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Delivering genomics to routine care
April 2012
by Jeffrey Bouley  |  Email the author


CAMBRIDGE, Mass.—Foundation Medicine Inc., a molecular information company that touts its ability to bring "comprehensive cancer genomic analysis to routine clinical care," announced in March a collaboration with Array BioPharma, headquartered in Boulder, Colo. In this collaborative effort, Foundation Medicine will use its genomic sequencing and analytic capabilities to assess potentially relevant molecular alterations and thus assist Array in identifying patients who are most likely to respond to treatment.
Array has a portfolio of targeted cancer agents that are in the early stages of clinical development, and through this collaboration with Foundation Medicine, Array seeks to determine the genetic profile of tumors of patients who are treated with certain anticancer agents in its pipeline. The ultimate goal is to increase knowledge about how to identify patients who may respond to a given targeted therapy and ensure that each patient gets the optimal drug to treat his or her individual disease.  
"Foundation Medicine has established a remarkable portfolio of collaborations around the discovery and clinical development of targeted cancer therapeutics," said
Dr. Michael J. Pellini, president and CEO of Foundation Medicine, in the news release about the deal. "The molecular information generated by our platform is designed to help biopharma companies like Array expedite the development of targeted drug candidates that impact the genomic pathways driving a specific cancer."
It's a good pairing of partners because Foundation Medicine's industry and academic partnerships will complement Array's core cancer diagnostics capability, which is a comprehensive cancer genomic test that provides physicians with genomic information to help match patients with treatments or clinical trials specific for the genomic profile of their tumor, Pellini tells ddn via email, echoing a similar point made in the official announcement.  
But looking at the bigger picture and Foundation Medicine's capabilities both in this deal and with respect to past and future collaborations, Pellini tells ddn that his company's "fully informative genomic profile capability is helping partners to better understand the molecular basis of their clinical trials' participants' cancer in order to conduct clinical trials more quickly and efficiently. It enables the partner to better stratify patients for the trials, to seek out better ways to identify responders and non-responders, to identify why certain patients might have adverse reactions, etc. Potentially we can develop companion diagnostics and help partners match the right patients with the right drug."  
Foundation Medicine's comprehensive cancer genomic test uses next-generation sequencing to analyze routine clinical specimens—typically, small amounts of formalin fixed, paraffin embedded tumor tissue—for molecular alterations in approximately 200 cancer-related genes.
The test is optimized for clinical-grade analysis of tumor tissues, reportedly overcoming multiple complexities—including purity, ploidy and clonality—inherent to tumor genomes. Test results are reported through a secure, interactive web site linking genomic data to a structured knowledge base of relevant, publicly available scientific and medical information. Foundation Medicine also aims to provide information on relevant clinical trials to enable a more rapid recruitment of patients into trials for targeted therapies.
According to the company, its test also is designed to accommodate "a broad landscape of cancer genome information and a growing repertoire of targeted treatments and clinical research opportunities."

Foundation Medicine, Dana-Farber identify genomic alterations in lung, colorectal cancer  
CAMBRIDGE, Mass.—Foundation Medicine Inc. also recently announced that the company and Dana-Farber Cancer Institute published results in Nature Medicine from their collaborative next-generation sequencing (NGS) study to assay cancer-relevant genes in 24 non-small cell lung cancer (NSCLC) and 40 colorectal cancer (CRC) cases.  
In the study, 59 percent of the samples were found to have genomic alterations directly associated with a clinically available targeted therapeutic or a relevant clinical trial of a targeted therapy. Two novel gene fusions, KIF5B-RET in NSCLC and C2orf44-ALK in CRC, were discovered among the potentially drugable alterations identified in the study. Both of these findings may expand therapeutic options for a subset of cancer patients, according to the collaborators. Further, they say the publication demonstrates that using targeted NGS to profile patient tumors for molecular alterations associated with therapeutic responses may have an important clinical impact in cancer treatment.
"In this collaboration, we detected clinically-relevant genomic alterations in more than half of the samples profiled, and because Foundation Medicine's NGS assay detects all classes of alterations with clinical-grade sensitivity, this research was able to identify both expected as well as completely novel alterations," says Dr. Maureen Cronin, senior vice president of research and product development at Foundation Medicine, and co-author of the study. "The discovery of novel rearrangements and fusions, such as KIF5B-RET and C2orf44-ALK, supports an important role for NGS in the clinical understanding and treatment of cancer."  
"In a common indication like NSCLC, identifying even a small subpopulation of individuals with gene fusions who may be responsive to a targeted therapy has the potential for major therapeutic impact," explains Dr. Phil Stephens, executive director of cancer genomics at Foundation Medicine, and a co-author of the study. "This joint research with Dana-Farber translates genomic research to the clinic and we expect that it may quickly have a positive impact for patients."
Code: E041219



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