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Thursday, February 26, 2015

AGBT Highlights, Day One: Advancing Human Reference Assembly & Sequencing in the Clinic

It is great to be here in Marco Island for the AGBT meeting! The 16th annual meeting hit the ground running with a pre-meeting workshop hosted by the Genome Reference Consortium (GRC) followed by an opening session that was more clinically focused than many attendees are used to at this tech-heavy conference. From the dynamic Q&A sessions, it was clear that these were precisely the kind of talks that people have been looking for as this meeting evolves downstream along with genomic science. The GRC workshop, entitled ‘Advancing the Human Reference Assembly’ included four speakers: Valerie Schneider (NCBI), Tina Graves-Lindsay…

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Tuesday, February 24, 2015

AGBT 2015: Seeing the Genome in a New Light (Sunshine?)

Like many others, we’re looking forward to an exciting week of science and sun at the 16th annual Advances in Genome Biology and Technology (AGBT) conference! We’re hosting a lunch workshop on Friday, February 27, in the Palms Ballroom from 12:00 pm to 2:00 pm EST. We hope you can join us onsite (please reserve your seat) and even if you’re not at the conference, you can watch the live stream. Here’s the agenda: Towards Comprehensive Genomics – Past, Present and Future The Human Genome: From One to One Million J. Craig Venter, Human Longevity Inc. Is Perfect Assembly Possible?…

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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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Monday, November 10, 2014

Nature Paper Offers Novel Sequence, Structural Variant Data for a More Complete Human Genome

A new paper out in Nature extends our view into the human genome and challenges current ideas about genetic variation. “Resolving the complexity of the human genome using single-molecule sequencing” comes from first author Mark Chaisson, senior author Evan Eichler, and their collaborators at the University of Washington, University of Bari Aldo Moro, and University of Pittsburgh. In the paper, the scientists describe an important effort to fill gaps and better characterize structural variation in the human genome by using Single Molecule, Real-Time (SMRT®) Sequencing data. The team sequenced a haploid human genome, using a hydatidiform mole cell line (CHM1),…

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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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Tuesday, October 21, 2014

Data Release: Whole Human Transcriptome from Brain, Heart, and Liver

In higher eukaryotic organisms, like humans, RNA transcripts from the vast majority of genes are alternatively spliced. Alternative splicing dramatically increases the protein-coding potential of eukaryotic genomes and its regulation is often specific to a given tissue or developmental stage. Using our updated Iso-Seq™ sample preparation protocol, we have generated a dataset containing the full-length whole transcriptome from three diverse human tissues (brain, heart, and liver). The updated version of the Iso-Seq method incorporates the use of a new PCR polymerase that improves the representation of larger transcripts, enabling sequencing of cDNAs of nearly 10 kb in length. The inclusion…

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Friday, October 10, 2014

ASHG 2014: A New Look at the Human Genome with Long-Read Sequencing

Scientists around the world are getting ready for the annual meeting of the American Society of Human Genetics taking place October 18-22 at the San Diego Convention Center. We’re looking forward to a number of excellent presentations and posters, and are delighted to see that many of them will focus on applying Single Molecule, Real-Time (SMRT®) Sequencing to human studies. If you’ll be among those attending ASHG, be sure to attend our workshop, A New Look at the Human Genome – Novel Insights with Long-Read PacBio Sequencing, taking place 12:30 – 2:00 p.m. on Tuesday, October 21. Register in advance to…

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Friday, June 27, 2014

At SFAF 2014, Great Science and High-Quality Genomes

It’s been a busy start to the summer, but we’re still basking in the top-notch presentations and posters from the Sequencing, Finishing, and Analysis in the Future meeting last month. Hosted by Los Alamos National Laboratory in Santa Fe, this has become a premier event for scientists working on sequencing protocols, analysis, and assembly methods. Many speakers presented data including reads from Single Molecule, Real-Time (SMRT®) Sequencing. Jeff Rogers from Baylor College of Medicine used long PacBio® reads with the PBJelly algorithm to fill gaps in many mammalian genomes, including sheep, rat, baboon, sooty mangabey, and mouse lemur. Tina Graves-Lindsay…

