March 2015
CIPA Journal
By Anthony C. Tridico, Ph.D.; Carla Mouta-Bellum, Ph.D.
As reported by Finnegan in the January CIPA Journal, the United States Patent and Trademark Office (USPTO) published a revised set of patent eligibility guidelines on December 16, 2014, entitled the "Interim Guidance on Patent Subject Matter Eligibility" ("new Guidance"). Judging by its name and accompanying request for comments, this is not the USPTO's final word on 35 U.S.C. § 101 and patent-eligible subject matter. In the meantime, however, the new Guidance, which includes practical hypothetical examples, should help examiners and practitioners throughout prosecution. For example, practitioners should be able to rely on these examples, much like they rely on case law precedent, to distinguish or analogize the facts from their case during prosecution. Interestingly, however, a survey of USPTO records on Public PAIR (portal.uspto.gov/pair/PublicPair) suggests that neither the Examining Corps nor applicants have taken advantage of the hypothetical examples that accompanied the previous version of the USPTO's published "Guidance On Patent Subject Matter Eligibility" ("the old Guidance"), issued in March of 2014.
To provide a better perspective on how practitioners can benefit from the Patent Office's Guidance, we followed the prosecution of thirteen pending applications directed to biotech inventions, in which §101 rejections were made since the old Guidance issued. In twelve of the thirteen applications, all claims remain rejected, even after arguments were made in support of patent eligibility. Of these twelve applications, we reviewed ten representative claims and summarize them in the table below. The remaining application (representative "claim 10" in the table) was allowed and its prosecution history (summarized in the table) reveals an interesting strategy: relying on the combination of natural principles as a means to overcome the rejection.
Applicant's arguments in support of patent eligibility showed some diversity around two main approaches, namely: (i) arguing that the Office has not met its burden to prove that the claim reads on a naturally occurring composition or product and (ii) relying on any difference identified between the claimed invention and natural products. On the latter, it remains unclear which differences would presumably rise to the level of "marked difference" and why, as all differences appear to have been afforded the same weight by both the applicants and the Office. Not surprisingly, the Office's rejections were most frequently based on the absence of a structural difference, without which no "marked difference" could be found. This approach by Examiners was effectively mandated by the old Guidance. Therefore, a key practice tip going forward is to focus on the functional difference examples provided in the new Guidance.
As can be seen in the table, structural and functional arguments are very factual and are essentially specific to each claim. Although we chose claims representative of diverse types of subject matter pursued in the biotech field, the winning argument is likely to rely on differences that distinguish the uniquely claimed subject matter and might not apply in another similar claim. Of note, success will also likely depend on whether the argued differences were recognized in the specification as filed. And well-drafted specifications may improve the likelihood of overcoming patent eligibility rejections during prosecution.
Based on our sampling, the Examining Corps under the old Guidance appear to emphasize, if not require, structural characteristics to confer patent eligibility. For example, Examiners reviewing claims 1, 4, 5, 6, and 7 were interested in structural differences only. And the Examiner reviewing claim 3 required structural changes to be evident, despite the applicant arguing functional differences. Based on the new Guidance these outcomes may be different.
The new Guidance is responsive to comments received on the old Guidance. In particular, the new Guidance explains that functional characteristics, in addition to structural characteristics, can evidence a marked difference for patent eligibility: "[N]ow changes in functional characteristics and other non-structural properties can evidence markedly different characteristics, whereas in the old Guidance only structural changes were sufficient to show a marked difference." The ability to rely on functional properties was strongly suggested by numerous commentators. Thus, the new Guidance provides an important new path for arguing subject matter eligibility.
This can be exemplified by considering how the Office treats the pomelo juice/preservative composition under both the old and new Guidance. Bacteria that are present in naturally occurring pomelo juice cause it to spoil easily in just a few days. Applicable claims are directed to a composition of pomelo juice and a preservative, which can either be a natural or an artificial compound. According to the specification, an "effective amount" of preservative in the claimed composition is an amount sufficient to prevent the pomelo juice from spoiling for at least three weeks. The same claimed composition was analyzed in both the old and the new Guidances, and the results were diametrically opposed. In particular, the "slower spoiling" property of the juice with a natural or non-natural preservative is now (but was not then) a marked difference sufficient to render the composition of natural products patent-eligible.
The differences, functional or structural, "cannot be an inherent or innate characteristic of the naturally occurring counterpart," nor come "about or were produced 'quite independently of any effort of the patentee'" nor be "uninfluenced by [applicant's] efforts." See Guidance and In re Roslin Inst. (Edinburgh), 750 F.3d. 1333 (Fed. Cir. 2014).
