Podcasts about pacbio

I'm joined by Christian Henry, CEO of PacBio, a company leading the way in high-accuracy long-read sequencing. We break down what that means in simple terms, how this technology is helping families solve their diagnostic odyssey, and why some genetic tests miss key information that PacBio can detect. Plus, if you've already had whole genome sequencing without finding an answer, Christian explains why it might be time to take another look. We also dive into the future of genetic testing, what needs to change for sequencing to become a routine part of medical care, and how families and advocates can help drive progress forward. This episode is all about hope, science, and the relentless pursuit of answers. Happy Rare Disease Day, and thank you for being part of this incredible community! Topics Covered: ✅ What is long-read sequencing, and how is it different from traditional genetic testing? ✅ How PacBio's technology is solving rare disease mysteries faster and more accurately. ✅ Why some families don't get answers from whole genome sequencing—and why they should consider trying again. ✅ The biggest barriers to making genetic testing more accessible and routine in rare disease care. ✅ How long-read sequencing could help lead to future treatments, not just diagnoses. ✅ What the next five years of genomic sequencing could look like. ✅ How rare disease families and advocacy groups can collaborate with PacBio to accelerate discoveries. Resources & Links:

Bridger (Waleed) Ammar, PhD Dr. Ammar is an educator, engineer, research scientist, author, and a business owner. Before founding HIGG, Dr. Ammar was a senior research scientist at Google, where he helped develop transformer-based models for generating DNA sequences based on PacBio long-reads which significantly reduced variant-calling errors [Nature Biotech'22]. He also helped develop task-oriented dialog systems which are more robust to disfluencies, code-switching and user revisions [arXiv'23]. Prior to joining Google, Dr. Ammar led the Semantic Scholar research team's efforts to develop ML-based methods to facilitate access to the literature [e.g., NAACL 19], build a knowledge graph of the scientific literature [NAACL'18], and use this wealth of information to identify systemic social problems in science [JAMA'19]. He also led the product team for the Semantic Scholar APIs in 2023. Dr. Ammar occasionally teaches courses at UW linguistics and UW Computer Science as a visiting lecturer. In 2016, he earned his Ph.D. degree in artificial intelligence from Carnegie Mellon University. Before pursuing the Ph.D., Waleed was a research engineer at Microsoft Research and a web developer at eSpace Technologies. 1. I was recently invited to speak at GAIN (Global AI Now/Next/Never), and was surprised by the degree to which SCIENCE IS TRANSFORMING KSA (kingdom of Saudi Arabia). Happy to share my key observations on the what, the how, and why it matters to the listeners of the podcast. 2. We recently launched SeeChat x Ideas at https://seechat.ai to help scientists do what they do best, even better: SCIENTIFIC PROBLEM SOLVING. Happy to elaborate on some of the key features we launched and a sneak peek on some of the features in our roadmap. 3. We just launched a first-of-its-kind AI-powered scientific problem solving competition for university students in Egypt at https://lnkd.in/gPCSiPKq. The goal is to HELP EGYPTIAN STUDENTS DO THEIR BEST WORK & SHINE in a highly competitive field, and a brutal job market. Happy to elaborate on the what, the how and why we think that IMPACT CHALLENGE: EGYPT has the potential to make a dent in the Egyptian economy.

