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 .
Applicant's amendments and remarks, filed, 07/25/2025, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of Claims
Claims 1-17 are presently under examination.
Claims 12-17 are newly added.
Priority
This application is a continuation of U.S. Patent Application Number 16/093,396, filed 10/12/2018 (and abandoned on 02/08/2024), which is a National Stage Entry of International Application Number PCT/EP2017/058866, filed 04/12/2017, and claimed priority to European Patent Application No. 16165319.1, filed on 04/14/2016.
Information Disclosure Statement
After careful consideration, the information disclosure statement filed 07/25/2025 is in compliance with 37 CFR 1.98(a)(2). The examiner has found legible copies of the cited references in parent application 16/093,396.
Specification
The amended specification filed 07/25/2025 is acceptable.
Claim Rejections - 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 1-17 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Guidance Step 1:
Under the broadest reasonable interpretation, the claimed invention is directed to a method of determining an antimicrobial resistance drug profile (claims 1, 6, and 8 being representative). Therefore, the claims fall into one of the four statutory categories.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the claimed invention includes the following steps that encompass an abstract idea for the following reasons:
Claim 1
analyzing the nucleic acid sequences of the first data set of nucleic acid sequences for at least two genetic variations of the nucleic acid sequences comprising at least one genetic variation in a chromosome and at least one genetic variation in at least one plasmid to obtain a third data set of structural variants;- providing a second data set of antimicrobial drug resistance and/or susceptibility of the plurality of clinical isolates of the microorganism;
correlating the data set of structural variants with the data set of antimicrobial drug resistance and/or susceptibility and statistically analyzing the correlation to develop a pangenome (PG)model using a decision tree, random forest, neural network, bayesian classification, or support vector machine approach;
determining with the PG model an antimicrobial drug resistance profile for the microorganism comprising the genetic variations in the nucleic acid sequences of the microorganism associated with antimicrobial drug resistance
Claim 6
determining with a pangenome (PG) model the presence of at least two genetic variations of the nucleic acid sequences comprising at least one genetic variation in the chromosome and at least one genetic variation in at least one plasmid, wherein the PG model was developed from correlation of a data set of structural variants with a data set of antimicrobial drug resistance and/or susceptibility and statistical analysis of the correlation using a decision tree, random forest, neural network, bayesian classification, or support vector machine, wherein the presence of said at least two genetic variations of the nucleic acid sequences comprising at least one genetic variation in the chromosome and at least one genetic variation in at least one plasmid is indicative of an infection with an antimicrobial drug resistant microorganism in said patient.
Claim 8
b) determining with a pangenome (PG) model the presence of at least two genetic variations of the nucleic acid sequences comprising at least one genetic variation in the chromosome and at least one genetic variation in at least one plasmid, wherein the PG model was developed from correlation of a data set of structural variants with a data set of antimicrobial drug resistance and/or susceptibility and statistical analysis of the correlation using a decision tree, random forest, neural network, bayesian classification, or support vector machine, wherein the presence of said at least two genetic variations of the nucleic acid sequences comprising at least one genetic variation in the chromosome and at least one genetic variation in at least one plasmid is indicative of a resistance to one or more antimicrobial drugs;
c) identifying said at least one or more antimicrobial drugs;
d) selecting one or more antimicrobial drugs different from the ones identified in step c) and being suitable for the treatment of the infection with the microorganism; and e) treating the patient with said one or more antimicrobial drugs identified in d).
Mental Processes
In this case, the above italicized steps are all nominally recited without any details specifying how these functions are being performed and generally encompass performing analysis and/or calculations, and making decisions based on said analysis. In addition, Accordingly, the above steps clearly fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III [Step 2A, Prong 1: YES].
