DETAILED ACTION
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 6-14, 16-18, 21-26, 28-31, 33, 34, 36, 38, 41, 43, 44, and 47-51 were canceled in an earlier amendment. Claim 32 is currently cancelled. Applicant states that claims 1 and 45 have been amended. Claim 53 is new. Claims 1-5, 15, 19, 20, 27, 35, 37, 39, 40, 42, 45, 46, 52, and 53 pending and under examination. Claim 1, and 52 are independent claims.
Claim Objections
The amendment to the claims filed on Aug. 17, 2026, does not comply with the requirements of 37 CFR 1.121(c) because claims 27, 39, 42 are designated “(Previously Presented)” in the amendment filed Aug. 17, 2026. A claim so designated must be presented in the same form as the immediately preceding entered version of that claim, with no changes. See 37 CFR 1.121(C)(3). Further Claim 45 is designated “(Currently Amended)” and is identical to the preceding entered version of that claim, with no changes.
The immediately preceding entered version of claim 27, from the amendment filed Dec. 4, 2025, recites, “…wherein the single-cell analysis involves single-cell RNA sequencing to determine, quantitate, or identify one or more of RNA splicing, lincRNA, microRNA, mRNA, tRNA and circRNA analysis…” The version of claim 27 presented in the Aug. 17, 2026, amendment instead recites “wherein the single-cell analysis involves single-cell RNA sequencing to determine, quantitate, or identify one or more of RNA splicing, RNA-protein interaction, RNA modification, RNA structure or lincRNA, microRNA, mRNA, tRNA and circRNA analysis…” The phrase “RNA-protein interaction, RNA modification, RNA structure or” was struck from the claim in the previous amendment.
The immediately preceding entered version of claim 39, from the amendment filed Dec. 4, 2025, recites, “…wherein the plurality of oligonucleotides comprises at least one oligonucleotide comprising a transposase recognition sequence…” The version of claim 39 presented in the Aug. 17, 2026, amendment instead recites “…wherein the plurality of oligos oligonucleotides comprises at least one oligo oligonucleotide comprising a transposase recognition sequence…” The phrase “oligo(s)” was struck from the claim in the previous amendment.
The immediately preceding entered version of claim 42, from the amendment filed Dec. 4, 2025, recites, in the relevant part: “…the target region comprises primer binding sites, a polyadenine region comprising at least 4 consecutive adenine nucleic acids…” The version of claim 42 presented in the Aug. 17, 2026, amendment instead recites: “…the target region comprises one or more primer binding sites, a polyadenine region comprising at least 4 consecutive adenine nucleic acids…” The phrase “one or more” was struck from the claim in the previous amendment.
Because claims 27, 39, and 42 submitted Aug. 17, 2026, is not identical to the immediately preceding entered version, it is improperly designated “(Previously Presented)”. To the extent that the Applicant intends to reintroduce these phrases into claims 27, 39 or 42, the claim must instead be designated “(Currently Amended),” with all changes relative to the immediately preceding entered version shown by underlining for insertion and strikethrough or bracketing for deletions, as required by 37 CFR 1.121(C)(2). Appropriate correction is required.
Amendments to the claims filed on or after July 30, 2003, must comply with 37 CFR 1.121(c) which states:
(c) Claims. Amendments to a claim must be made by rewriting the entire claim with all changes (e.g., additions and deletions) as indicated in this subsection, except when the claim is being canceled. Each amendment document that includes a change to an existing claim, cancellation of an existing claim or addition of a new claim, must include a complete listing of all claims ever presented, including the text of all pending and withdrawn claims, in the application. The claim listing, including the text of the claims, in the amendment document will serve to replace all prior versions of the claims in the application. In the claim listing, the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered).
(1) Claim listing. All of the claims presented in a claim listing shall be presented in ascending numerical order. Consecutive claims having the same status of “canceled” or “not entered” may be aggregated into one statement (e.g., Claims 1–5 (canceled)). The claim listing shall commence on a separate sheet of the amendment document and the sheet(s) that contain the text of any part of the claims shall not contain any other part of the amendment.
(2) When claim text with markings is required. All claims being currently amended in an amendment paper shall be presented in the claim listing, indicate a status of “currently amended,” and be submitted with markings to indicate the changes that have been made relative to the immediate prior version of the claims. The text of any added subject matter must be shown by underlining the added text. The text of any deleted matter must be shown by strike-through except that double brackets placed before and after the deleted characters may be used to show deletion of five or fewer consecutive characters. The text of any deleted subject matter must be shown by being placed within double brackets if strike-through cannot be easily perceived. Only claims having the status of “currently amended,” or “withdrawn” if also being amended, shall include markings. If a withdrawn claim is currently amended, its status in the claim listing may be identified as “withdrawn—currently amended.”
(3) When claim text in clean version is required. The text of all pending claims not being currently amended shall be presented in the claim listing in clean version, i.e., without any markings in the presentation of text. The presentation of a clean version of any claim having the status of “original,” “withdrawn” or “previously presented” will constitute an assertion that it has not been changed relative to the immediate prior version, except to omit markings that may have been present in the immediate prior version of the claims of the status of “withdrawn” or “previously presented.” Any claim added by amendment must be indicated with the status of “new” and presented in clean version, i.e., without any underlining.
(4) When claim text shall not be presented; canceling a claim.
(i) No claim text shall be presented for any claim in the claim listing with the status of “canceled” or “not entered.”
(ii) Cancellation of a claim shall be effected by an instruction to cancel a particular claim number. Identifying the status of a claim in the claim listing as “canceled” will constitute an instruction to cancel the claim.
(5) Reinstatement of previously canceled claim. A claim which was previously canceled may be reinstated only by adding the claim as a “new” claim with a new claim number.
