What It Is, Not What It Does: The Written Description Requirement and Carnegie Mellon University v. Hoffman-La Roche

This article first appeared in the Spring 2009 edition of the Philadelphia Intellectual Property Law Association Newsletter and was also a topic presented by Glenn Murphy at the Twenty-Fifth Annual Joint Patent Practice Seminar on April 30, 2009.

I. INTRODUCTION

Joining a growing body of cases applying written description in the context of biotechnological inventions, Carnegie Mellon Univ. v. Hoffman-La Roche, Inc., 541 F.3d 1115 (Fed. Cir. 2008) reaffirms that written description is a separate requirement apart from enablement under 35 U.S.C. § 112, ¶ 1, and that the written description forms part of the quid pro quo, in which the public receives meaningful disclosure of an invention in exchange for being excluded from practicing it for a certain time. Holding that disclosing a single gene from a single bacterial source encoding one DNA polymerase will not support claims directed to a genus claiming any bacterial source encoding any DNA polymerase, the court again used a relatively stringent standard for written description of biotechnological inventions begun with the Regents of the Univ. of California v. Eli Lilly case, which emphasizes the need to disclose the structure of DNAs or the proteins they encode. 119 F.3d 1559 (Fed. Cir. 1997).

This paper reviews the Carnegie Mellon case and considers its implications for future prosecution and enforcement of patents relating to biotechnological inventions.

II. THE LAW OF WRITTEN DESCRIPTION IN BIOTECHNOLOGY

35 U.S.C. § 112, ¶ 1 states:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same . . .

A landmark case applying the written description requirement in 35 U.S.C. § 112, ¶ 1 to biotechnological patent claims is Regents of the University of California v. Eli Lilly. In Eli Lilly, the court held that a specification that disclosed only a single example of a plasmid that encoded rat insulin did not describe generic claims covering a genus of recombinant plasmids encoding any vertebrate or mammalian insulin, nor dependent claims to plasmids encoding human insulin. The court wrote that adequate description of a DNA requires more than describing its function or a method for obtaining it. Rather, description of a DNA required disclosure of its relevant structural or physical characteristics. “A definition by function . . . does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is.” Id. at 1568, citing Fiers v. Revel, 984 F.2d 1164, 1169-71 (Fed. Cir. 1993). “A description of a genus of cDNAs may be achieved by means of a recitation of a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or of a recitation of structural features common to the members of the genus, which features constitute a substantial portion of the genus.” Id. at 1569. The decision in Eli Lilly signaled a trend in biotechnology cases emphasizing that written description of claims to DNA often requires a disclosure of a precise sequence of nucleotides.

The need to describe genetic materials by disclosing a specific sequence in the specification has been questioned. In Enzo Biochem, Inc. v. Gen-Probe Inc., 323 F.3d 956 (Fed. Cir. 2002), the court noted it is not correct “that all functional descriptions of genetic material fail to meet the written description requirement.” Id. at 964. The issue before the court in Enzo was whether claims to nucleic acid probes that preferentially hybridize to the DNA of one Neisseria species over another were described by a specification that did not disclose the nucleotide sequences of the probes but rather disclosed the ATCC deposit of three samples, in the form of recombinant DNA within an E. coli host. The court reversed its earlier decision and held that the ATCC deposit of the probes constituted a written description of the specific deposited nucleotides, but that material issues of fact remained on whether those deposits described the claimed subsequences or variants of those nucleotides or the functionally-defined genus of nucleotides generally. Id. at 965-68. On remand the case was decided on other grounds. Enzo is notable for its holding, for its adoption of the U.S.P.T.O.’s Guidelines for Examination of Patent Applications Under the 35 U.S.C. 112, ¶ 1 “Written Description” Requirement (now M.P.E.P. § 2163), and for the concurring and dissenting opinions on the court’s refusal to reconsider the case en banc, which argued whether written description constitutes a separate statutory requirement for patentability under section 112, ¶ 1.

