DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. This action is in response to the amendment filed on 24 April 2026 . Applicant's arguments and amendments to the claims have been fully considered but do not place the application in condition for allowance. All rejections not reiterated herein are hereby withdrawn.
This action contains new grounds of rejection and is made non-final.
Claim Status
3. Claims 2-12 and 15-18 are pending and have been examined herein.
Terminal Disclaimer
4. The terminal disclaimer filed on 24 April 2026 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of U.S. Patent No. 1218403 and U.S. Patent No. 12031177 has been reviewed and is accepted. The terminal disclaimer has been recorded.
Maintained / Modified Claim Rejections - 35 USC § 103
5. 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 2-12 and 15-18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al (WO 2021/252747) in view of Du et al (Analytical Chemistry. 2017. 89(22): 12433-12440; previously cited).
Kim et al. (abstract) teaches:
"Provided herein is a fluid delivery method for permeabilizing a biological sample. The method includes delivering the fluid to a first substrate and/or a second substrate. At least one of the first substrate and the second substrate includes a spacer. The method further includes assembling, subsequent to the delivering, a chamber comprising the first substrate, the second substrate, the biological sample, and the spacer. The spacer may be disposed between the first substrate and second substrate. The spacer may be configured to maintain the fluid within the chamber and maintain a separation distance between the first substrate and the second substrate. The spacer may be positioned to at least partially surround an area on the first substrate on which the biological sample is disposed and/or at least partially surround the array disposed on the second substrate “
Kim et al., at page 8, fourth paragraph, teach "the biological sample is a tissue section".
Kim et al., at page 8, last paragraph, teach:
“In some embodiments, a plurality of capture probes are attached to the bead. In some embodiments, a capture probe of the plurality of capture probes comprises (i) a capture domain; and (ii) a spatial barcode unique to the feature.”
Kim et al., at page 18, penultimate paragraph, teach:
“A capture probe can also include a nucleic acid sequence that is complementary to a sequence of a universal forward and/or universal reverse primer. A capture probe can also include a cleavage site (e.g., a cleavage recognition site of a restriction endonuclease), a photolabile bond, a thermosensitive bond, or a chemical-sensitive bond.”
Kim et al., at page 21, first full paragraph, teaches: “In some embodiments, a biological sample is permeabilized with one or more permeabilization reagents. For example, permeabilization of a biological sample can facilitate analyte capture.”
Kim et al., at page 21, fourth paragraph, teaches: In some embodiments, the capture probe includes a barcode (e.g., a spatial barcode and/or a unique molecular identifier (UMI)) and a capture domain).
Kim et al., at page 31, first paragraph, teach: “A tissue ( e.g., fresh-frozen, formalin-fixed paraffin-embedded (FFPE), or the like) may be sectioned and placed in proximity to a slide with thousands of barcoded spots, each containing millions of capture oligonucleotides with spatial barcodes unique to that spot.”
Kim et al., at page 32, last paragraph, teach: “FIG. 7 shows an exemplary spatial analysis workflow 700 in accordance with some example implementations. The workflow 700 includes preparing a biological sample on a slide ( e.g., a pathology slide) 701, fixing the sample, and/or staining 702 the biological sample for imaging.”
FIG. 13A and 13B of Kim et al. are set forth below:
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Regarding capture probe, Kim et al., teach:
"In some embodiments, a capture probe of the plurality of capture probes comprises (i) a capture domain; and (ii) a spatial barcode unique to the feature. In some embodiments, the capture domain of the capture probe comprises a poly(T) sequence. In some embodiments, the capture probe includes one or more of: a functional domain, a cleavage domain, a unique molecular identifier, or any combination thereof.” (See bridging paragraph, pages 8-9).
