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 .
Election/Restrictions
Applicant’s election without traverse Species Group I, Species A, claims 9-10 and Species Group II, Species B, claim 37 in the reply filed on 02/18/2026 is acknowledged.
Claim Status
Claims 1-13 and 21-27, and 29-35 are pending.
Claims 1-10, 12, 21-27, and 29-35 are examined on the merit.
Claims 11,13 and 36 are withdrawn from further consideration.
Claims 14-20, 28, and 36-37 are canceled.
Priority
The instant application claims the benefit of priority as a continuation of U.S. Application No. 16/903,231 filed 12/28/2020, and 16/389/753 filed on 04/19/2019 and 14/495,791 filed 24 September 2014. The ‘791 application claims the benefit of priority as a continuation of International Application No. PCT/AU2013/001088 filed 20 September 2013. The claim to the benefit of priority as a continuation of U.S. Application No. 14/495,791 filed 24 September 2014 as set forth on the Application Data Sheet and International Application No. PCT/AU2013/001088 filed 20 September 2013 is acknowledged.
The ‘088 applications claim the benefit of priority to U.S. Provisional Application No. 61/830,571 field 3 June 2013 and as a continuation in part of U.S. Application No. 13/842,209 filed 15 March 2013. The ‘209 application further claims the benefit of priority to U.S. Provisional Application No. 61/703,512 filed 20 September 2012.
Claim 1, and those claims dependent therefrom, recite calculating a first methylation level based on respective numbers of cell-free DNA molecules that are hypermethylated at the plurality of sites. This limitation is not supported by the ‘512 application. Therefore, claims 1-10, 12, 21-35, and 37 are not granted the claim to the benefit of priority to the ‘512 application.
Claim 5 recites treating the cell-free DNA molecules with sodium bisulfite as part of Tet- assisted bisulfite conversion or oxidative bisulfite sequencing. This limitation is not support by the ‘512, ‘209 or ‘571 applications. Therefore, claim 5 is not granted the claim to the benefit of priority to the ‘512, ‘209 and ‘571 applications.
Claims 21-22 recite limitations for analyzing the hypermethylation of CpG islands. These limitations are not supported by the disclosure of the ‘512 or ‘209 Applications. Therefore, claims 21-22 and 25 are not granted the claim to the benefit of priority to the ‘512 and ‘209 Applications.
In this action, all claims are examined as though they had the above-mentioned effective filing dates. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further analysis of the disclosure(s) of the priority application(s).
Withdrawn Rejections/Objections
Rejections and/or objections not reiterated from previous office actions are hereby
withdrawn in view of the amendments filed 07/02/2026.
The 35 U.S.C. 112(a) rejections to claims 28 in the office action filed 04/03/2026 has been withdrawn in view of the 07/02/2026 amendment canceling the claim.
The 35 U.S.C. 101 rejections in the office action filed 04/03/2026 has been withdrawn in view of amendments received 07/02/2026, at least in view of the analysis Step 2A, 2nd prong, 1st consideration relating to an improvement over the previous state of the technology field integrating possible judicial exceptions into a practical application (MPEP 2106.04(d) applied to the field of cancer screening, in this instance comprising more sensitive and specific cancer detection, equivalent to increased accuracy. This accuracy improvement is analogous to the reasoning in MPEP-cited case law including Cardionet v. Infobionic (955 F.3d 1358, Fed. Cir. 2020). In this regard, Applicant's 07/02/2026 remarks at p. 11 support withdrawal of the rejection.
In the alternative, the 101 rejections are withdrawn at least in view of the analysis Step 2B relating to a non-conventional additional element causing the claim to read on significantly more than any recited JE (MPEP 2106.05(d)), the non-conventional additional element in this instance comprising at least enriching from the biological sample a plurality of cell-free DNA molecules originating from at least 3,000 specific genomic regions, wherein the at least 3,000 specific genomic regions comprise genomic regions with a methylation differential between cancer and non-cancer for a tissue, wherein the enriching comprises contacting the plurality of cell-free DNA molecules with hybridization probes; performing methylation-aware sequencing to determine sequences of the enriched cell-free DNA molecules. In this regard, Applicant's 07/02/2026 remarks at pp. 15 support withdrawal of the rejection.
