yt:channel:UCyYzBOE7oC1GqV2mYwjLhVw UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2012-07-18T02:32:33+00:00 yt:video:h0D3Qwib_HM h0D3Qwib_HM UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-12-10T20:33:21+00:00 2016-01-29T21:38:18+00:00 Applying New Exome Sequencing in Medical & Translational Research | Roche Sequencing Join us for a 60-minute talk entitled "Applying a New Exome Sequencing Method in Medical and Translational Research." Today’s speakers are: Dr. Michael Brockman is Manager of Research Informatics at Roche NimbleGen and Dr. Shrikant Mane, the director of the Yale Center for Genome Analysis. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .:  Contact Us: http://sequencing.roche.com/contact-us.html .:  Twitter:  https://twitter.com/RocheSequencing .:  LinkedIn: https://www.linkedin.com/company/roche-sequencing ____ TRANSCRIPTION____ Dr. Michael Brockman: Today I want to give you a brief introduction to the SeqCap EZ MedExome and give you a little bit of insight into what went on in the development team when we made this product. For MedExome we started with coding sequence and miRNA gene annotation. We were pleasantly surprised to see that the coding sequence annotations for these multiple sources actually agreed quite well. We didn't see one annotation source standing apart from the others, like they have in the past, for coding sequence. But also in recent years we've seen annotation for medically relevant regions become more widely available. We also included these definitions-with some filtering-into MedExome. For example, information from gene tests, excluding genes on the mitochondrial genome, gene variance from ClinVar filtered to use pathogenic or likely pathogenic annotations. The set of coding sequences from 4,600 genes identified by a consortium of Emory Genetics Lab, Harvard Lab of Molecular Medicine and CHOP, and then some additional regions based on customer input. So we took the regions identified in these annotation sources and created an initial design which we then subjected to extensive empirical testing and optimizations. As shown here, with probe design we were able to cover all of our annotation sources quite well. You may also notice that although MedExome used hg38 or GRCh38 annotation sources and genome build natively, we're also providing the hg19/GRCh37 target files for those not yet ready to switch to the new assembly. One outcome of the customer conversations and formal interviewsk, that we conducted early on, was the strong desire for a validated SeqCap EZ workflow which required less DNA input and less hybridization time. We prioritized this work and our current workflow, released earlier this year, is now validated down to 100 ng input into library prep, reduced from a mcg and 16-20 hours hybridization time, reduced from 60-72 hours. These are also the conditions which were used throughout MedExome development, including the empirical optimizations, that I believe resulted in MedExome's strong performance. One aspect of that performance that we observed was a strikingly uniform coverage across MexExome targets-even with varying GC composition, especially compared to a competitor exome as shown at right there. This is, again, due to the additional optimizations that we performed for MedExome using empirical experiments. In this type of GC plot here, the ideal sequencing depth of coverage profile is flat across the GC bins. Which is what we observed for MedExome in the plot at the left. In this type of plot you also see the width of the box indicating the number of targets in the GC composition bins. The ones at the ends are less targets at those levels in the GC bins so those boxes are thinner. Overall performance for the MedExome design is quite strong and here MexExome capture shows a high on-target rate of about 85% or higher. About 95% of the design is covered at 20X or higher – the conditions that we tested. Then compared to the competitor’s clinical exome, the SeqCap EZ MedExome kit exhibited greater percent on-target, higher coverage of the overall target and better snip sensitivity and specificity. Really overall, quite a strong performing exome. That concludes my brief introduction to the SeqCap EZ MedExome To hear Dr. Shrikant Mane talk about their experience at Yale about testing the MedExome, watch the video. --- For More Information about Roche Sequencing, please visit: http://sequencing.roche.com/ yt:video:j5KTRjueBAI j5KTRjueBAI UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-12-10T20:28:14+00:00 2016-01-29T21:37:28+00:00 Targeted Sequencing: Understanding Genetic Basis of Transplant Rejection | Roche Sequencing Targeted Sequencing as a Tool to Understand the Genetic Basis of Transplant Rejection | A Webinar by Dr. Brendan J. Keating, Assistant Professor of Pediatrics and Surgery, Perelman School of Medicine, University of Pennsylvania in conjunction with Roche Sequencing. http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .:  Contact Us: http://sequencing.roche.com/contact-us.html .:  Twitter:  https://twitter.com/RocheSequencing .:  LinkedIn: https://www.linkedin.com/company/roche-sequencing _____ Transcript_______ With their ever-growing suite of tools for targeted DNA sequencing, Roche is enabling the life science community to achieve their research goals more efficiently in order to understand the association genomics and epigenomics have with diseases and biological processes. Today’s speaker is Dr. Keating, who designed and developed large-scale snip panels for cardiovascular-related diseases which have resulted in about a hundred metabolic and cardiovascular related genetic discoveries. He is involved in a number of large-scale genomic association meta-analyses projects across a spectrum of cardiovascular and metabolic related traits, through a number of U.S. and European consortia. Dr. Keating's current research interests focus on large-scale genome wide association studies in transplantation and the analysis of micro RNA, mRNA and polymorphisms of donor, recipients, genomes and solid-organ transplantations. His group aims to predict genetic signals that may underpin graft rejection and complications of rejection and to ultimately deliver individualized treatment of immunosuppression therapies post transplant. First of all, I'll give you an overview of the complications of transplantation, including rejection, and other