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 .
Election/Restrictions
Applicant's election with traverse of Group I, claims 1,2,5, 13, 14, 16, 19, 29, 42, 59, 65, 66, 71, 82, 84, and 93-96 in the reply filed on 4/20/2026 is acknowledged.
The traversal is on the ground(s) that “M.P.E.P. §803 requires showing of burden on the search it is believed that the claims of the present application would be part of an overlapping search area. Furthermore, electronic searching allows for a search of many, or theoretically all, relevant subclasses without substantial additional effort… whereas it would be a serious burden on the Applicant to prosecute and maintain separate applications.” This is not found persuasive. As set forth in the restriction requirement, examination of the claimed inventions would impose a serious search and examination burden because the inventions are directed to independent and/or distinct subject matter requiring materially different searches and examination. The existence of electronic searching does not eliminate the statutory authority for restriction under 35 U.S.C. § 121 or the examination burden recognized in MPEP §§803 and 808.02. Applicant’s assertion that searching multiple subclasses electronically would not require substantial additional effort is unsupported and does not address the different search strategies, prior art, and examination required for the distinct inventions. Further, applicant’s argument regarding the cost of pursuing divisional applications is not the legal standard governing restriction practice.
The traversal on the grounds that there is no showing of lack of unity between the groups. This is not found persuasive because the lack of unity is demonstrated. The shared technical feature between the two groups of invention “probes comprising target and adaptor binding domains and tag sequences comprising barcodes, does not make a contribution over the prior art cited in the international search report and written opinion (WO 2020/140693 A1), as stated in the previous Restriction Requirement. Accordingly, the traversal is not persuasive.
The requirement is still deemed proper and is therefore made FINAL.
Claim Status
Claims 1, 2, 5, 13, 14, 16, 19, 29, 42, 59, 65, 66, 69, 71, 82, 84, and 93-96 are pending and under examination. Claims 177 and 184 are withdrawn from consideration following the election of Group I invention in the Response to Election/Restriction filed 04/20/2026. Claim 1 is the only independent claim.
Priority
This application is a 371 of PCT/CN2022/097049 filed 06/06/2022. PCT/CN2022/097049 claims foreign priority to CHINA 202110631874.7 filed 06/07/2021.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Should applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d) prior to declaration of an interference, a certified English translation of the foreign application must be submitted in reply to this action. 37 CFR 41.154(b) and 41.202(e).
Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Drawings
The drawings are objected to because the table in Fig. 3 appears to be missing the headers that describe the contents of the columns. Without the headers it is impossible to determine that this table is supposed to display the “gene expression results of region 1 (eye) of mouse tissue in Fig. 2” as described in the Brief Description of the Drawings. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. Figure 3, top row contains a nucleotide sequence that is not described.
Required response – Applicant must provide:
Replacement and annotated 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 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 Rejections - 35 USC § 112
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.
Claim 65,66, 71, and 84 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.
Regarding claims 65 and 66, claim 1 established antecedent basis for “a first tag sequence” and “a second tag sequence,” which are thereafter referred to in claim using the definite article (“the first tag sequence”)). Claim 65 recites “administering a first tag molecule containing a first tag sequence to the first region of the sample,” and claim 66 recites the parallel limitation “administering a second tag molecule containing a second tag sequence to the second region of the sample.” The use of the indefinite article “a” in claims 65 and 66 to reintroduce “first tag sequence” and “second tag sequence”, terms already given definite antecedent basis in claim 1 renders it unclear whether the tag sequence recited in claims 65/66 is the same first/second tag sequence already recited and attached to the probe in claim 1, or is a new and distinct tag sequence not previously introduced. If the former is intended, claims 65 and 66 should be amended to recite “the first tag sequence” and “the second tag sequence,” respectively, consistent with claim 1’s antecedent basis. If the latter is intended, it is unclear what relationship, if any, this newly-introduced tag sequence bears to the first/second tag sequence already recited as attached to the probe in claim 1, and the claims should be amended to clarify that relationship. Applicant’s specification does not resolve this ambiguity, as the corresponding specification passage (see [0074]) mirrors the same indefinite article construction found in the claims.
Claim 71 recites the limitation "the second binding domain of the adapter in the first tag sequence" in lines 5-6. There is insufficient antecedent basis for this limitation in the claim.
Claim 84 recites the limitation "the second binding domain of the adapter in the second tag sequence" in lines 5-6. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 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 (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 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.