The 35 U.S.C. 103 rejections in the office action filed 04/03/2026 has been withdrawn in view of the 07/02/2026 amendments. The amendments necessitated new art rejection.
The non-statutory double patenting rejection to U.S. Patent No. 12,518,854, U.S. Patent application No. 16/930,231, U.S. Patent No. 10,706,957, U.S. Patent No. 10,392,666, and U.S. Patent No. 9,732,390 has been withdrawn in view of terminal disclaimer filed 12/16/2024.
The following rejections and/or objections are either maintained or newly applied. They constitute the complete set presently being applied to the instant application.
Terminal Disclaimer
The 07/02/2026 terminal disclaimer has been approved.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 05/07/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered in full by the examiner. A signed copy of the corresponding 1449 form has been included with this Office action.
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 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)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 29, and d30 are rejected under 35 U.S.C. 102(a)(2) as anticipated by Deciu (US20130338933A1; as cited in the attached 892 form).
Regarding claims 1, 29, and 30, Deciu discloses methods, processes and apparatuses for non-invasive assessment of genetic variations (abstract).
Deciu further discloses identifying of one or more genetic variations or variances involves the analysis of cell-free DNA [0008].
Deciu further discloses that genomic DNA target sequences used for the determination of total DNA are present in every genome copy (e.g. is present in fetal DNA and maternal DNA, cancer DNA and normal DNA, pathogen DNA and host DNA) [0214]; reading on limitations of a method of analyzing a biological sample of an organism, the biological sample comprising cell-free DNA originating from normal cells and potentially from cells associated with cancer.
Deciu further discloses enriching a sample nucleic acid for one or more polymorphic nucleic acid targets… A plurality of polymorphic targets can comprise two or more targets. For example, a plurality of polymorphic targets can comprise 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, or more targets [0258]. Deciu further discloses determining one or more elevations from normalized or non-normalized counts of all or some of the 2 to about 100,000 genomic sections of a genome [0470], where one or more elevation is methylation [0610] [0614].
Deciu further discloses that the one or more loci comprise one or more methylation regions [0012].
Deciu further discloses enrichment of fetal DNA based on the methylation-specific separation of differentially methylated DNA [0224].
Deciu further discloses analysis is a quantitative methylation assay useful for determining DNA methylation levels at specific gene loci, where PCR amplification of the bisulfite converted DNA is performed using primers specific for the interested CpG islands, followed by restriction endonuclease digestion, gel electrophoresis, and detection using specific, labeled hybridization probes [0233]; reading on limitations of enriching from the biological sample a plurality of cell-free DNA molecules originating from at least 3,000 specific genomic regions, wherein the at least 3,000 specific genomic regions comprise genomic regions with a methylation differential between cancer and non-cancer for a tissue, wherein the enriching comprises contacting the plurality of cell-free DNA molecules with hybridization probes.
Deciu further discloses that enriched (e.g., amplified) polymorphic nucleic acid targets are sequenced by a sequencing process [0267], wherein sequencing is methylation-aware sequencing [0232]; reading on limitations of performing methylation-aware sequencing to determine sequences of the enriched cell-free DNA molecules.
Deci further discloses mapping nucleotide sequence reads (i.e., sequence information from a fragment whose physical genomic position is unknown) can be performed in a number of ways, and often comprises alignment of the obtained sequence reads with a matching sequence in a reference genome [0382].
Deciu further discloses bar graph plots of the methylation differences obtained from the microarray analysis (dark bars) and the mass spectrometry analysis (light grey bars) with respect to their genomic location [0100]; reading on imitations of determining a location of each enriched cell-free DNA molecule in a genome of the organism; and determining whether each enriched cell-free DNA molecule is methylated at one or more sites.
Deciu further discloses determining the fraction of non-methylated and the methylated DNA [0099]; reading on limitations of determining a respective number of enriched cell-free DNA molecules at the site that are methylated at one or more sites.
