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Genomic Health Plans to Move Next-Gen Sequencing into Commercial Test Development within Two Years


By Monica Heger

This story was originally published Feb. 17.

Genomic Health plans to eventually move its molecular diagnostics testing platform from quantitative RT-PCR to next-generation sequencing, the company reported this month in an earnings call with investors.

Near term, Genomic Health expects next-gen sequencing to have an impact on biomarker identification, but over the next two to four years, the company plans to move the technology into its commercial development process.

While the company has previously expressed interest in moving into next-gen sequencing (IS 8/31/2010), officials last week provided further specifics on the firm's plans for immediate and long-term investment in sequencing, as well as how it plans to develop products based on the technology.

Already, over the past year, the company has transitioned its "entire research program to next-generation sequencing technology for all discovery projects" and has made "significant investments" in its IT infrastructure "to support the increase in data and data analysis associated with that expansion," Genomic Health's CEO Kim Popovits said in the call.

In 2011, next-gen sequencing will comprise one of the company's "key areas of investment," along with expanding its international business and developing a prostate cancer test, said Joffre Baker, the company's chief scientific officer. In order to support those investments, the company is targeting a net income of between $3 million and $5 million for 2011, consistent with its 2010 net income of $4.3 million.

As part of the investment, the company is looking to hire about a half dozen employees to "shore up our bioinformatics group," Baker added. "In the world of next-gen sequencing the top of the iceberg is generating the data, and the analysis is the other 90 percent of the iceberg. We're investing heavily in that aspect of our business," he said.

Near term, next-gen sequencing will have an impact on biomarker identification for breast, colon, and prostate cancer, and already has begun to identify a "bevy of clinical markers," said executive chairman Randy Scott. The company has been using next-gen sequencing in clinical studies of breast cancer, and plans to expand to colon and prostate cancer.

At the Advances in Genome Biology and Technology conference earlier this month, Genomic Health presented initial findings from its NGS-based biomarker discovery program. The company performed transcriptome sequencing on the Illumina platform to identify "hundreds of coding and non-coding transcripts that are differentially expressed in tumor versus normal, non-cancerous breast tissue, including a subset of genes statistically associated with the recurrence of breast cancer."

The study, which compared gene expression profiles between 12 normal and 12 tumor formalin-fixed breast specimens, also identified "new candidate biomarkers linked to breast cancer recurrence from regions outside of the previously identified protein-coding sections of the genome," the company said.

Currently, Genomic Health further develops these biomarkers for tests using quantitative RT-PCR, but over the next two to four years, the company plans to implement next-gen sequencing technology into its clinical development process, Scott said.

He explained that the company's product development cycle is between three to four years, and noted that next-generation sequencing is "not so different from the classical clinical perspective." In the next year and a half the company expects to decide on a sequencing platform for the clinical development of its products, which it will then integrate "in that three- to four-year product development cycle," he said.

"In the next two years you'll see next-gen sequencing itself become a platform that we begin to move into clinical development and begin moving to market," said Scott. The first product based on sequencing will likely be for a "second generation Oncotype DX product," he added.

"There is still a lot of work to do to bring [next-gen sequencing] into the clinical laboratory, but every year that goes by the technology improvements are just amazing and we think this is truly going to redefine cancer and really have an impact on healthcare," Scott said.

A key aspect of the company's current research with next-gen sequencing is a protocol it has developed for extracting RNA from formalin-fixed paraffin embedded tissue, which it presented in a poster at last fall's Beyond the Genome conference (IS 10/19/2010). That method has contributed to a 60,000-fold increase in the amount of information screened for the company's use in biomarker discovery, Popovits said.

Technology that enables the development of assays using small amounts of tissue is an area that the company has been focused on, said Genomic Health's chief medical officer, Steve Shak, so next-gen sequencing makes sense because it enables the company to "build on our expertise." Looking ahead, developing tests that can run with small amounts of tissue will be "important for many of our future clinical applications."

Have topics you'd like to see covered by In Sequence? Contact the editor at mheger [at] genomeweb [.] com.

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