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  • Looks like some bad news to be announced , having said that I don't think it will come as a surprise to anyone
  • Genome Assembly Advances Featured in Genome Research Special Issue
    Wednesday, May 24, 2017

    The May issue of Genome Research is a special edition focusing on advances in sequencing technologies and genome assembly techniques. The research papers selected for this special issue cover reference-grade genome assemblies, structural variant detection, diploid assemblies, and other features enabled by new high-quality sequencing tools.

    The issue kicks off with a perspective from NHGRI’s Adam Phillippy, who reflects on the history of sequencing and assembly. Dusting off publications from as early as 1979, he illustrates the remarkable pace of advances in this field for the past four decades. Phillippy has worked with just about every kind of sequence data, so his view of the current landscape is particularly instructive. “The biggest gains in contig lengths have come from single-molecule sequencing,” he writes. “Critically, 10-kb reads are longer than the most common repeats in both microbial and vertebrate genomes and can therefore generate highly continuous assemblies. In fact, the complete reconstruction of bacterial genomes—a process that used to require teams of people—is now automated and routine.” Phillippy also notes that long-read sequencing assemblies have spurred “a renewed interest in repetitive sequences, which can be properly analyzed for the first time” and are “even revealing new variation in the human genome.”

    We are very pleased that more than half of the papers in this special issue feature our sequencing data and genome assemblies derived therefrom, underscoring PacBio’s leading role in long-read sequencing and de novo assembly. We congratulate all the authors for their exciting contributions to this special issue and encourage you to review these excellent publications:

    Human Genome

    Discovery and genotyping of structural variation from long-read haploid genome sequence data: Scientists used SMRT Sequencing to scan human genomes for structural variants, finding that more than 89% of those found had been missed in the 1,000 Genomes Project.
    Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly: An exploration of the latest human reference assembly, which expands the number of alternate loci and for the first time includes sequence coverage of centromeres.
    Plant and Animal Genomes

    Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data: This project used SMRT Sequencing data to generate genomes of three relatives of the model plant Arabidopsis thaliana,assembling all three genomes into only a few hundred contigs. Integration of optical mapping and chromosome conformation capture techniques yielded chromosome-scale assemblies of these repetitive plant genomes. The scaffolds even revealed some of the heterochromatic regions which are not present in gold standard reference sequences.
    Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster: Long-read PacBio sequencing allowed scientists to characterize complex satellite DNA regions, which have been challenging to resolve due to their repetitive nature.
    Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications: This analysis of Eurasian crow genomes found that assembling two high-quality genome references using SMRT sequencing, combined with optical mapping, made it possible to recover missing regions and correct errors in a previous short-read-only assembly.
    An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations: Scientists use SMRT Sequencing of full-length cDNAs for genome annotation of a new wheat genome assembly, identifying protein-coding genes and noncoding RNA genes with high confidence.
    New Tools for Long-Read Data

    Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm: Scientists present a new hybrid assembly algorithm to combine short-read and long-read data for optimal accuracy and contiguity.
    Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation: Based on Celera Assembler, Canu was designed for long-read data and significantly reduces computational time for genome assembly.
    HINGE: long-read assembly achieves optimal repeat resolution: This assembler focuses on resolving challenging repeats.
    Fast and accurate de novo genome assembly from long uncorrected reads: For long-read assembly, scientists pair Racon with miniasm to rapidly generate high-quality consensus sequences without an error-correction step.
    HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies: This tool performs fast, high-resolution haplotype assembly from data produced by long-read sequencing, short-read sequencing, and other genome analysis technologies.
    HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies: This method calls structural variants from human genomes using short-read and long-read sequence data; tests showed it improved detection rates for several types of variants.
  • They keep pounding the table on long reads saying that short reads are no match and erroneous. Why no one scientists listens to them? I thought scientists were smart people am I wrong
  • With all the negativity on this message board, I must say that the turn around today was pretty impressive. I am, and will be adding to my position. As far as I'm concerned, nothing has changed. It's still a great long term investment. I get as frustrated as everyone else, but I'm in for the long haul.
  • Nasdaq up over 14% YTD and we are hitting a 52 week low. I'm still holding quite a few shares but I can't say it's not painful. I was against a buyout before but at this point I'm almost hoping for one at the right price. Wish management was doing a better job but still believe in the product.
  • ILMN CEO on CNBC Hunkapillar should learn something from him. It is all about selling your product.
  • Hi,
    I´m sure we all were aware of the recent patent dispute between Pacbio and oxford nanopore regarding the use of the single molecule technology. Well, Pacbio has lost its dispute and if i´m right the main reason being the fact that a single molecule is not defined the same way.
    Pacbio defines a single molecule as a sequence (read base per base) where as a molecule for Oxford nanopore defines a molecules as an ensembl of signals including channel, amplitude width-- affecting the recorded signal. In other words Pacbio detects a DNA sequence where as Nanopore detects an ensembl of signals to obtain a molecule (including a dna sequence).

