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 .
Status of the Claims
Applicant’s election with traverse of Group III in the response filed January 30, 2025, and made final in the office action mailed May 7, 2025, is reiterated for the record. It is acknowledged that Applicant amended claims 36, 38, 41, 42, 45, and 46 and the specification in the response filed November 6, 2025.
Claims 1, 2, 4, 8-10, 12, 16 and 36-46 are pending.
Claims 1, 2, 4, 8-10, 12, 16 were withdrawn from consideration as being directed to non-elected invention.
Claims 36-46 are currently under examination.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Summary of Response to Applicant’s Arguments
This action is in response to the papers filed November, 6, 2025. Applicant’s remarks and amendments have been fully and carefully considered but are not found to be persuasive. Detailed arguments are documents on pages 17-21 of this office action. Any new grounds of rejection presented in this Office Action are necessitated by Applicant’s amendments. Any rejections or objections not reiterated herein have been withdrawn. This action is made FINAL.
As a result of the amendments to the claims, prior rejections under 35 U.S.C. 103 have been modified and new rejections have been raised against amended claims 41 and 42. These are set forth below.
Priority
This application is a 371 of International Application No. PCT/CA2019/051403, filed October 1, 2019, and claims the benefit of the filing date of Application No. 62/739,602, filed October 1, 2018.
Claim Rejections - 35 USC § 103
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.
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.
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.
Claim(s) 36 and 45 are/remain rejected under 35 U.S.C. 103 as being unpatentable over Olkhov-Mitsel et al. (Sci Rep., 2014 Mar 21:4:4432) in view of Ballhause et al. (US8962246B2, 2015) and Haldrup et al. (J Clin Oncol, 2013 Sep 10;31(26):3250-8).
Olkhov-Mitsel teaches materials for detecting prostate cancer in biological samples from patients, including a mastermix (pg. 5, Application of the multiplex MethyLight assay to measure DNA methylation in patient samples) and probes and primers for a selected methylation site in the APC gene (pg. 6, col. 2, Methods para. 3, MethyLight Assays).
Regarding claim 36, Olkhov-Mitsel teaches a mastermix for detecting prostate cancer in genomic DNA from a biological sample obtained from a subject (pg. 5, Application of the multiplex MethyLight assay to measure DNA methylation in patient samples and pg. 6, Methods, Patient samples and cell lines and DNA extraction and sodium bisulfite modification). Olkhov-Mitsel refers to the mastermix as a PCR reaction. The set of reagents taught by Olkhov-Mitsel is equivalent to a “kit” since no further structure is required in the claim than the mastermix and the probes and primers (i.e. there is no requirement for a box to contain the reagents, for example).
Olkhov-Mitsel teaches a mastermix comprising reaction buffer, deoxyribonucleotide triphosphate (dNTP); about 3.2 mM MgCl2, and ROX reference dye (pg. 2, col 2, para. 1). Olkhov-Mitsel teaches dNTPs within a range of 200-600 uM – this overlaps the claimed 200 uM with sufficient specificity that the limitation is considered to have been met. Olkhov-Mitsel teaches a range of MgCl2 concentrations from 3.5-10.5mM were tested in the mastermix. In Olkhov-Mitsel, 10.5mM MgCl2 was the optimal concentration for the MethyLight assay when used with 400 uM dNTPs, 1.0 units of Taq polymerase enzyme, primer concentrations of 8.0 uM for APC, HOXD3 and TGFB2, and 1.0 uM for ALU, probe concentrations of 2.66 uM for APC and TGFB2, 2.0 uM for HOXD3 and 0.1 uM for ALU. However, Olkhov-Mitsel teaches that optimization of reaction conditions is an important parameter for development of multiplex detection (pg. 2, Results) as discussed further below.
Regarding claim 45, Olkhov-Mitsel teaches the biological sample is selected from fresh prostate tissue, frozen prostate tissue, archival prostate tissue including formalin fixed tissue and paraffin embedded (FFPE tissue), blood, and urine (Introduction, last paragraph).
Olkhov-Mitsel does not explicitly teach the limitations (i) the mastermix comprises about 0.25U of DNA polymerase, and the mastermix comprises a concentration of BSA that stabilizes the DNA polymerase and neutralizes any potential inhibitors, (ii) primers and probes for a selected methylation site in each of the GAS6, GSTP1 and HAPLN3 genes recited in independent claim 36.
