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 with traverse of group I, claims 149-168, ADRA1D, MAX.chr4.184, ITGA5, and NRN1, NHL and blood sample in the reply filed on 10/6/2021 is acknowledged. The traversal is on the ground(s) that Applicant respectfully disagrees and submits that the present claims recite active steps other than bisulfate sequencing, including "amplifying the treated genomic DNA using a set of primers specific for at least one CpG site for one or more genes" and "determining a methylation level of the at least one CpG site by methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfate pyrosequencing, or bisulfate genomic sequencing PCR,". This is not found persuasive because Chio teaches bisulfite modification, followed by PCR and whole genome bisulfite sequencing. Thus as the recited genes are in the genome, this anticipates the active steps of the claims.
Claims 151, 153-155, 158-162, 164, 167-171 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species or invention. Claims 151, 153-155 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species as they do not recite the entire combination of elected genes, there being no allowable generic or linking claim. Claims 158-162, 164, 16167-171 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species as they do not read upon the elected NHL or blood sample, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 10/6/2025.
Claims 149-150, 152, 156-157, 163, 165-166 are being examined.
Priority
The instant application was filed 02/17/2023 and is a national stage entry of PCT/US21/46494 with an international filing date: 08/18/2021 and claims priority from provisional application 63067592 , filed 08/19/2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/11/2023, 7/30/2025, 10/9/2025 are being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered. It is noted the examiner has not compared the IDS with references cited in the specification.
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1), 1.835(a)(2), or 1.835(b)(2) is missing, defective or incomplete.
Required response - Applicant must:
• Provide a substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Claim Objections
Claims 149-150, 152, 156-157, 163, 165-166 objected to because of the following informalities:
Claim 149 is objected to as it recites, “CpG,” “ADRA1D, DNAH14, FAM110B, FAM221A, FLRT2, GABRG3, GATA6, HOXA9, MAX.chr17:79367190-79367336, MAX.chr4.184644047- 184644181, MAX.chr5:74349626-74349841, MAX.chr6.19805123-19805338, MNX1, NRN1, SH3BP4, SYT6, VWA5B1, ZNF503, BNC1, TPBG, CACNG8, CDK20, EBF3, FOXP4, ITGA5, JUP, MAX.chrl.61508719-61508998, MAX.chr3.44038141-44038266, TGFB1Il,THBS1, MAX.chr6.19805195-19805266, MAX.chr:61508832-61508969, MAX. chr4.184644069-184644158, SYT2, and CALN1” but does not recite the full terminology for the acronym (or abbreviation). Claims are more concise when the first time an acronym (or abbreviation) is presented the full terminology is also presented. Finally an acronym (or abbreviation) may have alternative meanings to an artisan.
Appropriate correction is required.
Improper Markush Group
Claims 149-150, 152, 156-157, 163, 165-166 are rejected under the judicially approved ‘‘improper Markush grouping’’ doctrine. (See Federal Register, Vol. 76, No. 27, Wednesday, February 9, 2011, page 7166). This rejection is appropriate when the claim contains an improper grouping of alternatively useable species. See In re Harnisch, 631 F.2d 716, 719–20 (CCPA 1980). A Markush claim contains an ‘‘improper Markush grouping’’ if: (1) the species of the Markush group do not share a ‘‘single structural similarity,’’ or (2) the species do not share a common use. Members of a Markush group share a ‘‘single structural similarity’’ when they belong to the same recognized physical or chemical class or to the same art-recognized class. However, when the Markush group occurs in a claim reciting a process or a combination (not a single compound), it is sufficient if the members of the group are disclosed in the specification to possess at least one property in common which is mainly responsible for their function in the claimed relationship, and it is clear from their very nature or from the prior art that all of them possess this property. See MPEP § 803.02.
Here each species is considered to be genes which may be methylated.
