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 .
Response to Amendment
The Amendment filed 03/23/2026 has been entered. Claims 1-2, 7-9, 14, 19-20, 24-26, 28, 32, 34, 36, 45, 50, and 66-73 remain pending in the application. New grounds of rejections necessitated by amendments are discussed below.
Claim Rejections - 35 USC § 103
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.
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.
Claims 1-2, 7-8, 19, 24-26, 28, 32, 34, 36, 50, and 66-68 are rejected under 35 U.S.C. 103 as being unpatentable over Bornmann et al. (US 20190039061 A1) in view of Torre-Bueno et al. (US 20030231791 A1) and Hu (US 5939251 A).
Regarding claim 1, Bornmann teaches a method (abstract, paragraph [0002], and Figs. 1-4 teach looking at biological samples on a sample carrier; paragraph [0039] teaches analyzing a sample on a sample carrier), comprising:
(a) providing (i) an adapter (Figs. 4A-4B, teaches hydrophobic region 104 is provided) comprising a top surface (top surface of element 104), a bottom surface (bottom surface of element 104), and a through hole between the top surface and the bottom surface (Figs. 1-4 and paragraph [0054] teaches a through hole, between the top and bottom surfaces of element 104, comprising a region 103) and (ii) a biological sample (paragraph [0002] teaches biological samples; [0039] teaches placing a sample on a sample carrier);
(b) applying the adapter to a substrate (Figs. 2-4 and paragraph and paragraphs [0030]-[0031] teaches a hydrophobic region 104 is produced by a coating of a hydrophobic material to the surface of sample carrier 101, i.e. applying the adapter to a substrate), wherein: the biological sample is immobilized on the substrate (Figs. 1-4 teaches sample 201 located on substrate 101; paragraphs [0006],[0013], teaches a biological sample immobilized on a sample carrier; paragraph [0057] teaches cells are immobilized), such that the through hole of the adapter (Figs. 1-4 and paragraph [0054] teaches a through hole comprising a region 103) surrounds a region of interest in the biological sample immobilized on the substrate (Figs. 1-4 and paragraph [0054] teaches the hydrophobic region 104 surrounds a region 103 where a sample 201 immobilized on the substrate is located, i.e. region of interest in the biological sample) and the bottom surface of the adapter (Figs. 4A-4B, bottom surface of element 104) forms a substantially impervious seal with the substrate (Figs. 4A-4B and paragraphs [0031]-[0032] and [0054] teach a hydrophobic material coated on the surface 102 that contains a sample 201, therefore it is implied that the bottom surface of element 104 forms an impervious seal with sample carrier 101 since the sample is contained within the hydrophobic material), wherein an area of the adapter surrounding the region of interest is hydrophobic (paragraphs [0031]-[0032] and [0054] teach hydrophobic region 104 is a hydrophobic material, therefore, the area of the adapter surrounding the region of interest is hydrophobic); and
wherein the method does not comprise applying a cover to the adapter to enclose the region of interest (paragraph [0039] is silent on a step of applying a cover to enclose the region of interest).
Bornmann fails to teach: the biological sample is immobilized on the substrate prior to the applying the adapter to the substrate; and (c) delivering a hydrophilic composition to cover the region of interest in the biological sample on the substrate, wherein the hydrophilic composition covering the region of interest is contained in the through hole by the substantially impervious seal and the hydrophobic area surrounding the region of interest.
Bornmann teaches a step of placing a sample on a sample carrier (paragraph [0039]) and if an aqueous sample is placed on the sample side of the surface of the sample carrier, the sample collects in the hydrophilic region of the sample carrier, but is pushed away from the hydrophobic edges (paragraph [0032]). Bornmann teaches an aqueous sample is contained in the through hole by the substantially impervious seal and the hydrophobic area surrounding the region of interest (Figs. 4A-4B). Bornmann teaches biological samples can include cells and tissues (paragraph [0012]). Bornmann teaches a microscope can be provided with a fluorescent unit (paragraph [0014]) for fluorescence analysis (paragraph [0042]).
Torre-Bueno teaches a method and apparatus for automated analysis of transmitted and fluorescent labeled biological samples by acquiring images of samples having different staining agents (abstract), wherein the sample can include cells and tissue (paragraph [0057]). Torre-Bueno teaches fluorescent in situ hybridization is known, where a fluorescently labeled probe is added to a tissue sample on a microscope slide for visualization and imaging on a fluorescent microscope (paragraphs [0004]-[0005], [0171]), where FISH has the advantage that the individual cells containing the DNA sequences being tested can be visualized in the context of the tissue (paragraphs [0004],[0171]). Torre-Bueno teaches a sample may be stained or labeled with a first agent and examined by light and fluorescent microscopy, and then stained or labeled with a second agent, and examined by light and fluorescent microscopy (paragraph [0061]). Torre-Bueno teaches assays using FISH are used to determine genetic composition of a virus using fluorescently labeled probes (paragraph [0169]). Torre-Bueno teaches stains include dyes in water (paragraph [0160]), wherein water is interpreted as hydrophilic.
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 Bornmann to incorporate Bornmann’s teachings of fluorescence analysis of an aqueous sample that is placed within a hydrophilic region and pushed away from hydrophobic edges (paragraphs [0012],[0014],[0032],[0042]; Figs. 4A-4B) and the teachings of methods of fluorescent in situ hybridization comprising adding fluorescent stains to a sample for fluorescent analysis of Torre-Bueno (abstract; paragraphs [0004]-[0005],[0057],[0061],[0171]) to provide: (c) delivering a hydrophilic composition (e.g. solution comprising a stain or label) to cover the region of interest in the biological sample on the substrate (e.g. a region of interest of a tissue or cell sample), wherein the hydrophilic composition covering the region of interest is contained in the through hole by the substantially impervious seal and the hydrophobic area surrounding the region of interest. Doing so would have a reasonable expectation of successfully improving visual analysis of target components of individual cells as taught by Torre-Bueno (paragraphs [0004],[0169],[0171]).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. delivering the hydrophilic composition and the hydrophilic composition contained in the through hole) by known methods with no change in their respective functions (i.e. fluorescent analysis of samples that are contained within a hydrophobic region), and the combinations yielded nothing more than predictable results (i.e. delivering the hydrophilic composition and the hydrophilic composition contained in the through hole would yield nothing more than the obvious and predictable result of fluorescent analysis of sample components while containing the aqueous sample within the region for imaging). See MPEP 2143(A).
Modified Bornmann fails to teach: the biological sample is immobilized on the substrate prior to the applying the adapter to the substrate.
Hu teaches an enclosure dam for defining a sealed space between a slide and covering means for containing a mixture of target samples and reagents for carrying out a molecular biological reaction (abstract; Fig. 4). Hu teaches applying the dam to a slide that includes a sample (Fig. 4). Hu teaches it is known for samples to be fixed and mounted on microscopic slides for recognition after treatment (column 1, lines 63-67). Hu teaches the thickness, height, size, and shape defined by the surrounding dam can be controlled, such as automated to be controlled by a computer , where the dam is applied to surround a specimen mounted on the microscope slide (column 5, lines 36-47). Hu teaches depending on the size, shape and configurations of the tissues or cells, the surrounding dam can be flexibly formed to best suit the situations such that the required molecular biological reactions can be optimally performed in a seal space partly defined by the surrounding dam (column 5, lines 47-52).
