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Friday, March 14, 2014

AGBT 2014 Presentation Videos: SMRT Sequencing at CSHL, Uppsala U., and Baylor College of Medicine

There were several excellent talks showcasing SMRT® Sequencing data at the annual Advances in Genome Biology and Technology conference. If you didn’t have the opportunity to see them in person, you can watch the recordings: From Cold Spring Harbor Laboratory, Dick McCombie described the need for de novo sequencing, which preserves structural information that can be missed with resequencing. Organisms presented include yeast, Arabidopsis, and rice. McCombie notes that in many cases, full chromosomes are assembled into single contigs with long-read sequencing. He also presented the longest read seen at AGBT: more than 54 Kb. Watch video: A near perfect…

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Wednesday, January 29, 2014

At Plant & Animal Genome Workshop, Users Showcase Projects Enabled by SMRT Sequencing

Earlier this month, we hosted a workshop at the International Plant & Animal Genome (PAG) conference in San Diego entitled “A SMRT® Sequencing Approach to Reference Genomes, Annotation, and Haplotyping.” PacBio users presented data on various projects that have benefited from long-read sequence data, including several that had previously been attempted with short-read technologies without success. We were delighted to see reports on newer features of SMRT Sequencing, including full-length isoforms, automated haplotyping, and more. Here’s a recap, as well as links to video recordings of the presentations: Chongyuan Luo, a scientist from Joe Ecker’s lab at the Salk Institute…

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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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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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Monday, November 4, 2013

Comparative Transcriptome Analysis: Insights from a Single SMRT Cell

In a new paper published in the journal Gene, scientists from Rutgers University and King’s College London report the use of a single SMRT® Cell to sequence and assemble more than 400 wheat-storage protein transcripts from 10 strains of the crop. In “PacBio sequencing of gene families — A case study with wheat gluten genes,” authors Wei Zhang, Paul Ciclitira, and Joachim Messing note that traditional studies of these cDNA sequences are so costly and labor-intensive that they have not allowed for intensive study of “the variation of each orthologous gene copy among cultivars.” That kind of study for complex…

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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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Monday, October 7, 2013

Characterizing Structural Variation in the Human Genome: ASHG 2013 Workshop and Presentations

We are excited to participate in the annual American Society of Human Genetics meeting again this year on October 22-26 in Boston, MA. With so many new PacBio® technology advances since last year, we wanted to give you a preview of how users are applying SMRT® Sequencing to better elucidate a variety of complex regions in the human genome. On Thursday, October 24, we’ll be hosting a luncheon workshop from 12:30 p.m. to 2:00 p.m. entitled ‘Characterizing Structural Variation in the Human Genome Using Long-Read SMRT Sequencing.’ Join us in room 152 of the convention center (BCEC) to hear from…

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Thursday, October 3, 2013

New Chemistry for PacBio RS II Provides Average 8.5 kb Read Lengths for Complex Genome Studies

Our R&D team has been focusing on chemistry improvements for the PacBio® RS II sequencer and today we are pleased to announce our newest reagent combination, the P5 DNA polymerase with C3 chemistry (P5-C3). Together, they extend our industry-leading sequencing read lengths to an average of approximately 8.5 kb, with the longest reads exceeding 30,000 bases. The new chemistry includes photo-protected dyes to shield the P5 polymerase from laser-induced damage. With this new protection, the sequencing polymerase is able to generate much longer reads from a single DNA-template molecule.  Our previously released chemistry, P4-C2, has been successfully used by many…

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Wednesday, August 21, 2013

New DNA Polymerase P4 Delivers Higher-Quality Assemblies Using Fewer SMRT Cells

Pacific Biosciences is pleased to announce the introduction of DNA/Polymerase Binding Kit P4. This P4 enzyme has average read lengths of >4,300 bp when paired with the C2 sequencing chemistry and >5,000 bp when paired with the XL chemistry. The enzyme’s accuracy is similar to C2, reaching QV50 between 30X and 40X coverage. The resulting P4 attributes will provide you with higher-quality assemblies using fewer SMRT® Cells, and with improved variant calling. The P4 binding kit is compatible with PacBio® RS and PacBio RS II Systems with the latest version of Instrument Control Software (v1.3.3.1 and v2.0.1 respectively), and with…

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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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Wednesday, July 3, 2013

Genome Biology Commentary Discusses the Advantages of SMRT Sequencing

A new commentary in Genome Biology from highly respected scientific authors, including a Nobel Prize winner, highlights the benefits of Single Molecule, Real-Time (SMRT®) Sequencing.  The commentary, entitled “The advantages of SMRT sequencing,” comes from Richard Roberts at New England BioLabs, Mauricio Carneiro at the Broad Institute, and Michael Schatz at Cold Spring Harbor Laboratory. The authors begin with the premise that the PacBio® RS is sometimes overlooked as a next-generation sequencing option, even though it serves as “ideal approach to the complete sequencing of small genomes.” The commentary focuses on three advantages of SMRT Sequencing: extraordinarily long reads, methylation…

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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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Monday, April 29, 2013

PNAS: Copy Number Analysis in Maize Sheds Light on Tolerance for Acidic Soil

A new study of maize sheds light on the importance of copy-number variation in genes related to stress tolerance with implications to boost crop yield in suboptimal soil environments. A paper published in PNAS, “Aluminum tolerance in maize is associated with higher MATE1 gene copy number,” was published by senior author Leon Kochian and a team of scientists at the US Department of Agriculture, Cold Spring Harbor Laboratory, University of Arizona, and several other institutions. The authors report on the discovery of aluminum stress-tolerance modulation through changing copy-number variation of a rare allele found in maize that has survived in…

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Thursday, April 18, 2013

Guest Blog: Michael Schatz shares his perspective on the new PacBio RS II

Michael Schatz, Ph.D. Assistant Professor of Quantitative Biology at Cold Spring Harbor Laboratory, shares some thoughts about his experience with the PacBio RS and his hopes for future work with the new PacBio RS II: “For several important genomic analysis, including de novo genome assembly, mapping structural variations, and discovering alternative splicing, we are principally limited by the read lengths of sequencing technology available. When it comes to assembling a genome, for example, read length is critically important for spanning repetitive sequences, as reads shorter than those repeats fundamentally just don’t have enough information for the assembler to determine the…

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Thursday, March 7, 2013

From In Sequence: Spotlight on PacBio Customers’ Data at AGBT 2013

A recent article from In Sequence highlights several of our customers and the great projects they’ve been working on with single molecule, real-time (SMRT®) sequencing. If you’re not a subscriber to the newsletter, you can access the story here. In the article, GenomeWeb’s Monica Heger reports on several PacBio customer talks from the Advances in Genome Biology & Technology meeting, including presentations from Eric Antoniou and Mike Schatz at Cold Spring Harbor, and Eric Schadt at Mt. Sinai. The article also reports on a talk given by our CSO, Jonas Korlach. According to the article, “Pacific Biosciences and several users recently…

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