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.
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
Sad folks are bailing.
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!!
I am with Chengis. I sold 2/3 today. what I don't like PACB: increasing legal cost (can't believe they spend $$ on lawyers than increasing their throughput, accelerating development time) $4M+ stock comp per q @ ~20% of their rev. New building...state of art... but without new orders of sequels $$$ Q2 rev. will be lower than Q1 dilution second half of 17 and the worst is: let us blame slow sales on the government budget!!!
agreed, BuyOut is the only out for this bunch.
Longs I did sell all of my 60,000 shares around 4.00 taking a 60% loss, I will buy again if this bunch of guys runningng the show gets fired, it was morey which was doing nothing for me. I really believe with right leadership company can do justice to this great technology. Best of luck to longs and hope to buy backk for a great reason soon.
Hard to believe that such a scientifically advanced instrument is such a financial still born.
This webinar will provide an overview of an RNA-seq protocol that has been optimized to study small RNA species such as microRNAs.
Our speaker, Neelanjan Mukherjee of the Berlin Institute for Medical Systems Biology, will discuss the use of this protocol, based on PerkinElmer's NEXTflex Small RNA Sequencing kits, within the context of his research into the role of RNA regulatory networks in cancer and steroid hormone metabolism. Achieving a quantitative understanding of RNA regulatory mechanisms is a critical aspect of this work. Thus, it is necessary to have unbiased and quantitative measurements of small RNA species.
PacBio's Juliet Minor Variant Software
By Bio-IT World Staff
May 8, 2017 | At PacBio’s SMRT scientific symposium and developers meeting last week held at the Leiden University Medical Center in the Netherlands, Lance Hepler, with PacBio, announced three apps coming in the next SMRT Analysis release: minor variants, structural variation, and multiplexed microbe WGS.
Juliet is the new unified minor variant software pipeline, Hepler said. The pipeline is extensible for new disease areas and organisms, offers a targeted amplicon approach, with reference-guided, one-click analysis. Juliet can handle de novo codon variants now. Insertion and deletion variants are currently being ignored; support will be added in a future version.
The challenge, Hepler said, is to reliably identify 1% variants from sequencing noise. Juliet can do that, he said, with coverage of 6000x. The false-positive and false-negative rates he reported are below 1% and 0.001% (10-5), respectively. Juliet can distinguish between minor variants and PCR heteroduplex. Official release of the Juliet pipeline will be in SMRT Link 5.0, though it’s available as-is on Github now.
Hepler, of course, touted the strength of long reads, especially for revealing structural variations. He quoted a Genome Biology story from 2011 that theorized that structural variants are the major limitation to better diagnostics from exome sequencing, and credited structural variations with diseases, traits, and evolutionary processes (10.1186/gb-2011-12-9-128).
PacBio discovers 20,000 structural variants in a human genome, compared to 4,000 revealed by Illumina sequencing, Hepler reported, combining several published findings from 2015 and 2016 in Nature, Nature Communications, and Genome Research (DOIs: 10.1038/nature20098; 10.1101/gr.214007.116; 10.1038/ncomms12065; and 10.1038/nature15394).
In fact, Hepler claimed, most structural variants in the human population remain undiscovered today. Increased sample sizes will yield higher rates of structural variant discovery, he said, but doesn’t require deep sequencing of every individual. Volume, not depth of sequencing, will reveal more of variants in lower frequency in the population.
Hepler presented models claiming that nearly 100% of variants in the population at 5%, 1% and 0.5% frequencies could be detected by sequencing 1,000 humans at 50-fold, given that reads are long enough to identify all variants. The model didn’t suffer much at just 5-fold coverage; only variants of 0.5% frequency fell to less than 100% sensitivity.
For microbial whole genomes sequencing, Hepler called PacBio the gold standard, and reiterated that multiplexing bacterial samples is the key to maximizing throughput, efficiency, and cost on the Sequel System.
PacBio has released an end-to-end workflow for bacterial multiplexing compatible with both the PacBio RSII and Sequel systems. Hepler recommended one SMRT cell for two microbes on the PacBio RSII system, and 12-16 microbes per SMRT cell on the Sequel System.
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Anyone seeing a large volume spike at approximately 11am EST? Looks like it was for 251K shares and brought the price down from about $4.09 to about $4.03. That's what Yahoo shows at least. TIA
Genome assembly and characteristics
Assembly characteristics and genome characterization features for each genome included in this study are summarized in S1 Table. As expected, Pacific Biosciences (PacBio) Single-Molecule Real-Time (SMRT) sequencing resulted in longer read lengths and fewer contigs but lower average genome depth coverage compared to Illumina sequence data. Complete closed genomic sequences were generated for 17 of 25 (68%) isolates sequenced with the PacBio platform; the remaining eight consisted of ≤ 6 contigs. Nucleotide accuracy of PacBio sequences was > 99.85% as determined by alignment with Illumina reads. On average, 759 genes were predicted in the resulting genome sequences, which was comparable to the results of available M. pneumoniae reference genomes [11, 53]. Using Gubbins, 19 regions were identified as potential recombination sites (all <300 bp), yet the phylogenetic tree remained unchanged after masking these regions (data not shown) and thus was not considered supportive evidence of recombination driving the evolution of M. pneumoniae.
