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 .
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.
Claim 16 is 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 16, the phrase “such as” which is considered equivalent to the phrases: “preferably,” “for example,” “in particular,” “specifically,” and “or the like,” is considered indefinite. The metes and bounds of the claim scope are not clear. It is not clear if the claim limitation is optional or not. These phrases/expressions have no limiting effect on the scope of the claim. The feature following such an expression is to be regarded as entirely optional, and results in an unclear definition of the subject matter for which protection is sought. Furthermore, without knowing this information, one of ordinary skill in the art would not know whether they are infringing on the claims or not.
Note Regarding Prior Art
Examiner cites particular sections, columns, line numbers, paragraphs and figures, in the references as applied to the claims below for the convenience of the applicant. Although the specified citations are representative of the teachings in the art and are applied to the specific limitations within the individual claim, other passages and figures may apply as well. It is respectfully requested that, in preparing responses, the applicant fully consider the references in their entirety as potentially teaching all or part of the claimed invention, as well as the context of the passage as taught by the prior art or disclosed by the examiner.
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 – 13, 15 – 22, 24 and 26 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ruthernburg et al. (WO 2015/117145 A1; hereinafter “Ruthernburg”).
Regarding claim 1, Ruthernburg teaches throughout the publication a method comprising:
providing a biologically derived nucleosome preparation which contains a defined amount or concentration of nucleosomes expressed in absolute units of mass or concentration (an internal standard comprising recombinant and semi-synthetic protein-DNA complexes that include nucleosomes (paragraphs 47 – 49, 56, 57 and 85; the standards are added at differing concentrations (paragraph 62) and at known precise molar concentrations (paragraph 72)); and
using the preparation as a calibrant in a comparative analytical procedure (e.g., ICeChIP assay; paragraphs 49, 84 and 87).
Regarding claim 2, Ruthernburg teaches the method of claim 1, wherein the comparative analytical procedure is for the measurement of a level of a histone post translational modification in a sample (histone-containing samples can be prepared from biopsy tissue to detect the histone PTM (post translational modification) state associated with cancer; paragraph 85).
Regarding claim 3, Ruthernburg teaches the method of claim 1, wherein the biologically derived nucleosome preparation contains a defined amount or concentration of a type of nucleosomes comprising a specified epigenetic feature (histones, which comprise the nucleosomes, can be modified to include a plurality of epitopes and post-translational modifications referred to as “epigenetic marks” or epigenetic features; paragraphs 3 and 4).
Regarding claim 4, Ruthernburg teaches the method of claim 1, wherein the biologically derived nucleosome preparation contains defined amounts or concentrations of a multiplicity of nucleosome types, each comprising one or more specified epigenetic feature (an internal standard comprising recombinant and semi-synthetic protein-DNA complexes that include the nucleosomes that comprise the histones (paragraphs 47 – 49 and 57; the standards are added at differing concentrations (paragraph 62) and at known precise molar concentrations (paragraph 72)).
Regarding claim 5, Ruthernburg teaches the method of claim 4, wherein the biologically derived nucleosome preparation contains a combination of multiple different nucleosome types, and optionally other chromatin fragments, comprising multiple epigenetic features as a combined calibrant (numerous standards of different types may also constitute a standard (paragraph 10); and can include standard histone fragments (paragraph 13)).
Regarding claim 6, Ruthernburg teaches the method of claim 4, wherein the one or more specified epigenetic feature is a histone post translational modification (histones, which comprise the nucleosomes, can be modified to include a plurality of epitopes and post-translational modifications referred to as “epigenetic marks” or epigenetic features; paragraphs 3, 4 and 10).
Regarding claim 7, Ruthernburg teaches the method of claim 6, wherein the histone isoform is H3.1 (in a preferred embodiment, the protein part of a DNA-protein complex is a core histone octamer complex containing core histones H2A, H2B, H3 and H4; paragraphs 50 and 127).