Deciu further discloses that various methylation analysis procedures are known in the art, and can be used in conjunction with the present technology, such as, DNA sequencing of bisulfite-treated DNA, PCR (for sequence-specific amplification), Southern blot analysis, and use of methylation-sensitive restriction enzymes, and COBRA analysis is a quantitative methylation assay useful for determining DNA methylation levels at specific gene loci [0229-0233]; reading on limitations of calculating a first methylation level using the respective numbers of enriched cell- free DNA molecules that are methylated at the plurality of one or more sites.
Further regarding claim 29, Deciu discloses performing Genomic DNA sodium bisulfite conversion [0238] [1070]; reading on limitations of treating cell-free DNA molecules from the biological sample with sodium bisulfite.
Further regarding claim 30, Deciu discloses that MBD-FC was used to capture the methylated fraction of each DNA sample. See FIGS. 145 [0285] [1066]; reading on limitations of contacting cell-free DNA molecules from the biological sample with a protein that binds methylated DNA.
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 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 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.
Claims 1-4, 25-28, 29-30, and 37 are rejected under 35 U.S.C. 103 as unpatentable over Deciu, as applied to claims 1, 29, and 30 above, in view of Korshunova et al. (2008: Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA, 18:19-29; as previously cited in the 892-form dated 04/03/2026).
Claim 2 depends on claim 1. Limitations of claim 1 has been taught in the above rejections.
Regarding claim 2, Deciu discloses that various methylation analysis procedures are known in the art, and can be used in conjunction with the present technology. These assays allow for determination of the methylation state of one or a plurality of CpG islands within a DNA sequence. In addition, the methods maybe used to quantify methylated nucleic acid. Such assays involve, among other techniques, DNA sequencing of bisulfite-treated DNA, PCR (for sequence-specific amplification), Southern blot analysis, and use of methylation-sensitive restriction enzymes [0232]. Deciu further discloses genomic sequencing is a technique that has been simplified for analysis of DNA methylation patterns and 5-methylcytosine distribution by using bisulfite treatment. Deciu further discloses that the sequencing is sequencing-by-synthesis and reversible terminator-based sequencing (e.g. Illumina's Genome Analyzer; Genome Analyzer II; HISEQ 2000; HISEQ 2500 (Illumina, San Diego Calif.)). With this technology, millions of nucleic acids (e.g. DNA) fragments can be sequenced in parallel [0360].
Further, Deciu discloses determining one or more elevations from normalized or non-normalized counts of all or some of the 2 to about 100,000 genomic sections of a genome [0470], where one or more elevation is methylation [0610] [0614].
Further regarding claim 2, Deciu does not expressly disclose performing the methylation-aware assay sequencing of the enriched cell-free DNA molecules comprises sequencing of at least 60,000 cell-free DNA molecules. Korshunova discloses analysis of the DNA-methylation landscape present in just over 700,000 patient derived DNA fragments from cancer-free breast tissue, infiltrating ductal breast carcinomas, and sera obtained from a collection of 50 patients using a massively parallel bisulphite sequencing strategy (pg. 20, col. 1, last para.); reading on limitations of performing the methylation-aware assay comprises sequencing of at least 60,000 cell-free DNA molecules.
Regarding claim 3, Deciu discloses PCR amplification of the bisulfite converted DNA [0120] [0165]; reading on limitations of performing the methylation-aware assay further comprises amplification of the cell-free DNA molecules prior to said sequencing.
Regarding claim 4, Deciu discloses treating the cell-free DNA molecules with sodium bisulfite [0205] [0226]; reading on limitations of treating the cell-free DNA molecules with sodium bisulfite prior to the enrichment.
Regarding claim 25, Deciu discloses genomic regions are on a plurality of chromosomes [0102] [0160] [0283].
Additionally, Korshunova discloses that the genomic loci under the study are chromosomes (Figure 1). Tynan discloses detecting the presence or absence of fetal aneuploidy, the amount of fetal nucleic acid may be determined at multiple loci on one or more target chromosomes (e.g., chromosomes 13, 18 or 21) and on one or more reference chromosomes [0041] [0094] [0267] [0371].
