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Tuesday, July 30, 2013

Single-Molecule Sequencing Technology Q&A with Nobel Laureate Rich Roberts

BioMed Central has published an interesting Q&A session on its Biome blog with Nobel Laureate Richard Roberts about why he believes in SMRT Sequencing and thinks non-users should take another look at it, too. He also discusses the critical need for funding to support the functional annotation of the genomes being sequenced, including for new bioinformatics tools. “We should be greatly increasing our efforts to gain functional insights into the millions of genes we are discovering by sequencing and for which we either have no idea of what they do, or many of our predictions are simply wrong,” he says.…

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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

New Genomes for 100K Pathogen Project Sequenced and Finished with PacBio Technology

The 100K Foodborne Pathogen Genome Project announced the contribution of 20 newly finished genomes of microbes responsible for foodborne disease, and we’re pleased to report that they were sequenced and assembled using automated PacBio® pipelines. The 100K Genome Project aims to sequence the genomes of 100,000 bacterial and viral genomes with the goal of speeding up the diagnosis and treatment of foodborne diseases and shortening the outbreak time. The global effort is led by the University of California, Davis, the Center for Food Safety and Applied Nutrition of the US Food and Drug Administration, and Agilent Technologies; Pacific Biosciences is…

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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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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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Wednesday, July 3, 2013

Using PacBio Sequencing, Scientists Find No Evidence of Horizontal Gene Transfer in Haitian Cholera Strain

A new analysis from public health scientists has found that the cholera strain responsible for the 2010 outbreak in Haiti has a limited ability to add to its genetic repertoire through horizontal gene transfer. The paper, “Evolutionary Dynamics of Vibrio cholerae O1 Following a Single-Source Introduction to Haiti,” from lead author Lee Katz and senior author Cheryl Tarr, both from the US Centers for Disease Control and Prevention, came out this week in mBio, a journal published by the American Society for Microbiology. Because the 2010 epidemic represents the first known arrival of cholera in Haiti, the outbreak served as…

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