DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
2. 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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 18 September 2025 has been entered. 3. Applicant's arguments and amendments to the claims presented in the reply of 18 September 2025 have been fully considered but do not place the application in condition for allowance. All rejections not reiterated herein are hereby withdrawn.
Claim Status
4. Claims 26-28, 31, 38, 39, 43, 47, 48 and 51-56 are pending.
Claims 27, 31, 47, 48 and 51-56 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim. Note that claims 27, 31, 47, 48 were amended in the reply of 04 March 2025 to recite a non-elected combination of genes.
Claims 26, 28, 38, 39 and 43 read on the elected invention and have been examined herein.
Maintained / Modified Claim Rejections - 35 USC § 103
5. In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 26, 28, 38, 39 and 43 is/are rejected under 35 U.S.C. 103 as being unpatentable over Allawi et al (U.S. 20170335401, published 23 Nov 2017; cited in the IDS of 05/26/2021), in view of Chen et al (J. Pathol. 2015. 235: 397-407; cited in the IDS of 05/26/2021) and Feng et al (Epigenomics. Jan 2017. 9(2): 137-153; cited in the IDS of 03/04/2024).
Allawi et al teaches methods, compositions and kits for detecting differentially methylated DNA regions of markers in test samples, wherein the markers include the BARX1, FLJ45983, ZNF781 and SOBP genes (e.g., para [0004-0005] and [0007]).
For instance, Allawi (para [0007]) teaches:
“While not limiting the invention to any particular application or applications, the method finds use, e.g., in characterizing samples from a subject having or suspected of having lung cancer, when the methylation state of the methylation marker is different than a methylation state of that marker assayed in a subject that does not have a neoplasm. In preferred embodiments, the methylation marker comprises a chromosomal region having an annotation selected from BARX1, LOC100129726, SPOCK2, TSC22D4, MAX.chr8.124, RASSF1, ZNF671, ST8SIA1, NKX6_2, FAM59B, DIDO1, MAX_Chr1.110, AGRN, SOBP, MAX_chr10.226, ZMIZ1, MAX_chr8.145, MAX_chr10.225, PRDM14, ANGPT1, MAX.chr16.50, PTGDR_9, ANKRD13B, DOCK2, MAX_chr19.163, ZNF132, MAX_chr19.372, HOXA9, TRH, SP9, DMRTA2, ARHGEF4, CYP26C1, ZNF781, PTGDR, GRIN2D, MATK, BCAT1, PRKCB_28, ST8SIA_22, FLJ45983, DLX4, SHOX2, EMX1, HOXB2, MAX.chr12.526, BCL2L11, OPLAH, PARP15, KLHDC7B, SLC12A8, BHLHE23, CAPN2, FGF14, FLJ34208, B3GALT6, BIN2_Z, DNMT3A, FERMT3, NFIX, S1PR4, SKI, SUCLG2, TBX15, ZDHHC1, and ZNF329.”
Allawi teaches that B3GALT6 can be used in the methylation detection assays as a reference gene (para [0144]).
Allawi teaches that differentially methylated regions are preferably detected using a flap endonuclease assay (e.g., (para [0018]). The flap endonuclease assay comprises treating test sample DNA with bisulfite, which is a methylation-specific reagent that changes a nucleotide sequence of the DNA in a manner that reflects a methylation status of the DNA, amplifying bisulfite-converted DNA with primers specific for differentially methylated regions in target nucleic acids, and contacting the amplified nucleic acids with a flap oligonucleotide and an invasive oligonucleotide and then contacting the resulting complexes with a FEN-1 endonuclease (e.g., para [0018], [0065], [0073] and [0305-0306]).
Allawi exemplifies primers and flap oligonucleotides for detecting differentially methylated regions in each of the BARX1, FLJ45983, ZNF781 and SOBP marker genes (Table 3).
The reference further teaches providing the reagents required to practice the methylation detection methods disclosed therein in a kit, including primers that hybridize to bisulfite-converted DNA, flap oligonucleotides that hybridize to bisulfite converted DNA and bisulfite (e.g., para [0019], [0022] and [0077])).
Allawi (para [0105]) also teaches:
“reagents (e.g., primers, probes) specific for one or more markers are provided alone or in sets (e.g., sets of primers pairs for amplifying a plurality of markers). Additional reagents for conducting a detection assay may also be provided (e.g., enzymes, buffers, positive and negative controls for conducting QuARTS, PCR, sequencing, bisulfite, or other assays). In some embodiments, the kits containing one or more reagent necessary, sufficient, or useful for conducting a method are provided. Also provided are reactions mixtures containing the reagents. Further provided are master mix reagent sets containing a plurality of reagents that may be added to each other and/or to a test sample to complete a reaction mixture.”
