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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 03/30/2026 has been entered.
Applicant's amendments and remarks, filed 03/30/2026, 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 Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.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 1-12 and 14-17 are under examination. Claim 13 is cancelled.
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.
Withdrawn Rejections
The rejection of claims 1-17 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112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement (for new matter) is withdrawn in view of applicant’s amendments.
The rejection of claims 1-17 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 (PLoS ONE, 2013, 8(2):e55582, pp.1-10) is withdrawn in view of applicant’s amendments.
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.
The following rejection is modified in view of applicant’s amendments.
Claims 1-3, 5-12 and 14-17 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 with a pangenome (PG) model that is a decision tree, random forest, neural network, bayesian classification, or support vector machine…;
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 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 is a decision tree, random forest, neural network, bayesian classification, or support vector machine 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, wherein the PG model is for one or more…, 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 is a decision tree, random forest, neural network, bayesian classification, or support vector machine 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, wherein the PG model is for one or more…, 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 that is 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;
e) treating the patient for the infection with the microorganism with said one or more antimicrobial drugs identified as suitable for the treatment… (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).
With regard to the “treating” step (claim 8), this 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, 9-12, 14-17 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, 9-12, 14-17, 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 03/30/2026, 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 by using a PG model to determine an antimicrobial resistance drug profile, and further asserts that the claimed model is not well understood. In response, neither Applicant nor the specification provides any objective evidence of an improvement to the technology, nor does the specification explain the details of an unconventional technical solution expressed in the claim, or identify technical improvements realized by the claim over the prior art. See MPEP 2106.04(d)(1) and MPEP 2106.05(a). Furthermore, the steps for “determining” an antimicrobial resistance profile (as well as the PG model) have been interpreted as part of the abstract idea (Step 2A, prong 1) and applicant is essentially arguing that the inventive concept is the abstract idea. However, it 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 also 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.
Applicant additionally argues that claim 8 is patent eligible in view of the amendments to clarify the step of “treating” the patient. In response, this step does not recite a particular treatment for the reasons set forth above (Step 2A, prong 2). 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 at least these reasons, the rejection is maintained.
In the interest of advancing prosecution, it is noted that claim 4 is not rejected under 35 USC 101 since it recites particular drugs. For a list of considerations when evaluating whether additional elements integrate a judicial exception into a practical application see MPEP 2106.04(d)(1) lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
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 1-12 and 14-17 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 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:
Claim 1 recites, inter alia, obtaining or providing a data set of coding and non-coding nucleic acid sequences of a plurality of clinical isolates of the microorganism, wherein at least a part of the nucleic acid sequences of the data set are assembled; and/or obtaining or providing a data set of coding and non-coding nucleic acid sequences of a plurality of clinical isolates of the microorganism and aligning the nucleic acid sequences of the data set of nucleic acid sequences to at least one reference sequence;- analyzing the nucleic acid sequences of the data set of coding and non-coding 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 data set of structural variants; providing a 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 with a pangenome (PG) model that is a decision tree, random forest, neural network, bayesian classification, or support vector machine, wherein the PG model is for one or more Acinetobacter, Escherichia, Enterobacter, Klebsiella, Proteus, Pseudomonas,Salmonella, Serratia, Shigella and/or Staphylococcus species…;
With regards to the “obtaining” and “analyzing” steps, it is unclear how the “coding” and “non-coding” nucleic acid sequence data of a plurality of clinical isolates is actually being obtained. The claims are not limited to any particular acts or operations, nor are they limited to any particular sequences. A review of the specification fails to provide any evidence of techniques necessary for obtaining such information. Moreover, one of ordinary skill in the art would recognize that discriminating coding from non-coding nucleic acid has become an important biological and computational problem that is generally achieved through computational/bioinformatics analysis (see, e.g. Liu et al., PLoS Genet, 2006, 2(4): e29, pp.529-536). However, a review of the specification does not provide any significant details with regards to how the reader is actually obtaining/identifying coding and non-coding sequence data for use in determining antimicrobial drug resistance. As a result, it is also unclear how the practitioner would be able to analyze the coding and non-coding data in order to obtain “structural variants”. A review of the specification fails to provide any evidence of computational techniques necessary for obtaining such information, and fails to provide any evidence that applicant has sufficient knowledge of the structural variants associated with coding and non-coding sequence data, as claimed. As such, the instant specification fails to provide evidence of physical and/or computational methods for achieving the above functions for the full scope of microorganisms being claimed.
With regards to the ‘analyzing’ and ‘correlating’ steps, the claims are still not limited to any particular genetic variants (e.g. SNPs) or structural variants (e.g. CNVs). A review of the specification does not provide sufficient correlations between the full scope of variants and drugs being claimed, i.e. what variants confer antibiotic resistance. One of ordinary skill in the art would recognize that knowledge of such information 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. As such, the instant specification fails to provide evidence of genetic and structural variations for achieving the above functions for the full scope of microorganisms being claimed.