complications of immunosuppressant therapy. I'll then move on to give you an overview of some of the surveillance of rejection that we're doing using biomarkers, genomics. Then I'll move on to second generation sequencing to actually discover what are the genetic underpinnings between a donor and a recipient that we think may precipitate rejection. I will discuss specifically the SeqCap capture system for prospective for NIH clinical study that was run out of Penn and some other U.S. centers. I'll go through some of the results for those. Then I'll talk about some of the ongoing clinical studies and future directions for these studies. So, to give you some historical perspective for those who are not in the transplant arena, the first transplants for heart, were conducted in the early 1970s and this was before there was decent immune suppression therapies or even pathology to assess rejection from biopsies. Then in the subsequent decade there were advances on a number of fronts, outlined here on the biopsies, surveillance biopsies. Also, some of the steroids started to transition into better immune suppression therapies, as outlined here. Still, even with advances in immune suppression therapy and surgical techniques, the graft -life survival for a heart is now about 11 years. This is a lot of time if you are having severe issues in your 50s or 60s but when you put this in perspective of a young child, they may only have a couple of transplants over their lifetime. So any significant increase in the graft life that we can provide through better surveillance, or through better matching would obviously a major advancement in the field. An important note here for audience members, unless explicitly stated otherwise, all Roche products and services referenced in this webinar are intended for life science research and not for use in diagnostics procedures. Learn more about Roche Sequencing at: http://sequencing.roche.com yt:video:brRFEO0h9Sc brRFEO0h9Sc UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-08-26T15:06:13+00:00 2016-01-19T22:53:34+00:00 Characterizing Methylomes by Next Generation Capture Sequencing | Roche Sequencing Characterizing Methylomes by Next Generation Capture Sequencing Identifies Novel Disease Associated Variants. Dr. Elin Grundberg, Assistant Professor of Human Genetics, McGill University. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - I guess most of you know that complex diseases means that there are multi-factorial underlying factors with genetic and environmental playing both equally important roles. On the genetic side, again I think most of you also know that the large efforts from genome-wide association studies in the past decade have really been successful in identifying underlying genetic factors for these complex diseases, and we've seen a large number of those traits. Each trait has a large number of common genetic variants being associated, but one key finding from these studies is that these genetic variants actually have very small effect sizes. Another important finding from these studies is that most of these genetic variants are actually mapping to non-coding regions, which makes it more difficult to understand the mechanistic function of these variants. One approach that my group, and many others, have been applying is to use cellular phenotypes or, more specifically, gene expression traits in eQTL as studies to understand what's the functional role of genetic variants involved in disease susceptibility. This approach of eQTLs has been very successful too. We have elucidated multiple layers of the impact for these common disease variants. What we know now from these functional genomic studies is that using cellular phenotypes is very powerful, but it really has to be assessed in cells or tissues that are directly targeted to the disease of interest. More recently, now, we've also been able to expand these functional genomics studies to understand genetic contributions to complex diseases by also looking at epigenetic traits or epigenomic phenotypes. Maybe one of the most common epigenetic traits that we have been able to study is DNA methylation. I guess also many of you know that DNA methylation is a chemical modification on the cytosine base in our genome. We have around 30 million of these DNA methylation sites. They're mostly occurring in a CpG. Also, the important role of these epigenetic modifications in DNA methylation in relation to gene regulation and also its very close association to the different chromatin states that we have recently seen great efforts from the large consortiums, such as ENCODE and RoadMap, that have really shown this link between these DNA methylation patterns and the different chromatin states involved in the gene regulation machinery. Another feature that we know from DNA methylation patterns is that it's a quantitative trait, but also that the pattern of DNA methylation is really variable across individuals and across tissue. But there's also been a challenge, given the large amount of DNA methylation sites in the CpG [contact], to understand which proportion of these sites are just random, stochastic or versus those that actually have a functional role in altering the genome regulation or the genome function. We also know that DNA methylation is playing an important role in disease susceptibility. It is pioneered in cancer association and also that this trait, which I will talk about more from our research, is the fact that the genetic traits are impacted by both genetic and environmental factors. yt:video:AAd8OWVG-s4 AAd8OWVG-s4 UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-08-14T14:52:30+00:00 2016-01-19T23:04:20+00:00 Long Genomic DNA Fragment Capture & SMRT Sequencing | Roche Sequencing Dr. Lawrence Hon (Senior Manager, Bioinformatics, Pacific Biosciences) and Dr. Denise Raterman (R&D Scientist, Sequence Capture, Roche NimbleGen). ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Diane: Today’s talk is entitled "Long Genomic DNA Fragment Capture & SMRT Sequencing Enables Accurate Phasing of Cancer & HLA Loci." . Capitalizing on the efficiencies inherent with parallel enrichment, researchers can now design economical and time-saving next-generation sequencing experiments. Next generation sequencing combined with sequence capture probe pools offer researchers a clear understanding of genomic structure and function in order to understand the impact of genes on biological processes. Roche is part of the innovations in sequencing solutions for life science research. Our first speaker, Dr. Denise Raterman, is a Scientist at Roche NimbleGen with experience in leading protocol and product development for sequence capture. She received her undergraduate degree at the University of Wisconsin in Madison, with a double major in Wildlife, Ecology and Genetics. She earned her PhD in Evolution, Ecology and Organismal Biology at the University of California in Riverside, studying the molecular evolution of mammalian fertilization genes. Denise joined Roche NimbleGen after obtaining her PhD, and leads the development of the long fragment target enrichment protocol, using the Roche NimbleGen SeqCap technology, and is currently working on continued development of this and other next generation targeted enrichment technologies. Our second speaker for today is Dr. Lawrence Hon, who is a Bioinformatics Manager at Pacific Biosciences with a broader experience in bioinformatics analysis, algorithm development and software design. He works with customers to help them understand PacBio data, design experiments and analyze their data with an eye towards developing new messages and applications. He received his undergraduate degree in Computer Science from Stanford University and a Bioinformatics PhD from the University of California in San Francisco where he studied transcription factor binding side modeling. He then did an industry postdoc at Genentech, research of which included studying microRNA behavior by intersecting gene and microRNA expression data. Before PacBio, he worked at 23andMe, developing a Relative Finder feature that connects distant relatives using identity-by-descent estimated from SNP microarray data. And now to our first speaker, Dr. Denise Raterman. Dr. Raterman: Thank you, Diane, and thank you to everyone for attending and welcome. Before we begin, we’d like to remind everyone that the applications and products discussed in today’s talk are intended for life science research only. Today, I will talk about Roche NimbleGen technology and long fragment capture and library prep. Dr. Lawrence Hon will discuss Sequencing Data and Results and Phasing and Haplotype Creation. In today’s talk, Dr. Hon and I will be discussing how target enrichment can be combined with long read sequencing to address challenging research applications. yt:video:F0MEcttn4rQ F0MEcttn4rQ UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-08-12T16:51:40+00:00 2016-01-19T23:10:50+00:00 Roche NimbleGen Improved Next Generation Sequencing | Roche Sequencing Roche recognizes that user experience is just as important as the technology behind them. Roche is committed to the continuous improvement of its products and their usability. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Roche NimbleGen, part of Roche Sequencing, develops target enrichment solutions for targeted, next-generation sequencing. These technologies help the life sciences community efficiently target DNA sequences of interest in the genome, through either focused exomes or custom-designed gene panels. One of our innovations is best-in-class, hybridization base sequence capture technology. Customers around the world are using SeqCap line of target enrichment products for a wide variety of applications. To improve their user experience and efficiency, we implemented a workflow enhancement that greatly shortens the time it takes to prepare sequencing-ready DNA. Dan: The latest update to our target enrichment workflow allows researchers to perform the whole process, from sample to sequencing, in a much, much faster time. Instead of several days to get a hybridized approach to your sample, now you can do that overnight. And you can now run more experiments in a week. In addition to that, we've validated the recent lower amounts of DNA input into the process, which provides researchers greater flexibility to design experiments the way they have to. A lot of our customers have limited DNA for sample input amounts available to them, and this provides them the flexibility that they need. The improvements we have introduced lately have reduced the time and cost it takes to do a targeted enrichment experiment considerably, which allows customers to process more samples faster and achieve results more quickly. yt:video:AnsYU3qdj8c AnsYU3qdj8c UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-06-11T19:04:47+00:00 2017-04-20T23:23:30+00:00 The Future of Sequencing with Nanopore Chemistry | Roche Sequencing Leadership Series: Advancing the Future of Sequencing. Stefan Roever, CEO, and Roger Chen, CTO, of Genia Technologies discuss their serendipitous meeting that lead to founding the company. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Stefan: Yeah. I was at Starbucks, getting a cappuccino. Starbucks on Sand Hill Road where all the VCs are. Roger: I had been working in my garage and had met with some setbacks and I needed a break. I was reading a book on the origin of life. In sweat pants, disheveled, and Stefan approached me. Stefan: So I go to him and say, "Hey, I just read something on that." So we start talking and after about a half an hour, he tells me he's working on a DNA sequencing technology in his garage. I go, "DNA sequencing? What's that?" And he goes, "It's going to change the world." He says it will allow you to do diagnostics faster and cheaper. I say, "Well, that's cool." Roger: I gave him my address and said, "Come by." I wasn't sure. Seems like a strange thing, a guy with disheveled hair would have a DNA sequencing machine in his garage. Stefan: So I go there, I visit him and lo and behold there in his garage he's got this little prototype and it's got this little tiny black dot on it. He says, "Watch this dot and it'll turn white." Roger: Well, I had a concept in my head after leaving Santa Cruz that these nanopores can be very useful, but they just needed a way to be mated with semiconductor technology. Stefan: I had no clue what I was really looking at, but he convinced me that this would one day be able to sequence DNA. I go, "That's great. Do you have any money for it?" He goes, "No." Roger: You know, I built tons of little circuit boards. Most of them are complete junk that I went through for months and months and months trying to figure out how you would make these technologies. Stefan: I said, "Do you have a business plan?" "No." I said, "Do you have a team?" "No." "All right. Well, let me help you with that." You can think of the Genia chip as being very similar to a camera sensor. There are camera sensors in your digital cameras, in you cell phones and these camera sensors have millions of pixels. Each pixel picks up a tiny amount of light and converts that into an image. Our chip operates very similarly. It also has millions of pixels, but these pixels don't measure light, they measure electrical current. That current comes from the molecules of the DNA that we put on the chip. There may be millions on the chip. And as we're analyzing that DNA, we're picking up a tiny current from that DNA and that's what we interpret and that's what gives us the DNA sequence. Roger: Probably the biggest excitement of working with the single-molecule technology is you get to see things that nobody else gets to see. Stefan: What really differentiates Genia's technology is that it's a combination of highly integrated semiconductor technology on the one end that goes into our chip. Then we put a specifically developed chemistry on top of that and that's the nanopore chemistry. Roger: I see our sequencing technology being really widely deployed because of its cost effectiveness. The lack of a need for heavy infrastructure to operate this technology is a key thing. Where I see it going is everywhere. Stefan: When we engaged with Roche, we shared our vision for sequencing, which was this idea of a de-central deployment of the instrument where you could take a sample and you could put it on a reader and you could analyze it almost in real time. Then move that data into the cloud and do central analysis of it so that a doctor or a patient could then access that data through an Internet browser from anywhere in the world. Beth: Roche has been a pioneer in sequencing through introducing the second generation sequencing technology and now we are continuing with investments in third and fourth generation. Genia's single-molecule nanopore sequencing technology is the next evolution in sequencing. Roche is confident that we'll be able to introduce a differentiated product that will improve affordability, speed and accuracy. Stefan: What we found when we engaged with Roche is that that was really the same vision that the Roche team had for where sequencing should go and how diagnostics would change once you have this technology. So it was really refreshing to see a company like Roche that had been scouting for technologies, really had the same vision that we had. I though it made it a very good fit. yt:video:O0XZqBu1Ftc O0XZqBu1Ftc UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-06-11T12:04:16+00:00 2016-01-29T22:00:46+00:00 Personalized Health Care from Bench-to-Bedside | Roche Sequencing Personalized Health Care - Learn more from our leadership team about the potential future of clinical diagnostics using sequencing technologies. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Tom: The big differentiator for Roche in the sequencing space is that we have a wealth of experience in developing true diagnostic tests. We are a very large, a very experienced diagnostic company. There's basically no one who's more effective at taking very complex technologies and making them into something that's a very hardened package. Beth: We offer products in the full continuum from research through diagnostics and therapeutics. We also have an expansive commercial presence and a very strong technical support, which really allows us to push sequencing into the clinical market. Andrew: It's the mission of the Roche group in terms of personalized health care and bringing together and further our diagnostics division. I think sequencing fits really firmly in the heart of this mission and vision. It's going to be a fundamental part of medicine in the future, understanding what function that code is. Paul: The way that Roche sequencing helps support the ‘bench-to-bedside’ is that there's nothing more personal to an individual than their genome in a certain respect. We're developing disruptive technology that allows us to sequence this so that at the end the patient gets the correct treatment decision. Tom: What sequencing is doing now is sort of the epitome of doing now, what patients need next. Sequencing will provide you basically the operating system on which lots of therapies and therapeutic choices are going to be made. Infectious diseases, oncology, prenatal testing, genetic disorders, all of these things require you to understand the molecular basis of what's driving them before you can really pick the appropriate therapies. Lin: Traditionally I read tests. I read diagnostic tests. It will tell you a result, either a test positive or a test negative. Sequencing adds another layer of the information for the physicians. Not only it will tell you the genetic makeup of the patients but also on top of that, it will tell you multiple biomarkers or multiple genetic makeups of this particular patient Andrew: I think the long-term vision of sequencing is having a sequencer in the doctor's office so they can take a sample, get a result and give immediate feedback to the patient. Paul: The doctor will actually have a cockpit to help integrate the different technologies to end up with the correct answer for the treatment decision. Beth: When sequencing reaches its full potential, it will really enable individuals to make personal health care plans and choices based on genetic composition. Lin: We're coming from different functions of different areas, coming with different expertise. We have a whole lot more disease knowledge and need a very comprehensive tool to study the disease, to diagnose the disease, and that's what Roche sequencing is about. Andrew: This is where Roche has an incredible opportunity because we're going to see sequencing move from research into the clinic and into clinical practice. And for Roche, we have this great history in terms of diagnostics and in vitro diagnostics presence in the clinic. And I think it's a great opportunity for Roche to be involved in rapidly evolving technology and help bring it to the patients. yt:video:ICnfLq4NKoc ICnfLq4NKoc UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-06-11T11:02:11+00:00 2017-04-30T05:24:20+00:00 New Sequencing Workflow with Liquid Biopsy | Roche Sequencing Enriching the Power of Sequencing. Discover how we’re incorporating target enrichment, focused assays and challenging sample prep methods into development of our portfolio of products. