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 .
DETAILED ACTION
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 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.
Status of the claims
Claims 1-4, 9, 12, 14-17, 19, 21-24, 26-28, 30, 32 and 34-37 are examined on merits in this office action.
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 1-4, 9, 12, 14-17, 19, 21-24, 26-28, 30, 32 and 34-37 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.
Claims 1 and 4 as amended recites ‘trimming DNA associated with the released chromatin fragments by treating with a nuclease to standardize DNA length” (in step e of claim 1 and in step g in claim 4). The claims also recite activating the nuclease (inactive nuclease of step c of claim 1 and inactive nuclease of step e of claim 4) to digest chromatin in a targeted manner to release chromatin fragments. It is unclear as to whether the nuclease in the trimming step is the same nucleosome used in the previous step or a different nucleosome. The trimming step in the specification has not clearly been described or defined and the nuclease utilized in the trimming step has not been clearly described. Moreover, “standardize DNA length” with various nucleases have not been clearly described in the specification and thus the types of nuclease and the length encompassed by the “standardize DNA length” with the nuclease is vague and indefinite.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-4, 9, 12, 14-17, 19, 21-24, 26-28, 30, 32 and 34-37 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of an application. These include “level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient.” MPEP § 2163. While all of the factors have been considered, a sufficient amount for a prima facie case are discussed below.
Further, to provide evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include: a) the scope of the invention; b) actual reduction to practice; c) disclosure of drawings or structural chemical formulas; d) relevant identifying characteristics including complete structure, partial structure, physical and/or chemical properties, and structure/function correlation; e) method of making the claimed compounds; f) level of skill and knowledge in the art; and g) predictability in the art.
Claims 1, 2, 3 and 4 are drawn to a method for measuring the total amount of a chromatin target epitope in a biological sample, the method comprising steps of: a. obtaining a biological sample comprising chromatin; b. contacting the chromatin within the biological sample with a detection reagent that binds a chromatin target epitope to form a complex; c. contacting the complex with a detection reagent-binding agent linked to an inactive nuclease, wherein the detection reagent-binding agent comprises protein A (pA), protein G (pG) or protein A protein G (pAG); d. activating the nuclease to digest the chromatin in a targeted manner to release chromatin fragments; e. trimming DNA associated with the released chromatin fragments by treating with a nuclease to produce a uniform length; f. isolating the released chromatin fragments; and g. quantifying the amount of DNA associated with the released chromatin fragments.
“Chromatin target epitope” has not been clearly defined in the specification but in paragraph [0052] “target epitope” is exemplified by histone or DNA modification and in claim 14, chromatin target epitope is disclosed as histone modification, histone variant, histone mutation, unmodified histone, unmodified DNA, DNA modification and/or protein the indirectly or directly binding chromatin. Thus, in the absence of a definition of detection reagent that binds a chromatin target epitope, the claim encompasses various types of compounds that bind to the above exemplified epitopes. As for example, just for unmodified histone, the binding reagent the binds histone can be histone-binding agent epigallocatechin-3-O-gallate, RAPTA-C, FACT, NAP1L1, Nucleoplasmin, and histone regulator A (HIRA), to exemplify a few. Similar situation exists for, histone variants, DNA, DNA modification and protein, where an inordinately a large number of different types of binding reagents for “detection reagents” are encompassed in the claim, for which the specification does not have a clear descriptive support. The “detection reagent-binding agent linked to an inactive nuclease”, as claimed encompasses various binding compounds complementary (capable of binding) to the above exemplified enormous types of detection reagents and the inactive nuclease encompasses various types of nucleases in inactive form and the nucleases encompasses restriction endonuclease (e.g. HindIII), EcoRV, BamH, DNase1, Lambda exonuclease, Mung bean nuclear, to exemplify a few. Thus claim encompasses the various detection-reagent binding compound linked to the various above nuclease in inactive form, for which the specification does not have a clear descriptive support. The specification fails to provide a representative number of species for the claimed generic detection reagent and detection reagent-binding agent linked to an inactive enzyme.
