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 .
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 08/28/2025; 11/26/2025; 05/11/2026 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of claims / Response to Amendment
This office action is in response to Applicant's Response to Election / Restriction filed on May 11, 2026. No claims amendment are made in the response filed on 05/11/2026.
In amended claims filed on November 26, 2025: Applicant amended claims 1 and 13; added new claims 50-53.
Claims 1, 8-11, 13-14, 17, 19, 26, 42-47 and 50-53 are currently pending, with claims 13-14, 17 and 50-51 withdrawn.
Claims 1, 8-11, 19, 26, 42-47 and 52-53 are under consideration.
All of the previously presented rejections have been withdrawn as being obviated by the amendment of the claims.
Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
This office action contains new grounds for rejection necessitated by amendment.
Election/Restrictions
Applicant’s election without traverse of Group 1 (claims 1, 8-11, 19, 26, 42-47 and 52-53) in the reply filed on May 11, 2026 is acknowledged.
Claims 13-14, 17 and 50-51 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention.
Examination on the merits commences on claims 1, 8-11, 19, 26, 42-47 and 52-53.
Priority
For the instant claims 1, 8-11, 19, 26, 42-47 and 52-53, the applicant claims priority of 15 US provisional applications 62/819,449; 62/819,477; 62/819,458; 62/819,456; 62/819,496; 62/819,468; 62/819,444 ; 62/819,448; 62/819,439; 62/819,453; 62/819,495; 62/819,467; 62/819,486; 62/819,478 and 62/819,470, they share the same filling date on March 15, 2019.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, claim 1 recites "spatial barcode," which is described in the specification as follows:
"A “spatial barcode” is a contiguous nucleic acid segment or two or more non-contiguous nucleic acid segments that function as a label or identifier that conveys or is capable of conveying spatial information. In some embodiments, a capture probe includes a spatial barcode that possesses a spatial aspect, where the barcode is associated with a particular location within an array or a particular location on a substrate.
A spatial barcode can be part of an analyte, or independent from an analyte (e.g., part of the capture probe). A spatial barcode can be a tag attached to an analyte (e.g., a nucleic acid molecule) or a combination of a tag in addition to an endogenous characteristic of the analyte (e.g., size of the analyte or end sequence(s)). A spatial barcode can be unique. In some embodiments where the spatial barcode is unique, the spatial barcode functions both as a spatial barcode and as a unique molecular identifier (UMI), associated with one particular capture probe. " (page 80)
Accordingly, under BRI and in light of the specification, the term "spatial barcode" is interpreted to encompass any nucleic acid sequence contiguous or non-contiguous, as any nucleic acid sequence can be used as a label. For example, as explicitly described in the specification, a unique molecular identifier (UMI) is a "spatial barcode."
For the purpose of applying prior art, claim 1 recites "capture domain," which is described in the specification as follows:
"As discussed above, each capture probe includes at least one capture domain. The “capture domain” can be an oligonucleotide, a polypeptide, a small molecule, or any combination thereof, that binds specifically to a desired analyte. In some embodiments, a capture domain can be used to capture or detect a desired analyte. " (page 69)
Accordingly, under BRI and in light of the specification, the term "capture domain" is interpreted to encompass any entity capable of capturing or detecting an analyte.
For the purpose of applying prior art, claim 1 recites "removable coating," which is described in the specification as follows:
" As used herein, a “removable coating” refers to a coating that can be removed from the surface of a substrate upon application of a releasing agent. As an example, a removable coating can include a hydrogel. A “hydrogel” as referred to herein includes a cross-linked three-dimensional (3D) network of hydrophilic polymer chains. " (page 374).
Accordingly, under BRI and in light of the specification, the term "removable coating" is interpreted to encompass any coating material capable of being removed from a surface of a substrate. For example, as explicitly described in the specification, a hydrogel is a species of "removable coating."
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.
Claims 1, 8, 10-11, 19, 42-47 and 52-53 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Srinivasan (WO2018089910A2 - Compositions and methods for the simultaneous genomic, transcriptomic and proteomic analysis of single cells; Published on : 2018-05-17); as evidenced by
Helgeson (Helgeson et al. Hydrogel microparticles from lithographic processes: novel materials for fundamental and applied colloid science. Curr Opin Colloid Interface Sci. 2011 Apr 1;16(2):106-117. doi: 10.1016/j.cocis.2011.01.005. PMID: 21516212; PMCID: PMC3079890).