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Andrew: When we think about sequencing, at Roche we're really looking at what does this mean from the sample in, to the results out and everything in between. Rebecca: Roche wants to build a complete sequencing workflow and this is what's going to be required in the diagnostic setting in the future so target enrichment is a piece of that workflow. Having solutions for every kind of assay is what we're there to build. Tom: We're constantly looking to identify new aspects of the sequencing workflow, such as new sample prep methods, new sequencing instrumentation, new core technologies that may eventually become a sequencing instrument. Andrew: The sequencer is the heart of sequencing, but we want to look across the whole workflow and come up with a great solution. We want to make sure that if I'm a physician, what I'm interested in is, what is the sample and what is the result. And I want to make sure that, everything in between is as easy and as automated as possible. Rebecca: Roche is investing heavily in the target enrichment area. We're not only investing in improving our existing technologies, but we're investing in new technologies that are going to make everything easier, more efficient and get it to an answer as fast as possible to inform the patient care. New products coming will include amplification-based methods and we're looking at some new technologies that will allow you to do target enrichment directly from a biological specimen such as a liquid biopsy that will get you to your result faster. Tom: We are doing partnerships in the area of sample prep where there are disruptive methods that let you maybe take a blood sample from a person, do some analysis and have the DNA sample that's ready to go onto a sequencer in a very fast, easy workflow. For example, at Vitro Molecular, a small multi-specialty anatomic pathology laboratory company that sells interesting sample prep that may allow us to skip the DNA sample prep process itself and take samples directly from blood, for example, and put that directly into a sequencing box at the end of the workflow. Rebecca: Another area that we're trying to expand the portfolio in is working with precious or very difficult samples. So that might be highly fragmented DNA, FFPE samples or very low amounts where you have a very rare piece of sample that you need to get DNA from. This allows you to work with sample sets that you haven't had access to before, which allows you to get more information out of the samples and get more knowledge about the disease type. It also allows you to non-invasively gather samples from patients, which makes the whole experience much easier and perhaps can improve their care because you can actually sample them more often during their diagnosis and treatment. We're expanding the target enrichment portfolio. We have our existing sequence capture products, which have been very successful in the market over the last few years. We have just launched SeqCap Epi for expanding that into the epigenomics market and we have also launched SeqCap RNA for looking at RNA sequencing and making that more cost effective and informative for the customers. I think Roche has a real eye towards diagnostic sequencing and very a clear focus and path to get there. We are very interested in the research and translational markets as well, but the clear focus is getting to a diagnostic product that will benefit patients. I think the patient's behind everything we're doing, people working in the medical technology field, that's the end point we're looking for is to help the patient and I think Roche sequencing will play a big role in understanding disease and understanding an individual patient's response to disease. yt:video:eSBqVWQ65sk eSBqVWQ65sk UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-06-11T11:01:48+00:00 2016-12-12T14:25:15+00:00 Sequencing Innovation from Sample In to Result Out | Roche Sequencing Innovation Through Collaboration - Learn more from our leaders about how we’re partnering with experts around the world to develop the next breakthrough technologies in sequencing. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Tom: My role is basically to be thinking long-term about which technologies and which applications we need to bring in-house to make sure that we are competitive in the marketplace for many years to come. Andrew: We’re looking at the next generation of technologies that can really lead to breakthroughs in sequencing. Tom: So we’re using an open innovation model to seek out what we think are the best, most disruptive technologies. There are so many researchers out there at so many universities and small companies that are really taking potentially huge risks but have huge rewards that could come from those risks. Andrew: We know that there are great ideas all over the world and we want to be partners with the people who’ve got the best ideas so that together that we can bring those ideas through development and bring them ultimately to the market, to the medical community, and to patients. Beth: We’re looking for partners that share Roche's philosophy of taking customer needs and placing them at the forefront of product development decisions. We’re also looking for partners that have truly innovative new technologies. Tom: We are searching for partners in two key areas. The first of which is new and disruptive sequencing technologies, technologies that can improve the sample prep, the sequencing box itself, and the way that we can do data analysis. The second aspect of our partners that we’re looking for are partners that have made inroads into certain application areas, such as oncology or prenatal testing. Andrew: When we think about sequencing, we can really focus on the sequencer, but I think for Roche we’re really looking at what does this mean from the sample in to the result out and everything in between. Tom: For example, we are seeking partnerships in very advanced sequencing technology, such as graphene, for example, or other nanopore-based technologies, which can be very powerful and disruptive. Andrew: In Roche, we're not bound to today's sequencing technology. We really want to make sure