Claims 1, 2, 5, 13, 19, 29, 42, 59, and 93-96 are rejected under 35 U.S.C. 102(a)(1)/102(a)(2) as being anticipated by Oki et al. (US 2022/0251639 A1, the English translation of WO 2020/235563 A1, published Nov. 26 2020).
In regards to claim 1, Oki is in the field of oligonucleotides and omics analysis and discloses a method comprising “contacting at least one target molecule in a sample with at least one probe, the at least one probe containing a target molecule binding domain capable of specifically binding to the at least one target molecule and at least one reaction blocking modification, under a condition of specifically binding the at least one probe to the at least one target molecule”. Oki discloses an oligonucleotide comprising a target binding portion (e.g., a poly-T sequence that hybridizes to the poly-A tail of an mRNA, or a transposon sequence for genomic DNA) and “an additional sequence for detecting a nucleic acid… wherein at least one nucleotide in the additional sequences is modified with a photolabile protecting group” (see Oki [0008], [00046], [0049]), the protecting groups “inhibit formation of a hydrogen bond between the base and a base complementary to the base,” which reads on the claimed “reaction blocking modification.” Oki further disclose the exposure step in which this oligonucleotide is exposed to mRNA or DNA in a tissue section under hybridizing conditions (see Oki [0057]-[0059]).
Oki further discloses “carrying out a first processing on a first region of the sample, the first processing being capable of at least partially removing a reaction blocking modification on a probe in the first region, to cause the probe in the first region to be attached to a first tag sequence.” Oki discloses irradiating a part of the tissue section with UV light, whereupon “the photolabile protecting group is decomposed, the region complementary to the base sequence from the nucleotide modified with the photolabile protecting group to the 5’ end in the oligonucleotide is elongated” (see Oki [0054]), such that a second strand complementary to and including the full additional (tag/barcode) sequence is synthesized only in the illuminated region (see Oki [0055], [0073] (disclosing that in the transposase embodiment, “the fill-in reaction is established only when a protecting group is cleaved by irradiation with light”). This reads on removal of the reaction blocking modification causing the probe to become attached to a first tag sequence.
Oki further discloses “carrying out a second processing on a second region that is different from the first region in the sample, the second processing being capable of at least partially removing a reaction blocking modification on a probe in the second region, to cause the-probe in the second region to be attached to a second tag sequence, the second tag sequence being different from the first tag sequence.” Oki discloses irradiating “a circular portion having a diameter of about 1.2 mm in each of the neural tube and posterior limb” of the same tissue section (see Oki [0128], Example 2), i.e., sequential processing of two distinct, non-overlapping regions. Oki further discloses a kit embodiment comprising “a first oligonucleotide including a first barcode sequence… and a second oligonucleotide including a second barcode sequence, of which the base sequence is different from the base sequence of the first barcode sequence” (see Oki [0079]), reading on the distinct tag sequences at different regions.
Additionally, Oki discloses “determining a composition of the-probe attached to the first tag sequence and the probe attached to the second tag sequence, and determining a presence and/or content of a target molecule of the first region and the presence and/or content of a target molecule of the second region in the sample from the composition of the probe.” Oki discloses that “the cDNA included in the library includes an additional sequence at an end. Thus, sequence analysis and the like can be performed through the additional sequence” (see Oki [0063]), and Example 2 demonstrates region-resolved target determination (see Oki [0137], Fig. 8).
In regards to claim 2, Oki discloses that the sample comprises a tissue section (see Oki [0058]).
In regards to claim 5, Oki discloses that the tissue section is fixed (see Oki [0120]).
In regards to claim 13, Oki discloses that the first and second regions are substantially non-overlapping regions on the same tissue section, the neural tube and posterior limb ROIs of Example 2 (see Oki [0128], Fig. 7).
In regards to claim 19, Oki discloses that the molecule comprises a nuclei acid: mRNA in the CEL-Seq2 embodiment (see Oki [0059]), and genomic DNA in the transposase embodiment (see Oki [0070]-[0072]).
In regards to claim 29, Oki discloses that the reaction blocking modification is a photosensitive group, the photolabile protecting group bonded to a base of a nucleotide (see Oki [0011], [0049]), which is decomposed by light exposure (see Oki [0054]).
In regards to claims 42 and 59, Oki discloses that the first and second processing is illumination, UV irradiation at 340-380 nm (see Oki [0060]), though the second illumination is applied to a second ROI (see Oki [0128]).
In regards to claim 93, Oki discloses performing in situ hybridization between the target molecule and the probe, the oligonucleotide hybridizing to mRNA within the intact tissue section (see Oki [0058]-[0059], Example 2).
