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 .
The claims dated 5/3/2024 are under consideration.
Priority
The present application is a 371 national stage entry of PCT/KR2022/017269 (filed 11/4/2022), and claims benefit of REPUBLIC OF KOREA 10-2021-0151412 (filed 11/5/2021).
An English translation of the foreign priority document has not been received.
Drawings
The drawings dated 5/3/2024 are objected to because it is unclear if applicant intends the application to include colored figures as copies were submitted in which Fig. 1 and 12 include color.
If applicant intends the application to include colored drawings, the following information is provided.
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
If applicant intends the application to not include colored drawings, it is suggested a grayscale or black and white copy of the drawings be filed.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because of the following informalities: the priority information is not consistent with that in the ADS.
Appropriate correction is required.
The disclosure is objected to because of the following informalities: on p. 8 the specification states “uucleoside” rather than “nucleoside”.
Appropriate correction is required.
Claim Objections
Claim 1 is objected to because of the following informalities: in line 2, the claim recites “predict cancer patient’s” rather than “predict a cancer patient’s”. Appropriate correction is required.
Claim 6 is objected to because of the following informalities: in line 3, the claim recites “bisulfige” rather than “bisulfite”. Appropriate correction is required.
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 1-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
The claims are drawn to methods, one of the four statutory categories.
The claim(s) recite(s) the following elements:
In claim 1, “assessing the methylation disorder of adjacent CpG sites in one or more regions in the genomic DNA”. The recitation encompasses an abstract idea that may be performed purely in the human mind or with the aid of pen and paper. The amount of data to be considered, e.g., two CpG sites in one genomic region, is limited such that it may be considered mentally.
In claim 9, the claim sets forth abstract ideas in the form of mathematical equations and data processing that may carried out in the human mind or with the aid of pen and paper. The amount of data to be considered, e.g., two CpG sites in one genomic region, is limited such that it may be considered mentally.
In claims 10 and 11, the claim sets forth abstract ideas in the form of mathematical equations and data processing that may carried out in the human mind or with the aid of pen and paper. The amount of data to be considered, e.g., two CpG sites in one genomic region, is limited such that it may be considered mentally.
In claim 13, a natural phenomenon that is the natural relationship between the degree of methylation disorder and reactivity to anticancer drugs.
The judicial exceptions are not integrated into a practical application because the claims do not involve:
improvements to the functioning of a computer or to any other technology or technical field;
applying or using the judicial exceptions to effect a particular treatment or prophylaxis for a disease or medical condition;
applying the judicial exception with, or by use of, a particular machine; or
effecting a transformation or reduction of a particular article to a different state or thing.
The claimed limitations add insignificant extra-solution activity to the judicial exceptions as they are mere data gathering, which is the overall purpose of the method as set forth in the preamble
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims encompass the use of known methodologies as described on page 8-9.
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 1-14 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.
Regarding claim 1, it is not clear how the recited preamble is intended to breathe life and meaning into the claims. The preamble of the claim recites a “method for assessing the methylation status of adjacent CpG sites in genomic DNA in order to provide information necessary to predict cancer patient's reactivity to anticancer drugs”. However, the method steps in the claim only require:
a) isolating genomic DNA from a biological sample isolated from a subject;
(b) measuring the methylation status of CpG sites in the isolated genomic DNA; and
(c) assessing the methylation disorder of adjacent CpG sites in one or more regions in the genomic DNA.
Thus, it is unclear if applicant intends to cover any method of performing those steps, or if the method is intended to somehow require more to accomplish the goal set forth in the preamble. If it is the later, then it appears that the claims are incomplete, as they fail to provide any active steps related to “cancer patients”, “predicting”, etc.
Claims 2-14 depend from claim 1 and are rejected for the same reason.
Regarding claim 6, the claim contains the trademark/trade name EpiTYPER®. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a methylation assay and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2-4 and 13 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Regarding claims 2-4, the claims further describe elements set forth in the preamble. The preamble does not limit the scope of the claims and these additional descriptions do not alter how steps (a) to (c) are carried out. Thus, the claims fail to further limit claim 1.
Regarding claim 13, the claim further describe a property of the methylation disorder. The description does not limit the scope of claim 1 and does not alter how steps (a) to (c) are carried out. Thus, the claims fail to further limit claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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.
(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.
Claim(s) 1-8 and 13-14 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Gaiti (Nature. 2019. 569:576).