that we are open to looking at the next opportunities in sequencing, the new technologies coming through and we want to work with the people who have those technologies to bring them forward. This isn’t about having the one-size-fits-all approach to deal making. It’s saying, “How can we together with our partners bring technology forward and make the technology a success?” We need to build relationships over time. Collaborations are not finished on the day that the deal is signed. Actually in business development we can focus a lot on getting the deal done, but that’s only the beginning. In many ways, the real work begins once the deal is signed. The future for Roche sequencing, I think, is really bright and really exciting. We’ve made some important investments in sequencing technologies. I think that we’re going to see this continue in the next few years because we really need to build the whole portfolio. Beth: We do intend to continue to build upon these opportunities and invest further in strengthening our technology, building out our menu and our community of experts. Andrew: I think that’s something that we pride ourselves on at Roche is having a very open view about what sort of technology and what sort of partnership we can be entering into. We want to be networked with the whole of the scientific community because our mission is to bring the best sequencing technologies to patients. yt:video:akDauYIZIqo akDauYIZIqo UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-06-11T10:58:38+00:00 2017-02-27T08:18:04+00:00 Deep Sequencing Expertise for Patient Care | Roche Sequencing The Commitment of Roche Sequencing – Our leadership team discusses how we’re building our sequencing pipeline to support the future of clinical diagnostics. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Dan: Roche has been a pioneer in sequencing for over 10 years and I think this is one of the well-kept secrets about Roche. Andrew: I think when we think about the sequencing unit itself, we're actually a small but rapidly growing unit. We have the energy and excitement of a startup company, but we also have the support a large company that's allowing us to make some significant investments at the moment. Dan: Our vision is "Roche Sequencing: changing science, changing lives." And to me, those few words speak volumes of what we do. We are the only sequencing company that has deep expertise in clinical diagnostics. We're the number one clinical diagnostics company in the world. And we're the only clinical diagnostics company with deep sequencing expertise. And so we think we have a tremendous advantage from our heritage and from our experience in clinical diagnostics to really bring sequencing into the clinic and to really make a difference in patients' lives. Andrew: In Roche, we're not bound to today's sequencing technology. We really want to make sure that we are open to looking at the next opportunities in sequencing, the new technologies coming through, and we want to work with the people who have those technologies to bring them forward. Dan: Right now, we're on a mission to build our pipeline. To build our pipeline of products so that we would have truly a differentiated sequencing system and at the same time we're trying to build our pipeline of people. Lin: We're coming from different functions of different areas, coming with different expertise from Roche Diagnostics and we get together and then we talk about our strategies and we really want to define our own pathways to bring this clinical sequencing into the routine lab as fast as we can. Dan: I love the people on the team. I was fortunate enough to be able to hand-pick our leadership team and so we have a real camaraderie together and it's just fun working with the organization. Tom: What sequencing is doing now is sort of the epitome of doing now what patients need next. Sequencing will provide you basically the operating system on which lots of therapies and therapeutic choices are going to be made. Dan: You can see every day and you can sense the excitement in the scientific and clinical community about the potential for sequencing. If you think about being able to have a simple blood test in the future to detect cancer, this would be a revolution for the diagnosis and the treatment of cancer. Tom: It's very gratifying to really think about the fact that we could really improve human health care in ways that just a few years ago we could dream of. I love this field. I have the best job in the world right now. yt:video:W5n3IRHlURQ W5n3IRHlURQ UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-06-06T12:15:48+00:00 2017-04-14T06:54:11+00:00 Preventing Pandemic Outbreaks by Unknown Pathogens | Roche Sequencing A documentary discussing the actual possibility of a world wide pandemic similar to the one depicted in the film Contagion, and our ability to deal with such an outbreak. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Host: With the release of the film "Contagion," an opportunity exists for the scientific community to engage in the public discussion regarding the real world possibility of a pandemic outbreak caused by an unknown pathogen. We've interviewed five highly regarded virologists and microbiologists to discuss the current state of understanding and preparedness and the scientific methodologies they employ for just such an outbreak. Dr Lipkin, MD: A couple of years ago, I had a meeting with Scott Burns and Laurie Garrett to talk about a movie that would be concerned with an outbreak of infectious disease. Soderbergh and Burns, the director and the screenwriter, had been on another film where someone had sneezed. And this was the catalyst for talking about what might happen if somebody became ill on set and this expanded and became a major outbreak. So we met to talk about various scenarios about how an outbreak might emerge and how it might evolve and how it could be addressed and what are some of the issues that might come up, political, economics, scientific, logistical and so forth. A number of outbreak stories have been covered in film. One of them was called "Outbreak." There were some others as well. "I am Legend," you've even got "Invasion of the Body Snatchers," if you want to think about that as an infectious disease. But this is different and this is why we became involved in this project because it was a commitment on the part of the director