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Thursday, November 14, 2019

Webinar Summary: Need accurate isoform-level characterization? Iso-Seq is the answer

Traditional RNA-Seq is done by fragmenting cDNA, and then sequencing the fragmented reads with paired-end sequencing. The problem comes when trying to identify the full-length isoform during assembly. This is computationally challenging, and sometimes intractable.  Iso-Seq is a method of full-length transcript sequencing that eliminates the need for assembly The solution? Long-read isoform sequencing, according to PacBio Principal Scientist Elizabeth Tseng and PacBio user Gloria Sheynkman, a research fellow at Dana-Farber Cancer Institute. The two recently participated in a webinar, sharing their experiences using PacBio’s Iso-Seq method. Tseng started by explaining the method and some of its applications.  “In contrast…

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Wednesday, September 4, 2019

Webinar: No-Amp Targeted Sequencing Yields Base-Level Resolution of Hard-to-Amplify Regions

Until recently, enriching for certain regions of the genome has been virtually impossible. Repeat expansions, extreme GC regions, and other genomic elements are very difficult to target using traditional enrichment methods. That’s why our new “No-Amp” targeted sequencing application  — a streamlined, amplification-free approach based on the CRISPR/Cas9 system — is a valuable addition to the SMRT Sequencing toolbox. No-Amp targeted sequencing combines the CRISPR/Cas9 enrichment method with SMRT Sequencing. Pacific Biosciences does not sell a kit for carrying out the overall No-Amp Targeted Sequencing method. Use of these methods may require rights to third-party owned intellectual property. The method…

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Monday, April 22, 2019

Rapid Response: A Role for SMRT Sequencing in Infectious Disease Control

Researchers rely on PacBio long-reads for richness and resolution when probing genomes, and these same attributes are becoming increasingly relevant in clinical settings. One field where the technology shows particular promise is infectious disease control. When a disease outbreak hits a hospital, it is crucial that the pathogen and its transmission path are rapidly and accurately identified. As PacBio researchers demonstrated in CLP magazine, current microbial detection techniques that rely solely on short-read DNA sequences can misidentify pathogens, resulting in incorrect prognosis and misinformed treatment decisions. SMRT Sequencing, on the other hand, can paint a complete picture of entire genomes,…

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Thursday, April 11, 2019

Microbial Sequencing Used to Unravel Mysteries of Aquatic Environments

Dr. Cody Sheik While some microbiologists can study their organisms of interest by growing them in cultures in the lab, many don’t have that luxury. Most microbes and algae cannot be cultured, which is why environmental microbiologist Cody Sheik relies so heavily on DNA sequencing and why he is especially excited to use the PacBio platform for metagenomic studies using both targeted and shotgun sequencing approaches. Sheik’s first exposure to PacBio sequencing came shortly after joining the faculty at the University of Minnesota at Duluth, where the sulfate-reducing bacterium Desulfovibrio desulfuricans strain G11 was being used as a model organism.…

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Monday, April 8, 2019

Complete Genomes Within Reach: Multiplexing Enables Efficient Microbial Sequencing

Research interest in the human microbiome and the roles our bacterial, viral, and single-cell eukaryote co-inhabitants play in health, nutrition, immunity, and disease has exploded. Yet accurately measuring the composition of these microbial communities remains complex. Sequence-based approaches allow the genetic material from complete collections of microbes to be analyzed without the need to cultivate the microorganisms. But each step in the process of collecting, extracting, preparing, sequencing and analyzing the DNA and data introduces its own set of errors and biases. At the Innovation Lab of the University of Minnesota Genomics Center, research scientist Ben Auch and his colleagues…

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Tuesday, September 4, 2018

Webinar Summary: Developing Benchmark Sets for Structural Variants

Justin Zook A map of every individual’s genome will soon be possible, but how will we know if it is correct? Benchmarks are needed in order to check the performance of sequencing, and any genomes used for such a purpose should be comprehensive and well characterized. Enter the Genome in a Bottle Project (GIAB), a consortium of geneticists and bioinformaticians committed to the creation and sharing of high-quality reference genomes. Unlike other initiatives, such as the 1000 Genomes Project, that are seeking to sequence many representatives of different populations, GIAB is interested in sequencing just a few individuals, but deeply…

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Thursday, June 14, 2018

For Reference-Grade Human Genome Assemblies, SMRT Sequencing Yields Optimal Results

SMRT Sequencing is a go-to technology for generating reference-grade human genome assemblies, according to speakers in a recent webinar. In their presentations, Tina Graves-Lindsay from Washington University and Adam Ameur from Uppsala University spoke about diploid assemblies, discovering novel sequence, improving diversity of the current human reference genome, and much more. Finally, our own Paul Peluso gave a presentation that included the technology roadmap showing the next several upgrades for the Sequel System. Graves-Lindsay began with efforts from the Genome Reference Consortium to “represent the full range of genetic diversity in humans,” a task requiring the generation of many population-specific references.…

