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Mayo oral cancer study shows full tumor genome

23.02.2010
Novel method speeds analysis for individualized medicine

Mayo Clinic researchers along with collaborators from Life Technologies are reporting on the application of a new approach for sequencing RNA to study cancer tumors. Their findings from a proof-of-principle study on oral carcinomas appear in the current issue of PLoS One, the online science journal.

To explore the advantages of massively parallel sequencing of genomic transcripts (RNA), the researchers used a novel, strand-specific sequencing method using matched tumors and normal tissues of three patients with the specific cancer. They also analyzed the genomic DNA from one of the tumor-normal pairs which revealed numerous chromosomal regions of gain and loss in the tumor sample.

The key finding of this work was that alterations in gene expression which can arise from a variety of genomic alterations frequently are driven by losses or gains in large chromosomal regions during tumor development.

In addition to the specific tumor findings, this study also demonstrated the value of this RNA sequencing (RNA-Seq) method. It will allow researchers to measure strand-specific expression across the entire sample's transcriptome. This technology reveals far more detail about genome-wide transcription than traditional microarrays.

"This method allows us to investigate genetic changes at a level that we were never able to see before," says David Smith, Ph.D., Mayo Clinic genomics researcher and corresponding author of the study. "This provides us with much more information about alterations during cancer development that could reveal important therapeutic targets. We can more completely understand the relationship between an individual's genome and the alterations to that which result in disease.

This is a huge step in speed, detail and diagnostic power for the field of individualized medicine. This transforms how we are going to study cancer -- and how we're going to practice medicine -- in the very near future."

The urgency of this condition points to the need for more efficient technologies and methods. Head and neck cancers are the sixth most prevalent carcinomas in the world. Advanced stage oral and throat cancers have a five-year survival rate of only 50 percent in the United States. Information provided by these and continued studies will help to better characterize the molecular basis of cancer development. That information can hopefully define better therapeutic strategies for treating an individual's specific cancer.

Others involved in the research include co-first author Rebecca Laborde, Ph.D.; Kerry Olsen, M.D.; Jan Kasperbauer, M.D.; Eric Moore, M.D.; and Yan Asmann, Ph.D.; all of Mayo Clinic; and co-first author Brian Tuch, Ph.D.; Xing Xu, Ph.D.; Christina Chung, Ph.D.; Cinna Monighetti, Ph.D.; Sarah Stanley, Adam Broomer, Ruoying Tan, Ph.D.; Pius Brzoska, Ph.D.; Matthew Muller, Asim Siddiqui, Ph.D.; Yongming Sun, Ph.D.; Melissa Barker; and Francisco De La Vega, Ph.D.; all of Life Technologies, Foster City, Calif.

The research was supported by Mayo Clinic and Life Technologies. The funders had no role in study design, data collection, analysis or publishing. Some authors are or have been employed by Life Technologies, which makes technology and materials used in the study. Data and materials will be shared.

About Mayo Clinic

For more than 100 years, millions of people from all walks of life have found answers at Mayo Clinic. These patients tell us they leave Mayo Clinic with peace of mind knowing they received care from the world's leading experts. Mayo Clinic is the first and largest integrated, not-for-profit group practice in the world. At Mayo Clinic, a team of specialists is assembled to take the time to listen, understand and care for patients health issues and concerns. These teams draw from more than 3,700 physicians and scientists and 50,100 allied staff that work at Mayo Clinic's campuses in Minnesota, Florida, and Arizona; and community-based providers in more than 70 locations in southern Minnesota, western Wisconsin and northeast Iowa. These locations treat more than half a million people each year. To best serve patients, Mayo Clinic works with many insurance companies, does not require a physician referral in most cases and is an in-network provider for millions of people. To obtain the latest news releases from Mayo Clinic, go to www.mayoclinic.org/news. For information about research and education visit www.mayo.edu. MayoClinic.com (www.mayoclinic.com) is available as a resource for your general health information.

Robert Nellis | EurekAlert!
Further information:
http://www.mayo.edu
http://www.mayoclinic.com

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