DETAILED ACTION
The amendment filed on 10/01/2025 has been entered. No new matter has been added.
Claims 157, 160, 161, 163, 164, 174, and 175 were amended in the claim set filed on 10/01/2025.
Claim 171 was canceled in the claim set filed on 10/01/2025.
Claim 177 was newly added in the claim set filed on 10/01/2025.
Claims 157-170 and 172-177 in the claim set filed on 10/01/2025 are pending and currently under examination.
Response to the Arguments
Objection to the Specification in the previously mailed non-final has been withdrawn in light of applicants Abstract amendments.
Applicant’s arguments regarding previous rejection(s) of claim(s) 157-176 under 35 U.S.C. 112 have been fully considered and are persuasive. The 35 U.S.C. 112 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim amendments and arguments on Pg. 7-8.
Applicant’s arguments regarding previous rejection(s) of claim(s) 157-176 under 35 U.S.C. 103 have been fully considered and are persuasive. Applicant’s argument on Pg. 6-7, states that “Applicant has amended independent claim 157 to recite "wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample" and "wherein a first semi-porous material of the one or more semi-porous materials retains one or more second analytes". Applicant submits that the asserted combination of Frisen, Belgrader, and Schulze fails to render the claims as obvious at least because the references (when considered alone or in any combination) do not meet all of the elements of amended claim 157 and fails to provide a motivation to be modified or combined to arrive at the claimed invention with a reasonable expectation of success.” The 35 U.S.C. 103 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim amendments and arguments on Pg. 6-7. However, upon further search and consideration of claim amendments, new grounds of rejection for claims 157-176 under 35 U.S.C. 103 have been documented below in this Final Office Action on Pg. 7-7.
Applicant’s arguments regarding previous rejection(s) of claim(s) 157-176 under 35 U.S.C. 103 have been fully considered and are persuasive. As necessitated by amendment to the claim, new grounds of rejection for claims 157-170 and 172-177 under Non-Statutory Double Patenting is documented below in this office action on Pg. 12-15.
As necessitated by abandonment of U.S. Application 17/312,638, rejection for claim 12 under Non-Statutory Double Patenting is withdrawn.
The rejections are documented below in this Final Office Action are necessitated by claim amendments filed on 10/01/2025.
Priority
This application claims priority to U.S. Provisional Application No. 63/157,521, filed March 5, 2021. Accordingly, the priority date of instant claims is determined to be March 5, 2021, the filing date of U.S. Provisional Application No. 63/157,521.
Claim Rejections - 35 USC § 103
Claim interpretations: Regarding claims 157-170 and 172-177, first and/or second semi-porous materials is interpreted as any material that is semi-porous or permeable, allowing at least some molecules through the materials, which can be the same type of material or different types of materials.
Claims 157, 159, 170, 172 and 176-177 are rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (“Frisen”; US Patent App. Pub. No. US 20150344942 A1, Dec. 12, 2015) in view of Schulze et al. (“Schulze”; JP 5596568 B2, Sept. 24, 2014, English translation provided).
Frisen discloses present invention relates to methods and products for localized or spatial detection and/or analysis of RNA in a tissue sample or a portion thereof, comprising: (a) providing an object substrate on which at least one species of capture probe, comprising a capture domain, is directly or indirectly immobilized such that the probes are oriented to have a free 3′ end to enable said probe to function as a reverse transcriptase (RT) primer; (b) contacting said substrate with a tissue sample and allowing RNA of the tissue sample to hybridize to the capture probes; (c) generating cDNA molecules from the captured RNA molecules using said capture probes as RT primers; (d) labelling the cDNA molecules generated in step (c), wherein said labelling step may be contemporaneous with, or subsequent to, said generating step; (e) detecting a signal from the labelled cDNA molecules; and optionally (f) imaging the tissue sample, wherein the tissue sample is imaged before or after step (c). (Abstract)
Regarding claim 157, Frisen teaches a method comprising “spatial detection of nucleic acid in a tissue sample or a portion thereof. …, so as to obtain spatial information about the localization, distribution or expression of genes in a tissue sample, for example in an individual cell. The present invention thus enables spatial transcriptomics” (Para.1). Frisen teaches a method comprising “the invention is particularly based on array technology and may be coupled with high throughput DNA sequencing technologies. The methods of the invention allow the nucleic acid molecules (e.g. RNA molecules) in the tissue sample, particularly mRNA, to be captured on an object substrate (e.g. a slide or chip, which may be an array) and labelled, which may include the incorporation of a positional tag. The labelled molecules may be visualized to determine or assess the efficacy of the conditions used to capture the nucleic acid molecules. Alternatively or additionally, the captured nucleic acid molecules (or a subset thereof, e.g. a portion of the nucleic acid molecules captured from the tissue sample) may be analyzed further, e.g. by sequence analysis. For instance, the captured nucleic acid molecules may be used to template the synthesis of DNA molecules which are sequenced and analyzed to determine which genes are expressed in all or one or more parts of the tissue sample” (Para. 3).
