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 Response
Applicant’s response, filed 10/27/2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn.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.
Claims Status
Claims 2-6 and 8-12 are canceled.
Claims 1, 7, and 13-15 are pending.
Claims 1, 7, and 13-15 are examined.
Withdrawn Objections/Rejections
The rejection of claims 1, 4-7, and 10-15 under 35 USC 112(a) is withdrawn in view of the amendments submitted.
The rejection of claims 1, 4-7, and 10-15 under 35 USC 112(b) from the Office Action mailed 06/27/2025 is withdrawn in view of the amendments submitted.
The rejection of claims 1, 7, 13, and 14 under 35 USC 102(a)(2) over Wang et al. is withdrawn in view of the amendments submitted.
The rejection of claim 15 under 35 USC 103 over Wang et al. in view of Pandolfi et al. is withdrawn in view of the amendments submitted.
Claim Objections
Claim 15 is objected to because of the following informalities:
In claim 15, “the gene is NFKBIE gene or PAK 1” should read “the gene is NFKBIE
Appropriate correction is required.
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, 7, and 13-15 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
With respect to claims 1, 7, and 13, the claims recite the limitation of “selecting the single gene as a companion diagnostic biomarker”. The claims are indefinite because it is unclear which gene is being selected, if it is the “single gene” use to divide the patient group, or if instead a gene that is compared is selected, because the comparison step does not recite a gene and simply states comparing the prognostic association values.
With further respect to claims 1, 7, and 13, in claim 1 line 27, claim 7 line 26 and claim 13 line 24, the claims reiterate “wherein the prognostic association value is calculated based on gene expression levels, disease recurrence periods, and recurrence status”. This limitation is already recited in the calculating step, and thus it is unclear in what manner the claim is being limited.
With respect to claim 15, the claim recites the limitation of “wherein the gene is NFKBIE gene or PAK1 gene”. The claim is indefinite because it is unclear which gene is being referred to. Claim 13, from which claim 15 depends, recites “specifying a single gene and dividing”, “calculating, for each gene among all genes”, and “selecting the single gene as a companion diagnostic biomarker”. Thus, it is unclear which gene is being limited.
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, 7, and 13-15 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more. Any newly recited portion is necessitated by claim amendments.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims recite a system and methods.
With respect to step (2A)(1): The claims recite abstract ideas of mental processes and mathematical concepts.
“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). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mental processes recited in claims 1 and 7:
specifying a single gene and dividing patient into a high-expression patient group and a low-expression patient group with respect to the single gene based on a reference expression value comprising an average value or a StepMiner threshold
selecting the single gene as a companion diagnostic biomarkers based on the comparison
selecting a novel target protein based on the prognostic association value in the high-expression patient group or the low-expression patient group based on the biomarkers
Mathematical concepts recited in claims 1 and 7:
calculating, for each gene among all genes represented in gene expression profiles of the patients, a prognostic association value based on gene expression levels, disease recurrence periods, and recurrence status, separately within the high-expression patient group and the low-expression patient group, using a method selected from a long-rank test, a Cox hazard ratio, or an iterative patient portioning method, to generate a set of prognostic association values of all genes for the high-expression group and a set of prognostic association values of all genes for the low-expression group
comparing the set of prognostic association values of the high-expression patient group with the set of prognostic association values of the low-expression patient group using a method selected from a Pearson correlation coefficient, a Euclidean distance, a Mahalanobis distance, or a Tanimoto coefficient
wherein the prognostic association value is calculated based on gene expression levels, disease recurrence periods, and recurrence status
Mental processes recited in claim 13:
specifying a single gene and dividing a high-expression patient group and a low-expression patient group with respect to the single gene based on a reference expression value comprising an average value or a StepMiner threshold
selecting the single gene as a companion diagnostic biomarker based on the comparison
selecting a novel targeting protein based on the prognostic association value in the high-expression patient group or the low-expression patient group
Mathematical concepts recited in claim 13:
calculating, for each gene among all genes represented in gene expression profiles of the patients, a prognostic association value based on gene expression levels, disease recurrence periods, and recurrence status, separately within the high-expression patient group and the low-expression patient group, using a method selected from a log-rank test, a Cox hazard ratio, or an iterative partitioning log-rank test, to generate a set of prognostic association values of all genes for the high-expression patient group and a set of prognostic association values of all genes for the low-expression patient group
comparing the set of prognostic association values of the high-expression patient group with the set of prognostic association values of the low-expression patient group using a method selected from a Pearson correlation coefficient, a Euclidean distance, a Mahalanobis distance, or a Tanimoto coefficient
wherein the prognostic association value is calculated based on gene expression levels, disease recurrence periods, and recurrence status
Dependent claims 14 and 15 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claim 12 and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claim 14: “wherein the disease is cancer”
Claim 15: “wherein the gene is NFKBIE gene or PAK1 gene”
The abstract ideas in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes and mathematic concepts because the claims recite no more than the comparison of data in order to select a characteristics by which to sort it with.
