Delivering genomics to routine care

CAMBRIDGE, Mass.—Foundation Medicine Inc., a molecularinformation company that touts its ability to bring "comprehensive cancergenomic analysis to routine clinical care," announced in March a collaborationwith Array BioPharma, headquartered in Boulder, Colo. In this collaborativeeffort, Foundation Medicine will use its genomic sequencing and analyticcapabilities to assess potentially relevant molecular alterations and thusassist Array in identifying patients who are most likely to respond totreatment.

Array has a portfolio of targeted cancer agents that are inthe early stages of clinical development, and through this collaboration withFoundation Medicine, Array seeks to determine the genetic profile of tumors ofpatients who are treated with certain anticancer agents in its pipeline. Theultimate goal is to increase knowledge about how to identify patients who mayrespond to a given targeted therapy and ensure that each patient gets theoptimal drug to treat his or her individual disease.

"Foundation Medicine has established a remarkable portfolioof collaborations around the discovery and clinical development of targetedcancer therapeutics," said
Dr. Michael J. Pellini, president and CEO of Foundation Medicine, in the newsrelease about the deal. "The molecular information generated by our platform isdesigned to help biopharma companies like Array expedite the development oftargeted drug candidates that impact the genomic pathways driving a specificcancer."

It's a good pairing of partners because FoundationMedicine's industry and academic partnerships will complement Array's corecancer diagnostics capability, which is a comprehensive cancer genomic testthat provides physicians with genomic information to help match patients withtreatments or clinical trials specific for the genomic profile of their tumor,Pellini tells ddn via email, echoing asimilar point made in the official announcement.

But looking at the bigger picture and Foundation Medicine'scapabilities both in this deal and with respect to past and futurecollaborations, Pellini tells ddn thathis company's "fully informative genomic profile capability is helping partnersto better understand the molecular basis of their clinical trials'participants' cancer in order to conduct clinical trials more quickly andefficiently. It enables the partner to better stratify patients for the trials,to seek out better ways to identify responders and non-responders, to identifywhy certain patients might have adverse reactions, etc. Potentially we candevelop companion diagnostics and help partners match the right patients withthe right drug."

Foundation Medicine's comprehensive cancer genomic test usesnext-generation sequencing to analyze routine clinical specimens—typically,small amounts of formalin fixed, paraffin embedded tumor tissue—for molecularalterations in approximately 200 cancer-related genes.

The test is optimized for clinical-grade analysis of tumortissues, reportedly overcoming multiple complexities—including purity, ploidyand clonality—inherent to tumor genomes. Test results are reported through asecure, interactive web site linking genomic data to a structured knowledgebase of relevant, publicly available scientific and medical information.Foundation Medicine also aims to provide information on relevant clinicaltrials to enable a more rapid recruitment of patients into trials for targetedtherapies.

According to the company, its test also is designed toaccommodate "a broad landscape of cancer genome information and a growingrepertoire of targeted treatments and clinical research opportunities."

Foundation Medicine, Dana-Farber identify genomicalterations in lung, colorectal cancer

CAMBRIDGE, Mass.—Foundation Medicine Inc. also recentlyannounced that the company and Dana-Farber Cancer Institute published resultsin Nature Medicine from theircollaborative next-generation sequencing (NGS) study to assay cancer-relevantgenes 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 havegenomic alterations directly associated with a clinically available targetedtherapeutic or a relevant clinical trial of a targeted therapy. Two novel genefusions, KIF5B-RET in NSCLC and C2orf44-ALK in CRC, were discovered among thepotentially drugable alterations identified in the study.

Both of these findings may expand therapeutic options for asubset of cancer patients, according to the collaborators. Further, they saythe publication demonstrates that using targeted NGS to profile patient tumorsfor molecular alterations associated with therapeutic responses may have animportant clinical impact in cancer treatment.

"In this collaboration, we detected clinically-relevantgenomic alterations in more than half of the samples profiled, and becauseFoundation Medicine's NGS assay detects all classes of alterations withclinical-grade sensitivity, this research was able to identify both expected aswell as completely novel alterations," says Dr. Maureen Cronin, senior vicepresident of research and product development at Foundation Medicine, and co-authorof the study. "The discovery of novel rearrangements and fusions, such asKIF5B-RET and C2orf44-ALK, supports an important role for NGS in the clinicalunderstanding and treatment of cancer."

"In a common indication like NSCLC, identifying even a smallsubpopulation of individuals with gene fusions who may be responsive to atargeted 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 translatesgenomic research to the clinic and we expect that it may quickly have a positiveimpact for patients."