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Monday, September 22, 2014

Maryland Scientists Produce High-Quality, Cost-Effective Genome Assembly of Loa loa Roundworm Using SMRT Sequencing

A paper just released in BMC Genomics details what authors call “the most complete filarial nematode assembly published thus far at a fraction of the cost of previous efforts.” The project was performed using the PacBio® RS II DNA Sequencing System by scientists at the University of Maryland School of Medicine’s Institute for Genome Sciences and the Laboratory of Parasitic Diseases at the National Institute of Allergy and Infectious Diseases. In this genome sequencing effort, scientists generated a de novo assembly of Loa loa, a roundworm that infects humans. L. loa, transmitted to humans by deer flies, causes loiasis. The…

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Tuesday, September 9, 2014

Genome Analysis of Unicellular Organism Reveals Frequent, Massive Reshuffling

A recent publication from senior author Laura Landweber at Princeton University offers a remarkable and unexpected look at sweeping genomic rearrangements in a unicellular organism. “The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development,” published in Cell, comes from lead authors Xiao Chen and John Bracht as well as other collaborators from Princeton, the Icahn School of Medicine at Mount Sinai, Benaroya Research Institute, and other institutions. The project focused on Oxytricha trifallax, a single-celled eukaryote that lives in ponds. Despite its unicellular simplicity, the organism has an extensive ability to scramble and rearrange its…

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Wednesday, March 26, 2014

Importance of Finished Microbial Genome Highlighted for Ethanol-Generating Clostridium

A paper in BioMed Central’s Biotechnology for Biofuels journal demonstrates how finished microbial genomes using Single Molecule, Real-Time (SMRT®) Sequencing are having an impact on the biotechnology industry. The publication, “Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia,” comes from scientists at Oak Ridge National Laboratory, the University of Tennessee, and New Zealand-based biofuels company LanzaTech. Lead authors Steven Brown and Shilpa Nagaraju and their colleagues used PacBio® sequencing to generate a finished genome sequence for a complex class III microbe that previously could not…

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Wednesday, November 20, 2013

New Publication Demonstrates Long-Read Sequences Needed to Thoroughly Resolve Short Tandem Repeats

In a new paper reporting a protocol for using short-read sequence data to locate short tandem repeats (STRs), scientists find that long-read sequence information is necessary to resolve regions with repeat complexity, extreme GC content, and other challenging factors. Their solution is to use short-read data to find STRs, and then to use long-read sequencing to fully characterize those repeat expansions. The Bioinformatics publication is entitled “Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing” and came from scientists Koichiro Doi, Shinichi Morishita, et al. at the University of Tokyo. They focused on resolving STRs across…

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Thursday, November 14, 2013

ASHG Workshop Recordings: Resolving Structural Variation in Human Genomes

We hosted a structural varation workshop at the annual meeting of the American Society of Human Genetics, and were pleased to see that the speakers’ presentations really resonated with attendees – the event was standing-room-only! Jonas Korlach, PacBio CSO, opened the session by sharing a brief update on SMRT® technology, noting that the new P5-C3 chemistry delivers 50% of bases in 10 kb or longer reads. View presentation recording Evan Eichler, Howard Hughes Medical Investigator from the University of Washington discussed his use of the PacBio® system to study difficult-to-sequence regions of the human and chimp genomes. Eichler has identified a…

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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, 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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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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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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Sunday, February 24, 2013

AGBT Day 3 Highlights: Long-Read Sequence Data Makes a Difference for Human, Crop Studies

The third day of sessions has wrapped up at AGBT, and we’ve got one day left to go. It’s the last leg of the marathon! We’ve been having a great time here, enjoying the opportunity to meet with old friends and make new acquaintances as well. Today’s talks included two of particular interest to us: one from Eric Schadt and another from Mike Schatz. Eric Schadt, founder and director of the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai School of Medicine in New York, gave a talk during the afternoon session entitled “Whole Human Genome SMRT® Sequencing…

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Monday, February 11, 2013

SMRT Sequencing Offers First Look at Fragile X Syndrome Repeat Expansion Disorder Sequence

Scientists at the University of California, Davis, School of Medicine have used the PacBio® RS to sequence a previously “unsequenceable” region of highly repetitive DNA on the X chromosome, providing a critical leap forward in understanding the genetic complexity of repeat expansion disorders such as Fragile X Syndrome. Paul Hagerman, a professor of biochemistry and molecular medicine at the University of California, Davis, has spent the better part of the last 30 years trying to parse the molecular biology of Fragile X Syndrome. The FMR1 genetic mutation responsible for the syndrome is a leading cause of heritable cognitive impairment and…

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