A federal court invalidated a Sequenom-licensed patent covering the detection of fetal cell-free DNA in the bloodstream of pregnant women, upholding a challenge from Ariosa Diagnostics.

Judge Susan Illston of the U.S. District Court for the Northern District of California issued a summary judgment Wednesday in favor of Ariosa, declaring that U.S. Patent No. 6,258,540 covered patent-ineligible subject matter—namely the presence of fetal DNA in the mother’s blood, which the judge said fell into the natural-phenomenon exemption from patentability under Section 101 of the U.S. Patent Code. Judge Illston added that claims covering detection of that DNA were unpatentable because they involved conventional genetic techniques.

Sequenom used the patent to protect its MaterniT21 Plus noninvasive prenatal diagnostic test, which poses a lower risk of miscarriage than older techniques such as amniocentesis or chorionic villus sampling.

Ariosa, formerly Aria Diagnostics, sued Sequenom in December 2011, seeking a declaratory judgment that its Harmony™ Prenatal Test did not infringe the patent. Ariosa cited what it called repeated public threats made against the company by Sequenom regarding enforcement of the patent—for which Sequenom holds an exclusive license from Isis Innovations. Judge Illston held a hearing October 11.

In its federal court case (No. C 11-06391), Ariosa contended that Sequenom unsuccessfully spent almost two years trying to prevent Ariosa from making and selling the Harmony Prenatal Test. Harmony is designed to assess whether a fetus is at risk of having Down syndrome and other chromosomal abnormalities, based on the drawing of blood from pregnant women.

Ariosa responded to the summary judgment yesterday with a statement hailing the court’s action as “a complete victory” that “validates Ariosa’s long-standing view that it has freedom to develop new, innovative, and market-leading technologies to provide improved genetic testing for pregnant women.”

Sequenom said it “vigorously disagrees with the order and, following entry of judgment pursuant to the order, intends to appeal the decision to the Federal Circuit Court of Appeals,” in a Form 8-K filing by the publicly traded company yesterday to the U.S. Securities and Exchange Commission.

The summary judgment comes nearly five months after the U.S. Supreme Court’s mixed decision in a closely watched case involving gene patents. The high court ruled against Myriad Genetics’ patent claims for breast cancer susceptibility genes BRCA 1 and 2, maintaining they are naturally occurring DNA segments and thus products of nature—but also holding that companies can patent composite DNA (cDNA) and other synthetic genetic materials that do not meet the “product of nature” exemption from patentability.

Since the June 13 Supreme Court decision, Myriad has filed separate suits against three companies alleging that they infringed its patents for a predictive cancer diagnostic test; the companies have promised to defend themselves in court. Earlier this month, BioReference Laboratories became the third company to be challenged by Myriad, joining Ambry Genetics and Gene by Gene.

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