Update on Patentability of Diagnostic Claims: Australia (Part 1 of an 8-part Series)

This is an update to our 2014 10-part series “The Thorny Problem of Patentable Eligible Subject Matter.” Since that series, the U.S Patent and Trademark Office (USPTO) issued further guidance on December 16, 2014, updated in July 2015 and May 2016 (May 2016 Update), for evaluating subject matter eligibility under Section 101 (Guidance). The new Guidance superseded the March 4, 2014 Guidance.

On July 16, 2016, the USPTO issued a memo commenting on recent decisions by the U.S. Supreme Court (Supreme Court) and the U.S. Court of Appeals for the Federal Circuit (Federal Circuit) in two subject matter eligibility cases directed to life sciences method claims: Sequenom v. Ariosa and Rapid Litigation Management v. CellzDirect, (Rapid Litigation Management) respectively. The memo concludes that neither decision changes the subject matter eligibility framework and that the existing Guidance and training examples are consistent with these cases; however, the memo also notes that the Rapid Litigation Management decision further clarifies the inquiry involved in determining whether a claim is directed to a judicial exception. In particular, the Federal Circuit stated that the “directed to” analysis of a process claim requires more than “merely identify[ing] a patent-ineligible concept underlying the claim” and instead requires an analysis of whether “the end result of the process, the essence of the whole, was a patent-ineligible concept.”

The May 2016 Update provided more detailed instructions for Examiners regarding the formulation of a rejection under Section 101 and evaluation of an Applicants response thereto. Specifically, Examiner’s must identify the exception to patentable subject matter, referred to as a “judicial exception,” that is being claimed, explain what is recited  in the claim and why it is an exception, and identify any additional elements that define claim features/limitations/steps that are beyond the exception. The Examiner must then explain why the additional elements individually AND in combination do not result in the claim as a whole amounting to “significantly more” than the exception.

The May 2016 Update also provided additional examples for application of the Guidance to specific types of life science claims, which were not well represented in the December 2014 Guidance.

As discussed in our 2014 series, the basic requirements for patentability in Australia are found in section 18(1) of the Patents Act (1990) (Act) which states that a claimed invention is patentable if  it (a) is a manner of manufacture within the meaning of section 6 of the Statute of Monopolies; and (b) when compared with the prior art base as it existed before the priority date of that claim: (i) is novel; and (ii) involves an inventive step; and (c) is useful; and (d) was not secretly used in the patent area before the priority date of that claim by, or on behalf of, or with the authority of, the patentee or nominated person or the patentee’s or nominated person’s predecessor in title to the invention.

In Australia, the general test for patentable subject matter is that an invention is patentable (i.e. a manner of new manufacture) if it provides something that is industrially useful or provides an “artificially-created state of affairs” in a field of economic significance (National Research Development Corporation v Commissioner of Patents (1959) 102 CLR 252). Patentable subject matter in Australia, however, has largely been defined by case law. For example, methods of medical treatment of human beings, including surgery and the administration of therapeutic drugs were deemed patentable inventions under section 18 of the Act in Apotex Pty Ltd v. Sanofi-Aventis Australia Pty Ltd., [2013] HCA 50 (4 December 2013). Recently, however, the High Court of Australia (HCA) ruled in Yvonne D’Arcy v Myriad Genetics Inc., that claims covering isolated DNA are not patent eligible, finding that the creation of this category of important rights is best left to “legislative determination.”  D’Arcy v Myriad Genetics Inc (S28-2015) [2015] HCA 35.

Regarding diagnostic method claims, unlike the U.S., there is no recent Australian decision that negatively impacts the patentability of diagnostic claims. In general, diagnostic claims are considered to be directed to an “artificially-created state of affairs,” as they are man-made processes that produce useful and concrete results.

We at the BRIC Wall thought it would be insightful to update our analysis of subject matter eligibility under Australian patent law for diagnostic method claims based on the May 2016 updated Guidance and Life Science examples.

Analysis of Life Sciences Examples from May 2016 Update to USPTO Guidance

Example 29 – Diagnosing and Treating Juliti

Background: Example 29 of the May 2016 Update relates to a hypothetical situation relating to an autoimmune disease called “Julitis.” An Applicant for a patent discovered that Julitis could be diagnosed by detecting the presence of the hypothetical “JUL-1” protein in patients’ plasma, skin, hair and nails. Applicant has disclosed detecting JUL-1 using anti-JUL-1 antibodies that may be naturally occurring (e.g., a human anti-JUL-1 antibody isolated from a patient known to have julitis), or non-naturally occurring (e.g., a porcine anti-JUL-1 antibody created by injecting pigs with JUL-1, or a specific monoclonal antibody named “mAb-D33”).

Two representative claims from this Example are analyzed below.

