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/Restriction
Applicant's election without traverse of Species A (claim 99), Species B (claim 105), and Species C (claim 112) in the response filed 06/23/2026 is acknowledged. Regarding Species B, after further consideration, claim 104 is rejoined due to lack of search burden and this species election is withdrawn.
Claims 100, 101, 108-111, 114-117 are hereby withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Status of Claims
Claims 97-118 are pending.
Claims 100, 101, 102, 108-111, 114-117 are withdrawn.
Claims 97-99, 103-107, 112-113, 118 are under examination.
Priority
This application claims the benefit of priority to U.S. Provisional Application Ser. No. 62/901,175, filed September 16, 2019.
Information Disclosure Statement
The three (3) information disclosure statement (IDS) document(s) submitted are in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS document(s) has/have been fully considered by the examiner.
However, it is noted that at least one of the IDS documents is over twelve pages long. Applicant is reminded that it is desirable to avoid the submission of long lists of documents if it can be avoided. See MPEP 2004. Applicant's duty of disclosure of material and information is not satisfied by presenting a patent examiner with "a mountain of largely irrelevant material from which he is presumed to have been able, with his experience and with adequate time, to have found the critical [material]. It ignores the real world conditions under which examiners work." Rohm & Haas Co. v. Crystal Chemical co., 722 F.2d 1556, 1573 [220 USPQ 289] (Fed. Cir. 1983), cert. Denied, 469 U.S. 851 (1984). Patent applicant has a duty not just to disclose pertinent prior art references but to make a disclosure in such a way as not to "bury" it within other disclosures of less relevant prior art; see Golden Valley Microwave Foods Inc. v. Weaver Popcorn Co. Inc., 24 USPQ2d 180i (N~D. Ind. 1992); Molins PLC v. Textron Inc., 26 USPQ2d 1889, at 1899 (D.Del 1992); Penn Yan Boats, Inc. v. Sea Lark Boats, Inc. et aL, 175 USPQ 260, at 272 (S.D. FI. 1972).
Drawings
The drawings filed 03/16/2022 are objected to as failing to comply with 37 CFR 1.84 because several of the Figures are not legible. See at least Figures 1A, 8, and 9. Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
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 97-99, 103-107, 112-113, 118 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 Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and ‘as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355).
Guidance: Step 1. Under the broadest reasonable interpretation, the claimed invention (claims 1 being representative) is directed to a method for performing a process (determine a treatment regimen) and therefore falls within 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 following steps of claim 1 recite an abstract idea:
classifying, using the obtained molecular data as features within a molecular class prediction tool, the biological sample into an integrative cluster subgroup associated with aggressiveness and high risk of relapse;
determining a treatment regimen for the individual based on the classification of the biological sample into the integrative cluster subgroup, wherein the treatment regimen includes at least one of: chemotherapy, endocrine therapy, targeted therapy, immunotherapy, or health professional surveillance.
Mental Processes
Under MPEP §2111, during patent examination, claims must be interpreted in their broadest reasonable manner consistent with the specification. This means that examiners consider the claim language in light of the specification as understood by a person of ordinary skill in the art, ensuring that the claims are not unduly narrowed by implicit limitations not explicitly recited in the claim (37 CFR 1.75(d)(1)).
Under the BRI, the recited acts of classifying and determining are generically recited and set forth or describe observing and/or analyzing data (which scientists can perform using their brains or a pencil and paper). As such, these steps encompass a mental process of observing data and/or manipulating data. MPEP 2106.04(a)(2), section III.
It is important to note that “Claims that recite performing information analysis as well as the collection and manipulation of information related to such analysis, have been determined by our reviewing court to be an abstract concept that is not patent eligible. See SAP, 898 F.3d, 1165, 1167, 1168 (Claims reciting "[a] method for providing statistical analysis" (id. at 1165) were determined to be "directed to an abstract idea" (id. at 1168)); see also Content Extraction & Transmission LLC v. Wells Fargo Bank, Nat'l Ass 'n, 776 F.3d 1343, 1345, 1347 (Fed. Cir. 2014). [Step 2A, Prong 1: YES].
