Heavily manipulated. Check the new Seeking Alpha story. What a joker.
barring any global calamity, this trends up till Christmas. There are no further negative pulls. GLTALs
Idk about you guys but I'm not seeing much of a dent in ILMN stock. If you think PACB is going to overtake them any day soon with their tech I think you're going to be deeply disappointed. That one is going UP!
Stupid dummy Hello where IS you!
I'm betting Pac-B is well on this but it's one of the risks of doing biz in China. Not sure how Illumina get's around not turning over their IP to their partner in China, or if they had to. 'The request for an investigation will focus on Beijing’s practices of coercing American companies doing business in China to partner with local firms, which require them to turn over proprietary technological secrets as part of what American officials described as a coordinated effort to steal intellectual property.'
Trump Cautious on China Inquiry Over Intellectual Property Theft
The president is seeking to fulfill hard-edge campaign promises on trade without alienating Beijing during the crisis over North Korea’s nuclear weapons program.
In Bake-Off, SMRT Sequencing Generates Highest-Quality, Cost-Effective Bacterial Assembly Tuesday, August 15, 2017
From CDC/Courtesy of Larry Stauffer, Oregon State Public Health Laboratory Scientists from the University of Hong Kong recently reported results of a head-to-head comparison of long-read and short-read platforms for sequencing and assembly of a bacterial genome. They determined that only SMRT Sequencing was capable of generating highly accurate, complete assemblies. “Completing bacterial genomes should no longer be regarded as a luxury, but rather as a cost-effective necessity,” the team reports.
“PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome” was published in Frontiers in Microbiology by lead author Jade Teng, senior author Patrick Woo, and collaborators. For this project, scientists compared performance of the PacBio RS II Sequencing System with the Illumina HiSeq 1500. Their target was Burkholderia pseudomallei, which has at least 68% GC content as well as “highly repetitive regions and substantial genomic diversity,” the authors report.
After sequencing, the team attempted both hybrid and single-source assemblies. Working with Illumina data alone “resulted in a draft genome with more than 200 contigs,” they note, pointing out that the platform’s reliance on PCR amplification is inherently problematic for GC-rich genomes. Three different short-read assemblers were not able to improve results. The hybrid assembly of both sequencers’ data was also “not successful,” producing 74 contigs, the team reports.
Assembling only PacBio data, which was generated from a single SMRT Cell, led to a very different result. The approach “achieved complete closure of this two-chromosome B. pseudomallei genome without additional costly bench work and further sequencing, demonstrating its utility in the complete sequencing of bacterial genomes, particularly those that are well-known to be difficult-to-sequence,” the scientists write. The chromosome contigs of the assembly aligned to the organism’s reference genome with better than 99.9% accuracy. Importantly, the assembly accurately characterized “the number of CDSs and their distributions in each subsystem, four ribosomal operons, the highest number of core and virulence proteins (coverage of query protein sequence and amino acid identity ≥80%), and MLST gene loci,” the team adds.
The Illumina assembly, on the other hand, was unable to resolve these elements. “Extraordinarily high coverage of Illumina reads were observed in several collapsed repeat regions, including regions containing varying copies of mobile element proteins and ribosomal operon,” Teng et al. report. “We reasoned that Illumina sequencing was not able to resolve these repeat regions as their sequence reads were not long enough to span different kinds of repeats with unique flanking sequences.”
The scientists also included an assessment of project cost. “To completely sequence a bacterial genome using Sanger sequencing or the second generation sequencing platforms, the main bulk of the cost, labor and time is spent in the gap-filling phase,” they write. “It has been estimated that when using these second generation sequencing platforms, around 95% of the money and time are spent in completing the last 1% of the bacterial genome.” But the calculation is very different for SMRT Sequencing. “Although the cost per base is more expensive for the PacBio RS II platform compared to short-read sequencing technology, no additional manual work after de novo assembly is required,” the team concludes, “and the benefit of obtaining an accurate number of individual replicons and an intact assembly of repetitive regions and mobile genetic elements justify the initial cost.”
