Federal Circuit Looks for Inventive Concept in Sequenom Patent

10 November 2014 PharmaPatents Blog

On November 7, 2014, the Federal Circuit heard oral arguments in Aria Diagnostics, Inc. v. Sequenom, Inc., where Sequenom is appealing the district court’s summary judgment of invalidity under 35 USC § 101. The active questioning by the judges suggests that they are wrestling with how to apply the Supreme Court’s decision in Mayo to different types of inventions. 

The Patent at Issue


The Sequenom patent at issue was U.S. Patent 6,258,540, owned by Isis Innovation Limited and exclusively licensed to Sequenom.

Claim 1 recites:

A method for detecting a paternally inherited nucleic acid of fetal origin performed on a maternal serum or plasma sample from a pregnant female, which method comprises amplifying 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.

When the case previously was before the Federal Circuit after the district court denied Aria’s motion for a preliminary injunction, the Federal Circuit  described the invention as follows:

The ’540 patent discloses methods to identify fetal genetic defects by analyzing … maternal plasma or serum. The ’540 patent discloses that non-nucleated free floating fetal DNA (the cffDNA) exists in maternal blood. … The specification explains that not only does analysis of cffDNA permit more efficient determination of genetic defects (for example, trisomy of chromosome 21) but that a pregnant woman carrying a fetus with certain genetic defects will have more cffDNA in her blood than do women with normal fetuses. … In other words, the ’540 patent claims methods to detect fetal genetic characteristics by analyzing cffDNA obtained from a maternal blood sample. These new tests presented fewer risks and a more dependable rate of abnormality detection.

(You can read more about the first Federal Circuit decision here.)

The Previous Proceedings

The case previously was before the Federal Circuit after the district court denied Sequenom’s motion for a preliminary injunction against Aria’s Harmony test for Down’s Syndrome. The previous Federal Circuit decision (authored by then Chief Judge Rader and joined by Judges Dyk and Reyna) focused on claim construction, but also instructed the district court to “examine subject matter eligibility [under the Myriad Supreme Court decision]” on remand.

The Oral Arguments 

Oral arguments were heard by Judges Reyna, Linn, and Wallach. I was not able to attend in person, but have listed to the recording. In the summary below, I have done my best to identify which judge was speaking. Mr. Malacek argued for Sequenom.  Mr. Gindler and Mr. Reines argued for Aria, but I treat their comments together.

Before Sequenom’s counsel was able to complete his first sentence, Judge Reyna jumped in with his first question:

Looking at the claims themselves … where is the “inventive concept” within the claims?

Show me in the claim limitations the “inventive concept” ….

The presence of paternal DNA in the fetal sample is a natural phenomenon, and the activities that are used to detect are conventional, so where is the inventive concept?

Sequenom’s main response to this line of questioning was that while the general techniques are conventional, it was “radically different” to use them in the claimed context, which uses a sample that had previously been discarded.  Judge Linn appeared to be interested in these comments, but also noted that the fact that paternal DNA may be present in the fetal sample is a natural phenomenon. Aria’s counsel argued that Sequenom’s position turned Alice on its head, because Alice shows that conventional steps are not “new” because they are applied to a natural phenomenon. According to Aria’s counsel, Alice requires the following analytical framework:

Under Alice, eliminate the natural phenomenon, see what’s left, and ask if that’s new.

Judge Wallach raised another issue:

Is cell-free DNA that has been amplified physically and chemically different from naturally-occurring DNA?

While Sequenom argued that it is, Aria’s counsel pointed out the claims did not recite any difference, and so any difference could not support patent eligibility under In re Roslin Institute.

Sequenom’s counsel emphasized that the claims did not preclude others from detecting paternal DNA by other methods, but the judges were not satisfied that the claims were sufficiently circumscribed. This led to the following point of discussion:

When we engage in a section 101 analysis … are we restricted to the claim language and the claims, or can we look at the patent as a whole–the written description and the claims …?

Judge Linn asked Aria’s counsel why the claims can’t be characterized as a new use of known techniques, which is decidedly patent-eligible. In response, Aria’s counsel argued that because the new use relates to a natural phenomenon it must be treated differently under the Supreme Court decisions in Parker v. Flook and Myriad.

Predicting the Outcome


I can’t tell from the oral arguments how the Federal Circuit will rule on this case, and am left with the feeling that even the judges are still uncertain of the outcome. Judge Linn may have captured the conundrum best with this comment:

Once you recognize that [there is paternally inherited information in the fetal sample] then there’s nothing beyond that other than applying conventional techniques to go find it … I’m not saying that shouldn’t be rewarded with a patent, but I’m living under a regime set by the Supreme Court.

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