and the screenwriter and the producers to make something that would be viable, would be plausible. It would describe the various aspects of emergence of an infectious disease and would both entertain as well as educate. And I used the term "education" in a very broad sense. It would actually highlight some of the things that we needed to address, weaknesses in our current public health system. Dr. Skowronski.: The Tahoe Research Initiative is a small business that is pushing diagnostics and discovery technology out internationally in order to support United States government priorities and goals and surveillance and detection of infectious disease. We've been in operation about a year and a half. Our major focus right now is that we're working in the Philippines. We have two partners out there, Saint Luke's Medical Center in Quezon City at the Research in Biotechnology Division and at the University of the Philippines Los Baños, where the Veterinary School is. And so what we're doing is we're putting some technology in the field. Those are handheld thermocyclers, microarray technology and, of course, the keystone of this project is the 454 GS Junior that we have at Saint Luke's Medical Center. It's an interesting program because in the Philippines they are Anti-Biopiracy Laws where you can't export either the microbes themselves or any of their derivatives, such as proteins or nucleic acids. So if you're going to do the kinds of work we want to do, defining the local microbial biodiversity, doing sequencing, doing detection work, you have to do it in-country. You can't farm it out to other parts of Asia or back to the United States. So right now what we're doing is we have the sequencer running. We have a couple of projects right now where we're working on two separate outbreaks, one of Cholera in the island of Palauan where we have environmental samples as well as a couple of clinical examples and we're trying to match what we suspect is the source of the Cholera with the exact strain of the bug that's coming out of the patients. So that's the kind of work that we're doing. We're trying to enable. We talk about pushing the technology to the problem and not trying to bring the problem to the technology. And so the GS Junior is what we're using right now to do the very nitty-gritty, fine detail discovery of what bugs are making people sick, where they're at in the environment and how they compare with other strains that we know from other sequencing projects around the world. yt:video:SvKnIZbvcTc SvKnIZbvcTc UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-06-04T21:42:15+00:00 2016-01-19T19:46:55+00:00 SeqCap Hybridgized Approach from Sample to Sequencing | Roche Sequencing SeqCap Target Enrichment: Enjoy Improved User Experience, Get Answers Faster - Across SeqCap probe design and workflow. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - Announcer: Roche NimbleGen, part of Roche sequencing, develops target enrichment solutions for targeted next-generation sequencing. These technologies help the life sciences community efficiently target DNA sequences of interest in the genome through either focus exomes or custom design gene panels. One of our innovations is best in class hybridization base sequence capture technology. Customers around the world are using our SeqCap line of target enrichment products for a wide variety of applications. To improve their user experience and efficiency, we implemented a workflow enhancement that greatly shortens the time it takes to prepare sequencing-ready DNA. Dan: The latest update to our target enrichment workflow allows researchers to perform the whole process from sample to sequencing in a much, much faster time so instead of several days to hybridized approach to your samples, now you can do that overnight and run more experiments in a week. In addition to that, we’ve validated the use of lower amounts of DNA input into the process, which provides the researcher greater flexibility to design experiments the way they have to. A lot of our customers have limited DNA for a sample. You put amounts available to them and this provides them the flexibility they need. The improvements we have introduced lately have reduced the time and cost it takes to do a targeted enrichment experiment considerably, which allows customers to process more samples faster and achieve results more quickly. yt:video:tgSgZthXBvo tgSgZthXBvo UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-06-04T21:39:49+00:00 2016-04-21T23:54:48+00:00 Intelligent & Custom Sequence Capture Tutorial | NimbleGen | Roche Sequencing NimbleDesign is a free online tool which enables you to quickly and easily design probes to SeqCap EZ and SeqCap RNA Target Enrichment Systems. Learn more about creating your custom design. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - This tutorial will provide a brief overview of NimbleDesign features and functions. We will walk you through the steps of creating a custom Sequence Capture design using this powerful web-based tool. NimbleDesign is an intelligent probe design tool for SeqCap target enrichment products. It capitalizes on years of design experience, which has resulted in our Optimized Probe Database and Design Process for proven probe selection. You will discover how these unique advantages help you create your optimal design. New NimbleDesign features include an intuitive user interface from start to finish that allows you to shorten your turnaround time for custom designs. We have added the flexibility to input genomic coordinates, gene names, or other commonly used gene identifiers to maximize your convenience when entering desired regions of interest. NimbleDesign now includes the ability to design to human or mouse genomes and for DNA or RNA applications. This design tool is set up with 24/7 access for easy creation and approval of the custom human or mouse target enrichment designs within the Roche NimbleGen website. The NimbleDesign process is a step-by-step workflow designed to guide you through the development of your custom SeqCap enrichment design. The updated NimbleDesign now has a Document Center, which contains documents pertaining to the web application, as well as important notes regarding updates that have been made. The Messages and Recent Design section provides information regarding designs that have been created using NimbleDesign. To begin