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 .
Election/Restrictions
Applicant’s election of the species (A) the combination of all six of the listed markers as the specific combination in the reply filed on September 9, 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Any reference to Keibish et al in the restriction mailed on July 9, 2026 was done in error and is not relevant to the prosecution of this application.
Claims 1-13 are under consideration in this office action.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(a)-(d) or (f), 365(a) or (b), or 386(a) is acknowledged. The application is the national stage entry of PCT/EP2022/066456, which claims benefit to CH00752/21, filed June 29, 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on December 27, 2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS is being considered by the examiner.
Claim Objections
Claims 1-13 are objected to because of the following informalities:
Claims 1-3, 10, and 13 use acronyms without first defining what they represent in the independent claims (THBS1, LUM, FN1, LG3BP, MMP9, and PSA). While the claims can reference acronyms, the material presented by the acronym must be clearly set forth at the first use of the acronym.
Dependent claims 2-13 recite “Method according to claim”. In order to improve clarity, application should amend the claims to recite “The method of claim”, so that the claim clearly refers back to, and encompasses all the limitations of the claims from which the claim depends.
Claims 3 and 9 are objected to for awkward claim construction; it is suggested that “a first step being performed by contacting” be amended to recite “a first step of contacting”.
In claim 11, there should be a comma after “5-7” to properly offset this limitation in the claim.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-13 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.
Claims 1-2, 11, and 13 recite “Method…involving…”. These claims are indefinite for reciting the language “involving”, and it is suggested that Applicant amend the claims to use typical transitional language “comprising” (e.g., “The method…comprising quantitative detection”) in the interest of improving clarity of the record, particularly since the language “involving” does not clearly communicate that the claims require the active step of detection or preparation. For example, in claim 1, “involving the quantitative detection” may be interpreted as requiring performance of quantitative detection or as using data obtained in a previously performed quantitative detection. Both interpretations are reasonable and materially different.
Claim 1 recites the limitation “the systems” without previously introducing this term in the claim. “[T]he systems” lacks clear antecedent basis.
Regarding claims 3 and 9, the term "preferably" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 5, which is dependent on claim 1, recites the limitation "the combined score” in line 1. There is insufficient antecedent basis for this limitation in the claim, as there is no score in claim 1.
Claim 8, which depends from claim 6, recites the limitation "the case of AP”. There is insufficient antecedent basis for this limitation in the claim, as there is no mention of AP in claim 6.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 3 recites the broad recitation “at least one… affinity reagent” and the narrower statement of “at least … two”. Claims 6-7 also recite narrow numerical ranges that fall within a broader range in the same claim. For example, claim 6 recites the broad recitation b0 is in the range of (-2)-0 and also recites the range of (-1.5)-(-0.5), which is the narrower statement of the range/limitation, and claim 7 recites a threshold value of the combined score of below 50, below 47.3, or 40.4-54.1. Claim 8 recites the broad recitation “30-42” and the narrower statement of “36”. Also, claim 11 recites the broad recitation “several” and the narrower statement of “5-7”. The claims are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claims 3 and 9 also recite “using quantitative readout of the respective protein’s concentration… allowing the calculation of the respective concentration”. This language is indefinite because it is not readily clear if the recited language is implying the method involves a reader or some instrumentation that produces a readout as a display of data from a system or merely encompasses an observable result that can be used to calculate concentration. The claims do not recite a particular structural component used in the method that is an instrument/reader. Furthermore, the language is confusing because “a quantitative readout of the…concentration” suggests one is obtaining the concentration but then the claim also then additionally recites “allowing the calculation of the respective concentration”, which appears to contradict that the earlier “quantitative readout” is the concentration. The claim should be amended in order to clarify.