The recited alternative species in the groups set forth here do not share a single structural similarity, as each method relies on detection of different gene or nucleic acid. Each gene or nucleic acid position that could be detected is itself located in a separate region of the genome and has its own structure. The nature of gene or nucleic acid is that they are differentially methylated in different cells, tissues, subjects and species. The flanking nucleotides surrounding each gene or nucleic acid have a unique sequence relative to the others- they are not structurally the same when you consider the sequence required to identify one particular gene or nucleic acid relative to another gene or nucleic acid. The gene or nucleic acid recited in the instant claims, and the methods which detect them, do not share a single structural similarity since each consists of a different nucleotide sequence which is present in different location of the genome. The only structural similarity present is that all detected positions are part of nucleic acid molecules. The fact that the gene or nucleic acid comprise nucleotides per se does not support a conclusion that they have a common single structural similarity because the structure of comprising a nucleotide alone is not essential to the common activity of being methylated. The association between the claimed gene or nucleic acid is not considered as ‘property’ as the association is a statistical construct, it is a conclusion based on analysis of a specific population and may not be present in subject outside of the population assayed. Further there is no evidence the association was known in the prior art. While the instant specification asserts the gene or nucleic acid have a common function of being correlated with the asserted phenotype, the association between the claimed gene or nucleic acid is not clear from their very nature. If the instantly claimed gene or nucleic acid are placed in a group with an equal number of gene or nucleic acid the skilled artisan could not differentiate those associated with a phenotype from those that are not associated with a phenotype. Thus the one of skill in the art could not identify those gene or nucleic acid that are asserted to be associated with the phenotype by their very nature. Thus the instant claims have not met the requirements of a proper Markush group.
Following this analysis, the claims are rejected as containing an improper Markush grouping.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 149-150, 152, 156-157, 163, 165-166 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 149 recites, “primers specific for at least one CpG site.” The recitation of “specific for” suggests there are primers which are not specific for. Review and searching of the specification did not provide a definition or standard to differentiate specific for from non-specific for. Thus the metes and bounds are unclear.
Claim 149 recites, “MAX.chr17:79367190-79367336, MAX.chr4.184644047- 184644181, MAX.chr5:74349626-74349841, MAX.chr6.19805123-19805338, MAX.chrl.61508719-61508998, MAX.chr3.44038141-44038266, MAX.chr6.19805195-19805266, MAX.chr:61508832-61508969, MAX. chr4.184644069-184644158.” The recitation with respect to chr number followed by a number is vague, unclear and incomplete as it is unclear which database, build, species, etc. these recitations are relative to.
Claim 157 recites, “in the control sample.” The metes and bounds are unclear as neither the claim, nor claims 150 or 149 from which it depends recites “control sample.” Thus it is unclear what control sample is being referenced. This rejection can be overcome by amending the claim to provide an indefinite article prior to control sample.
Claim 166 recites, “ determining the methylation score of the at least one CpG site, and/or determining the methylation frequency of the at least one CpG site.” While the specification states, “The term "methylation score" as used herein is a score indicative of detected methylation events in a marker or panel of markers in comparison with median methylation events for the marker or panel of markers from a random population of mammals (e.g., a random population of 10, 20, 30, 40, 50, 100, or 500 mammals) that do not have a specific neoplasm of interest. “ The metes and bounds are unclear as the claim is not limited to a neoplasm of interest. Further the teachings of the specification do not teach how the score is calculated.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 156-157, 166 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a mental step without significantly more and/or a natural correlation. The claim(s) recite(s) the abstract idea or mental step of comparing. Further the claim recites, “comprising determining the presence of non-Hodgkin lymphoma when the methylation level of the one or more genes is higher than the methylation level of the corresponding gene in the control sample “ which is a natural law or correlation. Finally claim 166 states, “wherein determining the methylation level of the at least one CpG site for the one or more genes comprises determining the methylation score of the at least one CpG site, and/or determining the methylation frequency of the at least one CpG site.” This is a mental step or abstract idea. These judicial exceptions are not integrated into a practical application because if there is limitations depending from or otherwise integrating the judicial exception. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because as the independent claim provides generic limitations with respect to treating genomic DNA with a reagent capable of modifiying DNA in a methylation specific manner, amplifying and determining a methylation level of the at least one CpG site by methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, or bisulfite genomic sequencing PCR
Claim analysis
The instant claim 156 is directed towards further comprising comparing the methylation level of the one or more genes to a methylation level of a corresponding gene from a control sample without lymphoma. The comparing step is a mental step or abstract idea.
