Ariosa Diagnostics, Inc v Sequenom, Inc [2021] FCAFC 101 (18 June 2021)

Patents – method of diagnosis – manner of manufacture – sufficiency – fair basis – infringement

This case involved an appeal from the decision of Beach J in Sequenom, Inc v Ariosa Diagnostics, Inc [2019] FCA 1011, concerning Sequenom’s patent for a method of detecting the presence of a nucleic acid of foetal origin in a maternal serum or plasma sample.  The method used “cell free foetal DNA” (“cffDNA”) – that is, non-cellular DNA from a foetus.

The first appellant (“Ariosa”) conducts and licenses others (including the second and third appellants) to conduct a non-invasive prenatal test called the Harmony Test.  Sequenom sued Ariosa for infringement of claims of its patent (which is now expired).  At trial, Ariosa cross-claimed seeking revocation.  Ariosa convinced the Court to revoke one claim on the ground of fair basis.  Sequenom otherwise succeeded in its infringement claim.

Ariosa appealed on the bases that the judge erred in his conclusions in relation to manner of manufacture, lack of fair basis, lack of sufficiency, and aspects of the infringement findings. 

The Full Court (Middleton, Nicholas and Burley JJ) dismissed all of the appeal grounds relating to validity but allowed the appeal insofar as it related to the judge’s findings of infringement by use of the “send out test”.

Manner of manufacture

The primary judge had noted that there was no claim to cffDNA, but rather to a method to which the discovery of the existence of cffDNA could be put to practical use.  For this reason, the primary judge considered that the subject matter of the claims fell within the principles of National Resource Development Corporation v Commissioner of Patents [1959] HCA 67; 102 CLR 252 (Dixon CJ, Kitto and Windeyer JJ) (“NRDC”) and affirmed in D’Arcy v Myriad Genetics Inc [2015] HCA 35; 258 CLR 334 (“Myriad”), while not falling within the impermissible product claims rejected in Myriad. 

The primary judge said that the patent specification confirms that the invention is:

[…] not simply the presence of cffDNA in maternal serum or plasma but rather, “a detection method performed on a maternal serum or plasma sample from a pregnant female, which method comprises detecting the presence of a nucleic acid of foetal origin in the sample”. It is explained that the claimed method thus provides a “method of prenatal diagnosis”[…]

The primary judge identified that there were four classes of claims: a detection method (independent claim 1 and dependent claims 2, 3, 5, 6 and 9); a detection method within the first class for determining the sex of a foetus (dependent claim 13); a method of the first class which further comprises determining the concentration of foetal nucleic acid sequences in the maternal serum or plasma sample (dependent claim 14); and the provision of a “prenatal diagnosis” following the performance of the method in the first class (independent claim 22 and dependent claims 23, 25 and 26).  His Honour distinguished Myriad on the basis that the case does not concern product claims to naturally occurring nucleic acid molecules per se or naturally occurring genetic information.  He noted that the detection method inherently involved artificial steps requiring human action.  The primary judge concluded that all uses of the relevant method would be commensurate with the scope of the inventor’s new method of prenatal detection using cffDNA.  He concluded that the claimed invention was for an artificially created state of affairs, of economic significance, and that there would be no chilling effect and the decision would promote consistency in the application of the law.

On appeal, Ariosa asserted that the primary judge ought to have found that the end result does not at all, or sufficiently, involve an artificial effect or an artificially created state of affairs, but the detection of what is naturally occurring, and that in substance each of the relevant claims is to a mere discovery.  The appellants further contended that the primary judge erred in finding that the alleged invention did not concern a new class of claim and accordingly, that there was no need to apply the “other factors” identified by the plurality in Myriad, and in finding that those factors confirm the patentability of the invention claimed.

The Full Court analysed NRDC and noted that the distinction between mere discovery and an invention lies in its practical application to a useful end, and that the invention should be considered as a unitary concept, not segregated artificially into parts.  Their Honours observed that the approach of the appellants sought to disaggregate the discovery of cffDNA in maternal plasma or serum from the method used to harness that discovery, and therefore tended to overlook those matters.  Their Honours also noted that an invention may reside in an abstract idea that is then put to a useful end.

On the basis of their analysis of Apotex Pty Ltd v Sanofi-Aventis Australia Pty Ltd [2013] HCA 50; 253 CLR 284 (“Apotex”), the Full Court noted that, in respect of method claims, a “product” in the sense of a tangible thing is not required for patentability, and that in this respect, Myriad distinguished between product and method claims.  They relied upon these observations for the proposition that it is not necessary for a method or process claim to have as its outcome or result a tangible product or output in order to be a method that produces an economically useful outcome, provided there is “a new and useful effect”.  It may be observed that the “new and useful effect” in Apotex was the treatment of a disease in a human.  In this case, the “new and useful effect” was merely a method of detection (or diagnosis) as to presence of certain cffDNA or the nature of the foetus.