In this episode, we have a conversation with Cam McKenzie, VP of Commercial Operations at PacBio and a leader in the genomics and life sciences industry. McKenzie discusses the innovative transformation of PacBio's commercial operations under the guidance of CEO Christian Henry, focusing on overcoming challenges like siloed operations and minimal infrastructure through strategic Salesforce integration and omnichannel strategies.  We also delve into the potential for innovation at the intersection of technology and human collaboration. McKenzie emphasizes the importance of fostering a culture of continuous learning and adaptability to stay ahead in the rapidly evolving field of genomics. Show Highlights: Strategic transformation of PacBio's commercial operations, focusing on Salesforce integration and omnichannel strategies. Challenges faced by PacBio and the innovative solutions implemented. Insights into the complexities of PacBio's business model. The impact of technology in streamlining sales processes and improving customer interactions. Reflection on the importance of diverse perspectives and optimism for future innovation at the intersection of technology and human collaboration. Follow and Review: We'd love for you to follow us if you haven't yet. Click that purple '+' in the top right corner of your Apple Podcasts app. We'd love it even more if you could drop a review or 5-star rating over on Apple Podcasts. Simply select “Ratings and Reviews” and “Write a Review” then a quick line with your favorite part of the episode. It only takes a second and it helps spread the word about the podcast. Supporting Resources: Join the Commerce Cloud Community: http://sforce.co/commercecrew To learn more about Commerce Cloud Innovations, go here: https://www.salesforce.com/commerce/innovations/  Would you like to be on the podcast, or do you know someone who should? Check out the nomination form: http://sfdc.co/podnomination  *** Episode Credits If you like this podcast and are thinking of creating your own, consider talking to my producer, Emerald City Productions. They helped me grow and produce the podcast you are listening to right now. Find out more at https://emeraldcitypro.com. Let them know I sent you.

Estonia is working on becoming the first country to implement personalized health at scale through the Estonian National Biobank.The biobank uses genetic data to create a picture of the Estonian population, leading to the potential adaptation of public health systems. The Estonian Biobank has samples from 20% of the adult population; in comparison, UK biobanks only represent 0.7% of the population. With so much data, Estonia can determine risk factors for cancer, cardiovascular disease, mental and reproductive health, informing health investments to improves patient outcomes.The project seeks to predict patients' responses to certain medications based on their genetic makeup. As well as better patient outcomes, this approach could save health systems millions on ineffective prescriptions in the long run. It could also be a blueprint for other national health systems, including the NHS, to personalize healthcare at scale.Earlier this year, the Estonian Biobank announced the next phase of its European Commission funded project in collaboration with sequencing firm PacBio. On the podcast this week, we have Professor Lili Milani, head of the Estonian National Biobank, and Neil Ward, VP of EMEA at PacBio.01:27-04:06: What is the Estonian National Biobank?04:06-05:15: Background on PacBio05:15-06:43: What are the benefits of using genetic data to create a picture of the Estonian population?06:43-08:24: What data is collected, and how is it used?08:24-09:54: Protecting individual privacy09:54-11:24: Is the databank used regularly by Estonian citizens?11:24-12:35: Can the biobank help address disease earlier?12:35-16:30: Are there economic savings?16:30-17:16: How to expand the biobank program17:16-19:44: How does the biobank help personalize medicine?19:44-20:26: Are there regional differences?20:26-21:57: How can Estonia's system be applied to other countries?21:57-22:57: Has there been international interest in the biobank?22:27-22:52: Are pharma companies interested in the biobank?22:52-24:05: The partnership with PacBio24:05-26:15: Is AI being used in conjunction with the biobank?26:15-27:26: Is the biobank project similar to other PacBio work?27:26-29:00: What is the future for the biobank relationship with PacBio?29:00-31:30: What is the future for the biobank?Interested in being a sponsor of an episode of our podcast? Discover how you can get involved here! Stay updated by subscribing to our newsletter

The Daily Business and Finance Show - Tuesday, 16 July 2024 We get our business and finance news from Seeking Alpha and you should too! Subscribe to Seeking Alpha Premium for more in-depth market news and help support this podcast. Free for 14-days! Please click here for more info: Subscribe to Seeking Alpha Premium News Today's headlines: Musk moving SpaceX to Texas, calls California transgender law 'the final straw' Verizon is reportedly looking to sell thousands of towers in the U.S. Energy Transfer, Sunoco unveil Permian Basin crude oil joint venture Palantir slips pre-market following ratings downgrade from Mizuho Rithm Capital continues gain for seven straight sessions Warner Bros. Discovery reportedly to undergo a 'significantly smaller' round of layoffs Enphase Energy among most shorted S&P 500 technology stocks in June; Apple, Microsoft among least (corrected) PacBio jumps over 30%, biggest in five years Explanations from OpenAI ChatGPT API with proprietary prompts. This podcast provides information only and should not be construed as financial or business advice. This podcast is produced by Klassic Studios Learn more about your ad choices. Visit megaphone.fm/adchoices