Regarding claim 26, Deciu discloses analysis of disjointed portions of multiple chromosomes [0391]; reading on limitations of wherein the plurality of sites are from disjointed regions separated from each other.
Regarding claim 27, Deciu discloses contacting cfDNA with MBD-FC to capture methylated fraction [0166]; reading on limitations of the methylation-aware assay further comprises contacting the cell-free DNA molecules with a protein that binds methylated DNA.
Rationale for combining Deciu and Korshunova:
In KSR Int 'l v. Teleflex, the Supreme Court, in rejecting the rigid application of the teaching, suggestion, and motivation test by the Federal Circuit, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Applying the KSR standard to Deciu and Korshunova, the examiner concludes that the combination of Korshunova and Tynan represents the use of known techniques to improve similar methods. Both Deciu and Korshunova are directed to methylation profiling of cell-free DNA.
Deciu discloses analyzing a biological sample of an organism, the biological sample comprising cell-free DNA originating from normal cells and potentially from cells associated with cancer by enriching, performing methylation-aware sequencing, determining a location and methylation level. Deciu further discloses genomic sequencing for analysis of DNA methylation patterns and 5-methylcytosine distribution by using bisulfite treatment. Deciu further discloses that the sequencing is sequencing-by-synthesis and reversible terminator-based sequencing (e.g. Illumina's Genome Analyzer; Genome Analyzer II; HISEQ 2000; HISEQ 2500 (Illumina, San Diego Calif.)). With this technology, millions of nucleic acids (e.g. DNA) fragments can be sequenced in parallel [0360]. Deciu does not expressly disclose the number of cfDNA molecules sequenced. In the same field of research, Korshunova discloses analysis of the DNA-methylation landscape present in just over 700,000 patient derived DNA fragments from cancer-free breast tissue. Combining the method of Deciu with methylation profiling of Korshunova comprising sequencing at least 60,000 cfDNA molecules would have allowed for greater genomic coverage, higher sensitivity to mutations, and better handling the methylated DNA. One ordinary skilled in the art before he effective filing data of the claimed invention would have had a reasonable expectation of success at combining the method of Deciu and Korshunova. This combination would have been expected to have provided a more specific methylation profiling. Therefore, the invention would have been prima facie obvious to one of skill in the art before the effective filing date of the claimed invention, absent evidence to the contrary.
Claim 5 is rejected under 35 U.S.C. 103 as unpatentable over Deciu in view of Korshunova, as applied to claims 1-4, 25-27, and 29-30 above, and further in view of Booth (Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution, 18 MAY 2012 VOL 336 SCIENCE, p. 934-937; as cited in form 892 dated 04/03/2026).
Claim 5 depend on claim 4 and 1. The limitations of claims 1 and 4 have been taught in the above rejection.
Regarding claim 5, Deciu discloses bisulfite conversion methods, for example, MSP (methylation-sensitive PCR), COBRA, methylation-sensitive single nucleotide primer extension (Ms-SNuPE) or Sequenom MassCLEAVE™ technology [0255]. Deciu and Korshunova do not expressly disclose treating the cell-free DNA molecules with sodium bisulfite is part of Tet-assisted bisulfite conversion or oxidative bisulfite sequencing for a detection of 5-hydroxymethylcytosine. Booth discloses oxidative bisulfite sequencing (oxBS-Seq), the first method for quantitative mapping of 5hmC in genomic DNA (abstract).
Rationale for combining Deciu, Korshunova, and Booth:
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Deciu and Korshunova to have treated the DNA molecules with the sodium bisulfite as part of Tet-assisted bisulfite conversion or oxidative bisulfite sequencing for a detection of 5-hydroxymethylcytosine, as shown by Booth et al. (abstract). There would be a reasonable expectation of success in combining the technique of Booth to the method of Deciu and Korshunova because they all use bisulfite sequencing to reveal methylation patterns.