Claim 1. A method of detecting JUL-1 in a patient, said method comprising:

  1. obtaining a plasma sample from a human patient; and
  2. detecting whether JUL-1 is present in the plasma sample by contacting the plasma sample with an anti-JUL-1 antibody and detecting binding between JUL-1 and the antibody.

Claim 2. A method of diagnosing julitis in a patient, said method comprising:

  1. obtaining a plasma sample from a human patient;
  2. detecting whether JUL-1 is present in the plasma sample by contacting the plasma sample with an anti-JUL-1 antibody and detecting binding between JUL-1 and the antibody; and
  3. diagnosing the patient with julitis when the presence of JUL-1 in the plasma sample is detected.

Analysis of claims 1 and 2: Both claims would constitute patent eligible subject matter in Australia. In the U.S., claim 1 constitutes patent eligible subject matter, while claim 2 constitutes patent ineligible subject matter, as the May 2016 Update indicates that the claim is directed to a judicial exception (i.e., the correlation between the presence of JUL-1 and the presence of julitis in the patient) and as a whole does not amount to significantly more than the exception itself.

Example 31 – Screening for Gene Alterations

Background: Applicant discovered the “wild-type” sequence of the human BRCA1 gene (i.e., the typical sequence of the gene in humans), and has also discovered naturally occurring alterations from the wild-type sequence that are correlated with an increased likelihood of developing breast or ovarian cancer. Applicant’s disclosure provides methods of screening patients for alterations in the BRCA1 gene by comparing a patient’s BRCA1 sequence with the wild-type BRCA1 sequence. The compared sequences can be germline (genomic) DNA sequences, RNA sequences, or cDNA sequences.

At the time the invention was made and the application was filed, scientists routinely compared DNA sequences using two-data generating techniques: (1) hybridizing two different DNA molecules (e.g., a probe and DNA isolated from a patient sample), and detecting whether the molecules bind to each other and form a hybridization product and (2) amplifying (making copies of) at least part of a DNA molecule such as DNA isolated from a patient sample, by using a set of primers to produce amplified nucleic acids, and then sequencing the amplified nucleic acids. The probes and primers used in these techniques are short single-stranded DNA molecules that typically have a naturally occurring nucleotide sequence.

In one embodiment, Applicant discloses using a computer-implemented micromechanical method known as Scanning Near-field Optical Microscopy (SNOM) to detect hybridization of a single probe to its target. At the time the invention was made and the application was filed, the use of SNOM to study DNA hybridization had been discussed in several articles in widely-read scientific journals. However, scientists were not commonly or routinely using SNOM to study DNA hybridization at the time the invention was made and the application was filed. Instead, scientists at the time typically used autoradiography to detect hybridization products.

In another embodiment, Applicant discloses using Cool-Melt polymerase chain reaction (Cool-Melt PCR) to amplify BRCA1 DNA from the patient sample. Cool-Melt PCR uses lower melting and annealing temperatures than conventional PCR, which results in Cool-Melt PCR having a 20-fold higher sensitivity of mutation detection than conventional PCR. At the time the invention was made and the application was filed, Cool-Melt PCR was known and used by a few scientists in the field. Several years after filing the application, Cool-Melt PCR became a standard laboratory technique that appeared in virtually every laboratory manual and was conventionally used by most scientists in the field to amplify mutant nucleic acids.

Three representative claims from this Example are analyzed below.

Claim 1. A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue sample from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild-type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject.

Claim 70. The method of claim 1, wherein said comparing BRCA1 sequences further comprises:

  1. hybridizing a wild-type probe to a BRCA1 gene isolated from said sample; and
  2. detecting the presence of a hybridization product by measuring conformational changes in the probe that are indicative of hybridization to the BRCA1 gene with scanning near-field optical microscopy.

Claim 80. The method of claim 1, wherein said comparing BRCA1 sequences further comprises:

  1. amplifying by Cool-Melt PCR all or part of a BRCA1 gene from said sample using a set of primers to produce amplified nucleic acids; and
  2. sequencing the amplified nucleic acids.

Analysis of claims 1, 70, and 80: Claims 1, 70, and 80 would constitute patent eligible subject matter in Australia. In the U.S., claim 1 constitutes patent ineligible subject matter, as the May 2016 Update indicates that the “comparing” amounts to an abstract idea, which is a judicial exception, and the claim as a whole does not amount to significantly more than the exception itself.  In contrast, claims 70 and 80 are patent eligible in the U.S., as each claim recites additional elements that distinguishes the claim from well-understood, routine, or conventional techniques in the field (i.e., SNOM and Cool-Melt PCR, respectively), and, therefore, each of claims 70 and 80 as a whole amounts to significantly more than the exception itself.

In view of the above, it is clear that Australian patent law is considerably less restrictive to the patentability of diagnostic method claims as compared to U.S. patent law, at least for the foreseeable future.

This post was written by Lisa L. Mueller and Melissa E. Kolom of Michael Best and John Moore and Tony Davis of Griffith Hack.