Since Hu teaches forming a surrounding structure to contain a sample, similar to modified Bornmann, 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 biological sample of modified Bornmann to incorporate the teachings of automated control of creating a dam around a sample mounted on a slide and optimizing the dam based on the size, shape, and configurations of the tissues or cells of Hu (column 5, lines 36-52) and the teachings of mounting samples on a slide for analysis of Hu (column 1, lines 63-67; column 5, lines 36-47) to provide: the biological sample is immobilized on the substrate prior to the applying the adapter to the substrate. Doing so would have a reasonable expectation of successfully allowing for mounting and preparing of a sample on the substrate and optimizing the size and shape of the through hole to best suit the size and shape of the region of interest of a sample as taught by Hu (column 5, lines 47-52).
Regarding claim 2, modified Bornmann fails to teach: wherein the adapter comprises one or more positional markers or fiducial markers on the top surface, on the bottom surface, or within the adapter.
Torre-Bueno teaches digital imaging of a sample (paragraph [0092]), wherein imaging includes orientation matching, automated tasks such as fiducial recognition, and automated recognition of printed matter to be inspected, such as alignment marks (paragraph [0092]).
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 adapter of modified Bornmann to incorporate teachings of digital imaging including orientation matching, fiducial recognition, and recognition of alignment marks of Torre-Bueno (paragraph [0092]) to provide: wherein the adapter comprises one or more positional markers or fiducial markers on the top surface, on the bottom surface, or within the adapter. Doing so would have a reasonable expectation of successfully improving sample orientation and alignment when imaging of the sample in relation to the adapter.
Regarding claim 7, Bornmann further teaches wherein the adapter is composed of polypropylene, polytetrafluoroethylene (PTFE), a silica-based material, or a paraffin coated materials (paragraph [0031] teaches the hydrophobic material comprises polytetrafluoroethylene).
Regarding claim 8, Bornmann further teaches wherein the adapter comprises a hydrophobic coating (paragraphs [0030]-[0031] teach the hydrophobic region comprises a coating of hydrophobic material, i.e. adapter) on an inner surface of the through hole (Figs. 4A-4B, the through hole comprising a region 103 has an inner surface with a hydrophobic coating since the sides of hydrophobic material 104 comprising a coating of hydrophobic material defines inner surfaces of the through hole), or on the top surface of the adapter or a portion thereof surrounding the region of interest (paragraphs [0030]-[0031] and Figs. 4A-4B, the top surface of the hydrophobic region 104 is interpreted as comprising a coating of hydrophobic material since element 104 comprises a coating of hydrophobic material).
Regarding claim 19, Bornmann further teaches wherein the adapter (Figs. 4A-4B, hydrophobic region 104) is not secured to the substrate (sample carrier 101) by a clip, a clamp, or a sample cassette (Figs. 4A-4B shows hydrophobic region 104 is not secured to sample carrier 101 by a clip, clamp, or cassette).
Regarding claim 24, modified Bornmann fails to teach the method of claim 1, comprising selecting the adapter with a pre-configured through hole size or shape according to the size or shape of the region of interest, such that the selected adapter surrounds the region of interest upon application to the substrate.
Hu teaches an enclosure dam for defining a sealed space between a slide and covering means for containing a mixture of target samples and reagents for carrying out a molecular biological reaction (abstract; Fig. 4). Hu teaches applying the dam to a slide that includes a sample (Fig. 4). Hu teaches the thickness, height, size, and shape defined by the surrounding dam can be controlled, such as automated to be controlled by a computer (column 5, lines 36-47). Hu teaches depending on the size, shape and configurations of the tissues or cells, the surrounding dam can be flexibly formed to best suit the situations such that the required molecular biological reactions can be optimally performed in a seal space partly defined by the surrounding dam (column 5, lines 47-52).
Since Hu teaches forming a surrounding structure to contain a sample, similar to modified Bornmann, 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 modified Bornmann to incorporate the teachings of automated control of creating a dam and optimizing the dam based on the size, shape, and configurations of the tissues or cells of Hu (column 5, lines 36-52) to provide: the method of claim 1, comprising selecting the adapter with a pre-configured through hole size or shape according to the size or shape of the region of interest, such that the selected adapter surrounds the region of interest upon application to the substrate. Doing so would have a reasonable expectation of successfully optimizing the size and shape of the through hole to best suit the size and shape of the region of interest of a sample as taught by Hu (column 5, lines 47-52).
Regarding claim 25, modified Bornmann fails to teach the method of claim 1, comprising customizing the size or shape of the through hole according to the size or shape of the region of interest, such that the customized adapter surrounds the region of interest upon application to the substrate.
Hu teaches an enclosure dam for defining a sealed space between a slide and covering means for containing a mixture of target samples and reagents for carrying out a molecular biological reaction (abstract; Fig. 4). Hu teaches applying the dam to a slide that includes a sample (Fig. 4). Hu teaches the thickness, height, size, and shape defined by the surrounding dam can be controlled, such as automated to be controlled by a computer (column 5, lines 36-47). Hu teaches depending on the size, shape and configurations of the tissues or cells, the surrounding dam can be flexibly formed to best suit the situations such that the required molecular biological reactions can be optimally performed in a seal space partly defined by the surrounding dam (column 5, lines 47-52).
Since Hu teaches forming a surrounding structure to contain a sample, similar to modified Bornmann, 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 modified Bornmann to incorporate the teachings of automated control of creating a dam and optimizing the dam based on the size, shape, and configurations of the tissues or cells of Hu (column 5, lines 36-52) to provide: the method of claim 1, comprising customizing the size or shape of the through hole according to the size or shape of the region of interest, such that the customized adapter surrounds the region of interest upon application to the substrate. Doing so would have a reasonable expectation of successfully optimizing the size and shape of the through hole to best suit the size and shape of the region of interest of a sample as taught by Hu (column 5, lines 47-52).
Regarding claim 26, modified Bornmann fails to teach wherein the substrate is a pre-prepared or archived substrate comprising the biological sample immobilized thereon.
Hu teaches an enclosure dam for defining a sealed space between a slide and covering means for containing a mixture of target samples and reagents for carrying out a molecular biological reaction (abstract; Fig. 4). Hu teaches applying the dam to a slide that includes a sample (Fig. 4). Hu teaches it is known for samples to be fixed and mounted on microscopic slides for recognition after treatment (column 1, lines 63-67). Hu teaches the thickness, height, size, and shape defined by the surrounding dam can be controlled, such as automated to be controlled by a computer , where the dam is applied to surround a specimen mounted on the microscope slide (column 5, lines 36-47). Hu teaches depending on the size, shape and configurations of the tissues or cells, the surrounding dam can be flexibly formed to best suit the situations such that the required molecular biological reactions can be optimally performed in a seal space partly defined by the surrounding dam (column 5, lines 47-52).
