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:

New Publication Demonstrates Long-Read Sequences Needed to Thoroughly Resolve Short Tandem Repeats

Wednesday, November 20, 2013

In a new paper reporting a protocol for using short-read sequence data to locate short tandem repeats (STRs), scientists find that long-read sequence information is necessary to resolve regions with repeat complexity, extreme GC content, and other challenging factors. Their solution is to use short-read data to find STRs, and then to use long-read sequencing to fully characterize those repeat expansions.

The Bioinformatics publication is entitled “Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing” and came from scientists Koichiro Doi, Shinichi Morishita, et al. at the University of Tokyo. They focused on resolving STRs across whole genomes because of their links to genetic disease, noting that exome capture is insufficient to fully characterize these repeat units, which are often found in non-exonic regions of the genome.

Doi et al. report that short-read sequence data has traditionally proven inadequate for elucidating STRs that span more than 100 bp, the average length of a short read. In this project, they developed an efficient computational program along with ab initio procedures to sense and locate STRs by scanning massive short-read data sets and analyzing frequency distributions of approximate STRs based on length.

However, they note, “As genomic regions of GC content > 70% are difficult to cover with an ample number of Illumina® reads, our method is unlikely to detect long expansions of STRs with high GC contents. STRs in reads originating in centromeres, telomeres, or retrotransposons are too numerous to map to unique genomic positions.”

To fully analyze longer STRs, the team utilized Single Molecule, Real-Time (SMRT®) Sequencing on 11 samples from patients with a brain disease. Through this approach, they report, “we were able to determine a divergent set of [two] 3-3.1 kb STR sequences in eleven SCA31 samples, showing the instability of STR expansions.” By combining both methods — genome scanning with short-read data to find STR locations and sequencing those structural variants with the PacBio® platform — the scientists were able to rapidly hone in on long STRs implicated in human disease.

Looking ahead, the authors suggest that there is much to be learned about STRs longer than 1 kb and whether STR expansions occur more often in germline or somatic cells. “Analysis of the stability of STR expansions in germline and somatic cells of a specific disease might eventually lead to the recognition of a functional role of STRs,” they write.

Subscribe for blog updates:

Archives