Hosting PacBio User Group Meeting June 27/28: Win Sequencing on our Sequel System

For the 5th year in a row, we’re proud to be hosting the annual PacBio East Coast User Group Meeting (UGM) & Workshops on June 27 & June 28 at the School of Pharmacy.  The UGM is a great opportunity to hear how scientists are using SMRT Sequencing to advance their research, a chance to learn best practices, and an opportunity to hear about application success stories. The agenda features speakers from Johns Hopkins University, The Jackson Laboratory, New England Biolabs, Massachusetts General Hospital and Harvard Medical School, University of Massachusetts Medical School, North Carolina State University, University of Florida & more. In addition, PacBio staff will be on-hand to answer questions, share insights, and talk about the technology road map.

 

Two SMRT Sequencing interactive workshops take place on campus on June 27th:

  • From 9am – 1pm, the Bioinformatics Workshop will highlight new tools available within SMRT Analysis 4.x. The PacBio Bioinformatics team will share analysis guidance for ensuring genomes are publication ready, as well as discuss various multiplexed analyses available through SMRT Link and enabled by the latest protocols for the Sequel System.
  • From 2pm – 6pm, the Sample Prep Workshop will cover product updates, application updates, and sample preparation recommendations to achieve the longest reads possible. Interactive group breakout sessions will facilitate discussions about specific applications of SMRT Sequencing.

Register online to attend these events.

 

New to PacBio sequencing?  We’re offering a chance to win sequencing and analysis on our new Sequel System.  The Microbial SMRT Grant program is open until June 30 and entering is simple: just submit a brief application describing how you’d use the long reads, high accuracy, single-molecule resolution, and uniform coverage of SMRT Sequencing to fully characterize viruses, microbes, and/or their communities.

 

One winner will be chosen by a panel of scientists. Submit your entry today!

ASM SMRT Grant Winner: Squirrel Microbiome!

We’re pleased to announce the winner of this year’s SMRT Grant, which launched during the American Society for Microbiology annual meeting this summer. The grant program, co-sponsored by PacBio and the Institute for Genome Sciences (IGS), was very competitive, with over 100 submitted proposals. From this broad range of entries, our judges faced quite a task choosing just one recipient for the grant.

Congratulations to Jessica Sieber from the University of Minnesota Duluth, who impressed reviewers with her proposal, “Metagenomic analysis of the gut microbiota of the 13-lined ground squirrel, a model fat storing hibernator.”

Ground squirrels have been models for human health conditions from diabetes and obesity to longevity and hypothermia. These particular squirrels are scientifically interesting because they almost triple their weight before going into a six-month hibernation, during which they consume nothing. Sieber notes that the hibernation process involves reducing the squirrel’s body temperature to 4 degrees Celsius. While that should be a challenging environment for the animal’s gut microbes, in fact they appear to thrive and may be responsible for folate production to protect the squirrel’s brain during hibernation. A deeper understanding of the role these microbiota play in this process may have downstream implications for human health.

Sieber’s project involves using SMRT Sequencing to produce a high-resolution picture of these gut microbial communities, including how they withstand the cold hibernation temperature. We look forward to learning about the new insights she discovers as a result of this grant!

In addition to the grant winner, the submitters of the top 10 proposals will have the opportunity to conduct their projects through IGS with a 20% discount on SMRT sequencing. Thank you to all of the submitters who participated in the grant competition. We look forward to a number of exciting new projects in the coming months!

Do you have a project that could benefit from SMRT sequencing or any of our other sequencing and analysis services? If so, please contact us for a free project consultation.

The PacBio Sequel is here! Join us for the PacBio User Group Meeting – June 8

We are excited to announce that our PacBio Sequel System has arrived! The newest instrument from PacBio joins the RS II system which has been with us since 2011. The Sequel uses redesigned SMRT Cells containing more than one million ZMWs (zero mode waveguides), a significant increase over the 150,000 ZMWs on RS II cells. The increased capacity of the cells means a potential for up to 6x as many reads per run compared to the RS II system. Over the past several weeks, we have begun evaluating and optimizing the Sequel. While initial supplies of the new SMRT Cells are limited, we expect improved cells and the next chemistry release in the coming months. Our goal is to offer sequencing on the Sequel as part of our services portfolio this summer.

