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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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Monday, August 18, 2014

Genome-Wide Methylation in Human Microbiome Samples

Scientists in Florida and Finland recently published a report of their work studying methylation patterns in two human microbiome samples. While microbiome studies have become quite popular, the authors note there have been no prior papers detailing genome-wide methylation of bacteria found in those studies. Their goal was to ascertain how much added functional variation might occur based on methylation patterns. “The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei,” published in Frontiers in Microbiology, comes from lead author Michael Leonard and senior author Eric Triplett at the University of Florida plus a team of…

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Tuesday, July 29, 2014

Novel Study of Genome-wide PT Modifications in Bacteria Performed with SMRT Sequencing

A recent paper from scientists in China and the United States demonstrates a novel view of phosphorothioate (PT) DNA modifications in two bacterial genomes. Scientists from Shanghai Jiao Tong University, Massachusetts Institute of Technology, Wuhan University, and Pacific Biosciences teamed up to deploy Single Molecule, Real-Time (SMRT®) Sequencing to generate the first genome-wide view of PT modifications and to better understand their function. “Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences” by Cao et al. was published in Nature Communications. The authors note that PT modifications, which replace a non-bridging phosphate oxygen with sulphur, were only recently…

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Tuesday, July 1, 2014

Scientists Generate the First Personal Transcriptome Using SMRT Sequencing

A new paper from scientists at Stanford University and Yale University describes the use of Single Molecule, Real-Time (SMRT®) Sequencing to generate transcriptomes for three individuals. The work is believed to be the first personal transcriptome analysis using long-read sequencing. The paper, entitled “Defining a personal, allele-specific, and single-molecule long-read transcriptome,” was published in PNAS by Hagen Tilgner, Fabian Grubert, Donald Sharon, and Michael Snyder. Last year, the same authors published a study using SMRT Sequencing to analyze transcriptomes across tissue samples from human organs. In the PNAS publication, they compare metrics from the new data set to those from…

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Monday, June 2, 2014

ARCHIVED: Intro to the Iso-Seq Method: Full-length transcript sequencing

Since the launch of the Iso-Seq protocol in SMRT Analysis in 2014, the analysis pipeline has seen several improvements, as well a host of new tools. Please see our updated post to learn more about current applications of this increasingly popular method. With the recent launch of SMRT Analysis v2.2, we’re excited to introduce analysis software support for the new Iso-Seq™ method for sequencing full-length transcripts and gene isoforms, with no assembly required! Today we’ll take a deeper look at the Iso-Seq method to explain its unique scientific value and review publications from those already applying Single Molecule, Real-Time (SMRT®)…

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Tuesday, May 6, 2014

Retroviral Study Reveals Potential for Influencing HIV Replication

Scientists from the Icahn School of Medicine at Mount Sinai in New York City and the MRC National Institute for Medical Research in London published a paper using Single Molecule, Real-Time (SMRT®) Sequencing to gain a better understanding of how human endogenous retroviruses may be interacting with HIV infection. They pursued a new avenue of research that could shed light on how to interfere with HIV replication. “HIV-1 interacts with HERV-K (HML-2) Envelopes derived from human primary lymphocytes” was recently published in the Journal of Virology, a publication of the American Society for Microbiology. Daria Brinzevich and George R. Young…

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Thursday, April 24, 2014

SMRT Sequencing of Chicken Heart Transcripts Yields New Genes and Isoforms

The Gallus gallus (common chicken) genome was initially published in 2004, but the latest RefSeq and Ensembl annotations remain incomplete. The chicken is an important model organism, especially for research on embryogenesis and heart development. In a new paper published in PLOS One, researchers representing the Cardiovascular Development Consortium of the Bench to Bassinet Program and Pacific Biosciences describe work to improve the chicken genome annotation using SMRT® DNA Sequencing. In “Long-Read Sequencing of Chicken Transcripts and Identification of New Transcript Isoforms,” the consortium describes how they used SMRT sequencing to generate full-length cDNA reads from embryonic chicken hearts, combined…

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Tuesday, April 8, 2014

GC-Rich Genome of Pandoraea Bacterium Assembled with SMRT Sequencing

Scientists from the Institute of Biological Sciences at the University of Malaya recently published a description of Pandoraea sp. strain RB-44 in Genome Announcements, a journal from the American Society for Microbiology. The genome sequence was completed using Single Molecule, Real-Time (SMRT®) Sequencing. Pandoraea is a soil bacterium; this particular strain was collected from the site of a former landfill. Some strains of Pandoraea have been suggested as cystic fibrosis clinical pathogens, the authors report, though “their role in pathogenicity is still largely unknown.” Corresponding author Kok-Gan Chan and colleagues may have a new lead in that mystery. Their Pandoraea…

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Thursday, March 27, 2014

As Genome Editing Gains Traction, SMRT Sequencing Provides Accurate View of Results

A new paper published in Cell Reports describes how Single Molecule, Real-Time (SMRT®) Sequencing can be used to greatly improve outcome reporting for a variety of popular genome-editing approaches. “Quantifying genome-editing outcomes at endogenous loci with SMRT sequencing” comes from lead authors Ayal Hendel and Eric Kildebeck from the Porteus lab at Stanford University, along with other collaborators at Stanford and the Georgia Institute of Technology. The goal for this study was to contribute to the tremendous innovations occurring in the genome editing field — from CRISPR to TALENs and more — by finding a better tool to measure results…

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Wednesday, March 19, 2014

Assessment of Highly Complex Alternative Splicing of Neurexins Performed with SMRT Sequencing

A new paper in the Proceedings of the National Academy of Sciences from the laboratories of Stephen R. Quake and Thomas C. Südhof (both at Stanford University) describes the direct, full-length transcript sequencing of RNA molecules that are essential to synapse formation in the mammalian brain. The team used Single Molecule, Real-Time (SMRT®) Sequencing to analyze full-length mRNAs from different members of the neurexin gene family and used that information to examine alternative splicing events. In the publication entitled “Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing,” the scientists highlight the importance of understanding alternative splicing in…

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Monday, March 3, 2014

In Acinetobacter Study, Long Reads Aid in Defining Genomic Structure

A paper recently published in mBio, an open access journal from the American Society for Microbiology, reports on the sequencing and phylogenetic analysis of several drug-resistant strains of a pathogen found in hospitals. According to the authors, incorporating PacBio® sequence was critical for generating extremely long contigs for assembly and for accurately identifying chromosomal position and structure of genomic features associated with drug resistance. The publication, entitled “New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis,” from scientists at the J. Craig Venter Institute, as well as Case Western Reserve University and its…

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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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Friday, December 27, 2013

Breakpoint Detection in Cancer Structural Variants with PacBio May Yield Patient-Specific Data

A new publication from scientists at the University of California, San Diego, demonstrates the use of Single Molecule, Real-Time (SMRT®) Sequencing to identify structural variation (SV) breakpoints in cancer. “Amplification and thrifty single molecule sequencing of recurrent somatic structural variations” was published in Genome Research and comes from authors Anand Patel, Richard Schwab, Yu-Tsueng Liu, and Vineet Bafna. In the paper, the scientists report development of a new method — Amplification of Breakpoints, or AmBre — to detect important structural variant breakpoints. AmBre relies on a PCR-based approach for amplification of the structural variant, followed by sequencing on the PacBio®…

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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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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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