Throughout the specification, the detection reagent is very limited to target specific antibody specific for histone PMT, histones, nucleosomes or chromatin binding protein or DNA modification (para [0003], [0006], [0021], [0077], Fig.1). All the examples are limited to immune-targeted cleavage utilizing antibody to target chromatin target epitope. Throughout the specification, the detection reagent-binding agent is very limited to fusion protein comprising protein A and protein G fused to micrococcal nuclease MNase (pAG-MNase) wherein the pAG_MNase binds to antibody of the detection reagent by virtue of pAG and wherein MNase is inactive (no Ca2+) and can be activated by Ca2+. Specification teaches that immune-targeted cleavage by pAG-MNase is critical innovation to the present invention, providing high efficient method to digest target chromatin into mononucleosomes (i.e. ~150bp) for reliable quantification of various chromatin elements. For “standardize DNA length”, specification teaches targeted immune cleavage with pAG-MNase to standardize DNA length of ~150bp (para [0087], [0086]). The standardized DNA length has not been clearly described with various nuclease but specification (para [0087]) teaches that DNA length shorter than 147 bp suggest nucleosome being over digested and by contrast, antibody-targeted cleavage by pAG-MNase did not result in fragments shorter than 147 bp, suggesting that nucleosome integrity was maintained. Thus the only, disclosure is DNA length of ~150 bp and the use of antibody-targeted pAG-MNase for the digestion and trimming.
In summary, the specification fails to provide adequate written descriptive support for the genus of “detection reagent” and “detection reagent-binding agent linked to an inactive nuclease” by disclosing only antibody for detection reagent specific for some chromatin target epitope and pAG-MNase as detection reagent-binding agent linked to an inactive enzyme.
MPEP § 2163 states that, for a claimed genus, the written description requirement may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus:
A “representative number of species” means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that “only describe[d] one type of structurally similar antibodies” that “are not representative of the full variety or scope of the genus.”). The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure “indicates that the patentee has invented species sufficient to constitute the gen[us].” See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) (“[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.”). “A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed.” In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004).
Emphasis added.
Therefore, by disclosing only a single species representing “detection reagent” and “detection reagent-binding agent linked to an inactive nuclease”, the specification failed to adequately provide representative descriptive support for the claimed genus of “detection reagent” and “detection reagent-binding agent linked to an inactive nuclease“. Accordingly, the claims do not meet the written description provision of 35 USC 112(pre-AIA ), first paragraph.
Claim Rejections - 35 USC § 102
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.
Claims 1-4, 9, 12, 14-19, 21, 23-24, 26-28, 30, 32, 34, 36 and 37 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Henikoff et al (WO 2019060907A1, cite # 2 of Foreign Patent document of IDS filed 8/15/2024).
In regards to claims 1, 18, 19, 21, 24 and 28 Henikoff teaches a method for detecting the binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in a cell, including: contacting a permeabilized cell or nucleus with a specific binding agent that specifically recognizes the chromatin-associated factor of interest, wherein the specific binding agent is linked to a nuclease that is inactive or an activatable transposome; activating the nuclease or transposase, thereby excising the sequence of chromatin DNA bound to the chromatin-associated factor of interest; isolating the excised DNA; and determining the sequence of the excised DNA, thereby detecting binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in the cell (Abstract). Claim 1 of the reference discloses method for determining the binding site of a chromatin-associated factor of interest to DNA sequences in a cell, comprising:
contacting a permeabilized cell with a first antibody that specifically binds the chromatin- associated factor interest wherein the first antibody is coupled to a plurality of transposomes, each of the plurality of transposomes comprising:
at least one transposase; and
a transposon comprising:
a first DNA molecule comprising a first transposase recognition site; and a second DNA molecule comprising a second transposase recognition site;
activating the transposase, thereby excising and tagging the sequence of DNA bound to the chromatin-associated factor of interest with the DNA tag, wherein the at least one transposase integrates the first and second DNA molecules into chromatin DNA, thereby cleaving and tagging chromatin DNA with the first and second DNA molecules; Henikoff teaches nuclease comprising a chimeric fusion between Protein A and MNase (pA-MN) and activation by calcium (para [000129], [000135] & [000312]) and teaches uniform length of 120 and 150 bp fragment lengths (para [00015] & [000191]). In the absence of description of nuclease and standardize DNA length of the trimming step, the disclosed DNA length of Henikoff digested with pA-MN would be considered as the trimming to standardize DNA length.
isolating the excised DNA; and
determining the sequence of the excised DNA, thereby mapping binding of a chromatin- associated factor of interest to one or more sequences of DNA in the cell. The claims further teaches that the antibody is indirectly coupled to the at least one transposase.
