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Tuesday, January 21, 2014

Genome Research Paper: Resolve Complex Genomic Regions for a ‘Fraction of the Cost’ With SMRT Sequencing

A new Genome Research paper describes the application of Single Molecule, Real-Time (SMRT®) Sequencing to resolve repeat-heavy genomic regions in important reference genomes such as human and chimpanzee. In the process, the authors drew some important conclusions about cost, pooling, and coverage requirements for this type of work. “Reconstructing complex regions of genomes using long-read sequencing technology” comes from lead author John Huddleston and senior author Evan Eichler at the University of Washington, along with collaborators at Washington University, the University of Bari, Bilkent University, and Pacific Biosciences. In the paper, Eichler and his collaborators note the steep cost of…

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Thursday, January 16, 2014

Looking Ahead: The 2014 PacBio Technology Roadmap

By Jonas Korlach, Chief Scientific Officer 2013 was an eventful and exciting year for PacBio. As I described in the 2013 roadmap post a year ago, we have applied numerous improvements to SMRT® Sequencing, resulting in longer read lengths, greater sequencing throughput, new and improved data-analysis methods, and more efficient workflows. We are very pleased that these advances resulted in so many publications, conference presentations, and social media contributions, with the number of peer-reviewed scientific publications from the scientific community now exceeding 100. On behalf of all of us at Pacific Biosciences, I would like to express my heartfelt gratitude…

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Monday, January 13, 2014

Data Release: Preliminary de novo Haploid and Diploid Assemblies of Drosophila melanogaster

Model organisms such as yeast, Arabidopsis and Drosophila have been essential to progress in genetic and biomedical research for more than 100 years.  Model organisms are the best, fastest, most effective way to advance science especially when human experimentation may not be feasible. Numerous biological principles have been elucidated using model organisms, including Nobel-prize winning discoveries by Thomas Hunt Morgan that genes are carried on chromosomes; by Hermann Muller for the discovery that X-ray irradiation causes mutations; and by Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus for their discoveries revealing the genetic control of early embryonic development – all…

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Thursday, November 7, 2013

Event Recap: Fall User Group Meeting Presentations & Review

In September we were excited to have 100+ customers gather in Palo Alto, Calif., to discuss their use of Single Molecule, Real-Time (SMRT®) Sequencing and hear about what’s next for the PacBio® RS II. Many thanks to all the scientists who attended and shared their experiences. For anyone who couldn’t make it, we’ve included some highlights from each talk below (and links to full presentations when possible): Chongyuan Luo from the Ecker lab at the Salk Institute for Biological Studies spoke about studying the genome and epigenome of several Arabidopsis thaliana strains using SMRT Sequencing. Luo noted that Arabidopsis is…

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Wednesday, November 6, 2013

At Institute for Genome Sciences, Long Reads Offer New Path to Finished Genomes

The Genomics Resource Center (GRC) at the Institute for Genome Sciences (IGS) has a scientific pedigree and a sample-to-interpretation service commitment that place it in a league of its own. The team operates under a simple mantra: ‘If it can be sequenced, we can do it.’ Both GRC and IGS were founded in 2007 when a high-powered team of investigators formerly at The Institute for Genomic Research (TIGR), led by Claire Fraser, joined the University of Maryland School of Medicine. “The group of faculty and senior staff that came here to start the institute was heavily focused on infectious disease…

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Tuesday, October 22, 2013

Data Release: Long-Read Shotgun Sequencing of a Human Genome

In order to help evaluate the utility of long, unbiased sequence reads for characterizing structural variation in the human genome using our recently released P5-C3 scaffolding sequencing chemistry, we have collected 10x long-read, shotgun coverage of a human genome sample. The human genome harbors many structural variations, including variable number tandem repeats, deletions, insertions, inversions, and repetitive mobile elements, which are often difficult to resolve using short-read technologies. We hope this data set will be of value to the bioinformatic and scientific community studying various forms of structural variation across the human genome. To access the full data set, simply…

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Thursday, October 17, 2013

Stanford Team Finds Novel Transcripts Using Long-Read Isoform Sequencing

An advance online publication in Nature Biotechnology from Michael Snyder’s lab at Stanford University demonstrates the utility of long-read sequencing for assessing transcribed regions across the human genome. Long PacBio reads were able to completely cover full-length RNA molecules, characterizing genetic regions that have not been previously annotated. The paper, entitled “A single-molecule long-read survey of the human transcriptome,” reports the application of Single Molecule, Real-Time (SMRT®) Sequencing to studying RNA, comparing it to results from libraries sequenced with a 454® instrument. The scientists sequenced cDNA synthesized from pooled RNA gathered from 20 human organs and tissues in order to…

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Wednesday, October 9, 2013

Resolving Complex Regions in the Human Genome: SMRT Sequencing Fills Major Mucin Gap

