Commonwealth Scientific and Industrial Research Organisation v BASF Plant Science GmbH - [2018] APO 90

IP AUSTRALIA
AUSTRALIAN PATENT OFFICE
Commonwealth Scientific and Industrial Research Organisation v BASF Plant Science GmbH
[2018] APO 90

Patent Application: 2013273704

Title:Process for the production of polyunsaturated fatty acids in transgenic organisms

Patent Applicant:                   BASF Plant Science GmbH
Opponent:  Commonwealth Scientific and Industrial Research Organisation
Hearing Officer:  Dr S.D. Barker – Deputy Commissioner of Patents
Decision Date:  10 December 2018
Hearing Date:  Written submissions finalised on 26 September 2018

Catchwords: PATENTS – opposition to an amendment – "as a result of the amendment" – what matter was disclosed in the specification as filed – amendment allowable
Representation: Patent attorney for the applicant: Watermark Intellectual Property Pty Ltd
Patent attorney for the opponent: FB Rice Pty Ltd

IP AUSTRALIA
AUSTRALIAN PATENT OFFICE
Patent Application: 2013273704

Title:Process for the production of polyunsaturated fatty acids in transgenic organisms

Patent Applicant: BASF Plant Science GmbH
Date of Decision: 10 December 2018
DECISION
The opposition is unsuccessful.
The application is currently in a state of lapse due to failure to pay a continuation fee. Subject to the payment of the outstanding continuation fee, I allow the amendment.
I award costs according to Schedule 8 against the Commonwealth Scientific and Industrial Research Organisation.
REASONS FOR DECISION
Background