Frisen teaches a method comprising “high density nucleic acid arrays comprising capture probes for capturing and labelling” and “barcode sequences (or ID tags, defined herein as positional domains) incorporated into the arrayed nucleic acid probes” (Para. 83). Frisen teaches a method comprising “cells may be captured in a matrix (for example a gel matrix” (Para. 152). “gel matrix” is interpreted as semi-porous. Frisen also teaches a method wherein “In addition to a coating or surface treatment with poly-L-lysine, the substrate, in particular glass, may be treated by… a treatment with polyacrylamide” (Para. 93). Frisen teaches a method comprising “wherein the spatial distribution of the transcripts in the tissue sample is transferred directly to the surface of the object substrate.” (Para. 60). Thus, Frisen teaches a method for determining a location of one or more analytes in a biological sample, the method comprising: (a) providing an array comprising a plurality of capture probes, wherein a capture probe of the plurality of capture probes comprises: (i) a spatial barcode and (ii) a capture domain; (b) providing one or more semi-porous materials, wherein the one or more semi-porous materials are disposed between a biological sample and the array.
Frisen does not explicitly teach the limitations wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample and step (c) applying an electric field to the biological sample, the one or more semi-porous materials, and the array, wherein the electric field promotes the migration of one or more first analytes from the biological sample in the direction of the array, wherein the capture domain of the capture probe binds to a first analyte of the one or more first analytes, wherein the first analyte is a nucleic acid, wherein a first semi-porous material of the one or more semi-porous materials retains one or more second analytes.
Schulze discloses a method for processing a sample, which method comprises: a) contacting a binding phase, which binding phase is capable of binding an analyte, with the sample in the presence of a medium; b) applying across the medium a first alternating field composed of a plurality of pulses and having a first frequency, a first pulse duration and a first pulse rise time; c) optionally applying across the medium a second alternating field; and d) thereby influencing the sample and/or the binding phase in the medium.(Abstract)
Regarding claim 157, Schulze teaches a method comprising “the present invention can be used to purify an analyte, isolate an analyte, or sort an analyte. The method according to the present invention is preferably an assay method for detecting the presence or absence of an analyte in a sample. In this embodiment, the assay method may include quantification of the sample.” (Pg. 6, 2nd to last para.). Schulze teaches a method comprising “The medium used in the method of the present invention is any suitable medium including liquids, gels, and buffer solutions, allowing the analyte to move through the medium and bind to the binder phase” (Pg. 7, Para. 10). Schulze teaches a method comprising “Alternating electric fields are a variety of events that occur during the performance of the method, including bulk events such as analyte movement through the medium to the bonded phase, and surface limited events such as binding of the analyte to the bonded phase… electric field can be used to control the movement of the analyte through the medium to the binding phase, e.g., the movement of DNA through the medium to the binding phase. Binding of the analyte to the binding phase, e.g., DNA hybridization, can be controlled using … electric field” (Pg. 4, Para. 5, ln 3-7). Schulze teaches a method comprising “Techniques for purifying, isolating, sorting, and quantifying analytes in a sample are well known to those skilled in the art, and therefore the method according to the present invention can be easily adapted to perform a specific treatment on the required analyte” (Pg. 7, Para. 1). Schulze teaches a method comprising “a specific DNA target sequence can be captured by hybridization using a DNA probe. One skilled in the art can readily use a suitable capture probe depending on the analyte to be detected.” (Pg. 7, Para. 7). “purify an analyte, isolate an analyte, or sort an analyte” reads on “wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample” and “wherein a first semi-porous material of the one or more semi-porous materials retains one or more second analytes”. “a specific DNA target sequence can be captured by hybridization using a DNA probe” reads on “wherein the capture domain of the capture probe binds to a first analyte of the one or more first analytes, wherein the first analyte is a nucleic acid”. Thus, Frisen and Schulze teaches a method comprising wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample and step c) applying an electric field to the biological sample, the one or more semi-porous materials, and the array, wherein the electric field promotes the migration of one or more first analytes from the biological sample in the direction of the array, wherein the capture domain of the capture probe binds to a first analyte of the one or more first analytes, wherein the first analyte is a nucleic acid, wherein a first semi-porous material of the one or more semi-porous materials retains one or more second analytes.
