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 .
Claims 1-20 are currently pending and under examination.
Information Disclosure Statement
The Information Disclosure Statement filed July 12, 2023 has been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," 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 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/patents-application- process/filing-online/legal-framework-efs-web), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) 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 of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action 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:
Amend the Sequence Listing Incorporation by Reference paragraph at page 1 of the
specification. It is noted the Sequence Listing Incorporation by Reference paragraph lists the size of the ASCII text file as 51,900 bytes, whereas the ASCII text file itself lists the size as 2,779 bytes.
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 2 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.
Claim 2 is considered vague and indefinite for the following reasons:
Claim 2 recites the limitation “the two or more sources” in lines 2-3. There is insufficient antecedent basis for this limitation in the claim.
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.
Claims 1-10 and 14-20 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Pan et al. (U.S. Patent Application Publication US 2015/0368694 A1, published December 24, 2015, cited on the IDS filed July 12, 2023.
Regarding claim 1, Pan teaches a method for multiplexed detection of DNA methylation (Abstract, Page 5, [0046] and Page 17, [0189]). Pan teaches contacting a micrococcal nuclease (MNase) to two or more individual samples comprising genomic DNA (Abstract, Page 3, [0032] and Page 17, [0189]). Pan teaches purifying the MNase-contacted samples of step (a), whereby DNA samples comprising nucleosome-protected fragments are obtained (Page 3, [0028] and [0032], Page 9, [0092], Page 8, [0085], Pages 7-8, [0077] and Page 10, [0109], [0112] and [0114]). Pan teaches ligating sample-specific adapters to the nucleosome-protected fragments and each of the two or more samples comprises a unique adapter and wherein adapter ligated DNA libraries are generated (Page 2, [0016], Page 3, [0025], Page 5, [0045]-[0046], Page 6, [0065], Page 17, [0189] and Pages 22-23, [0257]). Pan teaches pooling the two or more adapter-ligated DNA libraries to generate a pooled DNA library (Page 5, [0046], Page 7, [0076], Page 8, [0085] and Pages 22-23, [0257]). Pan teaches performing methylated DNA immunoprecipitation on the pooled DNA library of step (d), thereby obtaining a pooled library enriched for methylated DNA (Page 2, [0016], Page 5, [0046], Page 6, [0065] and Pages 28-29, [0330]). Pan teaches amplifying the DNA of step (e) using primers having specificity for the unique adaptors (Page 4, [0038], Page 5, [0046], and Pages 22-23, [0257]). Pan teaches sequencing the amplified sample to detect DNA methylation (Page 3, [0032], Page 4, [0038], Page 5, [0046] and Page 29, [0339]).
Regarding claim 2, Pan teaches analyzing sequences obtained in step (g) to identify, if present, aberrant DNA methylation in genomic DNA from the two or more sources (Page 2, [0014]-[0015], Page 3, [0025], Page 5, [0046], Page 6, [0065] and Page 14, [152]).
Regarding claim 3, Pan teaches the pooled DNA library comprises genomic DNA from 2 to 15 individual sources (Page 3, [0025], Page 5, [0046], Page 6, [0065], Page 8, [0082], Page 14, [152] and Page 32, [0367]).
Regarding claim 4, Pan teaches the pooled DNA library comprises at least 5 ng genomic DNA of each individual source (e.g., Less than 1,000 cells of gDNA equates to about 6 ng of gDNA as well as less than 10,000 cells of gDNA equates to about 60 ng of gDNA therefore at least 5 ng, Abstract, Page 5, [0053], Page 19, [0216] and Page 20, [0223]).
Regarding claim 5, Pan teaches the pooled DNA library comprises at least 10 ng genomic DNA of each individual source (e.g., Less than 10,000 cells of gDNA equates to about 60 ng of gDNA therefore at least 10 ng, Abstract, Page 5, [0053], Page 19, [0216] and Page 20, [0223]).
Regarding claim 6, Pan teaches the pooled DNA library comprises less than 100 ng genomic DNA of each individual source (Less than 10,000 cells of gDNA equates to about 60 ng of gDNA (e.g., Less than 10,000 cells of gDNA equates to about 60 ng of gDNA therefore at least 10 ng, Abstract, Page 5, [0053], Page 19, [0216] and Page 20, [0223]).
Regarding claim 7, Pan teaches amplifying comprises quantitative polymerase chain reaction (qPCR) (Page 29, [0339]).
Regarding claim 8, Pan teaches sequencing comprises next generation sequencing (Page 5, [0047] and Page 25, [0292]).
Regarding claim 9, Pan teaches the method has specificity greater than 70% (Page 3, [0025] and [0032]-[0033], Page 5, [0046], Page 7, [0074], Pages 7-8, [0077], Page 31, [0358] and Figs. 18B and 19A-C).