The teachings of Allawi indicate that it is routine and well-within the skill of the ordinary artisan to combine primers for detecting differentially methylated regions of different genes in a reaction mixture and to perform multiplex amplification reactions. See, e.g., para [0061] which discloses conventional multiplex PCR assays; and para [0232], [0246-0258], [0274] and [0306-0307] which exemplify multiplex amplification reactions for the detection of differentially methylated DNA regions.
In particular, at para [0274], Allawi exemplifies reaction mixtures containing primers for amplifying 30 marker genes, including each of the BARX1, FLJ45983, ZNF781 and SOBP marker genes.
Accordingly, Allawi teaches kits and compositions comprising reaction mixtures comprising primer pairs configured to amplify differentially methylated regions of methylation markers, including BARX, FLJ45983, ZNF781, and SOBP, in sequence- converted DNA, wherein the sequence-converted DNA is formed by treating human DNA with a methylation-specific reagent that changes a nucleotide sequence of the DNA in a manner that reflects a methylation status of the DNA, flap oligonucleotides for each of the BARX, FLJ45983, ZNF781, and SOBP markers, wherein each flap oligonucleotide has a region that specifically hybridizes to a differentially methylated region of the marker and a 5' flap portion that is unpaired when the flap oligonucleotide specifically hybridizes to a differentially methylated region of a methylation marker in the sequence-converted DNA; a reference primer pair to amplify a reference nucleic acid, such as B3GALT6, and a reference flap oligonucleotide that includes a region that specifically hybridizes to portion the nucleic acid amplified by the reference primer pair and which includes a 5' flap portion that is unpaired when the reference flap oligonucleotide specifically hybridizes to the reference nucleic acid.
Allawi does not teach kits or compositions comprising reaction mixtures that further include primers for amplifying a differentially methylated region of bisulfite-converted IFFO1 and HOPX DNA, and flap oligonucleotides that specifically hybridize to differentially methylated sequences in amplified IFFO1 and HOPX DNA.
However, Feng teaches that IFFO1 is differentially methylated in small-cell lung cancer (SCLC), as compared to normal lung tissue (abstract; p. 147; and Figure 1 and Figure 3A). It is shown that hypermethylation of IFFO1 in lung cancer tissue correlates with decreased expression of IFFO1 (Figure 3A). Feng teaches that it has been previously shown that methylation of IFFO1 is a strong prognostic indicator for lung cancer (p. 149, col. 1).
Chen et al teaches that HOPX is differentially methylated in lung cancer and that HOPX hypermethylation is correlated with decreased HOPX expression (e.g., abstract; p. 400, col. 2). Chen (p.400, col. 2) states:
“The methylation status of HOPX was further analysed by methylation-specific-PCR (MSP) with primers designed in the promoter region. In line with the results from BS, MSP showed that HOPX was totally or partially methylated in lung cancer cell lines without HOPX expression…
The utility of the MSP primer encouraged us to analyse the methylation status of HOPX DNA in primary lung tumours. Univariate and multivariate analysis revealed that decreased HOPX protein expression was significantly correlated with HOPX DNA methylation (p=0.011 and p =0.004, respectively; Table 2).”
In view of the teachings of Feng and Chen, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the kits of Allawi so as to have included in the reaction mixture present in the kits primers for amplifying a differentially methylated region of bisulfite-converted IFFO1 and HOPX DNA, and flap oligonucleotides that specifically hybridize to differentially methylated sequences in amplified IFFO1 and HOPX DNA. One would have been motivated to have done so in order to have provided reagents for detecting additional biomarkers that could be used to diagnose and/or characterize lung cancer, thereby enhancing the use of the kit for screening for biomarkers of lung cancer. The skilled artisan would have had a reasonable expectation of success since Feng teaches differentially methylated sequences of IFFO1 that are correlated with lung cancer and Cheng teaches differentially methylated sequences of HOPX that are correlated with lung cancer.
Regarding claims 28 and 39, as discussed above, Allawi teaches use of the methylation-specific reagent of bisulfite to treat the DNA (e.g., [0018-0019] and [0046]).