Regarding claim 1, Srinivasan teaches a method for profiling a biological analyte present in a cell- containing biological sample (Figure 15, sequencing protocol for single bead, single cell capture; [0119]), the method comprising:
(a) providing a substrate comprising
(i) a removable coating (FIG. 15, PVA hydrogel coated on microchamber surface) and
(ii) a plurality of capture probes (FIG. 15J, seq-well beads comprising capture probes),
wherein a capture probe of the plurality of capture probes comprises a spatial barcode (FIG. 15J, UMI, which is a spatial barcode according to the specification of the present application (p.80, lines 12-13)) and a capture domain (FIG. 15J, poly T) ;
(b) distributing a plurality of cells from the cell-containing biological sample onto the substrate such that a cell from the plurality of cells occupies a distinct spatial position on the substrate from other cells in the plurality (FIG. 15; [0119]lines 8-9, “Final consumable consists of 1 bead and 1 cell per microchamber”; lines 12-13),
wherein the plurality of cells is from a disassociated tissue or tissue section, or a culture of cells (FIG. 15 discloses loading cells. A plurality of cells is either from tissue or a culture of cells; see also [072] “the single cell is a cancer cell.Cancer cells of the disclosure may be isolated, purified, derived and/or cultured from any tissue of the body”), and
wherein the plurality of cells is distributed onto the substrate using fluid flow ([0119] lines 12-13, cells are pipetted on to the surface of microchamber), a pressure gradient, a chemical concentration gradient, a temperature gradient, and/or a pH gradient;
(c) treating the plurality of cells such that the biological analyte from the cell is released and captured by the capture probe (FIG. 15I-J); and
(d) determining
(i) all or part of the sequence of the biological analyte, or a complement thereof, and
(ii) the sequence of the spatial barcode, or a complement thereof (FIG. 15L, single cell RNA sequencing ; FIG. 25), and
using the determined sequences of (i) and (ii) to profile the biological analyte as having been present in the cell from the cell-containing biological sample at the distinct spatial position on the substrate ([056] lines 4-5 “each chamber of the plurality of chambers comprises a single cell of the biological sample.” Therefore each single cell is at a distinct spatial position within a distinctly located chamber ; lines 12-17, “sequencing a target of the at least one capture agent:target complex to identify one or more intracellular targets of a single cell in a multiplexed analysis”).
Regarding claim 8, Srinivasan teaches the removable coating comprises a hydrogel and wherein the cell from the plurality of cells is immobilized on the substrate comprising the hydrogel (FIG. 15).
Regarding claim 10, Srinivasan teaches the cell from the plurality of cells is immobilized by using a labelling agent that facilitates attachment of the cell to the capture probe on the substrate (FIG. 15H, both capture antibody and beads comprising capture probes are immobilized on the chamber surface, thus the cell capture by the antibody indirectly links the cell with the capture probes on the substrate).
Regarding claim 11, Srinivasan teaches the substrate comprises streptavidin ([0119] line 8, “streptavidin functionalized surface”).
Regarding claim 19, Srinivasan teaches imaging the plurality of cells ([0122] line 11; Fig. 19A) .
Regarding claim 42, Srinivasan teaches the biological analyte is DNA ([030] line 2) .
Regarding claim 43, Srinivasan teaches the biological analyte is RNA ([030] line 2).
Regarding claim 44, Srinivasan teaches the biological analyte comprises two or more of a DNA, an RNA, a protein ([0126] lines 13-14 “simultaneous analysis of DNA, RNA, and proteome from individual cells” ).
Regarding claim 45, Srinivasan teaches the capture domain comprises a poly-dT sequence (FIG. 15J) .
Regarding claim 46, Srinivasan teaches the capture domain is configured to hybridize to a poly-A tail of a mRNA(FIG. 15J).
Regarding claim 47, Srinivasan teaches capture probe comprises a unique molecular identifier (UMI) and a functional domain (FIG. 15J, e.g. PCR handle).
Regarding claim 52, Srinivasan teaches the removable coating is a light-responsive hydrogel ([0119] UV crosslinkable PVA).
Regarding claim 53, Srinivasan teaches applying a releasing agent to remove the removable coating from the substrate by teaching coating the substrate surface with a PVA hydrogel using UV light, and later removing the surface from substrate for visualization ([0119] lines 3-4, forming a PVA hydrogel on microchamber surface using UV light; [0142] lines 7-8 “Once the intracellular components form complexes with the capture agents, the surface may be removed and visualized.”).
A skilled artisan would readily understand that UV light acts as releasing agent to create removable hydrogel blocks from substrate, as photolithography to create hydrogel particles is well known in the art. See Helgeson (Fig. 1).
