DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
The claims filed 8/6/2026 are under consideration in this Office action.
The amendments and arguments presented in the papers filed 8/6/2026 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 5/6/2026 listed below have been reconsidered as indicated.
a) The rejections of claims 47-48 and 54-63 under 35 U.S.C. 101 because the claimed invention is directed to a judicial exceptions without significantly more are withdrawn in view of the claim only requiring an active method step of “assaying” comprising: i) an amplifying step; and ii) a detecting step.
b) The rejections of claims 48, 56, 59 and 62 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, are withdrawn in view of the amendments to the claims.
c) The rejections of: claims 47-48 and 54-63 under pre-AIA 35 U.S.C. 102(a) as being anticipated by Cooperberg (Meeting Abstract: 2012 Genitourinary Cancers Symposium. February 10, 2012); and claim(s) 47-48 and 54-63 under pre-AIA 35 U.S.C. 102(a) as being anticipated by Cooperberg (The Journal of Urology. May 23, 2012. 187(4S):e580), are withdrawn. The Cooperberg references each teach CAPRA-S (Cancer of the Prostate Risk Assessment post-Surgical), which is distinct from CAPRA as claimed. CAPRA is not a genus of assessments but a particular “preoperative predictor of disease recurrence after radical prostatectomy” as described by Cooperberg (J UROL. 2005. 173:1938-1942). See paragraph 409 of the published application.
The Examiner’s responses to the Remarks are detailed below in this Office action.
New and modified grounds of rejection necessitated by amendment are detailed below and this rejection is made FINAL.
Claim Interpretation
Claim 47 requires a single active method step, which is “assaying cDNA derived from RNA obtained from a prostate cancer tumor sample from a patient with preoperative prostate cancer that has been assigned a Cancer of the Prostate Risk Assessment (CAPRA) score of 0-10”. It is noted that CAPRA scores range from 0-10 in view of para. 409 of the published application. Thus, the step broadly encompasses assaying preoperative prostate cancer samples from patients that are merely identified as having a CAPRA score, because their CAPRA score inherently has to be within the range of 0-10. This is true because CAPRA scores outside the range of 0-10 are not known to exist in view of the instant specification.
The “assaying” step is carried out by amplifying a set of marker genes in the cDNA, wherein the set of marker genes comprises at least three genes selected from the group consisting of ASFIB, ASPM, BIRC5, BUB1B, C18orf24, CDC2, CDC20, CDCA3, CDCA8, CDKN3, CENPF, CENPM, CEP55, DLGAP5, DTL, FOXM1, KIAA0101, KIF11, KIF20A, MCM10, NUSAP1, ORC6L, PBK, PLK1, PRC1, PTTG1, RAD51, RAD54L, RRM2, TK1, and TOP2A; and detecting an expression level of each gene in the set of marker genes by measuring the level of amplified cDNA for each gene in a set of marker genes.
Claim 47 concludes with a “wherein” clause. The clause does not set forth any additional active method steps. The clause merely provides information about how the data gathered from the “assaying” step may be utilized. The clause also sets forth a property the exists between a combined score generated from the expression level of the set of marker genes and the patient's CAPRA score and whether the cancer is likely to recur or result in cancer-specific death. This property, which is inherent because it is based on an underlying biological phenomenon, does not need to be known or identified by the prior art. MPEP 2112.II.
Claim 58 requires a single active method step, which is “assaying cDNA derived from RNA obtained from a prostate cancer tumor sample from a patient with preoperative prostate cancer that has been assigned a Cancer of the Prostate Risk Assessment (CAPRA) score of 0-10”. It is noted that CAPRA scores range from 0-10 in view of para. 409 of the published application. Thus, the step broadly encompasses assaying preoperative prostate cancer samples from patients that are merely identified as having a CAPRA score, because their CAPRA score inherently has to be within the range of 0-10. This is true because CAPRA scores outside the range of 0-10 are not known to exist.
The “assaying” step is carried out by amplifying a set of marker genes in the cDNA, wherein the set of marker genes comprises at least three genes selected from the group consisting of ASFIB, ASPM, BIRC5, BUB1B, C18orf24, CDC2, CDC20, CDCA3, CDCA8, CDKN3, CENPF, CENPM, CEP55, DLGAP5, DTL, FOXM1, KIAA0101, KIF11, KIF20A, MCM10, NUSAP1, ORC6L, PBK, PLK1, PRC1, PTTG1, RAD51, RAD54L, RRM2, TK1, and TOP2A; and detecting an expression level of each gene in the set of marker genes by measuring the level of amplified cDNA for each gene in a set of marker genes.
Claim 58 concludes with a “wherein” clause. The clause does not set forth any additional active method steps. The clause merely provides information about how the data gathered from the “assaying” step may be utilized. The clause also sets forth a property the exists between a combined score generated from the expression level of the set of marker genes and the patient's CAPRA score and whether the cancer is likely to recur or result in cancer-specific death. This property, which is inherent because it is based on an underlying biological phenomenon, does not need to be known or identified by the prior art. MPEP 2112.II.