Regarding claim 38, Allawi teaches compositions comprising a mixture of target nucleic acids that are bisulfite converted and oligonucleotides that hybridize to differentially methylated target nucleic acids that have been bisulfite converted (para [0024] and [0105]). It is disclosed that the compositions and kits can include additional reagents for performing the detection method, including enzymes (para [0077]) and that thermostable FEN-1 is used in the flap detection assays (e.g., para [0068]). Allawi states that in the flap detection assays, “(t)he first complex is a substrate for a flap endonuclease, e.g., a FEN-1 endonuclease, which cleaves the flap oligonucleotide to release the 5′ flap portion” (para [0073]).
Accordingly, modification of the flap detection method of Allawi so as to have included reagents for also detecting the methylation status of differentially methylated regions in IFFO1 and HOPX marker genes would have resulted in compositions comprising a reaction mixture comprising a solution comprising sequence-converted DNA formed by treating human DNA with a methylation-specific reagent that changes a nucleotide sequence of the DNA in a manner that reflects a methylation status of the DNA; ii) IFFO1, HOPX, BARX1, FLJ45983, ZNF781 and SOBP amplicon DNAs amplified from the sequence-converted DNA by extension of pairs of primers complementary to methylation markers IFFO1, HOPX, BARX1, FLJ45983, ZNF781, and SOBP in the sequence-converted DNA, the amplicon DNAs comprising differentially methylated regions of the methylation markers comprising nucleotide sequences changed by treatment with the methylation-specific reagent; and iii) a thermostable FEN-1 endonuclease.
Regarding claim 43, Allawi teaches that the reaction mixture for performing the flap detection assay / “QuARTS Assay” includes “3-(n-morpholino) propanesulfonic acid (MOPS)” (para [0231]).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have included 3-(n-morpholino) propanesulfonic acid (MOPS) in the modified compositions of Allawi because Allawi teaches that this is a typical reagent that is present in the reaction mixture used to perform the flap detection assay.Response to Remarks:
The response states:
“None of the cited references point to the selection of methylation markers BARX, FLJ45983, ZNF781 and SOBP as a group of four markers selected from the numerous markers disclosed by Allawi, for use together in combination with IFFO and HOPX. In making the rejection, the Examiner selects a subset of methylation markers from a larger set of markers disclosed by Allawi, and uses to instant claims to find HOPX as a methylation marker in one reference (Chen) and to find IFFO as a methylation marker in another reference (Feng), to arrive at the elements of Applicant's claimed kits and compositions. There is no evidence in the record that such a combination would be successful, e.g., that adding either HOPX or IFFO], or the combination of the two, would have any beneficial effect on, for example, the sensitivity and/or specificity of a PCR flap assay conducted using kits for amplifying differentially methylated regions of methylation markers BARX, FLJ45983, ZNF781 and SOBP in sequence-converted human DNA, or on compositions related to such PCR flap assays, as set forth in the instant claims. As such, the obviousness rejection is clearly based on an "obvious to try" logic - i.e., that it would be obvious to try the various potential additional markers to arrive at the claimed invention.”
These arguments have been fully considered but are not persuasive. Regarding the arguments pertaining to the need to select the subset of the four markers of BARX, FLJ45983, ZNF781 and SOBP from the 30 marker genes disclosed in Allawi, there is no reason that a subset of the methylation markers of Allawi would need to be selected since the present claims recite the open claim language of comprising and thereby include any number of additional methylation markers. The present claims are not directed to a reaction mixture that consists of only the seven primers that amplify a differently methylated region of each of the BARX, FLJ45983, ZNF781, SOBP, IFFO1, HOPX and B3GALT6 and the recited 8 flap oligonucleotides. The present claims do not exclude the presence of additional primers and flap oligonucleotides in the reaction mixture. Further, Allawi teaches that the methods disclosed therein include assaying for a subset of the markers, including “2 to 21 markers, preferably 2 to 8 markers, preferably 4 to 6 markers” (para [0008]). Thus, the teachings of Allawi do suggest reaction mixtures comprising primers to a subset of the marker genes including the BARX, FLJ45983, ZNF781, SOBP markers and the reference marker gene of B3GALT6.
