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 .
Claim Status
Claims 1-22 are pending and under examination. Claims 7, 9, 11, 12, 19, 21, and 22 have been amended. Claims 1, 21, and 22 are independent claims.
Response to Arguments
Objections Withdrawn
The objection to the specification is withdrawn following the applicant’s amendments.
Rejections Withdrawn
The rejection of claims 1-6, 9-10, 13-18 under 35 U.S.C. 102(a)(1)/102(a)(2) as being anticipated by Mok is withdrawn following the applicant’s amendments.
Rejections Maintained
Claims 1-22 are rejected under 35 U.S.C. 103 as being unpatentable over Mok in further view of Nicol and Assarsson is maintained.
Applicant's arguments filed 11/03/2025 have been fully considered but they are not persuasive. The applicant argues that Mok, Nicol and Assarsson fail to teach or suggest correlating the position of a target within a sequence concatemer with the original source and therefore fail to disclose every element of the claims. This argument is not persuasive. The rejection does not rely on any single reference to expressly state such “correlation.” Rather, Mok teaches concatenation of target nucleic acids for sequencing, including formation and sequencing of concatemers (see Abstract, Figs. 2, 4, 7, ¶0043-¶0047, ¶0056-¶0060, ¶0093-¶0094), wherein “each unit has a desired orientation, facilitating downstream identification and deconvolution of sequence information in each target molecule within the concatenate.” (see ¶0093); Nicol teaches directed assembly of DNA fragments using complementary overlap regions that enforce a predetermined and orientation-specific joining order (see Fig. 23); and Assarsson teaches multiplex detection assays generating distinct pools of target-derived nucleic acids (see Abstract). When fragments derived from different pools are engineered to contain complementary assembly sites as taught by Nicol (see Fig. 23, ¶0121), their structural positions within the resulting concatemer is dictated by the overlap design and therefore correspond to their source pool (see Figs. 21, 23, 24,28,29). The claimed step of assigning detected sequences to pools “based upon position within the concatemer” represents a predictable use of the ordered concatemer structure resulting from such directed assembly. A recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim.
The applicant further contends that the prior art provides no suggestion for modifying Mok in view of Nicol and Assarsson to arrive at the invention of the present claim. This argument is also not persuasive. Mok expressly recognizes the problem of tracking the source of nucleic acid fragments when multiple samples or targets are combined for sequencing (see ¶0071). Mok teaches the use of multiplex identifiers (MIDs) to identify the source of target nucleic acid, stating that target nucleic acids from different sources may be mixed and sequenced simultaneously and subsequently assigned back to their original source using the MID sequences (see ¶0071). Thus Mok clearly contemplates and addresses the very problem applicant characterizes as solved by the present claims, namely maintain source identity in multiplex sequencing workflows. Nicol teaches directed assembly of DNA fragments using complementary overlap regions to enforce predetermined fragment order (see e.g., Fig 23; as acknowledged in the applicants’ remarks filed 11/03/2025 on pg. 13 paragraph 4), and Assarsson teaches multiplex assay panels that generate distinct pools of reporter nucleic acids. In view of Mok’s recognition of the need to preserve source identity in pooled sequencing applications, one of ordinary skill in the art would have been motivated to apply Nicol’s known directed assembly techniques to the pooled nucleic acids generated in multiplex systems such as Assarsson in order to generate ordered concatemers that structurally encode fragment origin by position. Substituting or supplementing barcode-based tracking (as taught by Mok) with position-based identification through ordered assembly represents a predictable use of known techniques to achieve the same known goal of source attribution in multiplex sequencing. Accordingly, the combination is supported by articulate reasoning with rational underpinning, and applicant’s assertion that the prior art provide no suggestion to combine in not persuasive.
Conclusion
No claim is allowed.
THIS ACTION IS MADE FINAL. 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.
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/MATTHEW HAROLD RAYMONDA/Examiner, Art Unit 1684
/AARON A PRIEST/ Primary Examiner, Art Unit 1681