Mathematical Concept
In this case, above correlating and determining steps require developing a model using a decision tree, random forest, neural network, bayesian classification, or support vector machine which one of ordinary skill in the art would recognize as mathematical concepts. This position is also supported by applicant’s own specification [page 47], which shows mathematical models run using software packages. As such, these steps require mathematical concepts and/or mathematically relating data. Therefore, when read in light of applicant’s own specification, the claims are directed to a mathematical concept. See MPEP 2106.04 and 2106.05(II). [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception. In this case, the claimed steps that are not part of the abstract idea are as follows:
obtaining or providing a data set of nucleic acid sequences of a plurality of clinical isolates of the microorganism, wherein at least a part of the nucleic acid sequences of the first data set are assembled; obtaining and/or providing a data set of nucleic acid sequences of a plurality of clinical isolates of the microorganism (claim 1); obtaining or providing a sample containing or suspected of containing a microorganism from the patient; (claim 6); obtaining or providing a sample containing or suspected of containing a microorganism from the patient; (claim 8)
providing a data set of antimicrobial drug resistance and/or susceptibility of the plurality of clinical isolates of the microorganism; (claim 1)
d) selecting one or more antimicrobial drugs different from the ones identified in step c) and being suitable for the treatment of the infection with the microorganism; and e) treating the patient with said one or more antimicrobial drugs identified in d) (claim 8)
Under the broadest reasonable interpretation, the above obtaining, providing, and selecting steps amount to necessary gathering of data for use by the abstract idea and selecting a particular type of data. Therefore, after careful consideration, the above steps amount to “insignificant extra-solution activity”, i.e. activities incidental to the primary process or product that are merely a nominal or tangential addition to the claim. MPEP 2106.05(g). In addition, the “treating” step (claim 8) is not limited to any particular type of “antimicrobial drugs” nor it is associated with a particular disease/disorder (but merely a generically recited infection). The MPEP is clear that in order to qualify as a “treatment” or “prophylaxis” limitation for purposes of this consideration, the claim limitation in question must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. See MPEP 2106.04(d)(2). For example, consider a claim that recites “administering a lower than normal dosage of a beta blocker medication to a patient identified as having the poor metabolizer genotype.” This administration step recites a particular dosage and type of medication and it integrates the mental analysis step into a practical application. In this case, however, the claimed treating step is not particular, and is instead merely instructions to “apply” the exception in a generic way. Accordingly, the claims as a whole do not integrate the abstract idea into a practical application. [Step 2A, Prong 2: NO]
C. Guidance Step 2B:
Under the 2019 PEG, a conclusion that an additional element is insignificant extra-solution activity in Step 2A should be re-evaluated in Step 2B. In this case, the claims do not include additional steps and/or elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons:
As discussed above, the above non-abstract steps amount to nothing more than insignificant extra-solution activity and/or instructions to “apply” the exception in a generic way. Furthermore, it is the examiner’s position that methods for obtaining and aligning DNA sequences were routine and conventional in the art (see, e.g. Zhao et al. (Applied and Environmental Microbiology, 2016, vol. 82, no. 2, pp.459-466). Applicant’s own specification also teaches assays for obtaining sequence data and that drugs for treating infections in microorganisms were routine and conventional [pages 3, 39]. Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract steps. See MPEP 2106.05(d)(Part II). Taken alone or in combination, the additional steps/elements fail to transform the exception into a patent-eligible application of that exception. Therefore, based on the two-part analysis, the claims as a whole are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more. [Step 2B: NO]. For additional guidance, applicant is directed generally to the 2019 Revised Patent Subject Matter Eligibility Guidance published in the Federal Register (84 FR 50).
Dependent Claims
Dependent claims 2, 3, 5, 7, 9-17 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. Regarding claim(s) 2, 3, 5, 7, 9-17, these claims further limit the abstract idea (by adding additional functional limitations) or the nature of the data being used by the abstract idea. Accordingly, these claims are also abstract ideas that are not patent eligible for reasons discussed above (Step 2A, analysis). Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more.
Response to Arguments
Applicant’s arguments, filed 07/25/2025, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the claimed invention does not recite any mental steps because the amended claims recite correlating and determining steps that are beyond the capability of the human mind. In response, this argument is not persuasive since these steps the Office's eligibility guidance does not set limit on the number of calculations that can or cannot be performed mentally. MPEP § 2106.04(a)(2)III. Accordingly, these steps are reasonably interpreted as both a mental process and mathematical concept for reasons set forth above (Step 2A, prong 1).
Applicant additionally argues that the claims provide an improvement to the technology of antimicrobial drug resistance (via predicting drug resistance with improved accuracy). In response, the limitations set forth above have been interpreted as part of the abstract idea (Step 2A, prong 1). Accordingly, applicant is essentially arguing that the inventive concept is the abstract idea (and that the abstract idea is being used to obtain “better data”). However, Applicant is reminded that “[i]t has been clear since Alice that a claimed invention’s use of the ineligible concept to which it is directed cannot supply the inventive concept that renders the invention ‘significantly more’ than that ineligible concept.” BSG Tech LLC v. BuySeasons, Inc., 899 F.3d 1281, 1290 (Fed. Cir. 2018). On this point, the courts have recently instructed that “[t]he different use of a mathematical calculation, even one that yields different or better results, does not render patent eligible subject matter.” Board Of Trustees Of Leland Stanford Junior University, 991 F.3d 1245, 1251 (Fed. Cir. 2021). In summary, while appellant’s particular algorithmic approach may be a particular way to achieve an alternative solution for improving antimicrobial resistance, the claimed invention is, nevertheless, directed to an improved algorithmic analysis. As such, the claims do not integrate the recited judicial exception into a practical application. For at least these reasons, the rejection is maintained
Claim rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(a):
IN GENERAL.—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, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
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 and shall set forth the best mode contemplated by the inventor of carrying out his invention.