Secondly, the cited Feng and Chen references do provide the motivation to also assay for the methylation of the IFFO1 and HOPX genes since these references teach that these genes are differentially methylated in lung cancer. It is maintained that the skilled artisan would have had a reasonable expectation of success since Feng teaches differentially methylated sequences of IFFO1 that are correlated with lung cancer and Cheng teaches differentially methylated sequences of HOPX that are correlated with lung cancer. Further, even though there is a large number of alternative genes with differentially methylated regions that could be selected to be included in the method of assaying for differential methylation as indicative of lung cancer and the characteristics of lung cancer (and thereby a large number of different reaction mixtures comprising primers and flap oligonucleotides for detecting differentially methylated genes), selecting alternative or additional biomarker genes to be assayed would have been obvious and well within the skill of the ordinary artisan given the teachings of Feng and Chen that the methylation level of IFFO1 and HOPX genes are indicative of lung cancer .
Applicant further argues that “the selecting the combination of BARX,FLJ45983, ZNF781 and SOBP of Allawi with the HOPX and IFFO is not suggested by any of the references, is not a "predictable" combination, and success or failure of making the combination cannot be predicted based on the teachings of the references.”
However, the claims are directed to kits and compositions comprising reaction mixtures comprising primers to the DMRs of the BARX, FLJ45983, ZNF781, SOBP, IFFO1, HOPX and B3GALT6 genes and the recited 8 flap oligonucleotides. The claimed kits and compositions do not require any particular outcome. Applicant does not provide any evidence or scientific arguments to support their conclusion that one would not have a reasonable expectation of success of combining primers to known DMR sequences in the BARX, FLJ45983, ZNF781, SOBP, IFFO1, HOPX and B3GALT6 genes and flap oligonucleotides that bind to the DMRs in the BARX, FLJ45983, ZNF781, SOBP, IFFO1, HOPX and B3GALT6 amplification products. The teachings of Allawi indicate that it is routine and well-within the skill of the ordinary artisan to combine primers for detecting differentially methylated regions of different genes in a reaction mixture and to perform multiplex amplification reactions. See, e.g., para [0061] which discloses conventional multiplex PCR assays; and para [0232], [0246-0258], [0274] and [0306-0307] which exemplify multiplex amplification reactions for the detection of differentially methylated DNA regions. Thus, it is maintained that combining the primers and flap oligonucleotide probes in a reaction mixture would have been obvious and well within the skill of the ordinary artisan.
Note that Applicant has not established any unexpected results obtained with the broadly claimed reaction mixtures comprising any primers and flap oligonucleotides for detecting any differentially methylated region in the BARX, FLJ45983, ZNF781, SOBP, IFFO1, and HOPX genes and the reference B3GALT6 gene. In the absence of evidence to the contrary, it is maintained that the broadly claimed reaction mixtures comprising the primers and flap oligonucleotides for the BARX, FLJ45983, ZNF781, SOBP, IFFO1, HOPX and B3GALT6 genes would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Modified Rejection / Double Patenting
6. 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 filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual 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/apply/applying-online/eterminal-disclaimer.
Claims 26, 28, 38, 39 and 43 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 65-72 of copending Application No. 17/638,840 in view of Allawi et al (U.S. 20170335401, published 23 Nov 2017; cited in the IDS of 05/26/2021).
Claim 71 of ‘840 recites a method comprising “c) extracting from blood sampled from the subject at least one methylation marker DNA and at least one reference marker DNA; d) measuring an amount of at least one methylation marker DNA; e) measuring an amount of at least one reference marker DNA; wherein the amount of the at least one methylation marker DNA as a percentage of the amount of the reference marker DNA is indicative of an amount of the at least one methylation marker DNA in the blood sampled from a subject” and claim 72 recites the method of claim 71 wherein “at least one methylation marker DNA comprises a nucleotide sequence associated with at least one of BARX, FLJ45983, HOPX, ZNF781,…SOBP, and IFFO1.”
Accordingly, the methods claimed in ‘840 encompasses determining the methylation status of differentially methylated target regions in the IFFO1, HOPX, BARX1, FLJ45983, ZNF781 and SOBP genes.
The claims of ‘840 do not specify the methodology used to detect the methylation status of the differentially methylated target regions in the IFFO1, HOPX, BARX1, FLJ45983, ZNF781 and SOBP genes and do not recite the present claimed kits and compositions comprising the reagents for detecting the methylation status of differentially methylated target regions in the IFFO1, HOPX, BARX1, FLJ45983, ZNF781 and SOBP genes.
However, Allawi et al teaches a quantitative method for detecting the methylation status of differentially methylated regions in target nucleic acids using flap oligonucleotides, and particularly discloses the “QUARTS assay” (e.g., para [0134]). Allawi teaches that the methods can be used to , detect differentially methylated DNA regions of markers in test samples, including the markers of BARX1, FLJ45983, ZNF781 and SOBP g (e.g., para [0004-0005] and [0007]). Allawi teaches that that the detection methods disclosed therein can also assay for the methylation status of the reference marker of B3GALT6 (para [0144]).