Episode 9 (February 16, 2024): Using CRISPR-Cas9 technology, British animal genetics firm Genus has generated a population of pigs that are resistant to the deadly porcine reproductive and respiratory syndrome (PRRS) virus. Exscientia has fired its founder, CEO, and principal executive officer Andrew Hopkins, PhD, and removed him from the company's board, after it concluded that he engaged in “inappropriate” relationships with two employees. Julianna LeMieux, PhD, Deputy Editor in Chief at GEN, provides a recap of her time at AGBT 2024.Plus, an interview with Christian Henry, president and chief executive officer at PacBio. Listed below are key references to the GEN stories, media, and other items discussed in this episode of Touching Base: CRISPRed Pigs: Precision Porcine Gene Editing Combats PPRS Virus ThreatBy Uduak Thomas, GEN, February 14, 2024 Exscientia Fires CEO for “Inappropriate” Relationships with Two EmployeesGEN, February 13, 2024 Sun, Spatial, and Sequencing: A Report from the First Day of AGBTBy Julianna LeMieux, PhD, and Jonathan D. Grinstein, PhD, GEN, February 7, 2024NanoString CSO Joe Beechem Insists the Company “Not Going Anywhere”By Julianna LeMieux, PhD, GEN, February 8, 2024 Hosted on Acast. See acast.com/privacy for more information.

Get Opto's best content every day by subscribing to our FREE Newsletter: www.cmcmarkets.com/en/opto/newsletterToday, we have the pleasure of introducing Arelis Agosto, Senior Healthcare Analyst at Global X. In this episode, we explore the transformative landscape of healthcare, diving into the latest breakthroughs in gene therapy & editing and genomic technology and the sector's increasing need for digitisation. Arelis shares insights from the latest J.P. Morgan Healthcare Conference, highlighting how the rapid pace of innovation drives immense investment potential in this space. She guides us through recent advancements in disease prevention strategies, such as soft therapy and enhanced diagnostics, set to reshape patient care. She also highlights key industry leaders, including Illumina, PacBio, and Nvidia, shedding light on why the latter plays a pivotal role in propelling progress, with healthcare now recognised as the world's foremost data-generating industry. Lastly, Arelis dives into Global X's Genomic & Biotechnology ETF [GNOM], designed to provide exposure to the genomic value chain. Before joining Global X in 2022, Arelis worked as a Senior Healthcare Analyst at Third Bridge, covering US life sciences, diagnostics, biotech, pharmaceutical services, and animal health.Check out our daily newsletter: https://www.cmcmarkets.com/en-gb/opto/newsletter---------Past performance is not a reliable indicator of future results.CMC Markets is an execution-only service provider. The material (whether or not it states any opinions) is for general information purposes only and does not take into account your personal circumstances or objectives. Nothing in this material is (or should be considered to be) financial, investment, or other advice on which reliance should be placed. No opinion given in the material constitutes a recommendation by CMC Markets or the author that any particular investment, security, transaction, or investment strategy is suitable for any specific person.The material has not been prepared in accordance with legal requirements designed to promote the independence of investment research. Although we are not specifically prevented from dealing before providing this material, we do not seek to take advantage of the material prior to its dissemination.CMC Markets does not endorse or offer opinions on the trading strategies used by the author. Their trading strategies do not guarantee any return and CMC Markets shall not be held responsible for any loss that you may incur, either directly or indirectly, arising from any investment based on any information contained herein for any loss that you may incur, either directly or indirectly, arising from any investment based on any information contained herein.