Kim et al., further teaches that:
"Spatial analysis methodologies described herein provide a vast amount of analyte level and/or expression data for a variety of multiple analytes within a sample at high spatial resolution, e.g., while retaining the native spatial context. Spatial analysis methods include, e.g., the use of a capture probe including a spatial barcode (e.g., a nucleic acid sequence that provides information as to the position of the capture probe within a cell or a tissue sample (e.g.,mammalian cell or a mammalian tissue sample) and a capture domain that is capable of binding to an analyte (e.g., a protein and/or nucleic acid) produced by and/or present in a cell. As described herein, the spatial barcode can be a nucleic acid that has a unique sequence, a unique fluorophore or a unique combination of fluorophores, a unique amino acid sequence, a unique heavy metal or a unique combination of heavy metals, or any other unique detectable agent. The capture domain can be any agent that is capable of binding to an analyte produced by and/or present in a cell (e.g., a nucleic acid that is capable of hybridizing to a nucleic acid from a cell (e.g., an mRNA, genomic DNA, mitochondrial DNA, or miRNA), a substrate including an analyte, a binding partner of an analyte, or an antibody that binds specifically to an analyte). A capture probe can also include a nucleic acid sequence that is complementary to a sequence of a universal forward and/or universal reverse primer. A capture probe can also include a cleavage site (e.g., a cleavage recognition site of a restriction endonuclease), a photolabile bond, a thermosensitive bond, or a chemical-sensitive bond.” (See page 18, 3ʳᵈ paragraph).
Kim et al. (2015) does not explicitly teach the limitation "applying light having a
wavelength of about 300 nm to about 400 nm to the nucleic acid capture probe" recited in step (b) of claim 2.
However, Du et el. (2015) teach "A microfluidic sample preparation multiplexer (SPM) and assay procedure is developed to improve amplification-free detection of Ebola virus RNA from blood. While a previous prototype successfully detected viral RNA following off-chip RNA extraction from infected cells, the new device and protocol can detect Ebola virus in raw blood with clinically relevant sensitivity. The Ebola RNA is hybridized with sequence specific capture and labeling DNA probes in solution and then the complex is pulled down onto capture beads for purification and concentration. After washing, the captured RNA target is released by irradiating the photocleavable DNA capture probe with ultraviolet (UV) light. The released, labeled, and purified RNA is detected by a sensitive and compact fluorometer. Exploiting these capabilities, a detection limit of 800 attomolar (aM) is achieved without target amplification. The new SPM can run up to 80 assays in parallel using a pneumatic multiplexing architecture. Importantly, our new protocol does not require time-consuming and problematic off-chip probe conjugation and washing. This improved SPM and labeling protocol is an important step toward a useful POC device and assay." (See Abstract).
Du et al., at page 12435, right column, teach that "After that, the SPM was placed under a 311 nm ultraviolet (UV) lamp (Kernel-4003B) to release captured nucleic acid targets from the beads (Figure S1c)."
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Kim et al. by using a wavelength of about 311 nm UV light to cleave the DNA capture probe since Kim et al teaches that this is an effective wavelength of light to use to cleave a photo-cleavable capture probe. In view of the well developed state of the art, one of ordinary artisan would had a most reasonable expectation of success of modifying the method of Kim so as to have used the wavelength disclosed by Du for cleaving the photocleavable linkage in the DNA capture probe.
Response to Remarks:
The response states that Kim is not prior art under the 35 U.S.C. 102(b)(2)C). It is stated that the present application has an effective filing date of June 22, 2022, which is within one year of the December 16, 2021 publication date of the Kim et al reference. Applicant states “as of the effective filing date of the instant application, Kim, and the instant application were co-owned by or subject to an obligation of assignment to 10X GENOMICS, INC. Accordingly, Kim falls under the 35 U.S.C. § 102(b)(2)(C) exception, and therefore it does not qualify as prior art under 35 U.S.C. §§ 102 or 103.”
By establishing common ownership as of the effective filing date of the claimed invention removes the Kim et al reference as prior art under 35 U.S.C. 102(a)(2).
However, Kim et al has a publication date of December 16, 2021, which is prior to the present effective priority date. Thus, Kim et al is prior art under 35 U.S.C. 102(a)(1). Note that the inventorship of the Kim et al reference includes additional inventors Siyuan Xing, Rajiv Bharadwaj, Bill Kengli Lin, Felice Alessio Bava, and Pratomo Putra Alimsijah, which are not listed as inventors of the present application. While Kim et al was published less than one year prior to the effective filing date of the present application, Kim et al is not an exception under 102(b)(1) because it has not been established that the Kim et al reference is by the inventor or was obtained from the present inventor. See MPEP 2152.06.
