Landmark patent granted for comprehensive genomic analysis in cancer

May 18, 2016 – CAMBRIDGE. The U.S. Patent and Trademark Office has issued U.S. patent number 9,340,830, entitled, “Optimization of Multigene Analysis of Tumor Samples” to¬†Foundation Medicine, Inc. The patent includes fundamental claims describing methods of analyzing a cancer patient’s tissue or blood specimen to detect multiple classes of genomic alterations, and carries a term extending to 2032. Foundation Medicine is also pursuing patent applications covering aspects of its genomic analysis platform with the European Patent Office and in other jurisdictions outside the United States.

According to the patent’s abstract, it covers “A method of analyzing a tumor sample comprising: (a) acquiring a library comprising a plurality of tumor members from a tumor sample; (b) contacting the library with a bait set to provide selected members; (c) acquiring a read for a subgenomic interval from a tumor member from said library; (d) aligning said read; and (e) assigning a nucleotide value (e.g., calling a mutation) from said read for the preselected nucleotide position, thereby analyzing said tumor sample.”

“Foundation Medicine has been at the leading edge of innovation in genomic analysis of cancer since our inception six years ago,” said Michael Pellini, M.D, chief executive officer for Foundation Medicine. “We believe this patent both acknowledges our pioneering efforts in research and development, and, importantly, it demonstrates our expertise in translating innovation into clinically validated, best-in-class assays that benefit cancer patients around the world. We are gratified that our contributions to the clinical and scientific communities are enabling new genomic analysis products in the fight against cancer.”

Dr. Pellini continued, “We believe patients and their physicians should have access to the full complement of test offerings that, when used appropriately, can meaningfully guide and inform treatment plans. We plan to evaluate strategies to maximize the value of this patent and our other intellectual property. That said, in leveraging this asset, we do not intend to block the use of methods covered by the patent in patient testing that may be offered by others. We are pleased with the issuance of this patent to strengthen Foundation Medicine’s intellectual property position and reinforce our overall leadership in transforming cancer care.”

Shortly after the patent issuance was announced on Tuesday, Foundation Medicine filed a lawsuit against competitor Guardant Health in the Eastern District Court of Texas. The suit does not specifically indicate how Guardant’s technology infringes on the patent rights of Foundation Medicine. In a comment made to the Business Insider, Steve Kafka, President of Foundation Medicine, said that “[w]e certainly intend to pursue the value of this patent.”