Claim 11 recites “the…assay to the respective protein is one obtained by using recombinant proteins of human THBS1, CTSD, ICAM1 and OLFM4, respectively and animal monoclonal antibodies generated through immunization of mice therewith”. The claim is indefinite because it is not clear how these limitations limit the claimed assay. Specifically, it is not understood what is meant by the assay is obtained “by using recombinant proteins”; for example, what role or how the is the method, particularly the assay step, being performed using the recombinant proteins, as it is the proteins which are being quantitatively determined. It is not clear if the recombinant proteins are being used as a reagent in the assay, or rather if the claim is referring to the monoclonal antibodies (i.e. the antibodies used in the assay to determine the proteins rely on monoclonal antibodies specific to the recombinant proteins).
Claim 11, line 5 recites the limitation "the same buffer” and “the same set of measurements". There is insufficient antecedent basis for this limitation in the claim, and it is unclear what limitation this language places on the claim. For example, it is not clear if this language means measuring the protein standards during the assay performed on the samples (“in the same set” as in at the same time), or if this means under the same assay conditions/using same steps as performed on the samples. Clarification is necessary.
Claim 11, which is dependent on claim 1, recites the limitations “such biomarkers”, “the same buffer”, and “the preparation”. There is insufficient antecedent basis for these limitations because there is no biomarker, buffer, or preparation limitation in claim 1.
Claim 12 recites “the quantitative detection… involves the determination…relative to an external protein standard, involving the preparation of a reference standard curve by measuring defined concentrations of several protein standards…to be measured in the same set of measurements of the samples”. The claim language “involves” and “involving” is indefinite because it is not readily clear if the method comprises the actual active steps of preparing a reference standard, and measuring concentrations of several protein standards as part of the method claimed. The scope of what is and is not encompassed by the language “involve” and “involving” is not such that one can readily determine the boundaries of the claim.
Claim 12, which depends from claim 1, recites the limitation "the Gleason grade”. There is insufficient antecedent basis for this limitation in the claim, as there is no mention of Geason grade in claim 1.
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 1-13 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. Based upon consideration of all of the relevant factors, the instant claims are determined to be directed to a natural phenomenon and an abstract idea. The judicial exception is not integrated into a practical application because the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. The rationale for this determination is explained below:
The claims recite a method for collecting information about the health status of a subject involving the quantitative detection, in serum, plasma, or blood of the subject, of the concentration of THBS1, LUM, FN1, LG3BP, MMP9, and PSA.
Under Step 1 of the 2019 Revised Patent Subject Matter Eligibility Guidance the claimed method is found to be drawn to one of the four statutory categories of inventions, a process.
Under Step 2A, prong 1, the claims have been determined to recite a natural phenomenon (detecting concentration of THBS2, LUM, FN1, LG3BP, MMP9, and PSA) and an abstract idea (mathematical concept).
Claims 1-13 recite: quantitative detection of a protein (claims 1-4, 9-13); calculation of the respective concentration and a combined score value (claims 5-8); comparing the score with a corresponding threshold (claims 4, 7-8); calculation of a combined score based on a formula (claims 5); determination of concentration of biomarkers relative to an external standard (claim 11). These limitations recite natural phenomena, mathematical calculations, and mental processes. The grouping of “mathematical concepts” in the 2019 PEG includes “mathematical calculations” as an exemplar of an abstract idea. 2019 PEG Section I, 84 Fed. Reg. at 52, accordingly the limitation falls into the “mathematical concept” grouping of abstract ideas.
Furthermore, limitations of claims 4 and 8 drawn to protein level/score and risk of adverse pathology or recurrence describe naturally occurring relationship between the THBS2, LUM, FN1, LG3BP, MMP9, and PSA expression level and the health status of a subject. Natural correlations are laws of nature that have been deemed ineligible subject matter because methods directed to the natural correlation without significantly more, preempt use of the natural correlation itself.
Taken together, claims 1-13 recite the judicial exceptions law of nature and abstract idea, and the analysis must therefore proceed to Step 2A Prong 2.