wherein the transposase is linked to a specific binding agent that specifically binds the first antibody and the method of claim 1, further comprising:
contacting the cell with a second antibody that specifically binds the first antibody, and wherein the transposase is linked to a specific binding agent that specifically binds the second antibody. Claim 30 of the reference teaches A method for detecting the binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in a cell, comprising: contacting an uncrosslinked permeabilized cell with a specific binding agent that specifically recognizes the chromatin-associated factor of interest, wherein the specific binding agent is linked to a nuclease or transposase in an inactive state; activating the nuclease or transposase, thereby excising the DNA bound to the chromatin- associated factor of interest; isolating the excised DNA to diffuse out of the cell; and determining the sequence of the excised DNA, thereby mapping binding of a chromatin- associated factor of interest to a sequence of DNA in the cell. Claim 40 teaches that wherein the nuclease, when activated, cleaves a DNA sequence on either side of a binding site of the chromatin-associated factor. Claims 40-42 teaches that wherein the nuclease is a MNase. And the nuclease is activated by Ca.sup.2+ ions. Henikoff teaches that the released DNA after digestion is quantitatively detected using picogreen intercalating dye (para 16 and Figs. 11A and aaB), thereby measuring the total amount of the chromatin target epitope.
In regards to claim 2, Henikoff teaches including reference standard in the process and is added as spike in DNA (para 100], [217], [014], [128], [361] and [765]).
In regards to claims 3 and 4, Henikoff teaches immobilization of the sample on a solid support (claims 9-10 and para [315], [318]).
In regards to claims 9 and 12, Henikoff teache cell samples (para [0052]). Henikoff also teaches various samples including biopsy (para [182]) and biological fluid (para [114]).
In regards to claim 14, Henikoff teaches chromatin target epitope includes protein modification such as transcription factors, DNA modification (para[0004]), and histone modifications (para [35] & [48]), among others.
In regards to claims 15 and 16, Henikoff teaches detection of histone modification (par [0035]) including histone H4 acetylation and histone H3 trimethylation of lysine H3K27me (par [0030] and [0061]).
In regards to claim 17, Henikoff teaches profiling multiple histone modification and chromatin factors (para [000778], [000786], [000925]-[000927]).
In regards to claim 23, Henikoff teaches uniform length of 120 and 150 bp fragment lengths (para [00015] & [000191]).
In regards to claim 24 and 26, as described above, Henikoff teaches nulcease comprising a chimeric fusion between Protein A and MNase (pA-MN) and activation by calcium (para [000129], [000135] & [000312]).
In regards to claim 27, Henikoff teaches that a preferred embodiment of the disclosure is the fusion protein pAG-MN (fusion protein of pA, pG and MNase) (para [000140]).
In regards to claims 28 and 37, as described above, Henikoff teaches that the released DNA after digestion is quantitatively detected using picogreen intercalating dye (para 16 and Figs. 11A and 11B), thereby measuring the total amount of the chromatin target epitope and the dye Picogreen is the intercalator dye as claimed in claim 37.
In regards to claim 30, Henikoff teaches fragmentation of genome for solubilization para [0004]) before, enzyme digestion.
In regards to claim 32, Henikoff teaches digestion of sample with proteinase K after digestion with the enzyme pA-MNase (para [0054]).
In regards to claim 36, Henikoff teaches sold support comprising ConA coated magnetic beads (para [000765]).
In regards to claims 2 and 34, Henikoff teaches using spike-in DNA at a single concentration as control or reference in the process (par [000100], [000280]) and teaches that by scaling to spike-in DNA, quantitative measurement of the amount of cleaved DNA fragments is possible (para [00032], [000128], [000217] and [000765).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-4, 9, 12, 14-19, 21-24, 26-27, 30, 32 and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Schmid et al (Molecular cell 2004) in view of Meers (eLife 2019 Jun 24:8:e46314, pp 1-16; Cite # 2 of Non-Patent Documents of IDS filed 05/01/2023 ).
In regards to claims 1, 3, 17-19 and 21, 24, 26-27, and 36 Schmid discloses genomic interaction sites of chromatin proteins utilizing antibody specific for target epitope tethered with enzyme. Schmidt discloses tethering fusion protein pA-MN (a fusion protein comprising micrococcal nuclease and protein A) to specifically bound antibody, wherein the nuclease is kept inactive during the tethering process (no Ca2+) and the specifically tethered nucleases are activated with Ca2+ ions to locally introduce double-stranded DNA breaks (Summary). Schmid teaches binding of antibody (primary antibody) specific to chromatin protein of interest (i.e. chromatin target epitope), binding of secondary antibody to the primary antibody, binding of the fusion protein pA-MN (detection reagent) to the secondary antibody, activating the nuclease MN moiety of pA-MN with Ca2+ ions to provide double-stranded DNA breaks (i.e. trimming) and gel analysis of the DNA fragment (see Figs. 1A and 1B). In the absence of description of nuclease and standardize DNA length of the trimming step, the digestion of pA-MN would be considered as the trimming to standardize DNA length because immune targeting with pA-MN would be expected to digest DNA to a certain length.