Claim Rejections - 35 USC § 103
The following is a quotation of the appropriate paragraphs of pre-AIA 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 –
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claim(s) 47, 48, 54, 55, 56, 57, 58, 59, 60, 61, 62 and 63 is/are rejected under pre-AIA 35 U.S.C. 102(b) as being anticipated by Cuzick (Lancet Oncol. 2011. 12:245-55; previously cited) in view of Lughezzani (European Urology. 2010. 57:562-568; previously cited).
The following rejections have been maintained.
Regarding claims 47, 48, 54, 55, 57, 58, 59, 60, 61 and 63, Cuzick teaches generating RNA and corresponding cDNA from prostate tissue (p. 247, Gene expression). The samples include pre-operative biopsy samples as patients treated with radical prostatectomy were excluded (p. 246, Transurethral resection of prostate (TURP) cohort).
The cDNA was used to assay for the expression of the recited genes of the claims, i.e., CCP genes (p. 246, CCP gene selection). CCP genes includes each of the recited genes of the claims. Expression was determined using amplification based TaqMan assays (p. 248).
Cuzick teaches providing an assessment of risk of recurrence or non-recurrence of prostate cancer based on a score that takes into account the expression of the CCP genes, PSA levels, tumor stage, Gleason score and margin status.
Regarding claims 56 and 62, Cuzick teaches the patients have been assigned a Gleason score (p. 249).
Cuzick does not specifically teach the sample is from a prostate cancer patient that has been assigned a CARPA score.
However, Lughezzani teaches pre-operative CARPA scores were known and are validated to assess a risk of prostate cancer recurrence.
Regarding claims 47, 56, 58 and 62, Lughezzani teaches that CARPA scores have a scale of 0 to 10 (p. 563, 2.3. Statistical evaluation). Lughezzani teaches the CARPA scores are based on PSA strata, an assigned Gleason sum strata, clinical tumour stage groupings, percentage of positive cores, and patient age (p. 563, 1. Introduction).
It would have been prima facie obvious to have modified the prostate samples provided for assessments of Cuzick and including samples from patients assigned a CARPA score. Cuzick provided assessments based on PSA levels, tumor stage, Gleason score and margin status, which as factors considered in a CARPA score. Thus, a CARPA score and those factors considered by Cuzick are based on overlapping factors. One would have been motivated to use the samples from patients assigned a CARPA score because CARPA scores are used and validated as being able to provide prostate cancer assessments to patients. There is a reasonable expectation of success as it simply modifies the type of samples analyzed by Cuzick and does not modify the actual assaying methodology of Cuzick.
Response to the traversal of the 103 rejections
The Remarks argue both the MPEP and the Federal Circuit have plainly instructed, "obviousness requires a suggestion of all limitations in a claim." And independent claims 47 and 59 have been amended to recite that "wherein the cancer is [or "is not, " respectively] likely to recur or result in cancer-specific death based on a combined score generated from the expression level of the set of marker genes and the patient's CAPRA score." The Remarks further argue neither Cuzick or Lughezzani disclose or suggest this limitation, and therefore both references fail to teach or suggest each and every limitation of amended independent claims 47 and 59, as required by MPEP § 2143. See p. 8.
The argument have been fully considered but are not persuasive. The amended “wherein” clauses of claims 47 and 59 do not limit how the positively, recited active method steps of claims 47 and 59 are performed. The “wherein” clause itself does not set forth any additional active method steps. The clause merely provides information about how the data gathered from the “assaying” step may be utilized. Therefore, the “wherein” clause is interpreted as not limiting the scope of the claimed method. See MPEP 2111.04.I. The clause also sets forth a property the exists between a combined score generated from the expression level of the set of marker genes and the patient's CAPRA score and whether the cancer is likely to recur or result in cancer-specific death. This property, which is inherent because it is based on an underlying biological phenomenon, does not need to be known or identified by the prior art. MPEP 2112.II.
Thus, in view of the broadest reasonable interpretation of the claims, the combination teaches and/or suggests all the elements of the positively recited active method steps of claims 47 and 58.
The Remarks argue the “wherein” clause contains a non-obvious combination because the specification shows that a combined score generated from the expression level of the set of marker genes and the patient's CAPRA score resulted in a p-value of <10-6, whereas the p-value of either the CAPRA or CCP score was reported as <10-4. The Remarks further argue in a multivariate model, the combined score generated from the expression level of the set of marker genes and the patient's CAPRA score resulted in a p-value of 0.0028, whereas the p-value for the CAPRA score was 0.58. See p. 8-9.
The arguments have been fully considered but are not persuasive. The arguments rely upon are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Claims 47 and 58 do not require active methods steps of “generating” a combined score. The claims merely require assaying the claimed samples by amplifying cDNA for a set of the recited genes and detecting the expression level of the amplified genes. As noted above, the amended “wherein” clauses do not limit the scope of the method’s positively recited active method steps.
