F.Hoffman-La Roche AG v New England Biolabs Inc
[2000] FCA 283
At a glance
Source factsCourt
Federal Court of Australia
Decision date
2000-04-28
Before
Emmett J
Source
Original judgment source is linked above.
Judgment (11 paragraphs)
EX TEMPORE REASONS FOR DECISION 1 I have before me two appeals arising out of opposition proceedings under the provisions of the Patents Act 1952 (Cth) ("the 1952 Act") as continued in force under the Patents Act 1990 (Cth) ("the 1990 Act"). F. Hoffman-La Roche AG ("the Applicant") claims a patent relating to a purified thermostable enzyme. The first claim in the Specification ("Claim 1") is in the following terms: "1. A purified thermostable DNA polymerase isolated from a Thermus species which catalyses combination of nucleoside triphosphates to form a nucleic acid strand complementary to a nucleic acid template strand, said polymerase having a molecular weight of about 86,000 to 95,000 daltons as compared to phosphorylase B by SDS-PAGE." Claims 2 to 7 are ancillary to Claim 1 and all relate to a purified thermostable DNA polymerase. There are 101 claims in all, but for present purposes, I do not think it is necessary to indicate the nature of Claims 8 to 101. 2 In proceedings before a delegate of the Commissioner of Patents, opposition to the grant of a patent to the Applicant was mounted by New England Biolabs Inc ("New England Biolabs"). The Delegate upheld the opposition in relation to Claims 1 to 7 but concluded that the application should proceed to grant in respect of the balance of the claims. The Applicant has appealed against the rejection of Claims 1 to 7 and New England Biolabs has appealed against the decision to permit the balance of the claims to proceed to grant. 3 One of the grounds of opposition relied on by New England Biolabs is that the alleged invention was published in Australia before the priority date of each of the claims. The principal publication relied on by New England Biolabs is a paper ("the Kaledin Paper") published in 1980 by A. S. Kaledin and others entitled "Isolation and Properties of DNA Polymerase from the Extremely Thermophilic Bacterium Thermus aquaticus YT1" Biokhimiya (1980) vol. 45, pp. 644-651. The paper begins with the following abstract: "A DNA polymerase was isolated from the thermophilic bacterium T. acquaticus YT1. As a result of six stages of purification an electrophoretically homogeneous preparation of the enzyme with a molecular weight of about 62,000 was obtained." 4 In a section of the Kaledin Paper entitled "Determination of Molecular Weight of Enzyme" the following appears: "The molecular weight of the enzyme was determined by two methods: by electrophoresis under denaturing conditions and by ultracentrifugation in a 5-20% sucrose density gradient. The data of electrophoresis in polyacrylamide gel containing sodium dodecyl sulfate…indicate that the enzyme behaves like a homogeneous protein. The molecular weight of the DNA polymerase was computed by comparing the mobility of the enzyme with the mobilities of marker proteins with known molecular weights and it was found to be 62,000 per monomeric unit. During analytical ultracentrifugation DNA polymerase sediments as one discrete symmetrical peak somewhat faster than bovine serum albumin. The approximate molecular weight of the enzyme, calculated using the equation of Martin and Ames…is 60,000. New England Biolabs contends that that anticipates Claims 1 to 7 of the Specification lodged on behalf of the Applicant. The Applicant, on the other hand, contends that the Kaledin Paper, while it may describe a DNA polymerase, does not anticipate all of the integers comprised in Claims 1 to 7 of the Specification. 5 A question arises as to precisely what it is that was disclosed by the Kaledin Paper. The Applicant contends that an essential integer of Claim 1 is the isolation of a DNA polymerase having a particular molecular weight, being a molecular weight of 86,000 to 95,000 daltons. New England Biolabs contends, on the other hand, that the reference to molecular weight in the Kaledin Paper is consistent with the enzyme described in Claim 1, notwithstanding that the figures are clearly different. New England Biolabs seeks to explain the difference in the figures in two ways. 6 Two different measurements are referred to in the Kaledin Paper. The first concerns a process known as sucrose density gradient measurement ("SDG"). The other is the process referred to in Claim 1, namely, a measurement involving the process known as electrophoresis, involving a polyacrylamide gel ("SDS-PAGE"). The measurement of the enzyme by SDG in the Kaledin Paper was stated to be 60,000 daltons. The measurement by SDS-PAGE was stated to be 62,000 daltons. New England Biolabs contends that there is an inconsistency on the face of the Kaledin Paper indicating an error from which it should be concluded that the molecular weight calculated by SDG is in fact in excess of 66,000 daltons. It is common ground that there is an inconsistency. The Applicant, however, contends that the figure of 60,000 is correct and that the error contained in the Kaledin Paper in that respect relates to what was observed in the SDG process. 