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 .
Priority
This application 17/630,304 filed on 01/26/2022 is a 371 national phase of PCT/CA2021/050837 and claims the benefit of provisional U.S. Patent Application No. 63/040,692, filed on 06/18/2020.
The priority date of claim 7 and its dependent claim 11 is determined to be 06/18/2020, the filing date of provisional U.S. Patent Application No. 63/040,692.
Status of Claims
Applicant’s amendments to claims filed 04/01/2026 in response to the Non-Final Rejection mailed 10/02/2025 are acknowledged.
Claim 7 is amended.
Claims 9, 10, and 12 have been canceled.
Claims 1-6 and 13-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Applicant’s election without traverse of (a) mRNA as the patient feature category; in the reply filed on 09/17/2025 is acknowledged. Claim 8 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim.
Claims 1-8, 11, and 13-15 are pending.
Claims 7 and 11 are under examination.
Response to Remarks filed 04/01/2026
The amendments and arguments presented in the papers filed 04/01/2026 ("Remarks”) have been thoroughly considered.
The issues raised in the Office action dated 10/02/2025 listed below have been reconsidered as indicated.
a) The objections to the specification regarding the use of trade names or marks are withdrawn in view of the amendments to the specification.
b) The 35 USC 112(a) written description rejection of claims 7 and 9-12 have been withdrawn in view of the amendments to claim 7 and the cancellation of claims 9, 10, and 12.
b) The 35 USC 112(b) indefiniteness rejections of claims 7 and 10 have been withdrawn in view of the amendments to claim 7 and cancellation of claim 10.
c) The rejection of claim 7 under 35 U.S.C. 103 as being unpatentable over Berman are withdrawn in view of the amendments to the claims.
d) The rejection of claims 9 and 12 under 35 U.S.C. 103 as being unpatentable over Berman and Williams are withdrawn as moot in view of the cancellation of the claims.
e) The rejection of claim 11 under 35 U.S.C. 103 as being unpatentable over Berman and Williams are withdrawn in view of the amendments to the claims.
f) The rejection of claim 10 under 35 U.S.C. 103 as being unpatentable over Berman and Williams are withdrawn in view of the amendments to the claims.
g) The nonstatutory double patenting rejections are being unpatentable over copending Application No. 17/612,695 are withdrawn in view of the amendments to the claims.
Note: The Priority section on page 3 of the Office Action mailed on 10/02/2025 contains the priority for a different application that was inadvertently transposed into the Office Action. The misplaced priority dates did not affect the examination or the remainder of the Office Action. The correct Priority statement is written above in the Priority section.
Note: The Remarks filed 04/01/2026 report that claim 8 is amended in the current claims. This appears to be a typographical error, as claim 7 was amended and claim 8 is withdrawn. The correct amended claim is written above in the Status of Claims section.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Claim Interpretation
Claim 7 recites the amended limitation “patient features comprising the mRNA, CNA, methylation and clinical features listed for ---”. The claim recites mRNA and applicants have elected the patient feature category “mRNA” as elected species pertaining to search burden for prior arts under 35 USC § 102 and 35 USC § 103. In this regard, Table 6 includes the category “RNA”. The RNA of Table 6 is interpreted to be the mRNA recited in step b) of amended claim 1 filed on 04/01/2026.
Claim Rejections - 35 USC § 101 - modified
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.
Claim 7 and 11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
This maintained rejection has been modified to address claim amendments.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106, part II.
Based upon consideration of the claims as a whole, as well as consideration of elements/steps recited in addition to the judicial exception, the present claims fail to meet the elements required for patent eligibility.
Step 1
The claimed invention is directed to the statutory category of a process.
Step 2A, Prong One
The claims are taken to be directed to abstract ideas, a judicial exception.
Claim 7 is directed to a method comprising “b) determining -- all of 94 patient features comprising the mRNA, CNA, methylation and clinical features, and at least one reference or control feature for each of the mRNA, CNA, methylation and clinical features”. This limitation is an abstract mental process (see MPEP 2106.04(a)(2)(III)). As written, the determining step encompasses the mental step of looking at data and/or reports of patient features.
Claim 7 is directed to a method comprising “c) comparing said patient features to the reference or control features”. This limitation is an abstract mental process (see MPEP 2106.04(a)(2)(III)). As written, the comparing step encompasses the mental step of encompasses the mental step of looking at more than one set of patient features and making a mental judgment regarding similarities and differences.
