called Prime Medicine, are able to affect specific DNA changes in the human genome.So if you can target CRISPR, which is an enzyme that cuts DNA together with a little program, the GPS signal is provided in the form of a short RNA molecule that tells the enzyme where to go, where to go in the genome. And then you have a couple of strategies. You can either cut the DNA at the appropriate target site, because you want to inactivate that gene, or you just want to scramble the sequence because you want to completely squash the expression of that gene. Or particularly using the newer forms of gene editing, like base editing, you can make a specific, a more nuanced, specific precision edit without, with one big potential advantage in the safety profile, which is, you're not completely cutting the DNA, you're just making a nick and then coaxing the cell's natural repair systems to make the change that you sort of you're able to prime.So there are many diseases where this is the way you want to go, but that does not in any way invalidate the great progress that we're making in traditional gene therapy. So for example today earlier today I was recording an interview or for one of my own programs with Laurence Reid, the CEO of Decibel Therapeutics, which is looking at therapies for hearing loss both genetic and other, other types of hearing disorders.And I pushed him on this. Aren't you actually joinomg with the gene editing wave? And he was very circumspect and said, no, we're very pleased, very happy with the results that we're getting using old fashioned gene replacement therapy. These are recessive loss of function disorders. And all we need to do is get the expression of some of the gene back. So you don't necessarily need the fancy gene editing tools. If you can just use a an AAV vector and put the healthy gene back into the key cells in the inner ear. So they're complimentary approaches which is great.Harry Glorikian: So, you know, in, in this podcast, I try to have a central theme when I'm talking to people. The relationships of big data, computation, advances in new drugs, and other ways to keep people healthy. So, you know, like question-wise, there's no question in my mind that the whole genomics revolution that started in the ‘90s, and I was happy to be at Applied Biosystems when we were doing that, would have been impossible in the absence of the advances in computing speed and storage in the last three decades. I think computing was the thing that held up the whole human genome, which gave us the book of life that CRISPR is now allowing us to really edit. But I wonder if you could bring us sort of up-to-date and talk about the way CRISPR and computation are intertwined. What happens when you combine precision of an editing tool like CRISPR with the power of machine learning and AI tools to find meaning and patterns in that huge genetic ball? Kevin Davies: Yeah. Well, yeah. I'm got to tread carefully here, but I think we are seeing papers from some really brilliant labs that are using some of the tools that you mentioned. AI and machine learning with a view to better understanding and characterizing some of the properties and selection criteria of some of these gene editing tools. So you mentioned earlier Harry, the need to look out for safety and minimize the concern of off-target effects. So I think by using some of these some algorithms and AI tools, researchers have made enormous strides in being able to design the programmable parts of the gene editing constructs in such a way that you increase the chances that they're going to go to the site that you want them to go to, and nnot get hung up latching onto a very similar sequence that's just randomly cropped up on the dark side of the genome, across the nucleus over there. You don't want that to happen. And I don't know that anybody would claim that they have a failsafe way to guarantee that that could never happen. But the you know, the clinical results that we've seen and all the preclinical results are showing in more and more diseases that we've got the tools and learned enough now to almost completely minimize these safety concerns. But I think everyone, I think while they're excited and they're moving as fast as they can, they're also doing this responsibly. I mean, they, they have to because no field, gene therapy or gene editing really wants to revisit the Jesse Gelsinger tragedy in 1999, when a teenage volunteer died in volunteering for a gene therapy trial at Penn of, with somebody with a rare liver disease. And of course that, that setback set back the, entire field of gene therapy for a decade. And it's really remarkable that you know, many of the sort of pioneers in the field refuse to throw in the towel, they realized that they had to kind of go back to the drawing board, look at the vectors again, and throw it out. Not completely but most, a lot of the work with adenoviruses has now gone by the wayside. AAV is the new virus that we hear about. It's got a much better safety profile. It's got a smaller cargo hold, so that's one drawback, but there are ways around that. And the, the explosion of gene therapy trials that we're seeing now largely on the back of AAV and now increasingly with, with non-viral delivery systems as well is, is very, very gratifying. And it's really delivery. I think that is now the pain point. Digressing from your question a little bit, but delivery, I think is now the big challenge. It's one thing to contemplate a gene therapy for the eye for rare hereditary form of blindness or the ear. Indeed those are very attractive sites and targets for some of these early trials because of the quantities that you need to produce. And the localization, the, the physical localization, those are good things. Those help you hit the target that you want to. But if you're contemplating trying something for Duchenne muscular dystrophy or spinal muscular atrophy, or some of the diseases of the brain, then you're going to need much higher quantities particularly for muscular disorders where, you run into now other challenges, including, production and manufacturing, challenges, and potentially safeguarding and making sure that there isn't an immune response as well. That's