Frisen and Schulze are both considered to be analogous to the claimed invention because they are in the same field of using nucleic acid arrays. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of spatial detection and analysis of nucleic acid analytes in a tissue sample as taught by Frisen to incorporate wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample and the claim limitations according to claim 157 step (c) as taught by Schulze and provide a method for identification and/ or characterization of analytes and determination of spatial location of analytes within a biological sample. Doing so would for allow for the localization of nucleic acid and/or protein analyte(s) based on a biological sample.
The teachings of Frisen and Schulze are documented above in the rejection of claim 157 under 35 U.S.C. 103. Claims 159, 170, 172 and 176-177 depend on claim 157.
Regarding claim 159, Frisen teaches a method wherein “Imaging Measurement of DNA and RNA Hybridization Adsorption onto DNA Microarrays (Para. 76). The present invention can be used for analysis of any complex biological sample, including blood, urine, cerebrospinal fluid, cells, and tissue, among others” (Para. 77). Thus, Frisen teaches a method further comprising imaging the biological sample.
Regarding claim 170, Schulze teaches a method wherein “Binding of the analyte to the binding phase, e.g., DNA hybridization, can be controlled using … electric field” (Pg. 4, Para. 5, ln 3-7). DNA hybridization is interpreted as DNA hybridization in an array. An array is interpreted as having a number of discrete areas Thus, Schulze teaches a method wherein the electric field is applied to a discrete area of the biological sample or is applied to a discrete area of the array.
Regarding claim 172, Frisen teaches a method wherein “tissue samples … arrays are also available or known for use in the context of sequence analysis … Such arrays may also be used as the substrate, e.g. array substrate in the context of the present invention, e.g. an Illumina bead array” (Para. 94). Frisen does not teach porous material, and/or the array are in direct contact with the buffer.
Regarding claim 172, Schulze teaches a method wherein “Since it is known that DNA migration and hybridization can be controlled using an electric field, an electric field is used for nucleic acid arrays based on microchips” (Pg. 2, Para. 4) and “suitable medium including liquids, gels, and buffer solutions, allowing the analyte to move through the medium and bind to the binder phase” (Pg. 7, Para. 10). Thus, Belgrader teaches a method wherein the biological sample, the one or more semi- porous materials, and/or the array are in direct contact with a buffer and wherein the biological sample is a tissue section or a fixed tissue section.
Regarding claim 176, Frisen teaches a method wherein “it may be useful to permeabilize the tissue sample to facilitate the transfer of nucleic acid to the substrate surface” (Para. 163) and “permeabilizing and/or fixing cells” (Para. 164). Thus, Frisen teaches a method further comprising a step of fixing and/or permeabilizing the biological sample.
Regarding claim 177, Frisen teaches a method wherein the invention is particularly based on array technology and may be coupled with high throughput DNA sequencing technologies (Para. 3). Frisen also teaches a method wherein “molecules, or amplicons…are analyzed to investigate (e.g. determine their sequence … The step of sequence analysis may identify the positional domain and hence allow the analyzed molecule to be localized to a position in the tissue sample” (Para. 219) Thus, Frisen teaches a method further comprising determining (i) the sequence of the spatial barcode, or a complement thereof, and (ii) all or a portion of the sequence of the nucleic acid, or a complement thereof, and using the sequences of (i) and (ii) to determine the location of the first analyte in the biological sample.
