DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 1-20 are pending and examined herein.
No claims are canceled.
Priority
As detailed on the 03 July 2023 filing receipt, the application claims priority as early as 10 March 2016. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Information Disclosure Statement
Information disclosure statements (IDS) were filed on 16 February 2023 and 24 June 2024. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the references are being considered by the examiner.
Claim Objections
Claims 10 and 16 are objected to because of the following informalities: the claims recite “data bases” rather than “databases” as in parent claim 1. Similarly, claims 11-15 are objected to because they recite “key words” while parent claim 10 recites “keywords.” Claim 20 is objected to because it recites “an epitope mimic peptides,” where the singular article “an” disagrees with the plural “peptides.”
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 17 and 20 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 17 recites two list elements – analyzing alternative sequences and identifying alternative sequences – but they are not joined by a conjunction and thus it is unclear whether either or both is required.
Claim 20 recites “the human protein” but a human protein lacks antecedence because it does not appear in parent claim 1, rendering “the human protein” unclear.
35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-20 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements both individually and in combination, do not amount to significantly more than the abstract idea of identifying epitope mimics.
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of
nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to a method, which falls within one of the categories of statutory subject matter. [Step 1: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
The independent claim recites assigning curation, which are interpreted as mental steps of listing proteins and their functions, which the human mind is practically equipped to perform. The independent claim recites computing probable epitopes in each protein. This claim is interpreted as reciting a metric of probability, which requires a mathematical calculation to determine, and thus is considered to be a mathematical concept. The independent claim recite identifying the core peptide, where a core peptide is defined in the specification as the central five amino acids in a nine amino acid sequence (pg. 25, lines 10-13). The human mind is practically equipped to evaluate which five amino acids are the central ones in a string of nine. The independent claim recites computing probable epitopes for a protein of interest, which is interpreted as a mathematical concept for the reasons explained above. The independent claim recites identifying the core peptide of the query sequence, which is interpreted as a mental process for the reasons explained above. The independent claim recites comparing core peptides in the database and query, where comparing sequence data is a step the human mind is practically equipped to perform as data evaluation or judgment. The independent claim recites identifying peptides that are identical in the database and query core peptides, which is a more specific data evaluation or judgment as explained above and thus a mental process. The independent claim recites identifying the function of the host proteins, which is interpreted as referencing the protein database, which is a step the human mind is practically equipped to perform.
Claims 2-3 recite additional information about the data assembled in the database, where data is a non-statutory category and thus interpreted as abstract.
Claim 4-7 recite additional information about the metric for selection of probable B cell epitopes, where a criterion for selection is interpreted as related to selection, which the human mind is practically equipped to perform.
Claims 8-9 recite additional data about the epitope evaluation of the epitopes from the database and query, where data is a non-statutory category and thus interpreted as abstract.
Claim 10 recites using keywords to search a database, where searching a database by keyword is a step the human mind is practically equipped to perform.
Claims 11-16 recite additional information about using keywords and the keywords themselves for searching a database, and so are considered additional details about the mental process described above.
Claim 17 recites analyzing alternative sequences and identifying alternative sequences, where analyzing and identifying sequences are steps the human mind is practically equipped to perform.
Claim 18 recites analyzing a biopharmaceutical, identifying epitope mimics, and preparing a report. Analyzing and identifying epitopes are abstract ideas for the reasons explained above. Preparing a report is interpreted as including, under a broadest reasonable interpretation, mental steps before production of a physical report and as such may be interpreted as a mental process.
Claim 19 recites determining identical matches by comparison with homologous proteins, where determining matches is previously discussed as a mental process of data evaluation which the human mind is practically equipped to perform. Claim 19 further recites selecting an animal model, where making a selection is a mental step the human mind is practically equipped to perform.
Claim 20 recites identifying mimics, which is a mental process for the reasons described above.
Hence, the claims explicitly recite numerous elements that, individually and in combination,
constitute abstract ideas. The claims must therefore be examined further to determine whether they
integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
The independent claim recites additional elements that are not abstract ideas: "a computer readable medium,” “entering a sequence… into a computer,” and assembling databases. The dependent claims also recite “providing a synthetic protein,” “contacting said synthetic protein with serum,” and identifying the presence of antibodies (claim 20).
The elements of using a non-transitory computer readable medium and a computer itself are interpreted as using a general purpose computer to perform the abstract steps, which does not integrate the abstract idea into a practical application (MPEP 2106.05(f)).