Later decisions by the Federal Circuit have often followed Eli Lilly to find claims to biotechnological subject matter lacking proper written description, notably Noelle v. Lederman, 355 F.3d 1343 (Fed. Cir. 2004), In re Wallach, 378 F.3d 1330 (Fed. Cir. 2004), and In re Alonso, 88 U.S.P.Q.2d 1849 (Fed. Cir. 2008). Other cases have applied Eli Lilly analogously to invalidate claims not specifically claiming or requiring a DNA. See University of Rochester v. G.D. Searle & Co., Inc., 358 F.3d 916 (Fed. Cir. 2004) and Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co., 2009 U.S. App. LEXIS 6915, (Fed. Cir. April 3, 2009). Notable exceptions distinguishing Eli Lilly include Invitrogen Corp. v. Clontech Labs., Inc., 429 F.3d 1052 (Fed. Cir. 2005) and Falkner v. Inglis, 448 F.3d 1357 (Fed. Cir. 2006).

III. THE CARNEGIE MELLON CASE

Carnegie Mellon clearly falls into the Eli Lilly line of cases requiring the specification to disclose the structure of a claimed chemical entity, and in particular the nucleotide sequence of a claimed genetic material. At issue in Carnegie Mellon were: U.S. Patent 4,767,708, “Enzyme Amplification and Purification” (‘708 patent); U.S. Patent 5,126,270, “Enzyme Amplification and Purification” (‘270 patent); and U.S. Patent 6,017,745, “Enzyme Amplification and Purification Process for Producing DNA Polymerase” (‘745 patent). The three patents form a family relating to plasmids that contain gene coding regions for the expression of the enzyme DNA polymerase I, which catalyzes the synthesis of DNA.

DNA polymerase I (Pol I) is encoded by the gene known as polA. ‘708 patent col. 1, ll. 14-15. The polA gene contains two regions – the gene coding region, which codes for DNA polymerase I, and the promoter region, which is a DNA sequence involved in initiating transcription of the enzyme. Carnegie Mellon, 541 F.3d at 1118. Researchers seeking to clone the polA gene into plasmids to express the Pol I enzyme found that uncontrolled expression of the enzyme beyond natural levels proved fatal to the host organism. The ‘708, ‘270, and ‘745 patent inventors discovered that damaging or excluding portions of the natural promoter sequence of the polA gene could limit expression of the enzyme in a host organism to non-lethal levels. Id. at 1118-19.

Thus in the ‘708 patent they claimed:
1. A recombinant plasmid containing a cloned complete structural gene coding region isolated from a bacterial source for the expression of DNA polymerase I, under operable control of a conditionally controllable foreign promoter functionally linked to said structural gene coding region, said foreign promoter being functional to express said DNA polymerase I in a suitable bacterial or yeast host system.

Claim 1 of the ‘270 patent reads:
1. A recombinant plasmid providing for Nick-translation activity isolated from a bacterial source, said plasmid capable of being placed in a bacterial host system such that the host system can grow and divide.

Similarly, claim 1 of the ‘745 patent reads:
1. A recombinant plasmid containing a DNA coding sequence for the expression of DNA polymerase activity, wherein said DNA coding sequence is derived from a source that encodes a bacterial DNA Polymerase, said source not containing an amber mutation affecting expression of said DNA polymerase activity, such that when said plasmid is transformed into a bacterial host system the host system can grow and divide thereby replicating said plasmid.

Carnegie Mellon sued Roche in August, 1994, alleging that Roche’s plasmid pLSG5 infringed the ‘708 and ‘270 patents. Id. at 1119. On Roche’s motions, the district court granted summary judgment that certain claims of the ‘708 and ‘270 patents were invalid for lack of written description. Id. at 1120. In 2001 Carnegie Mellon sued Roche on the ‘745 patent; again, the court granted Roche’s motion for summary judgment that certain claims of the ‘745 patent were invalid under the written description requirement. Id. The district court entered final judgment on all three patents in May, 2007, and Carnegie Mellon appealed. Id. at 1120-1121.