Damn 08/15/2017 - felt like throwing up!
More fantastic updates on PACB tech from the research departments.
Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line | bioRxiv
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Anyone have access to genomeweb's article on China called- PacBio Upgrades Sequel; Sees Potential for Clinical Partnerships in China
Can't access it. Thanks.
Please join us for our West Coast User Group Meeting (UGM) on Thursday, September 7 hosted by the Puglisi Laboratory at the Stanford University School of Medicine.
The UGM will allow you to discover and understand how your peers are using SMRT Sequencing to power their research, a chance to learn best practices, and an opportunity to hear about application success stories. In addition, PacBio staff will be on-hand to answer your questions, share insights, and talk about the company’s technology road map.
User Group Meeting: Thursday, September 7, Paul Berg Hall, Li Ka Shing Center, Stanford University 8 a.m. – 5 p.m. (Reception to follow)
Confirmed Speakers Include: Alicia Clum, Joint Genome Institute Peter Myler, Center for Infectious Disease Research Tom Poorten, University of California, Davis Jeremy Schmutz, Hudson Alpha Institute for Biotechnology Birgitt Schuele, Parkinson’s Institute and Clinical Center Faramarz Valafar, San Diego State University We are also offering a Bioinformatics workshop and a Sample Preparation workshop at Stanford University the day before the UGM.
Workshops: Wednesday, September 6, Paul Brest Hall, Stanford University Sample Preparation: 9 a.m. – 1 p.m. Bioinformatics: 2 p.m. – 6 p.m We welcome the participation of those who are considering adopting SMRT Sequencing to join in the discussions and hear directly from existing users. Feel free to share this email with others who may be interested in attending.
We look forward to seeing you,
The PacBio Team
Iso-Seq Analysis Reveals Differential Expression in Male and Female Abalones Wednesday, August 9, 2017
Photo by Toby Hudson Earlier this year, scientists from Korea reported results from a transcriptome study of Pacific abalone. In this paper, the team used SMRT Sequencing to demonstrate that alternative splicing and gene expression have sex-specific signatures in these organisms.
“Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai” comes from lead authors Mi Ae Kim and Jae-Sung Rhee, senior author Young Chang Sohn, and collaborators. They focused on abalone, a marine gastropod, because of its importance to Korean aquaculture: the species they studied is estimated to represent about 10,000 metric tons of production each year.
As H. discus hannai has grown in economic importance, new genomics resources have become available, including a genetic linkage map and some RNA-seq data. This latest project was designed to glean more information about abalone to provide a clearer view of its biological function. Scientists chose to focus on sex-specific transcriptomes, using the Iso-Seq method to study gene content in male and female members of the species. They analyzed several tissue types — including gonads, muscle, gills, and more — and defined 15,110 protein-coding genes in females and 12,145 in males. Of those, 519 genes in female and 391 genes in male produced alternatively spliced transcripts.
To validate these findings, the team investigated expression profiles for six genes known to be sex-preferential in related organisms. Two of the three female-specific genes and all three male-specific genes were highly expressed in their respective samples. “Taken together, these studies strongly suggest the intactness of the sex-specific isoform DB of the Pacific abalone,” the authors write.
“The information obtained in this study represents the first significant contribution to sex-specific genomic resources, as well as isoform information,” the scientists conclude. “These data will provide an essential genomic reference that could be used for further diverse genetics- and physiology-based research using abalones.”
PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome
Although PacBio third-generation sequencers have improved the read lengths of genome sequencing which facilitates the assembly of complete genomes, no study has reported success in using PacBio data alone to completely sequence a two-chromosome bacte
SMRT Sequencing Shines at ISAG: First Sequel System Bovine Genome Presented Monday, August 7, 2017
If you weren’t at the 36th International Society for Animal Genetics Conference in Dublin, you missed more than a chance to drink Guinness and practice an Irish brogue. The PacBio team had a great time at ISAG, learning about the latest in animal science and updating attendees on the advantages of SMRT Sequencing for generating high-quality genome assemblies and annotations.