However, (i) Ballhause teaches a mastermix used for detecting cancer by DNA methylation patterns of genomic DNA in a biological sample from a subject (pg. 26, col 3-4). Ballhause further teaches the method in PPFE prostate samples (Example 12 pg. 66 col 84). Ballhause refers to a sample as a biopsy.
Regarding claim 36, Ballhause teaches the mastermix comprised reaction buffer (col 44, lines 42-49), dNTPs, MgCl2 and DNA polymerase (Col. 29, lines 36-44 and 59-67, continued in col. 30, line 1). Ballhause further teaches the DNA polymerase could be in the range 0.05-0.3 U/μl or 0.08-0.25 U/μl (sec. 29, lines 36-44 and 59-67), and thus could comprise about 0.25U of DNA polymerase. Ballhause further teaches the mastermix could comprise a concentration of BSA that stabilizes the DNA polymerase and neutralizes any potential inhibitors; (col. 83, lines 2-4). Ballhause teaches that the concentration of MgCl2 in the reaction mixture is adjusted to the concentration of nucleotides in the reaction mixture as it is well known for those skilled in the art (col 29 para. 4 – col. 30 para. 1). Ballhause further teaches, for example, a master mix containing 4mmol/l MgCl2 with either 0.25 mmol/l or 0.5mmol/l of each dNTP (col. 83, first para.) and a master mix containing 3mmol/l MgCl2 with 0.25 mmol/l of each dNTP (col 83, second para.).
It would have been obvious before the effective filing date of the claimed invention to have modified the master mix taught by Olkhov-Mitsel so as to include a concentration of BSA that stabilizes the DNA polymerase and neutralizes any potential inhibitors in the mastermix as taught by Ballhause because both Olkhov-Mitsel and Ballhause teach a mastermix used in detecting prostate cancer in genomic DNA in a biological sample from a subject.
It would have been obvious to one of ordinary skill in the art modify the master mix taught by Olkhov-Mitsel in view of Ballhause to include a concentration of BSA that stabilizes the DNA polymerase and neutralizes any potential inhibitors in the mastermix to achieve the predictable result providing a master mix that can be used for the detection of methylation in target genes.
The combined teachings of Olkhov-Mitsel and Ballhause do not teach primers and probes for a selected methylation site in each of the GAS6, GSTP1 and HAPLN3 genes.
However, (ii) Haldrup teaches detecting prostate cancer using primers and probes for selected methylation sites in the CCDC181, GAS6, GSTP1 and HAPLN3 genes (Abstract and pg. 3252, Results para. 3). In Haldrup, the CCDC181 gene is referred to as C1orf114.
Regarding claim 36, Haldrup teaches primers and probes for a selected methylation site in each of the GAS6, GSTP1 and HAPLN3 genes (pg. 3252, Results para. 3 and Data Supplement, pg. 43, Table A). Haldrup further teaches that diagnostic and prognostic tools for prostate cancer (PC) are suboptimal, causing overtreatment of indolent PC and risk of delayed treatment of aggressive PC (Abstract). Haldrup teaches that the GAS6, GSTP1 and HAPLN3 genes were novel candidate DNA methylation markers for PC with promising diagnostic and prognostic potential (Abstract). Haldrup further teaches that the precise clinical utility of these new candidate methylation markers for PC diagnosis should be further investigated in studies including other PC sample types (pg. 3255, first column).
One of ordinary skill in the art, upon reading Haldrup would have recognized the well-established hybridization and PCR techniques for detecting prostate cancer using primers and probes for selected methylation sites taught by Olkhov-Mitsel in view of Ballhause with the primers and probes for a selected methylation site in the GAS6, GSTP1 and HAPLN3 genes taught by Haldrup to provide diagnostic and prognostic tools for prostate cancer (PC).
It would have been obvious before the effective filing date of the claimed invention to modified the reagents taught by Olkhov-Mitsel in view of Ballhause so as to include primers and probes for selected methylation site in each of the GAS6, GSTP1 and HAPLN3 genes because Haldrup teaches that the GAS6, GSTP1 and HAPLN3 genes were novel candidate DNA methylation markers for PC with promising diagnostic and prognostic potential (Abstract of Haldrup et al.).