another, another issue that is always percolating in the background.But given where we were a few years ago and the clinical progress that we've talked about earlier on in the show it, I think you can safely assume that we've collectively made enormous progress in, in negating most, if not all of these potential safety issues.Harry Glorikian: No, you know, it's funny, I know that people will say like, you know, there was a problem in this and that. And I look at like, we're going into uncharted territories and it has to be expected that you just…you've got people that knew what they were doing. All of these people are new at what they are doing. And so you have to expect that along the way everything's not going to go perfectly. But I don't look at it as a negative. I look at it as, they're the new graduating class that's going to go on and understand what they did right. Or wrong, and then be able to modify it and make an improvement. And, you know, that's what we do in science. Kevin Davies: Well, and forget gene editing—in any area of drug development and, and pharmaceutical delivery, things don't always go according to plan. I'm sure many guests on Moneyball Medicine who have had to deal with clinical trial failures and withdrawing drugs that they had all kinds of high hopes for because we didn't understand the biology or there was some other reaction within, we didn't understand the dosing. You can't just extrapolate from an animal model to humans and on and on and on. And so gene editing, I don't think, necessarily, should be held to any higher standard. I think the CRISPR field has already in terms of the sort of market performance, some of the companies that we've mentioned, oh my God, it's been a real roller coaster surprisingly, because every time there's been a paper published in a prominent journal that says, oh my God, there's, there's a deletion pattern that we're seeing that we didn't anticipate, or we're seeing some immune responses or we're seeing unusual off target effects, or we're seeing P53 activation and you know, those are at least four off the top of my head. I'm sure there've been others. And all had big transient impact on the financial health of these companies. But I think that was to be expected. And the companies knew that this was just an overreaction. They've worked and demonstrated through peer review publications and preclinical and other reports that these challenges have been identified, when known about, pretty much completely have been overcome or are in the process of being overcome.So, you know, and we're still seeing in just traditional gene therapy technologies that have been around for 15, 20 years. We're still seeing reports of adverse events on some of those trials. So for gene editing to have come as far as it's common, to be able to look at these two big New England Journal success stories in sickle cell and ATTR amyloidosis, I don't think any very few, except the most ardent evangelists would have predicted we'd be where we are just a few years ago. [musical transition]Harry Glorikian: I want to pause the conversation for a minute to make a quick request. If you're a fan of MoneyBall Medicine, you know that we've published dozens of interviews with leading scientists and entrepreneurs exploring the boundaries of data-driven healthcare and research. And you can listen to all of those episodes for free at Apple Podcasts, or at my website glorikian.com, or wherever you get your podcasts.There's one small thing you can do in return, and that's to leave a rating and a review of the show on Apple Podcasts. It's one of the best ways to help other listeners find and follow the show.If you've never posted a review or a rating, it's easy. All you have to do is open the Apple Podcasts app on your smartphone, search for MoneyBall Medicine, and scroll down to the Ratings & Reviews section. Tap the stars to rate the show, and then tap the link that says Write a Review to leave your comments. It'll only take a minute, but it'll help us out immensely. Thank you! And now back to the show.[musical transition]Harry Glorikian:One of your previous books was called The $1,000 Genome. And when you published that back in 2010, it was still pretty much science fiction that it might be possible to sequence someone's entire genome for $1,000. But companies like Illumina blew past that barrier pretty quickly, and now people are talking about sequencing individual genome for just a few hundred dollars or less. My question is, how did computing contribute to the exponential trends here. And do you wish you'd called your book The $100 Genome?Kevin Davies: I've thought about putting out a sequel to the book, scratching out the 0's and hoping nobody would notice. Computing was yes, of course, a massive [deal] for the very first human genome. Remember the struggle to put that first assembly together. It's not just about the wet lab and pulling the DNA sequences off the machines, but then you know, the rapid growth of the data exposure and the ability to store and share and send across to collaborators and put the assemblies together has been critical, absolutely critical to the development of genomics.I remember people were expressing shock at the $1,000 genome. I called the book that because I heard Craig Venter use that phrase in public for the first time in 2002. And I had just recently published Cracking the Genome. And we were all still recoiling at the billions of dollars it took to put that first reference genome sequence together. And then here's Craig Venter, chairing a scientific conference in Boston saying what we need is the $1,000 genome. And I almost fell off my chair. “what are you? What are you must you're in, you're on Fantasy Island. This is, there's no way we're going to get, we're still doing automated Sanger sequencing. God bless Fred Sanger. But how on earth are you going to take that technology and go from billions of dollars to a couple of thousand dollars. This is insanity.” And that session we had in 2002 in Boston. He had a local, a little episode of America's Got Talent and he invited half a dozen scientists to come up and show what they had. And George Church was one of them. I think Applied