Assembling a database, whether based on all proteins in a host proteome or of core proteins, is interpreted as using storing data, which is preparatory step related to data gathering and thus insignificant extra-solution activity which does not integrate the abstract idea into a practical application (MPEP 2016.05(g)).
Meanwhile, the steps of providing a synthetic protein, contacting it with serum from a subject, and identifying the presence of antibodies are interpreted as instructions to apply the abstract ideas (MPEP 2106.05(f)). It is not clear than an improvement is asserted, a treatment is administered, or a transformation is occurring. [Step 2A Prong Two: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself. Step 2B of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05). The claims recite the following additional elements that are not abstract ideas: "a computer readable medium” (claim 1), “entering a sequence… into a computer,” (claim 1), assembling databases (claim 1), “providing a synthetic protein” (claim 20), “contacting said synthetic protein with serum” (claim 20), and identifying the presence of antibodies (claim 20).
Entering data into a computer with memory is interpreted as receiving or transmitting information using a computer, which is a conventional computer task (buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014); MPEP 2106.056(d)).
Storing data in a database is a conventional computer function (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93) ); MPEP 2106.056(d)).
Doores (Chemistry: A European Journal 12(3): 656-665, 2006; newly cited) teaches analysis of a synthetic epitope mimic to validate a mimic selection process (pg. 662, col. 1, first paragraph), which involves contact with the serum and antibody detection.
Therefore, the recited additional elements, alone or in combination with the judicial exceptions, do not appear to provide an inventive concept. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-10, 12-13, and 16-19 are rejected under 35 U.S.C. 103 as being unpatentable over Berglund (Protein Science 17: 606-613, 2007; newly cited) in view of Camon (Genome Research 13: 662-672, 2003; newly cited), Rubinstein (BMC Bioinformatics 10(287): 6 pgs., 2009; newly cited), and Kanduc (Current Pharmaceutical Design 14: 289-295, 2008; previously cited on the 16 February 2023 IDS form).
Claim 1 recites assembling a database of all proteins in the host proteome.
Berglund teaches determining all possible fragments of the human proteome (pg. 607, col. 2, last paragraph).
Claim 1 recites assigning a curation to each protein based on its reported function.
Berglund teaches that the proteome consists of the Ensembl database (pg. 607, col. 2, last paragraph), which may include protein function, but does not explicitly teach assigning a curation to each protein based on its reported function.
Claim 1 recites computing the probable B cell epitopes in each protein of said host proteome database that is curated by function, which is not taught by Berglund.
Berglund teaches description of B-cell epitopes (pg. 606, col. 1, second paragraph) and screening proteomes using a sliding scale (pg. 613, col. 1, third paragraph), but not detecting B-cell epitopes specifically.
Claim 1 recites identifying the core peptide of said probable B cell epitopes in each protein of the host proteome. A core peptide is defined in the specification as the central five amino acids in a nine amino acid sequence (pg. 25, lines 10-13).
Berglund teaches identifying at least 8-mers (pg. 607, col. 2, last paragraph) and not the core peptides as defined as pentamers or 5-mers.
Claim 1 recites assembling a database of said core peptides of said probable B cell epitopes from each protein of the host proteome in a computer readable medium.
Claim 1 recites entering a sequence of a protein of interest into a computer with access to said database.
Berglund teaches using a protein sequence as input to search for an epitope (pg. 607, col. 1, second paragraph).
Claim 1 recites computing probable B cell epitopes in the protein of interest.
Berglund teaches prediction of epitopes using a protein sequence as input, where the epitopes may be B-cell epitopes (pg. 607, col. 1, second paragraph).
Claim 1 recites identifying the core peptide of said probable B cell epitopes in said protein of interest.
Berglund teaches determining a sliding window of different k-mer sizes of a query protein (pg. 607, col. 2, last paragraph) but not core peptides.
Claim 1 recites comparing said core peptide of said probable B cell epitope in a protein of interest to the core peptides contained in said database of peptides from the host proteome.
Berglund teaches comparison of a query protein to a protein database (pg. 607, col. 2, last paragraph), but not specifically comparing the core peptide pentamer.
Claim 1 recites identifying core peptides in predicted B cell epitopes in said protein of interest which are identical to core peptides in predicted B cell epitopes in one or more proteins of the host proteome.
Berglund teaches identical amino acids in a hit and query (pg. 608, Fig. 1 caption) but not core peptides.
Claim 1 recites identifying the function of the host proteome proteins which comprise the identical core peptides matching the core peptides of the protein of interest.
Berglund does not teach determining the function of a protein of interested based on the curated function from the database.