Accordingly, Applicant has provided evidence in this file showing that the claimed invention and the subject matter disclosed in the prior art reference were owned by, or subject to an obligation of assignment to, the same entity as 10X GENOMICS not later than the effective filing date of the claimed invention, or the subject matter disclosed in the prior art reference was developed and the claimed invention was made by, or on behalf of one or more parties to a joint research agreement in effect not later than the effective filing date of the claimed invention. However, although Kim et al has been excepted as prior art under 35 U.S.C. 102(a)(2), it is still applicable as prior art under 35 U.S.C. 102(a)(1) that cannot be excepted under 35 U.S.C. 102(b)(2)(C).
Applicant may rely on the exception under 35 U.S.C. 102(b)(1)(A) to overcome this rejection under 35 U.S.C. 102(a)(1) by a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application, and is therefore not prior art under 35 U.S.C. 102(a)(1). Alternatively, applicant may rely on the exception under 35 U.S.C. 102(b)(1)(B) by providing evidence of a prior public disclosure via an affidavit or declaration under 37 CFR 1.130(b).
New Grounds of Rejection:
6. Claim(s) 2-12 and 15-18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Iyer et al (WO 2020/176788, published 03 September 2020; cited as reference “1129” in the first IDS filed on 09/03/2024).
Iyer teaches a method of detecting a target analyte in a cell using a plurality of capture probes that migrate to and penetrate a cell, wherein the capture probes comprise a spatial barcode, a capture domain that is specific for a target analyte, and a photocleavable domain (e.g., p. 3, lines 10-20; p. 80, lines 6-17; p. 90 line 30 to p. 81, line 7; p. 298, line 9 to p. 299, line 12; and Figure 21).
Iyer (p. 298, lines 9-20) states:
“In some embodiments, a cell-tagging agent comprises a cell-penetrating agent (described below). In some embodiments, a cell-penetrating agent transports the cell-tagging agent into the cells of a biological sample. When a cell-tagging agent comprises a barcode (e.g., a nucleic acid that includes a spatial barcode), the barcode also penetrates into the cell. In some embodiments, a plurality of cell-tagging agents are cleaved (e.g., photocleaved) from an array via a cleavage domain, thus freeing the cell-tagging agents from the array and allowing at least one capture probe of the plurality to penetrate a cell. The cell-tagging agent can then interact with an intracellular biological analyte via the capture domain. In some embodiments, the plurality of capture probes is migrated from the array into cells of the biological sample via cell-penetrating agents. In some embodiments, migrating a plurality of capture probes from the array to cells of the biological sample includes applying a force (e.g., mechanical, centrifugal, or electrophorectic) to the biological sample.” (Emphasis added).
Iyer teaches that the sample is a tissue sample (e.g., p. 7, lines 23-25; and p. 10, lines 12-16). Iyer also teaches that the capture probes are attached to a surface, such as a solid array (p. 18, lines 33-34).
Accordingly, Iyer teaches a method comprising:
a) contacting a tissue section with a substrate comprising an array comprising a plurality of nucleic acid capture probes, wherein a nucleic acid capture probe in the plurality of nucleic acid capture probes comprises: (i) a cleavage domain, (ii) a nucleic acid spatial barcode, and (iii) a nucleic acid capture domain comprising a sequence capable of hybridizing to a nucleic acid analyte; (b) cleaving the nucleic acid capture probe at the cleavage domain from the array to generate a cleaved nucleic acid capture probe; (c) migrating the cleaved nucleic acid capture probe into the tissue section, thereby spatially tagging the nucleic acids of the cell in the tissue section; and (d) hybridizing the cleaved nucleic acid capture probe to the nucleic acid analyte
Iyer (p. 80 line 34 to p. 81, line 1) states “When a photo-cleavable linker is used, the cleavable reaction is triggered by light, and can be highly selective to the linker and consequently biorthogonal.”