المرة دي حندردش مع د وليد عمار عن الذكاء الصناعي و تأثيره على المجتمع, د وليد من خبراء الذكاء الصناعي و من اللي اشتغلوا في المجال سواء من أكثر من زاوية, سواء من زاوية الأكاديميا و البحث العلمي, أو من الناحية التطبيقية و العملية. - Did scientific innovation (eg, AI) improve our lives? - How does early stage scientific innovation translate into economic progress? - Can AI be used to build more advanced weapon? - Who is in charge? Waleed Ammar is the co-founder of a mission-driven AI startup and a product manager at the Allen Institute for Artificial intelligence (AI2). Before rejoining AI2 this year, Waleed was a senior research scientist at Google, where he helped develop transformer-based models for generating DNA sequences based on PacBio long-reads which significantly reduced variant-calling errors [Nature Biotech'22]. He also helped develop task-oriented dialog systems which are more robust to disfluencies, code-switching and user revisions [arXiv'23]. Prior to joining Google, Waleed led the Semantic Scholar research team's efforts to develop ML-based methods to facilitate access to the literature [e.g., NAACL 19], build a knowledge graph of the scientific literature [NAACL'18], and use this wealth of information to identify systemic social problems in science [JAMA'19]. He also occasionally teaches courses at UW linguistics as an affiliate faculty member. In 2016, Waleed received a Ph.D. degree in artificial intelligence from Carnegie Mellon University. Before pursuing the Ph.D., Waleed was a research engineer at Microsoft Research and a web developer at eSpace Technologies. Outside work, Waleed spends most of his time on the water or in dancing studios.

1:32 Labiotech.eu news4:02 PacBio34:02 Sierra Space57:12 JLLThis week, we have two longer interviews. We have conversations with Neil Ward, VP of PacBio EMEA, and Marc Giulianotti, senior manager in space biomanufacturing at Sierra Space.We also have our weekly contribution from global commercial real estate services company JLL, with Travis McCready. Sierra Space and UC San Diego to develop first stem cell research institute in spaceSierra Space and University of California San Diego, one of the world's top 15 research universities and a leader in microgravity research, have formed a new agreement with the goal of defining the future of human health care research in space.In a new memorandum of understanding between the two organizations, Sierra Space and UC San Diego will collaborate on Orbital Reef, the first commercial space station in low Earth orbit (LEO), to expand the university's Integrated Space Stem Cell Orbital Research (ISSCOR) program, which is currently operational on the International Space Station (ISS). Together they will help define and shape the future of biotech and biopharma research and development in microgravity.PacBio launches Onso and Revio sequencing systemsPacBio recently announced beta testing of its Onso Sequencing System. The benchtop short-read DNA sequencing platform is expected to provide a new level of accuracy by utilizing PacBio's sequencing by binding (SBB) technology.The Onso Sequencing System has been designed for compatibility with the rich ecosystem of products currently available for short-read sequencers and supports a diverse set of library preparation types, single cell analysis solutions, whole-genome sequencing and other targeted methods, such as amplicon and hybridization capture panels. It is anticipated to deliver 500 million reads per run and offer 200 and 300 cycle kits enabling paired and single end reads, at a list price of US $259,000 per system.The Revio long-read sequencing system will enable customers to scale their use of PacBio's HiFi sequencing technology. Revio is designed to provide customers with the ability to sequence up to 1,300 human whole genomes per year at 30-fold coverage for less than $1,000 per genome. PacBio believes Revio will enable the use of HiFi sequencing for large studies in human genetics, cancer research, agricultural genomics, and more.Scientists have achieved many ‘firsts' with HiFi sequencing on PacBio's Sequel IIe sequencing system – the first complete telomere-to-telomere assembly of a human genome (Nurk 2022), the first haplotype-resolved methylomes in a rare disease cohort (Cheung 2022), the first population surveys of structural variation with long reads (All of Us Research Program), the first single-cell full isoform catalogs (Al'Khafaji 2021), and the first complete assembly of the highly complex oat genome (European Seed 2020). Revio uses the same HiFi chemistry – producing accurate native long reads with uniform coverage, extraordinary application performance for variant calling and assembly, and accurate DNA methylation detection – but at a much larger scale.SponsorInterested in sponsoring one or more episodes of the podcast? Learn more here!Leave a review on Apple podcastsReviews are hugely important because they help new people discover this podcast. If you enjoyed listening to this episode, we would love to hear your feedback!Connect with uslabiotech.euSubscribe to our newsletter