Regarding claim 10, Pan teaches the method has specificity greater than 90% (Page 3, [0025] and [0032]-[0033], Page 5, [0046], Page 7, [0074], Pages 7-8, [0077], Page 31, [0358] and Figs. 18B and 19A-C).
Regarding claim 12, Pan teaches the micrococcal nuclease (MNase) reaction of step (a) is maintained at about 55 °C (Page 20, [0219] and Page 21, [0234]).
Regarding claim 14, Pan teaches a kit for multiplexed detection of DNA methylation comprising micrococcal nuclease and an antibody specific for methylated DNA (Page 5, [0046], Page 3, [0032], Page 7, [0076], Page 17, [0189], Page 18, [0201], Pages 28-29, [0330]-[0332] and Pages 31-32, [0364]).
Regarding claim 15, Pan teaches sample-specific adapters and reagents for ligating the adapters to nucleosome-protected fragments (Page 2, [0016], Page 3, [0025], Page 5, [0045]-[0046], Page 6, [0065], Page 7, [0076], Page 17, [0189] and Pages 22-23, [0257]).
Regarding claim 16, Pan teaches primers that hybridize with the sample-specific adapters (Page 5, [0045]-[0046], Page 15, [0165] and Page 17, [0187]).
Regarding claim 17, Pan teaches reagents for amplifying the nucleosome-protected fragments (Page 3, [0028]-[0029] and [0032], Page 9, [0092], Page 8, [0085]-[0086], Pages 7-8, [0077] and Page 10, [0109], [0112] and [0114]).
Regarding claim 18, Pan teaches the reagents for amplifying comprise reagents for polymerase chain reaction (PCR) (Page 3, [0031] and [0033] and Page 4, [0038]).
Regarding claim 19, Pan teaches the reagents for PCR comprise a high-fidelity polymerase (Page 21, [0231]).
Regarding claim 20, Pan teaches reagents for next generation sequencing (Page 5, [0047] and Page 25, [0292]).
Pan teaches each and every limitation of claims 1-10 and 14-20, and therefore Pan anticipates claims 1-10 and 14-20.
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.
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.
Claims 11 and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Pan et al. (U.S. Patent Application Publication US 2015/0368694 A1, published December 24, 2015, cited on the IDS filed July 12, 2023, as applied to claims 1-10, 12 and 14-20 above, in view of Shema-yaacoby et al. (WIPO International Application Publication WO 2017/034970, published March 02, 2017).
Regarding claim 11, Pan teaches identifying 5-methylcytosine (Page 8, [0079] and Page 16, [0182]).
Regarding claim 13, Pan teaches the micrococcal nuclease reaction of step (a) as discussed above. Pan teaches isolating different size fragments of DNA that correlate to different portions of chromatin such as mono-nucleosomal DNA and di-nucleosomal DNA (Page 10, [0108] and [0112]).
Pan does not teach or suggest the method can differentiate between 5-methylcytosine and 5-hydroxymethylcytosine. Pan does not teach or suggest the micrococcal nuclease reaction of step (a) results in about 30% mono-nucleosomal DNA and about 25% di-nucleosomal DNA.
Shema-yaacoby teaches a method for multiplex detection of DNA methylation that can differentiate between 5-methylcytosine and 5-hydroxymethylcytosine using micrococcal nuclease (MNase) (Page 12, [0046], Page 16, [0056], Page 77, [00192] and Example 8). Shema-yaacoby teaches using multiplex split pool analysis (Page 22, [0075] and Page 33, [00110]). Shema-yaacoby teaches contacting two or more samples of genomic DNA with micrococcal nuclease (MNase) (Pages 7-8, [0029]-[0031], Page 22, [0075], Pages 28-29, [0099] and Page 77, [0192]). Shema-yaacoby teaches purifying the MNase-contacted samples and the DNA sample comprises nucleosome protected fragments (Page 4, [0018], Pages 7-8, [0029], Page 76, [00188] and Pages 7-8, [0029]-[0031]). Shema-yaacoby teaches the micrococcal nuclease reaction results in about 30% mono-nucleosomal DNA and about 25% di-nucleosomal DNA (Page 8, [0033], Page 9, [0034] and Page 28, [0096]). Shema-yaacoby teaches using this method advantageously allows for labeling and detection of single nucleosomes which can advantageously allow the characterization of the combinatorial pattern of histone modifications on a single nucleosome, which can provide significant utility in the study of epigenetics (Pages 61-62, [00149]-[00152]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to modify the teachings of Pan with the teachings of Shema-yaacoby, using a micrococcal nuclease reaction resulting in about 30% mono-nucleosomal DNA and about 25% di-nucleosomal DNA. This would advantageously allow for labeling and detection of single nucleosomes which can advantageously allow the characterization of the combinatorial pattern of histone modifications on a single nucleosome, which can provide significant utility in the study of epigenetics as taught by Shema-yaacoby (Pages 61-62, [00149]-[00152]).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684