Thus, it would have been obvious to one of ordinary skill in the art to try the primers and probes for a selected methylation site in each of the GAS6, GSTP1, HAPLN3 genes to provide DNA hypermethylation biomarkers highly specific for PC (Haldrup, pg. 3254, Discussion, first para.).
Claim 37 is/remains rejected under 35 U.S.C. 103 as being unpatentable over Olkhov-Mitsel in view of Ballhause and Haldrup as applied to claims 36 and 45 above, and further in view of Ashour et al. (Prostate, 2014 Sep;74(12):1171-82).
The combined teachings of Olkhov-Mitsel et al., Ballhause et al. and Haldrup et al. as they relate to the elements of claim 37 that require primers and probes for a selected methylation site in the CCDC181 gene are documented above in the 103 rejection of claim(s) 36 and 45.
The combined teachings of Olkhov-Mitsel et al., Ballhause et al. and Haldrup et al. do not teach primers and probes for a selected methylation site in each of the GSTM2 and RASSF1 genes as recited in claim 37.
However, Ashour teaches materials for detecting prostate cancer in genomic DNA from a biological sample obtained from a subject (pg. 1173, column 2, para.1 and pg. 1176, Table II).
Regarding claim 37, Ashour teaches primers and probes for a selected methylation site in the GSTM2 and RASSF1 genes (pg. 1176, Table II).
Ashour further teaches a prostate cancer gene hypermethylation profile could identify groups of genes to be used for the early detection of neoplasia and that specifically discriminate populations of patients with different levels of risk of mortality from the disease (Abstract and Introduction para. 3). Ashour further teaches that the GSTM2 and RASSF1a genes are hypermethylated in prostate cancer (pg. 1176, Table II).
One of ordinary skill in the art, upon reading Ashour, would have recognized the desirability of trying the materials taught by Ashour for detecting prostate cancer using primers and probes for selected methylation sites in genes taught by Olkhov-Mitsel in view of Ballhause and Haldrup with the primers and probes for selected methylation sites in the GSTM2 and RASSF1a genes taught by Ashour because Ashour teaches that a prostate cancer gene hypermethylation profile could identify groups of genes to be used for the early detection of neoplasia and that specifically discriminate populations of patients with different levels of risk of mortality from the disease (Abstract and Introduction para. 3).
One of skill in the art would reasonably have expected the GSTM2 and RASSF1a genes to be applicable to a hypermethylation profile because Ashour teaches that the GSTM2 and RASSF1a genes were hypermethylated in prostate cancer (pg. 1176, Table II).
Thus, it would have been obvious to one of ordinary skill in the art to have tried the primers and probes for a selected methylation site in each of the GSTM2 and RASSF1a genes taught by Ashour to provide a prostate cancer gene hypermethylation profile for the early detection of neoplasia and that specifically discriminate populations of patients with different levels of risk of mortality from the disease (Ashour, Abstract and Introduction para. 3).
Claims 39 and 40 are/remain rejected under 35 U.S.C. 103 as being unpatentable over Olkhov-Mitsel in view of Ballhause and Haldrup as applied to claims 36 and 45 above, and further in view of Baden et al. (US 2008/0213781Al, 2008).
The combined teachings of Olkhov-Mitsel et al., Ballhause et al. and Haldrup et al. are documented above in the 103 rejection of claim(s) 36 and 45 above.
The combined teachings of Olkhov-Mitsel et al., Ballhause et al. and Haldrup et
al. does not teach the limitations of the SEQ ID NOs. recited in claim 39 and claim 40.
Regarding claim 39, Haldrup teaches probes including SEQ ID NOs. 23 and 35 for the GAS6 and HAPLN3 genes respectively (Table A, Supplementary Materials part A, pg. 43). Table A from Haldrup, Supplementary materials part A, listing the qMSP primers and probes taught by Haldrup, and the alignments of the Haldrup primers and probes to SEQ ID 23 and 35 are shown below.
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632
779
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91
401
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82
512
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Regarding claim 40, Haldrup teaches primers for the GAS6 gene that are functional equivalents of SEQ ID NOs. 22 and 24 of the claimed invention (See Haldrup, Data Supplement, pg. 43, Table A, qMSP primers). It is therefore inherent that the probe taught by Haldrup is for a methylation site between a forward primer of SEQ ID NO: 22 and a reverse primer of SEQ ID NO: 24.