Today's guest is Michael Eberle, VP of Computational Biology at PacBio in California. Founded in 2004, PacBio have created the world's most advanced sequencing systems to provide you the most complete and accurate view of genomes, transcriptomes and epigenomes. They are passionate about developing products that empower scientists to explore the full spectrum of genetic variation in any organism, from unraveling the mystery of rare diseases to improving the world's food supply. Michael joined PacBio in February 2022 and is responsible for leading a team that is combining data science and population genetics methods to develop novel variant calling methods for researchers using HiFi sequence data. They are prioritizing methods that elucidate the genetic variations in the difficult regions of the genome with a focus on identifying the genetic cause of patients with rare and undiagnosed genetic diseases. In the episode, Michael will chat about: The interesting work they do in genetic sequencing, Applying AI and Data within Computational Biology, Common challenges they need to overcome, An insight into the AI team and plans for growth, and Why PacBio is a great place to work

Last week with a crowd of 1,200 customers in a Los Angeles nightclub, sequencing company Pacific Bioscience launched two new sequencers, both long and short read, Revio and Onso. It was a night of great technology, music, and anticipation. Their customers have waited a long time for this moment. Revio offers long read whole genomes at scale for under $1,000.

I'm joined by Simon Barnett, genomics analyst at Ark Invest, to discuss the latest developments in the genomics revolution and investment opportunities. Interview recorded on June 23, 2022. Simon Barnett on Twitter: https://twitter.com/sbarnettARK Timestamps: 00:00 - Introduction 02:00 - Top key defining trend in genomics today 04:00 - How does a machine sequence DNA? 19:23 - Why it took so long to sequence the entire genome? 25:17 - short-read vs long-read DNA sequencing 31:18 - Downsides of PacBio and Nanopore's approach 38:10 - Ultima Genomics 42:48 - Singular Genomics Systems 47:45 - Illumina 52:30 - Approaching valuation to genomics stocks 53:30 - Big stock price drop with genomic stocks 1:05:00 - Importance of diagnostics and liquid biopsies 1:07:00 - Declining costs of liquid biopsies 1:10:30 - How liquid biopsy tests work? 1:25:25 - Tackling cancer - where is this headed? 1:32:18 - What are the cancers that can be detected with liquid biopsies now? 1:36:11 - Wright's Law on liquid biopsies? 1:38:07 - Dealing with inefficiencies of Pharma system 1:42:27 - Invitae 1:47:11 - Exact Sciences Social

Pacific Biosciences has introduced a new method for detecting DNA methylation simultaneously with DNA sequencing. They are calling it 5-base sequencing. Today on the program, Jonas Korlach, PacBio's Chief Scientific Officer, and Tomi Pastinen, the Director of the Genomic Medicine Center at Children's Mercy Research Institute in Kansas City join us to describe the new breakthrough and connect it to clinical possibilities.

In a genomics first, Pacific Biosciences has introduced a new method for detecting DNA methylation simultaneously with DNA sequencing. They are calling it 5-base sequencing. Today on the program, Jonas Korlach, PacBio's Chief Scientific Officer, and Tomi Pastinen, the Director of the Genomic Medicine Center at Children's Mercy Research Institute in Kansas City join us to describe the new breakthrough and connect it to clinical possibilities.

In a joint interview, Sean George, CEO of diagnostics firm, Invitae, and Christian Henry, CEO of sequencing tools company, Pacific Biosciences, say that “it was clear in the first five minutes of a phone call that they shared a vision for doing something big together.” What comes through the interview is that this partnership is built on a big vision: speeding up the adoption of whole genome sequencing into clinical medicine as the preferred method for genetic testing.

Christian Henry, CEO of PacBio, on long read DNA sequencing applications.

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. 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.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.