Response to Arguments
Applicant' s arguments filed 10/01/2025 (Pg.9-14) do not apply to the new grounds of rejections with respect to claim 157, 159, 170, 172 and 176-177. To clarify some instances argued in the response filed 10/01/2025 see responses to each argument made by Applicant below:
Applicants’ argument: “Applicant submits that the asserted combination of Frisen, Belgrader, and Schulze fails to render the claims as obvious at least because the references (when considered alone or in any combination) do not meet all of the elements of amended claim 157 and fails to provide a motivation to be modified or combined to arrive at the claimed invention with a reasonable expectation of success.” (Pg. 9)
Response: Applicant's argument filed 10/01/2025 has been fully considered but is not persuasive because, as stated in the new grounds of rejection under 35 U.S.C. 103 (documented above on Pg. 4-9) towards claim 157, Frisen and Schulze in combination do teach the elements of the amended claim 157 with a reasonable expectation of success. In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, as recited above, Frisen and Schulze are both considered to be analogous to the claimed invention because they are in the same field of using nucleic acid arrays. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of spatial detection and analysis of nucleic acid analytes in a tissue sample as taught by Frisen to incorporate wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample and the claim limitations according to claim 157 step (c) as taught by Schulze and provide a method for identification and/ or characterization of analytes and determination of spatial location of analytes within a biological sample. Doing so would for allow for the localization of nucleic acid and/or protein analyte(s) based on a biological sample.
Applicants’ argument: “Belgrader also does not teach or suggest all elements of the above limitation. According to Para. 344 of Belgrader, "[a] scaffold [(e.g., a gel bead)] loaded with a non-covalently bound reagent may be made using any method of incorporating an agent in a solid substance." (Emphasis added). The "presence or absence of an electric field for electric charge-/field-responsive hydrogel material" is one of various conditions "that causes the scaffold to swell and the pores defined by the polymer scaffold to enlarge." (Belgrader, Para. 344). The application of an electric field that causes one or more semi-porous materials to swell and pores to enlarge in Belgrader does not provide that the one or more semi-porous materials are configured to separate analytes from other analytes in a biological sample, nor that the electric field promotes the migration of the one or more analytes in the direction of an array comprising a plurality of capture probes. Nowhere in Belgrader's disclosure provides a method of"(b) providing one or more semi-porous materials, wherein the one or more semi-porous materials are disposed between the biological sample and the array, wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample; (c) applying an electric field to the biological sample, the one or more semi-porous materials, and the array, wherein the capture domain of the capture probe binds to a first analyte of the one or more first analytes, wherein the first analyte is a nucleic acid, wherein a first semi-porous material of the one or more semi-porous materials retains one or more second analytes ..." as claimed.” (Pg. 10)
Response: Applicant's arguments filed 10/01/2025 do not apply to the new grounds of rejections.
Applicants’ argument: “However, Schulze does not actually teach or suggest the claimed limitations of "wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample" and/or "wherein the capture domain of the capture probe binds to a first analyte of the one or more first analytes, wherein the first analyte is a nucleic acid, wherein a first semi-porous material of the one or more semi-porous materials retains one or more second analytes." (Pg. 11)
Response: Applicant's argument filed 10/01/2025 has been fully considered but is not persuasive Schulze does actually teach or suggest the claimed limitations of "wherein the one or more semi-porous materials are configured to separate analytes from other analytes in the biological sample" and/or "wherein the capture domain of the capture probe binds to a first analyte of the one or more first analytes, wherein the first analyte is a nucleic acid, wherein a first semi-porous material of the one or more semi-porous materials retains one or more second analytes. Please see the new grounds of rejection documented above in the rejection of claim 157 under 35 U.S.C. 103.
Claims 158, 160-162, 167-169 are rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (“Frisen”; US Patent App. Pub. No. US 20150344942 A1, Dec. 12, 2015) in view of Schulze et al. (“Schulze”; JP 5596568 B2, Sept. 24, 2014, English translation provided), as applied to claim 157, and further in view of Belgrader et al. (“Belgrader”; US 20180179590 A1, Jun. 28, 2018).