But is the ability to rely on function, not just structure, enough to significantly alter prosecution course? Quite possibly. From the results compiled in the table below, patent eligibility rejections under § 101 in biotech art units relate mostly to "natural products" (peptide fragments, nucleic acids, vaccines, host cells, compositions) or "natural laws" (screening and diagnostic methods). Functional differences should help most applicants in these technologies and these art units. Another approach some applicants have taken is to switch from product claims to method claims. However, after both Non-Final and Final Actions, (through Request for Continued Examination), the USPTO promptly refused to allow this change in course because applicants had already received the allotted Office Action on the merits of the originally presented invention. Thus, the ability to change claim type during examination may be available only in a continuing application.
Going forward, two main question remain. One, is any functional difference sufficient to make a claim patent-eligible? Recent, post-new Guidance case law, suggests that only a "significantly new function" might justify patent eligibility. See Univ. of Utah Res. Foundation et al. v. Ambry Genetics Corp., No. 2014-1361 (Fed. Cir. Dec. 17, 2014) (emphasis added). Here, while the Federal Circuit recognized that primers have the new role of serving as starting material for PCT, which distinguishes them from DNA within the genome, the court did not find this was a significantly new function because priming, according to the Court, is "a function that is performed because the primer maintains the exact same nucleotide sequence as the relevant portion of the naturally occurring sequence . . . . Thus, just as in nature, primers utilize the innate ability of DNA to bind to itself." Id.
Second, how often will one find functional differences without some accompanying difference in structure? Neither the old nor the new Guidance exemplify this situation. Ultimately, this could mean that structural differences will be necessary but maybe not sufficient to show patent eligibility, and the resulting difference in function will nonetheless be the required "marked" impact of the observed change.
Although it is the USPTO's burden to establish that the claimed subject matter is a natural product, current practice appears to shift the burden to applicants to show that (structural or functional) differences exist. The USPTO's default position appears to be one of equality, i.e., the claimed subject matter is structurally and functionally the same as the natural product. And practitioners should expect to receive, at least initially, a patent eligibility rejection under § 101. This practice effectively shifts the burden to practitioners to come forward with evidence of structural or functional differences. To do so, practitioners, as well as inventors and applicants, will need to (i) better understand the scientific intricacies of the claimed subject matter and claim those properties, (ii) incorporate those intricate differences into the specification to avoid relying on ex post facto reasoning, and (iii) be capable of explaining those intricacies to an Examining Corps that has diverse scientific backgrounds.
Claim | Applicant's Argument | Rejection |
1. An immunogenic composition comprising neisserial hia homologue (Hsf) and Ope antigens, wherein the Hsf antigen is a polypeptide comprising the amino acid sequence of SEQ ID NO: 2 and the Ope antigen is a polypeptide comprising the amino acid sequence of SEQ ID NO: 4, wherein either one or both of the Hsf antigen and Ope antigen is purified and wherein the immunogenic composition is non-toxic. | It is the Office's burden to provide factual support for concluding that the claims read on a naturally occurring composition. Office must support a conclusion that the naturally occurring antigens present on or in naturally occurring Neisseria would be non-toxic, and this has not been done. |
Claimed composition not structurally different from the antigens, which are intrinsically comprised in naturally occurring Neisseria. The limitation "non-toxic" did not render the antigen elements structurally markedly different. |
2. A vaccine comprising the immunogenic composition of claim 1 and a pharmaceutically acceptable carrier. | A pharmaceutically acceptable carrier is approved for use in humans, unlike the naturally occurring elements as they exist in nature referred to by the Office Action. | A generic pharmaceutically acceptable carrier is not markedly different from a naturally occurring adjuvanting cell wall element, LPS, or a proteoglycan of the Hsf, Ope, and FHbp proteins-containing natural Neisseria (Funk Brothers). Term 'vaccine' amounts to nothing more than a mere field of use. |
3. An immunogenic polypeptide fragment comprising a deletion relative to the polypeptide of SEQ ID NOs: 3-18, which increases solubility of the fragment as compared to the applicable full length polypeptide of SEQ ID NOs: 3-18 and wherein the fragment raises a substantially similar immune response in a subject as provides at least 70% of protection in a subject provided by the applicable full length polypeptide of SEQ ID NOs: 3-18. | Claimed polypeptide fragments demonstrate marked structural and functional differences compared to the naturally occurring proteins. Claimed fragments exhibit increased solubility compared to the corresponding full-length proteins. Specification describes how the orf405 protein showed "limited or no solubility" when expressed as a full-length protein. This feature renders the protein incapable of serving as a vaccine antigen. Fragments provide protection against sepsis and infection. In contrast to the claims in Myriad, the pending claims expressly define the isolated fragments in terms of their chemical composition (i.e., amino acid sequence) and explicitly call out chemical changes that result from the fragmentation, such as increasing solubility. Unlike Myriad, the pending claims are not directed to the information encoded by a unique amino acid sequence per se, but rather the chemical properties of the three-dimensional proteins having those sequences, including immunogenicity and solubility. |