Claim 7 is directed to a method comprising “d) computing a prediction score using a classifier that takes said patient feature values as input, the classifier having been previously trained on said patient features in samples from a population of early prostate cancer patients”. This limitation is an abstract mental process, a mathematical concept (see MPEP 2106.04(a)(2)). As written, the computing step encompasses mathematical concepts such as mathematical calculations.
Claim 7 is directed to a method comprising “d) – classifying the patient tumour into a pathological Gleason Grade Group (GG) class”. This limitation is an abstract mental process (see MPEP 2106.04(a)(2)(III)). As written, the classifying step encompasses the mental step of looking at data in a report and making a mental judgement to sort and categorize the data.
Claim 11 depends from claim 7, and requires the same steps of determining, comparing, computing and classifying.
Step 2A, Prong Two
The exception is not integrated into a practical application of the exception. The claims do not recite any additional elements that integrate the exception into a practical application of the exception.
While claim 7 recites “providing a sample containing RNA and DNA material from tumour cells”, and “measuring all of 94 patient features…” , these are not integrations of the exception into a practical application. Instead, these elements are data gathering required to perform the method.
Claim 7 further recites “if the patient is classified into the pathologic GG2 class, further comprising treating the patient with surgery, endocrine therapy, chemotherapy, radiotherapy, hormone therapy, gene therapy, thermal therapy, or ultrasound therapy” and claim 11 recites “managing the patient with active surveillance” these are not integrations of the exception into a practical application, but are rather generalized instructions to treat which are well understood, routine and conventional. Simply appending them is not enough to qualify as significantly more when recited in a claim with a judicial exception. The recited treatments are at such a high level of generality that they do not constitute a particular treatment for prostate cancer.
Step 2B
The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. The claim does not add a specific limitation other than what is well-understood, routine, and conventional in the field. Steps directed to “providing a sample”, “measuring” patient features, and optional step of “treating the patient with surgery, endocrine therapy, chemotherapy, radiotherapy, hormone therapy, gene therapy, thermal therapy, or ultrasound therapy” are techniques that are routine, conventional, and well-known in the art (See pages 12-18 of Non-Final for relevant prior arts in this regard).
For these reasons, the claims are rejected under section 101 as being directed to non-statutory subject matter.
Response to Arguments against Claim Rejection - 35 U.S. C § 101
The response asserts that claim 7 is not properly characterized as "mental." The claim recites (i) "providing a sample containing RNA and DNA material from prostate tumour cells," and (ii) "determining or measuring all of 94 patient features comprising the mRNA, CNA, methylation and clinical features" for PRONTO-m. The response asserts that these limitations require wet-lab and instrumented molecular measurement of nucleic-acid features from a physical biological sample, which cannot practically be performed in the human mind (p. 8-9).
Applicant's arguments have been fully considered but are not persuasive.
Although limitations of the claim require wet-lab and instrumented molecular measurement of nucleic-acid features from a physical biological sample, these are methods that are routine, well-known and conventional in the art and in this instance are used merely for the purposes of data gathering necessary for performing the method.
Further it is noted that the claimed clinical features do not require wet-lab and instrumented molecular measurement of nucleic-acid features.
The further response asserts that “computing a prediction score using a classifier—” is not a mere human "judgment," but application of a trained machine-learning classifier to a high dimensional, measured patient feature profile and do not recite a “mental process” judicial exception (p. 9).
Applicant's arguments have been fully considered but are not persuasive.
As described above, the computing step is considered a mathematical concept (i.e. calculating, etc.), a judicial exception. See MPEP 2016.04(a)(2)(I)(C).
The response asserts that even assuming arguendo that the scoring step implicates mathematics, claim 7 integrates any such computation into a concrete medical application. Applicant argues that this is not a result-only "apply it" instruction, but a specific diagnostic-and-treatment workflow grounded in the disclosed molecular profiling and classifier-training pipeline that was developed to provide an "objective biomarker of prostate cancer grade" despite biopsy inaccuracy (p. 9).
Applicant's arguments have been fully considered but are not persuasive.
The instant claims recite treating steps at a high level of generality and do not require a specific or particular treatment in response to a specific classification or prediction score. As such, the claim is directed to the relationship and is not a
practical application of the judicial exception.
Claim Rejections - 35 USC § 112(a)- New Matter
The following is a quotation of the first paragraph 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 the first paragraph of pre-AIA 35 U.S.C. 112:
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 7 and 11 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
This is a new matter rejection necessitated by amendments to the claims.