In regards to claim 94, Oki discloses digesting the sample after the in situ hybridization to obtain the probe attached to the tag sequences, “proteinase K… was dropwise added to lyse the tissue section”(see Oki [0133]).
In regards to claim 95, Oki discloses amplifying the probes attached to the first and second tag sequences, PCR amplification of the library (see Oki [0063], [0113]).
In regards to claim 96, Oki discloses sequencing the amplified probes to determine the composition, sequences analysis performed through the additional/barcode sequence following library amplification (see Oki [0062]-[0064]).
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 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1, 2, 5, 13, 14, 16, 19, 29, 42, 59, 69, 71, 82, 84, and 93-96 are rejected under 35 U.S.C. 103 as being unpatentable over Oki et al. (US 2022/0251639 A1, the English translation of WO 2020/235563 A1, published Nov. 26 2020) as applied to claims 1, 2, 5, 13, 19, 29, 42, 59, and 93-96 above and included here for reasons supra, in view of Frenz et al. (US 2022/0145361 A1, filed Mar. 4, 2020).
In regards to claims 14 and 16, Oki discloses all of the limitations of claim 1 as set forth above, for which claim 14 and 16 depend. Oki’s disclosed embodiments operate at the tissue-section/cell0mass scale. (e.g., 1.2 mm-diameter ROIs encompassing many cells, Example 2) and do not disclose resolving the sample to the level of a single cell.
Frenz, however, is directed to the same field of endeavor, spatial profiling of biological analytes using region, or feature specific capture probes on a substrate and expressly discloses achieving single-cell spatial resolution. Frenz discloses “distributing a plurality of cells onto the solid support such that at least one cell occupies a distinct feature on the solid support” (Embodiment A1; see also Frenz [0219] (disclosing “the cells are distributed onto the substrate such that at least one cell occupies a distinct spatial feature on the substrate”), and further discloses that “the spatial location of the biological analyte in the biological sample is resolved to a single cell” (see Frenz [0018]). Frenz discloses that “In some embodiments the biological sample is a single cell” (see Frenz [1335]), and further discloses methods “for profiling at least one biological analyte present in a cell” (see Frenz [1333]). Frenz further discloses that the single cell may be fixed (see Frenz [0013], [1419]-[1420]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify Oki’s method by distributing individual optionally fixed cells onto discrete substrate locations (or single cell sized features) as taught by Frenz, rather than applying Oki’s illumination gated probes to bulk tissue sections encompassing many cells. One of ordinary skill in the art would have been motivated to do so because Frenz expressly teaches that resolving capture to individual, distinctly-positioned cells increases the spatial resolution of the resulting analyte data down to single cell resolution (see Frenz [0073]), which is a recognized and desirable improvement over ROI0scale resolution for applications requiring cell-type specific or single cell analyte information. Further, Oki’s transposase-tagmentation embodiment achieves “a limited region of 1 µm2 or less” of illumination (see Oki [0065]), showing that a skilled artisan applying Oki’s blocking group removal mechanism would have had every reason to combine it with Frenz’s teaching of discretizing the sample into single cell unites to realize single cell resolved output, rather than being limited to Oki’s own exemplified mm-scale ROIs. This is the combination of prior art element (Oki’s illumination gated tag attachment mechanism and Frenz’s single cell resolve feature architecture) according to their established functions to yield the predictable results of single-cell resolved, illumination gated spatial barcoding.
In regards to claims 69, 71, 82, and 84, Frenz discloses a “splint oligonucleotide,” defined as “an oligonucleotide that, when hybridized to other polynucleotides, acts as a "splint" to position the polynucleotides next to one another so that they can be ligated together,” which “can include a nucleotide sequence that is partially complimentary to nucleotide sequences from two or more different oligonucleotides” and “assists in ligating a ‘donor’ oligonucleotide and ‘acceptor’ oligonucleotide” (see Frenz [0143]), reading on the claimed ‘oligonucleotide adapter’ comprising a “probe binding domain” (complementary to a first binding domain in the probe) and a “tag binding domain” (complementary to a second binding domain in the tag sequence), together forming a partially double-stranded splint bridged structure. Frenz further discloses this mechanism specifically in the context of joining a capture domain to a target-bound oligonucleotide (see Frenz [0305]) and in the context of array-probe construction (see Frenz [0502]-[0506]). This splint architecture is disclosed generically as applicable to any pair of donor/acceptor oligonucleotides, and therefore reads equally on the second region limitations of claims 82 and 84 without modification.