Since Hu teaches forming a surrounding structure to contain a sample, similar to modified Bornmann, 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 modified Bornmann to incorporate the teachings of automated control of creating a dam around a sample mounted on a slide and optimizing the dam based on the size, shape, and configurations of the tissues or cells of Hu (column 5, lines 36-52) and the teachings of mounting samples on a slide for analysis of Hu (column 1, lines 63-67; column 5, lines 36-47) to provide: wherein the substrate is a pre-prepared or archived substrate comprising the biological sample immobilized thereon. Doing so would have a reasonable expectation of successfully allowing for mounting and preparing of a sample on the substrate and optimizing the size and shape of the through hole to best suit the size and shape of the region of interest of a sample as taught by Hu (column 5, lines 47-52).
Regarding claim 28, modified Bornmann fails to teach wherein the adapter is applied to the substrate according to the location of the biological sample on the substrate or according to the location of the region of interest in the biological sample.
Hu teaches an enclosure dam for defining a sealed space between a slide and covering means for containing a mixture of target samples and reagents for carrying out a molecular biological reaction (abstract; Fig. 4). Hu teaches applying the dam to a slide that includes a sample (Fig. 4), where the dam is applied according to locations of samples or regions of interest on the substrate (Fig. 4). Hu teaches the thickness, height, size, and shape defined by the surrounding dam can be controlled, such as automated to be controlled by a computer (column 5, lines 36-47). Hu teaches depending on the size, shape and configurations of the tissues or cells, the surrounding dam can be flexibly formed to best suit the situations such that the required molecular biological reactions can be optimally performed in a seal space partly defined by the surrounding dam (column 5, lines 47-52).
Since Hu teaches forming a surrounding structure to contain a sample, similar to modified Bornmann, 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 modified Bornmann to incorporate the teachings of automated control of creating a dam according to the location of samples on a substrate and optimizing the dam based on the size, shape, and configurations of the tissues or cells of Hu (column 5, lines 36-52) to provide: wherein the adapter is applied to the substrate according to the location of the biological sample on the substrate or according to the location of the region of interest in the biological sample. Doing so would have a reasonable expectation of successfully optimizing the position, size, and shape of the through hole to best suit the size and shape of the region of interest of a sample as taught by Hu (column 5, lines 47-52).
Regarding claim 32, Bornmann wherein the biological sample is not embedded in a matrix (Figs. 4A-4B, sample 201 is interpreted as not embedded in a matrix).
Regarding claim 34, Bornmann further teaches an opening on the top of the adapter (Figs. 2, 3, and 4A-4B shows an opening on the top surface of element 104, therefore forming a hydrophilic region 103). Modified Bornmann fails to teach the method of claim 1, comprising delivering the hydrophilic composition to the through hole via the opening on the top surface of the adapter.
Bornmann teaches a step of placing a sample on a sample carrier (paragraph [0039]) and if an aqueous sample is placed on the sample side of the surface of the sample carrier, the sample collects in the hydrophilic region of the sample carrier, but is pushed away from the hydrophobic edges (paragraph [0032]). Bornmann teaches an aqueous sample is contained in the through hole by the substantially impervious seal and the hydrophobic area surrounding the region of interest (Figs. 4A-4B). Bornmann teaches biological samples can include cells and tissues (paragraph [0012]). Bornmann teaches a microscope can be provided with a fluorescent unit (paragraph [0014]) for fluorescence analysis (paragraph [0042]).
Torre-Bueno teaches a method and apparatus for automated analysis of transmitted and fluorescent labeled biological samples by acquiring images of samples having different staining agents (abstract), wherein the sample can include cells and tissue (paragraph [0057]). Torre-Bueno teaches fluorescent in situ hybridization is known, where a fluorescently labeled probe is added to a tissue sample on a microscope slide for visualization and imaging on a fluorescent microscope (paragraphs [0004]-[0005], [0171]), where FISH has the advantage that the individual cells containing the DNA sequences being tested can be visualized in the context of the tissue (paragraphs [0004],[0171]). Torre-Bueno teaches a sample may be stained or labeled with a first agent and examined by light and fluorescent microscopy, and then stained or labeled with a second agent, and examined by light and fluorescent microscopy (paragraph [0061]). Torre-Bueno teaches assays using FISH are used to determine genetic composition of a virus using fluorescently labeled probes (paragraph [0169]).
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 modified Bornmann to incorporate Bornmann’s teachings of fluorescence analysis of an aqueous sample that is placed within a hydrophilic region and pushed away from hydrophobic edges (paragraphs [0012],[0014],[0032],[0042]; Figs. 4A-4B) and the teachings of methods of fluorescent in situ hybridization comprising adding fluorescent stains to a sample for fluorescent analysis of Torre-Bueno (abstract; paragraphs [0004]-[0005],[0057],[0061],[0171]) to provide: the method of claim 1, comprising delivering the hydrophilic composition to the through hole via the opening on the top surface of the adapter. Doing so would have a reasonable expectation of successfully allowing for placement of the hydrophilic composition (e.g. a solution of reagents or stains) to the region of interest.
Regarding claim 36, modified Bornmann fails to teach wherein the adapter comprises one or more barcodes.
Torre-Bueno teaches slides are identified with a unique barcode; and upon reading the barcode, the instrument recognizes the slide as part of a control set, and runs the appropriate application (paragraph [0159]).
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 adapter of modified Bornmann to incorporate the teachings of barcodes for slides of Torre-Bueno (paragraph [0159]) to provide: wherein the adapter comprises one or more barcodes. Doing so would have a reasonable expectation of successfully improving sample identification and recognition and automation of sample processing.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. barcodes) by known methods with no change in their respective functions (i.e. providing identification information about a sample), and the combinations yielded nothing more than predictable results (i.e. providing the adapter with one or more barcodes would yield nothing more than the obvious and predictable result of providing identification information about a sample). See MPEP 2143(A).
Regarding claim 50, Bornmann further teaches wherein the method does not comprise applying a cover slip to the adapter to enclose the region of interest (paragraph [0039] is silent on a step of applying a cover slip to the adapter to enclose the region of interest).
Regarding claim 66, Bornmann further teaches wherein the biological sample comprises adherent cells (paragraphs [0012],[0057] teaches cells that adhere, i.e. adherent cells).
Regarding claim 67, Bornmann further teaches wherein the biological sample comprises a tissue sample (paragraph [0012] teaches the sample can include tissue).
Regarding claim 68, modified Bornmann fails to teach: wherein the biological sample is a formalin-fixed and paraffin-embedded (FFPE) sample.
Bornmann teaches samples can included tissues, fixed cells or fixed dead cells (paragraph [0012]).
Torre-Bueno teaches a sample can include tissue, which is prepared by embedding the tissue in paraffin (paragraphs [0058]-[0059]). Torre-Bueno teaches a tissue sample may be a conventionally fixed tissue sample that are fixed by fixing fluids such as formalin (paragraph [0059]).