Mathematical Concept
Under the BRI, the recited act of classifying requires using a molecular class prediction tool, and thus sets forth or describes a mathematical relationship when read in light of the specification. For example, the specification teaches molecular prediction tools that include logistic regression, a support vector machine with a linear kernel, a support vector machine with a gaussian kernel, or a neural network [0029-0031] which are all well-known mathematical techniques. While no specific equation is being claimed, Applicant is reminded that there is no particular word or set of words that indicates a claim recites a mathematical calculation. See MPEP 2106.04(a)(2). Similar to the ineligible claims at issue for In re: Board of Trustees of the Leland Stanford Junior University, 991 F.3d 1245 (Fed. Cir. 2021), the instant claims are written effectively as a method for mathematically manipulating or relating data to ascertain additional data. As such, this step recites a mathematical concept. MPEP 2106.04(a)(2) Section I. [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
Having made that determination, under the 2019 Guidance, the examiner next determines whether there are additional elements beyond the recited abstract idea(s) that integrate them into a practical application.
In this case, the additional steps/elements that are not part of the abstract idea are as follows:
obtaining molecular data derived from a biological sample of an individual;
With regards to said obtaining, this step is recited at a high level of generality and requires collecting data for use by the abstract idea. Accordingly, this step amounts to insignificant extra-solution activity and is not indicative of an integration into a practical application. See MPEP 2106.05(g). Notably, the claim does not include any computer or a specific machine for practicing the claimed invention. Even when viewed in combination, these additional elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO].
C. Guidance Step 2B:
This part of the eligibility analysis evaluates whether the claim 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. See MPEP 2106.05.
As discussed above, the non-abstract steps/elements amount to nothing more than insignificant extra-solution activity. Moreover, applicant’s own specification teaches well understood, routine, and conventional methodologies for obtaining molecular data [0033]. Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract elements/steps. See MPEP 2106.05(d)(Part II). Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
Dependent Claims
Dependent claims 98-99, 103-107, 112-113, 118 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) 98-99, 118, these are directed to limitations that further limit the specificity of the abstract idea set forth above or the nature of the data being used by the abstract, and therefore are also recite mathematical concepts for reasons discussed above in the Step 2A (prong 1) analysis. Regarding claim(s) 103, this claim further limits the type of samples used. Accordingly, this amounts to insignificant extra-solution activity and/or generally linking the use of a judicial exception to a particular technological environment or field of use as set forth above. MPEP 2106.04(g) and (h).
Regarding claim(s) 104-107, 112, 113, these claims further limit the type of treatment. However, it is noted with particularity that parent claim 99 does not require administering a treatment but merely requires “determining a treatment regimen” (which is not equivalent and in fact reads on determining information or providing advice). Accordingly, the aforementioned dependent claims do not effect a particular treatment and thus do integrate the mental analysis step into a practical application. See MPEP 2106.04(d)(2). Therefore, the claims as a whole are not patent eligible. For additional guidance, applicant is directed generally to MPEP 2106.
Claim rejections - 35 USC § 112a
The following is a quotation of 35 U.S.C. 112(a):
(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.
Claims 97-99, 103-107, 112-113, 118 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.
Regarding claim(s) 97, the specification fails to provide written description support for the following steps:
classifying, using the obtained molecular data as features within a molecular class prediction tool, the biological sample into an integrative cluster subgroup associated with aggressiveness and high risk of relapse;
determining a treatment regimen for the individual based on the classification of the biological sample into the integrative cluster subgroup, wherein the treatment regimen includes at least one of: chemotherapy, endocrine therapy, targeted therapy, immunotherapy, or health professional surveillance.
In this case, the above steps are not limited to any particular acts or operations and amount to functional language specifying desired results and/or specific functions. Without reciting the particular structure, materials or steps that accomplish the function or achieve the result, all means or methods of resolving the problem may be encompassed by the claim. As a result, it is unclear what the “molecular class prediction tool” is and how it is being used in the “classifying” step achieves the claimed function. A review of the specification generically lists examples of molecular prediction tools that include logistic regression, a support vector machine with a linear kernel, a support vector machine with a gaussian kernel, or a neural network [0029-0031, 0053]. However, given the breadth of the claim, this does not provide any sufficient technical details with regards to the claimed “tool” that would serve to clarify its structure, how it was trained, or other specific details with regards to how it operates. The specification does disclose classifiers that include a specific CTS5 algorithm [0167]. However, it is improper to import narrowing limitations from the specification into the claims. MPEP 2111.01. In other words, the “molecular class prediction tool” as claimed is essentially using a black box to achieve the claimed function. Moreover, one of ordinary skill in the art would recognize that methods for predicting treatment regimes based on model classification are not trivial.
