PacBio Blog

Thursday, October 1, 2015

ASHG 2015: Workshop, Presentations, and First Chance to See the Sequel System

We’re looking forward to the year’s biggest scientific meeting focused on human genetics next week — the American Society of Human Genetics (ASHG) 2015 annual meeting, taking place in Baltimore, Maryland. SMRT® Sequencing will be featured in 36 scientific presentations, as well as our lunchtime workshop. Even if you’re not attending you can attend our workshop virtually to learn more about our newest SMRT Sequencer – the Sequel™ System — and about the latest uses of SMRT Sequencing for human biomedical applications.

Our workshop, “Addressing Hidden Heritability through Long-Read Single Molecule, Real-Time (SMRT) Sequencing” will be held on Wednesday, October 7, from 1:00-2:30 p.m. Eastern Time at the Sheraton Inner Harbor Hotel, Baltimore. The event will be hosted by Michael Hunkapiller and Jonas Korlach from Pacific Biosciences, and include talks by Richard Gibbs from Baylor College of Medicine and Richard Wilson from Washington University in St. Louis. Sign up to attend in person or virtually.

Podium Presentations

The depth and breadth of scientific talks presented at ASHG this year demonstrate how long-read SMRT Sequencing is opening up new frontiers by helping the genome sequencing community create gold-standard genome references, characterize complex regions, resolve structural variation, and unlock isoform diversity. Highlights include the following podium presentations:

Wednesday, October 7

2:30 p.m.
Long read single-molecule real-time (SMRT) full gene sequencing of cytochrome P450 2D6 (CYP2D6) #27
Yang, Icahn School of Medicine at Mount Sinai

3:15 p.m.
Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing #14
Nattestad, Cold Spring Harbor

3:30 p.m.
Evolution and structural diversity of the complement factor H related gene cluster #47
Cantsilieris, University of Washington School of Medicine

Friday, October 9

2:15 p.m.
Building a platinum assembly from single haplotype human genomes generated from long molecule sequencing #227
Meltz Steinberg, Washington University

2:30 p.m.
Building a Better Human Genome Reference and Targeting Structure using Single Molecule Technologies #228
Sebra, Icahn School of Medicine at Mount Sinai

2:45 p.m.
Genome in a Bottle: You may have sequenced, but how well did you do? #229
J.M. Zook, National Institute of Standards and Technology

3:30 p.m.
A Diploid Personal Human Genome Reference from Diverse Sequence Data – A Model for Better Genomes #232
K.C. Worley, Baylor College of Medicine

Saturday, October 10

10:45 a.m.
Full-length mRNA sequencing uncovers a widespread coupling between transcription and mRNA processing #71
S.Y. Anvar, Leiden University Medical Center

Additional Activities at ASHG

Research conducted using SMRT Sequencing will also be featured in at least 28 poster presentations. Check out the full list of PacBio-related ASHG meeting research and activities. Attendees can also visit the PacBio booth (#907) to learn more about the new Sequel System.

We hope to see you in Baltimore!

Wednesday, September 30, 2015

Introducing the Sequel System: The Scalable Platform for SMRT Sequencing

We are excited to announce our newest Single Molecule, Real-Time sequencer, the Sequel™ System. Visit our new website to learn about this exciting evolution in SMRT® Sequencing.

The Sequel System provides higher throughput, more scalability, a reduced footprint and lower sequencing project costs compared to the PacBio® RS II System, while maintaining the benefits of SMRT technology. The core of the Sequel System is the capacity of its redesigned SMRT Cells, which contain one million zero-mode waveguides (ZMWs) at launch, compared to 150,000 ZMWs in the PacBio RS II. Active individual polymerases are immobilized within the ZMWs, providing windows to observe and record DNA sequencing in real time.

With about seven times as many reads per SMRT Cell as the PacBio RS II, customers should be able to realize lower costs and shorter timelines for sequencing projects, with approximately half the up-front capital investment compared to previous technology. The Sequel System occupies a smaller footprint — less than one-third the size and weight — compared to the PacBio RS II. Since the new system is built on the company’s established SMRT Technology, most aspects of the sequencing workflow are unchanged.

