DETAILED ACTION
Status of the Claims
Claims 323-347 are currently pending.
Claims 323-337 have been withdrawn as being drawn to non-elected subject matter (see below).
Claims 338-347 are examined herein.
The following Office Action is in response to Applicant’s communication dated 12/31/2025. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. The following rejection(s) and/or objection(s) are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Response to Restriction Requirement
Applicant’s election without traverse of Group II (claims 338-347) in the reply filed on 02/17/2025 is acknowledged.
Claims 323-337 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected group, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 02/17/2025.
Drawings
The objection to the drawings because Figure 5 and Figure 6 were mis-labeled in the BRIEF DESCRIPTION OF THE DRAWINGS section of the specification is withdrawn in light of Applicant’s amended specification submitted 12/31/2025.
Maintained Claim Rejections – 35 U.S.C. 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 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.
Drmanac et al.
Claims 338-347 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Drmanac et al. (U.S. PGPub 2016/0017414, cited in IDS of 11/17/2023, of record).
Regarding claim 338, Drmanac discloses a method comprising:
delivering a plurality of nucleic acids to a plurality of binding sites on a surface of a flow cell (e.g., flow cell as per ¶¶0086-0087), wherein the plurality of binding sites comprising at least 10,000 binding sites separated by disjunctions (e.g., high density as per ¶0034 and/or the Abstract), wherein the disjunctions are irregular (e.g., random arrays as per ¶0018, ¶0028, and/or Fig. 1);
obtaining a plurality of images of the flow cell (e.g., multiple section images acquired as per ¶0118);
aligning the disjunctions in a plurality of flow cell images to align the plurality of flow cell images (e.g., aligning images using empty regions as per ¶0118); and
sequencing the plurality of nucleic acids (e.g., “large scale sequence determination” as per ¶0097).
Regarding claim 339, Drmanac discloses the above, wherein the nucleic acids are concatemers that are rolling circle amplification (RCA) products (e.g., products of rolling circle replication as per ¶0033 and Fig. 1).
Regarding claim 340, Drmanac discloses the above, further comprising performing rolling circle amplification (RCA) in solution by extending an amplification primer or a splint primer with a plurality of templates to generate the concatemers, prior to depositing the concatemers on the binding sites (e.g., conjugates can be formed prior to disposal to the array as per ¶0041).
Regarding claim 341, Drmanac discloses the above, wherein the concatemer is bound to an intermediate nucleic acid, and wherein the intermediate nucleic acid is a DNA tile (e.g., a “macromolecular structure” such as concatemers made by rolling circle amplification as per ¶0040 and/or Fig. 1E).
Regarding claim 342, Drmanac discloses the above, comprising forming concatemers on the binding sites of the flow cell by rolling circle amplification (RCA) of a target nucleic acid from splint oligonucleotides (e.g., as per ¶0041 and/or Fig. 1I).
Regarding claim 343, Drmanac discloses the above, wherein the splint oligonucleotides are each presented by a DNA tile bound to a binding site of the plurality of binding sites (e.g., as per ¶0041 and/or Fig. 1G-1I).
Regarding claim 344, Drmanac discloses the above, wherein the DNA tile comprises a plurality of capture sequences each comprising a portion of a splint oligonucleotide (e.g., as per ¶0041 and/or Fig. 1G-1I).
Regarding claim 345, Drmanac discloses the above, comprising:
providing a plurality of asymmetric DNA tiles;
providing a plurality of concatemers;
binding individual concatemers to a first side of individual DNA tiles in solution;
and depositing the DNA tiles on the surface of the flow cell such that a second side of the individual DNA tiles binds to the binding sites of the surface while the first side of the individual DNA tiles remains bound to a concatemer (e.g., as per ¶0041 and/or Fig. 1G-1I).
Regarding claim 346, Drmanac discloses the above, wherein at least 50% of the binding sites comprise a single monoclonal nucleic acid cluster (e.g., substantially all as per the Abstract and/or ¶0008).
Regarding claim 347, Drmanac discloses the above, further comprising sequencing the concatemers (e.g., “large scale sequence determination” as per ¶0097).
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Response to Arguments
The 12/31/2025 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks assert that Drmanac does not disclose nucleic acid binding sites on a surface separated by irregular disjunctions, as required by the present claims, but instead cites para 0028 of Drmanac and states that this portion of Drmanac “confirms that the discrete spaced apart regions, i.e., the binding sites, on the surface are in a regular array, while single molecules are randomly distributed on the discrete spaced apart regions”.
In response, as noted by Applicant, the DNA molecules were deposited and bound randomly to locations on the surface. Accordingly, it is reasonable to interpret these randomly spaced sites where the DNA bound as being “binding sites”. Such random binding sites are evident in the assorted embodiments of Fig. 1 and as detailed in the rejection above. Therefore, the rejection is proper and is maintained.
Conclusion
No claims are allowed.
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 extension fee 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 date of this final action.
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/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684