creation of a new design, click on Create New Design button. In the Design tab, you will input basic information and select organism, genome build, and application for your desired design. In the Customer Design Identifier, type in a name for your design. This name will be included in the final design name. Next, select the organism, followed by genomic build and application. In this demo, we will be choosing homo sapiens, HG19 genomic build, and RNA application. Use the Description field to add more information on this design. At any time during the process, you can click on the Summary to see your selections. Click Next to go to the Target Regions tab. In the Target Regions tab, NimbleDesign provides you with three different selection methods for defining your genomic regions. By default, manual entry is selected. Click Select Input Type to choose from greater than 20 options for manual entry. The most common input type is to enter the genomic coordinates, which includes chromosome, start, and stop for your desired regions of interest. Click on Add Regions to upload it. The second method is to upload a file. Click Choose File or Browse, depending on your internet browser, to browse through the tab to limited files containing your coordinates, gene names, or other commonly used identifiers. Click Next or Open to upload it. Once the file is successfully uploaded, click Add Regions. The third method is to search genes using the Enter a Gene Identifier box. Type in a gene name in the box, which automatically pulls up associated genes found in the database. Choose the appropriate gene. Click Add Features to List to upload it. Once all regions have been added, click Next to move to the Parameters section. NimbleDesign has two parameters for selecting close matches in the genome. Preferred Close Matches default value is three. Maximum Close Matches default value is 20. Type a new number into the Value field or use the slider to modify. The default values are based on review of optimal coverage in a variety of designs. By definition, the Preferred Close Matches is the limit applied to initial selection of probes from the database. yt:video:fUk1_Lb6WUA fUk1_Lb6WUA UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-04-01T21:35:06+00:00 2016-01-19T22:12:40+00:00 Innovation for Changing Lives with Personalized Care | Roche Sequencing Roche Sequencing is Changing Science and Changing Lives. What does Roche Sequencing do that enables us to do so? Watch this video to know. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing yt:video:LCTGhx3d2a0 LCTGhx3d2a0 UCyYzBOE7oC1GqV2mYwjLhVw Roche Sequencing https://www.youtube.com/channel/UCyYzBOE7oC1GqV2mYwjLhVw 2015-02-19T23:18:02+00:00 2016-01-26T19:00:19+00:00 Quantitative Accuracy with In-Depth Transcriptome Research | Roche Sequencing Dr. Mercer and Dr. Tan will present a novel targeted RNA sequencing method and elaborate on experiences with targeted RNA sequencing. ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - - ► Learn more: http://sequencing.roche.com/ ► NimbleGen SeqCap: http://sequencing.roche.com/products/nimblegen-seqcap-target-enrichment.html ► 454 Sequencing: http://sequencing.roche.com/products/454-sequencing-systems.html ► LET'S CONNECT .: Contact Us: http://sequencing.roche.com/contact-us.html .: Twitter: https://twitter.com/RocheSequencing .: LinkedIn: https://www.linkedin.com/company/roche-sequencing - - - - Transcript - - - -Essentially, I want to start off with talking about this technology we've been developing of targeted RNA sequencing. I want to start off with, I guess, a bit of a background. The problem is when you look in the cell, the human transcriptome, most transcriptomes are hugely unequal. There's a huge gap, a huge distance between the most-abundant expressed gene and the lowest-abundant expressed gene. You can see here from these calculations, probably about the top sort of 1% of genes - these are genes like GAPDH, tubulin, actin - they comprise about 40% of the RNA molecules within a cell and when you look at the other end of the spectrum, the lower half of the least abundant genes expressed within the cell actually contribute only 1% of the RNA molecules. Now, this actually presents an almost insurmountable problem for technology such as RNA sequencing because it means that, within a library, you're basically sequencing the same 1% of genes over and over again while those low-abundance genes which might be of interest to you essentially attract really sad sequencing coverage. We actually estimate, and this is probably a lower limit, that it will require about two terabytes of sequencing to start approaching one-fold coverage of the human transcriptome. This wide dynamic range presents a huge challenge for RNA sequencing. Like I said, my original research interest is in things like long-noncoding RNAs which are quite lowly expressed. So to try and address this problem, we developed this technique which we took that targeted RNA sequencing or capture sequence. It's not rocket surgery. It's essentially a kind of hack job we performed on the DNA exome capture kits. What it essentially involves is the design of oligonucleotide probes that are complementary to our genes of interest or to our genomic regions of interest. We use those probes to capture the RNAs and wash away all the other unwanted RNAs. Those captured RNAs that we're left with, we can then focus our sequencing on them. So, this essentially allows a huge magnification of sequencing coverage and it basically allows, often, quite an exquisite sensitivity. One of the concerns which invariably gets raised when we present this work is whether the actual technique is quantitative or does that initial hybridization, that washing step, obscure any underlying measurements of gene expression. Now, to address this concern, we actually performed a couple of sets of experiments where we spiked in RNA standards across a range of concentrations. Then what we did is we essentially measured the abundance of these RNA spike-ins following capture sequencing and also as a sort of comparison, we also just sequence straight with RNA sequencing, the same library. Now, you can see here, this is a plot, a comparison of the known abundance of these spikes-ins. For the capture sequencing, the first thing you will notice particularly here, up in the top corner, is the fact that the spike-ins actually tail off.