Berglund does not teach assigning a curation to each protein based on its reported function or identifying function of a determined protein of interest.
Camon teaches an ontology for molecular function (pg. 662, col.1, last paragraph) which can be applied to Ensemble (pg. 663, col. 2, last paragraph) to match a protein with its function.
Berglund teaches description of B-cell epitopes (pg. 606, col. 1, second paragraph) and screening proteomes using a sliding scale (pg. 613, col. 1, third paragraph), but not detecting B-cell epitopes specifically.
Rubinstein teaches predicting probable B-cell epitope regions (abstract).
Berglund teaches identifying at least 8-mers (pg. 607, col. 2, last paragraph) and not the core peptides as defined as pentamers or 5-mers.
Kanduc teaches use of pentamers for comparison in a proteome database to compare to host sequences (pg. 289, col. 1, third paragraph).
Claim 2 recites said host proteome is selected from the group consisting of a human proteome and a murine proteome.
Berglund teaches “the human proteome” (pg. 608, col. 2, first paragraph).
Claim 3 recites said host proteome is a non-human primate proteome.
Berglund teaches generating antibodies using the proteome of species “other species than humans, such as mouse, rat, dog, or primates” (pg. 612, col. 2, first paragraph).
Claim 4 recites the probable B cell epitope in said protein of interest is in the top 25% most probable B cell epitopes in said protein of interest.
Rubinstein teaches a probability score (pg. 4, Fig. 1) and the regions with the most significant score (pg. 5, Fig. 2C). While a 25% threshold is not taught, the probability is interpreted as a results effective variable. Optimization of a results-effective variable within known prior art ranges (of up to 100% by virtue of being a probability) is insufficient to patentably distinguish the invention from the prior art, and there does not appear to be an argument regarding why the specific threshold of 25% is selected (MPEP 2144.05).
Claim 5 recites said probable B cell epitope in said protein of interest is in the top 10% most probable B cell epitopes in said protein of interest.
Rubinstein teaches a probability score (pg. 4, Fig. 1) and the regions with the most significant score (pg. 5, Fig. 2C).While a 10% threshold is not taught, the probability is interpreted as a results effective variable. Optimization of a results-effective variable within known prior art ranges (of up to 100% by virtue of being a probability) is insufficient to patentably distinguish the invention from the prior art, and there does not appear to be an argument regarding why the specific threshold of 10% is selected (MPEP 2144.05).
Claim 6 recites the probable B cell epitope in said host proteome protein is in the top 40% most probable B cell epitopes in said protein of interest.
Rubinstein teaches a probability score (pg. 4, Fig. 1) and the regions with the most significant score (pg. 5, Fig. 2C).While a 40% threshold is not taught, the probability is interpreted as a results effective variable. Optimization of a results-effective variable within known prior art ranges (of up to 100% by virtue of being a probability) is insufficient to patentably distinguish the invention from the prior art, and there does not appear to be an argument regarding why the specific threshold of 40% is selected (MPEP 2144.05).
Claim 7 recites the probable B cell epitope in said host proteome protein is in the top 25% most probable B cell epitopes in said protein of interest.
Rubinstein teaches a probability score (pg. 4, Fig. 1) and the regions with the most significant score (pg. 5, Fig. 2C).While a 25% threshold is not taught, the probability is interpreted as a results effective variable. Optimization of a results-effective variable within known prior art ranges (of up to 100% by virtue of being a probability) is insufficient to patentably distinguish the invention from the prior art, and there does not appear to be an argument regarding why the specific threshold of 25% is selected (MPEP 2144.05).
Claim 8 recites the core peptide in said probable B cell epitope in said protein of interest comprises a sequence of five contiguous amino acids.
Kanduc teaches pentamers being used to scan the host proteome (pg. 289, col. 2, second paragraph).
Claim 9 recites the core peptide in said probable B cell epitope in said host proteome protein of interest comprises a sequence of five contiguous amino acids.
Kanduc teaches pentamers being used to scan the host proteome (pg. 289, col. 2, second paragraph).
Claim 10 recites the database of core peptides in said data base of host proteome proteins is searched by application of a list of keywords to select to a subset of peptides with functions of interest.
Berglund teaches a model for determining epitope profiles for clinical diagnosis, where the proteins are significant for treatment of cancer (pg. 609, col. 2, only paragraph), where a keyword for the function of the protein is interpreted as reading on, for instance, a region therapeutically important to trastuzumab.
Claim 12 recites said key words define a group of proteins with enzymatic function.