The claims are broadly drawn to method of treating a subject with prostate cancer, the method comprising predicting disease progression risk by providing a sample from prostate tumor cells, determining or measuring all of 94 patient features comprising the mRNA, CNA, methylation and clinical features, and at least one reference or control feature for each of the mRNA, CNA, methylation and clinical features, comparing said patient features to the reference or control features, computing a prediction score and selecting treatment or surveillance based on a threshold for the prediction score.
Claim 7 is drawn to “determining or measuring all of 94 patient features comprising the mRNA, CNA, methylation and clinical features, and at least one reference or control feature for each of the mRNA, CNA, methylation and clinical features”. The claim further recites mRNA features consisting of 64 listed mRNAS, CNA features consisting of 14 listed genes, methylation features consisting of 12 genes, and clinical features consisting of 4 categories.
The claim uses open language (94 patient features comprising the mRNA, CNA, methylation and clinical features) that includes the 94 listed individual features of the claim but is not limited to those features. The determining or measuring step (b) encompasses any and all patient features; and “the method comprising ---” recited in the preamble of claim 7 allows recitation of more steps that encompasses any additional patient features.
To provide evidence of possession of a claimed genus, the specification must provide sufficient distinguishing/identifying characteristics of the genus. The factors to be considered include disclosure of complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of
making the claimed product, or any combination thereof.
The instant specification does not provide sufficient written description for the claimed set of any and all patient features encompassed by the scope of amended claim 1 filed on 04/01/2026. There is a lack of support in the claims and/or specification as to what selection criteria must be used for the selection or combining of the subset of class features. Further the specification does not
As a relevant consideration regarding the scope of amended claim 1 filed on 04/01/2026, Table 6 of the specification lists 466 candidate features for classifiers listed under data type as methylation, RNA, clinical, CN (Nanostring), CN (MLPA). No guidance is provided within the specification for identifying or selecting the required patient features of the instant claim. The specification does not teach the identity of any and all patient features that may be determined or measured. No guidance is provided for identifying or selecting other patient features or as to what features distinguish relevant patient features.
The ordinary artisan would not have been able to identify the claimed “all of 94 patient features comprising the mRNA, CNA, methylation and clinical features” that are capable of predicting disease progression risk and the applicant is considered not in possession of all patient features that meet this limitation.
Further claim 7 recites “at least one reference or control feature for each of the mRNA, CNA, methylation and clinical features”. Given the broadest interpretation of the specification, features listed in Table 6 zeros in both the PRONTO-e and PRONTO-m columns are reference or control features. However, the specification Table 6 only includes features listed as methylation (2 entries) or CN (Nanostring) (92 entries) that could be considered reference or control features. The specification does not identify control or reference features for (i) each of mRNA, CNA, methylation and clinical features, or, further, for (ii) any and all individual features.
No guidance is provided within the specification for identifying or selecting the required control or reference features of the instant claim. The specification does not teach the identity of any and all control or reference features that may be determined or measured. No guidance is provided for identifying or selecting other control or reference features or as to what features distinguish relevant control or reference features.
The ordinary artisan would not have been able to identify the claimed control or reference features that are necessary for comparing to patient features and the applicant is considered not in possession of all control or reference features that meet this limitation.
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 7 and 11 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.
Claim 7 recites the limitation “at least one reference or control feature for each of the mRNA, CNA, methylation and clinical features”. It is unclear what features are intended to be reference or control features. It is unclear if “at least one reference or control feature” is required for each of the four patient feature categories (mRNA, CNA, methylation and clinical), or if “at least one reference or control feature” is required for each of the 94 genes or elements of the four patient feature categories.
Claim 7 recites the limitation “comparing said patient features to the reference or control features”. The specification recites reference or control features in Table 6. However, there is no column in Table 6 indicating reference or control features. For the purposes of examination, it is interpreted that features with zeros in both the PRONTO-e and PRONTO-m columns are reference or control features, however there appear to be no reference or control features for mRNA or clinical features. It is unclear how “comparing” is intended to be performed across feature categories or individual patient features when reference or control features are not provided for all different types of patient features, e.g., mRNA, CNA, methylation, etc.
Claim 7 recites the limitations “wherein the clinical features consist of Gleason Grade (GG)--;” and “d) computing a prediction score using a classifier that takes said patient features as input --; wherein determining the prediction score comprises classifying the patient tumour into a pathological Gleason Grade Group (GG) class; the patient tumour is classified in the pathologic GG2 class if the score is > 0.5 or the pathologic GG1 class if the score is < 0.5;”. It is unclear how the clinical feature Gleason Grade (GG) is used in computing a prediction score and also classified as a class (GG1 or GG2) that is determined by the prediction score.
Conclusion
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.
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/JESSICA GRAY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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