Pre-natal diagnostic claims employing conventional DNA techniques held unpatentable under Myriad

In Ariosa Diagnostics Inc. v Sequenom Inc., the US District Court for the Northern District of California held that several claims of a US patent disclosing a method to detect the presence of paternally inherited DNA of fetal origin (cffDNA), through the screening of maternal serum or plasma, do not constitute eligible subject matter and are invalid under 35 USC 101.

In 2011, Ariosa had filed a declaratory judgment action, seeking a declaration that its non-invasive prenatal test 'Harmony' did not infringe US Patent No. 6,258,540, exclusively licensed by Sequenom from Isis Innovation Ltd. Sequenom had filed a counterclaim for infringement, seeking a preliminary injunction against Ariosa. The court had denied the motion for a preliminary injunction, but the Federal Circuit had vacated the court's order, remanding the case for further proceedings and directing the court to examine subject matter eligibility of the asserted claims in light of the Supreme Court’s recent decision in Association for Molecular Pathology v Myriad Genetics Inc. Both Ariosa and Sequenom had filed motions for summary judgment of whether claims 1, 2, 4, 5, 8, 19-22, 24 and 25 of the '540 patent were drawn to patent-eligible subject matter.

The independent claims at issue in the case were the following:

1. 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.
24. A method for detecting a paternally inherited nucleic acid on a maternal blood sample, which method comprises:
removing all or substantially all nucleated and anucleated cell populations from the blood sample,
amplifying a paternally inherited nucleic acid from the remaining fluid and
subjecting the amplified nucleic acid to a test for the Paternally [sic] inherited fetal nucleic acid.
25. A method for performing a prenatal diagnosis on a maternal blood sample, which method comprises:
obtaining a non-cellular fraction of the blood sample
amplifying a paternally inherited nucleic acid from the non-cellular fraction and
performing nucleic acid analysis.

The court highlighted that, although the patent law has a wide scope (Diamond v. Chakrabarty), 'laws of nature, natural phenomena, and abstract ideas are not patentable' (Mayo Collaborative Servs. v Prometheus Labs. Inc.). Then it proceeded to examine the case law of the Supreme Court on subject matter eligibility:

• in Funk Bros. Seed Co. v. Kalo Inoculant Co., the Supreme Court held that 'patent cannot issue for the discovery of the phenomena of nature', explaining that the aggregation of specific strains of bacteria in a product, in light of the absence of harmful effects to the properties of either, does not constitute eligible subject matter;
• in Gottschalk v. Benson, the Supreme Court ruled that a method for converting binary-coded decimal numerals into pure binary numerals was ineligible subject matter, as the formula was an abstract idea and would have conferred a patent on the underlying algorithm itself;
• in Parker v Flook, the court stated that a mathematical formula 'cannot support a patent unless there is some other inventive concept in its application'; even if the claim does not wholly preempt the formula and discloses it as a solution for a specific purpose, it remains ineligible for patent protection;
• in Diamond v Diehr, instead, a process that employed a well-known mathematical equation was deemed patentable, as the claim merely sought 'to foreclose from others the use of that equation in conjunction with all the other steps in their claimed process';
• in Bilski v Kappos, dealing with a patent application claiming a procedure for instructing buyers and sellers of commodities in the energy market on how to best deal with price fluctuations, the Supreme Court ruled that the concept of hedging is an unpatentable abstract idea;
• in Mayo v Prometheus, the court rejected the patentability of a process that helped doctors determine whether a given dosage of thiopurine drug was too low or too high, relying on the presence of certain metabolites in the blood, as the claim merely recited a law of nature;
• in Association for Molecular Pathology v Myriad Genetics Inc., concerning claims directed towards the human genes BRCA1 and BRCA2 and related diagnostic tests, the Supreme Court held that 'a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated, but that cDNA is patent eligible because it is not naturally occurring'.

In the case decided by Judge Susan Illston, the parties agreed on the fact that neither cffDNA, nor its discovery in maternal plasma or serum is patentable, because its presence is a natural phenomenon. The court thus identified the key issue: 'whether the steps of the claimed methods in the ’540 patent, applied to that natural phenomenon, are sufficient to render the claims patentable'. Ariosa argued that the limitations embedded in the claims essentially applied well-understood, routine, and conventional activity to the natural phenomenon. The court agreed, noting that Ariosa had proved that the amplification and detection of DNA sequences in plasma or serum was well known by 1997, as confirmed by Sequenom's own expert. Thus, '[b]ecause the claimed processes at issue - apart from the natural phenomenon of paternally inherited cffDNA - involve no more than well-understood, routine, conventional activity, previously engaged in by those in the field, they are not drawn to patent eligible subject matter and are invalid under § 101'.

Judge Susan Illston
© Jason Doly/The Recorder

The judge dismissed Sequenom's arguments aimed at drawing a distinction between patentability of cffDNA, not permitted, and of its use, allegedly allowed. The decision noted that the Supreme Court has never stated that the use of a naturally occurring phenomenon in patentable. To the contrary, it has clarified that only an innovative or inventive use is entitled to patent protection: such use cannot rely on the simple addition of conventional steps to a non-eligible subject matter. Further, citing Flook, the court held that 'use of a newly discovered natural phenomenon, law of nature, or abstract idea will not render a claim patentable if the use of that natural phenomenon, law of nature or abstract idea is the only innovation contained in the patent'. Applying this reasoning to the case, the judge found that paternally inherited cffDNA does not become patentable just because the claims assert that it can be detected using conventional methods.

Relying on the recent judgment in Myriad, the court held that:

[E]ven though Myriad involved composition claims rather than method claims, that decision also supports the Court’s conclusion. The claims in Myriad gave the patentees the exclusive right to isolate the BRCA1 and BCRA2 genes. Although the Supreme Court was not presented with method claims, the Court explained "[h]ad Myriad created an innovative method of manipulating genes while searching for the BRCA1 and BRCA2 genes, it could possibly have sought a method patent. But the processes used by Myriad to isolate DNA were well understood by geneticists at the time of Myriad’s patents". Similarly, had the inventors of the ’540 patent created an innovative method of performing DNA detection while searching for paternally inherited cffDNA, such as a new method of amplification or fractionation, those claims would be patentable. But, the claims presently before the Court simply rely on processes to detect DNA that - as Sequenom concedes - were conventional techniques by those in the field at the time of the invention.

Evaluating the risk that the claims may preempt the underlying natural phenomenon, judge Illston accepted Ariosa's arguments, observing that preemption is not only triggered by the absence of practicable alternative methods, but also by the lack of commercially viable alternatives. In this perspective, although practicable alternatives for detecting cffDNA existed, the court found that Sequenom's failure to provide evidence of the existence of commercially viable alternative methods suggested that 'the claims at issue pose a substantial risk of preempting the natural phenomenon of paternally inherited cffDNA', supporting the court's conclusion on the unpatentability of the asserted claims.