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 biological sample to incorporate Bornmann’s teachings of fixed samples (paragraph [0012]) and Torre-Bueno’s teachings of paraffin embedded or formalin fixed samples (paragraphs [0058]-[0059]) to provide: wherein the biological sample is a formalin-fixed and paraffin-embedded (FFPE) sample. Doing so would have a reasonable expectation of successfully improving processing and analysis of tissue or cell samples.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. a formalin-fixed and paraffin-embedded (FFPE) sample) by known methods with no change in their respective functions (i.e. analysis of a fixed sample), and the combinations yielded nothing more than predictable results (i.e. providing a formalin-fixed and paraffin-embedded (FFPE) sample would yield nothing more than the obvious and predictable result of enabling proper preparation of a sample for analysis). See MPEP 2143(A).
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Bornmann in view of Torre-Bueno as applied to claim 1 above, and further in view of Yang et al. (US 20030194709 A1).
Regarding claim 9, modified Bornmann fails to teach: wherein the adapter has a thickness between the top surface and the bottom surface of no more than about 0.5 mm, no more than about 0.4 mm, no more than about 0.3 mm, no more than about 0.2 mm, no more than about 0.1 mm, no more than about 90 um, no more than about 80 um, no more than about 70 um, no more than about 60 um, no more than about 50 um, no more than about 40 um, no more than about 30 um, no more than about 20 um, or no more than about 10 um.
Yang teaches a method of making and using an assay chip having a hydrophilic region bounded by a hydrophobic region, which allows the user to deposit reagents in an aqueous medium on the hydrophilic region while the hydrophobic region prevents the reagents from flowing away from the hydrophilic region; hence, the reagents can be isolated in the hydrophilic region to minimize any loss or dilution of the reagents (abstract). Yang teaches a hydrophobic layer (paragraph [0029]; Figs. 1,3G-3H), wherein the hydrophobic layer is a 1 um thick CYTOP, an amorphous fluorocarbon polymer from Asahi Glass Company (with hydrophobic properties similar to polytetrafluoroethylene (paragraph [0036]).
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 thickness of the adapter of modified Bornmann to incorporate the teachings of a 1 um thick hydrophobic layer of Yang (abstract; paragraphs [0029],[0036]; Figs. 1, 3G-3H) to provide: wherein the adapter has a thickness between the top surface and the bottom surface of no more than about 0.5 mm, no more than about 0.4 mm, no more than about 0.3 mm, no more than about 0.2 mm, no more than about 0.1 mm, no more than about 90 um, no more than about 80 um, no more than about 70 um, no more than about 60 um, no more than about 50 um, no more than about 40 um, no more than about 30 um, no more than about 20 um, or no more than about 10 um. Doing so would have a reasonable expectation of successfully improving prevention of an aqueous solution from flowing away from a hydrophilic region, therefore improving isolation of the hydrophilic region to minimize any loss or dilution of the aqueous solution as discussed by Yang (abstract).
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Bornmann in view of Torre-Bueno as applied to claim 1 above, and further in view of Lauber et al. (US 20210349061 A1; effectively filed 05/05/2020).
Regarding claim 14, modified Bornmann fails to teach the method of claim 1, comprising modifying the area of the adapter surrounding the region of interest to be hydrophobic or more hydrophobic than prior to the modifying.
Lauber teaches the use of vapor deposition coated flow paths for improved sample analysis (abstract). Lauber teaches at least a portion of a wetted surface can be coated to tailor hydrophobicity (paragraph [0047]). Lauber teaches the deposited coatings can be used to adjust the hydrophobicity of internal surfaces of the fluidic flow path that come into contact with a fluid (paragraph [0055]). Lauber depositing a coating to adjust the contact angle or hydrophobicity of the coating, wherein a second coating can be additionally deposited to tailor the flow path (paragraph [0057]). Lauber teaches precursor materials are infiltrated into the flow path of the component to deposit one or more coatings along the wetted surfaces to adjust the hydrophobicity (paragraph [0059]).
Since Lauber teaches hydrophobic coatings for sample analysis, similar to Bornmann, 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 modified Bornmann to incorporate the teachings of providing additional hydrophobic coatings to tailor the hydrophobicity of surfaces of Lauber (paragraphs [0047],[0055],[0057],[0059]) to provide: the method of claim 1, comprising modifying the area of the adapter surrounding the region of interest to be hydrophobic or more hydrophobic than prior to the modifying. Doing so would have a reasonable expectation of successfully improving tailoring of the contact angle or hydrophobicity of the area surrounding the region of interest as taught by Lauber (paragraphs [0047],[0055],[0057],[0059]).
Claims 20 and 69-73 are rejected under 35 U.S.C. 103 as being unpatentable over Bornmann in view of Torre-Bueno as applied to claim 1 above, and further in view of Daugharthy et al. (WO 2021168326 A1; cited in the IDS filed 11/23/2022).
Regarding claim 20, while Bornmann teaches a hydrophobic region can be a plastic material (paragraph [0031]), modified Bornmann fails to teach the method of claim 1, wherein:
(ii) the bottom surface of the adapter is adhesive; or
(ii) the bottom surface of the adapter is bonded to the substrate by an adhesive material; or
(iii) the top surface of the adapter is adhesive.
Daugharthy teaches a sample slide for sample analysis (abstract). Daugharthy teaches in some embodiments, at least a portion of the support is covered by a removable mask or boundary attached to the support using an adhesive (paragraph [0008]), the removable mask is impermeable to formaldehydes, waxes, polyolefins, alcohols or glycols (paragraph [0008]), and the removable boundary forming a well (paragraph [0008]). Daugharthy teaches the removable boundary is attached to the surface of the support with an adhesive, wherein the adhesive forms a seal between the removable boundary and a surface of the support (paragraph [0008]). Daugharthy teaches the mask can be a non-sticking mask, a film, an adhesive coating or soft material, and can be attached to the support using an adhesive (paragraph [0098]).
Since Daugharthy teaches a boundary that forms a well on a support, similar to modified Bornmann, 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 modified Bornmann to incorporate the teachings of masks and boundaries attached to the surface of a support with an adhesive to form a well that is sealed between the boundary and support of Daugharthy (paragraphs [0008],[0098]) and the teachings of a hydrophobic plastic material provided on a support of Bornmann (paragraph [0031]; Figs. 1-4) to provide: wherein: (ii) the bottom surface of the adapter is adhesive; or (ii) the bottom surface of the adapter is bonded to the substrate by an adhesive material; or (iii) the top surface of the adapter is adhesive. Doing so would have a reasonable expectation of successfully improving sealing and fixing of the adapter to the substrate while ensuring a seal between the adapter and substrate as taught by Daugharthy (paragraphs [0008],[0098]).
Regarding claim 69, while Bornmann teaches a hydrophobic region can be a plastic material (paragraph [0031]), modified Bornmann fails to teach: wherein the adapter is an adhesive tape.