The Full Court noted that the claims in Myriad were to an isolated nucleic acid molecule, which the plurality concluded was not made or artificially created, and that the plurality of the High Court rejected the finding that the claims were of economic significance.  On that basis, the plurality in Myriad found that the subject matter of the claims lay at the boundaries of the concept of manner of manufacture because it was not an artificially created state of affairs of economic utility, that there was a chilling effect, that to extend the concept of manner of manufacture to include the invention claimed would not contribute to the coherence of the law, and that Australia’s international obligations did not suggest otherwise.  The Full Court noted that the facts upon which Myriad was based were materially different, most particularly because the claim in issue was a product claim (the isolated BRCA1 gene sequence). 

The Full Court noted that Myriad makes it clear that it is of importance to consider what in substance is the invention as claimed.  They concluded that the relevant claims represent a manner of manufacture, having regard to the disclosure of the specification (which informs the skilled reader that the invention provides a detection method) and the substance of the invention claimed in the relevant claims (which are to a detection method performed on a maternal serum or plasma sample from a pregnant female, which method comprises detecting the presence of nucleic acid of foetal origin in the sample). 

Their Honours found that the correct identification of the invention lay not in the mere observation that cffDNA is to be found in maternal plasma or serum, but in the explanation as to how that knowledge may be unlocked for others to use (the explanation of how to extract cffDNA from plasma or serum).  The idea, with a practical means of application, makes the invention.  The Full Court agreed with the primary judge’s conclusion that the artificially created state of affairs is the detection of cffDNA in the tested sample, which is by definition the result of human action and is not naturally occurring, and not just the information encoded by the naturally occurring cffDNA.

Their Honours also found that the detection of nucleic acid of foetal origin is of economic utility. 

The Full Court found that NRDC and Apotex compelled rejection of Ariosa’s submission that the output of the method is mere information and accordingly not a manner of manufacture, because their Honours concluded the claim, construed as a whole, necessarily involves an artificially created state of affairs yielding an outcome that is of economic utility.

The Full Court also found that, because the concept fell firmly within the concept of a manner of manufacture (as that term may be understood having regard to the authorities, being an artificially created state of affairs of economic utility), it did not represent a new class of claim involving a significant new application or extension of the concept.

Lack of sufficiency

Ariosa, relying on Tramanco Pty Ltd v BPW Transpec Pty Ltd [2014] FCAFC 23; 105 IPR 18 (“Tramanco”) also contended that there were three embodiments in the patent, each representing a different invention, and that each needed to be fully described.  These three embodiments were the performance of a diagnosis by reference to the quality of the foetal DNA, specifically whether the maternal serum or plasma includes any targeted sequences not possessed by the mother (“qualitative method”), the performance of a diagnosis by reference to the quantity of the foetal DNA, directed to determining the total levels of cffDNA (“correlative quantitative method”), and the performance of a diagnosis by reference to the quantity of foetal DNA, directed to measuring the level of foetal DNA markers on different chromosomes (“comparative quantitative method”).  Ariosa said that the correlative quantitative method and the comparative quantitative method were not sufficiently described.

The primary judge had found that there was only one invention around which the claims were drawn, which was the method of detecting cffDNA in an artificially created plasma or serum sample isolated from blood extracted from a pregnant female.  Against the prospect that he was wrong, his Honour considered the disclosure of a correlative quantitative method and concluded that the suggestion of use of cffDNA in such a method was not supported by any conclusive study nor implemented in practice.  His Honour agreed with Ariosa that implementing a comparative quantitative method would have constituted a significant research project, and it was doubtful the method could have been implemented in 1997.  However, the primary judge concluded the examples were only two of a wide range of uses for the invention described and claimed, and were described in very qualified terms as potential future applications.  His Honour concluded the relevant claims did not lack sufficiency, because a skilled person could perform something falling within the scope of each of the relevant claims.

On appeal, Ariosa contended that the primary judge ought to have found that each of the relevant claims was directed to more than one method, each of which needs to be described fully, and that in the case of the correlative quantitative method, the specification does not provide sufficient description.

The Full Court found that Kimberly-Clark Australia Pty Ltd v Arico Trading International Pty Ltd [2001] HCA 8; 207 CLR 1 (“Kimberly-Clark”) does not require an enabling disclosure across the breadth of the claim, because the High Court concluded at [25] that it was adequate consideration for the monopoly for the patentee to provide one means of utilising the invention.  This approach was affirmed in Lockwood Security Products Pty Ltd v Doric Products Pty Ltd [2004] HCA 58; 217 CLR 274 (“Lockwood”) at [60].  Their Honours said that an approach that seeks to move from consideration of the extent to which the claim was enabled by the body of the specification to the consideration of whether more than one invention is disclosed in the body of the specification tends to distract attention from the correct analysis, and reflects the law as amended by the Raising the Bar amendments, rather than the law which applied to the patent in issue. 

The Full Court concluded that there was only one invention described, being a detection method for prenatal diagnosis.  The Full Court also noted discussion of the correlative and comparative quantitative methods was tentative and qualified, and described the methods as possibilities.  The Full Court said that the recognition that the invention may have several applications, some described more fully and others less fully, does not yield the result that the concept as set out in the embodiment of the invention must be sub-divided.  The standard set by s 40(2)(a) and described in Kimberly-Clark may be satisfied by supplying a means of performing the invention, not every means. 