The Federal Circuit began its analysis by affirming that written description is a requirement of § 112, ¶ 1 separate and distinct from enablement that ensures the public receives meaningful disclosure of an invention in exchange for being excluded from practicing it for a certain time. Carnegie Mellon, 541 F.3d at 1121-22. Satisfaction of the written description requirement is a factual inquiry that depends on the nature of the invention and the knowledge of those of skill at the time the invention was made. Id. at 1122. Ultimately the applicant must convey to those of skill in the art that he or she invented or possessed what is claimed. Id. The court recounted its holdings in Eli Lilly that written description of a DNA requires a precise definition, such as by structure, formula, chemical name, or physical properties, and that description of a genus of cDNAs may be achieved by reciting a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or reciting structural features common to the members of the genus, which features constitute a substantial portion of the genus. Id.

Under this standard, the Federal Circuit agreed with Roche that there were no genuine issues of material fact regarding whether the ‘708, ‘270, and ‘745 patents failed to adequately describe what they claimed. The court determined that the claims of each patent covered coding sequences originating from any bacterial species. 541 F.3d at 1128. On the other hand, the common specification only disclosed the polA coding sequence from a single bacterial source, E. coli. 541 F.3d at 1125. The court further found that while the patents disclosed that the polA gene was “critical” to the claimed invention, the record established that DNA polymerase I was not a single enzyme, but a family of enzymes, encoded not by a single gene, but by a family of genes, varying across potentially millions of bacterial sources for polA genes. Id.

The court found persuasive authority in the U.S.P.T.O.’s Guidelines for Examination of Patent Applications Under the 35 U.S.C. 112, ¶ 1 “Written Description” Requirement, which provide that:
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species . . .

A “representative number of species” means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
* * *
Satisfactory disclosure of a “representative number” depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features of the elements possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus.

66 Fed. Reg. at 1106, cited at 541 F.3d at 1124 (emphasis by the court).
The court explained:
We agree with the district court that the narrow disclosure of the E. coli polA gene is not representative of and fails to adequately support the entire claimed genus under Eli Lilly. To satisfy the written description requirement in the case of a chemical or biotechnological genus, more than a statement of the genus is normally required. One must show that one has possession, as described in the application, of sufficient species to show that he or she invented and disclosed the totality of the genus. In light of the specifications’ disclosure concerning the careful construction of the claimed recombinant plasmids, such that the natural promoter of the polA gene is severely damaged or eliminated, and given the record evidence that the polA gene varied among the numerous bacterial species, as well as the absence of any polA gene sequence for any bacteria other than E. coli, we conclude that that requirement was not met here.

Carnegie Mellon, 541 F.3d at 1126.

IV. CONCLUSION

The Carnegie Mellon case at the most basic level affirms that, for the time being, the written description requirement remains a separate and independent statutory test for patentability. By its approving use of the U.S.P.T.O.’s written description Guidelines, it also more closely aligns the Federal Circuit’s treatment of written description in the biotechnological arts with U.S.P.T.O. practice. For prosecuting attorneys and litigators representing patentees, it means recognizing the limits of claims, biotechnological or not, that define subject matter in terms of function rather than structure. Claims that define a chemical entity by function and thereby create a large genus of chemical entities should be supported by adequate examples. It is clear where the members of the genus have significant, unpredictable, or unknown structural variation, a single example is unlikely to satisfy the written description requirement. Obtaining and enforcing broad claims to genetic materials described solely by their function and supported by a single example or limited or structurally unrepresentative examples will continue to present problems. On the other hand, counsel representing infringement defendants or potential infringement defendants may find in cases like Carnegie Mellon new opportunities to avoid or limit infringement concerns.

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