Claim 1 is drawn to a “method for assessing the methylation status of adjacent CpG sites in genomic DNA in order to provide information necessary to predict cancer patient's reactivity to anticancer drugs”; however, the active method steps do not explicitly require “predicting” a cancer patient’s reactivity to anticancer drugs. MPEP 2111.02 states:
If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention's limitations, then the preamble is not considered a limitation and is of no significance to claim construction.
Accordingly, the claim language of “a method for assessing the methylation status of adjacent CpG sites in genomic DNA in order to provide information necessary to predict cancer patient's reactivity to anticancer drugs” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims. The claims are given the broadest reasonable interpretation as requiring:
a) isolating genomic DNA from a biological sample isolated from a subject;
(b) measuring the methylation status of CpG sites in the isolated genomic DNA; and
(c) assessing the methylation disorder of adjacent CpG sites in one or more regions in the genomic DNA.
It is noted step (c) does not refer to or rely upon the methylation status of CpG sites measured in step (b).
Regarding claim 1, Gaiti teaches isolating genomic DNA from a biological sample isolated from a subject (Methods, Human subjects, sample collection and genotyping).
Gaiti teaches measuring the methylation status of CpG sites in the isolated genomic DNA using single-cell reduced representation bisulfite sequencing (scRRBS) (Methods, Multiplexed scRRBS library construction).
Gaiti teaches assessing methylation disorder of adjacent CpG sites in genomic regions by calculating the proportion of discordant reads (PDR) (Methods, PDR analysis).
Regarding claim 2, claim 2 refers to an element of the preamble of claim 1, which as described about does not limit the scope of the claim.
Gaiti anticipates the broad scope of claim 2 for the same reason it anticipates claim 1.
It is noted that the samples include B cells obtained from patients with chronic lymphocytic leukaemia (CLL) (Methods, Human subjects, sample collection and genotyping).
Regarding claim 3, claim 3 refers to an element of the preamble, which as described about does not limit the scope of the claim.
Gaiti anticipates the broad scope of claim 3 for the same reason it anticipates claim 1.
Regarding claim 4, claim 4 refers to an element of the preamble, which as described about does not limit the scope of claim 1.
Gaiti anticipates the broad scope of claim 4 for the same reason it anticipates claims 1 and 3.
Regarding claim 5, Gaiti teaches the biological samples are cancerous B cells obtained from patients with CLL (Methods, Human subjects, sample collection and genotyping).
Regarding claims 6 and 7, Gaiti teaches using scRRBS to measure CpG methylation status as described above.
Regarding claim 8, Gaiti teaches the one or more genomic regions include CG islands and promoters (Extended Data Fig. 3).
Regarding claim 13, claim 13 sets forth an inherent property that describes methylation disorder and reactivity to anticancer drugs. The prior art does not need to recognize this property at the time of filing. MPEP 2112.II.
Gaiti anticipates claim 13 for the same reason as claim 1.
Regarding claim 14, Gaiti teaches the subject is a human as described above, a vertebrate animal.
Claim(s) 1-9 and 12-14 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Landau (Cancer Cell. 2014. 26(6):813-825).
Claim 1 is drawn to a “method for assessing the methylation status of adjacent CpG sites in genomic DNA in order to provide information necessary to predict cancer patient's reactivity to anticancer drugs”; however, the active method steps do not explicitly require “predicting” a cancer patient’s reactivity to anticancer drugs. MPEP 2111.02 states:
If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention's limitations, then the preamble is not considered a limitation and is of no significance to claim construction.
Accordingly, the claim language of “a method for assessing the methylation status of adjacent CpG sites in genomic DNA in order to provide information necessary to predict cancer patient's reactivity to anticancer drugs” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims. The claims are given the broadest reasonable interpretation as requiring:
a) isolating genomic DNA from a biological sample isolated from a subject;
(b) measuring the methylation status of CpG sites in the isolated genomic DNA; and
(c) assessing the methylation disorder of adjacent CpG sites in one or more regions in the genomic DNA.
It is noted step (c) does not refer to or rely upon the methylation status of CpG sites measured in step (b).
Regarding claim 1, Landau teaches isolating genomic DNA from a biological sample isolated from a subject (p. 11 of 29, Sample acquisition).
Landau teaches measuring the methylation status of CpG sites in the isolated genomic DNA using WGBS or RRBS (p. 11-12 of 29, WGBS and RRBS).