It is disclosed that the flap endonuclease assay comprises treating test sample DNA with bisulfite, which is a methylation-specific reagent that changes a nucleotide sequence of the DNA in a manner that reflects a methylation status of the DNA, amplifying bisulfite-converted DNA with primers specific for differentially methylated regions in target nucleic acids, and contacting the amplified nucleic acids with a flap oligonucleotide and an invasive oligonucleotide and then contacting the resulting complexes with a FEN-1 endonuclease (e.g., para [0018], [0065], [0073] and [0305-0306]).
Allawi also exemplifies primers and flap oligonucleotides for detecting differentially methylated regions (DMRs), including DMRs in each of the BARX1, FLJ45983, ZNF781 and SOBP marker genes (Table 3).
Allawi further teaches providing the reagents required to practice the flap methylation detection assays disclosed therein in a kit, wherein the kits include primers that hybridize to bisulfite-converted DNA, flap oligonucleotides that hybridize to bisulfite converted DNA and bisulfite (e.g., para [0019], [0022] and [0077])).
Allawi also exemplifies multiplex PCR mixtures comprising primers to multiple target nucleic acid sequences. The teachings of Allawi indicate that it is routine and well-within the skill of the ordinary artisan to combine primers for detecting differentially methylated regions of different genes in a reaction mixture and to perform multiplex amplification reactions. See para [0061] which discloses conventional multiplex PCR assays; and para [0232], [0246-0258], [0274] and [0306-0307] which exemplify multiplex amplification reactions for the detection of differentially methylated DNA regions.
In particular, at para [0274], Allawi exemplifies reaction mixtures containing primers for amplifying 30 marker genes, including each of the BARX1, FLJ45983, ZNF781 and SOBP marker genes.
Accordingly, Allawi teaches kits and compositions comprising reaction mixtures comprising primer pairs configured to amplify differentially methylated regions of methylation markers, including BARX, FLJ45983, ZNF781, and SOBP, in sequence- converted DNA, wherein the sequence-converted DNA is formed by treating human DNA with a methylation-specific reagent that changes a nucleotide sequence of the DNA in a manner that reflects a methylation status of the DNA, flap oligonucleotides for each of the BARX, FLJ45983, ZNF781, and SOBP markers, wherein each flap oligonucleotide has a region that specifically hybridizes to a differentially methylated region of the marker and a 5' flap portion that is unpaired when the flap oligonucleotide specifically hybridizes to a differentially methylated region of a methylation marker in the sequence-converted DNA; and a reference primer pair to amplify a reference nucleic acid, such as B3GALT6, and a reference flap oligonucleotide that includes a region that specifically hybridizes to portion the nucleic acid amplified by the reference primer pair and which includes a 5' flap portion that is unpaired when the reference flap oligonucleotide specifically hybridizes to the reference nucleic acid.
In view of the teachings of Allawi of the flap detection method for effectively detecting methylation of DMRs in target marker genes and the disclosure of Allawi of kits comprising reaction mixtures containing the necessary reagents for performing such assays, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have packaged the reagents required to practice the method claimed in ‘840 in a kit, including the reagents of a mixture of primer pairs for amplifying DMRs in bisulfite-converted the IFFO1, HOPX, BARX1, FLJ45983, ZNF781 and SOBP DNA; flap oligonucleotides that specifically hybridize to DMRs in amplified the IFFO1, HOPX, BARX1, FLJ45983, ZNF781 and SOBP DNA; and a primer pair for amplifying a region of the reference nucleic acid of B3GALT6, and a flap oligonucleotide that specifically hybridizes to a region of the reference nucleic acid of B3GALT6 amplified with the primer pair for B3GALT6. One would have been motivated to have done so in order to have provided the advantages of convenience and cost-effectiveness for practioners wishing to perform multiplex assays to detect the methylation status of the IFFO1, HOPX, BARX1, FLJ45983, ZNF781 and SOBP DNA and the reference nucleic acid of B3GALT6 using the flap detection assay of Allawi.
Regarding claim 38, the claims of ‘840 do not recite compositions comprising the reagents for performing the methylation assay, including the solution of present claim 38.
