The Doom and Gloom lifts: patentability of Gene Marker-Trait Correlation Methods in Australia

Dr. Victoria Longshaw, Dr. Nigel Parker and Dr. Elizabeth Houlihan

The Australian Federal Court has provided welcome reassurance to patent owners in the biotechnology fields of gene association analyses and quantitative genetics.

In the aftermath of D’Arcy v Myriad Genetics Inc [2015] HCA 35 (“the Myriad case”), in which isolated nucleic acids encoding naturally-occurring information were excluded from patentability, there has been uncertainty as to the scope of this exclusion. Is the use of naturally-occurring gene sequences patentable?

The Federal Court has now answered this question: “yes”. In Meat & Livestock Australia Limited v Cargill, Inc [2018] FCA 51, handed down on 9 February 2018, the Court held that methods using gene markers to identify a trait in an animal are patentable in Australia.

A brief history of the case

This case involved an appeal from an IP Australia Opposition Decision by Meat & Livestock Australia Limited and Dairy Australia Limited (the Appellants, collectively referred to as “MLA”). The Appellants are industry research bodies that invest in, and act on behalf of, agricultural industries in Australia.

MLA had unsuccessfully opposed Australian Patent Application No. 2010202253 (“the Patent Application”), filed in the name of Cargill, Inc and Branhaven, LLC (“the Respondents”). The Patent Application is directed to methods for identifying a trait in a bovine subject from a nucleic acid sample of that subject. Specifically, the claimed invention was directed to identifying single nucleotide polymorphisms (“SNPs”) associated with bovine traits of economic importance using a high-density SNP map of the bovine genome.

MLA’s key argument was that the claimed invention was not patentable because it did not comprise a “manner of new manufacture” according to Subsection 18 (1)(a) of the Patents Act 1990 which states:

“an invention is a patentable invention for the purposes of a standard patent if the invention, so far as claimed in any claim is a manner of manufacture within the meaning of section 6 of the Statute of Monopolies.”

This argument relied heavily upon the outcome of D’Arcy v Myriad Genetics Inc [2015] HCA 35 (“the Myriad case”), in which isolated nucleic acids containing the same information as naturally-occurring nucleic acids were considered not patent eligible. The Decision in the Myriad case was handed down after MLA had initiated the Opposition Proceedings against the Patent Application.

MLA argued that the Claims of the Patent Application lacked an inventive step in light of over 130 documents, which were later limited to Venter J C et al. (2001)(1), the seminal publication of the human genome, and a general review paper on the use of SNPs as markers in animal genetics (2).

Accordingly, it was argued, the inventors of the Patent Application had merely used routine methods, in a routine manner, to address a problem that any skilled person, applying experience acquired from human genome analysis, could have solved and, in so doing, had inevitably arrived at the bovine SNPs of the invention. MLA contended that obviousness should be decided on whether or not SNPs, as opposed to other markers, were an obvious choice to use. However, this argument was rejected, the Delegate concluding that it was not obvious to arrive at the specific SNPs claimed in the Patent Application.

The Opposition failed on all grounds except for a minor clarity issue of Claim 13 that could be rectified by amendment. The only ground upon which MLA was successful was a minor clarity issue in Claim 13. That is, the Delegate regarded Claim 13, which is directed to a polynucleotide identified using the method of the invention, as a reach-through Claim that would have lacked patent eligibility if it has been clear.

MLA appealed the Decision to the Federal Court.

The question before the Federal Court

MLA’s principal attack centred on whether or not the Claims of the Patent Application satisfy the “manner of manufacture” requirement for patent eligibility, in light of how the High Court interpreted this requirement in the Myriad Decision.

MLA argued that the Claims are directed to known methods that use naturally-occurring markers for gene sequences (SNPs). Furthermore, such use was not appropriately defined by any sequence, making the Claims so broad in scope that bona fide research in the field would be prevented, contrary to the public interest. All the inventors had done, in MLA’s view, was to discover naturally occurring associations between specified SNPs and bovine traits. Accordingly, in light of the Myriad case, it would be anomalous if a claim to a product was not patentable, but a Claim to the use of that product in a method Claim was patentable, particularly a method using known techniques.