Biosystems may have given some sort of talk during that session. And then a guy, a young British guy from a company we'd never heard of called Celexa showed up and showed a couple of pretty PowerPoint slides with colored beads, representing the budding DNA sequence on some sort of chip. I don't know that he showed any data. It was all very pretty and all very fanciful. Well guess what? They had the last laugh. Illumina bought that company in 2006. And as you said, Harry you know, I think when, when they first professed to have cracked the $1,000 dollar genome barrier, a few people felt they needed a pinch of salt to go along with that. But I think now, yeah, we're, we're, we're well past that. And there are definitely outfits like BGI, the Beijing Genomics Institute being one of them, that are touting new technologies that can get us down to a couple of hundred. And those were such fun times because for a while there Illumina had enormous competition from companies like 454 and Helicose and PacBio. And those were fun heady times with lots and lots of competition. And in a way, Illumina's had it a little easy, I think over the last few years, but with PacBio and Oxford Nanopore gaining maturity both, both in terms of the technology platforms and their business strategy and growth, I think Illumina' gonna start to feel a little bit more competition in the long read sequence space. And one is always hearing whispers of new companies that may potentially disrupt next-gen sequencing. And that would be exciting because then we'd have an excuse to write another book. Harry Glorikian: Well, Kevin, start writing because I actually think we're there. I think there are a number of things there and you're right, I think Illumina has not had to bring the price down as quickly because there hasn't been competition. And you know, when I think about the space is, if you could do a $60 genome, right, it starts to become a rounding error. Like what other business models and opportunities now come alive? And those are the things that excite me. All right. But so, but you have a unique position as editor of the journal of CRISPR and the former editor of a lot of prominent, you know, publications, Nature Genetics, Bio-IT World, Chemical & Engineering News. Do you think that there's adequate coverage of the biological versus the computing side of it? Because I, I have this feeling that the computing side still gets a little overlooked and underappreciated. Kevin Davies: I think you're right. I mean I think at my own company Genetic Engineering News, we still have such deep roots in the wet lab vision and version of biotechnology that it takes a conscious effort to look and say, you know, that's not where all the innovation is happening. Bio-IT World, which you mentioned is interesting because we launched that in 2002. It was launched by the publisher IDG, best-known from MacWorld and ComputerWorld and this, this whole family of high-tech publications.And we launched in 2002 was a very thick glossy print magazine. And ironically, you know, we just couldn't find the advertising to sustain that effort, at least in the way that we'd envisioned it. And in 2006 and 2007, your friend and mine Phillips Kuhl, the proprietor of Cambridge Healthtech Institute, kind of put us out of our misery and said, you know what I'll, take the franchise because IDG just didn't know what to do with it anymore. But what he really wanted was the trade show, the production. And even though at the magazine eventually we fell on our sword and eventually put it out of its misery, the trade show went from strength to strength and it'll be back in Boston very soon because he had the vision to realize there is a big need here as sort of supercomputing for life sciences.And it's not just about the raw high-performance computing, but it's about the software, the software tools and data sharing and management. And it's great to go back to that show and see the, you know, the Googles and Amazons and yeah, all the big household names. They're all looking at this because genome technology, as we've discussed earlier has been one of the big growth boom areas for, for their services and their products.Harry Glorikian: Right. I mean, well, if you look at companies like Tempus, right. When I talked to Joel Dudley over there on the show it's, they want to be the Amazon AWS piping for all things genomic analysis. Right. So instead of creating it on your own and building a, just use their platform, basically, so it's definitely a growth area. And at some point, if you have certain disease states, I don't see how you don't get you know, genomic sequencing done, how a physician even today in oncology, how anybody can truly prescribe with all the drugs that are being approved that have, you know, genomic biomarkers associated with them and not use that data.Kevin Davies: On a much lower, lo-fi scale, as I've been doing a lot of reading about sickle cell disease lately, it's clear that a lot of patients who are, of course, as you, as you know, as your listeners know, are mostly African-American because the disease arose in Africa and the carrier status gives carriers a huge health advantage in warding off malaria. So the gene continues to stay, stay high in in frequency. Many African-American patients would benefit from some generic drugs that are available in this country that provide some relief, but aren't aware of it and maybe their physicians aren't completely aware of it either. Which is very sad. And we've neglected the funding of this disease over many decades, whereas a disease like cystic fibrosis, which affects primarily white people of Northern European descent that receives far more funding per capita, per head, than than a disease like sickle cell does. But hopefully that will begin to change as we see the, the potential of some of these more advanced therapies.I think as far as your previous comment. I think one of the big challenges now is how we tackle common diseases. I think we're making so much progress in treating rare Mendelian diseases and we know thousands of them. But it's mental illness and asthma and diabetes you know, diseases that affect millions of people, which have a much more complicated