Originally Published as The Niche PodcastSequencing technology, decentralized Alzheimer's trials, busts in gene therapy and microbiomes, and a $2.4B oncology collaboration Find out more athttps://thenichepod.comStory Referenceshttps://tinyurl.com/Niche-060-1https://tinyurl.com/Niche-060-2https://tinyurl.com/Niche-060-3https://tinyurl.com/Niche-060-4https://tinyurl.com/Niche-060-5Music by Luke Goodsonhttps://www.soundcloud.com/lukegoodsonLife Science Today is your source for stories, insights, and trends across the life science industry. Expect weekly highlights about new technologies, pharmaceutical mergers and acquisitions, news about the moves of venture capital and private equity, and how the stock market responds to biotech IPOs. Life Science Today also explores trends around clinical research, including the evolving patterns that determine how drugs and therapies are developed and approved. It's news, with a dash of perspective, focused on the life science industry. 

DNA. Três letrinhas que podem dizer muito sobre quem você é e como você se comporta e interage com tudo. Sabendo disso, o BeP desta semana vem falar sobre as técnicas de sequenciamento de DNA existentes, desde o método químico até as mais recentes nanopore e PacBio. Mas é claro, a gente nunca fala sério 100% do tempo, então o programa também tem fofoca briga pra toda família. Aliás, você sabe o que Ben Affleck, Fábio Porchat e Padre Marcelo Rossi têm em comum? Dá o play e descobre! Elenco: Anderson Freitas, Gabriel Nunes e Rickson Santana. Campanha apoia-se: https://apoia.se/biotecempauta2 (pontual - doação única); https://apoia.se/biotecempauta1 (contínua - seja assinante) Vinheta: Cold Funk by Kevin MacLeod Link: https://incompetech.filmmusic.io/song/3522-cold-funk License: https://filmmusic.io/standard-license Background: Wholesome by Kevin MacLeod Link: https://incompetech.filmmusic.io/song/5050-wholesome License: https://filmmusic.io/standard-license

Will there be a fourth surge of COVID here in the U.S.? Already that we’re asking the question and it’s not an inevitability is a good sign. It’s become a race between vaccination clinics and viral variants. The U.S. was a bit slow to this race, but we are catching up. Viral surveillance has become a key part of any nation’s pandemic strategy. This past month, PacBio and Labcorp announced a partnership that brings the tool of long read sequencing to this effort.

At the beginning of the year, we were all holding our breath for the future of PacBio. And by all, I mean all. It seems everyone has been rooting for this sequencing technology company. And why? It’s simple. Pretty much everyone is in agreement that they have the highest quality reads on the market.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.15.383273v1?rss=1 Authors: Ren, J., Chaisson, M. Abstract: It is computationally challenging to detect variation by aligning long reads from single-molecule sequencing (SMS) instruments, or megabase-scale contigs from SMS assemblies. One approach to efficiently align long sequences is sparse dynamic programming (SDP), where exact matches are found between the sequence and the genome, and optimal chains of matches are found representing a rough alignment. Sequence variation is more accurately modeled when alignments are scored with a gap penalty that is a convex function of the gap length. Because previous implementations of SDP used a linear-cost gap function that does not accurately model variation, and implementations of alignment that have a convex gap penalty are either inefficient or use heuristics, we developed a method, lra, that uses SDP with a convex-cost gap penalty. We use lra to align long-read sequences from PacBio and Oxford Nanopore (ONT) instruments as well as de novo assembly contigs. Across all data types, the runtime of lra is between 52-168% of the state of the art aligner minimap2 when generating SAM alignment, and 9-15% of an alternative method, ngmlr. This alignment approach may be used to provide additional evidence of SV calls in PacBio datasets, and an increase in sensitivity and specificity on ONT data with current SV detection algorithms. The number of calls discovered using pbsv with lra alignments are within 98.3-98.6% of calls made from minimap2 alignments on the same data, and give a nominal 0.2-0.4% increase in F1 score by Truvari analysis. On ONT data with SV called using Sniffles, the number of calls made from lra alignments is 3% greater than minimap2-based calls, and 30% greater than ngmlr based calls, with a 4.6-5.5% increase in Truvari F1 score. When applied to calling variation from de novo assembly contigs, there is a 5.8% increase in SV calls compared to minimap2+paftools, with a 4.3% increase in Truvari F1 score. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.11.09.374140v1?rss=1 Authors: Klasberg, S., Schmidt, A. H., Lange, V., Schöfl, G. Abstract: Background: High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation. Results: Here, we report on DR2S, an R package that leverages the strengths of two sequencing technologies - the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio's SMRT sequencing or ONT's nanopore sequencing - to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised for HLA and KIR genes, DR2S is applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. In addition, DR2S integrates supporting tools for easy visualisation and quality control of the reconstructed haplotype to ensure suitability for submission to public allele databases. Conclusions: DR2S is a largely automated workflow designed to create high-quality fully-phased reference allele sequences for highly polymorphic gene regions such as HLA or KIR. It has been used by biologists to successfully characterise and submit more than 500 HLA alleles and more than 500 KIR alleles to the IPD-IMGT/HLA and IPD-KIR databases. 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

