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Thursday, September 24, 2015

At Genome in a Bottle Workshop, Progress on New Reference Materials

Genome in a Bottle consortium The National Institute of Standards and Technology held its latest Genome in a Bottle workshop last month in Gaithersburg, Md., and we were honored to attend. NIST has performed pivotal work to establish reference materials for the genomics community, starting with its RNA spike-in standards (ERCC spike-in controls) and continuing now with the GIAB consortium. These standards are essential for quality control and we’re pleased to be working with NIST to help ensure the highest accuracy in human genome sequencing.Last year, GIAB released its first reference standard, based on the well-studied NA12878 human genome (NIST RM…

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Thursday, July 9, 2015

The Festival of Genomics Review: A Celebration of Long Reads

At the inaugural Festival of Genomics event in Boston, more than 1,500 people turned out to see what was billed as a conference unlike any other. The meeting was indeed unique, featuring a play (starring well-known scientists), a giant chess board, and a Genome Dome, in addition to the more familiar lineup of excellent speakers and workshops. To help kick off the festival, genomic luminaries Craig Venter and James Lupski presented plenary talks on day 1 and set the stage for some exciting science to follow. Lupski’s talk was particularly impactful, as he described how his team at Baylor recently…

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Thursday, April 30, 2015

In Study, Continuous Long Reads Outperform Synthetic Long Reads for Resolving Tandem Repeats

Scientists from Argentina and Brazil published the results of a study comparing long-read approaches to characterize the genome structure of a highly complex region of the Y chromosome in Drosophila melanogaster. They found that Single Molecule, Real-Time (SMRT®) Sequencing outperformed synthetic long reads in accurately representing tandem repeats. The study aimed to resolve the structure of the autosomal gene Mst77F, which had previously been found to have multiple tandem copies; the region, however, was known to be grossly misassembled in the reference. The scientists, from Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas and Universidade Federal…

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Friday, April 24, 2015

On DNA Day, Celebrating New Firsts

Hooray for DNA!  We’re excited to celebrate this day as it it honors two major accomplishments in the field: the 1953 publication of the structure of DNA, and the 2003 completion of the Human Genome Project. With the amount of attention DNA has received in the past century, it is hard to believe that in some ways we are still just getting acquainted with the molecule. Here at PacBio, we are proud to be helping life sciences researchers achieve new firsts with DNA. Because it does not use amplification, our Single Molecule, Real-Time (SMRT®) Sequencing platform provides the purest view…

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Friday, April 17, 2015

AACR 2015: A Novel Look at Cancer, and a New SMRT Sequencing Grant Program

We’re looking forward to the annual meeting of the American Association for Cancer Research, which kicks off this weekend in Philadelphia. From directly phasing variants to sequencing full-length gene isoforms and other complex events, many scientists are already using SMRT® Sequencing to make exciting discoveries in cancer research. We hear from customers that the single-molecule approach opens the door for experiments they could not have done any other way. If you’ll be at AACR, we encourage you to attend the talk from UCSF’s Catherine Smith on Monday at 10:40 a.m. in room 201. Her presentation, “Polyclonal and heterogeneous resistance to…

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Tuesday, March 3, 2015

AGBT Highlights, Day Three: Genomic Medicine, Population Specific Genomes, Goats & Influenza

Day 3 of the AGBT conference was packed with interesting talks - we've covered a few highlights below.  Admittedly, it took a little more caffeine than usual to power through the day..... In the clinical session, Euan Ashley from Stanford told attendees that genomic medicine is no longer something that we’re aiming for; it’s already here and being used routinely. He expressed concerns about accurate mapping of short-read sequence data for clinical utility, adding that the community needs to make progress in understanding complex genomic regions. Ashley noted that we still don’t have a gold-quality human genome with every single…

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Thursday, December 11, 2014

Review Article: Long-Read Sequencing Offers Better Understanding of Pluripotency

A new review article offers a nice overview of attempts to characterize the transcriptome of human stem cells using RNA-seq, the Iso-Seq™ method, and more. Kin Fai Au and Vittorio Sebastiano, scientists at the University of Iowa and Stanford University, respectively, contributed the review to Current Opinion in Genetics & Development. “The introduction of the RNA-Seq technology based on [second-generation sequencing technology] has provided a remarkable step forward providing a fast and inexpensive way to determine the transcriptome of a given cell type and several remarkable works have been done using this type of approach,” Au and Sebastiano write. “Nonetheless…

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Wednesday, November 12, 2014

New Transcript Study Offers Clues to Pathogenesis of Repeat Disorders Linked to FMR1