The alignments of SEQ ID NOs. 22 and 24 and the Haldrup primers and probes are shown below.
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68
467
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62
476
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Further regarding claim 40, Haldrup teaches primers for the HAPLN3 gene that
are functional equivalents to a forward primer of SEQ ID NO: 34 and a reverse primer of SEQ ID NO: 36 (See Haldrup, Data Supplement, pg. 43, Table A, qMSP primers). It is therefore obvious to detect the selected methylation site of the HAPLN3 gene comprising a region between a forward primer of SEQ ID NO: 34 and a reverse primer of SEQ ID NO: 36. The alignments of SEQ ID NOs. 34 and 36 and the Haldrup primers and probes are shown below.
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63
496
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65
493
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Haldrup further teaches that diagnostic and prognostic tools for prostate cancer
(PC) are suboptimal, causing overtreatment of indolent PC and risk of delayed
treatment of aggressive PC (Abstract). Haldrup teaches that the GAS6 and
HAPLN3 genes were novel candidate DNA methylation markers for PC with promising
diagnostic and prognostic potential (Abstract). Haldrup further teaches that the precise clinical utility of these new candidate methylation markers for PC diagnosis should be
further investigated in studies including other PC sample types (pg. 3255, first column).
One of ordinary skill in the art, upon reading Haldrup would have recognized the
desirability of trying to detect prostate cancer using a primers and probes
for selected methylation sites taught by Olkhov-Mitsel in view of Ballhause with the
probes including SEQ ID NOs 23 and 35 for the GAS6 and HAPLN3 genes comprising selected methylation sites between SEQ ID NO. 22 and 24 and SEQ ID NO. 34 and 36, respectively taught by taught by Haldrup to provide diagnostic and prognostic tools for prostate cancer.
It would have been obvious before the effective filing date of the claimed
invention to have modified the reagents taught by Olkhov-Mitsel in view of Ballhause so as to include primers and probes for selected methylation site in each of
the GAS6 and HAPLN3 genes because Haldrup teaches that the GAS6 and HAPLN3 genes were novel candidate DNA methylation markers for PC with promising diagnostic and prognostic potential (Abstract).
Thus, it would have been obvious to one of ordinary skill in the art to try the
primers and probes for a selected methylation site in each of the GAS6 and
HAPLN3 genes to provide DNA hypermethylation biomarkers highly specific for PC (Haldrup, pg. 3254, Discussion, first para.).
Olkhov-Mitsel in view of Ballhause and Haldrup does not teach (i) a probe including SEQ ID NO. 8 as recited in claim 36 and (ii) the selected methylation site of the GSTP1 gene comprises a region between a forward primer of SEQ ID NO: 7 and a reverse primer of SEQ ID NO: 9 as recited in claim 40.
However, Baden teaches materials for detecting prostate cancer in genomic DNA from a biological sample obtained from a subject using methylation markers. Baden further teaches that the methylation status of GST genes such as GSTP1 can have important prognostic and diagnostic value for prostate cancer (pg. 1, para. 3). Baden further teaches that interrogation of different methylation sites within a CpG island of a gene could provide a more complete molecular portrait of a tumor (pg. 4, para 1.)
Regarding claim 39, Baden teaches (i) a probe including SEQ ID NO. 8 (pg. 10, SEQ ID NO. 1). The alignment of the probe taught by Baden is shown below.
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95
481
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Regarding claim 40, Baden teaches (ii) primers comprising SEQ ID NO, 7 (pg. 13, SEQ ID NO. 15) and SEQ ID NO. 9 (pg. 10, SEQ ID NO. 1) It is therefore inherent that the primers taught by Baden will hybridize to a selected methylation site of the GSTP1 gene comprising a region between a forward primer a forward primer of SEQ ID NO: 7 and a reverse primer of SEQ ID NO: 9. The alignments of the Baden sequences to the claimed SED ID NOs. 7 and 9 are shown below.
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71
443
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72
498
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One of ordinary skill in the art, upon reading Baden would have recognized the desirability of detecting prostate cancer using primers and probes for selected methylation sites taught by Olkhov-Mitsel in view of Ballhause and Haldrup using the selected methylation site of the GSTP1 gene including a probe comprising SEQ ID NO. 8 and comprising a selected methylation site region between a forward primer of SEQ ID NO: 7 and a reverse primer of SEQ ID NO: 9 as taught by Baden for interrogation of different methylation sites within a CpG island of a gene.