With respect to step (2A)(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone or in combination to determine if the judicial exception is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exception, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
Claims 1 and 7 recite the following additional elements that are not abstract ideas:
one or more processors
Claim 13 recites the following additional elements that are not abstract ideas:
treating the patient by administering a therapeutic agent that targets the novel target protein to the patient
The element of one or more processors is directed to generic computer elements. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. ... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)). With respect to claim 13, although the claim recites a specific treatment, the treatment does not integrate all of the judicial exceptions into a practical application. The therapeutic agent is administered based on it targeting the novel target protein, however, the step of selecting a novel target protein and the step of “selecting the single gene as a companion diagnostic biomarker” do not connect with each other. Therefore, the treatment application does not fully integrate the judicial exceptions into a practical application.
None of the dependent claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application. Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims will be analyzed under step (2B) to determine if the claims amount to significantly more than the judicial exception.
Lastly, the claims have been evaluated with respect to step (2B): Under said analysis, Applicant is reminded that the judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.07(a).III, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106.05(d).II as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claims 1 and 7: The additional element of one or more processors does not rise to the level of significantly more than the judicial exception. With respect to the generic computer elements, as exemplified in the MPEP at 2106.05(f) with reference to Alice Corp. 573 US at 223, 110 USPQ2d at 1983 “claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible”. Therefore, the device constitutes no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the abstract idea (see MPEP 2105(b)I-III). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
With respect to claim 13: The additional element of treating the patient by administering a therapeutic agent that targets the novel target protein to the patient does not rise to the level of significantly more than the judicial exception. The prior art to Yang et al. (“Overexpression of PAK1 Correlates with Aberrant Expression of EMT Markers and Poor Prognosis in Non-Small Cell Lung Cancer”, Journal of Cancer, June 2017) discloses routine of treating cancer (page 1484, column 2). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found lacking.
Response to Arguments
Applicant states that the claims “are expressly limited to computer-implemented methods and system (‘one or more processors configured to…’) or therapeutic method (‘treating the patient by administering a therapeutic agent’). The claims therefore recite a concrete technological process of processing patient gene expression profiles and clinical recurrence data to concurrently discover a companion diagnostic biomarker and a novel target protein”.
It is respectfully submitted that this is not persuasive. It is the additional elements of the claims that are analyzed to determine whether the claims are integrated into a practical application (MPEP 2106.04(d).I; MPEP 2106.05(a-h)). The use of a computer to implement the method is not sufficient to integrate the claims into a practical application (see MPEP 2106.05(f)). Regarding claim 13, the treatment does not integrate all of the judicial exceptions into a practical application. The therapeutic agent is administered based on it targeting the novel target protein, however, the step of selecting a novel target protein and the step of “selecting the single gene as a companion diagnostic biomarker” do not connect with each other. Therefore, the treatment application does not fully integrate the judicial exceptions into a practical application. Thus, the rejection under 35 USC 101 is maintained.
Furthermore, Applicant states that the claims are not “directed to mere ‘mathematical relationships’ but to generating sets of prognostic association values for high-expression and low-expression patient groups, comparing those sets using specified statistical methods (Pearson correlation, Euclidean distance, Mahalanobis distance, Tanimoto coefficient), and selecting biomarker and target protein candidates based on those results. These are particular data processing steps integrated into a technological process, analogous to Enfish v. Microsoft, 822 F.3d 1327 (Fed. Cir. 2016), where a new data structure rendered the claims patent-eligible.”
It is respectfully submitted that this is not persuasive. The technological process recited in the claims is interpreted as applying judicial exceptions to a generic computer. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc. ... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)). Therefore, the rejection under 35 USC 101 is maintained.
Furthermore, Applicant states that “Claim 13 further recites ‘treating the patient by administering a therapeutic agent that targets the novel target protein to the patient.’ This step ties the discovery process to a concrete therapeutic application, directly analogous to Vanda Pharmaceuticals v. West-Ward, 887 F.3d 1117 (Fed. Cir. 2018), where treatment claims applying biomarker-based patient stratification were found eligible. Therefore, the amended claims are not directed to abstract ideas but to a specific technological process with real-world medical application, satisfying Step 1 and Step 2A/2B of the Alice/Mayo framework.”
It is respectfully submitted that this is not persuasive. Although claim 13 recites a specific treatment, the treatment does not integrate all of the judicial exceptions into a practical application. The therapeutic agent is administered based on it targeting the novel target protein, however, the step of selecting a novel target protein and the step of “selecting the single gene as a companion diagnostic biomarker” do not connect with each other. Therefore, the treatment application does not fully integrate the judicial exceptions into a practical application and the rejection under 35 USC 101 is maintained.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1 and 7 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Guo et al. (“Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival”, Artificial Intelligence in Medicine, June 2012). This is a new grounds of rejection as necessitated by claim amendments clarifying claim limitations.