genetic and in part environmental basis.And what can we learn, to your point about having a full genome sequence, what can we glean from that that will help the medical establishment diagnose and treat much more common diseases, not quite as simple as just treating a rare Mendelian version of those diseases? So that's, I think going to be an important frontier over the next decade.Harry Glorikian: Yeah. It's complicated. I think you're going to see as we get more real-world data that's organized and managed well, along with genomic data, I think you'll be able to make more sense of it. But some of these diseases are quite complicated. It's not going to be find one gene, and it's going to give you that answer.But I want to go back to, you can't really talk about CRISPR without talking about this specter of germline editing. And a big part of your book is about this firestorm of criticism and condemnation around, you know, the 2018 when the Chinese researcher He Jankui, I think I said it correctly.Yep.Kevin Davies: He Jankui is how I say it. Close. Harry Glorikian: He announced that he had created twin baby girls with edits to their genomes that were intended to make them immune to HIV, which sort of like—that already made me go, what? But the experiment was, it seems, unauthorized. It seems that, from what I remember, the edits were sloppy and the case spurred a huge global discussion about the ethics of using CRISPR to make edits that would be inherited by future generations. Now, where are we in that debate now? I mean, I know the National Academy of Sciences published a list of criteria, which said, don't do that. Kevin Davies: It was a little more nuanced than that. It wasn't don't do that. It was, there is a very small window through which we could move through if a whole raft of criteria are met. So they, they refuse to say hereditary genome editing should be banned or there should be a moratorium. But they said it should not proceed until we do many things. One was to make sure it is safe. We can't run before we can walk. And by that, I mean, we've got to first demonstrate—because shockingly, this hasn't been done yet—that genome editing can be done safely in human embryos. And in the last 18 months there've been at least three groups, arguably the three leading groups in terms of looking at genetic changes in early human embryos, Kathy Niakan in London, Shoukhrat Mitalipov in Oregon, and Dieter Egli in New York, who all at roughly the same time published and reports that said, or posted preprints at least that said, when we attempt to do CRISPR editing experiments in very early human embryos, we're seeing a mess. We're seeing a slew of off-target and even on-target undesirable edits.And I think that says to me, we don't completely understand the molecular biology of DNA repair in the early human embryo. It may be that there are other factors that are used in embryogenesis that are not used after we're born. That's speculation on my part. I may be wrong. But the point is we still have a lot to do to understand, even if we wanted to.And even if everybody said, “Here's a good case where we should pursue germline editing,” we've gotta be convinced that we can do it safely. And at the moment, I don't think anybody can say that. So that's a huge red flag.But let's assume, because I believe in the power of research, let's assume that we're going to figure out ways to do this safely, or maybe we say CRISPR isn't the right tool for human embryos, but other tools such as those that we've touched on earlier in the show base editing or prime editing, or maybe CRISPR 3.0 or whatever that is right now to be published somewhere. [Let's say ] those are more safe, more precise tools. Then we've got to figure out well, under what circumstances would we even want to go down this road? And the pushback was quite rightly that, well, we already have technologies that can safeguard against families having children with genetic diseases. It's called IVF and pre-implantation genetic diagnosis. So we can select from a pool of IVF embryos. The embryos that we can see by biopsy are safe and can therefore be transplanted back into the mother, taken to term and you know, a healthy baby will emerge.So why talk about gene editing when we have that proven technology? And I think that's a very strong case, but there are a small number of circumstances in which pre-implantation genetic diagnosis will simply not work. And those are those rare instances where a couple who want to have a biological child, but have both of them have a serious recessive genetic disease. Sickle cell would be an obvious case in point. So two sickle cell patients who by definition carry two copies of the sickle cell gene, once I have a healthy biological child preimplantation genetic diagnosis, it's not going to help them because there are no healthy embryos from whatever pool that they produce that they can select. So gene editing would be their only hope in that circumstance. Now the National Academy's report that you cited, Harry, did say for serious diseases, such as sickle cell and maybe a few others they could down the road potentially see and condone the use of germline gene editing in those rare cases.But they're going to be very rare, I think. It's not impossible that in an authorized approved setting that we will see the return of genome editing, but that's okay. Of course you can can issue no end of blue ribbon reports from all the world's experts, and that's not going to necessarily prevent some entrepreneur whose ethical values don't align with yours or mine to say, “You know what, there's big money to be made here. I'm going offshore and I'm going to launch a CRISPR clinic and you know, who's going to stop me because I'll be out of the clutches of the authorities.” And I think a lot of people are potentially worried that that scenario might happen. Although if anyone did try to do that, the scientific establishment would come down on them like a ton of bricks. And there'll be a lot of pressure brought to bear, I think, to make sure that they didn't cause any harm.Harry Glorikian: Yeah. It's funny. I would like to not call them entrepreneurs. I like entrepreneurs. I'd like to call