It is also noted the property of any combined score does not need to be described in the prior art as it inherent because a natural biological phenomenon underlies the combined score.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 47-48 and 54-63 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 of U.S. Patent No. 10,876,164 B2 in view of Lughezzani (European Urology. 2010. 57:562-568; previously cited).
The following are new rejections necessitated by amendments to the claims.
Although the claims at issue are not identical, they are not patentably distinct from each other. The difference lies in the description the patient from which the prostate sample was obtained.
However, Lughezzani teaches an analysis that produces a CARPA score as described in the above rejections.
It would have been obvious to apply the gene expression analysis and prostate cancer patients having an assigned CARPA score.
The additional elements of the ‘164 patent are encompassed by the full scope of the present claims based on the use of the open term “comprising” in the preamble.
Claims 47-48 and 54-63 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 of U.S. Patent No. 10,954,568 B2 in view of Lughezzani (European Urology. 2010. 57:562-568; previously cited).
The following are new rejections necessitated by amendments to the claims.
Although the claims at issue are not identical, they are not patentably distinct from each other. The difference lies in the description the patient from which the prostate sample was obtained.
However, Lughezzani teaches an analysis that produces a CARPA score as described in the above rejections.
It would have been obvious to apply the gene expression analysis and prostate cancer patients having an assigned CARPA score.
The additional elements of the ‘568 patent are encompassed by the full scope of the present claims based on the use of the open term “comprising” in the preamble.
Claims 47-48 and 54-63 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 10,519,513 B2 in view of Lughezzani (European Urology. 2010. 57:562-568; previously cited).
The following are new rejections necessitated by amendments to the claims.
Although the claims at issue are not identical, they are not patentably distinct from each other. The difference lies in the description the patient from which the prostate sample was obtained.
However, Lughezzani teaches an analysis that produces a CARPA score as described in the above rejections.
It would have been obvious to apply the gene expression analysis and prostate cancer patients having an assigned CARPA score.
The additional elements of the ‘513 patent are encompassed by the full scope of the present claims based on the use of the open term “comprising” in the preamble.
Claims 47-48 and 54-63 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-7 of U.S. Patent No. 11,174,517 B2 in view of Lughezzani (European Urology. 2010. 57:562-568; previously cited).
The following are new rejections necessitated by amendments to the claims.
Although the claims at issue are not identical, they are not patentably distinct from each other. The difference lies in the description the patient from which the prostate sample was obtained.
However, Lughezzani teaches an analysis that produces a CARPA score as described in the above rejections.
It would have been obvious to apply the gene expression analysis and prostate cancer patients having an assigned CARPA score.
The additional elements of the ‘517 patent are encompassed by the full scope of the present claims based on the use of the open term “comprising” in the preamble.
Claims 58-63 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 27, 30-34 and 37-39 of copending Application No. 17/678,357 (reference application).
The following are new rejections necessitated by amendments to the claims.
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 47-48 and 54-57 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 27, 30-34 and 37-39 of copending Application No. 17/678,357 (reference application) in view of Lughezzani (European Urology. 2010. 57:562-568; previously cited).
The following are new rejections necessitated by amendments to the claims.
Although the claims at issue are not identical, they are not patentably distinct from each other. The difference lies in the description the patient from which the prostate sample was obtained.
However, Lughezzani teaches an analysis that produces a CARPA score as described in the above rejections.
It would have been obvious to apply the gene expression analysis and prostate cancer patients having an assigned CARPA score.
The additional elements of the ‘357 application are encompassed by the full scope of the present claims based on the use of the open term “comprising” in the preamble.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 47-48 and 54-63 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 38-45 of copending Application No. 16/664,216 (reference application) n view of Lughezzani (European Urology. 2010. 57:562-568; previously cited).
The following are new rejections necessitated by amendments to the claims.
Although the claims at issue are not identical, they are not patentably distinct from each other. The difference lies in the description the patient from which the prostate sample was obtained.
However, Lughezzani teaches an analysis that produces a CARPA score as described in the above rejections.
It would have been obvious to apply the gene expression analysis and prostate cancer patients having an assigned CARPA score.
The additional elements of the ‘216 application are encompassed by the full scope of the present claims based on the use of the open term “comprising” in the preamble.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to the traversal of the double patenting rejections
The Remarks argue the rejections did not address the amended limitations of the claims (p. 7).
The rejections have been reconsidered and have been maintained because the claims are rendered obvious in view of the above detailed claim interpretation.
The Remarks argue the rejections over the ‘357 and ’216 should be withdrawn if the other rejections of record are overcome because they were filed later than the present application (p. 7-8).
The rejections have been maintained. Once allowable subject is identified, the rejections will be reconsidered.
Conclusion
No claims 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 JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/ Primary Examiner, Art Unit 1682
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