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Wednesday, May 28, 2014

The Sequence Analysis Meeting: SFAF 2014

The Sequencing, Finishing, and Analysis in the Future (SFAF) meeting kicks off today in Santa Fe, New Mexico. The conference is hosted by Los Alamos National Laboratory and focuses on the analytical details that are so important as the community assesses how to get the most out of all this sequence data. This year, we will have two PacBio speakers, and there will be a number of other talks from users of our long-read sequence data. Steve Turner, our CTO, will speak on Wednesday morning about the use of Single Molecule, Real-Time (SMRT®) Sequencing for generating highly contiguous genome assemblies…

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Tuesday, May 13, 2014

A New Approach for HLA Typing: SMRT Sequencing

Two recent news announcements demonstrate the utility of our Single Molecule, Real-Time (SMRT®) Sequencing technology in the challenging realm of HLA typing.  HLA typing — or analysis of genes in the human leukocyte antigen region of the human genome — is of critical importance for research in tissue transplantation matching, autoimmune disease-association studies, drug hypersensitivity research, and other applications. But analyzing those genes, which are highly polymorphic and contain thousands of alleles that code for proteins important in recognizing foreign antigens, has proven difficult with most technologies. Use of Sanger or short-read sequencing technologies has required other methods for confirmation…

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Saturday, February 15, 2014

AGBT Day 1 & 2 Highlights: Hello GRCh38 & SMRT Sequencing for Pathogen Screening

AGBT 2014 is off to a roaring start – the opening reception was hastily moved indoors when an impressive thunderstorm joined the party. Wednesday’s kickoff plenary session offered an insightful view of the recently released human genome reference, known as GRCh38, which is available with GenBank accession GCA_000001405.15. Valerie Schneider from the National Center for Biotechnology Information gave a presentation on the latest build, highlighting improvements that range from alternate loci to modeled centromeres to error correction of individual bases. The Genome Reference Consortium resolved more than 1,000 reported issues from build 37 with the release of this new build…

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Wednesday, February 12, 2014

Data Release: ~54x Long-Read Coverage for PacBio-only De Novo Human Genome Assembly

We are pleased to make publicly available a new shotgun sequence dataset of long PacBio® reads from a human DNA sample. We previously released sequence data using Single Molecule, Real-Time (SMRT®) Sequencing of ~10x coverage of this sample, sufficient for reference-based detection of structural variation. Today we expand on that release with additional data that increases the total sequencing coverage to ~54x.  This long-read data has enabled the generation of the first de novo human genome assembly from PacBio-only sequence reads. Download the 54x long-read coverage dataset. The dataset was generated from sequencing a well-studied human cell line (CHM1htert), which…

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Tuesday, February 11, 2014

AGBT 2014 Preview: Long reads, long flight, long days!

We are flying cross-country to Marco Island, Florida, to attend the fifteenth annual Advances in Genome Biology and Technology conference and, as we have done for years now, we are proud to be sponsoring the event. This year we look forward to connecting with the many researchers who already work with SMRT® Sequencing data, and to meeting others whose scientific efforts could benefit from our technology’s uniquely long reads and base modification information. Here are some of the presentations we’ll be attending: Evan Eichler, University of Washington, “Advances in Sequencing Technology Identify New Mutations, Genes and Pathways Related to Autism” …

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Tuesday, January 21, 2014

Genome Research Paper: Resolve Complex Genomic Regions for a ‘Fraction of the Cost’ With SMRT Sequencing

A new Genome Research paper describes the application of Single Molecule, Real-Time (SMRT®) Sequencing to resolve repeat-heavy genomic regions in important reference genomes such as human and chimpanzee. In the process, the authors drew some important conclusions about cost, pooling, and coverage requirements for this type of work. “Reconstructing complex regions of genomes using long-read sequencing technology” comes from lead author John Huddleston and senior author Evan Eichler at the University of Washington, along with collaborators at Washington University, the University of Bari, Bilkent University, and Pacific Biosciences. In the paper, Eichler and his collaborators note the steep cost of…

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Thursday, January 16, 2014

Looking Ahead: The 2014 PacBio Technology Roadmap

By Jonas Korlach, Chief Scientific Officer 2013 was an eventful and exciting year for PacBio. As I described in the 2013 roadmap post a year ago, we have applied numerous improvements to SMRT® Sequencing, resulting in longer read lengths, greater sequencing throughput, new and improved data-analysis methods, and more efficient workflows. We are very pleased that these advances resulted in so many publications, conference presentations, and social media contributions, with the number of peer-reviewed scientific publications from the scientific community now exceeding 100. On behalf of all of us at Pacific Biosciences, I would like to express my heartfelt gratitude…

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