It would have been obvious before the effective filing date of the claimed invention to have modified the reagents taught by Olkhov-Mitsel in view of Ballhause and Haldrup so as to have included primers and probes for detecting a methylation site of the GSTP1 gene as taught by Baden because Baden teaches that the methylation status of GST genes such as GSTP1 can have important prognostic and diagnostic value for prostate cancer (pg. 1, para. 3).
Thus, it would have been to one of ordinary skill in the art to try including a selected methylation site of the GSTP1 gene comprising a region between a forward primer of SEQ ID NO: 7 and a reverse primer of SEQ ID NO: 9 as taught by Baden because Baden teaches that doing so could provide a more complete molecular portrait of a tumor (pg. 4, para. 1).
Claims 41 and 42 are rejected under 35 U.S.C. 103 as being unpatentable over Olkhov-Mitsel in view of Ballhause and Haldrup as applied to claims 36, further in view of Ashour, as applied to claim 37, and further in view of Barekati et al. (published July 27, 2010; Barekati et al. Obstet Gynecol Int. 2010; 2010:870865) and UniProt CCDC181 (publicly available Sept 2018; UniProt #Q5TID7), UniProt GSTM2 (publicly available Sept 2018; UniProt #P28161), UniProt RASSF1 (publicly available Sept 2018; UniProt #Q9NS23), and UniProt APC (publicly available Sept 2018; UniProt #P25054).
The limitations of claim 36 are addressed in the rejection over Olkhov-Mitsel in view of Ballhause and Haldrup above, and the limitations of claim 37 are addressed in the rejection over Olkhov-Mitsel in view of Ballhause, Haldrup, and Ashour above.
Regarding claims 41 and 42, Olkhov-Mitsel, Ballhause, Haldrup, and Ashour do not explicitly teach the primers and probes as follows:
Gene Target
Primers (forward, reverse)
Probes
CCDC181
SEQ ID NO: 10, 12
SEQ ID NO: 11
GSTM2
SEQ ID NO: 19, 21
SEQ ID NO: 20
RASSF1
SEQ ID NO: 4, 6
SEQ ID NO: 5
APC
SEQ ID NO: 31, 33
SEQ ID NO: 32
However, as discussed above, Haldrup does teach at least CCDC181 (as C1orf114) and APC as differentially methylated gene targets relevant to the diagnosis of prostate cancer (Abstract; pg. 3252, col. 1, par. 1), Ashour does at least teach GSTM2 and RASSF1 as differentially methylated gene targets relevant to the diagnosis of prostate cancer (Abstract; Pg. 1172, col. 1, par. 3; Table II), and Olkhov-Mitsel does teach at least APC as a differentially methylated gene target relevant to the diagnosis of prostate cancer (pg. 2, col. 1, par. 2).
Regarding claims 41 and 42, Barekati teaches the design of primers and probes in DNA methylation profiling assays (Table 1; pg. 3-4).
The genomic sequences and gene names/functions of the appropriate gene targets were known at the time of filing, as shown by the UniProt references for CCDC181, GSTM2, RASSF1, and APC.
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Olkhov-Mitsel, Ballhause, Haldrup, and Ashour with the teachings of Barekati to arrive at the primers and probes recited in claims 41 and 42. One would have been motivated to do so in order to achieve high analytical sensitivity and precision (Barekati: pg. 3, col. 1, par. 1). One would have had reasonable expectation of success because Barekati demonstrates that the principles of primer/probe design in the context of methylation-sensitive PCR are known (pg. 3-4: “Methylation-Specific PCR (MSP) Primers” and “Guidelines for Probe Designing”) and that resources are widely available (pg. 4: “Online Web Tools for Methylation Study”).
Claims 38, 43, 44 and 46 are/remain rejected under 35 U.S.C. 103 as being unpatentable over Mandelker et al. (Cancer Res. 2005 Jun 1;65(11):4963-8) in view of Olkhov-Mitsel et al. (Sci Rep., 2014 Mar 21:4:4432) and Ballhause et al. (US8962246B2, 2015).
Mandelker teaches materials for detecting esophageal cancer in genomic DNA from a biological sample obtained from a subject (Abstract and pg. 4964, column 1 last para.). Mandelker teaches primers and probes identical to those recited in the instant application for the UCHL1 gene. Thus, the probe taught by Mandelker inherently hybridizes to a region between the two primers and detects methylation status of a CpG site between the primers.
