DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 2/9/2026 has been entered.
The claims filed 1/6/2026 are under consideration in this Office action.
The amendments and arguments presented in the papers filed 1/6/2026 ("Remarks”) entered with the RCE dated 2/9/2026 have been thoroughly considered. The issues raised in the Office action dated 11/12/2025 listed below have been reconsidered as indicated.
a) The rejections of: claim(s) 47-48 and 54-57 under pre-AIA 35 U.S.C. 102(b) as being anticipated by Cuzick (Lancet Oncol. 2011. 12:245-55); and claim(s) 58-63 under pre-AIA 35 U.S.C. 102(b) as anticipated by or, in the alternative, under pre-AIA 35 U.S.C. 103(a) as obvious over Cuzick (Lancet Oncol. 2011. 12:245-55), are withdrawn because Cuzick is silent regarding CAPRA scores.
b) The rejections of claim(s) 58-63 under pre-AIA 35 U.S.C. 102(b) as anticipated by or, in the alternative, under pre-AIA 35 U.S.C. 103(a) as obvious over Stone (WO 2010/080933 A1), are withdrawn because Stone is silent regarding CAPRA scores.
c) The provisional rejections of claims 47-48 and 54-57 on the ground of nonstatutory double patenting as being unpatentable over claims 64-83 of copending Application No. 17/484,179 (reference application) in view of Lughezzani (European Urology. 2010. 57:562-568) are rendered moot in view of the abandonment of the ‘179 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.
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 47-48 and 54-63 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exceptions without significantly more.
The following are new rejections addressing the amendments to the claims.
The claims recite a series of steps and thus are processes, one of the four statutory classes.
The claim(s) recite(s) a step of:
“providing an assessment that the cancer is likely to recur or result in cancer-specific death based on the expression level of the set of marker genes and the patient’s CAPRA score” (claim 47); or
“providing an assessment that the cancer is not likely to recur or result in cancer-specific death based on the expression level of the set of marker genes and the patient’s CAPRA score” (claim 58).
The steps represent an abstract idea in that they: 1) encompass a mental process of “providing” an assessment by reaching a conclusion based on the expression level and the patient’s CAPRA score; and/or 2) encompass the coordination of human activity by having one human “provide” information to another human.
The claims include the following additional limitations of:
(claim 47) 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, wherein the assaying comprises:
(i) 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 ASF1B, ASPM, BIRC5, BUB1B, C18orf24, CDC2, CDC20, CDCA3, CDCA8, CDKN3, CENPF, CENPM, CEP55, DLGAP5, DTL, FOXM1, KIAA0101, KIF11, KIF20A, MCM10, NUSAPI, ORC6L, PBK, PLK1, PRC1, PTTG1, RAD51, RAD54L, RRM2, TK1, and TOP2A; and
(ii) 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; or
(claim 58) 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, wherein the assaying comprises:
(i) 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 ASF1B, ASPM, BIRC5, BUB1B, C18orf24, CDC2, CDC20, CDCA3, CDCA8, CDKN3, CENPF, CENPM,CEP55, DLGAP5, DTL, FOXM1, KIAA0101, KIF11, KIF20A, MCM10, NUSAPI, ORC6L, PBK, PLK1, PRC1, PTTG1, RAD51, RAD54L, RRM2, TK1, and TOP2A; and
(ii) 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.
The judicial exceptions are not integrated into a practical application because the claims do not involve:
improvements to the functioning of a computer or to any other technology or technical field;
applying or using the judicial exceptions to effect a particular treatment or prophylaxis for a disease or medical condition;
applying the judicial exception with, or by use of, a particular machine; or
effecting a transformation or reduction of a particular article to a different state or thing.
The claimed limitations add insignificant extra-solution activity to the judicial exceptions. The additional limitations constitute data gathering.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims encompass using polymerases to amplify and detect DNA which the courts have recognized as well-understood, routine and conventional laboratory activity. See MPEP 2106.05(d). The claims encompass the use of a well-known gene panel in view of the instant specification (e.g., para. 46) and the references of record and the use of any known techniques as described in the instant specification (e.g., para. 49, 54, 56, 142 and 182). The claims do not require anything that is not routine and conventional in the field of measuring and analyzing expression levels.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 48, 56, 59 and 62 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.