    Frankly speaking this is crazy and the interpretation of what is a single molecule is just awesome and hard to understand for a scientist (that would not see any different in between them). Have no idea what Pacbio will say about but hopes they say something.

    The document is available at edis. You need to login (free registration).
    Search for Certain Single-Molecule Nucleic Acid Sequencing Systems and Reagents, Consumables, and Software for Use with Same; Inv. No. 1032

    https://edis.usitc.gov/

    USITC - EDIS Home
    edis.usitc.gov
  • DAVID, what are you looking at? That is the start of thelawsuit against them. NO new info yet.......
  • Looks like they are finally listening to me and other shareholders requests to put news out for the investing public to see too. Most of the exciting stuff going on is only seen via their website and twitter. They need to continue puttout information in the form of presss releases like this on a more regular basis.https://finance.yahoo.com/news/recent-publications-demonstrate-rapid-adoption-113000013.html.....

  • Technically speaking I think we will see a reversal
  • Is today the annual shareholder meeting?
  • hair of the dog, baby! I averaged my position down with 5K more shares @$3.99. i hold 15k shares. she's gonna pop mates. Mark it!
  • Lately, some of the leading HLA labs have adopted long-read, SMRT sequencing as an alternative approach to HLA typing. Long reads can capture full-length HLA gene sequences, phase alleles and detect rare and novel variants that are difficult to discover with other methods.

    At the Anthony Nolan Research Institute, for instance, scientists assessed the feasibility of using SMRT sequencing for HLA analysis with a pilot study of seven previously typed samples3. Each full-length gene sequenced to a mean quality value of 70 or greater produced high-resolution sequence information for all exons and introns. The researchers determined that SMRT sequencing yielded concordant results for all samples, and also detected novel alleles that had been missed by the other typing technologies. Remarkably, the long-read sequence information even identified and corrected an error in the reference sequence database. The entire workflow took just three days, generating results more quickly than established methods.

    In the paper reporting these results, the scientists wrote “The implications of this technology in the field of HLA typing could be enormous, allowing for true allelic HLA typing in a single experimental set-up and making redundant the need for multiple experiments on different typing platforms, cross-referencing of results and/or the need for re-sequencing using an allele-specific protocol.”

    A follow-up study from the Anthony Nolan team demonstrated that SMRT sequencing was successful in accurately phasing all the HLA alleles. An assessment of 45 samples from various DNA sources determined that this approach was 100% accurate and reliable for phasing variants in the HLA genotyping process4.

    SMRT sequencing is also now routinely used at HistoGenetics, a commercial laboratory that has been a pioneer in sequence-based HLA typing services. Scientists there are deploying long-read sequencing to type thousands of HLA samples each week; in a recent project, they used this approach to type 60,000 samples for the National Marrow Donor Program’s Be the Match registry. During a conference presentation earlier this year, HistoGenetics CEO Nezih Cereb said that sequencing full-length HLA genes are now the gold standard for accurate HLA typing, replacing current exon-based genotyping methods or short-read sequencing methods that only analyze portions of the genes or known variants5.

    Looking Ahead

    The advent of full-length gene sequencing promises to dramatically improve the accuracy and resolution of HLA typing for several important clinical applications, including drug hypersensitivity research, autoimmune disease studies, and transplantation. For the first time, long-read sequencing allows scientists to analyze and phase variants throughout this complex genomic region for a better understanding of the biology and its impact on clinical function. This comprehensive approach will offer new insight into the HLA region — its ability to detect novel alleles even in previously typed samples is early evidence of that — and could lead to greater precision in matching donor organs to transplant recipients.
  • Is future option - (date,strike price, amount) issuance to management a public information? Where can I find that?
    Can that be a motivation for management to keep the price down, by not revealing any good information - such as orders in pipeline
  • What PACB needs is a 'killer app'. Some new application for long reads that would be considered essential and worth the additional cost. I was thinking the article on haplotyping was a sign of more such things to come. Of course, it could also be a series of smaller applications that all add to the demand for PACB sequencing. But it would definitely be great to see a 'cure for cancer' type of discovery that required long reads. I think we will see such needs arise as genetics progresses, but the question is whether PACB runs out of time/money before that. Place your bets!
  • Sad folks are bailing.
  • Annual shareholders meeting was yesterday.

    https://www.sec.gov/Archives/edgar/data/1299130/000129913017000040/pacb-20170525x8k.htm

    8-K Annual meeting 5-24-17
    www.sec.gov
  • It has gote thru previous resistance of 3.79, very easily, no confidence in this management, they should all be fired allng with the board.
  • PAC will partner with someone local. forget this Swiss cheese b-s. Bay Area is where the goods are for high tech. Europe is a joke. Ox Nan is in England? Give me a break they can't even get their electrical and sewer lines correct how in the world will they ever compete with the Bay Area in this complex tech market you must be kidding me!!