Daugharthy teaches a sample slide for sample analysis (abstract). Daugharthy teaches in some embodiments, at least a portion of the support is covered by a removable mask or boundary attached to the support using an adhesive (paragraph [0008]), the removable mask is impermeable to formaldehydes, waxes, polyolefins, alcohols or glycols (paragraph [0008]), and the removable boundary forming a well (paragraph [0008]). Daugharthy teaches the removable boundary is attached to the surface of the support with an adhesive, wherein the adhesive forms a seal between the removable boundary and a surface of the support (paragraph [0008]). Daugharthy teaches the mask can be a non-sticking mask, a film, an adhesive coating or soft material, and can be attached to the support using an adhesive (paragraph [0098]).
Since Daugharthy teaches a boundary that forms a well on a support, similar to modified Bornmann, 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 modified Bornmann to incorporate the teachings of masks and boundaries attached to the surface of a support with an adhesive to form a well that is sealed between the boundary and support of Daugharthy (paragraphs [0008],[0098]) and the teachings of a hydrophobic plastic material provided on a support of Bornmann (paragraph [0031]; Figs. 1-4) to provide: wherein the adapter is an adhesive tape (e.g. the adapter including an adhesive surface). Doing so would have a reasonable expectation of successfully improving sealing and fixing of the adapter to the substrate while ensuring a seal between the adapter and substrate as taught by Daugharthy (paragraphs [0008],[0098]).
Regarding claim 70, modified Bornmann fails to teach: wherein the adhesive tape has a thickness between the top surface and the bottom surface of about 20 um to about 100 um.
Daugharthy teaches a sample slide for sample analysis (abstract). Daugharthy teaches in some embodiments, at least a portion of the support is covered by a removable mask or boundary attached to the support using an adhesive (paragraph [0008]), the removable mask is impermeable to formaldehydes, waxes, polyolefins, alcohols or glycols (paragraph [0008]), and the removable boundary forming a well (paragraph [0008]). Daugharthy teaches the removable boundary is attached to the surface of the support with an adhesive, wherein the adhesive forms a seal between the removable boundary and a surface of the support (paragraph [0008]). Daugharthy teaches the mask can be a non-sticking mask, a film, an adhesive coating or soft material, and can be attached to the support using an adhesive (paragraph [0098]). Daugharthy teaches a thin gel coating may provide strong adhesion and may have a thickness at least about 100 um (paragraph [0088]). Daugharthy teaches an adhesive mask can function as a protective film for a sample and can function as a spacer to prepare a coating with a thickness of at least about 50 microns (paragraph [0091]).
Since Daugharthy teaches a thickness of an adhesive being about 100 um (paragraph [0088]), which overlaps with the claimed range of about 20 um to about 100 um, 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 adhesive tape of modified Bornmann to provide wherein the adhesive tape has a thickness between the top surface and the bottom surface of about 20 um to about 100 um. I.e., it would have been prima facia obvious to have selected the overlapping portion of the range (i.e. about 100 um) from the taught range of at least about 100 um (Daugharthy, paragraph [0088]) (In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); see MPEP 2144.05 (I)).
Regarding claim 71, modified Bornmann fails to teach: the method of claim 1, further comprising: (d) allowing a reaction between a molecule at a location in the region of interest in the biological sample and one or more agents in the hydrophilic composition; (e) dipping an objective of a microscope in the hydrophilic composition; (f) detecting a signal associated with the reaction or a product thereof at the location, thereby detecting the molecule in situ in the biological sample.
Bornmann teaches a step of placing a sample on a sample carrier (paragraph [0039]) and if an aqueous sample is placed on the sample side of the surface of the sample carrier, the sample collects in the hydrophilic region of the sample carrier, but is pushed away from the hydrophobic edges (paragraph [0032]). Bornmann teaches an aqueous sample is contained in the through hole by the substantially impervious seal and the hydrophobic area surrounding the region of interest (Figs. 4A-4B). Bornmann teaches biological samples can include cells and tissues (paragraph [0012]). Bornmann teaches a microscope can be provided with a fluorescent unit (paragraph [0014]) for fluorescence analysis (paragraph [0042]).
Torre-Bueno teaches a method and apparatus for automated analysis of transmitted and fluorescent labeled biological samples by acquiring images of samples having different staining agents (abstract), wherein the sample can include cells and tissue (paragraph [0057]). Torre-Bueno teaches fluorescent in situ hybridization is known, where a fluorescently labeled probe is added to a tissue sample on a microscope slide for visualization and imaging on a fluorescent microscope (paragraphs [0004]-[0005], [0171]), where FISH has the advantage that the individual cells containing the DNA sequences being tested can be visualized in the context of the tissue (paragraphs [0004],[0171]). Torre-Bueno teaches a sample may be stained or labeled with a first agent and examined by light and fluorescent microscopy, and then stained or labeled with a second agent, and examined by light and fluorescent microscopy (paragraph [0061]). Torre-Bueno teaches assays using FISH are used to determine genetic composition of a virus using fluorescently labeled probes (paragraph [0169]). Torre-Bueno teaches one method of sample preparation is to react a sample with an agent that specifically interacts with a molecule in the sample and detecting the reaction (paragraphs [0170]-[0171])
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 Bornmann to incorporate Bornmann’s teachings of fluorescence analysis of an aqueous sample that is placed within a hydrophilic region and pushed away from hydrophobic edges (paragraphs [0012],[0014],[0032],[0042]; Figs. 4A-4B) and the teachings of methods of fluorescent in situ hybridization comprising adding fluorescent stains to a sample to allow for a reaction to occur for fluorescent analysis of Torre-Bueno (abstract; paragraphs [0004]-[0005],[0057],[0061],[0170]-[0171]) to provide: the method of claim 34, further comprising: (d) allowing a reaction between a molecule at a location in the region of interest in the biological sample and one or more agents in the hydrophilic composition; and (e) detecting a signal associated with the reaction or a product thereof at the location, thereby detecting the molecule in situ in the biological sample. Doing so would have a reasonable expectation of successfully improving visual analysis of target components of individual cells as taught by Torre-Bueno (paragraphs [0004],[0169]-[0171]).
Modified Bornmann fails to teach: (e) dipping an objective of a microscope in the hydrophilic composition.
Daugharthy teaches a sample slide for sample analysis (abstract). Daugharthy teaches in some embodiments, at least a portion of the support is covered by a removable mask or boundary attached to the support using an adhesive (paragraph [0008]), the removable mask is impermeable to formaldehydes, waxes, polyolefins, alcohols or glycols (paragraph [0008]), and the removable boundary forming a well (paragraph [0008]). Daugharthy teaches the system includes objective lenses for imaging, such as a single water dipping objective lens, which provides for higher image quality by eliminating the refractive index mismatch occurring at the interface between two media with distinct refractive indexes, such as an air-water interface or water-glass interface (paragraph [00145]). Daugharthy teaches wetting of the objective lens including dipping the lens into a medium (paragraph [00147]).
Since Daugharthy teaches an imaging system and a boundary that forms a well on a support, similar to modified Bornmann, 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 modified Bornmann to incorporate the teachings of imaging systems including objective lenses that are dipped into a medium of Daugharthy (paragraphs [00145],[00147]) to provide: (e) dipping an objective of a microscope in the hydrophilic composition. Doing so would have a reasonable expectation of successfully improving image quality by eliminating the refractive index mismatch occurring at the interface between two media with distinct refractive indexes as taught by Daugharthy (paragraphs [00145],[00147]).