Step 2A, prong 2
This part of the eligibility analysis evaluates whether the claims as a whole integrate the recited judicial exception into a practical application of the exception. This evaluation is performed by (a) identifying whether there are any additional elements recited in the claim beyond the judicial exception, and (b) evaluating those additional elements individually and in combination to determine whether the claims as a whole integrate the exception into a practical application. 2019 PEG Section III(A)(2), 84 Fed. Reg. at 54-55.
The above discussed limitations are insufficient to integrate the judicial exceptions into a practical application because steps corresponding to collecting data, mathematical calculations, and mental concepts are themselves insufficient to constitute a practical application (as these are the judicial exceptions, not a practical application thereof).
The claimed limitations directed to judicial exceptions, the claims also recite that the method is “involving the quantitative detection, in serum, plasma or blood of the subject, of the concentration of THBS1, FN1, LG3BP, MMP9 as well as PSA” and “calculating… a combined score value”. These steps of detecting and calculating are insufficient to integrate the judicial exceptions because the purpose is merely to obtain the data. The limitations do not go beyond insignificant presolution activity, i.e., mere data gathering steps necessary in order to use the judicial exceptions/necessary to the judicial exceptions (steps to obtain the input data), similar to the fact pattern in In re Grams, 888 F.2d 835 (Fed. Cir. 1989) and Ariosa Diagnostics, Inc. v. Sequenom, Inc. (Fed. Cir. 2015). Additionally, these steps (determining the concentrations, calculating combined scores) are recited at a high level of generality.
The claims fail to recite additional (in addition to the judicial exceptions themselves) steps/elements that apply, rely on or use the judicial exception(s) in a manner that impose a meaningful limit on the judicial exception.
Step 2B
This part of the eligibility analysis evaluates whether the claims as a whole amount to significantly more than the recited exception, i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. MPEP 2106.05. The additional steps/elements fail to go beyond activity that was considered well-known, routine, and conventional in the art at the time the application was filed.
See Steuber et al (instant PTO-892), which teaches a method comprising collecting information about the health status of a subject (health status related to prostate health, see abstract), the method comprising quantitative detection of THBS1 and free PSA using Proclarix, a blood based-test which combines THBS1, total PSA, and free PSA, as well as age, to generate a risk score (page 322, col. 1, para 3, see page 323, col 1, para 2 blood collected and the assay performed). Steuber is collecting, as one method, all the information about health, consistent with the present claims.
Even further, while Steuber does teach considering together all the collected data as claimed, it also supports that each biomarker/measurement individually is recognized in the prior art as a known biomarker/indicator, see for example the reference acknowledges PSA is a recognized/known indicator in the art (referring to current guidelines recommended for use or risk calculators (page 322, col. 1, para 1) and that THSB1 is already known/measured in relation to prostate health/risk determination (page 322, col. 1, para 3).
Regarding these limitations which are performed in order to gather the data, there is nothing to suggest or indicate that the data is obtained or collected in a non-routine or unconventional way.
Claims 9-11 require the quantitative detection of the respective concentrations using a sandwich enzyme linked immunosorbent assay or a sandwich bead-based antibody assay and a protein standard. However, these elements are routine methods for an ordinary skilled person in the art. For example, Thermo Scientific teaches a standard protocol for ELISA. In ELISA, optimization is routinely performed, including optimizing sample concentration, blocking buffer, standard diluent, signal detection (Thermo Scientific, ELISA technical guide and protocols, Publication Year: 2010, instant PTO-892), and thus limitations drawn to ELISA assay and related standard curves do not add an inventive concept to the claims.
Additionally, MPEP 2106.05(d) II teaches that:
The courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity.
i. Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
ii. Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
iii. Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
iv. Immunizing a patient against a disease, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
v. Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
vi. Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119 USPQ2d at 1375;
vii. Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014); and
viii. Hybridizing a gene probe, Ambry Genetics, 774 F.3d at 764, 113 USPQ2d at 1247.
For all of these reasons, the claims fail to include additional elements that are sufficient to amount to significantly more than the judicial exception(s).