Claim 157 is drawn to, “further comprising determining the presence of non-Hodgkin lymphoma when the methylation level of the one or more genes is higher than the methylation level of the corresponding gene in the control sample.” This is a mental step and/or natural correlation.
Claim 166 recites, “wherein determining the methylation level of the at least one CpG site for the one or more genes comprises determining the methylation score of the at least one CpG site, and/or determining the methylation frequency of the at least one CpG site. This is a mental step or abstract idea.
The independent claim provides generic limitations with respect to treating genomic DNA with a reagent capable of modifiying DNA in a methylation specific manner, amplifying and determining a methylation level of the at least one CpG site by methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, or bisulfite genomic sequencing PCR are routine and conventional.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, abstract idea and law of nature or natural phenomena.
The instant claim 156 is directed towards further comprising comparing the methylation level of the one or more genes to a methylation level of a corresponding gene from a control sample without lymphoma. The comparing step is a mental step or abstract idea.
Claim 157 is drawn to, “further comprising determining the presence of non-Hodgkin lymphoma when the methylation level of the one or more genes is higher than the methylation level of the corresponding gene in the control sample.” This is a mental step and/or natural correlation.
Claim 166 recites, “wherein determining the methylation level of the at least one CpG site for the one or more genes comprises determining the methylation score of the at least one CpG site, and/or determining the methylation frequency of the at least one CpG site. This is a mental step or abstract idea.
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as there are no claims which depend from or otherwise integrate the judicial exception.
Step 2B. Does the claim recite additional elements that are significantly more then the judicial exceptions? No, The independent claim provides generic limitations with respect to treating genomic DNA with a reagent capable of .modifying DNA in a methylation specific manner, amplifying and determining a methylation level of the at least one CpG site by methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, or bisulfite genomic sequencing PCR are routine and conventional.
The specification teaches:
For example, in some embodiments the methylation state is measured by a genome scanning method. For example, one method involves restriction landmark genomic scanning (Kawai et al. (1994) Mol. Cell. Biol. 14: 7421-7427) and another example involves methylation-sensitive arbitrarily primed PCR (Gonzalgo et al. (1997) Cancer Res. 57: 594- 599). In some embodiments, changes in methylation patterns at specific CpG sites are monitored by digestion of genomic DNA with methylation-sensitive restriction enzymes followed by Southern analysis of the regions of interest (digestion-Southern method). In some embodiments, analyzing changes in methylation patterns involves a PCR-based process that involves digestion of genomic DNA with methylation-sensitive restriction enzymes or methylation-dependent restriction enzymes prior to PCR amplification (Singer-Sam et al. (1990) Nucl. Acids Res. 18: 687). In addition, other techniques have been reported that utilize bisulfite treatment of DNA as a starting point for methylation analysis. These include methylation-specific PCR (MSP) (Herman et al. (1992) Proc. Natl. Acad. Sci. USA 93: 9821- 9826) and restriction enzyme digestion of PCR products amplified from bisulfite-converted DNA (Sadri and Hornsby (1996) Nucl. Acids Res. 24: 5058-5059; and Xiong and Laird (1997) Nucl. Acids Res. 25: 2532-2534). PCR techniques have been developed for detection of gene mutations (Kuppuswamy et al. (1991) Proc. Natl. Acad. Sci. USA 88: 1143-1147) and quantification of allelic-specific expression (Szabo and Mann (1995) Genes Dev. 9:
3097-3108; and Singer-Sam et al. (1992) PCR Methods Appl. 1: 160-163). Such techniques use internal primers, which anneal to a PCR-generated template and terminate immediately 5'9 of the single nucleotide to be assayed. Methods using a "quantitative Ms-SNuPE assay" as described in U.S. Pat. No. 7,037,650 are used in some embodiments. Upon evaluating a methylation state, the methylation state is often expressed as the fraction or percentage of individual strands of DNA that is methylated at a particular site (e.g., at a single nucleotide, at a particular region or locus, at a longer sequence of interest, e.g., up to a -100-bp, 200-bp, 500-bp, 1000-bp subsequence of a DNA or longer) relative to the total population of DNA in the sample comprising that particular site. Traditionally, the amount of the unmethylated nucleic acid is determined by PCR using calibrators. Then, a known amount of DNA is bisulfite treated (or non-bisulfite treated (see, Liu et al., 2019, Nat Biotechnol. 37, pp. 424-429)) and the resulting methylation-specific sequence is determined using either a real-time PCR or other exponential amplification, e.g., a QuARTS assay (e.g., as provided by U.S. Pat. Nos. 8,361,720; 8,715,937; 8,916,344; and 9,212,392).