Claims 6-8, 21-22, and 31-35 are rejected under 35 U.S.C. 103 as unpatentable over Deciu in view of Korshunova, as applied to claims 1-4, 25-27, and 29-30 above, and further in view of Melnikov (US20080261217A1; as cited in form 892 dated 04/03/2026).
Claims 6 and 7 depend on claim 1. Limitations of claim 1 has been taught in the above rejections.
Regarding claims 6 and 7, Deciu discloses comparing methylation levels to a cutoff value [0100] [0303]. Korshunova discloses analyzing cytosine-methylation topography within the samples; the methylation pattern of each molecule and methylation density (or the percent of the methylated residues from the total number of residues sequenced per molecule). The average methylation density of a region is the mean methylation occupancy per CG across a region; allowing characterization of the methylation level of the molecular population without analyzing prevalence of any molecular configuration; The goal of the analysis was to identify either a configuration or a regional methylation density where the relative abundance of each may be diagnostic of breast cancer (pg. 23, col. 2, para. 1). Korshunova further discloses performing discriminative analysis for classification of tumor (pg. 2, col. 2, last para.); determining the methylation levels [0369]; genomic regions were classified as being not differentially methylated when the group showed less than eight samples with a p value <0.01 and less than six samples with a p value <0.001[0390].
Further regarding claims 6 and 7, Deciu and Korshunova do not expressly disclose determining the first classification of the level of cancer based on the first methylation level. Melnikov discloses that the methylation profile of the subject may be compared to a standard methylation profile (e.g., a standard methylation profile for non-cancerous samples, a standard methylation profile for cancerous samples, or both) [0020] [0046]. Melnikov further discloses using thresholds for methylated fragments defining methylated and unmethylated calls for diagnosis of cancer [0090].
Regarding claim 8, Melnikov discloses methods of identifying methylation patterns in genes associated with specific cancers (abstract). Melnikov further discloses a) reacting isolated genomic DNA from the subject and a methylation-sensitive restriction enzyme; wherein the genomic DNA comprises a plurality of promoters from different genes, and the enzyme cleaves unmethylated CpG sequences in the promoters and does not cleave methylated CpG sequences in the promoters; (b) contacting the genomic DNA thus reacted and a plurality of pairs of specific primers in an amplification mixture, the pairs of specific primers being configured to hybridize to the genomic DNA and to amplify a plurality of different promoters through a region comprising an uncleaved CpG sequence; (c) reacting the amplification mixture; (d) detecting one or more amplified promoters in the reacted amplification mixture or the absence thereof, thereby diagnosing cancer in the subject selected from the group consisting of ovarian cancer, lung cancer, prostate cancer, pancreatic cancer, and colon cancer (claim 1); a cell-free assay is provided in which a cancer marker gene, protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the cancer marker gene, protein or biologically active portion thereof is evaluated [0116].
Melnikov further discloses distinguishing normal from cancer status and cancer classification [0262-0268]; reading on limitations of the first classification indicates that cancer exists for the organism, the method further comprising identifying a type of cancer associated with the organism.
Regarding claims 21 and 22, Deciu discloses determining differential DNA methylation of CpG sites using a paired T Test with those sites considered differentially methylated if the p-value (when comparing placental tissue to PBMC) is p<0.05 [1140].
Korshunova discloses variety of molecular methylation patterns recovered from each run including CpG sites (pg. 23, col. 1, para. 1; Table 2; Figure 1). Tynan discloses separating fetal and maternal nucleic acid based on the methylation status of a CpG-containing genomic sequence in the sample [0009]; assays allowing for determination of the methylation state of one or a plurality of CpG islands within a DNA sequence [0216]; PCR amplification of the bisulfite converted DNA is then performed using primers specific for the interested CpG islands, followed by restriction endonuclease digestion, gel electrophoresis, and detection using specific, labeled hybridization probes. Methylation levels in the original DNA sample are represented by the relative amounts of digested and undigested PCR product in a linearly quantitative fashion across a wide spectrum of DNA methylation levels [0218] [0457].
Melnikov discloses providing differential methylation of CpG islands (claim 1) [0092] [0094]; demonstration of increased frequency of CpG methylation over normal [0223].
