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UPDATE: Appeals Court Upholds Invalidity of Sequenom Patent

This article has been updated to include a comment from Sequenom.

NEW YORK (GenomeWeb) – A US Court of Appeals for the Federal Circuit upheld a ruling by the US District Court for the Northern District of California that found a key Sequenom patent invalid.

Sequenom's US Patent No. 6,258,540 has been the focal point of a series of lawsuits that began in 2011 involving Sequenom, Ariosa, and Natera. Illumina's Verinata Health was previously involved as well, but last year, Illumina and Sequenom entered into a patent pool agreement and settled their litigation.

In 2013, the US District Court for the Northern District of California found the '540 patent invalid. The judge in the 2013 ruling said that the '540 patent covers a phenomenon of nature, which is unpatentable. Sequenom appealed that decision, arguing that the patent covered the detection method, not a phenomenon of nature.

In its decision upholding the district court's ruling, the court of appeals agreed that the patent covered a phenomenon of nature and standard methods. It based its decision primarily on the case Mayo Collaborative Services v. Prometheus Laboratories, which set forth two steps for distinguishing between patents that claim laws of nature and patents that claim applications of such phenomena.

In the first step, the court found that the method concerns the natural phenomenon of circulating cell-free DNA. That in and of itself does not make the patent invalid, but the patent must also include an "inventive concept sufficient to 'transform' the claimed naturally occurring phenomenon into a patent-eligible application," the court wrote.

The court determined that because the '540 patent used techniques that were "well-understood, routine, conventional activities," the method claims did not "result in an inventive concept that transforms the natural phenomenon of cffDNA into a patentable invention."

Nevertheless, Circuit Judge Richard Linn, while agreeing with the court's ruling, did so reluctantly, and wrote that he was "bound by the sweeping language" of the Mayo v Prometheus case. Had it not been for that decision, "I see no reason, in policy or statute, why this breakthrough invention should be deemed patent ineligible."

Last September, the US Patent and Trademark Office board also declared certain of the '540 claims unpatentable.

The firm said in a statement released after the close of the market Friday that it believes the ruling "has little business impact, as it has been operating under the District Court's invalidity ruling since October 2013, and due to the pooling arrangement of NIPT intellectual property entered into with Illumina," which includes other patents. It also noted that it holds "valid and enforceable patents with claims equivalent to those of the '540 Patent … in Europe, Japan, Hong Kong, Canada, and Australia."

Previously, Ariosa's vice president of intellectual property and legal affairs, Dianna DeVore had told GenomeWeb that the invalidation ruling would give other companies the freedom to "innovate in the field of the use of cell-free DNA in pregnant women."