Patent application 2013273704 was filed by BASF Plant Science GmbH (BASF). The grant of a patent was opposed by the Commonwealth Scientific and Industrial Research Organisation (CSIRO). That opposition is still proceeding. BASF has sought amendments under section 104, and CSIRO has filed an opposition to the allowance of the amendments. The present decision relates to the latter opposition only.
The legislation
The application was filed on 19 December 2013. As a consequence, substantive amendments of the Patents Act 1990 (the Act) brought about by the Intellectual Property Laws Amendment (Raising the Bar) Act 2012 (the Raising the Bar Act) apply to the present application. This includes an amendment to subsection 102(1) which precludes the inclusion of subject matter extending beyond the original disclosure.
Section 104 states that the applicant is entitled to request amendments:
(1) An applicant for a patent or a patentee, may, subject to this Act, and subject to and in accordance with the regulations, ask the Commissioner for leave to amend the relevant patent request or complete specification, or any other filed document, for any purpose including either or both of the following:
(a)removing a lawful ground of objection to the request or specification, whether that objection is raised in the course of an examination or re-examination or otherwise;
(b)correcting a clerical error or an obvious mistake.
Section 104(4) provides for opposition to an amendment:
(4) The Minister or any other person may, subject to and in accordance with the regulations, oppose allowing an amendment.
Section 104(5) then sets out the criteria for allowability of an amendment:
(5) The Commissioner must not allow an amendment that is not allowable under section 102.
Section 102(1) as amended by the Raising the Bar Act states:
(1) An amendment of a complete specification is not allowable if, as a result of the amendment, the specification would claim or disclose matter that extends beyond that disclosed in the following documents taken together:
(a) the complete specification as filed;
(b) other prescribed documents (if any).
The documents that have been prescribed for the purposes of paragraph 102(1)(b) are set out in regulation 10.2A. For the purposes of this decision, it is not necessary to consider these documents.
The Explanatory Memorandum to the Intellectual Property Laws Amendment (Raising the Bar) Bill 2011 makes it clear that section 102 as amended is intended to prevent the addition of new matter to the description:
"The item introduces a provision preventing amendment of a complete patent specification after filing to add new matter that would go beyond the disclosure contained in the specification at its filing date. An applicant would not be able to amend the specification to add any material that the hypothetical skilled person could not directly derive by reading the information in the specification as filed."[1]
[1] Item 29, at page 61.
The opposition
The statement of grounds and particulars identifies the ground of opposition as section 102(1) – in that the amended specification would both claim and disclose matter extending beyond that disclosed in the specification as filed. Evidence in support consists of a declaration from Dr Surinder Singh (Singh) accompanied by Exhibits SPS-12 and 14-21. There is no evidence in answer. The opposition was heard on the basis of written submissions filed by the parties.
The matters that are relevant to this opposition are:
·whether as a result of the amendment the specification claims matter that extends beyond that disclosed in the specification as filed, and
·whether as a result of the amendment the specification discloses matter extending beyond that disclosed in the specification as filed.
The expression "as a result of the amendment" was a feature of section 102 before the recent amendments and had been considered on many occasions. In RGC Mineral Sands Ltd v Wimmera Industrial Minerals Pty Ltd[2] Carr and Sundberg JJ discussed section 102(1) as it stood at that time:
"That subsection requires one first to identify precisely what is the amendment. In this case that is done by identifying the difference between the specification as accepted (and as it stood at the hearing of the motion at first instance) on the one hand and, on the other hand, as the specification would read if amended in the manner sought. … The subsection focuses on the amendment proposed and it must be that amendment which has the result of pushing the claimed matter over the line defined by the expression ['matter that extends beyond that disclosed'] … The key point to keep in mind is, as counsel for the respondent contended (in our view correctly), that the words 'as a result of the amendment' are not to be confused with the expression 'after the amendment'."
[2] [1998] FCA 1358, 42 IPR 353 at page 360.
Deficiencies that do not arise "as a result of the amendment" are not properly matters that can be considered in an opposition under section 104. Such deficiencies may be relevant to the opposition under section 59.
The specification
The specification relates to the production of polyunsaturated fatty acids (which can be abbreviated to PUFAs). PUFAs are essential for the health of mammals, having a role in the development of the child brain, functionality of eyes, synthesis of hormones and prevention of cardiovascular disorders. Fish oils are a well-known source of PUFAs. The specification goes on to note that there have been attempts to identify the genes involved in synthesis of fatty acids and their triglycerides, and to produce genetically modified organisms to produce PUFAs:
"there is therefore a great need for means and measures for a simple inexpensive production of these polyunsaturated fatty acids, specifically in eukaryotic systems. The object of the present invention would therefore be the provision of such means and measures."[3]
[3] Specification at page 6.
The specification as filed then sets out the nature of the invention in the following terms:
"The invention, the subject of the present application, is directed to the following:
·a CoA-dependent delta-6 desaturase having the substrate specificity of the delta-6 desaturase shown in SEQ ID NO: 14, and
·the above CoA-dependent delta-6 desaturase which has a preference for conversion of alpha linolenic acid compared to linoleic acid."[4]
[4] Specification as filed at page 6 – 7.
The second dot point appears to me to be reference to a delta-6 desaturase (which can be abbreviated to D6D) that has the substrate specificity of SEQ ID NO: 14 and a preference for alpha-linolenic acid over linoleic acid. During examination this passage was deleted and replaced by a very different passage which does not contain equivalent text.
The specification discusses several polypeptides that are involved in the biosynthesis of PUFAs. Having regard to the claims as they now stand, the important polypeptides are desaturases,[5] particularly the D6Ds. The specification discusses the polynucleotide that codes for the polypeptide, vectors that include the polynucleotide, the introduction of a vector into prokaryotic or eukaryotic cells, expression of the gene in cells (including in plants), and production of PUFAs using the cells.
[5] Desaturases are enzymes that facilitate removal of two hydrogen atoms from the carbon chain of a fatty acid so as to create a carbon-carbon double bond.
The specification exemplifies the cloning of several desaturase genes. SEQ ID NO 13 is presented as the nucleic acid sequence that codes for a D6D. SEQ ID NO 14 is presented as the polypeptide sequence of a D6D.
The amendments
There are two aspects to the amendments. First there is an amendment to the description. Second there is an amendment to the claims. The nature of the amendments is discussed in detail below.
Is the amendment of the description allowable
Amendment item 6 was filed on 2 October 2017. This amendment corrects some typographical errors on pages 72 and 73. No objection was taken to this aspect of the amendment, so I do not need to consider those changes. The significant aspect of the amendment is the addition of a new sentence into page 7b:
