CTNF 18/685,199 CTNF 80332 DETAILED ACTION Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Drawings The drawings filed on 02/20/2024 are acceptable. 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/PatentLegalFramework), 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 - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”. Required response - Applicant must provide: A "Sequence Listing" part of the disclosure; together with An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2) ; A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3). If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide: A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of: A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); A copy of the amended specification without markings (clean version); and A statement that the substitute specification contains no new matter. If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide: A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and A statement according to item 2) a) or b) above. Specific deficiency - This application contains sequence disclosures in accordance with the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 - 1.825. The sequence disclosures are located in figure 3. Required response – Applicant must provide: A "Sequence Listing" part of the disclosure, as described above in item 1); as well as An amendment specifically directing entry of the "Sequence Listing" part of the disclosure into the application in accordance with 1.825(b)(2) ; A statement that the "Sequence Listing" includes no new matter in accordance with 1.825(b)(5); and A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(b)(4). If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide: A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of: A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); A copy of the amended specification without markings (clean version); and A statement that the substitute specification contains no new matter; If the "Sequence Listing" part of the disclosure is submitted according to item 1) b), c), or d) above, Applicant must also provide: A replacement CRF in accordance with 1.825(b)(6); and Statement according to item 2) a) or b) above. Claim Rejections - 35 USC § 112(b) 07-30-02 AIA 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. 07-34-01 Claims 1-8 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. 07-34-07 AIA The claims are generally narrative and indefinite, failing to conform with current U.S. practice. They appear to be a literal translation into English from a foreign document and are replete with grammatical and idiomatic errors. It is unclear what is encompassed by the method steps of the claims. Claim 1 requires a step of identifying by using a first primer and a step of identifying by using a second primer but the only active step of identifying is using a first primer and using a second primer with no actual step of identifying anything. Additionally the wherein clause requires mobility of a second reaction product obtained by the second primer extending a complementary strand on the other target polynucleotide is smaller than a mobility of a first reaction product obtained by the first primer extending a complementary strand on the one target polynucleotide. There are no steps of obtaining a rection product, detecting mobility or a sequence, or any steps that require the first or second primer to be extended. Claims 5-7 recite the first reaction product and the second reaction product and this recitation renders the claim indefinite. Claim 5 additionally recites the extension reaction. Claim 1 while it recites a reaction product and extending a complementary strand, this recitation is with respect to the wherein clause defining the mobility, claim 1 does not recite producing a first and second reaction product nor require a step an extension reaction and it is unclear what product is being produced and what extension reaction is being performed in the method of claim 1 that is being limited by claims 5-7. Claims 2-8 depend from claim 1 and are indefinite for the reasons applied to claim 1. Claim Rejections - 35 USC § 112 (d) 07-36 AIA The following is a quotation of 35 U.S.C. 112(d): (d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers. The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph: Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers. 07-36-01 AIA Claim s 5-7 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claims 5-7 recite the first reaction product and the second reaction product and depend from claim 1. Claim 1 does not produce a first and second reaction product. The only recitation of a reaction product is with respect to the wherein clause of defining the mobility of the reaction products however the claims do not require a reaction product. Claims 5-7 do not further limit claim 1 as claim 1 does not require a reaction product only a step of using a primer. Claim 5 recites a ddNTP contained during the extension reaction is labeled with a fluorescent substance. Claim 1 does not require performing an extension reaction, claim 5 does not further limit claim 1 as claim 1 does not require a step of extension and only recites extension with respect to the wherein clause for defining a mobility . Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements. Claim Rejections - 35 USC § 102 07-07-aia AIA 07-07 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 – 07-08-aia AIA (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. 07-15 AIA Claim s 1-5 and 7-8 are rejected under 35 U.S.C. 102( a)(1 ) as being anticipated by McGinnis (US6635419 B1) . For the purposes of compact prosecution, the claims have been interpreted to be directed to a method for identifying a sequence in a target nucleic acid by using a first and second primer, wherein the second primer comprises a mobility compound and a stop reaction site. With regard to claim 1-4 and 8, McGinnis teaches a method for determining a sequence of one or more nucleotides in a target polynucleotide. McGinnis teaches a target specific primer is contacted with a polynucleotide sample for the primer to anneal to the complementary region and form a target-primer hybrid. McGinnis teaches the primer comprises a target binding segment and a mobility reducing moiety that does not significantly bind the target (claim 3). McGinnis teaches the primer extension products are separated by electrophoresis (See column 3, lines 33-54). McGinnis teaches the target is double stranded nucleic acid (see column 7, lines 15-18). McGinnis teaches the primers contain a target binding site and a mobility reducing moiety. McGinnis teaches a first primer and a second primer and teaches the second primer comprises the mobility reducing moiety which is longer than the first primer(see ex 1) (claim 2 and 4). McGinnis teaches the mobility reducing agent is a non-polynucleotide polymer that can be branched (see column 10, lines 60-64) (claim 8). McGinnis teaches the mobility reducing agent comprise amino acids (see column 11, lines 2-5). McGinnis teaches adding the mobility reducing agent to the 5’ end (see column 11, lines 29-31). Amino acids are both mobility reducing agents and a reaction stop, as evidence by the instant specification. The specification exemplifies a reaction stop compound includes an amino acid residue (see para 21) and a mobility reduction site is an amino acid residue (see para 22). While McGinnis does not explicitly state the mobility reducing agents include a stop compound, the specification teaches the stop compound and mobility reduction site comprise the same compounds (See para 21 and 22), as such the mobility reducing agents of McGinnis encompass both a mobility reducer and a stop agent, as defined by the instant specification. With regard to claim 5 and 7, McGinnis teaches fluorescently labeled nucleotides and radioactive isotopes (see column 9, lines 3-15). McGinnis teaches ddNTP fluorescently labeled. McGinnis teaches direct labels include radioisotopes labels (see column 8, lines 31-32) . Claim Rejections - 35 USC § 103 07-20-aia AIA 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. 07-20-02-aia AIA 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. 07-21-aia AIA Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over McGinnis (US6635419 B1, cited on IDS) in view of Ju (Analytical Biochem, 1995, 231, pp 131-140) . McGinnis teaches a method of sequencing double stranded DNA using a first primer and a second primer, wherein the second primer comprises a mobility compound and a stop reaction site. McGinnis does not teach a primer comprising a fluorescent label. However using fluorescently labeled primers in sequencing reactions was known in the art. Ju teaches using fluorescence energy transfer dye labeled primers in DNA sequencing and analysis. Ju teaches the fluorescently labeled primers provide better results and higher sensitivity. Ju teaches higher quality sequencing data can be obtained with much less template DNA (see pg. 137, 1 st column). It would have been obvious to one of ordinary skill in the art at the time the claimed invention was made to apply fluorescently labeled primers in the method of McGinnis for the expected benefit of better results, higher sensitivity and higher quality sequencing data with less template DNA as known in the art taught and taught by Ju. Conclusion No claims are allowable. Any inquiry concerning this communication or earlier communications from the examiner should be directed to SARAE L BAUSCH whose telephone number is (571)272-2912. The examiner can normally be reached M-F 9a-4p. 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, Fereydoun Sajjadi can be reached at 571-272-3311. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. 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If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /SARAE L BAUSCH/Primary Examiner, Art Unit 1699 Application/Control Number: 18/685,199 Page 2 Art Unit: 1699 Application/Control Number: 18/685,199 Page 3 Art Unit: 1699 Application/Control Number: 18/685,199 Page 4 Art Unit: 1699 Application/Control Number: 18/685,199 Page 5 Art Unit: 1699 Application/Control Number: 18/685,199 Page 6 Art Unit: 1699 Application/Control Number: 18/685,199 Page 7 Art Unit: 1699 Application/Control Number: 18/685,199 Page 8 Art Unit: 1699 Application/Control Number: 18/685,199 Page 9 Art Unit: 1699 Application/Control Number: 18/685,199 Page 10 Art Unit: 1699 Application/Control Number: 18/685,199 Page 11 Art Unit: 1699 Application/Control Number: 18/685,199 Page 12 Art Unit: 1699
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