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 factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-4 and 9-13 are rejected under 35 U.S.C. 103 as being unpatentable over Cima et al published February 22, 2011 (instant PTO-892) and Hadler-Olsen et al published May 17, 2013 (instant PTO-892) in view of Kim et al published June 1, 2020 (instant PTO-892).
Cima et al teaches the identification of dysregulated glycoproteins in the serum of a mouse model of prostate cancer (PTEN inactivation mouse) (abstract). Using applied proteomics, Cima et al detected and quantified 39 human ortholog candidate biomarkers in prostate cancer patients and controls (abstract). These proteins include fibronectin (FN1; pg 3345, column 1, para 0), lumican (LUM; Figure 4), galectin 3 binding protein (LG3BP; Figure 4), and thrombospondin-1 (THBS1; Figure 3), as in the systems of claims 1-2. Furthermore, see Dataset S3 of Cima et al for FN1, LUM, LG3BP, and THBS1 in the list of identified targets. Cima et al also teaches that PSA is a widely used diagnostic serum biomarker for prostate cancer (pg 3344, column 2, para 0). Cima et al teaches that application of these biomarkers can be applied for the prognosis of prostate cancer (pg 3345, column 2, para 0), as in the health status limitation of claim 1.
Cima et al teaches the detection of protein concentration and calculating concentration in the original serum, as in claim 3, as well as methods using sandwich enzyme linked immunosorbent assay for the detection of proteins (Supplemental methods, pg 2, column 2), as in claims 9-11. For the ELISA, the antibody-antigen complex is transferred to a plate coated with recombinant protein for 2 hours to detect the unbound endogenous antigen-antibody fraction (Supplemental methods, pg 2, column 2), as in the recombinant proteins and the sandwich enzyme linked immunosorbent assay of instant claim 10. In ELISA, as evidenced by “Thermo Scientific, ELISA technical guide and protocols”, optimization is routinely performed for sample reference standard curve, concentration, standard diluent buffer, and signal detection, as in the limitations of 11 drawn to determining concentration of each biomarker with respect to a standard protein curve.
In Cima et al, the Gleason grade is less than 7 (Supplemental methods, pg 2, column 2), as in instant claim 12.
Cima et al provides no teaching regarding the protein MMP9 in prostate cancer.
Hadler-Olsen et al teaches that MMP-9 is upregulated in the blood from prostate cancer patients; furthermore, patients with metastatic prostate cancer had higher levels of MMP-9 than patients with organ-confined carcinomas and healthy controls (pg 2046, “Prostate cancer”), as in the MMP-9 and health status limitations of claims 1-2. Increased expression of MMP-9 is also associated with increased risk of biochemical recurrence (pg 2046, “Prostate cancer”), as in instant claim 4.
Given that Cima et al teaches a method for collecting information about the health status of a subject involving the quantitative detection of THBS1, LUM, FN1, LG3BP, and PSA, and further given that Hadler-Olsen teaches that MMP-9 is elevated in prostate cancer and is a prognostic marker for disease (i.e. information about the health status of a subject), it would have been prima facie obvious to one of ordinarily skill in the art at the time the invention was filed to include the biomarker of Hadler-Olsen with the biomarkers of Cima et al and have a reasonable expectation of successfully collecting data about the health status and risk of a subject in need. Such would amount to combining prior art elements according to know methods to yield predictable results, see MPEP 2143. Thus, Cima et al and Hadler-Olsen teach the 6 systems of instant claims 1 and 13.