Dartmann et al. (US2017/0067118) teaches a method for predicting treatment effectiveness in breast cancer patients. In particular, unlike the claimed method, Dartmann teaches obtaining expression levels from a specific set of genes associated with breast cancer and then evaluating those expression levels using well-defined mathematical models to yield classification scores and administer therapeutic treatments [ref. claims 1-5, 0023, 0024, 0060, 0083, 0108, 0118, 0119], wherein a high combined score is indicative of benefit from a more aggressive therapy, e.g. cytotoxic chemotherapy [0075]. Dartmann also teaches analyzing the performance of different predictive algorithms using different treatments [0118-0121, Tables 1-6].
Gehrmann et al. (WO2010003773A1) teaches algorithms for outcome prediction in patients with node-positive chemotherapy-treated breast cancer. In particular, unlike the claimed invention, Gerhrmann also teaches obtaining expression levels from a specific set of genes associated with cancer and then evaluating those expression levels using well-defined mathematical models to yield classification scores and selected appropriate therapeutic treatments [ref. claims 1-5].
Furthermore, one of ordinary skill in the art would understand that diseases such as breast cancer have different stages and evolve over time and that predictive models and survival analysis vary based on the treatment modality [as discussed in applicant’s own specification on ¶0239, ¶0246]. In this case, however, a review of the specification does not provide any evidence to suggest that applicant has sufficient knowledge of mathematical correlations between molecular classification data used by said prediction tool and the treatment regimens for the full scope of what is presently encompassed by the claim. Therefore, the specification does not establish a reasonable structure-function correlation between classifier/molecular data and treatment regimen data. “[A] sufficient description of a genus . . . requires the disclosure of either a representative number* of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can 'visualize or recognize' the members of the genus” (AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69)(emphasis added). Accordingly, one of ordinary skill in the art would not have understood applicant to have invented a method/system of performing the claimed functions with no more than routine experimentation.
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).
Claim rejections - 35 USC § 112b
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 97-99, 103-107, 112-113, 118 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 97 are also rejected due to said dependency.
Claim 97 recites “classifying, using the obtained molecular data as features within a molecular class prediction tool….”. In this case, such generic functional claim language amounts to descriptions of problems to be solved and covers all means or methods of performing the claimed function. See MPEP 2173.05(g). Firstly, it is unclear as to the metes and bounds of the claimed “molecular class prediction tool” such that the artisan would recognize what internal structure of the “tool” is intended, i.e. is tool simply a computer, an algorithm, or otherwise. Secondly, as a result, it is unclear in what way the tool is being “used” to achieve the claimed function. A review of the specification generically lists an examples of molecular prediction tools that include logistic regression, a support vector machine with a linear kernel, a support vector machine with a gaussian kernel, or a neural network [0029-0031, 0053]. However, examples are not limited definitions and it is improper to import narrowing limitations from the specification into the claims. MPEP 2111.01. Moreover, a claim is indefinite where it merely recites a use without any active, positive steps delimiting how this use is actually practiced. See MPEP § 2173.05(q). As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. Clarification is requested via amendment. Applicant is also encouraged to import the limitations from claim 98 into claim 97 (although this would not clarify in what way the “tool utilizes” these different mathematical techniques).
Claim 97 recites “…the biological sample into an integrative cluster subgroup associated with aggressiveness and high risk of relapse.” The term “aggressiveness” and “high risk” are relative terms and the specification does not provide any limiting definitions, specific properties, or scoring criteria indicating the scope of these terms. As a result, it is unclear as to the metes and bounds of these terms, as the result is subjective and imperceptible, i.e. what quantitative metrics are indicative of a cluster that is ‘aggressive’ or ‘high risk’. Clarification is requested via amendment.