them a rogue scientist. Kevin Davies: So as you say, there's the third section of four in Editing Humanity was all about the He Jankui debacle or saga. I had flown to Hong Kong. It's a funny story. I had a little bit of money left in my travel budget and there were two conferences, one in Hong Kong and one in China coming up in the last quarter of 2018. So I thought, well, okay, I'll go to one of them. And I just narrowed, almost a flip of a coin, I think. Okay, let's go to the Hong Kong meeting.It's a bioethics conference since I don't expect it to be wildly exciting, but there are some big speakers and this is an important field for the CRISPR Journal to monitor. So I flew there literally, you know, trying to get some sleep on the long flights from New York and then on landing, turn on the phone, wait for the new wireless signal provider to kick in. And then Twitter just explode on my feed as this very, very astute journalists at MIT Technology Review, Antonio Regalado, had really got the scoop of the century by identifying a registration on a Chinese clinical trial website that he and only he had the foresight and intelligence to sort of see. He had met He Jankui in an off the record meeting, as I described in the book, about a month earlier. A spider sense was tingling. He knew something was up and this was the final clue. He didn't know at that time that the Lulu and Nana, the CRISPR babies that you mentioned, had actually been born, but he knew that there was a pregnancy, at least one pregnancy, from some of the records that he'd seen attached to this registration document. So it was a brilliant piece of sleuthing. And what he didn't know is that the Asociated Press chief medical writer Marilynm Marchion had confidentially been alerted to the potential upcoming birth of these twins by an American PR professional who was working with He Jankui in Shenzhen. So she had been working on an embargoed big feature story that He Jankui and his associates hoped would be the definitive story that would tell the world, we did this quote unquote, “responsibly and accurately, and this is the story that you can believe.” So that story was posted within hours.And of course the famous YouTube videos that He Jankui had recorded announcing with some paternal pride that he had ushered into the world these two gene edited, children, screaming and crying into the world as beautiful babies I think was [the phrase]. And he thought that he was going to become famous and celebrated and lauded by not just the Chinese scientific community, but by the world community for having the ability and the bravery to go ahead and do this work after Chinese researchers spent the previous few years editing human embryos. And he was persuaded that he had to present his work in Hong Kong, because he'd set off such a such an extraordinary firestorm. And I think you've all seen now you're the clips of the videos of him nervously walking onto stage the muffled, the silence, or the only sound in the front row, the only sound in the big auditorium at Hong Kong university—[which] was absolutely packed to the rim, one side of the auditorium was packed with press photographers, hundreds of journalists and cameras clicking—and the shutters clattering was the only, that was the applause that he got as he walked on stage.And to his credit, he tried to answer the questions directly in the face of great skepticism from the audience. The first question, which was posed by David Liu, who had traveled all the way there, who just asked him simply, “What was the unmet medical need that you are trying to solve with this reckless experiment? There are medical steps that you can do, even if the couple that you're trying to help has HIV and you're trying to prevent this from being passed on. There are techniques that you can use sperm washing being one of them. That is a key element of the IVF process to ensure that the no HIV is transmitted.”But he was unable to answer the question in terms of I'm trying to help a family. He'd already moved out and was thinking far, far bigger. Right? And his naiveté was shown in the manuscript that he'd written up and by that point submitted to Nature, excerpts of which were leaked out sometime later.So he went back to Shenzhen and he was put under house arrest after he gave that talk in Hong Kong. And about a year later was sentenced to three years in jail. And so he's, to the best of my knowledge that's where he is. But I often get asked what about the children? As far as we know, there was a third child born about six months later, also gene-edited. We don't even know a name for that child, let alone anything about their health. So one hopes that somebody in the Chinese medical establishment is looking after these kids and monitoring them and doing appropriate tests. The editing, as you said, was very shoddily performed. He knocked out the gene in question, but he did not mimic the natural 32-base deletion in this gene CCR5 that exists in many members of the population that confers, essentially, HIV resistance. So Lulu and Nana on the third child are walking human experiments, sad to say. This should never have been done. Never should have been attempted. And so we hope that he hasn't condemned them to a life of, you know, cancer checkups and that there were no off-target effects. They'll be able to live, hopefully, with this inactivated CCR5 gene, but it's been inactivated in a way that I don't think any, no other humans have ever been recorded with such modifications. So we, we really hope and pray that no other damage has been done. Harry Glorikian: So before we end, I'd love to give you the chance to speculate on the future of medicine in light of CRISPR. Easy, fast, inexpensive genome sequencing, give us access to everybody's genetic code, if they so choose. Machine learning and other forms of AI are helping understand the code and trace interactions between our 20,000 genes. And now CRISPR gives us a way to modify it. So, you know, it feels like [we have] almost everything we need to create, you know, precise, targeted, custom cures for people with genetic conditions. What might be possible soon, in your view? What remaining problems need to be solved to get