The teachings of Frisen and Schulze are documented above in the rejection of claim 157, 159, 170, 172 and 176-177 under 35 U.S.C. 103. Claim 158, 160, and 167-167 depend on claim 157. Claim 162 depends on claim 161, which depends on claim 160, which depends on claim 157. Frisen and Schulze do not explicitly teach the limitations of claims 158, 160-162, 164 and 167-169.
Belgrader discloses compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing. (Abstract)
Regarding claim 158, Belgrader teaches a method further comprising “the structure of the barcode oligonucleotides may include a number of sequence elements in addition to the oligonucleotide barcode sequence. One example of a barcode oligonucleotide for use in RNA analysis as described above is shown in FIG. 7. As shown, the overall oligonucleotide 702 is coupled to a bead 704 by a releasable linkage 706… The oligonucleotide may include functional sequences that are used in subsequent processing, such as functional sequence 708, … A barcode sequence 710 is included within the structure for use in barcoding the sample RNA. An mRNA specific priming sequence, such as poly-T sequence 712 is also included in the oligonucleotide structure... An additional sequence segment 716 may be provided within the oligonucleotide sequence...this additional sequence provides a unique molecular identifier (UMI) sequence segment” (Para. 258). Thus, Belgrader teaches a method wherein the capture probe further comprises one or more of: a cleavage domain, a functional domain, and a unique molecular identifier.
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Regarding claim 160, Belgrader teaches a method wherein “the first analyte is a nucleic acid molecule, such as genomic deoxyribonucleic acid (gDNA) or messenger RNA (mRNA).” (Para. 26). Belgrader teaches a method wherein “the first analyte and the second analyte are different types of analytes (e.g., DNA and RNA, DNA and protein, RNA and protein, or DNA, RNA and protein)” (Para. 372). Thus, Belgrader teaches a method wherein the first analyte is a mRNA and a second analyte is a protein.
Regarding claim 161, Belgrader teaches a method wherein “Each capture probe consists of a particle, binding moieties (e.g., proteins) capable of binding to an analyte” (Para. 16). Belgrader teaches a method wherein “Examples of antibody-binding proteins include proteins that bind to the constant (Fe) region of antibodies, such as Protein A, Protein G, Protein L, or fragments thereof” (Para. 322). Thus, Belgrader teaches a method wherein the first semi-porous material comprises a plurality of protein-binding moieties that specifically bind to one or more proteins.
Regarding claim 162, Frisen teaches a method wherein “In order to correlate the transcriptome information, e.g. signal intensity … obtained from the substrate, e.g. by imaging the substrate … the tissue sample is placed on the substrate, e.g. array, such that the position of a capture probe on the substrate, e.g. array, may be correlated with a position in the tissue sample. Thus, it may be identified where in the tissue sample the position of each species of capture probe (or each feature of the array) corresponds. In other words, it may be identified to which location in the tissue sample the position of each species of capture probe corresponds” (Para. 176). The step of imaging the tissue may use any convenient histological means known in the art, field, darkfield, phase contrast, fluorescence, reflection, interference, confocal microscopy or a combination thereof. Typically, the tissue sample is stained prior to visualization to provide contrast between the different regions” (Para. 188) and “the tissue sample is
visualized or imaged using fluorescence microscopy” (Para. 189). Thus, Frisen teaches a method wherein determining the location of the one or more probes, wherein determining the location of the one or more probes comprises the use of immunofluorescence staining and imaging the first semi-porous material; and correlating the immunofluorescence staining in the image of the first semi-porous material with an image of the biological sample. Frisen does not specifically teach a method of the localization of one or more proteins.
Regarding claim 162, Belgrader teaches a method wherein “the antibody-binding proteins may be engineered to have tags, e.g., fluorescent tags (e.g., by fusing with a fluorescent protein such as green fluorescence protein (GFP), red fluorescence
protein (RFP), yellow fluorescence protein (YFP)) and/or affinity tags for purification and visualization” (Para. 323). Thus, Belgrader teaches a method further comprising determining the location of the one or more proteins comprises the use of immunofluorescence staining and imaging.
Regarding claim 167-169, Belgrader teaches a method wherein “a gel bead may be a hydrogel bead” (Para. 132) and “Beads may be of uniform size or heterogeneous size.” (Para.153). Thus, Belgrader teaches a method wherein at least one of the one or more semi-porous materials has a substantially uniform pore size or non-uniform pore sizes.