Claim 97 recites “determining a treatment regimen for the individual based on the classification of the biological sample into the integrative cluster subgroup, wherein the treatment regimen includes at least one of: chemotherapy, endocrine therapy, targeted therapy, immunotherapy, or health professional surveillance.”. Firstly, it is unclear in what way determining a treatment regimen is “based on the classification of the biological sample into the integrative cluster subgroup”. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function, nor does it disclose any associated threshold values for purposes of comparison. As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. Secondly, it is unclear as to the metes and bounds of the term “health professional surveillance”. A review of the specification does not provide any limiting definition that would serve to clarify the scope of this term or clarify in what way “surveillance” is reasonably construed as a type of treatment regimen. Clarification is requested via amendment.
Claim 112 recites the term “IntClust6”. It is unclear as to the metes and bounds of this term. A review of the specification does not provide any limiting definition that would serve to clarify the scope of this term, and does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. Clarification is requested via amendment.
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.
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 97, 98, 99, 103, 104, 118 are rejected under 35 U.S.C. 103 as being unpatentable over Gehrmann et al. (WO/2010003773A1).
Gehrmann teaches algorithms for outcome prediction in patients with node-positive chemotherapy-treated breast cancer. Regarding claim(s) 97, Gerhrmann teaches obtaining expression level data (i.e. molecular data) associated with a specific set of genes associated with breast cancer from patient samples [ref. claim 1, pages 13-14, 19]. Gehrmann teaches the classifying patient data into different clinical categories, wherein the classification includes using various discriminant functions and wherein patients can be classified into high risk or low risk groups as well as different grades [ref. claims 1, 10, pages 8, 17, 18, 19]. Gehrmann does not specifically teach a “molecular data prediction tool”. However, Gehrmann makes obvious this feature since their discriminatory functions include mathematical techniques such as kNNs, SVMs, and linear regression models [page 8]. Gehrmann teaches therapies that include chemotherapies such as taxane [page 20, ref. claim 15]. Regarding claim(s) 98, Gehrmann teaches discriminatory functions that include mathematical techniques such as kNNs, SVMs, and linear regression models [page 8]. Regarding claim(s) 99, Gehrmann teaches obtaining and analyzing gene expression data.
Regarding claim(s) 103, Gehrmann teaches biological samples include cells, tissue, body fluids, lavage fluid, smear samples, biopsy specimens, blood, urine, saliva, sputum, plasma, serum, cell culture supernatant, and others [page 10]. Regarding claim(s) 104, Gehrmann teaches adjuvant therapy [pages 1, 20, ref. claim 15]. Regarding claim(s) 118, Gehrmann teaches discriminatory functions that classify patients or samples as high or low risk [page 8], which broadly reads on a risk stratification model.
Claims 105-107 and 112-113 are rejected under 35 U.S.C. 103 as being unpatentable over Gehrmann et al. (WO/2010003773A1), as applied to claims 97, 98, 99, 103, 104, 118, and further in view of Dartmann et al. (US2017/0067118) and Perez-Garcia et al. (The Breast, 2018, Vol. 37, pp. 126-133; Pub. Date: 11/20/2017).
Gehrmann teaches algorithms for outcome prediction in patients with node-positive chemotherapy-treated breast cancer, as set forth above.
Gehrmann does not specifically teach administering treatments that include endocrine therapy, as in claims 105, 106, 107, 112, 113.
Gehrmann does not specifically teach samples classified as “IntClust6”, as in claim 112. However, Gehrmann teaches high risk classification groups, as set forth above, which makes obvious this limitation absent any limiting definition to the contrary.
Moreover, Dartmann teaches methods for predicting an outcome of breast cancer in patients receiving endocrine therapy, including hormone receptor agonists or antagonists, hormone derivatives, tamoxifene therapy which modulates signaling of the estrogen receptor, or aromatase treatment which interferes with steroid hormone production [0026]. Additionally, Perez-Garcia teaches methods for treating breast cancer including FGFR pathway antagonists such as dovitinib [Section 5.2 and Table 2]. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Gehrmann by additionally administering endocrine therapy, as claimed, since such treatments were routine and conventional in the art, as taught by Dartmann and Perez-Garcia. The rationale would have been the predictable use of prior art elements according to their established functions. KSR, 550, U.S. at 417.
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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