to this new area of medicine? Kevin Davies: If you know the sequence that has been mutated to give rise to a particular disease then in principle, we can devise a, some sort of gene edit to repair that sequence. It may be flipping the actual base or bases directly, or maybe as we saw with the first sickle cell trial, it's because we understand the bigger genetic pathway. We don't have to necessarily go after the gene mutation directly, but there may be other ways that we can compensate boost the level of a compensating gene.But I think we, we should be careful not to get too carried away. As excited as I am—and hopefully my excitement comes through in Editing Humanity—but for every company that we've just mentioned, you know, you can go on their website and look at their pipeline. And so Editas might have maybe 10 diseases in its cross hairs. And CRISPR [Therapeutics] might have 12 diseases. And Intellia might have 14 diseases and Graphite has got maybe a couple. And Beam Therapeutics has got maybe 10 or 12. And Prime Medicine will hasn't listed any yet, but we'll hopefully have a few announced soon. And so I just reeled off 50, 60, less than a hundred. And some of these are gonna work really, really well. And some are going to be either proven, ineffective or unviable economically because the patient pool is too small. And we've got, how many did we say, 6,000 known genetic diseases. So one of the companies that is particularly interesting, although they would admit they're in very early days yet, is Verve Therapeutics. I touched on them earlier because they're looking at to modify a gene called PCSK9 that is relevant to heart disease and could be a gene modification that many people might undergo because the PCSK9 gene may be perfectly fine and the sequence could be perfectly normal, but we know that if we re remove this gene, levels of the bad cholesterol plummet, and that's usually a good thing as far as heart management goes. So that's an interesting, very interesting study case study, I think, to monitor over the coming years, because there's a company looking at a much larger patient pool potentially than just some of these rare syndromes with unpronounceable names. So the future of CRISPR and gene editing is very bright. I think one of the lessons I took away from CRISPR in Editing Humanity is, looking at the full story, is how this technology, this game-changing gene-editing technology, developed because 25 years ago, a handful of European microbiologists got really interested in why certain microbes were thriving in a salt lake in Southeastern Spain. This is not exactly high-profile, NIH-must-fund-this research. There was a biological question that they wanted to answer. And the CRISPR repeats and the function of those repeats fell out of that pure curiosity, just science for science's sake. And so it's the value of basic investigator-driven, hypothesis-driven research that led to CRISPR being described and then the function of the repeats.And then the story shifted to a yogurt company in Europe that was able to experimentally show how having the right sequence within the CRISPR array could safeguard their cultures against viral infection. And then five years of work people in various groups started to see, were drawn to this like moths to a flame. Jennifer Doudna was intrigued by this from a tip-off from a coffee morning discussion with a Berkeley faculty colleagues, Jill Banfield, a brilliant microbiologist in her own. And then she met meets Emmanuelle Charpentier in Puerto Rico at a conference, and they struck up a friendship and collaboration over the course of an afternoon. And that, why should that have worked? Well, it did, because a year later they're publishing in Science. So it's serendipity and basic research. And if that can work for CRISPR, then I know that there's another technology beginning to emerge from somewhere that may, yet trump CRISPR.And I think the beauty of CRISPR is its universal appeal. And the fact is, it's drawn in so many people, it could be in Japan or China or South Korea or parts of Europe or Canada or the U.S. or South America. Somebody is taking the elements of CRISPR and thinking well, how can we improve it? How can we tweak it?And so this CRISPR toolbox is being expanded and modified and updated all the time. So there's a hugely exciting future for genome medicine. And you know, whether it's a new form of sequencing or a new form of synthetic biology, you know, hopefully your show is going to be filled for many years to come with cool, talented, young energetic entrepreneurs who've developed more cool gadgets to work with our genome and other genomes as well. We haven't even had time to talk about what this could do for rescuing the wooly mammoth from extinction. So fun things, but maybe, maybe another time. Harry Glorikian: Excellent. Well, great to have you on the show. Really appreciate the time. I hope everybody got a flavor for the enormous impact this technology can have. Like you said, we talked about human genome, but there's so many other genomic applications of CRISPR that we didn't even touch. Kevin Davies: Yup. Yup. So you have to read the book. Harry Glorikian: Yeah. I will look forward to the next book. So, great. Thank you so much. Kevin Davies: Thanks for having me on the show, Harry. All the best.Harry Glorikian: Take care.Harry Glorikian: That's it for this week's show. You can find past episodes of MoneyBall Medicine at my website, glorikian.com, under the tab “Podcast.” And you can follow me on Twitter at hglorikian.  Thanks for listening, and we'll be back soon with our next interview.

The Big Ones Canada-based digital investment platform developer Wealthsimple received C$750m ($610m) in funding from investors including Allianz X, a subsidiary of Allianz, at a valuation of almost $4.1bn. Meritech Capital and Greylock Partners co-led the round, which also featured DST Global, Sagard, Iconiq Capital, Dragoneer, TCV, iNovia Capital, Base 10 Partners, Redpoint Ventures, Steadfast … Continue reading "10 May 2021 – Oxford Nanopore Pockets $280m in Equity Financing" The post 10 May 2021 – Oxford Nanopore Pockets $280m in Equity Financing appeared first on Global Venturing Review.