If you are interested in hearing more about PacBio applications and the Sequel System at GRC, please join us as we host the PacBio East Coast User Group Meeting on June 8.

Pacbio Sequel

The PacBio Sequel System next to the Pacbio RS II.

 SMRT Cells

Evolution of PacBio’s SMRT Cell.  From Left to Right: SMRT Cell V2, SMRT Cell V3, and SMRT Cell 1M.

SMRTest Microbe Grant Winner: Identifying antibiotic resistance mechanisms with SMRT Sequencing

Congratulations to the winner of our recent “SMRTest Microbe” grant competition, 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 over 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 these meropenum-resistant B. pseudomallei genomes 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.”

In addition to the grant winner, the submitters of the top 10 proposals will have the opportunity to conduct their projects through IGS with a 20% discount on SMRT sequencing. Thank you to all of the submitters who participated in the grant competition. We look forward to a number of exciting new projects in the coming months!

Do you have a project that could benefit from SMRT sequencing or any of our other sequencing and analysis services? If so, please contact us for a free project consultation.

 

IGS to Host Pacific Biosciences User Group Meeting

The Institute for Genome Sciences is pleased to once again host the PacBio Americas East Coast UGM and Workshops in Baltimore from June 16-18, 2015.

The UGM meeting is a day-long event on June 17th.  An optional half-day Bioinformatics workshop will be held on the afternoon of June 16th and the morning of June 18th, and an afternoon sample prep workshop will be held on June 16th. The bioinformatics workshop will cover large genome assembly with FALCON and analysis for the Iso-Seq™ method, among other topics. Special guests Jon Badalamenti and Sergey Koren will host on Tuesday and Thursday, respectively. The sample prep workshop will include talks on ultra-long DNA fragments, barcoding, targeted sequencing with solution-based capture, the Iso-Seq method, an intro to the SMRT Portal, and more.

View the agenda and register to attend.

GRC a PacBio Certified Service Provider; Co-sponsoring SMRTest Microbe Grant Program at ASM 2015

We are pleased to announce that the GRC is the first PacBio certified service provider on the East Coast. This recently announced program is a partnership between PacBio and select sequence providers who have completed the certification process and offer the highest quality sequencing and analysis services using the PacBio technology. We offer a full range of PacBio services, including whole genome sequencing, transcriptome sequencing via Iso-Seq, targeted amplicon sequencing, and other customized applications. Our analysis team has expertise in genome assembly and annotation, variant analysis, transcriptome analysis, and base modification detection. We look forward to continuing our strong partnership with PacBio and offering the highest quality sequencing and analysis to our customers and collaborators.

As part of this new partnership, the GRC is proud to co-sponsor the SMRTest Microbe Grant Program. One lucky winner will receive sequencing and analysis services from the GRC. To enter, submit a short grant application detailing your project and how it would benefit from the long reads and high consensus accuracy of SMRT Sequencing. The deadline for submissions is June 27, 2015.

For more information on our full range of sequencing and analysis services, visit our Laboratory Services and Analysis Services pages. Please contact us if you have any questions or would like a quote.

If you are attending ASM 2015 next week, please stop by the IGS booth (#776) to learn more about the grant program and all of our sequencing and analysis services. See you in New Orleans!

Automated Preparation of Long Insert PacBio Libraries

The GRC sequences thousands of microbial samples each year. The high throughput of our sequencers and the small genome sizes of these samples means that a lot of libraries are needed to keep our sequencers running at full capacity. Automation of library preps is key to keeping instruments busy, reducing error, and maximizing the productivity of our lab staff.