"[F]ragmentation does not confer a marked structural difference from the naturally occurring product" whose sequence comprise the claimed fragments." Markedly different inquiry focuses on the structural characteristics of the product and not the function of solubility in water. Protein fragments that occur in nature as proteins are routinely digested and broken down by proteases Proteins are built one amino acid at a time and, as such, every protein at some point exists as a two amino acid fragment, a three amino acid fragment, and so forth. An immune response is a property/function of the host and not the protein per se. Denatured and insoluble antigens can generate an immune response and there is no evidence in the specification that the full-length insoluble fragment is incapable of doing so. There is no evidence in the specification as filed regarding the lack of an immune response toward the full-length antigen. Argument is directly contrary to the claims, which state that the fragments provide "at least 70% of protection in a subject provided by the applicable full length polypeptide." Assertion of vaccines is not relevant to the claims as the claims are not drawn to vaccines. Mere fragmentation of a protein is similar to the 101 guidance for DNA primers, the primers are more soluble and have the function of being able to bind to the nucleic acid and provide for amplification because they are fragments. However, the structure is not markedly different. |
4. A nucleic acid vector capable of replication in a host cell, wherein the vector comprises a nucleic acid sequence having at least 96% or more, or complete (100% identical) sequence identity to SEQ ID NO: 1, wherein the nucleic acid encodes a polypeptide having nitrilase activity, or an enzymatically active fragment thereof, wherein the nucleic acid sequence is operably linked to a heterologous promoter. | Original claim amended to recite the underlined/bolded element; amended claim not yet examined. A polynucleotide wherein the nucleic acid sequence is operably joined to a heterologous promoter that, when combined with the nucleic acid sequence, is not a natural product. |
Claimed nucleic acid sequences not marked different in structure from nucleic acid sequences found in nature. |
5. A host cell comprising a KIR6.2 subunit in operable interaction with a polypeptide consisting of an amino acid sequence selected from the group consisting of SEQ ID N0:2 and SEQ ID N0:21, wherein the KIR6.2 and the polypeptide are heterologously expressed in the host cell. | The claim does not encompass naturally occurring cells. | "[H]eterologously expressed" limitation is interpreted as a "product-by-process" limitation and there is no recited feature in the claim that positively renders the K1R6.2 subunit, the polypeptide, and/or the host cell markedly different in structure from a naturally occurring cell, e.g., a murine cardiomyocyte. |
6. A method of identifying a compound that modulates a demethylase activity of a recombinant histone demethylase, the method comprising: (a) contacting the recombinant demethylase with a methylated protein substrate in the presence and absence of a test compound; (b) detecting the level of demethylation of the protein substrate in the presence and absence of the test compound under conditions sufficient for demethylation; and (c) determining whether there is a change in the level of demethylation of the protein substrate in the presence of the test compound as compared with the level of demethylation in the absence of the test compound, wherein a change in demethylation of the protein substrate in the presence of the test compound as compared with the level of demethylation in the absence of the test compound indicates that the test compound is a modulator of the demethylase activity of the recombinant demethylase; wherein the recombinant demethylase is selected from SEQ ID NOs X, Y, and Z. |
Claims are directed to methods that require the use of a non-naturally occurring, man-made, novel and nonobvious, recombinant protein. Claimed methods are not routine and nor were they well-understood or engaged in prior to the filing date. Art did not disclose or suggest the claimed demethylases nor how to use such demethylases in screening assays. Field of histone demethylases was highly unpredictable and poorly understood prior to the novel and nonobvious work claimed. |
"[R]ecombinant" fails to render the structure of the histone demethylase "markedly different" from a natural histone demethylase. Contrary to applicant's position, the art's teachings show that the elements/steps in addition to the judicial exception are well-understood, routine, conventional activity already engaged in by the scientific community. |
7. A composition comprising an NDV (Newcastle Disease Virus) HN (Hemagglutinin-Neuraminidase) polypeptide or antigen and a pharmaceutically or veterinarily acceptable carrier, excipient, vehicle or adjuvant, wherein the NDV HN polypeptide or antigen has the sequence as set forth in SEQ ID NO: 3, and wherein the NDV HN polypeptide or antigen is expressed in microalgae and glycosylated, and wherein the glycosylated HN polypeptide or antigen contains high-mannose type glycans. | NDV HN polypeptide produced contains high-mannose type glycans, which is unique in microalgae, and is structurally different from the HN protein produced in chicken eggs. An article shows the structural difference between the HN protein of the present invention and the HN protein produced in chicken. Article teaches that antibodies produced in chicken eggs contain both fully processed glycan (complex glycans) as well as unprocessed glycan (high mannose structures) in almost equal amounts. The HN protein produced in chicken eggs contains a mixture of complex glycans and high mannose structures in about equal amounts, and is structurally different from the claimed HN protein (containing high mannose glycans). |