Regarding claim 38, Mandelker teaches primers and probes for a selected methylation site in the UCHL1 gene (pg. 4964, Real-time quantitative PCR).
Regarding claim 43, Mandelker teaches a probe including SEQ ID NO. 44 (pg.4964, Real-time quantitative PCR, 5'-TTCGGTCGTATTATTTCGCGTTGCGTAC-
3').
Regarding claim 44, Mandelker teaches wherein the selected methylation site of
the UCHLJ gene comprises a region between a forward primer of SEQ ID NO: 43 and a
reverse primer of SEQ ID NO:45. (pg. 4964, Real-time quantitative PCR, PGP9.5
TAQF: 5'-CGGCGAGTGAGATTGTAAGGTT-3' and PGP9.5 TAQR: 5'-
GAACGATCGCGACCAAATAAATAC-3').
Regarding claims 38 and 46, Mandelker does not teach a set of reagents (i.e. a kit) that includes the claimed mastermix for detecting aggressive prostate cancer. Mandelker is silent as to the mastermix that was used.
However, the combined teachings of Olkhov-Mitsel in view of Ballhause as they relate to the elements of claims 38 and 46 that require a master mix, including the sample type, are documented in the first 103 rejection above of this office action.
With respect to the limitation recited in the preamble of independent claim 38 “for detecting aggressive prostate cancer -p--”, which amounts to the intended use of claimed kit, and does not distinguish the products taught in the combined references from the products claimed. The combination of reagents taught by Olkhov-Mitsel in view of Ballhause and Mandelker could be used to detect aggressive prostate cancer
One of ordinary skill in the art, upon reading Mandelker, would have recognized
the desirability of providing reagents for detecting prostate cancer using primers and probes for selected methylation sites taught by Olkhov-Mitsel in view of Ballhause with the primers and probes for a selected methylation site in the UCHL1 gene taught by Mandelker because Mandelker teaches that UCHL1 was identified as a methylated gene in multiple cancers (Introduction, para. 2 and Discussion, para. 1).
Further, Mandelker teaches that UCHL1 was found to be an independent
prognostic factor as a single DNA marker for cancer prognosis (Pg. 4967, last para).
It would have been obvious before the effective filing date of the claimed invention to have provided a set of reagents (i.e. a kit) that included the mastermix taught by Olkhov-Mitsel in view of Ballhause so as to include and the primers and probes for the UCHL1 gene taught by Mandelker because both Olkhov-Mitsel in view of Ballhause and Mandelker teach detecting cancer using selected methylation sites. Further, Mandelker, teaches that UCHL1 was identified as a methylated gene in multiple cancers (Introduction, para. 2 and Discussion, para. 1) and that UCHL1 was found to be an independent prognostic factor as a single DNA marker (Pg. 4967, last para).
Response to Arguments
In the reply filed November 6, 2025, Applicant argued that the teachings of Ballhause could not be adapted to teach the claimed assay in combination with Olkhov-Mitsel because there is no reason a priori to expect that the assay parameters in Ballhause (designed for maximizing recovery of any DNA) would be applicable to the assay of claims 36 and 38, and render the accuracy required for diagnostic purposes (for methylation-specific PCR of selected regions in the identified genes).
These arguments have been fully considered and are not found persuasive. To reiterate from the rejections above, both Olkhov-Mitsel and Ballhause are directed to the detection of prostate cancer in biological samples using nucleic acid amplification methods. Therefore, the teachings of Ballhause regarding the concentration of the polymerase, the presence of BSA, and the use of specific primers and probes would have been obvious to combine with the teachings of Olkhov-Mitsel, with reasonable expectation of success given the same field of endeavor. The fact that Ballhause’s assay was designed for archived samples does not preclude the use of Ballhause’s teachings in the combination, as there is no evidence to suggest that they would be inoperable in the claimed invention. While Ballhause explicitly describes use with paraffin-embedded and/or fixed-tissue samples, these are standard sample types used for diagnostic purposes. In fact, both Olkhov-Mitsel (pg. 2, col. 1, 2nd par.) and the instant application (claims 45 and 46) are directed to the use of nucleic acid amplification methods in the same kinds of samples, and Olkhov-Mitsel teaches optimization of reaction conditions as an important parameter of multiplex detection (pg. 2, Results). Furthermore, MPEP 2144.05(II)(A) states that “Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical.” Barring evidence that the claimed parameters are critical and not merely the result of routine optimization, the fact that Ballhause was not optimized for selected combinations of regions of genes is not relevant because the combination of Ballhause and Olkhov-Mitsel as a whole teaches the claimed limitations.
