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Cytokinetics, Incorporated Message Board

paulieme60 8 posts  |  Last Activity: Jul 1, 2014 8:20 PM Member since: Feb 12, 2002
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  • Improving potato genetics using the long read sequencing data
    Expected/Ideal Start Date 01 Aug 2014
    The successful applicant will use and optimise tools for assembling a large plant gene sequences and an entire genome using ultra-long Pacific Bioscience (and as available Nanopore) reads, as well as using shorter Illumina reads to verify and correct the assembly.

    (for link go to IHUB PACB M B)

  • Reply to

    Roche just bought Genia, not good for PACB

    by borgati4 Jun 3, 2014 3:36 PM
    paulieme60 paulieme60 Jun 13, 2014 10:59 PM Flag

    (Quote fom an expert) Nick Loman ‏ ·Jun 12 2014
    "PacBio is a great tech, but shame many can’t tell the conceptual difference between a $700k instrument and a $1000 portable USB sequencer." !!!!!!!!!!!!!!!!

  • "Their technology is interesting in that it uses both a biological nanopore and a polymerase. The polymerase sits atop the nanopore, and a template single molecule of DNA is provided to the polymerase. Single nucleotides are added to the mix and each nucleotide has a “NanoTag” tail. As the polymerase incorporates the nucleotides, the nanopore sucks in the NanoTag, and this event is measured electronically. The polymerase moves on and the nanopore measures the next base etc etc. " "Any guidance on the limits on measurement performance in terms of bases per second? 10bps wouldn’t be practical for anything but small viruses. This is quotes from experts in the field,such Mick Watson!

  • James!Gurtowski!
    5/29/2014 Near perfect de novo assemblies of eukaryotic
    genomes using PacBio long read sequencing! (for link go to IHUB PACB M B)

  • PacBio Blog - 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.

    The scientists conducted a study uniquely suited to the extremely long reads provided by the PacBio® platform, noting that this technology was needed to accurately parse the complexity in expression among a specific group of human endogenous retroviruses (HERVs). In this project, the scientists dug deeper into evidence that expression of the endogenous retroviruses that make up almost 5% of the human genome is upregulated when a person is infected with HIV-1. “HIV-1 infection in human cells is equivalent to a co-infection by several retroviruses,” -------------The team found nearly 4,000 HERV-K sequences in these lymphocytes, compared to a previous study from other scientists that found fewer than 1,000 of these sequences in 11 samples. They posit that the higher number seen here reflects the greater sensitivity of PacBio sequencing as well as the difference in cell types analyzed.

    In all, the authors identified more than 30 different transcripts for HERV-K envelopes, including two that produce full-length proteins — one of which was found to incorporate into HIV-1 particles. “These findings imply that some HERV-Ks interact specifically with HIV possibly shaping the properties of the lentivirus,” they write. “Future studies are needed to determine the extent of their influence on the HIV-1 life cycle and whether their expression can be harnessed to hinder HIV-1 replication.”
    (for full story,go to PACB web site, click on blog)

  • Reply to

    Innovation Centre in Quebec Uses PACBIO!!!

    by paulieme60 Apr 17, 2014 4:20 PM
    paulieme60 paulieme60 Apr 17, 2014 4:26 PM Flag

    High-quality assemblies aren’t just for bacteria. “We’ve shown recently that we can assemble a fungal genome of 20 or 30 megabases with four or eight SMRT Cells and get only 10 or 20 contigs — which often represents the number of chromosomes in the genome,” Montpetit says.

    Read the full case study to learn more about how the Innovation Centre has deployed SMRT Sequencing, their shift from hybrid to PacBio-only assemblies, and how they differentiate their bioinformatics analysis service. (For link Go to PACB website,click on Blogs)

  • Reply to

    Innovation Centre in Quebec Uses PACBIO!!!

    by paulieme60 Apr 17, 2014 4:20 PM
    paulieme60 paulieme60 Apr 17, 2014 4:23 PM Flag

    At the center, SMRT Sequencing has been used in diverse research areas. Some examples include generation of high-quality assemblies in microbial sequencing, analysis of long, repetitive genomic regions, and sequencing of full-length human gene isoforms. Microbial sequencing encompasses a number of applications, including biotech industry efforts to improve microbial biofermentation and microbiome studies, from environmental remediation projects on Alberta tar sands to veterinary research on microbes present in cattle rumen.
    In the two years they’ve been running the SMRT Sequencing platform, the Innovation Centre scientists have seen remarkable progress in what they have been able to achieve. Continued improvements in read lengths — partly due to new reagent kits from PacBio and partly due to more streamlined sample prep protocols developed at the center — have already made a major difference.
    One major step was achieving complete bacterial sequencing and assembly in less than a day, a feat that may enable the core facility to serve as a rapid response center for organizations that study pathogen outbreaks and other urgent problems. In 2013, tests conducted with researchers at the Canadian Food Inspection Agency and other government agencies demonstrated that the Innovation Centre scientists could sequence a sample and fully assemble the genome and plasmid elements — all in 20 hours or less.
    Indeed, the Innovation Centre team is routinely able to deliver affordable, high-quality, finished genomes. “A single bacterial genome, a library prep, and two SMRT Cells of sequencing — which is generally a little bit overkill — is less than $1,000,” Dewar says. “More and more often, we are getting a completely closed, finished-quality genome for that.” (part 2 of 3)

  • Innovation Centre in Quebec Uses SMRT Sequencing for
    Cost-Effective, Complete Microbial Genomes
    At the McGill University and Génome Québec Innovation Centre, many projects conducted in the sequencing core facility fall under the umbrella of life sciences rather than biomedical research. To the scientists responsible for making the core facility operate as smoothly as possible, that makes a world of difference.
    “When you’re in the life sciences in addition to human biomedical [research], you’re out there in the world of things that haven’t been sequenced before, or haven’t been sequenced particularly well,” says Ken Dewar, a principal investigator at the Innovation Centre.
    To navigate this type of uncharted territory, scientists at the center rely on long-read sequencing from their PacBio® RS II platform to cost-effectively close microbial genomes, traverse repeat-heavy genomic regions, and perform full-length transcript sequencing. By leveraging the dramatically increased read lengths PacBio sequencing provides, they have driven down costs and improved completeness of their assemblies.
    At the core facility, Alexandre Montpetit is dedicated to running the next-generation sequencing platforms. His primary affiliation is with Génome Québec, and he has an adjunct appointment at McGill. He and his colleagues have been champions of long-read sequencing for years, so when PacBio unveiled its platform with industry-leading read length, it was an obvious choice for the center to adopt the technology.
    “We’ve always had a focus on sequencing things for the first time or assembling genomes for the first time, not for the thousand-and-first time,” Dewar says. “PacBio was a natural fit.”
    (Part 1 0f 2)

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