Grounds of inutility, lack of novelty, lack of inventive step, lack of sufficiency, lack of clarity, and lack of fair basis were also raised.

Turning first to the field of the invention, the Court held that the skilled person in the field of the invention was a molecular geneticist with laboratory experience. MLA had not led any expert evidence from such a person. Thus, MLA’s inventive step attack was rejected, with the Court preferring the evidence provided by the expert witnesses for the Respondents.

The Court also distinguished the case from the Myriad Decision because it concerned method Claims rather than product Claims. That is, the reasoning in the Myriad case could not be applied to the method Claims in suit, or the product Claim dependent thereon, because they were not directed purely to genetic information. Rather, the Claims were directed to the practical application of the identification of SNPs in a bovine nucleic acid sample, which is within “the plain vanilla concept of manner of manufacture” (3) as interpreted by the Myriad case.

MLA’s argument that the Patent Application would have a “chilling effect” on research was disposed of by the Court identifying another patent, co-owned by MLA, that was similarly broad, such that MLA’s argument did not sit well with its own patent and the effect thereof. The breadth of the Claims was not considered to be indicative of a lack of patentable subject matter.

After considering the complex subject matter in detail and noting the substantial conflict in expert opinion evidence, the Court rejected MLA’s appeal on all grounds except for minor aspects of clarity and utility regarding Claim 1. These deficiencies could be rectified by amendment to include reference to a statistically significant p value, as suggested by the Court.

The position in Australia and the United States distinguished

Australian and US Courts have taken similar positions by excluding naturally-occurring nucleotide sequences from patentability. However, the positions of Australia and the US on gene marker-trait correlation methods may not be similarly aligned.

Diagnostic methods relying on the application of a law of nature have received considerable attention in the US where they have been held to lack patent eligibility (4). Such methods usually involve screening for the presence or absence of a disease, or a predisposition to develop a disease.

Australian Courts have not yet had the opportunity of reaching a similar conclusion. The present case is the first time that Australian Courts have had an opportunity to consider the patentability of methods employing naturally occurring compounds since the Myriad case which suggested that such methods may be patentable. Arguably, the claimed invention is not a diagnostic method because it does not involve the diagnosis of a disease using biological markers, but rather the correlation of a pre-existing or potential phenotypic trait with a biological marker. Nonetheless, to the extent that aspects of such correlation methods overlap with diagnostic methods, it appears that they are patentable in Australia but not in the US.

Take-home message

This case provides reassurance for biotechnology innovators in the field of gene marker-trait association analyses, when prosecuting and enforcing their Australian Patent Portfolio.

The Federal Court has now confirmed that methods of using gene sequences are not encompassed by the isolated nucleic acid exclusion defined by the Myriad case. These inventions are patent eligible subject matter in Australia.

Nonetheless, when pursuing patent protection for methods of gene association analysis in Australia, Applicants should pay particular attention to aspects of clarity and utility. For example, method Claims for gene marker-trait associations should define the word “associated” in terms of statistical significance (e.g. a p value of equal to or less than 0.01).

This case also provides an important reminder to select expert witnesses carefully when leading evidence in any Australian Patent Proceedings. Evidence from experts with practical experience in the specific field of the invention will be preferred by an Australian Court over a theoretical understanding of the invention provided by an advanced academic.

  1. Venter, J. Craig, et al. “The sequence of the human genome.” Science 291.5507 (2001): 1304-1351.
  2. Vignal, A., Milan, D., SanCristobal, M., & Eggen, A. (2002). A review on SNP and other types of molecular markers and their use in animal genetics. Genetics Selection Evolution, 34(3), 275.
  3. Meat & Livestock Australia Limited v Cargill, Inc [2018] FCA 51, 134 [428].
  4. Mayo Collaborative Services v.  Prometheus Laboratories, Inc. 132 S. Ct. 1289 (2012)