Regarding claim 72, modified Bornmann fails to teach: wherein the biological sample comprises a rolling circle amplification (RCA) product at a location in the region of interest, wherein the hydrophilic composition comprises a probe and a detectably labeled oligonucleotide, and wherein the probe hybridizes to the RCA product at the location, and the detectably labeled oligonucleotide hybridizes to the probe.
Bornmann teaches a step of placing a sample on a sample carrier (paragraph [0039]) and if an aqueous sample is placed on the sample side of the surface of the sample carrier, the sample collects in the hydrophilic region of the sample carrier, but is pushed away from the hydrophobic edges (paragraph [0032]). Bornmann teaches an aqueous sample is contained in the through hole by the substantially impervious seal and the hydrophobic area surrounding the region of interest (Figs. 4A-4B). Bornmann teaches biological samples can include cells and tissues (paragraph [0012]). Bornmann teaches a microscope can be provided with a fluorescent unit (paragraph [0014]) for fluorescence analysis (paragraph [0042]).
Torre-Bueno teaches fluorescent in situ hybridization is known, where a fluorescently labeled probe is added to a tissue sample on a microscope slide for visualization and imaging on a fluorescent microscope (paragraphs [0004]-[0005], [0171]), where FISH has the advantage that the individual cells containing the DNA sequences being tested can be visualized in the context of the tissue (paragraphs [0004],[0171]). Torre-Bueno teaches detecting the presence of these cellular abnormalities, including immunophenotyping with monoclonal antibodies, in situ hybridization using nucleic acid probes, and DNA amplification using the polymerase chain reaction (paragraph [0051]). Torre-Bueno teaches a sample may be stained or labeled with a first agent and examined by light and fluorescent microscopy, and then stained or labeled with a second agent, and examined by light and fluorescent microscopy (paragraph [0061]). Torre-Bueno teaches assays used to detect, prognoses, diagnose, or monitor various conditions, diseases, and disorders, or monitor the treatment thereof; and an agent can be detectably labeled such that the agent is detectable when bound or hybridized to its target marker or ligand (paragraph [0062]). Torre-Bueno teaches testing for Her2 gene amplification using a stain for the gene product and fluorescent imaging (paragraph [0156]). Torre-Bueno teaches assays using FISH are used to determine genetic composition of a virus using fluorescently labeled oligonucleotide probes (paragraph [0169]). Torre-Bueno teaches stains include dyes in water (paragraph [0160]), wherein water is interpreted as hydrophilic.
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 modified Bornmann to incorporate Bornmann’s teachings of fluorescence analysis of an aqueous sample that is placed within a hydrophilic region and pushed away from hydrophobic edges (paragraphs [0012],[0014],[0032],[0042]; Figs. 4A-4B) and the teachings of methods of fluorescent in situ hybridization comprising adding fluorescently labeled oligonucleotide probes to a sample and for fluorescent analysis of DNA or gene amplification products of Torre-Bueno (abstract; paragraphs [0004]-[0005],[0051], [0057],[0061],[0062], [0156], [0169], [0171]) to provide: wherein the biological sample comprises an amplification product at a location in the region of interest, wherein the hydrophilic composition comprises a probe and a detectably labeled oligonucleotide, and wherein the probe hybridizes to the amplification product at the location, and the detectably labeled oligonucleotide hybridizes to the probe. Doing so would have a reasonable expectation of successfully improving detecting presence of cellular abnormalities, and improving visual analysis of target components of individual cells such as amplification products of a sample as taught by Torre-Bueno (paragraphs [0004], [0051], [0061]-[0062][0156], [0169],[0171]). Additionally, doing so would have a reasonable expectation of successfully improving detecting, prognoses, diagnosis, or monitoring of various conditions, diseases, disorders or treatments thereof.
Modified Bornmann fails to teach: wherein the biological sample comprises a rolling circle amplification (RCA) product at a location in the region of interest, and wherein the probe hybridizes to the RCA product at the location.
Daugharthy teaches a sample slide for sample analysis (abstract). Daugharthy teaches in some embodiments, at least a portion of the support is covered by a removable mask or boundary attached to the support using an adhesive (paragraph [0008]), the removable mask is impermeable to formaldehydes, waxes, polyolefins, alcohols or glycols (paragraph [0008]), and the removable boundary forming a well (paragraph [0008]). Daugharthy teaches a procedure including detection by hybridizing detection probes with amplification products (paragraph [00111]). Daugharthy teaches immobilization of target molecules, such as derivatives of target molecules including amplicons, i.e. rolling circle amplification product (paragraph [00166]; note that the instant specification, paragraph [0088] states amplicons are rolling circle amplification products). Daugharthy teaches amplification methods can produce a targeted library of amplicons (paragraph [00173]).
Since Daugharthy teaches an imaging system and a boundary that forms a well on a support, similar to modified Bornmann, 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 and amplification product of modified Bornmann to incorporate the teachings of sample analysis including hybridizing detection probes with amplification products and immobilizing target molecules such as amplicons of Daugharthy (paragraphs [00111],[00166],[00173]) to provide: wherein the biological sample comprises a rolling circle amplification (RCA) product at a location in the region of interest, and wherein the probe hybridizes to the RCA product at the location. Doing so would have a reasonable expectation of successfully improving specificity and flexibility of detection of desired derivatives of target molecules, such as RCA products.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. hybridization of a RCA product with a labeled oligonucleotide) by known methods with no change in their respective functions (i.e. detection of a desired target molecule), and the combinations yielded nothing more than predictable results (i.e. providing the sample with the RCA product and the probe hybridizing to the RCA product would yield nothing more than the obvious and predictable result of improving specificity and flexibility of detection of desired derivatives of target molecules, such as RCA products). See MPEP 2143(A).
Regarding claim 73, modified Bornmann fails to teach: the method of claim 72, further comprising dipping an objective of a microscope in the hydrophilic composition and detecting the detectably labeled oligonucleotide hybridized to the probe which is hybridized to the RCA product at the location, thereby detecting the RCA product in situ in the biological sample.
Torre-Bueno teaches fluorescent in situ hybridization is known, where a fluorescently labeled probe is added to a tissue sample on a microscope slide for visualization and imaging on a fluorescent microscope (paragraphs [0004]-[0005], [0171]), where FISH has the advantage that the individual cells containing the DNA sequences being tested can be visualized in the context of the tissue (paragraphs [0004],[0171]). Torre-Bueno teaches a sample may be stained or labeled with a first agent and examined by light and fluorescent microscopy, and then stained or labeled with a second agent, and examined by light and fluorescent microscopy (paragraph [0061]). Torre-Bueno teaches assays using FISH are used to determine genetic composition of a virus using fluorescently labeled probes (paragraph [0169]). Torre-Bueno teaches one method of sample preparation is to react a sample with an agent that specifically interacts with a molecule in the sample and detecting the reaction (paragraphs [0170]-[0171])
Daugharthy teaches a procedure including detection by hybridizing detection probes with amplification products (paragraph [00111]). Daugharthy teaches immobilization of target molecules, such as derivatives of target molecules including amplicons, i.e. rolling circle amplification product (paragraph [00166]; note that the instant specification, paragraph [0088] states amplicons are rolling circle amplification products). Daugharthy teaches amplification methods can produce a targeted library of amplicons (paragraph [00173]). Daugharthy teaches the system includes objective lenses for imaging, such as a single water dipping objective lens, which provides for higher image quality by eliminating the refractive index mismatch occurring at the interface between two media with distinct refractive indexes, such as an air-water interface or water-glass interface (paragraph [00145]). Daugharthy teaches wetting of the objective lens including dipping the lens into a medium (paragraph [00147]).