The Sequel System is ideal for projects such as rapidly and cost-effectively generating high-quality, whole-genome de novo assemblies for larger genomes, such as human, plants, and animals. It can provide characterization of a wide variety of genomic variation types, including those in complex regions not accessible with short-read or synthetic long-range sequencing technologies, while simultaneously revealing epigenetic information. The system can also be used to generate data for full-length transcriptomes and targeted transcripts using the company’s IsoSeq™ protocol. The Sequel System’s increased throughput should also facilitate applications of SMRT Technology in metagenomics and targeted gene applications for which interrogation of larger numbers of individual DNA molecules is important.

In today’s press release, Michael Hunkapiller, Ph.D., CEO of Pacific Biosciences, commented: “We are extremely proud to introduce the Sequel System, which provides access to the existing benefits of SMRT Sequencing, including long reads, high consensus accuracy, uniform coverage, and integrated methylation information — a set of core attributes first pioneered with the PacBio RS. The system’s lower cost and smaller footprint represent our continued commitment to leveraging the scalability of our technology and the unique characteristics of SMRT Sequencing.”

“We will continue to support our PacBio RS II customers, and we expect to introduce improvements in sample prep, sequencing chemistry, and software that will extend the performance of that system, as we have done each year since the initial commercialization of the PacBio RS in 2011 and the PacBio RS II in 2013. We expect to make similar, substantial performance improvements each year for the Sequel System,” added Dr. Hunkapiller. “In addition, the Sequel architecture provides the ability to scale throughput by substantially varying the number of ZMWs on future SMRT Cells, thereby optimizing throughput and operating costs for specific applications.”

On Display at the ASHG Annual Meeting

We will showcase the Sequel System in our booth (#907) at the American Society of Human Genetics annual meeting taking place in Baltimore, Maryland, beginning October 6, 2015.

Whether or not you are attending the meeting, you can still attend our workshop, “Addressing Hidden Heritability through Long Read Single Molecule, Real-Time (SMRT) Sequencing,” on Wednesday, October 7, from 1:00-2:30 p.m. The event will be hosted by Michael Hunkapiller and Jonas Korlach from Pacific Biosciences, and include talks by Richard Gibbs from Baylor College of Medicine and Richard Wilson from Washington University in St. Louis. Those attending the conference in Baltimore can register here. We will also offer live streaming and access to the recording.

Friday, September 25, 2015

Marc Salit at NIST: Defining Standards for the Human Genome

In the first podcast of a new series on the applications of long-read sequencing, Mendelspod host Theral Timpson interviewed Marc Salit, leader of the Genome Scale Measurements Group at the National Institute of Standards and Technology. Their conversation focused on how and why NIST is involved in establishing baseline measurements for the human genome.

Salit, along with Justin Zook and their team at NIST, are managing the Genome in a Bottle (GIAB) Consortium to develop reference materials, data, and methods needed to assess whole human genome sequencing. Their goal is to establish a physical reference genome as a standard against which subsequent measurements can be compared, providing a foundation for the translation of whole genome sequencing into clinical practice.

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 8398). At this year's meeting, attendees from clinical sequencing groups shared their experiences with this reference material, which they are using to support clinical testing and validation. The reference is designed to help users make high-confidence variant calls across many types of variation. In addition, attendees from the FDA described how they anticipate using the reference material to assess device performance as part of the regulatory review process for diagnostics.

Wednesday, September 23, 2015

SMRTest Microbe Grant Winner: Identifying Antibiotic Resistance Mechanisms with SMRT Sequencing

We’re pleased to announce the winner of our recent “SMRTest Microbe” grant competition. Congratulations to Dr. Erin Price at the Menzies School of Health Research in Australia! The grant program, co-sponsored by PacBio and the Institute for Genome Sciences (IGS), was very competitive, with more than 100 submitted proposals.

Dr. Price will receive SMRT® Sequencing and analysis from IGS  — using up to 4 SMRTbell™ libraries and 8 SMRT Cells — to characterize the mechanisms behind the emergence of antibiotic resistance in Burkholderia pseudomallei, a highly pathogenic bacterium that causes the potentially deadly disease melioidosis. Dr. Price and colleagues have recently uncovered the development of meropenem resistance in local cases of B. pseudomallei infection, along with evidence that this resistance is linked to at least two mortalities in Australia so far.

