X

Quality Statement

Pacific Biosciences is committed to providing high-quality products that meet customer expectations and comply with regulations. We will achieve these goals by adhering to and maintaining an effective quality-management system designed to ensure product quality, performance, and safety.

X

Image Use Agreement

By downloading, copying, or making any use of the images located on this website (“Site”) you acknowledge that you have read and understand, and agree to, the terms of this Image Usage Agreement, as well as the terms provided on the Legal Notices webpage, which together govern your use of the images as provided below. If you do not agree to such terms, do not download, copy or use the images in any way, unless you have written permission signed by an authorized Pacific Biosciences representative.

Subject to the terms of this Agreement and the terms provided on the Legal Notices webpage (to the extent they do not conflict with the terms of this Agreement), you may use the images on the Site solely for (a) editorial use by press and/or industry analysts, (b) in connection with a normal, peer-reviewed, scientific publication, book or presentation, or the like. You may not alter or modify any image, in whole or in part, for any reason. You may not use any image in a manner that misrepresents the associated Pacific Biosciences product, service or technology or any associated characteristics, data, or properties thereof. You also may not use any image in a manner that denotes some representation or warranty (express, implied or statutory) from Pacific Biosciences of the product, service or technology. The rights granted by this Agreement are personal to you and are not transferable by you to another party.

You, and not Pacific Biosciences, are responsible for your use of the images. You acknowledge and agree that any misuse of the images or breach of this Agreement will cause Pacific Biosciences irreparable harm. Pacific Biosciences is either an owner or licensee of the image, and not an agent for the owner. You agree to give Pacific Biosciences a credit line as follows: "Courtesy of Pacific Biosciences of California, Inc., Menlo Park, CA, USA" and also include any other credits or acknowledgments noted by Pacific Biosciences. You must include any copyright notice originally included with the images on all copies.

IMAGES ARE PROVIDED BY Pacific Biosciences ON AN "AS-IS" BASIS. Pacific Biosciences DISCLAIMS ALL REPRESENTATIONS AND WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, NON-INFRINGEMENT, OWNERSHIP, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL Pacific Biosciences BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, PUNITIVE, OR CONSEQUENTIAL DAMAGES OF ANY KIND WHATSOEVER WITH RESPECT TO THE IMAGES.

You agree that Pacific Biosciences may terminate your access to and use of the images located on the PacificBiosciences.com website at any time and without prior notice, if it considers you to have violated any of the terms of this Image Use Agreement. You agree to indemnify, defend and hold harmless Pacific Biosciences, its officers, directors, employees, agents, licensors, suppliers and any third party information providers to the Site from and against all losses, expenses, damages and costs, including reasonable attorneys' fees, resulting from any violation by you of the terms of this Image Use Agreement or Pacific Biosciences' termination of your access to or use of the Site. Termination will not affect Pacific Biosciences' rights or your obligations which accrued before the termination.

I have read and understand, and agree to, the Image Usage Agreement.

I disagree and would like to return to the Pacific Biosciences home page.

Pacific Biosciences
Contact:

Innovation Centre in Quebec Uses SMRT Sequencing for
Cost-Effective, Complete Microbial Genomes

Wednesday, April 16, 2014

At the McGill University and Génome Québec Innovation Centre, many projects conducted in the sequencing core facility fall under the umbrella of life sciences rather than biomedical research. To the scientists responsible for making the core facility operate as smoothly as possible, that makes a world of difference.

“When you’re in the life sciences in addition to human biomedical [research], you’re out there in the world of things that haven’t been sequenced before, or haven’t been sequenced particularly well,” says Ken Dewar, a principal investigator at the Innovation Centre.

To navigate this type of uncharted territory, scientists at the center rely on long-read sequencing from their PacBio® RS II platform to cost-effectively close microbial genomes, traverse repeat-heavy genomic regions, and perform full-length transcript sequencing. By leveraging the dramatically increased read lengths PacBio sequencing provides, they have driven down costs and improved completeness of their assemblies.

At the core facility, Alexandre Montpetit is dedicated to running the next-generation sequencing platforms. His primary affiliation is with Génome Québec, and he has an adjunct appointment at McGill. He and his colleagues have been champions of long-read sequencing for years, so when PacBio unveiled its platform with industry-leading read length, it was an obvious choice for the center to adopt the technology.

“We’ve always had a focus on sequencing things for the first time or assembling genomes for the first time, not for the thousand-and-first time,” Dewar says. “PacBio was a natural fit.”

At the center, SMRT Sequencing has been used in diverse research areas. Some examples include generation of high-quality assemblies in microbial sequencing, analysis of long, repetitive genomic regions, and sequencing of full-length human gene isoforms. Microbial sequencing encompasses a number of applications, including biotech industry efforts to improve microbial biofermentation and microbiome studies, from environmental remediation projects on Alberta tar sands to veterinary research on microbes present in cattle rumen.

In the two years they’ve been running the SMRT Sequencing platform, the Innovation Centre scientists have seen remarkable progress in what they have been able to achieve. Continued improvements in read lengths — partly due to new reagent kits from PacBio and partly due to more streamlined sample prep protocols developed at the center — have already made a major difference.

One major step was achieving complete bacterial sequencing and assembly in less than a day, a feat that may enable the core facility to serve as a rapid response center for organizations that study pathogen outbreaks and other urgent problems. In 2013, tests conducted with researchers at the Canadian Food Inspection Agency and other government agencies demonstrated that the Innovation Centre scientists could sequence a sample and fully assemble the genome and plasmid elements — all in 20 hours or less.

Indeed, the Innovation Centre team is routinely able to deliver affordable, high-quality, finished genomes. “A single bacterial genome, a library prep, and two SMRT Cells of sequencing — which is generally a little bit overkill — is less than $1,000,” Dewar says. “More and more often, we are getting a completely closed, finished-quality genome for that.”

High-quality assemblies aren’t just for bacteria. “We’ve shown recently that we can assemble a fungal genome of 20 or 30 megabases with four or eight SMRT Cells and get only 10 or 20 contigs — which often represents the number of chromosomes in the genome,” Montpetit says.

Read the full case study to learn more about how the Innovation Centre has deployed SMRT Sequencing, their shift from hybrid to PacBio-only assemblies, and how they differentiate their bioinformatics analysis service.

Subscribe for blog updates:

Archives