The following are new rejections.
Regarding claims 48 and 59, the claim recites “the set of marker genes comprises at least four test genes”. It is unclear what distinguishes the “at least three genes” from the “at least four test genes” when selected from the recited group. It is unclear if the claim further limits the “at least three genes” to “at least four” or if the claim requires at least 7 genes, “at least three genes” and “at least four test genes”.
Regarding claims 56 and 62, the claims each recite “the Gleason score”. The recitation lacks proper antecedent basis in view of the amendments to independent claims 47 and 58.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 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 –
(a) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
Claim(s) 47-48 and 54-63 is/are rejected under pre-AIA 35 U.S.C. 102(a) as being anticipated by Cooperberg (Meeting Abstract: 2012 Genitourinary Cancers Symposium. February 10, 2012).
Regarding claims 47-48 and 54-63, Cooperberg teaches analyzing the expression of 31 CCP genes and CAPRA scores and making assessments of a prostate cancer patients likelihood of recurrence.
The ordinary artisan would recognize that determining the expression levels of the CCP genes involves making cDNA from RNA and detecting the levels of expression.
The ordinary artisan would recognize the “31 CCP genes” are the same 31 genes recited in the claims.
Claim(s) 47-48 and 54-63 is/are rejected under pre-AIA 35 U.S.C. 102(a) as being anticipated by Cooperberg (The Journal of Urology. May 23, 2012. 187(4S):e580).
Regarding claims 47-48 and 54-63, Cooperberg teaches analyzing the expression of 31 CCP genes and CAPRA scores and making assessments of a prostate cancer patients likelihood of recurrence.
The expression of the CCP genes is determined as described by Cooperberg by extracting RNA from paraffin-embedded RP specimens and converted to cDNA and the CCP genes were amplified and quantified in triplicate, and the CCP score was calculated as the normalized average of CCP gene expression.
The ordinary artisan would recognize the “31 CCP genes” are the same 31 genes recited in the claims.
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).
The following are new rejections necessitated by the amendments to the claims.
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 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 based on the expression of the CCP genes, PSA levels, tumor stage, Gleason score and margin status.
Regarding claims 56 and 62, Cuzick teaches a Gleason score of 7 based on primary and second Gleason scores of 3+4 or 4+3 (p. 249).
Cuzick does not specifically teach the CARPA score of the prostate cancer patient that provided the RNA is known or providing an assessment based on the CARPA score.
However, Lughezzani teaches CARPA scores were known and are validated to assess a risk of prostate cancer recurrence.
Regarding claims 47 and 58, 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, 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 provided assessments of Cuzick based on CCP gene expression and CARPA scores. 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 CARPA score in combination with the CCP gene expression levels because CARPA scores are used and validated as being able to provide prostate cancer recurrence assessments to patients. There is a reasonable expectation of success as Cuzick takes into consideration factors that contribute to the CARPA score and would provide the user with a more holistic view of the prostate cancer patient’s status.
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 54-57 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).
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 CARPA score to the prostate cancer patients in order to provide an assessment.
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 54-57 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).
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 CARPA score to the prostate cancer patients in order to provide an assessment.
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 54-57 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).
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 CARPA score to the prostate cancer patients in order to provide an assessment.
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 54-57 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).
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 CARPA score to the prostate cancer patients in order to provide an assessment.
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).
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 CARPA score to the prostate cancer patients in order to provide an assessment.
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.
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 38-45 of copending Application No. 16/664,216 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other.
The difference lies in the steps of “obtaining” a preoperative concentration of PSA and a Gleason score.
However, obtaining PSA levels and Gleason scores for prostate cancer patients, such as those encompassed by claim 27 of the ‘216 application, is well-known and routine.
It would have been prima facie obvious to have modified the methods of the ‘216 claims to include the steps of obtaining a preoperative concentration of PSA and a Gleason score, as it is routinely done for prostate cancer patients.
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 new rejections necessitated by amendments are described above.
The Remarks argue the rejections over the ‘179, ‘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.
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.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/JOSEPH G. DAUNER/ Primary Examiner, Art Unit 1682
Prosecution Insights