It would have been obvious to one of ordinary skill in the art before the effective filing date to performing Oki’s step of “cause the probe… to be attached to a tag sequence” would have looked to Frenz’s splint-oligonucleotide chemistry as a well-known, standard mechanism in the identical technical field for bridging and positioning a probe-side oligonucleotide and a tag-side oligonucleotide into a single hybridized complex suitable for ligation, since Frenz explicitly presents splint ligation as a standard tool for capture-probe construction. Combining Oki’s blocking group removal gated activation mechanism with Frenz’s splint-bridged tag-attachment chemistry is no more than the combination of prior art elements according to their established functions to yield the predictable result of sequence specific, splint-bridged attachment of a tag sequence to an unblocked probe.
Claims 1, 2, 5, 13, 14, 16, 19, 29, 42, 59, 65, 66, 69, 71, 82, 84, and 93-96 are rejected under 35 U.S.C. 103 as being unpatentable over Oki et al. (US 2022/0251639 A1, the English translation of WO 2020/235563 A1, published Nov. 26 2020) and Frenz et al. (US 2022/0145361 A1, filed Mar. 4, 2020) as applied to Claims 1, 2, 5, 13, 14, 16, 19, 29, 42, 59, 69, 71, 82, 84, and 93-96 above and included here for reasons supra, and further in view of Guo et al. (WO 2020/140693 A1, published Jul. 9, 2020, on IDS 12/06/2023).
In regards to claims 65 and 66, Oki discloses the limitations of claim 1 for which claim 65 and 66 depend, as set forth above. Oki does not disclose that, after the first (or second) processing, a first (or second) tag molecule containing a first (or second) tag sequence is administered to the region of the same as step distinct from and subsequent to the processing step. In Oki, the tag/barcode sequence is present as an integral, covalently linked part of the originally applied oligonucleotide from the outset of the exposure step, prior to irradiation (see Oki [0057]-[0060]) Following irradiation, Oki’s disclosed second-strand synthesis step introduces only generic enzymatic reagents, dNTP, RNaseH, DNA ligase, DNA polymerase (see Oki [0061]), and does not disclose administering any additional molecule containing a tag sequence to the processed region. Thus, in Oki, no first or second tag molecule is administered in the region of the sample after that region has been processed.
Guo, however, is directed to the same field of endeavor, enrichment and tagging of nucleic acids target regions using probe bearing a reaction blocking modification that is removed to enable subsequent tag attachment, and disclose precisely this administration step. Guo discloses a specific probe bearing a 3’ terminal blocking modification, which is amplified/extended on the target, whereupon “the blocking group is excised and the probe is activated” (capture extension step, correspond to the claimed first “first processing” removing the “reaction blocking modification”). Critically, Guo the discloses , as an express, separate, and subsequent step: “the 3’ end of the capture extension product provided in step (1) is ligated to a linker DNA to provide a ligation product.” That is, only after the blocking modification have been removed and the probe activated is a discrete linker DNA, a tag molecule distinct from and administered after the original probe, supplied to the reaction and ligated to the now activated probe. The linker DNA is expressly describe as carrying “a sample tag sequence, a molecular tag sequence,” i.e., a tag sequence withing the meaning of the instant claims.
It would have been obvious to one of ordinary skill in the art at the time of filling to modify Oki’s method such that, following the light-mediated removal of the photolabile blocking group in a given region of interest, a discrete tag molecule (analogous to Guo’s linker DNA) is separately administered to and ligated onto the new unblocked/activated probe in that region, rather than relying solely on in-situ extension of the pre-existing barcode sequence already present in the original probe backbone. One of ordinary skill in the art would be motivated to do so because Guo demonstrates that supplying the tag as a separately-administered ligated linker molecule rather than embedding it unalterably in the original probe prior to processing, allows the tag/barcode sequence to be selected, exchanged, or assigned at the point of ligation rather than fixed at the time of probe synthesis, providing greater flexibility in multiplexing different samples or regions with interchangeable barcode reagents without redesigning the probe oligonucleotide itself. This is no more than the combination of prior art elements (Oki’s blocking-group removal gated activation mechanism and Guo’s separately administered, ligated tag molecule) according to their established functions, to yield the predictable results of region specific tag molecule administration following processing. Whether it be the first processing as in claim 65 or the second processing as in claim 66, the mechanism is the same and would be obvious to one of ordinary skill in the art.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Matthew H Raymonda whose telephone number is (703)756-5807. The examiner can normally be reached Monday - Friday 10:00 am - 4:00 pm.
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/MATTHEW HAROLD RAYMONDA/Examiner, Art Unit 1684
/AARON A PRIEST/Primary Examiner, Art Unit 1681
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