Since Daugharthy teaches an imaging system and a boundary that forms a well on a support, similar to modified Bornmann, 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 modified Bornmann to incorporate the teachings of methods of fluorescent in situ hybridization comprising adding fluorescent stains to a sample to allow for a reaction to occur for fluorescent analysis of Torre-Bueno (abstract; paragraphs [0004]-[0005],[0057],[0061],[0170]-[0171]), the teachings of imaging systems including objective lenses that are dipped into a medium of Daugharthy (paragraphs [00145],[00147]), and the teachings of sample analysis including hybridizing detection probes with amplification products and immobilizing target molecules such as amplicons of Daugharthy (paragraphs [00111],[00166],[00173]) to provide: the method of claim 72, further comprising dipping an objective of a microscope in the hydrophilic composition and detecting the detectably labeled oligonucleotide hybridized to the probe which is hybridized to the RCA product at the location, thereby detecting the RCA product in situ in the biological sample. Doing so would have a reasonable expectation of successfully improving image quality by eliminating the refractive index mismatch occurring at the interface between two media with distinct refractive indexes as taught by Daugharthy (paragraphs [00145],[00147]).
Claim 45 is rejected under 35 U.S.C. 103 as being unpatentable over Bornmann in view of Torre-Bueno as applied to claim 34 above, and further in view of Guo et al. (US 20220026433 A1; cited in the IDS filed 11/23/2022; effectively filed 11/15/2018).
Regarding claim 45, modified Bornmann fails to teach the method of claim 34, further comprising:
(d) allowing a reaction between a molecule at a location in the region of interest in the biological sample and one or more agents in the hydrophilic composition,
(e) detecting a signal associated with the reaction or a product thereof at the location, thereby detecting the molecule in situ in the biological sample;
(f) removing the hydrophilic composition after the reaction from the through hole through the opening on the top surface; and
(g) delivering another hydrophilic composition to cover the region of interest.
Bornmann teaches a step of placing a sample on a sample carrier (paragraph [0039]) and if an aqueous sample is placed on the sample side of the surface of the sample carrier, the sample collects in the hydrophilic region of the sample carrier, but is pushed away from the hydrophobic edges (paragraph [0032]). Bornmann teaches an aqueous sample is contained in the through hole by the substantially impervious seal and the hydrophobic area surrounding the region of interest (Figs. 4A-4B). Bornmann teaches biological samples can include cells and tissues (paragraph [0012]). Bornmann teaches a microscope can be provided with a fluorescent unit (paragraph [0014]) for fluorescence analysis (paragraph [0042]).
Torre-Bueno teaches a method and apparatus for automated analysis of transmitted and fluorescent labeled biological samples by acquiring images of samples having different staining agents (abstract), wherein the sample can include cells and tissue (paragraph [0057]). Torre-Bueno teaches fluorescent in situ hybridization is known, where a fluorescently labeled probe is added to a tissue sample on a microscope slide for visualization and imaging on a fluorescent microscope (paragraphs [0004]-[0005], [0171]), where FISH has the advantage that the individual cells containing the DNA sequences being tested can be visualized in the context of the tissue (paragraphs [0004],[0171]). Torre-Bueno teaches a sample may be stained or labeled with a first agent and examined by light and fluorescent microscopy, and then stained or labeled with a second agent, and examined by light and fluorescent microscopy (paragraph [0061]). Torre-Bueno teaches assays using FISH are used to determine genetic composition of a virus using fluorescently labeled probes (paragraph [0169]). Torre-Bueno teaches one method of sample preparation is to react a sample with an agent that specifically interacts with a molecule in the sample and detecting the reaction (paragraphs [0170]-[0171])
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 Bornmann to incorporate Bornmann’s teachings of fluorescence analysis of an aqueous sample that is placed within a hydrophilic region and pushed away from hydrophobic edges (paragraphs [0012],[0014],[0032],[0042]; Figs. 4A-4B) and the teachings of methods of fluorescent in situ hybridization comprising adding fluorescent stains to a sample to allow for a reaction to occur for fluorescent analysis of Torre-Bueno (abstract; paragraphs [0004]-[0005],[0057],[0061],[0170]-[0171]) to provide: the method of claim 34, further comprising: (d) allowing a reaction between a molecule at a location in the region of interest in the biological sample and one or more agents in the hydrophilic composition; and (e) detecting a signal associated with the reaction or a product thereof at the location, thereby detecting the molecule in situ in the biological sample. Doing so would have a reasonable expectation of successfully improving visual analysis of target components of individual cells as taught by Torre-Bueno (paragraphs [0004],[0169]-[0171]).
Modified Bornmann fails to teach: (f) removing the hydrophilic composition after the reaction from the through hole through the opening on the top surface; and (g) delivering another hydrophilic composition to cover the region of interest.
Torre-Bueno teaches staining methods of applying a reagent to a sample and then rinsing the sample (paragraphs [0159],[0161]). Torre-Bueno teaches conventional preparation of slides for examination provides repeatable and known placement of the sample on the slide (paragraph [0087]). Torre-Bueno teaches a sample may be stained or labeled with a first agent and examined by light and fluorescent microscopy, and then stained or labeled with a second agent, and examined by light and fluorescent microscopy (paragraph [0061]).
Guo teaches methods for multiplexed in situ analysis of biomolecules in a tissue, which allows for investigation of different cell compositions and their spatial organizations in tissues through consecutive cycles of probe hybridization, fluorescence imaging, and signal removal (abstract). Guo teaches the method provides low-cost, high-throughput, comprehensive, and highly sensitive and high-quality methods for in situ molecular profiling capable of in situ analysis of target biomolecules (e.g., proteins, nucleic acids) in intact tissues with single-molecule sensitivity (paragraph [0004]). Guo teaches the method comprises contacting a tissue with HRP-conjugated targeting agents to bind to the target biomolecule, imaging the cell to detect a fluorescent signal, removing the fluorophore, and consecutively repeating the contacting, imaging, and removing steps, each time with a new plurality of HRP-conjugate targeting agents for each subsequent cycle, wherein each utilized plurality differs from each other utilized plurality due to being configured to specifically bind or hybridize to a different target biomolecule (paragraph [0005]). Guo teaches method can further comprise washing to remove unhybridized targeting agents and non-specifically hybridized targeting agents following each second contacting step (paragraph [0005]).