Applicant has not provided a quantitative argument related to the oligosacchardies structure of the HN as it naturally occurs on the NDVirus to the oligosaccharide structure of the HN protein expressed in microalgae. Recitation of the limitation "contains high-mannose type glycans" does not support any structural features and needs to be clarified to provide additional information such as % mannose and other sugars present on the oligosaccharide chain and how they compare to the oligosaccharide chain of the naturally occurring protein. |
8. A recombinant, isolated, or purified polypeptide encoded by a cDNA comprising a nucleotide sequence that has at least 85% identity to a nucleotide sequence as set forth in any one of SEQ ID NOs: 84-86. | Claimed polypeptides are recombinant, isolated, or purified. They CANNOT occur in nature because they are encoded by man-made codon-optimized cDNA that is not naturally occurring. | Protein is a naturally occurring isoform. Whether they are recombinantly produced from naturally-occurring nucleic acid or from codon-optimized nucleic acid or isolated from their natural source, there is no difference in their structure or activity. |
9. A product selected from the group consisting of an enzyme tablet, a granulate, a stabilized liquid, and a paste, the product consisting of (1) an isolated lactamase enzyme comprising the amino acid sequence of SEQ ID NO: 1 and (2) an excipient selected from the group consisting of lactose, glycerol, and albumin, the isolated lactamase enzyme obtained by a process comprising a step selected from the group consisting of (i) heterologous expression in E. coli and (ii) isolation from a recombinant strain of Salmonella. | No evidence that even suggests that any lactamase enzymes occur naturally in combination with such an excipient; the claim recites a meaningful limitation that narrows the scope of the claim, relates to the allegedly natural product in a significant way, and does more than describe the allegedly natural product with general instructions to use or apply it. If the USPTO's analysis were proper, no compositions containing any bacteria would ever be directed to patent-eligible subject matter. This goes against the fundamentals of patent law, as well as the public policy considerations for patent-eligible subject matter opined upon by the Supreme Court and USPTO. Elements/steps narrow the scope of the claim so that others are not substantially foreclosed from using the judicial exception(s). Claimed combinations were not well-known, routine, or conventional. |
Claims are drawn to natural products. Claims encompass an enzyme that is not markedly different in structure from the naturally occurring lactamase from fungi. Lactamase enzyme obtained from Salmonella retains the same structure and function as the enzyme found naturally in fungi despite being isolated from a different source. Addition of the excipients lactose, glycerol, or albumin does nothing to change the respective function of the lactamase outside of what nature intended. Funk Brothers. |
10. A method of identifying the presence of |
Method includes additional steps that integrate the natural principle into the claimed invention such that the natural principle is practically applied, and the combination of these elements is sufficient to ensure the claims amount to significantly more than the natural principle itself. A method which includes steps of using the combination of the expression level of the claimed genes to obtain a differential expression level, and then using that differential expression level to identify a viral or bacterial disease, is sufficient to ensure that the claim is significantly more than the natural principle itself with generalized instructions to "apply it." These additional steps, when viewed as a whole, are not well-understood, routine, conventional activity already engaged in by the scientific community. The combination of the genes currently claimed was not previously identified, therefore the use of this set of genes cannot be viewed as well-understood, routine, conventional activity. |
ALLOWED Rejection withdrawn in light of applicant's arguments/amendments thereto. Original rejection: Instant claims are drawn to methods of identifying the presence of an infectious disease by determining the expression level of certain biomarkers in a sample from a human subject. The relationship between the recited biomarkers and infectious disease is a natural principle. A claim that focuses on the use of a natural principle must also include additional elements or steps to show that the inventor has practically applied, or added something significant to, the natural principle itself. See Mayo 101 USPQ2d at 1966. Adding steps to a natural biological process that only recite well-understood, routine, conventional activity previously engaged in by researchers in the field would not be sufficient. |
Originally printed in CIPA Journal. This article is for informational purposes, is not intended to constitute legal advice, and may be considered advertising under applicable state laws. This article is only the opinion of the authors and is not attributable to Finnegan, Henderson, Farabow, Garrett & Dunner, LLP, or the firm's clients.
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