Iyer does not specifically recite the limitation of “applying light having a wavelength of 300 nm to 400 nm to the nucleic acid capture probe.”
However, Iyer (p. 81, lines 2-7) does teach:
“wavelength absorption for the photocleavable linker is located in the near-UV range of the spectrum. In some embodiments, /.max of the photocleavable linker is from about 300 nm to about 400 nm, or from about 310 nm to about 365 nm. In some embodiments, max of the photocleavable linker is about 300 nm, about 312 nm, about 325 nm, about 330 nm, about 340 nm, about 345 nm, about 355 nm, about 365 nm, or about 400 nm.”
Accordingly, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Iyer so as to have specifically applied a light having a wavelength of between 300nm to about 400 nm to cleave the capture probe having the photocleavable linker. One would have been motivated to have done so because Iyer teaches that this is an effective wavelength of light to cleave photocleavable linkers having a wavelength absorption near the UV range and particularly in the range from about 300nm to about 400 nm.
Regarding claim 3, Iyer teaches that the method comprises contacting the tagged nucleic acids of the cell with a plurality of molecules having a plurality of nucleic acid barcodes (p. 66, lines 5-10; p. 106, lines 20-31; p,. 296, line 22 to p 297 line 5).
Regarding claim 4, Iyer teaches separating the tagged nucleic acids of the cell from the tissue section (e.g., p. 296, line 22 to p.299 line 12).
Regarding claim 5, as discussed above, Iyer teaches that the nucleic acid capture domain of the nucleic acid capture probe hybridizes to the nucleic acid analyte, wherein the nucleic acid analyte comprises a nucleic acid barcode associated with the cell; wherein the nucleic acid analyte is comprised in the plurality of molecules having the plurality of nucleic acid barcodes.
Regarding claims 6 and 7, Iyer teaches that the array comprises a plurality of beads, wherein each bead occupies a unique position in the array and the capture probes are attached to the beads (e.g., p. 175, lines 21 to p.177, line 4).
Regarding claims 8 and 9, Iyer teaches that the capture probe can comprise a primer sequence with a cleavage domain 5’ to the primer sequence and a unique molecular identifier (e.g., p. 18, lines 25-27; p. 66 lines 27-32; p. 75 line 10 to 30).
Regarding claim 10, as discussed above, Iyer teaches that the cleavage domain comprises a photo-cleavable linker (e.g., p. 80, line 35 to p. 81, line 7; and p. 90, lines 30-31).
Regarding claim 11, Iyer teaches treating the biological sample, including the tissue section with a permeabilization buffer (e.g., p. 6 line 31 to p. 7 line 2; p. 51 line 12 to p. 52, line 16).
Regarding claim 12, Iyer teaches that the nucleic acid capture probe is attached by its 5' end to the substrate / array (p. 92, lines 3-4).
Regarding claim 15, Iyer teaches that the tissue section is a fresh-frozen tissue section (p. 217, lines 10-20 and p. 360, lines 1-2).
Regarding claims 16-17, Iyer teaches staining and imaging the tissue section (e.g., p. 40, lines 22-32; p. 73 lines 16 to p. 74, lines 2).
Regarding claim 18, Iyer (p. 56, line 32 to p. 57, line 10) states “a nucleic acid extension reaction includes using a DNA polymerase to extend the capture probe that is hybridized to the captured analyte (e.g., fragmented genomic DNA) using the captured analyte (e.g., fragmented genomic DNA) as a template. The product of the extension reaction includes a spatially-barcoded analyte (e.g., spatially-barcoded fragmented genomic DNA). The spatially barcoded analyte (e.g., spatially-barcoded fragmented genomic DNA) can be used to identify the spatial location of the analyte in the biological sample.” Thus, Iyer teaches extending the nucleic acid capture probe using the nucleic acid analyte as a template.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CARLA J MYERS whose telephone number is (571)272-0747. The examiner can normally be reached M-Th 6:30-5:00 EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached on 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CARLA J MYERS/Primary Examiner, Art Unit 1682
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