This new matter rejection is necessitated by applicant’s amendments.
Claims 1-17 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1, 6, and 8 recite a “pangenome (PG) model” developed using a decision tree, random forest, neural network, bayesian classification, or support vector machine approach. While there is no in haec verba requirement, newly added claims or claim limitations must be supported in the specification through express, implicit, or inherent disclosure. In this case, however, the examiner cannot find support for any such model in the original claims, drawings, or the specification as originally filed, and no basis has been pointed to for these new limitations in applicant's remarks. Therefore, the teachings of the specification are not commensurate in scope with what is being claimed. In the absence of support for the newly recited limitations, these claims and claims dependent thereon are deemed to constitute new matter.
Claim rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(a):
IN GENERAL.—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, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
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 and shall set forth the best mode contemplated by the inventor of carrying out his invention.
This is a written description rejection.
Claims 1-17 rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The written description requirement is separate and distinct from the enablement requirement. The specification must: (1) describe the claimed invention in a manner understandable to a person of ordinary skill in the art, and (2) show that the inventor actually invented the claimed subject matter. In this case, the claimed invention requires, inter alia:
Claims 1, 6, and 8 recite a “pangenome (PG) model” developed using a decision tree, random forest, neural network, bayesian classification, or support vector machine approach. However, a review of the specification does not provide any significant details with regards to how the claimed operations are actually being performed in order to develop the generically recited “PG model”. One of ordinary skill in the art would recognize that methods for developing mathematical models are not trivial and generally involve defining a problem, creating a mathematical representation using variables and equations, solving the equations, validating the model, and then optimizing model parameters to achieve optimal results. See e.g. Marion et al. (An Introduction to Mathematical Modelling, Bioinformatics and Statistics Scotland, 2008, pp.1-35). As such, the claimed “PG model” is essentially a black box and the instant specification fails to provide evidence of a mathematical model capable of determining antimicrobial drug resistance for the full scope of what is being claimed.
Regarding claim(s) 1, 6, 8, it appears that “genetic variations” (associated with antimicrobial resistance) and “structural variants” remain a critical aspect of the invention. However the claims are still not limited to any particular genetic variants and a review of the specification does not provide sufficient correlations between the full scope of variants and drugs being claimed. One of ordinary skill in the art would recognize that knowledge of such information (such that it can be identified or correlated to drug resistance) is not trivial. For example, Zhao et al. (Applied and Environmental Microbiology, 2016, vol. 82, no. 2, pp.459-466) teaches that sequence analysis methods for predicting antimicrobial resistance that require knowledge of specific genetic markers and specific disease phenotypes. Such information is not present in the instant specification. Therefore, the specification does not establish a reasonable structure-function correlation (with the structure is broadly interpreted as the computational techniques and associated data used by the computer system). “[A] sufficient description of a genus . . . requires the disclosure of either a representative number* of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can 'visualize or recognize' the members of the genus” (AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69)(emphasis added).
With regards to the steps for identifying and selecting antimicrobial drugs, these steps are generically recited and cover all means or methods of performing the claimed function without any significant details as to how they are actually being performed. Furthermore, after reading the specification, it immediately becomes unclear how one of skill in the art arbitrarily “identifies” or “selects” which drugs are suitable for treating the full scope of infections encompassed by the claims. As discussed above, there no evidence that applicant has actually disclosed sufficient correlations between genetic variations, disease, and statistical models for identifying drugs that are suitable as treatments for variants that are resistant to said anti-microbial drugs. Moreover, one of ordinary skill in the art would understand that the achieving the goal of determining which drugs are responsive to different genetic variations associated with antimicrobial resistance, as well as a comparative analysis between test and reference datasets (associated with a particular diseases) and data associated with therapeutic responses such that meaningful therapy determinations can be made. In this case, however, specification does not describe, to any appreciable extent, any algorithms or models that achieve this function for the full scope of what is being claimed. At best, the specification describes an example for predicting antimicrobial resistance that is limited to bacterial species, a few different drugs, and two generic models [pages 50-54]. Therefore, it is unclear how the artisan would understand (1) what criteria is being used to identify/select potential drug therapies and (2) what therapies are capable of being suitable for treatment as claimed. As a result, there is insufficient evidence of possession of this information for the full scope of genetic variants, diseases, and therapies encompassed by the claims. The specification does not need to spell out every detail of the invention, but the possession requirement demands that the written description show that the inventor actually invented what is claimed.
