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USPTO Board Rules Against Sequenom on Certain NIPT Patent Claims

NEW YORK (GenomeWeb) – A US Patent and Trademark Office board has declared that certain claims on a patent held by Sequenom are unpatentable, while it upheld other claims on the patent, US Patent No. 6,258,540.

In a final decision, the patent trial and appeal board of the USPTO recently ruled that Ariosa Diagnostics has shown that nine claims on the patent — claims 1, 2, 4, 5, 8, 19, 20, 24, and 25 — are unpatentable, but found that Ariosa did not demonstrate that seven other claims contained in the '540 patent — claims 3, 12, 13, 15, 18, 21, and 22 — were unpatentable.

Further, the board denied motions by Isis Innovations, which was assigned the '540 patent, to amend the claims and to exclude evidence. Sequenom holds an exclusive license to the '540 patent, which underlies its MaterniT21 Plus non-invasive prenatal diagnostic test, from Isis.

The decision by the USPTO board is the latest development in a nearly three-year long battle between Ariosa and Sequenom. In late 2011 Ariosa, then called Aria Diagnostics, sought a declaratory judgment from the US District Court for the Northern District of California that Ariosa's test, eventually called Harmony, did not infringe the '540 patent, as Clinical Sequencing News reported at the time.

Last October, the federal court delivered a blow to Sequenom by invalidating the patent, saying that it covers a phenomenon of nature, making it unpatentable. That decision is currently on appeal at the Court of Appeals for the Federal Circuit.

In declaring some of the claims unpatentable, the USPTO board found that, among other things, certain claims of the '540 patent were obvious,making them unpatentable. "[I]f the differences between the claimed subject matter and the prior art are such that the subject matter, as a whole, would have been obvious at the time the invention made to a person having ordinary skill in the art to which said subject matter pertains," the claim in question would be unpatentable, the board said.

Among the claims that it said are unpatentable is a "method for detecting a paternally inherited nucleic acid of fetal origin performed on a maternal serum or plasma sample from a pregnant female … [comprising the amplification of] a paternally inherited nucleic acid from the serum or plasma sample and detecting the presence of a paternally inherited nucleic acid of fetal origin in the sample," as described in the '540 patent.

The board's ruling could have a negative effect on Sequenom, Piper Jaffray analyst William Quirk said in a research note today. The ruling, along with the anticipated upcoming decision by the federal appeals court "could significantly weaken [Sequenom's] IP position, adding risk to [its] recent royalty/in-licensing strategy," he said, referring to Sequenom's agreement with Quest Diagnostics.

If the federal appeals court upholds the earlier decision that invalidated the '540 patent, royalties from in-licensing deals could be "materially impaired and/or third parties may opt to forego a deal entirely. …Irrespective, it implies lower future revenue from this strategy," Quirk said.

He added that he expects Sequenom will find it difficult to win its appeal.

Ariosa CEO Ken Song declined to comment on the USPTO board ruling, saying the firm does not comment on ongoing litigation. Sequenom officials could not be reached for comment.