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Tuesday, June 6, 2017

At CROPS 2017, SMRT Sequencing Powers Reference Plant Genome Assemblies

This week the HudsonAlpha Institute for Biotechnology and the University of Georgia are co-hosting CROPS 2017, a meeting focused on genomic technologies and their use in crop improvement and breeding programs. The three-day event attracts over 200 attendees involved in research and breeding for a range of important crop species. PacBio was proud to be a sponsor of the conference. HudsonAlpha’s Jeremy Schmutz kicked off the meeting with an introductory talk about trends in plant genomics, expanded transcriptome resources, and the improved representation of all plant genomes with many new genome assemblies. Schmutz, who also works with the Joint Genome…

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Friday, June 2, 2017

In Texas, New View of Klebsiella Strain Diversity and Antibiotic Resistance

A sweeping new report on Klebsiella pneumoniae sequence data from scientists at the Houston Methodist Research Institute, Weill Cornell Medical College, and other institutions found more diversity than expected in strains of the pathogen in a Texas population. The publication also indicates the emergence of a virulent, antibiotic-resistant strain of this organism. Published in mBio, “Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307” comes from lead author Wesley Long, senior author James Musser, and collaborators. K. pneumoniae is a dangerous source of infection, often acquired in hospitals and increasingly resistant to antibiotics. Scientists launched…

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Thursday, November 10, 2016

ASHI 2016: Long-read sequencing proves effective for full-length HLA gene sequencing

Last month we attended the annual meeting of the American Society for Histocompatibility and Immunogenetics (ASHI), where we were impressed to see the great progress in scientific research around transplantation, immunogenetics, HLA, vaccines and much more. There were an increasing number of presentations and posters showcasing new approaches to HLA sequencing. For the last few years, early protocols with NGS were focused purely on exon sequencing. Steady improvement in sequencing technologies has led to a new focus on full-length allele sequencing of all relevant MHC genes. It was great to see leading labs share their advice on the best methods…

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Thursday, June 23, 2016

Data Release: Zika-Susceptible Aedes aegypti De Novo Genome Assembly

We are excited about the release of a new genome assembly for the mosquito Aedes aegypti, which we hope will aid scientists in studying vector-pathogen dynamics, including those of the rapidly spreading Zika virus. The Aedes aegypti Aag2 cell line genome sequence was generated by a joint effort between Raul Andino’s lab at The University of California, San Francisco and PacBio. This cell line was derived by Peleg in 1975 and adapted in 1991 by Lan and Fallon. It was selected for sequencing based on its susceptibility to infection by many arboviruses, including Dengue, Chikungunya, Zika, Sindbis, and Rift Valley…

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Wednesday, September 30, 2015

Introducing the Sequel System: The Scalable Platform for SMRT Sequencing

We are excited to announce our newest Single Molecule, Real-Time sequencer, the Sequel™ System. Watch this short video to learn about this exciting evolution in SMRT® Sequencing. The Sequel System provides higher throughput, more scalability, a reduced footprint and lower sequencing project costs compared to the PacBio® RS II System, while maintaining the benefits of SMRT technology. The core of the Sequel System is the capacity of its redesigned SMRT Cells, which contain one million zero-mode waveguides (ZMWs) at launch, compared to 150,000 ZMWs in the PacBio RS II. Active individual polymerases are immobilized within the ZMWs, providing windows to…

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Friday, September 25, 2015

Marc Salit at NIST: Defining Standards for the Human Genome

In the first podcast of a new series on the applications of long-read sequencing, Mendelspod host Theral Timpson interviewed Marc Salit, leader of the Genome Scale Measurements Group at the National Institute of Standards and Technology. Their conversation focused on how and why NIST is involved in establishing baseline measurements for the human genome. Salit, along with Justin Zook and their team at NIST, are managing the Genome in a Bottle (GIAB) Consortium to develop reference materials, data, and methods needed to assess whole human genome sequencing. Their goal is to establish a physical reference genome as a standard against…

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Thursday, September 24, 2015