"According to an embodiment of the abovementioned process and use, the CoA-dependent desaturase preferentially converts alpha-linolenic acid compared to linoleic acid."
I note that this amendment to page 7b corresponds to the language of proposed claims 2 and 7. CSIRO's submissions seem to focus on the amendment to the claims, but the logic of those submissions also applies to the amendment to the description. I will treat the submissions as also applying to the description. As a result of the amendment to page 7b the description explicitly refers to the option that the D6D has a preference for alpha-linolenic acid. Does this statement disclose new matter that the hypothetical skilled person could not directly derive by reading the specification as filed?
CSIRO's case appears to hang on the contention that as a result of the amendment the specification discloses a specific group of D6Ds which:
i)do not have the same substrate specificity as SEQ ID NO: 14, and
ii)have a preference for conversion of alpha-linolenic acid compared to linoleic acid.
I note that point i) arises from the fact that a D6D with sequence identity as low as 75% would not necessarily have the same substrate specificity as SEQ ID NO: 14. It is CSIRO's submission that this specific group of desaturases constitutes information which is not found in the specification as originally filed.
On the other hand the main thrust of BASF's submissions is that the application has a broad and non-limiting disclosure (which I take to mean that the disclosure provides information on a variety of different embodiments without teaching away or excluding any in particular).
It follows that if the specific group of desaturases is not disclosed by the broad disclosure of the specification as filed, then the amendment is not allowable.
It is necessary to return to the passage of text spanning page 6 – 7 in the specification as filed, as this represents the clearest reference to the feature of alpha-linolenic acid preference. This text states:
"The invention, the subject of the present application, is directed to the following:
·a CoA-dependent delta-6 desaturase having the substrate specificity of the delta-6 desaturase shown in SEQ ID NO: 14, and
·the above CoA-dependent delta-6 desaturase which has a preference for conversion of alpha linolenic acid compared to linoleic acid."
This is an explicit reference to the substrate specificity of SEQ ID NO: 14 and a preference for alpha-linolenic acid. The specification as filed also states that the term "polynucleotide" includes variants,[6] and a variant having at least 75% identity is specifically listed.[7] The biological activity of the polypeptides is understood in the art. Notably the specification discloses at page 7 as filed that "especially preferably" the desaturases have substrate specificities and conversion rates that are "those of the respective enzymes from Ostreococcus lucimarinus", and the polynucleotide shown in SEQ ID NO. 13 was obtained from O. lucimarinus.
[6] Specification at pages 8 – 10.
[7] Specification at page 10.
Dr Singh considers that a D6D with 75% identity to SEQ ID NO: 14 would not have the same substrate specificity as SEQ ID NO: 14:
"Claims 1 and 5 and the description of the Opposed Application as accepted define the CoA-dependent Δ6-desaturase as having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO: 14 (the O. lucimarinus Δ6-desaturase). However, this definition of the CoA-dependent Δ6-desaturase does not equate with, and is unrelated to, a CoA-dependent Δ6-desaturase having the substrate specificity of the Δ6-desaturase shown in SEQ ID
[8] Singh at [44].
NO: 14."[8]
This leads Dr Singh to conclude that a D6D with 75% identity to SEQ ID NO: 14 and a preference for alpha-linolenic acid over linoleic acid is new matter:
"The sequence definition encompasses a large number of variants which do not have the same substrate specificity as SEQ ID NO: 14. When nucleotides are altered at multiple positions in a sequence, the likelihood of an impact on function increases. For example, changing up to 25% of the nucleotides (as permitted by a 75% identity claim) would in most cases result in a variant that does not have the same substrate specificity of the polypeptide shown in SEQ ID NO: 14."[9]
[9] Singh at [45].
It is clear that Dr Singh considers that a person skilled in the art would understand that 75% identity would likely lead to a different substrate specificity. It is not clear whether Dr Singh believes that the specification as filed disclosed variations of SEQ ID NO: 14 that have substrate specificity different to that of SEQ ID NO: 14. His evidence suggests to me that he considers the disclosure included variations having a different substrate specificity:
"The Opposed Application as filed does not describe which nucleotides can be changed while still retaining the substrate specificity of the encoded protein and as such, provides no structural guidance to distinguish functional species having the same substrate specificity of the polypeptide as shown in SEQ ID NO: 14 from species that do not have the substrate specificity of the polypeptide as shown in SEQ ID NO: 14."[10]
[10] Singh at [47].
I consider that the clear implication of Dr Singh's evidence is that the specification as filed would have been understood to disclose variations on SEQ ID NO: 14, and that these variations would have had different substrate specificities to SEQ ID NO: 14 when the degree of variation was at the level of 75% identity. It necessarily follows that the text spanning pages 6-7 discloses the subset which also has a preference for alpha-linolenic acid.
I conclude that the specification as filed disclosed the matter that is the subject of the amendment. It follows that the amendment to the description complies with section 102(1).
Is the amendment of the claims allowable
The claims of the specification as accepted (which is the current state of the claims) appear in the Annex at the end of this decision. Amendment item 5 filed on 7 June 2017 inserts new claims 2 and 7. New claim 2 is dependent on the existing claim 1. Claim 1 is directed to a process for producing PUFAs and derivatives by cultivating cells or organisms containing a polynucleotide that codes for a D6D. The polynucleotide is defined as:
"a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO: 14"
CSIRO described this requirement as "substrate specificity" in their written submissions. To the extent that there is any substrate specificity it is inherent in the sequence of the polypeptide.
Claim 2 as proposed to be inserted by the amendment reads as follows:
"The process according to claim 1, wherein the CoA-dependent delta-6 desaturase preferentially converts alpha-linolenic acid compared to linoleic acid."
It appears to me that this is imposing an additional limitation that the D6D is encoded by the sequence prescribed by claim 1 AND has a preference for alpha-linolenic acid compared to linoleic acid. Claim 2 is narrower in scope than claim 1.
New claim 7 is dependent on new claim 6 (claim 6 is simply the existing claim 5 renumbered to take account of the insertion of new claim 2). Claim 7 and its relationship to claim 6 is directly analogous to what I have said above in relation to new claim 2.
As a result of the amendment, the claims as a whole do not claim anything additional to what they claimed before the amendment. Since nothing arises "as a result of the amendment", the amendment to the claims complies with section 102(1).
Conclusion
It has not been shown that the amendments are not allowable. The opposition fails and I will allow the amendment.
Costs
I have found that the opposition fails, and I can see no considerations that persuade me to depart from the normal outcome that costs should follow the event. I will award costs against CSIRO.
Dr S.D. Barker
Deputy Commissioner of Patents
Annex: Claims as accepted
1. A process for the production of a substance which has the structure shown in the
general formula I hereinbelow:
where the variables and substituents are as follows:
R¹ = hydroxyl, coenzyme A (thioester), lysophosphatidylcholine, lysophosphatidylethanolamine, lysophosphatidylglycerol, lysodiphosphatidylglycerol, lysophosphatidylserine, lysophosphatidylinositol, sphingo base or a radical of the formula II

