SAIC-Frederick and Roche collaborate on technology advancements in sequencing cancer genes

National Cancer Institute contractor SAIC-Frederick, Inc., a wholly owned subsidiary of Science Applications International Corporation (NYSE: SAI), and Roche Applied Science, a division of Roche Diagnostics Corporation (SWX:RO) (SWX:ROG) (Pink Sheets: RHHBY), have signed a collaboration agreement to assess Roche’s advanced technologies to sequence the genomes of cancer research samples. These technologies include targeted enrichment with NimbleGen Sequence Capture and ultra-deep sequencing using the Genome Sequencer FLX System from 454 Life Sciences, a Roche Company. With these technologies, Roche Applied Science provides a complete solution for targeted re-sequencing of the human genome to further our understanding of disease associated regions.

Under the recently-signed agreement, SAIC-Frederick’s Core Genotyping Facility will assess the ability of a new solution-based sequence capture technology from Roche NimbleGen, the SeqCap EZ System, to capture specific regions of the genome of a cancer research sample. The captured DNA will then be sequenced on the ultra high-throughput Genome Sequencer FLX System. Implementation of this technology could accelerate the identification of genetic variants, such as DNA polymorphisms, that contribute to cancer outcomes.

The agreement was formed under the National Cancer Institute’s Advanced Technology Partnerships Initiative (ATPI). SAIC-Frederick aims to further NCI’s mission by rapidly translating the results of basic research into new preventive measures, diagnostic tests, and effective, patient-specific treatments for cancer patients. As a prime contractor at the National Cancer Institute at Frederick, SAIC-Frederick is facilitating ATPI partnerships for the government.

“Our ability to understand the impact of particular regions of the human genome with cancer phenotypes is rapidly advancing with the advent of next-generation sequencing technologies,” said Joseph Boland, Dedicated Scientific Operations Manager of the Core Genotyping Facility at SAIC-Frederick. “Our intent is to implement Roche NimbleGen’s solution-based sequence capture technology, SeqCap EZ, to rapidly advance our next-generation sequencing projects and in turn, increase our knowledge of cancer genetics.”

“Roche Applied Science is very pleased to work with the NCI to develop high-throughput methods of targeting large regions of the genome for next generation sequencing of research samples on cancer. Initial proof-of-principle studies show our solution-phase sequence capture technology, NimbleGen SeqCap EZ, is a robust and cost-effective alternative to long-range PCR and an ideal complementary technology for 454 Sequencing systems,” said Gerd Maass, CEO of Roche NimbleGen.

This collaboration is an exemplar study of the latest trend of using targeted resequencing as follow-up to genome-wide association studies (GWAS). For the past few years, cancer researchers have identified many genomic regions that are associated with cancer using GWAS. A daunting next step is to identify the mutations within these regions that are directly related to cancer outcomes. The new technology being developed and tested by Roche Applied Science and SAIC-Frederick holds great potential to simplify and streamline this important step in disease research studies.