Regarding claim 31, Melnikov discloses Predicted status for each sample (e.g. pCancer, pADH, pNormal, etc.) was compared with its true status (Cancer, ADH, Normal, etc). Intersection of predicted and true status for each type of cancer shows the sensitivity (e.g. 72.39% of Cancer samples are correctly identified, so the sensitivity of cancer classifier is 72.39%), while intersection of predicted and true status of normal indicates the specificity of the classifier (e.g. 74.74% of Normal samples are correctly identified by the cancer classifier, so its specificity is 74.74%) [0264]; The fraction of U calls for each tissue type is shown with p-values from Fisher's Exact Test for differential methylation on 2×2 tables for all pairwise comparisons [0267]; reading on limitations of identifying the type of cancer associated with the organism comprises comparing the first methylation level to a corresponding value determined from other organisms, wherein at least two of the other organisms are identified as having different types of cancer.
Regarding claims 32 and 33, Melnikov discloses that MethDet can be considered as the first-line test in combination with TVUS or other imaging techniques; While the accuracy of developed biomarkers needs additional refinement, even at this time the blood-based biomarker can be useful as a first-line screening tool in combination with imaging techniques [0333-0334]; radiological screening techniques include (mammography, ultrasonography, computed tomography, magnetic resonance imaging) [0004]; reading on limitations of identifying the type of cancer associated with the organism comprises radiological and/or imaging investigation, and wherein the imaging comprises computed tomography, magnetic resonance imaging, or positron emission tomography.
Regarding claims 34 and 35, Deciu discloses binding a sample nucleic acid to a methylation-specific binding agent (methyl-CpG binding protein (MBD), methylation specific antibodies, and the like) and separating bound nucleic acid from unbound nucleic acid based on differential methylation status [0285]. Melnikov discloses measuring the levels of CA125 [02910293]; reading on limitations of determining levels of one or more protein markers, wherein the one or more protein markers is selected from the group consisting of prostate specific antigen, carcinoembryonic antigen, alpha fetoprotein, CA125 and CA19-9.
Rationale for combining Deciu, Korshunova. and Melnikov:
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Deciu and Korshunova to have used their methylation profiling method to classify abnormalities such as cancer, as shown by Melnikov. There would be a reasonable expectation of success in combining the method of Melnikov with the method of Deciu and Korshunova because they all use methylation profiling to identify one or more abnormalities.
Claims 9-10, and 12 are rejected under 35 U.S.C. 103 as unpatentable over Deciu in view of Korshunova, as applied to claims 1-4, 25-27, and 29-30 above, in view of Melnikov, as applied to claims 6-8, 21-22, and 31-35 above, and further in view of Fackler (Quantitative Multiplex Methylation-Specific PCR Assay for the Detection of Promoter Hypermethylation in Multiple Genes in Breast Cancer, CANCER RESEARCH 64, 4442–4452, July 1, 2004; as cited in form 892 dated 04/03/2026).
Claims 9 depend on claims 1 and 7. Limitations of claim 1 and 7 have been taught in the above rejections.
Regarding claim 9, Freckle et al. discloses that the cutoff value is determined from other subjects not having cancer (Table 5, 6; p. 4448, cols. 1&2, The cumulative methylation profiles of 9 normal mammoplasty samples were compared with those of 19 invasive carcinomas).
Regarding claim 10, Fackler et al. discloses that the cutoff value is a specified distance from a reference methylation level established from another biological sample obtained from a healthy subject or a chromosomal region that does not have the abnormality (pg. 4447, col 2, paras 1 and 2, determining whether a CpG island is hypermethylated by using the Mann-Whitney test on the untransformed data; Figure 7, Cumulative promoter hypermethylation of RASSF1A, TWIST, Cyclin D2, and HIN1 in adjacent normal and malignant breast tissues).