We initially compared available genome sequences of the prototypical reference strains of M. pneumoniae, M129 (type 1) and FH (type 2), to those re-sequenced in the current study in terms of both genomic content and SNPs (S1 Fig). The original FH reference genome (NC_017504.1) lacked a 6 kb region shown to be present among newer constructs of the FH genome and all type 2 isolates , including those in the current study (n = 51). Thus, we used the sequence reported by Xiao et al.  (NZ_CP010546.1) as the reference genome for type 2 isolates for the remaining analysis. The type 1 strain M129 was >99.99% identical in nucleotide sequence to recent reference sequence (NC_020076.2) that was used as type 1 reference genome in the current study (S6 Table).
Finding A New Major Gene Expression Regulator in Fungi
Researchers report prevalent DNA base modification in the earliest fungal lineages
Linderina pennispora ZyGoLife Research Consortium Flickr CC BY-SA 2.0 The genome of the Linderina pennispora, a fungus belonging to the earliest branches of the fungal kingdom, was sequenced and annotated as part of the Nature Genetics study. (ZyGoLife Research Consortium, Flickr, CC BY-SA 2.0) Just four letters – A, C, T, and G – make up an organism’s genetic code. Changing a single letter, or base, can lead to changes in protein structures and functions, impacting an organism’s traits. In addition, though, subtler changes can and do happen, involving modifications of the DNA bases themselves. The best-known example of this kind of change is a methylation of the base cytosine at the 5th position on its carbon ring (5mC). In eukaryotes, a less-well known modification involves adding a methyl group to base 6 of adenine (6mA).
In the May 8, 2017 issue of Nature Genetics, a team led by scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, report the prevalence of 6mA modifications in the earliest branches of the fungal kingdom. Though fungi have been around for a billion years and collectively are capable of degrading nearly all naturally-occurring polymers and even some human-made ones, most of the species that have been studied belong to just two phyla, the Ascomycota and Basidiomycota. The remaining 6 groups of fungi are classified as “early diverging lineages,” the earliest branches in fungal genealogy. They comprise a little-explored realm of fungi, providing a repertoire of important and valuable gene products for DOE missions in bioenergy and environment.
The Importance of Exploring Understudied Lineages
Stephen Mondo, DOE JGI analyst Watch Stephen Mondo talk about the identification and proposed role of 6mA in early diverging fungi at the 2017 Genomics of Energy & Environment Meeting: http://bit.ly/JGI2017Mondo. “By and large, early-diverging fungi are very poorly understood compared to other lineages. However, many of these fungi turn out to be important in a variety of ways,” said study first author and DOE JGI analyst Stephen Mondo. “Consider the Neocallimastigomycetes – these fungi are one of the most powerful degraders of plant biomass currently known and have a tremendous arsenal of plant cell wall degrading enzymes which may be useful for bioenergy production. They are a good example of how exploring these understudied lineages leads to valuable biological and technological insights.”
Many of the fungal genomes used in the study were sequenced as part of the DOE JGI’s 1000 Fungal Genomes initiative aimed at producing at least one reference genome for every family of fungi. For the study, the team used 16 fungal genomes sequenced at the DOE JGI using the Pacific Biosciences sequencing platform. While the technology was used with the goal of attaining very high quality genome assemblies, DOE JGI scientists have now additionally taken advantage of this sequencing platform to explore epigenetic (5mC, 6mA) modifications. They discovered very high levels of 6mA in fungi, where up to 2.8% of all adenines were methylated, confirming these findings using multiple independent methods. The previous record holder for genomic 6mA, noted Mondo, is the alga Chlamydomonas reinhardtii (sequenced and annotated by the DOE JGI), in which just 0.4% of adenines were methylated.
6mA a Marker of Expression
“This is one of the first direct comparisons of 6mA and 5mC in eukaryotes, and the first 6mA study across the fungal kingdom,” said DOE JGI Fungal Genomics head and senior author Igor Grigoriev. “6mA has been shown to have different functions depending on the organism. For example, in animals it is involved in suppressing transposon activity, while in algae it is positively associated with gene expression. Our analysis has shown that 6mA modifications are associated with expressed genes and is preferentially deposited based on gene function and conservation, revealing 6mA as a marker of expression for important functionally-relevant genes.”
In addition to 6mA performing what seems to be the opposite role of 5mC (which suppresses expression), the team found that the presence of 5mC and 6mA are inversely correlated. Specifically, while 5mC is found at repetitive regions of the genome, the methylated adenines were clustered into dense “methylated adenine clusters” (MACs) at gene promoters. 6mA was also found consistently on both strands of DNA, which may enable propagation of methylation through cell division.
“Using genomics, we explore the diversity of fungi to develop catalogs of genes, enzymes, and pathways – parts lists for bio-based economy and bioenergy applications,” said Grigoriev. “A lot of this is encoded in early diverging fungi. In these fungi, we found that majority of expressed genes have 6mA MACs. Thus, the discovery of DNA methylation in early diverging fungi helps the research community better understand regulation of genes that encode the parts for bio-based economy and bioenergy applications.”
Mondo described the i
Right after SMRT Leiden was Oxford Nanopore Conference in London, most people are saying crowd in London was three times bigger and excitement was huge. Does anyone know something more.
Comey out. Next is McMaster!
Don't forget to vote beforeore May 26th. Hunkapillar and company need to go. You will not hear anything from them for next 3 months.