Landau teaches assessing methylation disorder of adjacent CpG sites in genomic regions by calculating the proportion of discordant reads (PDR) (Figure 1).
Regarding claim 2, claim 2 refers to an element of the preamble, which as described about does not limit the scope of the claim.
Landau anticipates the broad scope of claim 2 for the same reason it anticipates claim 1.
It is noted that the samples include B cells obtained from patients with chronic lymphocytic leukaemia (CLL) (p. 11 of 29, Sample Acquisition).
Regarding claim 3, claim 3 refers to an element of the preamble, which as described about does not limit the scope of the claim.
Landau anticipates the broad scope of claim 3 for the same reason it anticipates claim 1.
Regarding claim 4, claim 4 refers to an element of the preamble, which as described about does not limit the scope of claim 1.
Landau anticipates the broad scope of claim 4 for the same reason it anticipates claims 1 and 3.
Regarding claim 5, Landau teaches the biological samples are cancerous CLL cells obtained from patients with CLL (p. 11 of 29, Sample Acquisition).
Regarding claims 6 and 7, Landau teaches using RRBS to measure CpG methylation status as described above.
Regarding claim 8, Landau teaches the one or more genomic regions include CG islands and promoters (Figure 2).
Regarding claim 9, Landau teaches PDR is discordant reads divided by total number of reads (Figure 1), which is equivalent to the claimed equation B/(A+B). Landau further teaches averaging the PDR across regions (Figure 3; and Figure S1).
Regarding claim 12, Landau further teaches calculating methylation variation based on an entropy calculation (Figure S3).
Regarding claim 13, claim 13 sets forth an inherent property that describes methylation disorder and reactivity to anticancer drugs. The prior art does not need to recognize this property at the time of filing. MPEP 2112.II.
Landau anticipates claim 13 for the same reason as claim 1.
Regarding claim 14, Landau teaches the subject is a human as described above, a vertebrate animal.
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.
Claim(s) 10 and 11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gaiti (Nature. 2019. 569:576).
Claims 10 and 11 are drawn to a “method for assessing the methylation status of adjacent CpG sites in genomic DNA in order to provide information necessary to predict cancer patient's reactivity to anticancer drugs”; however, the active method steps do not explicitly require “predicting” a cancer patient’s reactivity to anticancer drugs. MPEP 2111.02 states:
If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention's limitations, then the preamble is not considered a limitation and is of no significance to claim construction.
Accordingly, the claim language of “a method for assessing the methylation status of adjacent CpG sites in genomic DNA in order to provide information necessary to predict cancer patient's reactivity to anticancer drugs” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims. The claims are given the broadest reasonable interpretation as requiring:
a) isolating genomic DNA from a biological sample isolated from a subject;
(b) measuring the methylation status of CpG sites in the isolated genomic DNA; and
(c) assessing the methylation disorder of adjacent CpG sites in one or more regions in the genomic DNA, where in the assessing is as described in claims 10 and 11.
It is noted step (c) does not refer to or rely upon the methylation status of CpG sites measured in step (b).
Regarding claims 10 and 11, Gaiti teaches isolating genomic DNA from a biological sample isolated from a subject (Methods, Human subjects, sample collection and genotyping).
Gaiti teaches measuring the methylation status of CpG sites in the isolated genomic DNA using single-cell reduced representation bisulfite sequencing (scRRBS) (Methods, Multiplexed scRRBS library construction).
Gaiti teaches assessing methylation disorder of adjacent CpG sites in genomic regions by calculating the proportion of discordant reads (PDR) (Methods, PDR analysis).
Gaiti does not teach the additional elements beyond those of claim 1 and specific to claims 10 and 11.
However, Gaiti teaches assessing a concordance odds ratio, which takes into account CpG methylation status between neighboring CpG sites as a function of genomic distance. The analysis involves the number of concordant pairs in reads at each distance divided by the CpG sites across the reads. An average of rate of decay of CORs is calculated based on each distance. See Extended Data Fig. 4 and Methods, Concordance odds ratio analysis.
It would have been prima facie obvious to the ordinary artisan at the time of filing to have modified the method of Gaiti by replacing the number of concordant pairs with the number of discordant pairs. This would allow one to identify genomic regions in which methylation is more variable providing information about unstable genomic regions. The modification has a reasonable expectation of success as it simply substitutes one value for another value within an equation.
Conclusion
No claims allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682
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