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.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over
Srinivasan (WO2018089910A2 - Compositions and methods for the simultaneous genomic, transcriptomic and proteomic analysis of single cells; Published on : 2018-05-17), in view of Voldman (Voldman J. Electrical forces for microscale cell manipulation. Annu Rev Biomed Eng. 2006;8:425-54. doi: 10.1146/annurev.bioeng.8.061505.095739. PMID: 16834563.) .
The teachings of Srinivasan are recited above and applied as for base claim 1.
Regarding claim 9, Srinivasan teaches immobilizing cell on a substrate by antibody capture (FIG. 15). Although Srinivasan does not explicitly teach immobilizing cells using electric force, a person of ordinary skill in the art would have found it obvious to substitute Srinivasan’s antibody-based immobilization with electric-force-based cell immobilization.
Using electric force to move and immobilize cells on substrates was well known in the art, as taught by Voldman (entire document, Figs. 5-8 for example). Because both approaches serve the same function of immobilizing cell on a substrate, this modification represents a simple substitution of one known element for another to obtain predictable results, see MPEP 2141.
Claim 26 is rejected under 35 U.S.C. 103 as being unpatentable over
Srinivasan (WO2018089910A2 - Compositions and methods for the simultaneous genomic, transcriptomic and proteomic analysis of single cells; Published on : 2018-05-17), in view of Jovanovich (US20180305681A1 - Method and apparatus for encoding cellular spatial position information; Published on: 2018-10-25), evidenced by
Golzio (Golzio et al. Direct visualization at the single-cell level of electrically mediated gene delivery. Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1292-7. doi: 10.1073/pnas.022646499. Epub 2002 Jan 29. PMID: 11818537; PMCID: PMC122183.)
The teachings of Srinivasan are recited above and applied as for base claim 1.
Regarding claim 26, it recites permeabilizing the cells. While Srinivasan teaches lysing cells with lysis reagents to release analytes within the cell, a skilled artisan with knowledge in the art would have found the claimed feature obvious because cell lysis and cell permeabilization are both known approaches for allowing analytes to contact assay reagents. The principle that electric force can be applied to permeabilize cells and allow exchange through the cell membrane was well known in the art, as evidenced by Golzio (page 1292, left-hand col, lines 5-10)
“Among physical methods, electropermeabilization, also named electroporation (see ref. 2 for review), a method based on the application of electric field pulses to cells was introduced in the early 1980s (3). Electropermeabilization indeed can be used to introduce a large variety of molecules into many different cells (4–6). ”
Jovanovich specifically teaches, in the context of cellular sequencing and barcoding, applying electric force to allow nucleic acid markers to enter cells for analyte analysis ([0134] lines 21-22; [0137]; Fig. 17). Accordingly, modifying Srinivasan’s method by substituting permeabilization for lysis would have been an obvious simple substitution.
Prior Art
Below are relevant prior art not used in rejection but pertinent to the claims or disclosure.
The application of hydrogel in spatial and cellular analysis methods is common with known benefits:
Gao (Gao, R., Asano, S.M. & Boyden, E.S. Q&A: Expansion microscopy. BMC Biol 15, 50 (2017). doi.org/10.1186/s12915-017-0393-3) teaches applying hydrogel matrix to spatial analysis for improved imaging quality, allowing for simultaneous, multiplex detection of nucleic acid and protein targets alike;
Tamura (Tamura, et al. Optical cell separation from three-dimensional environment in photodegradable hydrogels for pure culture techniques. Sci Rep 4, 4793 (2014). doi.org/10.1038/srep04793) teaches using photodegradable hydrogels for selective cell and beads separation;
Lan (WO2018119301A1 - Single cell genomic sequencing using hydrogel based droplets; 2018-06-28) teaches encasing and barcoding cells in hydrogel with tunable pore size that allows for permeable exchange of reagent molecule, yet retains larger structures for analysis ([00156]);
Khurana (WO2019028047A1 - Spatial indexing of genetic material and library preparation using hydrogel beads and flow cells ; Published on : 2019-02-07) teaches cells encapsulate in microenvironment for the controlled processing of nucleic acids within a hydrogel on a flow cell device, which allows for multiple reaction and washing steps within the hydrogel, the cross-linked gel is then washed out using a reducing agent, which uncrosslinks the gel (Fig. 13).
The following references also teach barcoding cells on a substrate comprising hydrogel:
Fodor (US20160253584A1 - Spatially addressable molecular barcoding; Published on 2016-09-01) ;
Gaublomme (US20180340939A1 - Multiplex analysis of single cell constituents; published 2018-11-29).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TIAN NMN YU whose telephone number is (703)756-4694. The examiner can normally be reached Monday - Friday 8:30 am - 5:30 pm.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
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