By Turna Ray
MOUNTAIN VIEW, Calif. – Genomic Health is planning to release a next-generation sequencing based research platform able to detect somatic mutations in 189 commonly mutated genes.
Speaking at the Personalized Medicine World Conference held here this week, Joffre Baker, Genomic Health's chief scientific officer, said that the company will make the platform available to its clinical and pharma collaborators in "several months."
The NGS offering will have 10,000-fold coverage and require low amounts of DNA from formalin-fixed paraffin-embedded samples. The company will use Agilent's SureSelect for sequence enrichment.
The genes included in the panel "are mutated in a broad spectrum of cancers, including solid tumors and hematopoietic malignancies," Baker told PGx Reporter. "All are drawn from published literature."
Genomic Health has been using NGS in the research setting for several years now. The company eventually plans to migrate all of its clinical diagnostics from an RT-PCR-based platform to an NGS platform. Earlier this month, Genomic Health announced it was "accelerating" its NGS research efforts into clinical development.
Genomic Health is currently in the process of testing and validating the somatic mutation panel. It has so far been used to detect mutations in FFPE breast and colon cancer specimens and has been tested in cell lines and FFPE tumors with known mutations. The company has also tested the sensitivity of the panel through cell-line mixing experiments.
"The panel will be used first for internal basic research, for example to probe whether there are mutations that distinguish [ductal carcinoma in situ] breast cancer from invasive breast cancer," Baker said, adding that going forward the company will use the platform in "programs" with outside collaborators.
At the conference Baker discussed the need for better tools to characterize the role of somatic mutations in cancer. Detection of somatic mutations in cancer tumors is currently challenged by tissue heterogeneity, analytical sensitivity of existing platforms, and chemical alterations in FFPE tissue. Additionally, there are bioinformatics challenges given the complexity of sequencing data.
Genomic Health didn't comment on whether it is planning to eventually commercialize its NGS-based somatic mutation platform as a cancer diagnostic.
Foundation Medicine, meanwhile, has also developed an NGS-based cancer assay that analyzes FFPE tissue for variations in over 200 cancer-related genes. The company then translates the results into "actionable information" that drug developers and doctors can use. The company is using the test in research efforts with several large pharmaceutical companies, and is planning to launch it as a lab-developed test later this year (see related story, in this issue).
Foundation Medicine's test routinely has 500x coverage, but in many cases, the company has performed the test with 1000x coverage. Foundation Medicine "soft launched" the test in the fourth quarter last year, and began accepting clinical samples for analysis. Currently the test gauges tumor samples from all solid tumors, but by the end of this year, Foundation Medicine will begin to analyze samples from hematological malignancies as well, CEO Michael Pellini said.
Separately, Genomic Health has so far conducted two early clinical studies using NGS to analyze paraffin-embedded tissue in more than 200 patients. At the San Antonio Breast Cancer Symposium last year Genomic Health presented data from a study that showed that the proprietary RNA-Seq method developed at the company can pick up validated genes that previously had been discovered by RT-PCR-based platform underlying the Oncotype DX tests. Additionally, this study also identified more than 1,800 new genomic associations with breast cancer recurrence.
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