Thus the claim does not provide additional steps which are significantly more.
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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 149-150, 152, 156, 163, 165 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Choi (2010) . PLoS ONE 5(9): e13020. doi: 10.137 1/journal.pone.0013020.
While the claim requires, “amplifying the treated genomic DNA using a set of primers specific for at least one CpG site for one or more genes.” The specification does not provide a standard to differentiate, “primers specific for at least one CpG site” from primers non-specific for at least one CpG site. Thus the broadest reasonable interpretation is any primer.
With regards to claim 149-150, 152, Choi teaches, “We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19+ B-cells using 454 sequencing technology. “ (Methodology/Principal Findings) Choi teaches, “These primers were designed to match the bisulfite converted linker primer sequences used in the ligation step “ (Bisulfite-PCR amplification)
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Choi thus teaches treating genomic DNA with bisulfite, amplifying and determining methylation by bisulfite genomic sequencing. Thus Choi anticipates the claims as written.
With regards to claims 156, Choi teaches comparison of methylation of normal control male and female (PBMCs) DNA (page 8, 1st column, top).
With regards to claims 163, Choi teaches blood samples (page 11, tissue samples and cell culture).
With regards to claim 165, Choi teaches methylation in promoter regions (promoter hypermethylation).
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.
Claim(s) 149-150, 152, 156, 163, 165-166 is/are rejected under 35 U.S.C. 103 as being unpatentable over Choi (2010) . PLoS ONE 5(9): e13020. doi: 10.137 1/journal.pone.0013020) and Yoon (The Korean Journal of Pathology 2008; 42: 16-20).
While the claim requires, “amplifying the treated genomic DNA using a set of primers specific for at least one CpG site for one or more genes.” The specification does not provide a standard to differentiate, “primers specific for at least one CpG site” from primers non-specific for at least one CpG site. Thus the broadest reasonable interpretation is any primer.
With regards to claim 149-150, 152, Choi teaches, “We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19+ B-cells using 454 sequencing technology. “ (Methodology/Principal Findings) Choi teaches, “These primers were designed to match the bisulfite converted linker primer sequences used in the ligation step “ (Bisulfite-PCR amplification)
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Choi thus teaches treating genomic DNA with bisulfite, amplifying and determining methylation by bisulfite genomic sequencing. Thus Choi anticipates the claims as written.
Choi does not specifically teach determining methylation frequency or methylation score..
However, Yoon teaches determining methylation frequency (table 3). Yoon teaches, “The frequencies of methylation for the two groups were compared using Fisher’s exact test or the 2 test. The methylation index (MI), as a reflection of the methylation status of all of the tested genes, is defined as the total number of genes methylated divided by the total number of genes analyzed. We calculated the MIs for each case to compare the extent of methylation for the panel of the examined genes16 and then we determined the mean for the different groups. Statistical analysis of MI between two variables was performed using the Mann-Whitney U nonparametric test”
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to determine methylation frequency and a methylation index or methylation score. The artisan would be motivated to as Yoon teaches the frequencies can be used as a calculation of methylation index to provide a score for methylation examined. The artisan would be motivated to provide a score of methylation or methylation index to examine total methylation or methylation of a subset of genes in a single value. The artisan would have a reasonable expectation of success as the artisan is merely using known methods of data analysis.
With regards to claims 156, Choi teaches comparison of methylation of normal control male and female (PBMCs) DNA (page 8, 1st column, top).
With regards to claims 163, Choi teaches blood samples (page 11, tissue samples and cell culture).
With regards to claim 165, Choi teaches methylation in promoter regions (promoter hypermethylation).
Summary
No claims are allowed.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday off.
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/Steven Pohnert/Primary Examiner, Art Unit 1683