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 modified Bornmann to incorporate Torre-Bueno’s teachings of applying a reagent to a sample and then rinsing the sample (paragraphs [0159],[0161]), repeatable steps for preparation of slides (paragraph [0087]), and repeating steps of staining and imaging with different agents (paragraph [0061]) and Guo’s teachings of repeated cycles of reacting a sample with an agent, detecting fluorescent signals, removing a fluorophore (paragraph [0005]) and washing to remove agents following each contacting step (paragraph [0005]) to provide: (f) removing the hydrophilic composition after the reaction from the through hole through the opening on the top surface; and (g) delivering another hydrophilic composition to cover the region of interest. Doing so would have a reasonable expectation of successfully improving in situ analysis of biomolecules in tissues utilizing different agents (i.e. hydrophilic compositions) to provide a low-cost, high-throughput, comprehensive, and highly sensitive and high-quality methods for in situ molecular profiling capable of in situ analysis of target biomolecules (e.g., proteins, nucleic acids) in intact tissues with single-molecule sensitivity (Guo, paragraph [0004]).
Response to Arguments
Applicant’s arguments, see page 7, filed 03/23/2026, with respect to the rejection under 35 U.S.C. 112(b) have been fully considered and are persuasive. The rejection under 35 U.S.C. 112(b) of 10/29/2025 has been withdrawn.
Applicant’s arguments, see pages 8-12, filed 03/23/2026, with respect to the rejection(s) of claims 1, 2, 7, 8, 19, 32, 34-36, and 50 under 35 U.S.C. 103, specifically regarding claim 1 and the limitations of “the biological sample is immobilized on the substrate prior to the applying…”, have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Bornmann et al. (US 20190039061 A1) in view of Torre-Bueno et al. (US 20030231791 A1) and Hu (US 5939251 A).
Applicant's arguments, see pages 8-10, filed 03/23/2026, with respect to the rejection of claim 1 under 35 U.S.C. 103, specifically regarding the limitations of “an adapter…” and “delivering a hydrophilic composition…” have been fully considered but they are not persuasive.
In response to applicant’s argument that Bornmann and Torre-Bueno do not teach or suggest providing an adapter comprising a top surface, a bottom surface, and a through hole, and applying the adapter to a substrate since Bornmann’s hydrophobic region 104 is not the claimed adapter (Remarks, page 9), the examiner disagrees.
Bornmann teaches: (a) providing (i) an adapter (Figs. 4A-4B, hydrophobic region 104) comprising a top surface (top surface of element 104), a bottom surface (bottom surface of element 104), and a through hole between the top surface and the bottom surface (Figs. 1-4 and paragraph [0054] teaches a through hole comprising a region 103) and (ii) a biological sample (paragraph [0002] teaches biological samples; [0039] teaches placing a sample on a sample carrier); (b) applying the adapter to a substrate (Figs. 2-4 and paragraph and paragraphs [0030]-[0031] teaches a hydrophobic region 104 is produced by a coating of a hydrophobic material to the surface of sample carrier 101, i.e. applying the adapter to a substrate). The BRI of “adapter” includes the interpretation of Bornmann’s hydrophobic region 104 structure.
In response to applicant’s argument that Bornmann and Torre-Bueno do not teach or suggest delivering a hydrophilic composition to the region of interest in the biological sample on the substrate and the modification would get rid of the sample of Bornmann and defeat its purpose (Remarks, page 10), the examiner disagrees.
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, Bornmann provides teachings of fluorescence analysis of an aqueous sample that is placed within a hydrophilic region and pushed away from hydrophobic edges (paragraphs [0012],[0014],[0032],[0042]; Figs. 4A-4B). Bornmann also provides teachings of sample including cells and tissue and fluorescent analysis of the sample (paragraphs [0012],[0014],[0042]).
Torre-Bueno provides teachings of a method and apparatus for automated analysis of transmitted and fluorescent labeled biological samples by acquiring images of samples having different staining agents (abstract), wherein the sample can include cells and tissue (paragraph [0057]); which is similar to the purpose of Bornmann. Torre-Bueno provides teachings of methods of fluorescent in situ hybridization comprising adding fluorescent stains to a sample for fluorescent analysis (abstract; paragraphs [0004]-[0005],[0057],[0061],[0171]), wherein stains include dyes in water (paragraph [0160]), wherein water is interpreted as hydrophilic. Torre-Bueno provides motivation of adding fluorescently labeled probes to a sample in order to visualize and image the sample (paragraphs [0004]-[0005], [0061], [0171]).
It would have been obvious to one of ordinary skill in the art to have modified the method of Bornmann to incorporate Bornmann’s teachings of fluorescence analysis of an aqueous sample that is placed within a hydrophilic region and pushed away from hydrophobic edges (paragraphs [0012],[0014],[0032],[0042]; Figs. 4A-4B) and the teachings of methods of fluorescent in situ hybridization comprising adding fluorescent stains to a sample for fluorescent analysis of Torre-Bueno (abstract; paragraphs [0004]-[0005],[0057],[0061],[0171]) to provide: (c) delivering a hydrophilic composition (e.g. solution comprising a stain or label) to cover the region of interest in the biological sample on the substrate (e.g. a region of interest of a tissue or cell sample), wherein the hydrophilic composition covering the region of interest is contained in the through hole by the substantially impervious seal and the hydrophobic area surrounding the region of interest. Doing so would have a reasonable expectation of successfully improving visual analysis of target components of individual cells as taught by Torre-Bueno (paragraphs [0004],[0169],[0171]).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. delivering the hydrophilic composition and the hydrophilic composition contained in the through hole) by known methods with no change in their respective functions (i.e. fluorescent analysis of samples that are contained within a hydrophobic region), and the combinations yielded nothing more than predictable results (i.e. delivering the hydrophilic composition and the hydrophilic composition contained in the through hole would yield nothing more than the obvious and predictable result of fluorescent analysis of sample components while containing the aqueous sample within the region for imaging). See MPEP 2143(A).
Therefore, 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 to have combined Bornmann with Torre-Bueno to arrive at the claimed limitations of “delivering…”.
In response to applicant’s arguments regarding dependent claims 9, 14, 20, 24-26, 28, and 45 (Remarks, pages 12-14), the examiner disagrees for the same reasons as discussed above regarding claim 1.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Chen et al. (US 20230013775 A1, effectively filed 07/13/2021; Note that Chen a common assignee with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2)) teaches methods for preparing biological samples for in situ analysis (abstract). Chen teaches methods of applying an adapter to the biological sample, where the adapter comprises one or more positioning markers and/or fiducial markers (paragraphs [0094]-[0095]).
Chen et al. (US 20160274008 A1) teaches a microscope slide for analyzing a tissue sample (abstract). Chen teaches an embodiment (Fig. 15) comprising an adapter (layer 1242) attached to a substrate (1212), wherein the adapter has a through hole (1250) surrounding a tissue sample (15).
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to HENRY H NGUYEN whose telephone number is (571)272-2338. The examiner can normally be reached M-F 7:30A-5:00P.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maris Kessel can be reached at (571) 270-7698. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/HENRY H NGUYEN/Primary Examiner, Art Unit 1758
Prosecution Insights