Regarding claim 12, Fackler et al. discloses comparing the first methylation level to the cutoff value includes: determining a difference between the first methylation level and a reference methylation level; and comparing the difference to a threshold corresponding to the cutoff value (pg. 4447, col 2, paras 1 & 2) the differences in the medians were highly significant for all genes tested… We chose to establish a cutoff (% M) for each gene at approximately the 10th percentile of the population, such that _90% of normal breast tissues would be at or below the cutoff. Using cutoffs of 2% M for RASSF1A and HIN1, 0.5% M for TWIST, and 0.2% M for Cyclin D2 in normal tissues, we considered values above the cutoffs “positive” for hypermethylation.
Rationale for combining Deciu, Korshunova, Melnikov, and Fackler:
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Deciu, Korshunova, and Melnikov to have used the cutoff values, as shown by Fackler (Para 4; pg. 4447, col 1, para 2 to pg. 4449, col 2, para 1; Figures 5-8; Tables 5-7) to distinguish between different states. There would be a reasonable expectation of success in combining the technique of Fackler to the method of Deciu, Korshunova, and Melnikov because they are all in the field of detecting hypermethylation in one or more abnormalities.
Claims 23-24 are rejected under 35 U.S.C. 103 as unpatentable over Deciu in view of Korshunova, as applied to claims 1-4, 25-27, and 29-30 above, and further in view of Wong (Quantitative Analysis of Tumor-derived Methylated p16INK4a Sequences in Plasma, Serum, and Blood Cells of Hepatocellular Carcinoma Patients, clinical Cancer Research, (2003) 9 (3): 1047–1052. 03/01/2003).
Claims 23-24 depend on claim 1. Limitations of claim 1 have been taught in the above rejections.
Regarding claims 23 and 24, Deciu discloses determining fractional concentration of fetal nucleic acids in the analyzed sample [0399] [1380].
Wong discloses method of quantifying methylated sequences and determining the fractional concentrations of circulating tumor DNA in plasma, serum, and peripheral blood cells (abstract). Wong further discloses that the fractional concentration of circulating tumor-derived DNA in plasma, the proportion of bisulfite converted unmethylated and methylated p16INK4a sequences that consisted of tumor-derived methylated p16INK4a sequences, was calculated for each methylation-positive plasma sample. For the 9 preoperative plasma samples, the p16INK4a methylation indices were 0.2, 0.4, 0.6, 21.3, 35, 46.7, 73.1, 85.3, and 100% (median methylation index = 35%; n = 9; Table 2). On the other hand, the p16INK4a methylation indices on the 8 postoperative plasma samples (for example, a reference methylation level) were 0.3, 0.3, 0.4, 1.6, 4.5, 11.2, 28, and 71.5% (median methylation index = 3.05%; n = 8; Table 2), corresponding to 10, 13, 32, 34, 34, 60, 77, and 103 genome-equivalents of methylated sequences/ml (median quantity = 34 genome-equivalents/ml); reading on limitations of determining whether a fractional concentration of tumor DNA in the biological sample is greater than a minimum value; and if the fractional concentration of tumor DNA is not greater than the minimum value, flagging the biological sample.
Rationale for combining Deciu, Korshunova, and Wong:
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Deciu and Korshunova to have used tumor fraction/fractional concentration of tumor DNA, as shown by Wong, to distinguish cancer-derived DNA from healthy blood cell DNA. There would be a reasonable expectation of success in combining the technique of Wong to the method of Deciu and Korshunova because they are all in the field of detecting hypermethylation in one or more abnormalities.
Response to Arguments
Applicant's 07/02/2026 arguments have been fully considered but they are not yet persuasive with regard to the revised art rejections herein. In response to the argument that Korshunova teaches away from using cell-free DNA (pg. 16, last para.), the revised rejection relies on Korshunova teaching evaluating circulating DNA as a non-invasive alternative to tumor DNA by applying massively parallel bisulfite pyrosequencing and compares them to those extracted from solid tumors.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GHAZAL SABOUR whose telephone number is (703)756-1289. The examiner can normally be reached M-F 7:30-5:00.
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, Larry D. Riggs can be reached at (571) 270-3062. 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.
/G.S./Examiner, Art Unit 1686
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
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