On the basis of their conclusion that only one invention was described (and given the concession that the qualitative method was enabled), the Full Court concluded that the disclosure of the specification supplied sufficient information to enable the person skilled in the art to produce something within any claim.  The Full Court held that the reasoning in Tramanco did not suggest a different analysis, because the comments there considered that if a claim had the effect of claiming three distinct alternative outcomes, each must be enabled.  But in the case before it, the Full Court concluded the broader disclosure was sufficient given the broader form of the invention.

The Full Court rejected specific challenges to claims 22, 23 and 25 on the same basis.

Interestingly, the Full Court noted that the claims might not have been enabled under post-Raising the Bar law.  However, as they observed, that did not assist Ariosa in this proceeding.  The observation reinforces the fact, which was already evident from the judgment in Merck Sharp and Dohme Corporation v Wyeth LLC [2020] FCA 1477, that the Raising the Bar amendments have achieved their aim of increasing the burden on patent applicants to provide disclosure to support the breadth of their claims.

Claim 14 – infringement and sufficiency

The Full Court also rejected an argument that claim 14 was confined to the absolute concentration of the foetal nucleic acid sequence in serum or plasma, rather than the relative concentration.  In reaching this conclusion, the Full Court endorsed the primary judge’s reasoning, which depended on the disclosure of absolute and relative concentration in the specification, dependent claims which specified relative concentration, and the expert evidence.

The Full Court rejected the argument that claim 14 was not sufficient because it did not enable the determination of relative concentration, because there was no dispute that the determination of absolute concentration was sufficiently described.

Lack of fair basis

Ariosa challenged the primary judge’s findings that the relevant claims were fairly based on the matter described in the specification, and submitted that:

• the primary judge ought to have found that the invention disclosed in the specification does not extend beyond targeting a DNA sequence of the foetus which is known in advance not to be possessed by the pregnant female, so as to detect the presence of that sequence in the maternal plasma or serum; and
• the primary judge ought to have recognised that the person skilled in the art would have read the broad disclosures of the patent as being informed by the specification as a whole and accordingly subject to limitations pointed to in the context of the examples.

The Full Court noted the test for fair basis in Lockwood.  Their Honours noted that the appellants did not contest the general characterisation of the invention by the primary judge (that is, that the patent as a whole describes an invention comprising the detection of cffDNA in a plasma or serum sample prepared from blood extracted from a pregnant female) but submitted this disclosure must by read down by reference to more express disclosure in the examples.  The Full Court rejected this ground of appeal, for four reasons.

First, the disclosure of the specification does not require advanced knowledge of the target sequence to detect the presence of the identified foetal nucleic acid.  There is a consistency between the broadest statement of the invention set out in the specification and the claims.  Second, it is not to be implied from specific embodiments that the scope of the invention is narrower than the broader statement of the invention – indeed, the specification states that the examples do not limit the invention.  Third, the experts did not understand that the patent required that the nucleic acid of foetal origin be known in advance to be of foetal origin.  Fourth, the Full Court did not agree that the primary judge had conflated the test for sufficiency with the test for fair basis – indeed, the primary judge had eschewed such an approach.

Infringement

A question arose as to whether a “send out” model used by Ariosa between December 2014 and March 2016, whereby the second and third appellants collected blood samples from pregnant women and sent them to Ariosa in the US, who sent back results via a file sharing platform, constituted exploitation.  The primary judge had concluded that the product of the use of the relevant Harmony tests was the results from that test. 

Ariosa argued that the test results were not a product resulting from the use of the method, and therefore that the primary judge erred in finding that the importation, supply, offer to supply or disposal of Harmony test results constituted infringement.  Ariosa said that the primary judge should have found that the Harmony test results were fundamentally information, not a product.

Ariosa said that not every method will result in a “product” within the definition of “exploit”. 

The Full Court agreed with Ariosa.  It noted that “product” is not defined in the Patents Act 1990 (Cth) but said that in the context of the definition of exploit (especially paragraph (b)) a product results from the use of the method or process, suggesting that the method or process must be one that manufactures the product, and that paragraph (a) suggests that a product is a tangible thing. 

The Full Court noted that there was no necessity in principle for a method or process to yield a product in order for that method or process to amount to a manner of manufacture, and that a number of manner of manufacture cases involve methods or processes which do not yield products (for example, NRDC, CCOM Pty Ltd v Jiejing Pty Ltd [1994] FCA 396, 51 FCR 260, Apotex).  They considered a construction of the word “product” which recognised that not all methods lead to a product was to be preferred. 

The Full Court concluded that the outcome that results from the use of the methods of detection or diagnosis of the relevant claims does not conform with the meaning of “a product resulting from such use” within the definition of “exploit”, and that the reference to “product” in exploit should not be interpreted as extending the patentee’s monopoly to information which could not itself constitute patentable subject matter.  The Full Court therefore concluded that sending the results of the “send out tests” to patients did not constitute infringement.