In the reply, Applicant argued that Haldrup does not reasonably suggest combining two of its six recited genes AOX1, C1orf11f (CCDC181), GAS6, HAPLN3, KLF8, and MOB3B for use with GSTP1 to provide GAS6, GSTP1, and HAPLN3 as DNA methylation markers for prostate cancer. Applicant argued also that Haldrup does not teach or suggest assays based on specific combinations or sub-combinations of the 10 genes targets of Table A as potential methylation biomarkers for prostate cancer and that any suggestion that the claimed three genes could be derived from Haldrup is based on hindsight.
These arguments have been fully considered and are not found persuasive. In response to applicant's argument that Haldrup does not explicitly teach the exact three-gene assay required by the claimed invention, the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). As stated in the original rejections and reiterated here, Haldrup discloses the use of GAS6, HAPLN3, and GSTP1 as markers for prostate cancer (pg. 3252, col. 1, par. 3). Haldrup explicitly discusses the need for better diagnostic/prognostic tools for prostate cancer (Abstract), the use of a multigene methylation signature for that purpose, and further investigation of the biomarkers (pg. 3255, col. 1). These elements provide motivation, with reasonable expectation of success, to combine the teachings of Haldrup with the teachings of Olkhov-Mitsel and Ballhause to arrive at the claimed invention. In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
In the response, Applicant questioned whether the Examiner intended to include the APC gene in the rejection of claim 37. It is noted that the office action dated May 7, 2025 addressed the APC gene on page 7-8, as taught by Olkhov-Mitsel.
In the response, Applicant argued that the listing of prostate cancer-related hypermethylation at the genes in Table II does not suggest or teach selecting GSTM2, RASSF1, and APC as candidates for use in a prostate cancer assay, and therefore suggestion of the claimed combination of genes is based on hindsight.
These arguments have been considered and found unpersuasive. As stated above, the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). Ashour teaches that RASSF1, GSTM2, and APC are genes significantly hypermethylated in prostate cancers (Table II), and that multi-gene prostate cancer hypermethylation profiles could be used diagnostically in prostate cancer patients (pg. 1172, col. 2, 1st par.). As discussed in the rejections above, the combined teachings of Olkhov-Mitsel, Ballhause, Haldrup and Ashour would have suggested assaying the claimed combination of genes to those of ordinary skill in the art. Regarding hindsight, as stated above, obviousness based on a reconstruction of hindsight reasoning is allowed so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure. The references relied upon in the rejections of the instant claims were publicly available before the effective filing date of the instant invention and represent knowledge within the level of ordinary skill for the claimed invention.
In the response, Applicant argued that “the rejection citing the combination of four references wherein Haldrup is relied upon as rendering obvious the selection of two of the genes and Baden is relied upon as rendering obvious the selection of the third gene in Applicants' claims, wherein each reference further discloses selections of other genes, lacks merit. There is no suggestion in the combined teachings of the references to select the specific combination of genes recited in the claims. Rather, the claimed combination of genes was deduced through the experiments and analyses described in Applicants' disclosure.” However, as discussed above, the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). The combination of references would render it obvious to target the genes recited in claims 39 and 40 because Haldrup teaches that the GAS6, GSTP1 and HAPLN3 genes are DNA methylation markers for prostate cancer with promising diagnostic and prognostic potential which should be further investigated further (Abstract; pg. 3255, first column) and Baden teaches that the methylation status of GST genes such as GSTP1 can have important prognostic and diagnostic value for prostate cancer (pg. 1, para. 3).
In the response, Applicant argued that amended claim 38 recites features that are not taught or suggested by Olkhov-Mitsel in view of Ballhause and/or Mandelker. This argument has been considered and found partially persuasive. As a result of the amendments to claims 36 and 38 regarding the concentration of dNTPs, the rejections have been modified and are set forth above.
Conclusion
No claims are 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.
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/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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