It’s been nearly two years since a team of scientists from the University of California, Davis, School of Medicine published the first-ever complete sequence of FMR1, the gene associated with a repeat expansion that causes Fragile X syndrome. That team is once again breaking new ground, this time characterizing alternative splicing and full-length transcripts of FMR1. For both studies, the scientists relied on Single Molecule, Real-Time (SMRT®) Sequencing because its uniquely long reads allowed them to span the gene and generate sequence and isoform data that would not have been possible any other way. The new paper, “Differential increases of…

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Wednesday, October 29, 2014

‘Revolutionizing HLA Typing’: Uppsala’s Ulf Gyllensten on How Long Reads Give Access to New Areas of the Human Genome

In a recent interview with Theral Timpson — part of Mendelspod’s series on long-read sequencing — Ulf Gyllensten, a scientist at Uppsala University, spoke about using PacBio® technology for HLA typing, human genome studies, transcriptomics, and more. Based in the medical genetics and genomics department, Gyllensten focuses on two areas: using systems biology to study biological variation in human physiology and studying the epidemiology of human papilloma virus and its genetic link to cervical cancer. He also works with the National Genomics Infrastructure, a national core facility in Sweden for genotyping and DNA sequencing, where he has access to all…

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Wednesday, October 15, 2014

New Chemistry Boosts Average Read Length to 10 kb – 15 kb for PacBio® RS II

We are pleased to announce the launch of our new reagent kit, P6-C4, which represents the next generation of our polymerase as well as our chemistry. This kit replaces the P5-C3 chemistry and is recommended for all SMRT® Sequencing applications, including de novo assembly, targeted sequencing, isoform sequencing, minor variant detection, scaffolding, long-repeat spanning, SNP phasing, and structural variant analysis. P6-C4 continues the steady read length improvement our users have seen since the instrument first launched. With this new chemistry, average read lengths increase to 10 kb - 15 kb, with half of all data in reads 14 kb or…

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Monday, October 6, 2014

‘The Quality of PacBio Data Is Beyond Compare’: Eric Schadt on Applications of SMRT Sequencing to Human Genetics

As part of its continuing series on long-read sequencing, last week Mendelspod aired an engaging interview with Eric Schadt, Professor & Chair of Genetics and Genomic Sciences, and Director of the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai. Having now spent three years in his role at the groundbreaking institute, he reports that they are making great progress in the quest to build better data-driven health profiles around individuals that may better guide healthcare choices. On short-read versus long-read sequencing Short-read sequencing technologies still maintain the advantage in terms of throughput, says Schadt, but there are a…

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Thursday, October 2, 2014

‘We’re Going to Find the Keys’: Dan Geraghty Discusses an Approach to Understanding Causal Genetic Variation

Dan Geraghty, a researcher at Fred Hutchinson Cancer Research Center and CEO of Scisco Genetics, has spent much of his career focused on the genetics of immune response. Recently he talked to Mendelspod host Theral Timpson as part of a continuing series of podcasts on the rise of long-read sequencing. Geraghty explained that while there have been decades’ worth of studies associating the genetics of the major histocompatibility complex (MHC), and the highly polymorphic HLA class 1 and 2 genes, we still haven’t found the key mutations for a variety of different autoimmune diseases such as type 1 diabetes, rheumatoid…

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Tuesday, September 23, 2014

Science Perspective: “Tracking Antibiotic Resistance”

In the current issue of Science there is an interesting Perspective by Scott Beatson and Mark Walker of the University of Queensland discussing research published this week in Science Translational Medicine by Conlan et al. who used SMRT® Sequencing to track plasmid diversity of hospital-associated infectious bacteria at the NIH Clinical Center. The article provides a nice overview of the paper, including an explanation of the important role that plasmids play in spreading antibiotic resistance. They illustrate why short-read DNA sequencing technologies are insufficient in resolving them and long reads are necessary for this work. “Plasmids may be viewed as…

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Monday, September 22, 2014

Maryland Scientists Produce High-Quality, Cost-Effective Genome Assembly of Loa loa Roundworm Using SMRT Sequencing

A paper just released in BMC Genomics details what authors call “the most complete filarial nematode assembly published thus far at a fraction of the cost of previous efforts.” The project was performed using the PacBio® RS II DNA Sequencing System by scientists at the University of Maryland School of Medicine’s Institute for Genome Sciences and the Laboratory of Parasitic Diseases at the National Institute of Allergy and Infectious Diseases. In this genome sequencing effort, scientists generated a de novo assembly of Loa loa, a roundworm that infects humans. L. loa, transmitted to humans by deer flies, causes loiasis. The…

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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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