Scientists from University of North Carolina at Chapel Hill, Duke University, and other institutions have teamed up to sequence an important region of the human genome that has until now proven impenetrable. In a paper entitled “Genome Reference and Sequence Variation in the Large Repetitive Central Exon of Human MUC5AC,” published in the American Journal of Respiratory Cell and Molecular Biology, corresponding authors Wanda O’Neal and Judith Voynow along with their collaborators describe the use of Single Molecule, Real-Time (SMRT®) Sequencing to characterize a complex mucin exon. MUC5AC, located on the P arm of chromosome 11, encodes one of the…

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Tuesday, August 27, 2013

Oklahoma Scientists Use SMRT Sequencing to Rescue Fungal Genome Assembly

Orpinomyces is found in cattle rumen. Scientists from Oklahoma State University and the University of Oklahoma teamed up with a sequencing service provider to study the genome of an anaerobic fungus found in the rumen of cows that may have implications for effective plant biomass degradation. What made this particular species so tricky to sequence were its extreme GC content — just 17 percent — and unusually high number of repeats. The study was reported in “The Genome of the Anaerobic Fungus Orpinomyces sp. Strain C1A Reveals the Unique Evolutionary History of a Remarkable Plant Biomass Degrader,” a paper published…

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Thursday, August 1, 2013

#SMRTSeq Tweet Chat: Users Weigh in on Current Applications and Future Outlook for PacBio Sequencing

Today offered something new for the PacBio® team: our SMRT® technology was the subject of a tweet chat hosted by Genome Biology. For one hour, editors at the journal along with two authors of a recent commentary article on SMRT Sequencing and additional guest panelists participated in a live discussion on Twitter about the PacBio platform. Thanks to scientists Mike Schatz, Mauricio Carneiro, Mario Caccamo, Jason Merkin, and Eric Johnson, as well as Genome Biology editors Clare Garvey and Naomi Attar, for managing the chat. You can check it out here. It was unclear how the Twitterati would manage a…

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Monday, July 29, 2013

As Cores Upgrade to PacBio RS II, Users Report Data and Progress

As PacBio customers are upgrading to the new PacBio® RS II System, some of our core lab users have already begun blogging about the improved results. At the University of Maryland’s Institute for Genome Sciences (IGS), for example, one blogger posted data comparing read length, read count, and throughput for the PacBio RS and PacBio RS II. The post reports a comparison of an 8 Kb Mycobacterium project run on the PacBio RS and again on the PacBio RS II, finding that with the upgrade, “we see an almost 3x increase in total yield [per SMRT Cell], while read lengths…

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Monday, July 22, 2013

Whole-Genome Microbial Epigenetics: ASM Workshop videos highlight emerging application of SMRT Sequencing

We recently participated in a workshop on whole-genome microbial epigenetics at the American Society for Microbiology annual meeting in Denver. Using SMRT® Sequencing, the three most common types of bacterial methylation can be studied at base resolution across an entire genome. An exceptional lineup of speakers shared their latest research and we’re pleased to be able to share video of the presentations. Our CSO Jonas Korlach opened the workshop with a brief introduction describing how SMRT Sequencing generates epigenetic information. His presentation was followed by Brian Anton, from New England BioLabs, who presented data on restriction-modification systems and orphan methylases…

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Wednesday, July 10, 2013

University of Oslo Scientists Use Long Reads for Unique Look at Cod Genome

Scientists at the University of Oslo’s Centre for Ecological and Evolutionary Synthesis (CEES) have used multi-kilobase sequence reads from the PacBio® RS sequencer to produce a dramatically improved genome assembly for the Atlantic cod.  In many ways the cod genome seemed like a puzzle that might never be fully solved, but the Single Molecule, Real-Time (SMRT®) Sequencing platform made significant inroads — and just in time, as the team of researchers working on cod recently received funding to resequence 1,000 more of them. Being able to base these new efforts on a reliable genome assembly will make future results far…

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Tuesday, June 18, 2013

Back from SFAF, and Eager for More Finished Genomes

Last month’s Sequencing, Finishing, Analysis in the Future  (SFAF) meeting in Santa Fe, New Mexico, hosted by Los Alamos National Laboratory, attracted terrific scientists and we really enjoyed hearing about their work as well as sharing our own technology advances. It was great to be at a meeting where genome finishing and analysis were key themes; it was an environment where our customers’ experience with HGAP and Quiver resonated, particularly around the automated finishing of microbial genomes. SFAF had a number of keynote speakers, including Mark Adams from the J. Craig Venter Institute, who spoke about antibiotic resistance in microbes.…

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Friday, June 14, 2013

Two Worlds of Genome Assemblers

by Jonas Korlach, Chief Scientific Officer Finished genomes were the focus of last month’s Sequencing, Finishing, Analysis in the Future (SFAF) meeting in Santa Fe, New Mexico. In addition to several presentations, including a talk by Adam Phillippy from the National Biodefense Analysis and Countermeasures Center that demonstrated the ability to generate high-quality, finished microbial genomes using just long-read PacBio data, several papers have appeared recently describing the same principle: the HGAP/Quiver Nature Methods paper, the FDA’s Salmonella Javiana outbreak genome publication, a blog entry by the University of Maryland using HGAP, and a preprint by Adam Phillippy and colleagues…

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