Rubinstein teaches keywords such as “enzyme” and “enzyme regulator” (pg. 670, Fig. 4).
Claim 13 recites said key words define a group of proteins which function in blood clotting and vascular permeability.
Rubinstein teaches the keyword “cell adhesion molecule” (pg. 670, Fig. 4), where cell adhesion is interpreted as reading on clotting.
Claim 16 recites the database of core peptides in said database of host proteome proteins is searched by application of a list of keywords to select to a subset of peptides with association with development of a specific disease syndrome.
Berglund teaches searching for proteins related to human breast cancer and specific regions in protein ERBB2 which have high sequence identity (pg. 609, col. 2, only paragraph).
Claim 17 recites the protein of interest is a biopharmaceutical protein or vaccine.
Kanduc teaches vaccine preparation (pg. 293, col. 2, last paragraph).
Claim 17 recites analyzing alternative sequences for the biopharmaceutical protein or vaccine.
Kanduc teaches “no-similarity segments” (pg. 293, col. 2, last paragraph), where an alternative reads on a sequence without similarity.
Claim 17 recites identifying alternative sequences for the biopharmaceutical protein or vaccine which do not contain epitope mimics.
Kanduc teaches “no-similarity segments” (pg. 293, col. 2, last paragraph), where an epitope mimic is interpreted as requiring a similar sequence and thus a no-similarity segment would not contain the epitope mimic.
Claim 18 recites the protein of interest is a biopharmaceutical protein or vaccine.
Kanduc teaches vaccine preparation (pg. 293, col. 2, last paragraph).
Claim 18 recites analyzing the biopharmaceutical protein or vaccine.
Kanduc teaches vaccine preparations based on segment similarity (pg. 293, col. 2, last paragraph), where analysis reads on determining segment similarity.
Claim 18 recites identifying potential epitope mimics in the human proteome. Parent claim 1 recites determining potential epitope mimics.
Claim 18 recites preparing a report identifying a spectrum of possible pathophysiologic interactions of the biopharmaceutical protein or vaccine.
Kanduc teaches the potential of side harmful cross reactions (pg. 293, col. 2, last paragraph), where pathophysiologic interactions reads on harmful cross reactions.
Claim 19 recites determining by comparison with epitope mimic matches identified in the human
proteome which other species have identical core peptides in their proteome proteins which are homologous in function to those in the human proteome that carry the core peptides matching said core peptides in said protein of interest.
Kanduc teaches similarity between peptide epitopes to the human proteome (abstract), where the comparator sequence is necessarily from a non-human proteome.
Camon teaches determining common properties from gene products from different species (pg. 662, col. 1, second paragraph), where homology of function is interpreted as reading on a common property.
Claim 19 recites selecting an animal model to study a disease or to test a vaccine or biopharmaceutical protein.
Berglund teaches “to generate antibodies toward proteins from other species than humans, such as mouse, rat, dog, or primates” (pg. 612, col. 2, first paragraph) for generating antibodies, and thus is interpreted as selecting an animal model for studying a disease.
Combining Berglund, Camon, Rubinstein, and Kanduc
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention.
One would have been motivated to combine the work of Berglund, which teaches comparing similarity of a query protein sequence to the entire human proteome, with the work of Camon, which teaches automatic annotation of genes in a database, because Camon the advantages of a dynamic, controlled vocabulary applied to protein databases to describe gene products in a standardized way (pg. 662, col. 1, last paragraph). A practitioner would recognize that the combination of the human proteome data of Berglund and the protein annotation of Camon would successfully result in a method of creating a database of core epitope sequences in the human proteome, screening therapeutic peptide sequences against this database, and displaying functional annotations of the proteins in the proteome that match subsequences of the therapeutic peptide.
One would be further motivated to combine with the work of Rubinstein because Rubinstein teaches detection of candidate B-cell epitopes (abstract), and Berglund teaches predicting B-cell epitopes (pg. 607, col. 1, second and third paragraphs). Rubinstein teaches a B-cell epitope prediction procedure that performs better than previous procedures that were inadequate for the method of Berglund. Given that both Berglund and Rubenstein are directed to predicting epitopes and immunogenicity from protein sequence, said practitioner would have readily predicted that the combination would successfully result in a method of creating a database of core sequences of linear B-cell epitopes in the human proteome.
Finally, one would be motivated to combine with the work of Kanduc because Kanduc teaches correlating a query and database entry based on a core 5-mer, where such a 5-mer would be desirable because “pentapeptides are minimal structural units critically involved in immune recognition” (pg. 289, col. 2, third paragraph). The previously combined art is concerned with immune recognition in the comparison of a query to a database of proteins, and a practitioner would recognize the strength of use of the minimally sized unit for search for matches.