Prior short-read-based attempts to sequence and assemble the genomes of these meropenum-resistant B. pseudomallei have suffered from the inability to scaffold across highly repetitive and paralogous loci, low genome complexity, high GC content, and genomic inversions. Dr. Price plans to use the long reads generated by SMRT Sequencing to overcome these assembly issues and close the genomes. As noted in her proposal, complete genome sequences “will provide significant insights into the molecular basis of meropenem resistance in this dangerous pathogen.”

Thursday, September 17, 2015

SMRT Data Analysis: Updates from our Developers Conference

Last month we hosted a SMRT® Informatics Developers Conference, bringing together 150 developers with a passion for improving tools and resources. Our team came back brimming with enthusiasm for tools that will be released in the coming months, and humbled by the commitment we saw from the bioinformatics community to help scientists make SMRT Sequencing data increasingly useful. Thanks to the National Institute of Standards and Technology for hosting our meeting on their campus right before the Genome in a Bottle workshop.

The big news we shared with attendees is that the PacBio® System will now output industry-standard BAM files instead of our usual HDF5 format — check out the new specifications.

Tuesday, September 8, 2015

Webinar: Long Fragment Capture for SMRT Sequencing

Roche recently posted this recording of a webinar walking through long fragment capture with SMRT® Sequencing. “Long Genomic DNA Fragment Capture and SMRT Sequencing Enables Accurate Phasing of Cancer and HLA Loci” is a great backgrounder for scientists interested in using the Roche NimbleGen SeqCap EZ System for target enrichment prior to sequencing on the PacBio® system.

The webinar features Denise Raterman from Roche NimbleGen and our own bioinformatics expert Lawrence Hon. Raterman provides a detailed review of the SeqCap EZ workflow, pointing out the specific steps that differ for SMRT Sequencing. The method can be used to capture up to 200 Mb of DNA. Hon presents a step-by-step guide for using SMRT Portal and other tools, including data from the MHC region and a targeted oncology panel, that demonstrate the even coverage generated across multi-kilobase genomic regions. He also explains the bioinformatics workflow for phasing and analyzing haplotypes.

Wednesday, August 26, 2015

In Bacterial Study, Scientists Link Epigenetic Switch to Virulence, Antibiotic Resistance, and More

Scientists from Griffith University, Ohio State University College of Medicine, and other institutions recently published a detailed study of phase-variable expression of a DNA methyltransferase in non-typeable Haemophilus influenzae, the predominant cause of pediatric middle ear infections. The team found that the bacterium’s epigenetic switch regulates proteins used in current vaccine candidates and influences important traits including antibiotic resistance, ability to evade the host immune system, and biofilm formation, which significantly contributes to chronic infection.

The paper, “A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae,” was published in Nature Communications last month by lead author John Atack, senior author Michael Jennings, and colleagues. Their study of H. influenzae used SMRT® Sequencing to elucidate the genome and epigenome of multiple bacterial strains collected across several decades. Closed genome assemblies were generated for all five bacterial strains sequenced.

Thursday, August 20, 2015

The Gapless Assembly: Scientists Describe Workflow for Producing Complete Eukaryote Genome

Sunflowers with verticillium wilt caused by V. dahliae
In a new mBio publication, scientists from Wageningen University and KeyGene in The Netherlands report results from several strategies used to assemble the genome of a filamentous fungus, and describe the specific pipeline they recommend for sequencing and assembling eukaryotic genomes.

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome” comes from lead authors Luigi Faino and Michael Seidl, senior author Bart Thomma, and collaborators. Using Verticillium dahliae as a model, which is a plant pathogen responsible for the damaging verticillium wilt disease in many crop species, they compared short-read and long-read sequencing approaches and incorporated optical mapping data to develop the method that generated the highest-quality assembly for the 36 Mb genome. This particular fungus was an ideal fit for the project, the authors note, due to its extensive genomic rearrangements and enrichment for repetitive elements.

Wednesday, August 12, 2015

Using SMRT Sequencing, Scientists Uncover Unexpected Transcript Diversity in Fungi

A new PLoS One publication from scientists at the Joint Genome Institute, University of Minnesota, and other organizations demonstrates that fungal genomes may contain far more transcript diversity than previously thought.

In “Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing,” lead author Sean Gordon, senior author Zhong Wang, and collaborators used long-read isoform sequencing to characterize four fungal species. In addition to widespread alternative splicing, they found evidence of polycistronic transcription units that could be important engineering targets for genetic manipulation of fungi.