Response to Arguments
Rejections Withdrawn
The rejection of claims 32 under 35 U.S.C. 103 as being unpatentable over So et al. (US 2018/0245142 A1 published Aug. 30, 2018) in view of Cusanovich et al. (Science, 2015, of record) is withdrawn following the cancellation of claim 32.
Rejections Maintained
The rejection Claims 1-5, 15, 19-20, 27, 35, 37, 39-40, 42, 45-46 and 52 are rejected under 35 U.S.C. 103 as being unpatentable over So et al. (US 2018/0245142 A1 published Aug. 30, 2018) in view of Cusanovich et al. (Science, 2015, of record).
Applicant's arguments filed 08/17/2026 have been fully considered but they are not persuasive. Applicant argues that neither So nor Cusanovich, alone or in combination, teach or suggest isolating intact barcoded nuclei from cells in an endogenous location within a tissue section where the cell have been previously frozen or fixed and, per new claims 53, permeabilized. This argument is not persuasive for the following reasons.
First, with respect to the newly added “previously frozen or fixed” and “permeabilized” limitations, So itself expressly discloses a formalin-fixed, paraffin-embedded (FFPE) tissue section that has been semi-permeabilized. So at paragraphs [0514] - [0516] and Fig. 50 (steps 5020, 5025, 5030) discloses placing a substrate bearing spatially addressed PCR primers atop semi-permeabilized FFPE tissue section, releasing the primers into the cellular space of the section, amplifying in situ, and collecting the tissue amplified DNA. Because FFPE tissue is, by definition, formalin-fixed, this passage of So (which the Applicant’s own remarks quote) discloses cells that have been previously fixed and permeabilized within a tissue section, as now recited in amended claim 1 and claim 54. Applicant’s assertion that “at no point does So teach” fixed or permeabilized cells is accordingly inconsistent with the very passage Applicant cites.
Second, Applicant argues that So’s disclosed embodiments involve disrupting the cellular matrix and collecting nucleic acids in bulk, and that this teaches away from preserving an intact nuclear envelope. This is not persuasive. A reference does not teach away from a claimed combination merely because it discloses a different or even a preferred embodiment. See MPEP 2145(X)(D)(1)“Furthermore, "the prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed…." In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004). So’s disclosure of a bulk collection workflow in one set of embodiments does not criticize or discourage preservation of nuclear envelope integrity in a nuclei-based workflow, it simply reflects an alternative embodiment directed to a different readout strategy. Nothing in the cited passage discourages a skilled artisan from adapting So’s spatially encoded, fixed-tissue barcoding platform to a single-nuclei workflows.
Third, in response to applicant's argument that Cusanovich is limited to cultured cell lines and does not teach isolating nuclei from fixed, frozen, permeabilized, or tissue-derived cells, and that a skilled artisan would have no motivation to introduce tissue-derived nuclei into Cusanovich’s workflow because doing so would add variability, this is a mischaracterization of Cusanovich’s work, as Cusanovich expressly states “this method’s simplicity and scalability may accelerate the characterization of complex tissues containing myriad cell types.” (see Cusanovich, pg. 914 left col. 2nd para.). Further the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). Cusanovich is relied upon for its teaching that transposase-mediated barcoding can be performed directly on intact nuclei without compromising nuclear envelope integrity, and that such barcoded nuclei can be recovered in suspension for downstream sequencing, not for its specific choice of cultured starting material. Further, the Applicant’s argument that “a skilled artisan would have no motivation to introduce tissue-derived nuclei into Cusanovich’s workflow” is in direct contradiction to Cusanovich itself which envision using the method on “complex tissue containing myriad cell types.” A skilled artisan seeking to obtain single-nucleus resolution from So’s fixed permeabilized, spatially, barcoded tissue platform would have been motivated to apply Cusanovich’s known intact nuclei indexing chemistry to that end, with a reasonable expectation of success, because both references operate on the same general class of biological starting material (permeabilized cellular material) and pursue compatible transposase mediated barcoding chemistries. This is precisely the type of combination of known elements according to known methods to yield predictable results outlined in KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007). See MPEP 2143(I)(A).
The Applicant’s remaining argument, that the rejection reflects impermissible hindsight, is conclusory and unsupported by any objective evidence. The rejection instead articulates explicit, evidence-based rationale grounding in the teachings of So and Cusanovich themselves. See KSR Int'l Co. v. Teleflex Inc., 550 U.S. 398, 415-421, 82 USPQ2d 1385, 1395-97 (2007); In re Kahn, 441 F.3d 977, 988, 78 USPQ2d 1329, 1336 (Fed. Cir. 2006).
For at least these reasons, the rejection under 35 U.S.C. 103 is maintained for.
New Rejections
Claim Rejections - 35 USC § 103
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1-5, 15, 19-20, 27, 35, 37, 39-40, 42, 45-46 and 52-53 are rejected under 35 U.S.C. 103 as being unpatentable over So et al. (US 2018/0245142 A1 published Aug. 30, 2018) in view of Cusanovich et al. (“Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing”, Science, 2015, of record) as applied to claims 1-5, 15, 19-20, 27, 35, 37, 39-40, 42, 45-46 and 52, included here for reasons supra.
Claim 53, depends on claim 1 and further recites the limitation that cells be permeabilized. As discussed previously, the combination of So and Cusanovich renders the limitations of claim 1 obvious. So discloses the use of formalin-fixed paraffin embedded tissue section that have been permeabilized (see So [0514] - [0516]).
Conclusion
No Claim is allowed.
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/MATTHEW HAROLD RAYMONDA/Examiner, Art Unit 1684
/AARON A PRIEST/ Primary Examiner, Art Unit 1681
