F. Hoffmann-La-Roche AG v Bresagen Ltd and New England Biolabs, Inc

[2005] APO 31

ABSTRACTS OF DECISIONS

DECISION OF A DELEGATE OF THE COMMISSIONER OF PATENTS

Application  :          No. 632857 in the name of F. Hoffmann-la Roche AG

Title:          Purified thermostable enzyme

Action: Final Determination of the oppositions under section 59 of the Patents Act 1990 by Bresagen Limited and New England Biolabs, Inc.

Decision:          Issued 4 July 2005

Abstract:

The issues raised by New England Biolabs inappropriately re-opened issues that had already been decided in the original substantive decision.  The amendments made to the specification by the applicant overcame the section 40 deficiencies identified in the original decision (paragraphs ii-iv above).  As a consequence, if the Court overturns the original decision in regard to novelty, the application will be in order for sealing

PATENTS ACT 1990

DECISION OF A DELEGATE OF THE COMMISSIONER OF PATENTS

Re:Patent Application No. 632857 by F. Hoffmann-la Roche AG and final determination of the oppositions under section 59 thereto by Bresagen Limted and New England Biolabs, Inc.

BACKGROUND

1. Patent application 632857 was filed in Australia on 8 October 1990 by Cetus Corporation as a divisional application of patent applications 77298/87 and 30629/89 both of which are now lapsed.  Through these applications, priority is ultimately based on a number of US basic documents, the earliest of which was US 899513 (with a priority date of 22 August 1986).  Cetus Corporation assigned their rights in the invention to F. Hoffmann-la Roche AG (Roche) on 11 December 1991 and the change of applicant was made in Australia under section 113 in March 1993.

2. The application was advertised accepted on 14 January 1993 and notices of opposition were filed by Bresatec Ltd and by New England Biolabs, Inc on 14 April 1993.  The hearing was heard in Canberra on 27-30 May 1997 with the office decision on the substantive (section 59) opposition being issued on 12 November 1997 (F Hoffmann-La Roche AG v Bresagen Limited and New England Biolabs Inc [1997] APO 57). I will refer to this decision as the "original decision" hereafter.

3. The applicant and one of the opponents (New England Biolabs, Inc) appealed the original decision insofar as it was contrary to its interests but New England Biolabs subsequently withdrew their appeal.  The applicant’s appeal of the original decision is still pending before the Court.  The applicant provided the Court with extra evidence disputing the Patent Office findings on novelty but made amendments to the specification under section 104 in an attempt to overcome the section 40 deficiencies noted in the original decision.

1. Before considering the appeal on the original decision, the Court (through the applicant) has referred the matter back to the Commissioner to determine whether the amended specification has the same section 40 problems as those identified in the accepted specification.  I provided a preliminary view to the parties that the amendments prima facie overcame the deficiencies noted in the original decision in regard to the accepted specification.  However, I also provided both parties with an opportunity to be heard on this view.  New England Biolabs advised that they wished to be heard and relied on written submissions filed before the hearing date of 4 July 2005.  The applicant then provided written submissions in response.  Neither party appeared in person.  The following decision is based on all these submissions.

ORIGINAL DECISION

1. In the original decision, I found the following deficiencies in the accepted specification:

   i.claims 1-7 and 86 of the specification were not novel in light of Kaledin et al Biokhimiya volume 45 pages 644-655 (Kaledin);

   ii.claims 8-11, 75-85 are not fairly based because the definition of “thermostable” provided in the specification is too broad;

   iii.claim 34 (and claims dependent thereon) do not define the invention because the word “part” in claim 34 has no size or functional limitations; and

   iv.there were certain typographical errors in claims 95-97 as accepted which should have referred to claims 90-94 rather than claims 79-83.

1. In note that the amendments have no bearing on the novelty findings in the original decision (paragraph i).  In any event, as the applicant noted, the novelty findings are on appeal before the Court and it is up to the Federal Court to rule on those claims.  This “final determination” hearing before the Commissioner is necessarily limited to the section 40 deficiencies noted in the original decision (paragraphs ii-iv above).  The submissions provided by New England Biolabs on the novelty issue are therefore irrelevant.

1. New England Biolabs did not make any submissions in regard to whether the amendments overcame the deficiencies noted in paragraph iv and in my view, the deficiencies noted in the paragraph have been resolved by the amendments.  The only remaining question for this determination is whether the deficiencies in paragraphs ii and iii have been overcome by amendment.

RELEVANT AMENDMENTS

1. There are two amendments to the specification which were intended to address the deficiencies noted in paragraphs ii and iii above.  The first amendment was made to address the deficiency noted in paragraph ii.  It concerned a change to the definition of "thermostable enzyme" set out of page 45 of the specification.  I have set out this amendment below with the changes marked. 

As used herein, the term "thermostable enzyme" refers to an enzyme which is stable to hear and is heat resistant and catalyses (facilitates) combination of the nucleotides in the proper manner to form the primer extension products that are complementary to each nucleic acid strand, and is stable to heat and is heat resistant to the extent that it would be effective for the amplification reaction described herein, ie, the enzyme does not become irreversibly denatured (inactivated) when subjected to the elevated temperatures for the time necessary to effect denaturation of double stranded nucleic acids."