The conference drew more than 750 scientists from around the world, and we were truly impressed by the quality of research they presented in talks and posters. Long-read PacBio sequencing is already making a difference for scientists in this community, many of whom are focused on improved breeding programs. Genome assemblies powered by SMRT Sequencing were presented for many economically important species, including chicken, sheep, goat, pig, cattle, horse, camel, and Atlantic herring. There were also several presentations featuring PacBio long-read sequencing data for immune region haplotypes such as the leukocyte receptor complex and the major histocompatibility complex.
We hosted a morning seminar that demonstrated how SMRT Sequencing provides comprehensive views of animal genomes and transcriptomes. John Williams from the University of Adelaide presented a preliminary assembly of the water buffalo genome generated with Sequel System data. A member of the International Buffalo Genome Consortium, Williams described limitations in contiguity and completion for previous sequencing efforts that used short-read data for this important livestock animal. Seeking a reference-grade assembly, the scientists turned to PacBio long reads, using FALCON-Unzip to phase more than half of the diploid genome. Though the assembly is not yet polished, Williams reported a stellar contig N50 of 18.7 Mb. The other seminar speaker was our own Emily Hatas, who discussed the chicken genome annotation generated by Richard Kuo at the Roslin Institute. In that project, scientists used the Iso-Seq method with SMRT Sequencing to identify 64,000 transcripts, including more than 17,000 long non-coding RNAs that had not been previously annotated.
As sponsors of the event, we also had fun encouraging attendees to snap creative photos with the toy animals we gave away at our booth. Check out the variety of clever snapshots!
TERESA8 seconds ago If you listened to the conf. call you would know why it's going up. Shorts see there's no reason to be short this one anymore. When they get that chinese partner this will run higher than what it did with roche. The chinese market is going all in with bio and sequencing. This had been way oversold, and it's just regaining a little of it's losses. Before the deciede on a partner, I wouldn't be surprised to see some other collaborations prior to that. They also stated there was no need for further dilution. Very positve call......
At Baltimore UGM, New Tools and Research Breakthroughs with SMRT Sequencing Thursday, August 3, 2017
We were delighted to be back at the University of Maryland this summer for our annual East Coast User Group Meeting. The day-long event, preceded by half-day workshops on sample prep and bioinformatics, exceeded our expectations. From the packed session hall to the terrific science and great discussions, the UGM facilitated the exchange of best practices and new suggestions for optimizing SMRT Sequencing performance for a variety of applications. Below is a recap of the day’s highlights, with several of the presentations available to download.
PacBio scientist Aaron Wenger presented the Structural Variant Calling application that is included in the SMRT Link v5.0 software release. The application utilizes the read aligner NGM-LR, and features both a command-line tool called pbsv and a web interface. Noting that most of the genetic difference between any two people lies in structural variation, he showed that short-read sequencers cannot detect the vast majority of these important variants. Wenger demonstrated that even low-coverage SMRT Sequencing can be used to discover structural variants; in an experiment, 10-fold coverage revealed almost 100% of homozygous variants and nearly 90% of heterozygous variants in a human individual.
Michael Schatz from Johns Hopkins University gave a talk entitled “In Pursuit of Perfect Genome Sequencing” in which he walked through three key metrics for evaluating genome quality: correctness (basepair accuracy), completeness (no gaps in the sequence), and contiguity (sequence ordered as on the physical chromosomes). Schatz compared the leading sequencing technologies available today, and explained that PacBio SMRT Sequencing is the most capable technology for all three metrics.