Furthermore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of determining the location of the one or more probes using immunofluorescence staining and imaging the first semi-porous material; and correlating the immunofluorescence staining in the image of the first semi-porous material with an image of the biological sample as taught by Frisen and Schulze to incorporate the method of the localization of one or more proteins as taught by Belgrader and provide a method for identification and/ or characterization of analytes and determination of spatial location of analytes within a biological sample. Doing so would for allow for the localization of nucleic acid and/or protein analyte(s) based on a biological sample.
Response to Arguments
Applicant's arguments filed 10/01/2025 do not apply to the new grounds of rejections. See above responses with regard to arguments towards amended claim 157.
Claims 163-166 are rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (“Frisen”; US Patent App. Pub. No. US 20150344942 A1, Dec. 12, 2015) in view of Schulze et al. (“Schulze”; JP 5596568 B2, Sept. 24, 2014), as applied to claim 157 above, and further in view of Natan et al. (“Natan”, US Application Pub. No. US 2002/0146745 A1, Oct. 10, 2002).
The teachings of Frisen and Schulze are documented above in the rejection of claims 157, 159, 170, 172 and 176-177 under 35 U.S.C. 103. Claim 163 depends on claim 157. Frisen and Schulze do not explicitly teach claim 163.
Natan discloses bifunctional capture probes used for multiplexed assays consist of particles bearing analyte-binding moieties and pairing oligonucleotides, which hybridize to an array of surface-bound capture oligonucleotides. Capture probes are combined with a sample containing analytes of interest, extracted from the sample, and then exposed to the oligonucleotide array. Based on their pairing oligonucleotide sequences, the capture probes self-assemble at particular array locations. Bound analytes are then detected using a method, such as mass spectrometry, that can be directed toward particular array locations. Because any number and combination of capture probes can be employed, the method is flexible and able to detect analytes at very low concentrations. Additionally, the method provides the ease of detection associated with position-addressable arrays. (Abstract)
Regarding claim 163, Natan teaches a method wherein “the capture probes are contacted with the array, the pairing oligonucleotides and capture oligonucleotides hybridize to form a binding complex. Preferably, different surface-bound capture oligonucleotides are located at particular … positions of the array. Different subsets of capture probes have different pairing oligonucleotides and binding moieties, so that particular binding moieties are directed to particular locations of the array. (Para. 17). Thus, Natan teaches a method wherein the one or more semi-porous materials comprises a second semi-porous material, wherein the second semi-porous material retains one or more third analytes, wherein the second semi-porous material comprises a plurality of analyte-binding moieties for the one or more third analytes.
Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of spatial detection and analysis of nucleic acid analytes in a tissue sample taught by Frisen and Schulze to incorporate the method of a semi-porous material comprising a plurality of analyte-binding moieties for one or more nucleic acid analytes as taught by Natan and provide a method for spatial detection of one or more nucleic acid analyte(s). Doing so would for allow for the localization of nucleic acid and/or protein analyte(s) based on a biological sample.
The teachings of Frisen, Schulze and Natan are documented above in the rejection of claim 163 under 35 U.S.C. 103. Claim 166 depends on claim 165, which depends on claim 164, which depends on claim 163.
Regarding claim 164, Belgrader teaches a method wherein “A sample may have a plurality of analytes of different types, such as a mixture of DNA and RNA molecules, or a mixture of nucleic acid molecules and labelling agents. (Para. 124). Thus, Belgrader teaches a method wherein the third analyte is a nucleic acid.
Regarding claim 165, Frisen teaches a method wherein “methods based on in situ hybridization provide only relative information of single mRNA transcripts” (Para. 26). Frisen teaches a method wherein “the abundance of the transcripts can be correlated directly with their position in the tissue sample” (Para. 60). Thus, Frisen teaches a method further comprising determining the location of the third analyte in the second semi-porous material, wherein determining the location of the third analyte in the second semi-porous material comprises in situ hybridization.
