Genomic Sequencing Method Speeds Analysis for Individualized Medicine for Oral Cancer

To explore the advantages of massively parallel sequencing of genomic transcripts (RNA), the researchers, from the Mayo Clinic (Rochester, MN, USA) along with collaborators from Life Technologies (Foster, City, CA, USA), utilized 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 major finding of this research was that alterations in gene expression that 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) technique. It will allow researchers to measure strand-specific expression across the entire sample's transcriptome. This technology reveals much 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,” said 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 disease 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% in the United States. Information provided by these and continued studies will help to better characterize the molecular basis of cancer development, according to the researchers.

The investigators' findings from the proof-of-principle study on oral carcinomas was published in the February 24, 2010, issue of PLoS ONE.

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