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Tuesday, November 15, 2016

‘Reveal Hidden Genetic Variation’
On-Demand Webinar Now Available

We recently co-sponsored a webinar with Springer Nature, and if you missed it live, you can now register to watch the recording. Moderated by Nature Publishing Group’s Jayshan Carpen, the webinar is entitled “Reveal hidden genetic variation by combining long-read target capture with SMRT Sequencing” and features several terrific speakers. We’d like to thank Tetsuo Ashizawa from Houston Methodist Research Institute, Melissa Laird Smith from the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai, and our own Meredith Ashby for taking the time to present fascinating data and answer audience questions. The webinar kicks off with a talk…

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Wednesday, April 27, 2016

Upcoming Webinars on Biomedical Research, Data Analysis, and Structural Variation

We’ve got several educational webinars coming up, and we hope you can join us! Our first event will be hosted by Front Line Genomics on April 28 (4:00 p.m. BST / 11:00 a.m. EST / 8:00 a.m. PST). “Applying PacBio Long-Read Sequencing for Human Biomedical Research” will include Adam Ameur of the National Genomics Infrastructure in Sweden; Giancarlo Russo from the Functional Genomics Center Zurich; and our CSO Jonas Korlach. Each participant will offer a brief presentation, with audience Q&A at the end. We’ve also teamed up with DNAnexus to offer two webinars on best practices for SMRT Sequencing data…

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Tuesday, September 8, 2015

Webinar: Long Fragment Capture for SMRT Sequencing

Roche recently posted this recording of a webinar walking through long fragment capture with SMRT® Sequencing. “Long Genomic DNA Fragment Capture and SMRT Sequencing Enables Accurate Phasing of Cancer and HLA Loci” is a great backgrounder for scientists interested in using the Roche NimbleGen SeqCap EZ System for target enrichment prior to sequencing on the PacBio® system. The webinar features Denise Raterman from Roche NimbleGen and our own bioinformatics expert Lawrence Hon. Raterman provides a detailed review of the SeqCap EZ workflow, pointing out the specific steps that differ for SMRT Sequencing. The method can be used to capture up…

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Tuesday, July 21, 2015

Webinar: Anthony Nolan’s Neema Mayor Reports on HLA Typing with Long Reads

Following the recent paper about HLA typing from scientists at Anthony Nolan Research Institute, we thought readers might enjoy this webinar from Neema Mayor, a scientist at the institute and lead author on the paper. The video offers a great foundation on HLA typing for beginners as well as more detailed information about typing technologies for advanced users. (Learn more about the institute’s plans for HLA typing in this GenomeWeb article.) Named for Anthony Nolan, a young boy whose need for a bone marrow transplant spurred his mother to start the world’s first registry of potential donors, the institute focuses…

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Wednesday, May 6, 2015

Tutorial on the Iso-Seq Method: Applications, Protocol, and Experimental Design

If you missed our recent webinar on isoform sequencing with the PacBio® platform, we’ve made the full recording available for on-demand access. “Iso-Seq™ Method: Sample Prep and Experimental Design for Full-Length cDNA Sequencing” offers an overview of the application, along with specific sample prep tips, factors to consider when designing an experiment, and suggestions about what kinds of projects can take advantage of this method. Hosted by our own Tyson Clark, the webinar begins with a look at why it’s important to capture full-length transcripts. There are known human genes that have very different functions depending on which splice variant…

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Friday, February 27, 2015

AGBT 2015: PacBio Workshop Review & Recording

Our AGBT workshop attracted more than 500 attendees thanks to the high-profile speakers who shared their perspectives on human genomic research. Because of the exclusivity of AGBT, we decided to live-stream our workshop to reach the broader scientific community. Thanks to the the hundreds of people who tuned in to our live webcast from afar! Here are some highlights from the presentations and the recording of the workshop is at the bottom of this post. Our CEO, Mike Hunkapiller, started the session with a reflection on the 15-year anniversary of the announcements of the first human genomes, noting these efforts…

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Tuesday, February 24, 2015

AGBT 2015: Seeing the Genome in a New Light (Sunshine?)

Like many others, we’re looking forward to an exciting week of science and sun at the 16th annual Advances in Genome Biology and Technology (AGBT) conference! We’re hosting a lunch workshop on Friday, February 27, in the Palms Ballroom from 12:00 pm to 2:00 pm EST. We hope you can join us onsite (please reserve your seat) and even if you’re not at the conference, you can watch the live stream. Here’s the agenda: Towards Comprehensive Genomics – Past, Present and Future The Human Genome: From One to One Million J. Craig Venter, Human Longevity Inc. Is Perfect Assembly Possible?…

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Thursday, January 29, 2015

Register Now: Isoform Sequencing Webinars Offer Tips on Method and Analysis

If full-length transcript information would be useful for your research, please join us for two upcoming webinars. Our scientists will offer tips for how to optimize the Iso-Seq™ method with the PacBio® System to meet your research goals. Our first webinar, Iso-Seq™ Method: Sample Prep and Experimental Design for Full-Length cDNA Sequencing,” will be presented by Tyson Clark, PacBio’s senior manager for next-generation applications and technologies. The talk will cover recent Iso-Seq template preparation protocol updates for creating full-length cDNAs, why full-length transcript sequence matters, and experimental design considerations. Sign up now at your preferred time: the webinar will take…

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