Good news for Biotech Innovators – Diagnostic Methods Remain Patentable in Australia

Background

 Sequenom, Inc. (Sequenom) sells a non-invasive test called “MaterniT® 21 PLUS” that is used to detect the presence of cell-free fetal DNA (cffDNA) in serum or plasma samples obtained from expectant mothers.  The test avoids the risks of widely-used  techniques that take samples from the fetus or placenta.  The test can be used to screen for certain chromosomal abnormalities that could affect a baby’s health and development, such as trisomy 21 (Down syndrome), sex chromosome aneuploidies (SCAs, abnormal numbers of X or Y chromosomes), and it can also be used to determine the gender of a baby.

Sequenom owns or has licensed a number of patent families that cover MaterniT® 21 PLUS. One such patent family is entitled “Non-invasive prenatal diagnosis” and includes U.S. Patent No. 6,258,540 B1 (the ‘540 patent), European Patent No. 0994963 B1 (the ‘963 patent) and Australian Patent No. 727919 B2 (the ‘919 patent).

Sequenom began offering its MaterniT® 21 PLUS test for sale in the U.S. in 2011.  Several other companies quickly followed suit, including Ariosa Diagnostics, Inc. (Ariosa) which began selling its own non-invasive test called “Harmony®”.  Not surprisingly, given the size of the pre-natal diagnostic market, patent litigation ensued between Sequenom and Ariosa in several jurisdictions, including the U.S., Great Britain, and Australia.

 U.S. Litigation

In 2015, the U.S. Federal Circuit found the claims of the ‘540 patent invalid as being directed to patent ineligible subject matter under 35 U.S.C. § 101 in Ariosa Diagnostics v. Sequenom, 788 F.3d 1371 (Fed. Cir. 2015).  Claim 1 of the ‘540 patent read as follows:

  1. A method for detecting a paternally inherited nucleic acid of fetal origin performed on 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. (emphasis added).

According to the Federal Circuit, the presence of the cffDNA in maternal blood was a natural phenomenon, thus the claims satisfied the first step of the Mayo test (Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. 66 (2012)).  With respect to the second step under Mayo, the Court concluded that the practice of the method claims did not contain an inventive concept sufficient to “transform” the natural phenomenon of cffDNA into a patentable invention.

UK Litigation

Not long after the U.S. litigation, corresponding litigation arose in Great Britain involving the ‘963 patent.  Claim 1 of the ‘963 patent reads as follows:

  1. 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.

In November 2017, in the High Court of Justice in Great Britain (Illumina, Inc v. Premaitha Health Plc [2017] EWHC 2930 (Pat)), Justice Henry Carr rejected the argument that claim 1 of the ‘953 patent was directed to excluded subject matter.  Specifically, he stated that:

“I do not accept that, properly construed, claim 1 is a claim to a discovery as such. The claims are not directed to information about the natural world, but rather to a practical process, namely a ‘detection method’ which uses information about the natural world. Claim 1 is directed to the detection of foetal DNA in a sample of plasma or serum. Such samples do not exist in the natural world and must be artificially created. The claimed method of detection is also an artificial process which does not exist in the natural world. The claim is to a practical process of implementing a discovery, for practical applications. The actual contribution, as a matter of substance, does not fall solely within the excluded subject matter and is technical in nature.”

Australian Litigation 

On June 27, 2019, the Federal Court of Australia adopted a similar approach to the UK and, in the highly anticipated decision Sequenom, Inc. v. Ariosa Diagnostics, Inc., [2019] FCA 1011, confirmed that diagnostic methods remain patent-eligible subject matter in Australia.

Sequenom commenced infringement proceedings against Ariosa and others alleging the promotion and supply of Ariosa’s Harmony® test in Australia infringed several claims of the ‘919 patent.  Claim 1 of the ‘919 patent, which was identical to claim 1 of the ‘963 Patent, was representative of the claims in dispute and read as follows:

  1. 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.

Ariosa cross-claimed for revocation of the ‘919 patent on various grounds, including that the claims at issue did not define patentable subject matter.

Patentable subject matter

For an invention to be patentable under Australian law, it must meet the statutory patentable subject matter requirement of being a “manner of manufacture”.

In D’Arcy v. Myriad Genetics Inc. [2015] HCA 35 (Myriad), the High Court of Australia (Australia’s ultimate appellate court) held that “isolated” nucleic acids (DNA) per se are not patentable subject matter because the “substance” of the invention is genetic information, which is not made by human intervention.  Interestingly, claims directed to diagnostic methods were not challenged in Myriad.  In Myriad the High Court set out the following general principles in relation to “manner of manufacture” (patentable subject matter):

  • the invention must involve an artificially created state of affairs in a field of economic utility (consistent with the High Court’s earlier decision in National Research Development Corporation v. Commissioner of Patents, [1959] HCA 67).
  • the starting point in assessing patentable subject matter is to determine the substance of the claim.

Most recently, the Federal Court’s decision in Meat & Livestock Australia Limited v. Cargill, Inc. [2018] FCA 51 (MLA) was the first to apply the principles set out in Myriad in relation to an invention concerning genetic information.  The claims at issue in MLA were directed to methods of identifying particular traits in cattle (such as meat tenderness) by analyzing DNA samples.  In that case, the Federal Court held that the claims were directed to patentable subject matter because they related to methods of using DNA sequences, rather than the DNA sequences per se.

The Federal Court’s decision

During the proceedings, Ariosa sought to rely on statements made by two of the seven judges (Gaegler and Nettle JJ) in Myriad, to support its argument tat the “substance” of the Sequenom claims was the mere discovery (and quantification) of a naturally occurring phenomenon, namely that cffDNA is detectable in maternal blood products, and that there is no practical application for that discovery provided in the claims.  Ariosa further submitted that none of the relevant claims provided an outcome that was an artificially created state of affairs.  Rather, even where human action was involved, the end result of each of these claims was mere “information”, e.g., a diagnosis.

However, Arisoa’s submissions were rejected by Beach J, who observed that, in contrast to the situation in Myriad, none of the Sequenom claims were directed to cffDNA per se.  Rather, Beach J noted that, as was the case in MLA, the Sequenom claims were directed to methods of identifying or detecting DNA having a particular characteristic, not the DNA per se.  The discovery of the existence of cffDNA in material blood can, in fact, be put to practical use – as explained in the patent, the invention offered a new non-invasive approach for prenatal diagnosis, including fetal abnormalities, blood typing and sex determination.  In particular, Beach J found that there was human intervention and an artificially created state of affairs in at least:

  1. the taking of a maternal blood from a pregnant female;
  2. the separation of the maternal blood into its component parts (plasma, white blood cells and red blood cells);
  3. the extraction of DNA from the plasma component of a maternal blood sample; and
  4. a step to discriminate between maternal and cffDNA in the sample.

Thus, Beach J concluded that while the substance of the claimed invention was premised on a naturally occurring phenomenon, i.e., the presence of cffDNA in material blood, it

“…builds on, uses, practically applies and reduces to practice a discovered substance found in nature, namely cffDNA in maternal blood, to provide a new, inventive, useful, artificial method of detection of cffDNA, and where the method is of economic significance.”

Accordingly, all relevant claims were found to define patentable subject matter, which is welcome news for biotech innovators.  As a result, any diagnostic methods that involve the practical application of a natural phenomenon remain patentable in Australia.

This post was written by Lisa Mueller, and Claire Gregg, Ph.D and Linda Govenlock, Ph.D of Allens Patent & Trade Mark Attorneys.