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(page 148).
Schmid does not mention isolating, profiling and quantifying chromatin fragment.
Meers teaches improved CUT & RUN utilizing His-tagged fusion protein comprising protein A, protein G, MNase, (His)6 and HA (PAG/MNase) useful for one step tagging of antibody without requiring secondary antibody and facile chromatin pull-down from a CUT&RUN supernatant (page 2). Meers teaches binding samples to activated concanavalin A-coated beads (pages 11-12). Meers teaches release of DNA fragments by digestion in the supernatant in the presence of Ca2+ (page 4) for detection and epigenomic profiling (Abstract). Meers teaches extracting total DNA from the released fragments (page 12, lines 14-17).
Therefore, since the basic concept of releasing chromatin fragments having specific chromatin target epitope for detection of associated DNA and epigenomic profiling by antibody targeted tethered MNase enzyme digestion has been described by Schmidt and Meers, and since Meers discloses extraction of total DNA from released chromatin fragment in the supernatant (Fig. 2 and lines 14-17 of page 12). it would be obvious to one of ordinary skilled in the art to easily envisage quantifying the amount of associated DNA from the released chromatin fragments as disclosed by Schmid and Meers, with the expectation of understanding the level of interaction between specific proteins and their associated DNA sequences for understanding the role of these proteins in gene regulation and the mechanism of epigenetic modification, with a reasonable expectation of success because both Schmid and Meers are directed to genomic mapping of chromatin proteins and epigenomic profiling of clinical samples. Meers teaches nucleosome associated DNA is about 150bp (pate 12, las 2 lines) and both Smidth and Meers teaches digestion with PA-MNase outside of the nucleosome (see the above diagram), which clearly indicates digestion/trimming around 150 bp and in the absence of description of nuclease and standardize DNA length of the trimming step, the digestion of pA-MN would be considered as the trimming to standardize DNA length.
Moreover, since the basic concept of antibody targeted digestion has been described, multiplexing utilizing two of more antibodies targeting to different epitopes and measuring of release chromatin DNA fragments after digestion for multiplexing, as claimed in claim 17, would be obvious to one of ordinary skilled in the art.
In regards to claims 2 and 4, Meers teaches including reference nucleosomes comprising the chromatin target epitope to from a reference sample (see calibration using E. coli carry-over DNA, page 7).
In regards to claim 9, Both Schmidt and Meers teaches cells as biological sample (see page 147 of Schmid and pages 11-12 of Meers).
In regards to claim 12 and 15, Meers teaches clinical sample and cell for histone modification (Introduction) but however, since the basic concept of cleaving of chromatin target epitope has been described by Schmidt and Meers, various types of samples including cell sample or sample of biological fluid (introduction) would be obvious to one of ordinary skilled in the art.
In regards to claim 14, Meers teaches histone modification (Introduction) and Schmid teaches myc DNA (page 148, last para of 1st col.).
In regards to claim 22, Meers, as described above, teaches biological sample immobilized on a solid support but does not disclose detection reagent (i.e. antibody) immobilized on a solid support. Since the basic concept of cleaving of chromatin target epitope by antibody targeted enzyme has been described, various variations including solid phase assay utilizing detection reagent immobilized on a solid support, would be obvious to one of ordinary skilled in the art.
In regards to claims 15 and 16, Meers teaches anti-H3K4me2 antibody for biding to H3K3me2 (histone H3 lysine 4 dimethylation) post translation histone 3 modification (Fig. 5, last row of page 9 table).
In regards to claim 23, Meers teaches nucleosome associated DNA is about 150bp (pate 12, las 2 lines).
In regards to claim 30, Schmid teaches breaking cell sample mechanically with glass beads (Last para of 2n col., page 147).
In regards to claim 32, Meers teaches treating sample with additional enzyme RNase after digestion with enzyme (page 12, lines 13-14).
Claims 1-4, 9, 12, 14-19, 21-24, 26-27, 30, 32 and 34-36 are rejected under 35 U.S.C. 103 as being unpatentable over Schmid et al (Molecular cell 2004) in view of Meers (eLife 2019 Jun 24:8:e46314, pp 1-16 ) as described for claim 1-4, 9, 12-15-19, 21-24, 26-27, 30, 32 and 36 above, and further in view of Grzybowski et al (Nat. Protoc. 2019).