Therefore, the invention is prima facie obvious.
Claims 11 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Berglund in view of Camon, Rubinstein, and Kanduc as applied to claims 1-10, 12-13, and 16-19 above and further in view of Alam-Faruque (Plos One 6(12): 9 pgs., 2011; newly cited).
Claim 11 recites said key words define a group of proteins with neurophysiological function.
Alam-Faruque teaches “negative regulation of neurogenesis” as a keyword (pg. 2, col. 1, first paragraph).
Claim 14 recites said key words define a group of proteins which function in inflammation.
Alam-Faruque teaches the gene ontology keyword “inflammatory response” (pg. 2, col. 1, last paragraph).
Combining Berglund, Camon, Rubinstein, Kanduc, and Alam-Faruque
The previously combined work, and in particular Camon, teaches a gene ontology in which descriptors or annotations are applied to describe molecular functions, processes, and components (pg. 662, col. 1, third paragraph). These descriptors or keywords include items such as enzyme or enzyme function, immunity protein, and more (pg. 670, Fig. 4). Alam- Faruque teaches further ontology keywords related to neurophysiology and inflammation. Both are simply descriptors for a protein used in classification. It would be obvious to one of ordinary skill in the art to apply different descriptors based on the disease condition in question with predictable results. Therefore, the invention is prima facie obvious.
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Berglund in view of Camon, Rubinstein, and Kanduc as applied to claims 1-10, 12-13, and 16-19 above and further in view of Feng (European Review of Medical and Pharmacological Sciences 19: 736-744, 2015; newly cited).
Claim 15 recites said key words define a group of proteins which have a function in arthritis.
Feng teaches determining differentially expressed genes in individuals with osteoarthritis (pg. 736, col. 2, last paragraph), which would result in proteins with a function in arthritis.
Combining Berglund, Camon, Rubinstein, Kanduc, and Feng
The previously combined work, and in particular Camon, teaches a gene ontology in which descriptors or annotations are applied to describe molecular functions, processes, and components (pg. 662, col. 1, third paragraph). These descriptors or keywords include items such as enzyme or enzyme function, immunity protein, and more (pg. 670, Fig. 4). Feng teaches further ontology keywords related to arthritis. The keywords are simply descriptors for a protein used in classification. It would be obvious to one of ordinary skill in the art to apply different descriptors based on the disease condition in question with predictable results. Therefore, the invention is prima facie obvious.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Berglund in view of Camon, Rubinstein, and Kanduc as applied to claims 1-10, 12-13, and 16-19 above and further in view of Doores and Davies (Immunology and Cell Biology 75: 113-126, 1997; newly cited).
Claim 20 recites providing a synthetic protein derived from the human protein which comprises epitope mimic peptides.
Doores teaches to design and synthesize a template-assembled oligomannose cluster to mimic the proposed 2G12 epitope (pg. 662, col. 1, first paragraph), interpreted as a protein comprising an epitope mimic.
Claim 20 recites contacting said synthetic protein with serum harvested from a subject at risk of being affected by an autoimmune disease and identifying the presence of antibodies with specific binding to mimic epitopes in said synthetic protein, thereby identifying the epitope mimics giving rise to an autoimmune disease.
Davies teaches inducing an autoimmune disease using epitope mimics in a host protein (pg. 113, col. 1, first paragraph), including teachings of host sera (Table 1) which would require contact.
Combining Berglund, Camon, Rubinstein, Kanduc, Doores, and Davies
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the previously combined works with those of Doores because Doores teaches analysis of a synthetic epitope mimic to validate a mimic selection process (pg. 662, col. 1, first paragraph), which involves contact with the serum and antibody detection, which is considered to be the natural next step after designing the epitopes as taught by Berglund. Further combination with Davies, which teaches inducing autoimmune responses using epitope mimics, would be useful because “a mimicking antigen sufficiently different from self proteins as to avoid tolerance, yet similar enough to self epitopes as to cross-react, primes a B cell that may produce antibodies that cross-react with a self protein” (pg. 121, col. 1, last paragraph) and would be useful for screening subjects for risk of autoimmunity (pg. 122, col. 1, first paragraph). The prior art is directed to the shared field of endeavor of epitope design and screening, and thus would be expected to succeed. The invention is considered prima facie obvious.
Conclusion
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/Robert J. Kallal/Examiner, Art Unit 1685