Regarding claim 8, Ruthernburg teaches the method of claim 6, wherein the histone post translational modification is selected from the group consisting of acetylation of lysine residues, methylation of lysine residues, ubiquitination of lysine residues, citrullination of arginine residues, methylation of arginine residues and phosphorylation of serine residues (paragraph 18).
Regarding claim 9, Ruthernburg teaches the method of claim 8, wherein the histone post translational modification is methylation of a lysine residue (paragraph 18).
Regarding claim 10, Ruthernburg teaches the method of claim 4, wherein at least one of the multiplicity of nucleosome types is nucleosomes per se (numerous standards of different types may also constitute a standard (paragraph 10); and can include standard histone fragments (paragraph 13)).
Regarding claim 11, Ruthernburg teaches the method of claim 1, wherein the biologically derived nucleosome preparation is produced from cells in cell culture (paragraphs 82 and 110).
Regarding claim 12, Ruthernburg teaches the method of claim 1, wherein the biologically derived nucleosome preparation is prepared by (i) isolation or purification of a nucleosome preparation for the desired nucleosomes (paragraphs 105 - 110).
Regarding claim 13, Ruthernburg teaches the method of claim 1, wherein the comparative analytical procedure is an immunoassay or clinical diagnostic test for a human or animal subject (paragraphs 132 – 135).
Regarding claim 15, Ruthernburg teaches the method of claim
Regarding claim 16, Ruthernburg teaches the method of claim 15, wherein the test sample is a human or animal body fluid sample, such as a blood (paragraph 133).
Regarding claim 17, Ruthernburg teaches an immunoassay method for the measurement of nucleosomes in a test sample, comprising: providing an immunoassay which comprises a calibrant comprised of a biologically derived nucleosome preparation assigned, or defined by, values expressed in absolute units of mass or concentration (e.g., immunoprecipitation (paragraphs 46 – 50); an internal standard comprising recombinant and semi-synthetic protein-DNA complexes that include nucleosomes (paragraphs 47 – 49 and 57; the standards are added at differing concentrations (paragraph 62) and at known precise molar concentrations (paragraph 72)).
Regarding claim 18, Ruthernburg teaches the immunoassay method according to claim 17, wherein said immunoassay comprises a binding agent that binds specifically to nucleosomes (via an affinity reagent; paragraphs 49 and 50).
Regarding claim 19, Ruthernburg teaches the immunoassay method according to claim 17, wherein the immunoassay employs a single binding agent (via an affinity reagent; paragraphs 49 and 50).
Regarding claim 20, Ruthernburg teaches the immunoassay method according to claim 17, wherein the immunoassay is a 2-site immunometric assay employing two binding agents (paragraphs 94 – 97, 104 and 129).
Regarding claim 21, Ruthernburg teaches the immunoassay method according to claim 18, wherein the binding agent is directed to a histone, nucleosome core, DNA epitope or a protein adducted to a nucleosome (paragraphs 94 – 97 and 129).
Regarding claim 22, Ruthernburg teaches the immunoassay method according to claim 18, wherein the binding agent is a chromatin protein or an antibody (paragraphs 94 – 97, 104 and 129).
Regarding claim 24, Ruthernburg teaches a comparative analytical procedure kits comprising; a biologically derived nucleosome preparation which contains a defined amount or concentration of nucleosomes expressed in absolute units of mass or concentration, and optionally instructions for use of the kit in a method of diagnosing and/or monitoring disease (paragraphs 94 – 97).
Regarding claim 26, Ruthernburg teaches the method of claim 9, wherein the methylation of a lysine residue is methylation of a histone 3 lysine residue (paragraph 18).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN J. SINES whose telephone number is (571)272-1263. The examiner can normally be reached 9 AM-5 PM EST M-F.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lyle Alexander can be reached at (571) 272-1254. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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BRIAN J. SINES
Primary Patent Examiner
Art Unit 1796
/BRIAN J. SINES/Primary Examiner, Art Unit 1796
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