Schmid in view of Meers has been described above that provides obviousness for the method of measuring chromatin in a sample as claimed in the above claims.
Meers as described in the rejection teaches spiking with reference sample in the process but however, does not mention the reference nucleosome present at a single concentration or multiple reference samples at different concentrations.
Grzybowski teaches spiking-in defined nucleosomal standards that provides absolute measurement of histone modification density at genomic loci on a biologically meaningful scale (Abstract; page 3275). Grzybowski teaches testing with multiple standards, for example, for anti H3K4me, suggest utilizing at least some mostly important available lysine methylation nucleosome standards for antibody specificity (page 3283) and the exact amount of the standards can vary (page 3283).
Therefore, from the description in mind of Grzybowski, it would be obvious to include single concentration or different concentration of one or more reference sample with a reasonable expectation of success.
Claims 1-4, 9, 12, 14-19, 21-24, 26-28, 30, 32 and 34-37 are rejected under 35 U.S.C. 102(a)(1) as being unpatentable over Henikoff et al (WO 2019060907A1) as described for claims 1-4, 9, 12, 14-19, 21, 23-24, 26-28, 30, 32, 34, 36 and 37 above, and further in view of Grzybowski et al (Nat. Protoc. 2019).
Henikoff has been described above, anticipating the process of claims 1-4, 9, 12, 14-19, 21, 23-24, 26-28, 30, 32, 34, 36 and 37. As described above, Henikoff teaches reference sample at a single concentration, but however, does not teach multiple reference samples.
Grzybowski teaches spiking-in defined nucleosomal standards that provides absolute measurement of histone modification density at genomic loci on a biologically meaningful scale (Abstract; page 3275). Grzybowski teaches testing with multiple standards, for example, for anti H3K4me, suggest utilizing at least some mostly important available lysine methylation nucleosome standards for antibody specificity (page 3283) and the exact amount of the standards can vary (page 3283).
Since Henikoff also teaches multiplexing (para [000925], [000926]), from the description in mind of Grzybowski, it would be obvious to include single concentration or different concentration of one or more reference samples, for multiplexing, with a reasonable expectation of success.
In regards to claim 22, Henikoff, as described above, teaches sample, as for example, cells, immobilized to ConA coated solid support (magnetic beads) but however, does not teach detection reagent (as for example, antibody bound to solid support). However, since the basic concept of cleaving of chromatin target epitope by antibody targeted enzyme has been described, and since Henikoff teaches solid support immobilized with sample and ELISA based detection, different variations including solid phase assay utilizing detection reagent immobilized on a solid support, would be obvious to one of ordinary skilled in the art.
Response to argument
Applicants’ arguments and amendments filed 07/23/2026 have been fully considered and are persuasive to overcome the rejections under 35 USC 112 (b) but however Applicant arguments regarding 35 USC 112(a), 35 USC 102(a)(1) and 35 USC 103 have been rendered moot in view of the modified rejections as described in this office action that are necessitated by Applicants’ amendments.
Applicant’s main argument is based claims with the added limitation of trimming DNA associated with the release chromatin fragments by treating with a nuclease to standardize DNA. Applicant argued that this step of trimming to standardize DNA length by treating with a nuclease has not been taught by Henikoff, Schmid, and Meers.
The above arguments have fully been considered but are not found persuasive. First as described above for 35 USC 112 (b) rejection, the trimming step in the specification has not clearly been described or defined and the nuclease utilized in the trimming step has not clearly been described. Moreover, “standardize DNA length” with various nucleases have not been clearly described in the specification and thus the types of nucleases and the length encompassed by the “standardize DNA length” with the nuclease is vague and indefinite. The references teach digestion of chromatin with a chimeric fusion between Protein A and MNase (pA-MN) and activation by calcium and the reference of Henikoff teaches uniform length of 120 and 150 bp fragment lengths. Meers teaches nucleosome associated DNA is about 150bp (pate 12, las 2 lines) and both Smidth and Meers teaches digestion with PA-MNase outside of the nucleosome (see the above diagram), which is highly expected to digestion/trimming around 150 bp. Since the nuclease digestion step of chromatin and trimming step is a nuclease has not been clarified or clearly claimed with specific nuclease and with specific DNA length and since the specification does not clearly describe the trimming steps, in the absence of description of nuclease and standardize DNA length of the trimming step, the disclosed DNA length of Henikoff digested with pA-MN and the digestion of pA-MN would be considered as the trimming to standardize DNA length.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/SHAFIQUL HAQ/Primary Examiner, Art Unit 1678
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