At Genome in a Bottle Workshop, Progress on New Reference Materials

Genome in a Bottle consortium  The National Institute of Standards and Technology held its latest Genome in a Bottle workshop last month in Gaithersburg, Md., and we were honored to attend. NIST has performed pivotal work to establish reference materials for the genomics community, starting with its RNA spike-in standards (ERCC spike-in controls) and continuing now with the GIAB consortium. These standards are essential for quality control and we’re pleased to be working with NIST to help ensure the highest accuracy in human genome sequencing. Last year, GIAB released its first reference standard, based on the well-studied NA12878 human genome…

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Wednesday, September 23, 2015

SMRTest Microbe Grant Winner: Identifying Antibiotic Resistance Mechanisms with SMRT Sequencing

We’re pleased to announce the winner of our recent “SMRTest Microbe” grant competition. Congratulations to Dr. Erin Price at the Menzies School of Health Research in Australia! The grant program, co-sponsored by PacBio and the Institute for Genome Sciences (IGS), was very competitive, with more than 100 submitted proposals. Dr. Price will receive SMRT® Sequencing and analysis from IGS  — using up to 4 SMRTbell™ libraries and 8 SMRT Cells — to characterize the mechanisms behind the emergence of antibiotic resistance in Burkholderia pseudomallei, a highly pathogenic bacterium that causes the potentially deadly disease melioidosis. Dr. Price and colleagues have…

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Thursday, September 17, 2015

SMRT Data Analysis: Updates from our Developers Conference

Last month we hosted a SMRT® Informatics Developers Conference, bringing together 150 developers with a passion for improving tools and resources. Our team came back brimming with enthusiasm for tools that will be released in the coming months, and humbled by the commitment we saw from the bioinformatics community to help scientists make SMRT Sequencing data increasingly useful. Thanks to the National Institute of Standards and Technology for hosting our meeting on their campus right before the Genome in a Bottle workshop. The big news we shared with attendees is that the PacBio® System will now output industry-standard BAM files…

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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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Wednesday, August 26, 2015

In Bacterial Study, Scientists Link Epigenetic Switch to Virulence, Antibiotic Resistance, and More

Scientists from Griffith University, Ohio State University College of Medicine, and other institutions recently published a detailed study of phase-variable expression of a DNA methyltransferase in non-typeable Haemophilus influenzae, the predominant cause of pediatric middle ear infections. The team found that the bacterium’s epigenetic switch regulates proteins used in current vaccine candidates and influences important traits including antibiotic resistance, ability to evade the host immune system, and biofilm formation, which significantly contributes to chronic infection. The paper, “A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae,” was published in Nature Communications last month by lead…

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Thursday, August 20, 2015

The Gapless Assembly: Scientists Describe Workflow for Producing Complete Eukaryote Genome

Sunflowers with verticillium wilt caused by V. dahliae In a new mBio publication, scientists from Wageningen University and KeyGene in The Netherlands report results from several strategies used to assemble the genome of a filamentous fungus, and describe the specific pipeline they recommend for sequencing and assembling eukaryotic genomes. “Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome” comes from lead authors Luigi Faino and Michael Seidl, senior author Bart Thomma, and collaborators. Using Verticillium dahliae as a model, which is a plant pathogen responsible for the damaging verticillium wilt disease in many crop species, they compared…

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Wednesday, August 12, 2015

Using SMRT Sequencing, Scientists Uncover Unexpected Transcript Diversity in Fungi

A new PLoS One publication from scientists at the Joint Genome Institute, University of Minnesota, and other organizations demonstrates that fungal genomes may contain far more transcript diversity than previously thought. In “Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing,” lead author Sean Gordon, senior author Zhong Wang, and collaborators used long-read isoform sequencing to characterize four fungal species. In addition to widespread alternative splicing, they found evidence of polycistronic transcription units that could be important engineering targets for genetic manipulation of fungi. The scientists turned to SMRT® Sequencing to escape the limitations of short-read transcriptome sequencing. “The…

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