This week on the podcast, Adam Knight of Pacific Biosciences joins us to discuss how PacBio uses ONTAP for all of its unstructured NAS workload requirements, with a focus on FlexGroup volumes!

Hello, I’m Thomas Locke and this is Five Minutes, the podcast that brings you closer to the malaria experts. All of our genetic material is made from DNA. It’s a chemical found in the nucleus of our cells, in long structures called chromosomes. The entire set of our genetic material forms our genome; each one of our is unique. Having reference genomes, a list of the genes always occur in a particular species is really important. It allows scientists to identify genes that cause disease, understand genetic inheritance and track migration patterns. Or in the case of malaria, understand insecticide resistance. Creating reference genomes for mosquitos is a challenge. But now, in a partnership between the Sanger Institute and PacBio, it can be done with just 100 nanograms of DNA. I speak with Sarah Kingan, a scientist who helped develop the new protocol.

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)

GEN Sounds of Science November 5, 2018 Illumina just purchased Pacific BioSciences (PacBio) for $1.2 billion. Shawn Baker formerly worked for Illumina as both a scientist and manager. He currently serves as the chief science officer for AllSeq and as a genomics startup advisor and consultant at SanDiegOmics.com. GEN asked Shawn about the significance of Illumina buying PacBio to the sequencing market and to obtain his take on what’s driving the Illumina deal?

Just hours after Illumina announced their buyout of Pacific Biosciences, Theral sits down with longtime sequencing Omics Omics blogger, Keith Robison, and the Chief Science Officer at sequencing marketplace, AllSeq, Shawn Baker, to discuss the news which has taken the industry by surprise. A special thanks to our sponsor, Sage Science, and the quick decision on this show.

We can all recognize that PacBio has laid down the railroad tracks in the frontier of long read sequencing. What many are asking is just how close on their caboose is Oxford Nanopore? And just what exactly will be the differences between the two technologies? Chia-Lin Wei is the Director of Genome Technologies at the Jackson Laboratories. When we called her up for today’s interview to talk about how she is using nanopore sequencing, she said, “I’ve been using nanopore for years, why the interest this year by the media?”

When 10X Genomics launched their GemCode sequencing instrument at last year’s AGBT conference, what they offered seemed too good to be true. 10X was promising researchers a machine that could generate long reads using Illumina’s short read technology at a price lower than what PacBio could offer with their “real” long read instruments. A year earlier, Illumina had announced they were buying Moleculo, a company that promised to offer long read data out of the short reads. But good data with the Moleculo platform failed to materialize.

Jonas Korlach is a natural storyteller—a rare trait in a scientist who is more comfortable presenting data than talking of himself. Jonas is the co-inventor of PacBio’s SMRT (single molecule, real time) sequencing, and we wanted to hear from him directly how it all got started, and also when the team realized that they had something big with long reads and close to 100X coverage. How many of us can boast of hitting it out of the park on our first try?

One of the popular questions on the program this past year is how those doing sequencing decide between the quality of Pacific Bioscience's long reads and the cheaper short read technology, such as that of Illumina or Thermo Fisher. Today’s guest provides the most clear and dramatic answer yet: use the PacBio system exclusively.

Guest: Mike Hunkapiller, CEO, Pacific Biosciences Bio and Contact Info Listen (4:58) What is the theme for 2014 at PacBio? Listen (2:50) Are you working on a clinical sequencer?