Since NVIDIA announced construction of the U.K.’s most powerful supercomputer — Cambridge-1 — Marc Hamilton, vice president of solutions architecture and engineering, has been (remotely) overseeing its building across the pond. Cambridge-1, which will be available for U.K. healthcare researchers to work on pressing problems, is being built on NVIDIA DGX SuperPOD architecture for a whopping 400 petaflops of AI performance. Located at KAO Data, a data center using 100% renewable energy, Cambridge-1 will rank among the world’s top 3 most energy-efficient supercomputers on the current Green500 list. Hamilton points to the concentration of leading healthcare companies in the U.K. as a primary reason for Cambridge-1’s location. AstraZeneca, GSK, Oxford Nanopore and more have already announced their intent to harness the supercomputer for research in the coming months.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.10.376871v1?rss=1 Authors: Wilks, C., Schatz, M. C. Abstract: Abstract Motivation: Long read sequencing has increased the accuracy and completeness of assemblies of various organisms' genomes in recent months. Similarly, spliced alignments of long read RNA sequencing hold the promise of delivering much longer transcripts of existing and novel isoforms in known genes without the need for error-prone transcript assemblies from short reads. However, low coverage and high-error rates potentially hamper the widespread adoption of long-read spliced alignments in annotation updates and isoform-level expression quantifications. Results: Addressing these issues, we first develop a simulation of error modes for both Oxford Nanopore and PacBio CCS spliced-alignments. Based on this we train a Random Forest classifier to assign new long-read alignments to one of two error categories, a novel category, or label them as non-error. We use this classifier to label reads from the spliced-alignments of the popular aligner minimap2, run on three long read sequencing datasets, including NA12878 from Oxford Nanopore and PacBio CCS, as well as a PacBio SKBR3 cancer cell line. Finally, we compare the intron chains of the three long read alignments against individual splice sites, short read assemblies, and the output from the FLAIR pipeline on the same samples. Our results demonstrate a substantial lack of precision in determining exact splice sites for long reads during alignment on both platforms while showing some benefit from postprocessing. This work motivates the need for both better aligners and additional post-alignment processing to adjust incorrectly called putative splice-sites and clarify novel transcripts support. Availability and implementation Source code for the random forest implemented in python is available at https://github.com/schatzlab/LongTron under the MIT license. The modified version of GffCompare used to construct Table 3 and related is here: https://github.com/ChristopherWilks/gffcompare/releases/tag/0.11.2LT Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.09.374165v1?rss=1 Authors: Lv, X., Chen, Z., Lu, Y., Yang, Y. Abstract: Oxford Nanopore sequencing is fastly becoming an active field in genomics, and it's critical to basecall nucleotide sequences from the complex electrical signals. Many efforts have been devoted to developing new basecalling tools over the years. However, the basecalled reads still suffer from a high error rate and slow speed. Here, we developed an open-source basecalling method, CATCaller, by simultaneously capturing global context through Attention and modeling local dependencies through dynamic convolution. The method was shown to consistently outperform the ONT default basecaller Albacore, Guppy, and a recently developed attention-based method SACall in read accuracy. More importantly, our method is fast through a heterogeneously computational model to integrate both CPUs and GPUs. When compared to SACall, the method is nearly 4 times faster on a single GPU, and is highly scalable in parallelization with a further speedup of 3.3 on a four-GPU node. Copy rights belong to original authors. Visit the link for more info

ナノレベルの分子構造をDNAシーケンシングから再構成する「DNA Nanoscope」と呼ばれる技術について、原著論文と分野の周辺を紹介しました。Show notes A DNA nanoscope that identifies and precisely localizes over a hundred unique molecular features with nanometer accuracy. (BioRxiv 2020)…今回Sohが紹介する論文はこれ。 研エンの仲…“研究者とエンジニアのカップルが、様々な話題について時にゆるく時に白熱した議論をするPodcast” 論理回路 (Wikipedia) Peng Yen Toehold switch (Wyss Institute) 原子間力顕微鏡/AFM (Wikipedia)…DNA Origamiの構造もAFMによる観察が行われている。 Researchat.fm ep16…光学顕微鏡を使わない新しいイメージングの方法DNA Microscopyや染色体の構造を解析するHi-Cについてはep16で話しました。 Design and self-assembly of two-dimensional DNA crystals. (Nature 1988)…SeemanによるDNA Nanotechnologyの大本の論文。 Folding DNA to create nanoscale shapes and patterns. (Nature 2006)…Paul W. K. RothemundによるDNA Origamiの元論文。 Primer Exchange Reaction…このビデオによる解説がとてもわかり易い。 Programmable autonomous synthesis of single-stranded DNA. (Nature Chemistry 2018)…Primer Exchange Reactionの元論文。 A DNA nanoscope via auto-cycling proximity recording. (Nature Communications 2017)…Auto-cycling proximity recordingの元論文。 Determination of bacteriophage lambda tail length by a protein ruler. (Nature 1987) … 自然界におけるmolecular rulerの研究。ファージ のtailの長さとそれを調整するタンパク質に関する論文。 Flap endonuclease (Wikipedia) Oxford Nanopore…長鎖DNAをシーケンスすることができるシーケンサーの一つ。 Editorial notes もうちょいうまく説明できた気がする…(soh) DNAを使った試みは何かワクワクしますね (tadasu) 全然関係ないですが、漫画とかで折り紙で戦うキャラって良いですよね(coela)

