DETAILED ACTION
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 .
Status of the Application
2. Applicant’s response filed on August 19, 2025 has been entered.
Claims 1-30 are pending and under examination.1
Response to Arguments
3. Applicant’s arguments filed on August 19, 2025 have been fully considered.
Objections to the Drawings
Applicant argues that the objections are moot in view of the amendments to the specification and Figure 2 (Remarks, page 11).
This argument was persuasive. The objections have been withdrawn.
Objection to the Specification
Applicant argues that the objection is moot in view of amendments to the specification (Remarks, page 11).
This argument was persuasive. The objection has been withdrawn.
Also, to clarify the record, it is noted that Applicant is correct that the specification objection made in the last Office action intended to refer to paras. 89 and 409 of the specification rather than paras. 87 and 409 (Remarks, page 11). The examiner regrets any inconvenience to the applicant resulting from this inadvertent typographical error.
Claim Objections
Applicant argues that the objections to claims 1, 3, 6, 8, 17, 21, 23, and 25 should be withdrawn in view of the claim amendments (Remarks, page 12).
This argument was persuasive. The objections have been withdrawn.
Rejection of claims 1-30 under 35 U.S.C. 112(b)
Applicant argues that the rejection should be withdrawn (Remarks, pages 12-13). More specifically, Applicant argues that the issues raised previously concerning claims 1-3, 8, and 9 are moot in view of the amendments to those claims (Remarks, pages 12-13). Applicant also argues that claim 14 is, in fact, definite (Remarks, page 13).
These arguments were persuasive. The rejection has been withdrawn.
Drawings
4. The replacement drawings filed on August 19, 2025 are objected to because the oligonucleotide sequences in Figure 1 are not identified with the appropriate sequence identifier. See MPEP 2412.06. As noted in this section of the MPEP, the required sequence identifiers may be added to the figure or the “Brief Description of the Drawings” section.
And more specifically, the sequences in Figure 1 are not identified with the appropriate sequence identifiers in view of the 8/19/25 amendment to para. 81 of the specification. The 8/19/25 version of para. 81 no longer contains the sentence with sequence identifiers, which was added in the preliminary amendment of December 1, 2023. Applicant could address the issue by amending para. 81 to include the last sentence in the version of para. 81 filed on December 1, 2023.
Nucleotide and/or Amino Acid Sequence Disclosures
5. Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, 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 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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 statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings. More specifically, the sequences in Figure 1 are not identified with the appropriate sequence identifiers in view of the 8/19/25 amendment to para. 81 of the specification. The 8/19/25 version of para. 81 no longer contains the sentence with sequence identifiers, which was added in the preliminary amendment of December 1, 2023. Applicant could address the issue by amending para. 81 to include the last sentence in the version of para. 81 filed on December 1, 2023.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, 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.
Claim Objections
6. Claims 7, 26, and 28 are objected to because their status identifiers are incorrect. These claims were examined in the last Office action and should have the status identifier “original” or “previously presented.”
Claim Rejections - 35 USC § 112
7. 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 1-30 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 1 is indefinite because the requirements of step (b) are unclear. More specifically, as written, options (i) and (ii) in step (b) encompass a method in which there is no difference between the two options, but this does not appear to be Applicant’s intention. The problem stems from the use of “modification status” in step (b). Based on the specification (see, e.g., paras. 3-4 63-66, 81, and 83), it appears that the intention for options (i) and (ii) in step (b) is to encompass conversion methods that alter the base pairing specificity of unmodified nucleotides while not affecting modified nucleotides (e.g., bisulfite conversion, which alters the base pairing specificity of unmethylated cytosine while not altering the base pairing specificity of methylated cytosine) and also conversion methods that function in the opposite way (i.e., to alter the base pairing specificity of modified nucleotides while not affecting unmodified nucleotides).
Use of the term “modification status” in step (b), though, creates confusion because the term encompasses modified or unmodified nucleotides. Therefore, options (i) and (ii) need not posses any differences from one another because “modification status” in each of line 2 of option (i) and the last line of option (ii) could be interpreted as “unmodified.” In that instance, options (i) and (ii) of step (b) would be reciting the same thing using different wording.
One possibility to address the rejection is amending step (b) to replace “modification status” with terms that clearly distinguish between modified and unmodified nucleotides. In that way, Applicant’s apparent intention for the claim would be better defined.
Lastly, since step (e) requires a clear understanding of step (b), the requirements of step (e) are also unclear in view of the indefiniteness issue in step (b).
Claims 2-30 are also indefinite since they depend from claim 1 and do not remedy its indefiniteness issue.
Conclusion
8. No claims are currently allowable.
The claims have not been rejected with prior art due to their indefiniteness issue. It is noted, though, that prior art disclosing Applicant’s inventive concept (i.e., quality control nucleotides in adapters, wherein the quality control nucleotides include modified and unmodified nucleotides) was not found. The closest prior art was cited and briefly discussed in the “Conclusion” section of the last Office action.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Angela Bertagna whose telephone number is (571)272-8291. The examiner can normally be reached 8-5, M-F.
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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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681
1 Claims 7, 26, and 28 have the status identifier “withdrawn,” but this is incorrect since these claims were examined in the last Office action.
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