A federal appellate court has invalidated Sequenom’s patent for a noninvasive prenatal DNA test, agreeing with a lower court that the patent was unenforceable.

The U.S. Court of Appeals for the Federal Circuit (CAFC) held Friday that Sequenom’s patent protected unpatentable “natural phenomena.” The ruling upheld a 2013 decision by the U.S. District Court for the Northern District of California that sided with Ariosa Diagnostics, which was acquired in January by Roche for up to $625 million.

The patent was at the center of infringement lawsuits filed starting in 2011 between Sequenom, Ariosa, and another prenatal diagnostics company, Natera. At issue was U.S. Patent No. 6,258,540, a key patent protecting Sequenom’s MaterniT21 test, a noninvasive prenatal test designed to detect fetal chromosomal abnormalities—from common (trisomies 21, 18 and 13) to more rare (fetal sex aneuploidies, trisomies 16 and 22, and select microdeletions).

The patent, issued in 2001 and commercialized via the MaterniT21 test, protected a method for detecting the small fraction of paternally inherited cell-free fetal DNA (cffDNA) in maternal plasma or serum to determine fetal characteristics, such as gender. Previously, cffDNA had been discarded as medical waste. The method, developed by Dennis Lo, M.D., Ph.D., and James Wainscoat, M.D., was designed to avoid risks of widely used techniques that took samples from the fetus or placenta.

“While Drs. Lo and Wainscoat’s discovery regarding cffDNA may have been a significant contribution to the medical field, that alone does not make it patentable,” the CAFC stated, in a decision authored by Circuit Judge Jimmie V. Reyna. “We do not disagree that detecting cffDNA in maternal plasma or serum that before was discarded as waste material is a positive and valuable contribution to science. But even such valuable contributions can fall short of statutory patentable subject matter, as it does here.”

The CAFC cited the U.S. Supreme Court’s 2012 decision in Mayo Collaborative Services v. Prometheus Laboratories decision. The high court unanimously held as patent-ineligible the methods of dosage calibration for thiopurine drugs for gastrointestinal and nongastrointestinal autoimmune diseases that had been patented by Nestle’s Prometheus’ Laboratories.

“To transform an unpatentable law of nature into a patent­ eligible application of such a law, a patent must do more than simply state the law of nature while adding the words “apply it,” the Supreme Court stated. “It must limit its reach to a particular, inventive application of the law.”

Circuit Judge Richard Linn said he concurred with the district court's decision “only because I am bound by the sweeping language of the test set out in Mayo.”  Otherwise, he added, “I see no reason, in policy or statute, why this breakthrough invention should be deemed patent ineligible.”

The CAFC also cited the 2013 Supreme Court decision in Association for Molecular Pathology (AMP) v. Myriad Genetics, in which the high court unanimously overturned seven of Myriad Genetics’ 24 patents related to its discovery of the precise location and sequence of breast cancer susceptibility genes BRCA 1 and 2.

Lisa A. Haile, J.D., Ph.D., a partner at the law firm DLA Piper, told GEN the CAFC decision was not surprising given these and other court cases on genetic tests in recent years.

“The way they're looking at these straightforward diagnostic claims which are considered to be routine steps, routine reagents, and what not, I think we have some clarity on the fact they are not patent eligible, and if they are issued, they should be reviewed for validity,” Dr. Haile said. “For the first time in a long time, I feel like there is some clarity as to where the courts stand on these types of claims.”

She said that clarity will not dampen the desire of diagnostics developers to develop new tests: “I think it's quite the opposite. I think that what the courts are saying is, have you added anything significantly more than just the routine steps?

“I think there is an opening for patents to be issued in this space,” Dr. Haile added, “but I think it will be difficult if all you're doing is obtaining samples and doing a straight comparison of DNA or proteins, whatever you’re looking at in a sample, versus a reference, and making an 'aha!' conclusion. Those are routine, so those are not going to be patentable.”

In a statement, Sequenom said it believes that the ruling has little business impact since it has been operating under the District Court's invalidity ruling since October 2013, and since it agreed with Illumina to pool all their owned and in-licensed IP covering noninvasive prenatal testing (NIPT) last December.

“In addition, valid and enforceable patents with claims equivalent to those of the '540 Patent are issued in Europe, Japan, Hong Kong, Canada and Australia,” Sequenom added.

Sequenom didn’t rule out another defense of the patents, adding: “The Company understands that patent eligibility under 35 U.S.C. Section 101 is an emerging and complex set of issues and is considering its options for further appeal.”

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