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:

Breakpoint Detection in Cancer Structural Variants with PacBio May Yield Patient-Specific Data

Friday, December 27, 2013

A new publication from scientists at the University of California, San Diego, demonstrates the use of Single Molecule, Real-Time (SMRT®) Sequencing to identify structural variation (SV) breakpoints in cancer.

Amplification and thrifty single molecule sequencing of recurrent somatic structural variations” was published in Genome Research and comes from authors Anand Patel, Richard Schwab, Yu-Tsueng Liu, and Vineet Bafna.

In the paper, the scientists report development of a new method — Amplification of Breakpoints, or AmBre — to detect important structural variant breakpoints. AmBre relies on a PCR-based approach for amplification of the structural variant, followed by sequencing on the PacBio® platform to resolve the exact breakpoints. The method was tested on several cancer cell lines that contained such extensive genomic rearrangements, including deletions of tumor suppressor genes.

The authors note that breakpoints of structural variation are far more individualized than the structural variants themselves; they posit that these breakpoints have “utility as patient specific tumor biomarkers.” A reliable way to detect breakpoints, then, could have clinical relevance for cancer patients. In addition, the method can also be used to validate structural variants found with other sequencing (exome or genome) or microarray-based methods.

The team used SMRT Sequencing of pooled amplicons in a single SMRT Cell as well as a custom-built algorithm to sort reads by breakpoint and then call a consensus sequence representing a particular structural variant. The AmBre approach was validated on cancer cell lines including A549, CEM, and Detroit562 by successfully identifying CDKN2A deletion breakpoints. It was then applied (and confirmed by Sanger sequencing) to cell lines MCF7 and T98G for which the breakpoints had not been identified in spite of previous efforts, including whole genome sequencing of the MCF7 cell line. Interestingly, the SNP-array estimate for the MCF7 breakpoint is 15 kb away from the AmBre detected breakpoint, likely due to repeat elements close to the upstream MCF7 breakpoint. The authors note that “Repetitive sequences are known to confound structural variation analysis and possibly explains why previous genome sequencing studies of MCF7, have not annotated the CDKN2A deletion breakpoints”.

The authors also show that AmBre captures more complex rearrangements, like interchromosomal translocations, by resolving the RUNX1-RUNX1T1 gene fusion which forms from a translocation between chromosome 21 and chromosome 8. In addition, “the AmBre assay, unlike other methods, can target DNA with a SV in the context of high background of germline DNA”, a feature “important for sensitive detection of tumor DNA and establishing a patient specific tumor DNA marker for monitoring tumor burden.” They demonstrate successful targeting of SVs by AmBre in heterogeneous samples where tumor DNA was present in as little as 1:1000 of the sample.

The paper was also reported on by In Sequence in an article entitled UCSD Team Develops PacBio Sequencing Method to ID Structural Variant Breakpoints (free access).

Subscribe for blog updates:

Archives