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:

CSHL Scientists Discuss Long-Read Sequencing for More Contiguous Assemblies and Complex Genomes

Thursday, March 24, 2016

Much like the “sharpen” tool in Photoshop brings a picture into tighter focus and enhances the fine detail, long-read sequencing offers enhanced resolution of genomic information, according to Cold Spring Harbor Laboratory colleagues Mike Schatz and Maria Nattestad. The scientists spoke with Mendelspod’s Theral Timpson about how long-read sequencing is advancing their research in unique and powerful ways; a brief recap of their conversation follows.

Schatz uses PacBio sequencing to establish incredibly accurate assemblies of microbial, crop, animal, and human genomes. Indeed, SMRT technology has significantly improved his work on the flatworm Macrostomum lignano, an organism with regenerative powers. With only a few reference genomes and limited functional studies available, the flatworm proved to be particularly challenging to sequence with short-read solutions. “We were quite frustrated by the results that we were getting, where the assembly was of very poor quality,” Schatz says. “It was also missing something like half of the genome that we expected to be there; it just wasn’t present at all in the assembly that took place.” At this point, the team realized that long reads would help them achieve a much improved reference genome. By collaborating with algorithm developers, PacBio, and the NIH, the team created an assembly that was about 100 times more contiguous than assemblies based on short-read data.

Long reads also appeal to Nattestad, who is using de novo assembly of the SK-BR-3 breast cancer cell line as a way to fully characterize not just SNPs, but also major structural variations. One of her interests in SK-BR-3 is to better understand Her2 oncogene amplification, and she has undertaken a historical, step-by-step reconstruction of its mutations using software she developed for that purpose. “Our focus here is not just to see how many copies of Her2 there are, or to see that it is Her2-amplified like you would in a diagnostic setting. Instead, we wanted to see how that amplification has happened over time in the genome, and try to reconstruct a history of steps that took place,” she says. Schatz notes that in SK-BR-3, the region around Her2 has undergone what they call ‘genome gymnastics,’ a very complicated series of amplifications, inverted duplications, and translocation events. He says that “trying to capture that level of complication and sophistication just from standard variant calling approaches is very challenging.” Nattestad plans to follow up with analyses of other oncogenes known to be amplified in this cell line.

This year, Schatz expects to see a number of reference-grade human genomes published using PacBio technology to create high-quality de novo assemblies. He says, “If you’re interested to do a de novo assembly of an entirely novel species, my strong recommendation — without any hesitation — is to do long-range PacBio sequencing, and I would advocate for 100x coverage of the longest reads you can possibly generate. … This will give you the most successful assembly.”  Structural variation studies are similar, he says: “You really want to use the long-read technology in order to capture those structural variations as accurately as possible.”

Subscribe for blog updates:

Archives