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More Genomic Tests Enhance Personalized Cancer Care

Genomics graphic

(National Human Genome Research Institute, NIH)

2 June 2016. A pilot study with cancer patients shows comprehensive genomic analyses can provide actionable treatment targets in 9 out of 10 cases, exceeding the performance of commercial diagnostic services available today. A team led by genomics professors Rong Chen and Eric Schadt at Mount Sinai medical school in New York published its findings yesterday in the journal Genome Medicine.

Chen, Schadt, and colleagues sought to determine the advantages to cancer patients of a comprehensive genomic analysis of their tumors, at more levels and detail than provided by current commercial diagnostic services. Mount Sinai medical center provides these expanded genomic tests as part of its personalized medicine programs. In addition, Chen and Schadt are scientific advisors or consultants to several companies applying genomic analysis to clinical diagnostics.

The researchers included the following set of tests for 46 patients with solid tumor cancers:

Whole exome sequencing from the tumor and patient-matched samples. Exomes represent about 2 percent of all base pairs in a genome, but still account for about 85 percent of disease-causing genetic variations.

Single nucleotide polymorphisms, or SNPs, small variations at specific points in the genome, also from tumor and patient-matched samples.

RNA sequencing, to identify tumor-specific mutations.

Copy number alterations, where sections of the genome are repeated, and patterns of these repeated sections are associated with occurrence of cancer.

Germline variations, mutations passed on from parents to children.

The comprehensive genomic analysis also brought in results from a commercial genomic test, the Ion AmpliSeq Cancer Hotspot Panel that analyzes known mutations associated with cancer, as well as gene fusions and changes in gene expression. The researchers integrated the test results into an individualized analysis for each of the 46 patients. Participants had an average age of 48, and 26 were women.

The findings show the comprehensive collection of genomic tests returned actionable results for 42 of the 46, or 91 percent of patients in the study. The tests identified on average 5 treatment targets per patient, from their somatic mutations, copy number variations, germline variations, and changes in gene expression. The comprehensive results identified 7.5 times as many targets as the Ion AmpliSeq Cancer Hotspot Panel alone, as well as twice as many targets as commercial cancer genome analytics offered by FoundationOne and the Oncomine Cancer Panel provided by ThermoFisher Scientific.

The authors say all results were returned to study participants and their physicians, which in several cases led to changes in treatment. “We launched this program with the idea that a more comprehensive view of that variant signature would make a difference in patient treatment,’ says Chen in a Mount Sinai statement, “but even we were surprised by just how much is being missed with current testing.”

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