Regarding claims 1 and 7, Guo et al. teaches a method for discovering a novel target protein and a companion diagnostic biomarker therefor, comprising:
specifying a gene and dividing the expression for each patient into up-regulated and down-regulated expression groups based on a reference expression value comprising an average value between (page 99, column 2, paragraph 2);
calculating, for each gene of the 6 genes differentially expressed, a prognostic association value based on gene expression levels, disease recurrence periods, and recurrence status, separately within the up-regulated and the down-regulated group using a Cox proportional hazard model (page 100, column 2, Section 3.5);
comparing the set of prognostic association values of the up-regulated and down-regulated group using a Pearson correlation coefficient (page 104, column 1, Section 3.8; Abstract, Results);
selecting the single gene as a companion diagnostic biomarker based on the comparison (Figure 6; page 104, column 1, Section 3.8);
selecting a novel target proteins based on the prognostic association value in the up-regulated group or the down-regulated group (page 102, column 2, Section 3.7; page 104, column 1, Section 3.8).
Furthermore, Guo et al. teaches a computer-implemented method as evidenced by the use of computer algorithms (page 98, column 1, paragraph 2) and thus inherently teaches a system comprising a processor configured to perform the method steps.
Response to Arguments
Arguments pertaining to the rejection under Wang are considered moot, as a new rejection is set forth in view of the amendments submitted clarifying the steps recited in the claims.
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.
Claims 13 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Guo et al., as applied to claims 1 and 7 above. This is a new grounds of rejection as necessitated by claim amendments.
Regarding claim 13, Guo et al. teaches a method for discovering a novel target protein and a companion diagnostic biomarker therefor, comprising:
specifying a gene and dividing the expression for each patient into up-regulated and down-regulated expression groups based on a reference expression value comprising an average value between (page 99, column 2, paragraph 2);
calculating, for each gene of the 6 genes differentially expressed, a prognostic association value based on gene expression levels, disease recurrence periods, and recurrence status, separately within the up-regulated and the down-regulated group using a Cox proportional hazard model (page 100, column 2, Section 3.5);
comparing the set of prognostic association values of the up-regulated and down-regulated group using a Pearson correlation coefficient (page 104, column 1, Section 3.8; Abstract, Results);
selecting the single gene as a companion diagnostic biomarker based on the comparison (Figure 6; page 104, column 1, Section 3.8);
selecting a novel target proteins based on the prognostic association value in the up-regulated group or the down-regulated group (page 102, column 2, Section 3.7; page 104, column 1, Section 3.8).
Furthermore, Guo et al. teaches that molecular network analyses can be used to identify disease genes and discover novel therapeutic targets (page 98, column 1, paragraph 1).
Although Guo et al. does not explicitly teach the claim elements of treating the patient by administering a therapeutic agent that targets the novel target protein, Guo et al. does teach that molecular network analyses can be used to identify disease genes and discover novel therapeutic targets (page 98, column 1, paragraph 1). Thus, it would have been prima facie obvious to one of ordinary skill in the art to use the method of Guo et al. to identify a target protein and then administering the therapeutic agent for this protein.
Regarding claim 14, the claim is directed to the disease being cancer. Guo et al. teaches the method of claim 13. Guo et al. also teaches the disease being lung cancer (Abstract).
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Guo et al., as applied to claims 1, 7, 13, and 14 above, in view of Yang et al. (“Overexpression of PAK1 Correlates with Aberrant Expression of EMT Markers and Poor Prognosis in Non-Small Cell Lung Cancer”, Journal of Cancer, June 2017). This is a new grounds of rejection as necessitated by claim amendments.
Regarding claim 15, the claim is directed to the gene being NFKBIE or PAK1. Guo et al. teaches the method of claim 13.
Guo et al. does not teach the claim element of the gene being NFKBIE or PAK1.
However, Yang et al. teaches that overexpression of PAK1 correlates with aberrant expression of EMT markers and poor prognosis in non-small cell lung cancer (abstract). Yang et al. teaches that PAK1 and EMT are key therapeutic targets in cancer (Abstract, Objective) and teaches that PAK1 may promote NSCLC progression and metastasis through EMT, thereby exhibiting the potential of an efficient prognostic predictor in NSCLC patients (Abstract, Conclusion).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have incorporated PAK1 as a gene biomarker to the method of Guo et al. because Guo et al. is directed to analyzing coexpression of genes in lung cancer (Abstract), specifically with regard to NSCLC (page 99,column 1, paragraph 1) and Yang et al. is directed to analyzing the correlation between two genes in NSCLC (Abstract). Thus, one of ordinary skill in the art would have had a reasonable expectation of success in combining the prior art references to analyze correlated genes in NSCLC and would have been motivated to analyze PAK1 and its correlation with EMT because these are key therapeutic targets in cancer, as taught by Yang et al.
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Emilie A Smith whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D Riggs can be reached at (571)270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/E.A.S./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686