Continuing the human genome theme, Ricardo Mouro Pinto from Massachusetts General Hospital spoke about using SMRT Sequencing to quantify CAG repeat instability in Huntington’s disease. Caused by a CAG repeat expansion, Huntington’s occurs when a person’s genome harbors 40 or more copies. Pinto noted that typically, the longer the repeat, the younger the person is at disease onset. The Huntington’s locus is difficult to enrich because it is resistant to PCR amplification. By using Cas9 digestion to perform non-amplification-based target enrichment followed by PacBio sequencing, Pinto’s team was able to capture wild type and disease alleles with no amplification bias. He noted that results are preliminary, and he hopes to expand the number of samples studied to get a better handle on CAG instability.
Representing the plant community, Hamid Ashrafi and Hamed Bostan from North Carolina State University tag-teamed a presentation on the blueberry genome and transcriptome. The fruit plant naturally occurs in diploid, tetraploid, and hexaploid genomes. The scientists generated a high-quality diploid assembly using SMRT Sequencing and noted that long reads were essential to get through the highly repetitive genome. Next, they used Iso-Seq to study several types of tissue from diploid, tetraploid, and hexaploid blueberry plants, finding many transcripts missed by short-read sequence data. Using both genome and transcriptome approaches was particularly important, Ashrafi noted, because SNPs explain only a small portion of natural variation for this plant, and he believes that alternative splicing and structural variants likely contribute a much larger proportion of variation. The team is still analyzing results but said that switching to long reads was “a dream come true.”
On the microbial front, Jethro Johnson from The Jackson Laboratory for Genomic Medicine gave a talk on full-length 16S rRNA sequencing, which is useful for taxa identification. By genotyping or using short-read data, Johnson said, so much of the information in the variable regions of 16S is missed that it often is impossible to accurately classify organisms. So, Johnson turned to SMRT Sequencing and circular consensus sequencing (CCS), which generates highly accurate long reads. Johnson applied CCS for a mock bacterial community of 36 species and found that SMRT Sequencing offered accurate results for identification. In studies of fecal samples, PacBio sequencing was able to provide a unique identification in cases where short-read sequencing generated ambiguous results. The team is now expanding SMRT Sequencing results to include internal transcribed spacer regions.
In a separate presentation, Phillip Tai from the University of Massachusetts Medical School highlighted the use of long-read sequencing for genome population sequencing of adeno-associated viruses. These harmless viruses have gained new interest recently as a vector for gene therapies, so Tai’s lab is interested in analyzing large groups of them to filter out any that would not be ideal vectors. By applying SMRT Sequencing to recombinant AAVs, they generate complete resolution of the vector genome, including the difficult-to-sequence inverted terminal repeats. This accomplishment could have tremendous value in the gene therapy field, he said.
The meeting also included some new tools and protocols from the community. New England Biolabs’ Bo Yan presented SMRT-cappable-seq, a method for characterizing operons across an entire bacterial genome. It involves capping the 5’ end of bacterial primary transcripts and using SMRT Sequencing to produce full-length transcripts. Yan said the protocol increases library prep efficiency and accurately defines and links the transcription start site and transcription termination site (something short reads cannot do). A validation project in E. coli revealed 840 novel operons, extending 40% of annotated operons in RegulonDB. In another talk, Manuel Tardaguila from the University of Florida discussed SQANTI, a new tool to perform quality control for long-read transcripts. The pipeline performs classification, curation, and quantification of transcripts to filter out any artifacts and ensure that scientists analyze only the highest-quality results. SQANTI incorporates PacBio data, a reference genome, and other resources to conduct its rigorous evaluation.
We’d like to thank our hosts for the meeting, the Genomics Resource Center, Institute for Genome Sciences at the University of Maryland, as well as our partners: Advanced Analytical Technologies, Diagenode, and Sage Science. And, of course, thanks to all the scientists who took time out of their busy schedules to make this event a success!
Did @PACB get us any update on the new chemical and new software and new anything to the boosting of throughput in the Q2 meeting?
IMHO, that is more important than selling 10 more Sequel...
Hehe now we know Hello's real name- Keith Speights. These short guys are rather pathetic. Spin Doctors, or just can't see the forest through the trees is all.