Claims 1, 6, and 8 recite “pangenome (PG) model...is a decision tree, random forest, …” in order to achieve the functions of analyzing the correlation and determining a drug resistance profile (claim 1) and determining generic variations (claims 6 and 8). In each case, a review of the specification lacks sufficient details with regards to the “pangenome model” and does not provide any significant structural or functional details with regards to how it was trained, validated, or how this model operates. The specification does describe a “statistical model” in terms of SVMs, decision trees, etc. [page 35], but this disclosure is not associated with the claimed “PG model” in any form or fashion and does not amount to a sufficient disclosure of a mathematical relationship between data and parameters which define the model (since the artisan would recognize that decision trees, random forests, etc. are all structurally distinct models). The specification additionally teaches that the term “PG model” generally refers to a model that takes into account both chromosomal and plasmid nucleic acid sequences [pages 42, 50], but this also does not amount to a sufficient disclosure of a mathematical relationship between data and parameters which define the model. Therefore, the specification does not establish a reasonable structure-function correlation between the model, data, and the intended function for the full scope of what is being claimed.
Claim 8 further recites “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 for the infection with the microorganism with said one or more antimicrobial drugs identified in d) as suitable for the treatment of the infection with the microorganism.” In this case, the claims are not limited to any particular drugs or means for identifying said drugs. As such, it is unclear how one of skill in the art “identifies” and “selects” which drugs are suitable for treating the full scope of infections encompassed by the claims. There is no evidence that applicant has actually disclosed sufficient correlations between genetic and/or structural variants and drugs that are suitable as treatments. 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, Tables 2-7, wherein only columns 4 and 5 refer to the “PG model”]. In addition, 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 varies depending on the type of drugs. 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 variants and drugs 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 03/30/2026, have been fully considered but are moot in view of the modified rejection as set forth above.
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 1-12 and 14-17 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 from claims 1, 6, 8 are also rejected herein due to said dependency.
Claim 1 recites “analyzing the nucleic acid sequences of the data set of coding and non-coding 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 data set of structural variants”. Such generic functional claim language amounts to descriptions of problems to be solved and/or functions, and covers all means or methods of performing the claimed functions. The specification teaches constructing pangenomes for purposes of determining genetic variants [page 38]. However, this is not commensurate in scope with what is claimed and it is improper to import narrowing limitations from the specification. MPEP 2111.01. It is additionally noted that claims 6 and 8 state the use of a “PG Model” for determining genetic variations. However, this is also not what is being claimed (in claim 1). Therefore, the claim(s) is/are indefinite for failing to point out the requisite computational techniques that are included or excluded by the claim language, such that the artisan would know how to avoid infringement. In addition, genetic variants are distinct from structural variants. Therefore, it is also unclear what limiting effect is intended by the intended-use phrase “…to obtain a data set of structural variants”, as this does not impose any limiting effect on the nature of the genetic variant. Clarification is requested via amendment.
Claims 1, 6, and 8 recite “pangenome (PG) model...is a decision tree, random forest, …”. In this case, it is unclear as to the metes and bounds of the claimed “pangenome model”, i.e. in what way is this model actually using or modeling pangenomic data. A review of the specification does not provide any limiting definition for this term that would serve to establish any mathematical relationship between data and parameters which define the model. The specification teaches that the term “PG model” generally refers to a model that takes into account both chromosomal and plasmid nucleic acid sequences [pages 42, 50] and also separately describes various types of “statistical model” (e.g. SVMs, decision trees, etc.) [page 35] and generating an ‘optimized model’ using decision tree analysis [page 47]. However, the later description is not associated with the claimed “PG model” in any form or fashion, and the artisan would recognize that decision trees, random forests, etc. are all structurally distinct models. Therefore, the claim(s) is/are indefinite for failing to clarify the boundaries of the claimed model such that the artisan would know how to avoid infringement. Clarification is requested via amendment.
Claims 1, 6, 8 recite “wherein the PG model is for one or more Acinetobacter, Escherichia, Enterobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Serratia, Shigella and/or Staphylococcus species.” In this case, the phrase “for one or more…” is an intended use recitation and applicant is reminded that intended use recitations impose no patentable distinction. Moreover, this limitation appears to further limit the type of microorganisms used by the claim (and not the nature of the model). As a result, it is unclear what structural and/or functional limitation of the claims “PG model” is intended by the above “wherein” clause, i.e. in what way is the model “for” a particular microorganism. Clarification is requested via amendment.
Claim 2 recites “wherein the genetic variations are annotated to a pan-genome”. It is unclear what positive process limitation is intended by the above “wherein” clause, which suggests an additional step (i.e. gene annotation) without explicitly requiring any such step. More specifically, 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 pangenome. Notably, the instant specification teaches that a pangenome must be constructed [page 24]. However, such limitations are not commensurate in scope with what is being claimed and Applicant is reminded that claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed. MPEP 2111.04. Therefore, it is unclear in what way the above “wherein” clause further limits the method of claim 1. Clarification is again requested via amendment. This rejection is maintained as applicant has not provided any illuminating arguments or clarifying amendments.
Examiner’s Comment
In the interest of advancing prosecution and clarifying the claimed invention, the examiner suggests the following amendments:
Amending claim 8 to include limitations from claim 2
Amending claim 8 to include limitations directed to constructing a pan-genome and mapping a model against the pan-genome [Specification, pages 40].
Amending claim 8 to include Deleting claims 1-7 (as they appear to be fully encompassed by claim 8 and/or incorporate problematic limitations for reasons set forth above, 35 USC 112b)
Conclusion
No claims are allowed.
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
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