Regarding claim 166, Frisen teaches a method wherein methods based on in situ hybridization provide only relative information of single mRNA transcripts. (Para. 26). Frisen teaches a method wherein “The methods allow the abundance of the transcripts from a tissue sample to visualized directly, e.g. by fluorescence, akin to a standard microarray… the abundance of the transcripts can be correlated directly with their position in the tissue sample. Advantageously, the detection of the labelled cDNA molecules in situ on the surface of the object substrate” (Para. 60). Thus, Frisen teaches a method wherein determining the location of the third analyte comprises: imaging the second semi-porous material; and correlating the in situ hybridization in the image of the second semi-porous material with an image of the biological sample.
Response to Arguments
Applicant's arguments filed 10/01/2025 do not apply to the new grounds of rejections. See above responses with regard to arguments towards amended claim 157.
Claim 173 is rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (“Frisen”; US Patent App. Pub. No. US 20150344942 A1, Dec. 12, 2015) in view of Schulze et al. (“Schulze”; JP 5596568 B2, Sept. 24, 2014) and Natan et al. (“Natan”, US Application Pub. No. US 2002/0146745 A1, Oct. 10, 2002), as applied to claim 163 above, and further in view of Zlatanova et al. (“Zlatanova”; (2001). Gel-immobilized microarrays of nucleic acids and proteins: production and application for macromolecular research. DNA Arrays: Methods and Protocols, 17-38).
The teachings of Frisen, Schulze and Natan are documented above in the rejection of claims 163-166 under 35 U.S.C. 103. Frisen and Schulze are documented above in the rejection of claims 157, 159, 170, 172 and 176-177 under 35 U.S.C. 103. Claim 173 depends on claim 163, which depends on claim 157. Frisen, Schulze and Natan do not explicitly teach claim 173.
Zlatanova discloses Gel-Immobilized Microarrays of Nucleic Acids and Proteins (Pg. 17, Section 2, Title)
Regarding claim 173, Zlatanova teaches a method wherein “crosslinks the protein to the gel” (Pg. 35, Para. 1; Figure 10). Thus, Zlatanova teaches a method further comprising crosslinking the one or more second analytes to the first semi-porous material, and optionally, crosslinking the one or more third analytes to the second semi-porous material.
Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of spatial detection and analysis of nucleic acid and protein analytes in a tissue sample taught by Frisen, Belgrader, and Schulze to incorporate the method of crosslinking the one or more second analytes by Zlatanova and provide a method for spatially capturing and crosslinking proteins to a semi-porous material. Doing so would for allow for the localization of nucleic acid and/or protein analyte(s) based on a biological sample.
Response to Arguments
Applicant's arguments filed 10/01/2025 do not apply to the new grounds of rejections. See above responses with regard to arguments towards amended claim 157.
Claims 174-175 is rejected under 35 U.S.C. 103 as being unpatentable over Frisen et al. (“Frisen”; US Patent App. Pub. No. US 20150344942 A1, Dec. 12, 2015) in view of Schulze et al. (“Schulze”; JP 5596568 B2, Sept. 24, 2014) and Natan et al. (“Natan”, US Application Pub. No. US 2002/0146745 A1, Oct. 10, 2002), as applied to claim 163 above, and further in view of Herr et al. (“Herr”; US Patent Application Pub No. US 20180217094 A1, Aug. 02, 2018).
The teachings of Frisen, Schulze and Natan are documented above in the rejection of claims 163-166 under 35 U.S.C. 103. Frisen and Schulze are documented above in the rejection of claims 157, 159, 170, 172 and 176-177 under 35 U.S.C. 103. Claims 174 and 175 depend on claim 163, which depend on claim 157. Frisen, Schulze and Natan do not explicitly teach claim 174-175.
Herr discloses isoelectric focusing devices configured for multiplex separation of sample components of interest in a polymeric separation medium are provided. Also provided are methods of using the devices as well as systems and kits that include the devices. The devices, systems and methods find use in a variety of different applications, including diagnostic and validation assays.
Regarding claim 174-175, Herr teaches a method wherein “Following assay completion, gels could be removed (Para. 280) and “protein photocapture to the gel matrix in the gel slide was done using UV light exposure” (Para. 253). Thus, Herr teaches a method further comprising removing the first semi-porous material after the first semi-porous material retains the one or more proteins, and optionally, removing the second semi-porous material after the second semi-porous material retains the one or more third analytes.
Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of spatial detection and analysis of nucleic acid and protein analytes in a tissue sample and a surface treated with semi-porous polyacrylamide as taught by Frisen, Schulze and Natan to incorporate the method of crosslinking the analytes to the gel and removing the gel after assay completion as taught by Herr and provide a method for spatially capturing analytes to one or more semi-porous material(s). Doing so would for allow for the detection and characterization of multiple types of analytes to be spatially localized to a biological sample.
Response to Arguments
Applicant's arguments filed 10/01/2025 do not apply to the new grounds of rejections. See above responses with regard to arguments towards amended claim 157.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 157 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 8 of U.S. Patent No. US 11,926,822 B1 (“U.S. Patent No. US ‘822”; Gohil et al., 10x Genomics, US Patent App No. 17/481810, published March 12, 2024) in view of Frisen et al. (“Frisen”; US Patent App. Pub. No. US 20150344942 A1, Dec. 12, 2015) and Schulze et al. (“Schulze”; JP 5596568 B2, Sept. 24, 2014). Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious the claims of U.S. Patent No. ‘822 in view of Frisen and Schulze.
The claims of U.S. Patent No. US ‘822” are drawn to:
A method for determining a location of an analyte in three-dimensional space in a tissue sample, the method comprising: (a) placing the tissue sample on an array and immobilizing the tissue sample by adding a hydrogel matrix to the tissue sample on the array, wherein the hydrogel matrix comprises a polymer; (b) adding a plurality of spatially-programmed capture probes to the hydrogel matrix, wherein a spatially-programmed capture probe in the plurality of spatially-programmed capture probes comprises: (i) a programmable migration domain that migrates to a z-axis location in the tissue sample; (ii) a detectable moiety; and (iii) a spatially-programmed capture domain that binds to the analyte; (c) migrating the plurality of spatially-programmed capture probes into the hydrogel matrix from a point distal to a surface of the hydrogel matrix; (d) hybridizing the spatially-programmed capture probe of the plurality of the spatially programmed capture probes to the analyte, thereby generating a hybridized spatially-programmed capture probe; (e) detecting a z-axis location of the detectable moiety of the spatially programmed capture probe in the tissue sample, thereby determining the z-axis location of the spatially-programmed capture probe and analyte in the tissue sample; (f) migrating the hybridized spatially-programmed capture probe to the array, wherein the array comprises a plurality of affixed capture probes, wherein an affixed capture probe of the plurality of affixed capture probes comprises a spatial barcode and a capture domain that hybridizes to the hybridized spatially-programmed capture probe; and (g) determining (i) a sequence of the hybridized spatially-programmed capture probe, or a complement thereof, (ii) a sequence of the spatial barcode, or a complement thereof, and (iii) all or part of the sequence of the analyte, or a complement thereof, and using the determined sequences of (i), (ii), and (iii), and the determined z-axis location in (e), to identify the location of the analyte in the three-dimensional space in the tissue sample.
The method of claim 1, wherein the migrating the hybridized spatially-programmed capture probe is performed using active migration, wherein the active migration uses an electric field, a magnetic field, a charged gradient, or any combination thereof.
Thus, the instant invention is made obvious over the U.S. Patent App. ‘822. U.S. Patent No. US ‘822” does not specifically teach one or more analytes. The teachings of Frisen and Schulze are documented above in the rejection of claims 157-162, 164-170, 172 and 176 under 35 U.S.C. 103.
It would have been obvious to someone of ordinary skill in the art to have modified the method of spatial detection and analysis of an analyte in a tissue sample taught by U.S. Patent No. US ‘822” to incorporate the method of one or more analytes as taught by Frisen and Schulze and provide a method for determining a location of one or more analytes in a biological sample. Doing so would for allow for the detection and characterization of multiple types of analytes to be spatially localized to a biological sample.
Response to Arguments
Applicant's arguments filed 10/01/2025 do not apply to the new grounds of rejections. See above responses with regard to arguments towards amended claim 157.
Conclusion of Response to Arguments
In view of the amendments, documented above in this Final Office Action are new grounds of rejections as well as responses to arguments. No claims are in condition for allowance.
Conclusion
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682