We have used automation to prepare large batches of libraries for Illumina sequencing for several years. Earlier this year, we began testing preparation of long-insert libraries for our PacBio RS II platform.

Our Biomek FXP (BeckmanCoulter) is a Dual Multi-channel Span-8 with an integrated thermal cycler. The combination of a 96-channel pipetting head and Span-8 pipetting head (which has eight independently controlled channels) allows for the preparation of up to 96 libraries at a time and the minimization of master mix dead volumes.

A script for preparing SMRTbell libraries developed by Todd Hartley at NCI/SAIC-Frederick was downloaded from Pacific Biosciences SMRT Community. We modified to the protocol to accommodate the specific tips and reagents tubes our lab uses, and to optimize reaction mixing.

 

Deck Layout

PB_Biomek_Deck

Prior to being loaded on the Biomek, samples are sheared with g-TUBEs (Covaris, Woburn, MA), targeting an average fragment size of 20kb. Master mixes for each reaction are prepared and placed in the robot. The following steps are performed by the Biomek:

  • DNA damage repair
  • End Repair
  • Ampure clean up
  • SMRTbell Ligation
  • Exonuclease
  • Ampure clean up

Once the run is complete, the libraries are removed and size-selection is performed using the BluePippin (Sage Science, Beverly, MA).

  manual preps robotic preps
Number of libraries (n) 91 27
Average input amount (ng of sheared gDNA) 4945 4951
Average library size (bp) 18507 18910
Average library concentration (nM) 5.1 3.5
Average recovery (ng) 902.8 707.4
Average recovery (%) 18.7 14.2

Above are data comparing libraries prepped manually and on the Biomek, from March 2014 to date. While the yields from the Biomek preps are slightly lower than manual preps, the yield is comparable and sufficient for sequencing multiple SMRT cells per library.

For more information on our full range of sequencing and analysis services, visit our Laboratory Services and Analysis Services pages. Please contact us if you have any questions.

 

Single Molecule Sequencing and Genome Assembly of a Clinical Specimen of Loa loa

Scientists Apply Successful Single Molecule Sequencing and de novo Genome Assembly to a Parasitic Worm that Infects Human Eyes and Skin

Investigators at the Institute for Genome Sciences (IGS) at the University of Maryland School of Medicine and the Laboratory of Parasitic Diseases at the National Institute of Allergy and Infectious Diseases (NIAID) at the National Institutes of Health (NIH) used the long-read, single-molecule Pacific Biosciences platform for the successful genome sequencing and de novo assembly of Loa loa round worms from a clinical sample. Their research, which generated the most complete genome sequence of a filarial nematode produced to date, provides a more comprehensive reference genome for this parasite in the hopes of developing better molecular diagnostics to decrease morbidity from filarial nematodes. Their findings appear in today’s issue of BMC Genomics.

Click here to access the abstract and complete article.

GRC Awarded Contract to Expand FDA Microbial Genome Database

IGS and the GRC have been awarded a contract to assist the U.S. Food and Drug Administration (FDA) in the expansion and curation of a public database of microbial genome sequences and associated metadata. This will serve as a valuable reference to evaluate and assess high-throughput sequencing based diagnostic devices. In addition to all publicly available microbial genome sequences, the database will include more than 550 newly sequenced, assembled, and annotated genomes from under-represented branches of the phylogenetic tree. For more information on the project, please click here or contact the GRC.

GRC Posters Presented at AGBT 2014

This year we are highlighting some of the work we’ve done in the past year.

The first poster provides an overview of how changes to our PacBio pipeline have increased our sequencing yields and read lengths, resulting in finished, high-quality microbial genomes, assembled using only PacBio data.

The second poster demonstrates how Next Gen sequencing can be used to investigate host and pathogen associations in cases of pulmonary non-tuberculous mycobacterial (PNTM) infections.

For more information on our full range of sequencing and analysis services, visit our Laboratory Services and Analysis Services pages. Please contact us if you have any questions.