However, Allawi teaches compositions for performing the flap detection assay which compositions comprise a mixture of target nucleic acids that are bisulfite converted and oligonucleotides that hybridize to differentially methylated target nucleic acids that have been bisulfite converted (para [0024] and [0105]). It is disclosed that the compositions and kits can include additional reagents for performing the detection method, including enzymes (para [0077]) and that thermostable FEN-1 is used in the flap detection assays (e.g., para [0068]). Allawi states that in the flap detection assays, “(t)he first complex is a substrate for a flap endonuclease, e.g., a FEN-1 endonuclease, which cleaves the flap oligonucleotide to release the 5′ flap portion” (para [0073]).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have prepared compositions for performing the modified methylation methods claimed in ‘840 modification, wherein the flap detection assay of Allawi is used to detect the methylation of the IFFO1, HOPX, BARX1, FLJ45983, ZNF781, and SOBP genes and the reference B3GALT6 gene. Such a modification of the methods claimed in ‘840 so as to have detected the methylation status using the flap detection assay of Allawi would have resulted in compositions comprising a solution comprising: i) sequence-converted DNA formed by treating human DNA with a methylation-specific reagent that changes a nucleotide sequence of the DNA in a manner that reflects a methylation status of the DNA; ii) IFFO1, HOPX, BARX1, FLJ45983, ZNF781, SOBP, and B3TGALT6 amplicon DNAs amplified from the sequence-converted DNA by extension of pairs of primers complementary to methylation markers IFFO1, HOPX, BARX1, FLJ45983, ZNF781, SOBP and B3TGALT6 in the sequence-converted DNA, the amplicon DNAs comprising differentially methylated regions of the methylation markers comprising nucleotide sequences changed by treatment with the methylation-specific reagent; and iii) a thermostable FEN-1 endonuclease.
Regarding claims 28 and 39, as discussed above, Allawi teaches use of the methylation-specific reagent of bisulfite to treat the DNA (e.g., [0018-0019] and [0046]).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have included bisulfite in the kits and reaction mixtures used to perform the modified methylation detection method claimed in ‘840 since this would have permitted the effective differentiation between methylated and unmethylated DNA.
Regarding claim 43, the claims of ‘840 do not recite compositions further comprising 3-(n-morpholino) propanesulfonic acid.
However, Allawi teaches that the reaction mixture for performing the flap detection assay / “QuARTS Assay” includes “3-(n-morpholino) propanesulfonic acid (MOPS)” (para [0231]).
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have included 3-(n-morpholino) propanesulfonic acid (MOPS) in the compositions formed performing the modified methods of ‘840. One would have been motivated to have done so because Allawi teaches that this is a typical reagent that is present in the reaction mixture used to perform the flap detection assay.
This is a provisional nonstatutory double patenting rejection.Response to Remarks:
Regarding the prior rejection, the response states that the instant application is earlier-filed than Application No. 17/638,840. Applicant cites the PTAB decision Ex Parte Baurin, Appeal 2024-002920, Appl. No. 17/135,529 (PTAB Nov. 6, 2024) and asserts that this decision “found that claims of a later-filed application cannot serve as reference claims against the claims of an earlier-filed application for purposes of nonstatutory double patenting.” Applicant concludes that “the claims of Application No. 17/638,840 therefore cannot serve as reference claims against the claims of the instant application for purposes of nonstatutory double patenting.”
These arguments have been fully considered but are not persuasive. It is first noted that the cited PTAB decision is not a precedential decision and is not binding. The PTAB decision is not consistent with USPTO guidance regarding provisional obviousness type double-patenting rejections set forth in MPEP 804 and 804.02. The rejection is maintained for the reasons set forth above. Note that the provisional nonstatutory double patenting rejection is not the only rejection remaining in the present application having the earliest effective U.S. filing date. See MPEP 804IB.7. The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Rousseaux et al (Science Translational Medicine. May 2013. 5(186), p. 1-11 and Supplementary Materials p. 1-211) teaches methods that identify genes containing differentially methylated regions that are correlated with an aggressive, mestastasis-prone lung cancer (see abstract; p. 6 final para to p. 7). Rousseaux also identified genes that showed a change in expression level in lung cancers characterized as being very aggressive and having a poor prognosis (the “P3 group”). Rousseaux discloses that there is a decrease in the expression level of the IFFO1 gene (Supplemental Material p. 174) and HOPX gene (Supplemental Material p. 206) in lung cancers having a poor prognosis (Table S12 beginning at p. 131).
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/CARLA J MYERS/Primary Examiner, Art Unit 1682