7 New England Biolabs also contends that the 62,000 dalton figure measured by SDS-PAGE is not a measurement of the enzyme itself but can most likely be explained as being a measurement of a contaminant in the solution, being a different enzyme that had some properties similar to that of the enzyme of interest. 8 The Applicant contends that, having regard to the factual matters involved in such assertions on the part of New England, it could never be concluded that the Kaledin Paper anticipated Claims 1 to 7 in the Specification. On the other hand, New England Biolabs seeks to adduce evidence designed to demonstrate that, on the balance of probabilities, there was in the solution produced as described in the Kaledin Paper an enzyme such as is described in at least Claim 1, albeit that the Kaledin Paper does not actually specify the molecular weight referred to in Claim 1. 9 In support of its contentions, New England Biolabs seeks to rely on evidence of Dr Dale William Mosbaugh, which it wishes to adduce in the form of an affidavit sworn on 3 September 1999. Dr Mosbaugh is a Professor in the Department of Environmental and Molecular Toxicology and Research Core Director and Centre Investigator in the Environmental Health Sciences Centre at Oregon State University in Corvallis, Oregon, United States of America. There does not appear to be, for present purposes, any issue as to the qualifications of Dr Mosbaugh to give evidence in relation to the matters to which he directs his attention. 10 Objection is taken to section 3 of Dr Mosbaugh's affidavit. Section 3 is headed "Isolation of Full-length Taq DNA Polymerase by Kaledin and by Chien". Alice Chien and others are the authors of another paper relied on by New England Biolabs as anticipating Claims 1 to 7, being "Deoxyribonucleic Acid Polymerase from the Extreme Thermophile Thermus Aquaticus", published in Journal of Bacteriology, Vol. 7 No. 3, September 1976 pages 1550-1557 ("The Chien Paper"). The Chien Paper is referred to in the Kaledin Paper. 11 I have heard extensive argument on the admissibility of section 3 of the affidavit, although I have not yet heard argument as to the form of the relevant paragraphs and their admissibility from that point of view. The objection at this stage has been taken at a level of principle. 12 First of all, it was said that the material is irrelevant, having regard to the principles to be applied in determining the question of novelty. Second, however, objection was taken on the basis that the nature of the proceeding is such that I should not entertain evidence of this nature at this stage. In the course of argument on that latter question, further questions of principle have been raised, which it is desirable to determine for the purposes of ruling on the admissibility of this evidence and the extent to which oral evidence on the question should ultimately be permitted. RELEVANCE 13 As I apprehend, there are three ultimate factual questions sought to be established by section 3 of the affidavit. They are as follows: 1. Certain techniques for measuring apparent molecular weight will result in an apparent molecular weight value lower than other techniques. In particular, an enzyme that will measure approximately 92,000 daltons by SDS-PAGE will measure approximately 72,000 daltons by SDG. 2. When, during the process of gel filtration chromatography, a protein tends to stick to a gel filtration resin, the interaction will cause it to exhibit a lower apparent molecular weight value than its actual molecular weight or than it would have using other techniques. 3. Full length Taq DNA polymerase binds to phosphocellulose and elutes at relatively high salt gradients. A fragment of the enzyme claimed by the Applicant, as referred to in the Specification and known as "the Stoffel Fragment",either does not bind to phosphocellulose or binds weakly and elutes at the beginning of the salt gradient identified in the Chien Paper. The enzyme described in the Chien Paper elutes well after the Stoffel Fragment does on the salt gradient. 14 I shall explain each of those matters and their significance.