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Large-Scale Cancer Gene Profiling Seen as Feasible

Stethoscope on DNA sheet

(National Heart, Lung, and Blood Institute)

18 November 2016. Genomic analysis of tumors, a growing practice for diagnosing cancer in individuals, is shown to be feasible when conducted routinely throughout a cancer care center. A study by a team from Dana-Farber Cancer Institute in Boston that appears in yesterday’s (17 November) issue of the journal JCI Insight, also points out some gaps in applying genomic profile data, when put into practice with patients.

The study, led by Laura MacConaill, scientific director of Dana-Farber’s Center for Cancer Genome Discovery, evaluated the Profile program that offers genomic profiling of tumors to all Dana-Farber patients, regardless of age, cancer type, or stage of the cancer. The research team that included participants from a number of other universities and institutions reviewed the experiences of 3,727 Dana-Farber patients, and those at Brigham and Women’s Cancer Center and Boston Children’s Hospital. who agreed to take part in Profile during 2013, the program’s first year. The program to date analyzed about 15,000 tumors.

Data from the study show results of the institution’s OncoPanel platform that analyzes some 300 genes in parallel from each tumor sample. The analysis seeks to identify genetic alterations in tumors, as well as therapies targeted to address those alterations. Dana-Farber stores patient genomic profiles in a database linked to other clinical data that the institute says provides a rich resource for precision cancer medical research and practice.

Where OncoPanel could make a genomic profile of a tumor, nearly all (96%) returned results of some kind. Nearly three-quarters (73%) showed an alteration providing new insights or considered actionable. In 19 percent of the cases, the analysis pointed to currently approved cancer treatments. In the remaining cases, the analysis could point patients to clinical trials of experimental drugs or currently approved drugs being tested for other disorders. The paper also notes cases where Profile identified genomic alterations that responded to targeted therapies, and gave examples where the analysis resulted in a different diagnosis or treatment strategy.

MacConaill and colleagues, however, also identified a number of obstacles that need to be addressed by Dana-Farber and other institutions considering a program like Profile. Among all of the samples collected, only about half had sufficient tumor material available for analysis. In addition, only in about 10 percent of the cases did genomic profiles result in actual changes in patient care.  The authors cite a number of factors in cancer care that must be coordinated with tumor profiling to make optimum use of the data, including the timing of the profile during the course of the patient’s disease progression, and access to targeted drugs and clinical trials.

Related to timing of the analysis is the amount of time needed to return results of tumor profiling. The authors report OncoPanel provided results in an average of 5.3 weeks, which Dana-Farber says is now down to 3 weeks. Genomic profiling of tumors is also expensive, “and this cost,” MacConaill notes in a Dana-Farber statement, “has been borne by our institutions.”

As reported on a number of occasions in Science & Enterprise, Foundation Medicine — a company spun off from Dana-Farber Cancer Institute, the Broad Institute, Harvard Medical School and MIT — commercializes a technology similar to Profile that examines and reveals genes altered in human cancers, and offers potential targets for therapies. Two of the paper’s authors, Matthew Meyerson and Levi Garraway, are co-founders of Foundation Medicine and serve as advisers to the company.

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