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.25.314252v1?rss=1 Authors: Feng, Z., Clemente, J., Wong, B., Schadt, E. Abstract: Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, co-infection of multiple pathogens. Detecting and phasing minor variants, which is to determine whether multiple variants are from the same haplotype, play an instrumental role in deciphering cellular genetic heterogeneity, but are still difficult because of technological limitations. Recently, long-read sequencing technologies, including those by Pacific Biosciences and Oxford Nanopore, have provided an unprecedented opportunity to tackle these challenges. However, high error rates make it difficult to take full advantage of these technologies. To fill this gap, we introduce iGDA, an open-source tool that can accurately detect and phase minor single-nucleotide variants (SNVs), whose frequencies are as low as 0.2%, from raw long-read sequencing data. We also demonstrated that iGDA can accurately reconstruct haplotypes in closely-related strains of the same species (divergence [≥] 0.011%) from long-read metagenomic data. Our approach, therefore, presents a significant advance towards the complete deciphering of cellular genetic heterogeneity. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.09.289793v1?rss=1 Authors: Hu, Y., Fang, L., Chen, X., Zhong, J. F., Li, M., Wang, K. Abstract: Long-read RNA sequencing (RNA-seq) technologies have made it possible to sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression over conventional short-read RNA-seq. However, long-read RNA-seq suffers from high per-base error rate, presence of chimeric reads and alternative alignments, and other biases, which require different analysis methods than short-read RNA-seq. Here we present LIQA (Long-read Isoform Quantification and Analysis), an Expectation-Maximization based statistical method to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read RNA-seq data. Rather than summarizing isoform-specific read counts directly as done in short-read methods, LIQA incorporates base-pair quality score and isoform-specific read length information to assign different weights across reads, which reflects alignment confidence. Moreover, given isoform usage estimates, LIQA can detect DAS events between conditions. We evaluated LIQA's performance on simulated data and demonstrated that it outperforms other approaches in rare isoform characterization and in detecting DAS events between two groups. We also generated one direct mRNA sequencing dataset and one cDNA sequencing dataset using the Oxford Nanopore long-read platform, both with paired short-read RNA-seq data and qPCR data on selected genes, and we demonstrated that LIQA performs well in isoform discovery and quantification. Finally, we evaluated LIQA on a PacBio dataset on esophageal squamous epithelial cells, and demonstrated that LIQA recovered DAS events on FGFR3 that failed to be detected in short-read data. In summary, LIQA leverages the power of long-read RNA-seq and achieves higher accuracy in estimating isoform abundance than existing approaches, especially for isoforms with low coverage and biased read distribution. Copy rights belong to original authors. Visit the link for more info

https://www.nhk.or.jp/snsenglish/news/n191206.html　東芝の癌検出の新技術について話しました。なぜ論文を読んでるはずなのにbaseすら口から出てこないのか？あと私が思い出してたのはマイクロアレイ法とOxford NANOPOREです。ほんと私の頭もっとちゃんとしてほしい

Long read sequencing technologies, such as Oxford Nanopore and PacBio, produce reads from thousands to a million base pairs in length, at the cost of the increased error rate. Trevor Pesout describes how he and his colleagues leverage long reads for simultaneous variant calling/genotyping and phasing. This is possible thanks to a clever use of a hidden Markov model, and two different algorithms based on this model are now implemented in the MarginPhase and WhatsHap tools. Links: Preprint: Haplotype-aware genotyping from noisy long reads (Jana Ebler, Marina Haukness, Trevor Pesout, Tobias Marschall, Benedict Paten)

Sequencing geeks are fresh off the trail from AGBT, and it’s time for our annual look at the sequencing tools space. This year we sit down with the longtime Omics! Omics! blogger, Keith Robison, who not only can answer all your questions about the topic, he even knows which sequencer you’re using right now, and in which department. Keith jauntily runs through the Big 3--Illumina, Pac-Bio, and Oxford Nanopore--and has a few odds and ends to say about the "niche developers."

Nanopore sequencing has arrived. Passing test after test this past year--including one we discuss today--this technology which was being hyped decades ago is delivering on its promise. Winston Timp joins us today. He's an assistant professor at Johns Hopkins and one of the leaders on a recent large scale project to directly sequence RNA on an array of nanopores. Winston's is the first in a series of shows we've lined up with users of Oxford Nanopore's technology. Why RNA-seq? Hasn’t this been done for years?

Mark Akeson has been working on nanopore sequencing at UC Santa Cruz’s biophysics lab for twenty years. Up until the past few years with the launch of Oxford Nanopore’s sequencers, that work was mostly the methodical toil of the quiet inventor. Today it is quite ordinary to see a sequencer the size of your wallet being taken out into the field for DNA work. But for years, the naysayers dominated. “Back in the day, the skeptics outnumbered the proponents 99 to 1,” Mark says in today’s show.

Oxford Nanopore is a British company, spun out of the University of Oxford in 2005 and founded on the science of Prof Hagan Bayley. It is developing new technology that has the potential to improve greatly the speed and cost of DNA sequencing.

Oxford Nanopore is a British company, spun out of the University of Oxford in 2005 and founded on the science of Prof Hagan Bayley. It is developing new technology that has the potential to improve greatly the speed and cost of DNA sequencing.