1. The second amendment was intended to address the deficiency noted in paragraph iii.  It involved the following marked changes to claim 34 (now claim 37):

A recombinant DNA comprising at least a sequence encoding all or part of a thermostable DNA polymerase when isolated from said Thermus aquaticus being characterised as having a molecular weight of about 86,000 to 95,000 daltons as compared to phosphorylase B by SDS-PAGE, wherein said part functions as a thermostable DNA polymerase.

DECISION

Lack of fair basis of claims 8-11, 75-85 because the definition of “thermostable” provided in the specification is too broad

1. New England Biolabs submitted that the first amendment does not overcome the lack of fair basis of claims 8-11, 75-85 identified in the original decision.  According to New England Biolabs, the amendment affects the definition of a specific term, namely "thermostable enzyme".  The term is used in the body of the specification but is not used in the relevant claims.  Claim 8 instead uses the term "thermostable DNA polymerase", which is not the subject of any definition in the specification.  Similarly, claim 75 (now claim 78) uses the term "thermostable polymerase" which is undefined.  New England Biolabs argued that the amended definition of "thermostable enzyme" cannot be read into the claims so as to qualify the clear meaning of the wording of the claims; cf Décor Corp Pty Ltd v Dart Industries Inc (1988) 13 IPR 385 at 410-411. As a consequence, the term "thermostable" has no clear meaning in the specification and claims 8-14 and 78-88 are not fairly based.

1. I do not accept this argument.  The definition of “thermostable enzyme” as set out on page 45 explicitly describes a specific enzymatic reaction (the combination of the nucleotides in the proper manner to form the primer extension products that are complementary to each nucleic acid strand).  DNA polymerase is the only enzyme disclosed in the specification which is able to catalyse this extension reaction and in my view the claimed DNA polymerase is therefore clearly encompassed in the dictionary definition of “thermostable enzyme" provided on page 45.  In addition, as the applicant noted in their submissions, there is nothing in the specification or in the evidence to suggest that the word “thermostable” would have a different meaning when used as an adjective for “enzyme” and for “polymerase”.

2. In any event, the only problem identified in the original decision was that the definition of "thermostable" did not clearly limit the enzyme as being sufficiently heat resistant to withstand the conditions of the PCR reaction.  The amendments made by the applicant (the "first amendments" described above) have added this limitation to the definition of "thermostable" and in my view, have overcome the problems identified in the original decision.  The alleged problem now being raised is that the definition of “thermostable” does not encompass DNA polymerase.  However, this problem would have equally applied to the definition at acceptance and does not arise as consequence of any of the amendments made to the specification.

3. I note that the accepted definition of “thermostable” was considered by the Commissioner in the original decision and there was no finding that the definition was problematic for the reasons now being raised by New England Biolabs.  The High Court decision in Ex parte Mole Engineering Pty. Ltd. (1981) 35 ALR 119 held that the Commissioner does not have the power to re-hear issues arising in an opposition that had been determined by an interim decision (see also Iluka Midwest Ltd v Technological Resources Pty Limited [ 2002] FCA 49 (6 February 2002) and BHP v American Can Company 29 ALR 424). If New England Biolabs disagreed with the findings of the original decision which did not find there to be the problem with the definition for the reasons now being raised by New England Biolabs, the proper recourse was for them to appeal the original decision. In this regard, I note that they appealed the original decision but have subsequently withdrawn that appeal.

Failure of claim 34 (and claims dependent thereon) to define the invention because the word “part” in claim 34 has no size or functional limitations

1. New England Biolabs submitted that the second amendment does not overcome the problem identified with claim 34 (now claim 37) in the original decision.  According to New England Biolabs, the added wording does not impose any effective size or functional limit commensurate with the description of the alleged invention in the body of the specification because no instructions are provided as to how much of a thermostable DNA polymerase is required in order for that part to function as a thermostable DNA polymerase. 

1. The amendments have not introduced the problem that New England Biolabs is now alleging.  If New England Biolabs's submissions are correct, the alleged deficiency would equally have existed in the specification at acceptance.  No such problem was identified in the original decision and it is not open to New England Biolabs to raise the issue at this stage.  If New England Biolabs disagreed with the findings of the original decision, the proper recourse was to appeal the original decision (but see paragraph 13 above).

1. In any case, I do not accept their argument.  The original decision found that the claims did not impose any size or functional limitations to the term "part".  As a consequence, the term was considered not to define the invention.  There is now a functional limitation which limits the claims to a functioning thermostable DNA polymerase and in my view this overcomes the deficiencies identified in the original decision.

CONCLUSION

1. The amendments made to the specification overcome the section 40 deficiencies identified in the original decision (paragraphs ii-iv above).  Therefore, if the Court overturns my original decision in regard to novelty, my view is that the amended application would be in order for sealing.

   COSTS

2. In matters before the Commissioner, costs generally follow the event.  I see no reason to depart from this practice in the current case.  New England Biolabs was unsuccessful in the present matter and I award costs in relation to this determination against them.

   Karen Ayers
   Delegate of the Commissioner of Patents

   Patent attorneys for the applicant:              Spruson & Ferguson, Sydney

   Patent attorneys for New England Biolabs: Houlihan², Melbourne