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
Status of the Application
1. Claims 1-5, 7-8, 10, 12, 14-15, 17, 21, 23, 25, 28, 31-33 and 35 are pending and are considered for examination. Claims 6, 9, 11, 13, 16, 18-20, 22, 24, 26-27, 29-30, 34 and 36-42 were canceled.
Priority
2. This application filed on May 10, 2024 is a CON of PCT/US2022/079757 filed on November 11, 2022 which claims priority to US 63/279,001 filed on November 12, 2021.
Informalities
3. The following informalities are noted:
(i) Claims 1, 7, recite method steps represented by a., b., c., which indicates a full stop at each method step. Amendment the claims to delete full stop of each step is suggested.
(ii) Claim 12 recites NaCl and Claim 33 recites MeCP2, MBD1, MBD2, MBD4. Expanding the terms at least once for the first time that they appear in the claims is suggested. Appropriate correction is required.
Specification
4. The disclosure is objected to because of the following informalities:
The use of the terms (fluorescent markers in para 0052, 0063, 0070, 0091), which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore, the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM, or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks. The fluorescent markers are not followed by generic names. Appropriate correction is required.
Claim Rejections - 35 USC § 112
5. 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.
A. Claim 15, 25 and 32 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 15 recites the limitation "the first methylated nucleotide" in line 2 of the claim. There is insufficient antecedent basis for this limitation in the claim because the claim 14 upon which the claim 15 depends lack support for a first labeled nucleotides. If the Applicant intend to refer to first oligonucleotide, amending the claim 15 to recite the first methylated oligonucleotide, would obviate the rejection. Further, claims 25 and 32 recites the limitation "the first and the second methylated oligonucleotides" in line 1-2 of the claim. There is insufficient antecedent basis for this limitation in the claim because the claim 17 upon which the claim 25 depends, and the claim 14 upon which the claim 32 depends, lack support for the second methylated oligonucleotide and it is unclear what the claims 25 and 32 are referring to.
B. Claim 23 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. The metes and bounds of the claim 23 are unclear and indefinite because Claim 23 is dependent on canceled claim 19 and it is not clear what the claim 23 is referring to.
C. Claim 32 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. The claim 32 recites ‘preferentially’. The metes and bounds of the claim 32 are unclear and indefinite because it is not clear if the claim requires the limitations followed by the term preferentially or do, they represent as preference.
Claim Rejections - 35 USC § 102
6. 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. Claims 1-5, 7-8, 10, 12, 14-15, 17, 21, 23, 25, 28, 31-33 and 35 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kennedy et al. (WO 2018/119452).
Note: claims 5, 12, 17 and 23 recite ‘optionally’. The limitations followed by the term ‘optionally’ are not considered as required limitations because they are optional limitations.
Kennedy et al. teach a method of claim 1, assaying a methylated DNA-binding protein, comprising:
a) contacting the methylated DNA-binding protein with a sample comprising at least a first oligonucleotide (sample comprising DNA or sample comprising DNA hybridized to an oligonucleotide (molecular tag) (para 00023-00024, 000337-000362, 00013, 00018,000132, 000316);
b) obtaining at least hypomethylated and hypermethylated partitions of the sample (para 00023-00024, 000337-000362, 00013, 000132-000147, 000316-000319); and
c) quantifying the first oligonucleotide in the hypomethylated and hypermethylated partitions (para 00023-00024, 000337-000362, 00013, 00018, 000132-000147, 000316-000319).
With reference to claim 2, Kennedy et al. teach that the methylated DNA-binding protein is immobilized on a solid support (para 000132, 000147).
With reference to claim 3, Kennedy et al. teach that the solid support comprises plate wells (para 000184).
With reference to claim 4-5, Kennedy et al. teach that the first oligonucleotide is quantified by measuring absorbance, wherein the first oligonucleotide is labeled (para 00072, 000316).
With reference to claim 7-8, 10, 12, Kennedy et al. teach that the hypomethylated partition comprises a first salt concentration, and the hypermethylated partition comprises a second salt concentration, wherein the second salt concentration is higher than the first salt concentration, wherein the first salt concentration ranges from 0 M to 1 M and/or b. the second salt concentration ranges from 1.0 M to 3.0 M and teach that the first salt or the second salt is a sodium salt and the first salt concentration is about 0.3 M or wherein the second salt concentration is about 2 M (para 000132-000147, 000337-000362).
With reference to claim 14, 17, 25, Kennedy et al. teach that multiple oligonucleotides, which comprises two or more oligonucleotides which include a first and a second methylated oligonucleotides, wherein the first and second methylated oligonucleotide comprises a methylated CpG (para 000132-000152).
With reference to claim 15, Kennedy et al. teach that the sample further comprises a labeled unmethylated oligonucleotide and the first methylated nucleotide is labeled, further wherein the labeled unmethylated oligonucleotide is differentially labeled relative to the first methylated oligonucleotide (para 000132-00147, 00025-00026).
With reference to claim 21, 25, Kennedy et al. teach that the first methylated oligonucleotide is labeled and the sample further comprises a second labeled methylated oligonucleotide, wherein the second labeled methylated oligonucleotide has a greater number of methylated positions than the first labeled methylated oligonucleotide, further wherein the second labeled methylated oligonucleotide is differentially labeled relative to the first labeled methylated oligonucleotide (para 000133, 00095-00098, 000211, 000372).
With reference to claim 23, 28, Kennedy et al. teach that the sample further comprises a labeled unmethylated oligonucleotide, wherein the labeled unmethylated oligonucleotide is differentially labeled relative to the first labeled methylated oligonucleotide and the second labeled methylated oligonucleotide, wherein the first labeled methylated oligonucleotide comprises 3 methylated CpGs (para 000372-000373, 00095-000104).
With reference to claim 32, Kennedy et al. teach that the first methylated oligonucleotide and/or the a second labeled methylated oligonucleotide binds to a methyl binding domain, a methyl binding protein (para 000132-000151).
With reference to claim 33, Kennedy et al. teach that the methylated DNA binding protein comprises MeCP2, MBD1, MBD2, MBD4, or a methyl-CpG binding zinc finger protein (para 000211, 000132, 000142).
With reference to claim 31, 35, Kennedy et al. teach that the method further comprising obtaining an intermediate partition or measuring a binding activity of the methylated DNA binding protein, wherein the binding activity is determined in units indicating an amount of protein capable of binding a predetermined fraction of a reference methylated oligonucleotide, wherein the reference methylated oligonucleotide comprises at least 1 methylated CpG (para 000337-000362, 000372-000373, 000212-000218). For all the above, the claims are anticipated.
Conclusion
No claims are allowable.
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/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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