In the remarks filed September 9, 2026, applicant asserts that the combination of references cited in the restriction do not offer evidence of the predictive value of the combination of biomarkers (remarks, pg 6-7). The five biomarkers of Cima et al are included in a list of almost 40 that are dysregulated in the serum of prostate cancer model mice. As such, there is no strong motivation to select the five proteins/systems claimed. At the time the application was filed, however, there were methods known in the art to assess the diagnostic/prognostic values of markers. For example, Kim et al teaches the successful identification of a diagnostic panel of 6 specific biomarkers from a total of 11 markers that are commonly expressed in pancreatic cancer (abstract). Kim et al teaches that each set of markers was validated (Table 2), as in the combined score value of claim 3. As Kim et al teaches a method for identifying a combination of proteins that are relevant for health status information, including evaluating candidate proteins based on their ability to provide information concerning a specific type of cancer, it would have been obvious to the ordinary artisan who was interested in improving methods for collecting information would have been motivated to use the method of Kim et al to optimize identification of markers/proteins relevant for assessment of disease risk. In view of this known methodology in the art for identifying and selecting proteins that are informative for health status, the selection of MMP-9 with the proteins of Cima et al would not have constituted an arbitrary or random selection from an essentially unlimited number of proteins. Rather, the skilled artisan would have had a recognized technical basis for evaluating and selecting proteins having relevance to health status. The combination of cited reference represents the predictable use of known methods to detect known proteins for their known purpose of obtaining information concerning health status. The cited references provide a reasoned basis for selecting the proteins and Kim et al teaches a known methodology for identifying informative sets of markers. Thus, the claimed combination would have been within the skill of the ordinary artisan and would have presented a reasonable expectation of success.
Claims 1-13 are rejected under 35 U.S.C. 103 as being unpatentable over Cima et al, published February 22, 2011, and Hadler-Olsen et al, published May 17, 2013, in view of Kim et al, published June 1, 2020, as applied to claims 1-4 and 9-13 above, and further in view of Landers et al, published December 17, 2004 (IDS from ??).
The teachings of Cima et al and Hadler-Olsen et al in view of Kim et al are discussed above. This combination of references does not teach the formula required by instant claims 5-8.
Landers teaches a method of using multiple biomarkers for a molecular diagnosis of prostate cancer (Title). Landers teaches a logistic regression (LR) analysis which can generate a combined score value (prediction score). The combined score value is calculated with the formula:
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30
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Where b0 is a constant, bi is the regression coefficient value for each biomarker and Qi is the level of expression (page 951, Statistical analysis), as in claims 5-6. Landers teaches that the regression coefficients as determined with an optimization using experimental data (this coefficient weighs each biomarker according to its importance in determining each individual’s risk of clinical diagnosis (page 951, Statistical analysis). Landers teaches that patients with a combined score surpassing a corresponding threshold value (> 0.5) is taken as positive prostate cancer information (pg 951, Statistical analysis).
Landers teaches that with four biomarkers, or three biomarkers, the model gave 100% correct prediction for all of the individuals (total 50) in both PCa and BPH categories (pg 952, col 2, para 2, and Table IV). Landers teaches that the logistic regression model provides the maximum predictive accuracy compared with other models such as neural networks and tree-based methods (pg 953, col 2, para 5). Landers further teaches that the value of the regression model and its application does not rely on specific functions of the biomarkers, therefore can be applied other biomarker combinations (pg 954, col 2, para 2).
As Cima et al teaches predictive regression models for tissue PTEN status and diagnosis and grading of prostate cancer (abstract), it would have prima facie been obvious to one of ordinarily skilled in the art at the time the invention was filed to apply logistic regression analysis to experimental data on THBS1, LUM, FN1, LG3BP, MMP9 and PSA as taught by Cima et al and Hadler Olsen to generate a combined score value and to predict disease state based on whether the value surpassing a threshold value (e.g. 0.5) as the instant claim 7-8, doing so would provide a simple value and the maximum predictive accuracy, as recognized by Landers (pg 953, col 2, para 5) and Cima et al.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JENNIFER BENAVIDES whose telephone number is (571)272-0545. The examiner can normally be reached M-F 9AM-5PM (EST).
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Jennifer Benavides
Examiner
Art Unit 1675
/JENNIFER A BENAVIDES/Examiner, Art Unit 1675