For the reasons discussed above, the specification does not satisfy the written description requirement with respect to the full scope of what is being claimed. For more information regarding the written description requirement, see MPEP §2161.01- §2163.07(b).
Response to Arguments
Applicant’s arguments, filed 07/25/2025, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the “determining” step now has sufficient written description in view of the claim amendments (which recite a “PG model”). In response, this argument is not persuasive for the reasons set forth above.
Applicant argues that the specification provides sufficient written description for the “genetic variants” as claimed in view of [0082-0092, 0166]. In response, a review of these sections provides nothing more than qualitative information associated with a number of isolates and a few specific types of isolates. As such, the examiner maintains that the claims are still not limited to any particular genetic variants and a review of the specification does not provide sufficient correlations between the full scope of variants and drugs being claimed.
Applicant argues that the “selecting” step does not lack written description in view of the specification [0132]. In response, this section merely states that the identification of the at least one or more antimicrobial, e.g. antibiotic, drug in step c) is then based on the results obtained in step b) and corresponds to the antimicrobial, e.g. antibiotic, drug(s) that correlate(s) with the structural variations and SNPs. Accordingly, the examiner maintains that this does not amount to sufficient correlations between genetic variations, disease, and statistical models for identifying drugs that are suitable as treatments for variants that are resistant to said anti-microbial drugs for the full scope of what is being claimed. Moreover, one of ordinary skill in the art would understand that the achieving the goal of determining which drugs are responsive to different genetic variations associated with antimicrobial resistance, as well as a comparative analysis between test and reference datasets (associated with a particular diseases) and data associated with therapeutic responses such that meaningful therapy determinations can be made. Accordingly, absent any evidence to the contrary, the rejection is maintained.
Claim rejections - 35 USC § 112
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 1-17 are 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 pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1, 6, 8 is/are also rejected due to said dependency.
Claim 1 recites “correlating the data set of structural variants with the data set of antimicrobial drug resistance and/or susceptibility and statistically analyzing the correlation to develop a pangenome (PG) model using a decision tree, random forest, neural network, bayesian classification, or support vector machine approach.” In this case, it is unclear what limiting effect is intended by the intended use phrase “to develop a pangenome (PG) model using a decision tree…”. Applicant is reminded that intended use recitations do not impose any limiting effect on the method as claimed. In addition, the artisan would understand that algorithms such as decision trees and SMVs are widely used for classification and regression tasks, i.e. they model decisions but do not necessarily result in “developing a model”. As a result, it is also unclear as to the metes and bounds of the claimed “pangenome model” such that the artisan would know how to avoid infringement. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed “model” (in terms structure). Accordingly, the claim is indefinite because it does not provide a discernable boundary on what operations are required to perform the specialized function. Clarification is requested via amendment.
Claims 6 and 8 recite “determining with a pangenome (PG) model the presence of at least two genetic variations of the nucleic acid sequences…, wherein the PG model was developed from correlation of a data set of structural variants with a data set of antimicrobial drug resistance and/or susceptibility and statistical analysis of the correlation using a decision tree, random forest, neural network, bayesian classification, or support vector machine.” In this case, it is unclear as to the metes and bounds of the claimed “pangenome model” such that the artisan would know how to avoid infringement. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed “model” (in terms structure). In addition, it is unclear what limiting effect is intended by the above “wherein” clause. For example, the artisan would understand that algorithms such as decision trees and SMVs are widely used for classification and regression tasks but are do not necessarily result in “developing a model”. Accordingly, the claim is indefinite because it does not provide a discernable boundary on what operations are required to perform the specialized function. Clarification is requested via amendment.
Claim 2 recites “wherein the genetic variations are annotated to a pan-genome”. Firstly, it is unclear as to the metes and bounds of the term “pan-genome” such that the artisan would know how to avoid infringement. A review of the specification teaches that a reference sequence can, for example, be one or more reference nucleic acid sequences, e.g. reference genomes, a pan-genome or one or more centroids. A pan-genome, also referred to as supra-genome, can describe the full complement of genes in a clade, e.g. a certain species in bacteria, which can vary among related strains [0059]. However, contrary to applicant’s arguments, this does not clarify the metes and bounds of the claimed “pan-genome” and applicant is reminded that examples are not limiting definitions. Clarification is requested via amendment. For purposes of applying prior art, this limitation is broadly interpreted as a genome. Secondly, it is unclear what positive process limitation is intended by the above “wherein” clause. In particular, one of ordinary skill in the art would understand that “gene annotation” is performed after a genome is sequenced and assembled, and generically describes the process of identifying and describing the structural and functional elements of a gene. However, in this case, there are no positive process limitations in the claims as written that are directed to sequencing or assembling a genome. Therefore, it is unclear in what way the above “wherein” clause further limits the method of claim 1. Clarification is requested via amendment. This rejection is maintained as applicant has not provided any illuminating arguments or clarifying amendments.