R² = hydrogen, lysophosphatidylcholine, lysophosphatidylethanolamine, lysophosphatidylglycerol, lysodiphosphatidylglycerol, lysophosphatidylserine, lysophosphatidylinositol or saturated or unsaturated C₂-C₂₄-alkylcarbonyl,
R³ = hydrogen, saturated or unsaturated C₂-C₂₄-alkylcarbonyl, or R2 and R3 independently of one another are a radical of the formula la:
and
wherein the process comprises the cultivation of:
(i) a host cell comprising an isolated polynucleotide comprising a nucleic acid
sequence coding for a CoA-dependent delta-6 desaturase having at least 75%
identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ
ID NO: 14, wherein the polynucleotide is operatively linked to an expression
control sequence; or
(ii) a transgenic, nonhuman organism comprising:
a) an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO:14,
b) a vector comprising an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO:14, wherein the polynucleotide is operatively linked to an expression control sequence, or
c) a host cell comprising an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO:14. wherein the polynucleotide is operatively linked to an expression control sequence,
under conditions which permit the biosynthesis of the substance.
2. The process according to claim 1, wherein the transgenic, nonhuman organism is an animal, a plant or a multicellular microorganism.
3. A process for the production of an oil, lipid or fatty acid composition, the process comprising the steps of the process according to claim 1 or claim 2 and the further step of formulating the substance as an oil, lipid or fatty acid composition.
4. The process according to claim 3, wherein the oil, lipid or fatty acid composition is formulated further to give a pharmaceutical, a cosmetic product, a foodstuff, a feeding stuff, or a food supplement.
5. The use of:
a) an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO:14,
b) a vector comprising an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO:14, wherein the polynucleotide is operatively linked to an expression control sequence,
c) a host cell comprising an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO: 14, wherein the polynucleotide is operatively linked to an expression control sequence, or
d) a transgenic, nonhuman organism comprising:
(i) an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO:14,
(ii) a vector comprising an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having at least 75% identity to a nucleotide sequence which codes for a polypeptide as shown in SEQ ID NO:14, wherein the polynucleotide is operatively linked to an expression control sequence, or
(iii) a host cell comprising an isolated polynucleotide comprising a nucleic acid sequence coding for a CoA-dependent delta-6 desaturase having the substrate specificity of the delta-6 desaturase shown in SEQ ID NO: 14. wherein the polynucleotide is operatively linked to an expression control sequence,
for the production of an oil, lipid or fatty acid composition.
6. The use according to claim 5, wherein the transgenic, non-human oragnism [sic] is an animal, a plant or a multicellular microorganism.
7. The use according to claim 5 or claim 6, wherein the oil, lipid or fatty acid composition is to be employed as a pharmaceutical, cosmetic product, foodstuff, feeding stuff, or food supplement.
8. The use according to any one of claims 5 to 7, wherein the feeding stuff is fish food.
9. The product of the process according to any one of claims 1 to 4.