Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
OBJECTION
2. Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps.
Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts.
NON-PRIOR ART REJECTION
3. 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 1-22 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.
A) These claims are indefinite because it cannot be determined what is encompassed in the second ‘wherein’ clause in independent claim 1 by the language ‘the detection sequence is 5’ to the nucleic acid template’. Typical language relating to relative position of one portion of a nucleic acid with respect to another portion is recited in claim 2. However, the language in claim 1 recites that the detection sequence is ‘5’ to’ the nucleic acid template, but the detection sequence is within the template, and is not a separate portion. It is unclear if the intention is that the detection sequence be at the 5’ end of the template. Clarification is required.
B) Claims 11, 13, and 18 are indefinite because of the language ‘such as’, as it cannot be determined exactly what is required. Correction is required.
C) Claims 16-17 are indefinite because ‘said’ or ‘the’ ‘partial nucleic acid target’ lacks proper antecedent basis. Correction is required.
PRIOR ART REJECTIONS
4. 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.
5. 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 1-16 and 18-22 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Vinayagamoorthy (US 2017/0166954).
Regarding independent claim 1, Vinayagamoorthy discloses a method comprising adding to a sample a template that partially hybridizes to a fragment of target nucleic acid, a polymerase, and dNTPs, such that an extension product is produced; removing, degrading, or masking the template; and contacting the extended product with a polymerase, dNTPs, and a primer, such that a strand complementary to the extended product is produced; wherein the template comprises a detection sequence and a capture sequence. See Fig. 6 and paragraphs 0004-0024, 0039, 0044, 0093, 0101-0110, 0114-0119, 0132-0134, 0144-0149, 0167-0183, 0216, and 0244—0246 (Example 2).
Regarding claim 2, Vinayagamoorthy discloses a template wherein a detection sequence is 5’ to a capture sequence (Fig. 6).
Regarding claims 3-4, Vinayagamoorthy discloses the use of one or more polymerase, which may be of different types (paragraphs 0170-0172).
Regarding claims 5-8, Vinayagamoorthy discloses the use of uracil bases in the template nucleic acid as well as a U-tolerant DNA polymerase and degradation of template nucleic acid (paragraphs 0162 and 0183).
Regarding claim 9, Vinayagamoorthy discloses enriching a sample for a target fragment (Example 2).
Regarding claim 10, Vinayagamoorthy discloses removing the template (paragraphs 0162 and 0173).
Regarding claims 11-13, Vinayagamoorthy discloses the use of magnetic beads (paragraph 0146).
Regarding claim 14, Vinayagamoorthy discloses degrading any remaining template (paragraphs 0162 and 0183).
Regarding claim 15, Vinayagamoorthy discloses a template in the length range of 15-2500 nucleotides (see SEQ ID NO:1, 115 nucleotides, paragraph 0229 in Example 1).
Regarding claim 16, Vinayagamoorthy discloses the use of DNA and DNA polymerase (paragraphs 0133 and 0172).
Regarding claim 18, Vinayagamoorthy discloses the use of RNA and RNA polymerase (paragraphs 0133 and 0172).
Regarding claims 19-21, Vinayagamoorthy discloses further adding a reverse primer and performing either linear or exponential amplification (paragraphs 0108, 0110, and 0177-0181).
Further regarding claim 21, Vinayagamoorthy discloses the use of a hybridization probe (paragraphs 0022 and 0211).
Regarding claim 22, Vinayagamoorthy discloses the use of urine as a sample (paragraph 0024 and Example 2).
The claimed methods cannot be distinguished from the methods of Vinayagamoorthy.
6. 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.
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 17 is rejected under 35 U.S.C. 103 as being unpatentable over Vinayagamoorthy in view of Bordelon et al. (2017).
The teachings of Vinayagamoorthy are discussed above.
Vinayagamoorthy does not disclose detecting a target nucleic acid or biomarker from Mycobacterium tuberculosis.
Bordelon teaches detecting a nucleic acid biomarker from Mycobacterium tuberculosis in a urine sample to diagnose tuberculosis (see entire document on pages 1-10, especially Materials and Methods on pages 3-5).
One of ordinary skill in the art would have been motivated to modify the method of Vinayagamoorthy by targeting a Mycobacterium tuberculosis nucleic acid biomarker because Bordelon taught the benefit of detecting such a biomarker in a urine sample to diagnose tuberculosis in patients. It would have been prima facie obvious to one of ordinary skill in the art at the time the application was filed to carry out the claimed method.
CONCLUSION
7. No claims are free of the prior art.
8. Dawson et al. (US 2009/0023151) and Slepnev (US 2007/0077582) are made of record as also disclosing detection of small nucleic acid fragments by hybridizing them to a larger template polynucleotide, performing an extension reaction to produce an extended product, and extending or amplifying the extended product.
9. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENNETH R HORLICK whose telephone number is (571)272-0784. The examiner can normally be reached Mon. - Thurs. 8:30 - 6:30.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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11/06/25
/KENNETH R HORLICK/ Primary Examiner, Art Unit 1681