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 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 following rejection is necessitated by amendment.
Claims 1-17 are rejected under 35 U.S.C. 103 as being unpatentable over Stoesser et al. (J Antimicrob Chemother, 2013; 68: 2234–2244) in view of Coelho et al. (PLoS ONE, 2013, 8(2):e55582, pp.1-10).
Stoesser teaches a method for predicting antimicrobial susceptabilities for microorganisms. Regarding claim(s) 1, 6, 8, Stoesser teaches obtaining sequence data from a plurality of clinical isolates including E. coli and K. pneumoniae; sequencing the isolates and mapping the sequence data against reference sequences [Abstract]. Stoesser teaches obtaining genetic loci data and sequence variant data known to be associated with antimicrobial drug resistance data from web-based resources and compiles them into a reference database [page 2235, col. 2]. Stoeser teaches analyzing sequence variations in both chromosomal and plasmid-associated genes using BLAST and correlating them with susceptibility profiles that were established for the clinical isolates with respect to seven commonly used antimicrobials, including amoxicillin, thereby identifying genetic variations that were associated with drug resistance [page 2236, entire, Table 1, Table 2], which reads on correlating variants with antimicrobial drug resistance as claimed. Stoesser also teaches determining genotypic profiles associated with resistance in various microorganisms [page 2241, col. 1].
Stoesser does not specifically teach analyzing the correlation “to develop a PG model” using the various claimed learning algorithms (decision tree, SVM, etc), as in claim 1, or determining with a pangenome (PG) model the presence of at least two genetic variations of the nucleic acid sequences…, wherein the PG model was developed from correlation of a data set of structural variants with a data set of antimicrobial drug resistance and/or susceptibility and statistical analysis of the correlation using a decision tree, random forest, neural network, bayesian classification, or support vector machine. However, applicant is reminded that intended use recitations and product-by-process type limitations directed to how the model was obtained do not impose any limiting effect on the method as claimed. Accordingly, these limitations are not given patentable weight. That being said, Stoesser at a minimum suggests using a “pangenome model” since their method requires using an algorithm (i.e. model) for predicting antimicrobial resistance using a prediction algorithm as discussed above [page 2241, col. 2, page 2242, col. 1], i.e. it achieves the same function, and since the instant claims do not impose any boundaries on the structure of the claimed model. Moreover, Coelho teaches methods for analyzing antibiotic susceptibility using various machine learning algorithms including decision trees [pages 3-4 and Figure 1]. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to alter the method of Stoesser by alternatively using various machine learning algorithms for classifying data, as taught by Coelho, since applying classification analysis would have been well within the capabilities of the artisan and since Stoesser already uses predictive models for processing antimicrobial resistance data. The rationale would have been to use the model that classifies the patient data with the highest accuracy.
Regarding claim(s) 2, Stoesser teaches labelling (i.e. annotating) the genetic variations [page 2240, col. 2 and Table 5]. Regarding claim(s) 3, 4, 5, Stoesser teaches determining resistance to a plurality of different antimicrobial drugs including amoxicillin [Tables 1-5]. Regarding claim(s) 7, 12-17, Stoesser teaches clinical isolates obtained from Escherichia coli and Klebsiella pneumoniae. [Discussion, page 2241]. Regarding claim(s) 8, Stoesser does not specifically teach selecting and treating patients using antimicrobial agents, as claimed. However, drug selection is considered a results-effective variable that is routinely optimizable. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date to have modified the teachings of Stoesser by selecting the drug with the least amount of antimicrobial resistance and treating a patient with said drug since Stoesser already teaches selecting antimicrobial drugs and optimizing the process for clinical applications [Abstract, Tables 1, 2], and since one of skill in the art would recognize that drug selection can easily be optimized based on the information generated by Stoesser. The motivation would have been to improve patient care by providing predictive methods for selecting suitable drugs. Regarding claim(s) 11, Stoesser makes obvious the use of a computer program product since their methods require using a computational algorithm and infrastructure that necessarily requires a suitably programmed computer to achieve functionality [page 2242, col. 2].
Response to Arguments
Applicant’s arguments, filed 07/25/2025, have been fully considered but are moot in view of the newly applied rejection set forth above which is necessitated by amendment.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619