DETAILED ACTION
Notice of AIA Status
The present application, filed on 5/20/24, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Claims 1-20 are pending.
Claims 1-2, 4-5, 7-13 and 16-20 are rejected.
Claims 3, 6 and 14-15 are objected to.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 10, 12 and 18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Sims (US20210254143).
With respect to claim 1, Sims (US20210254143) teaches a single-cell observation and sequencing system (system in [0004]) comprising:
a platform (microwell device in [0117]) defining one or more cellular wells (plurality of microwells in [0004]), each cellular well configured to capture a single cell of a target of interest (see [0074], which recites “the device described herein is a solid state device that allows for single cell isolation”) (see [0049], which recites “single cell lysates (green) are trapped in individual microwells);
a sequencing element (a plurality of dual barcode oligonucleotide capture beads in [0028]) comprising one or more barcoded solid phase polymerase chain reaction (PCR) probes (a first plurality of oligonucleotide sequences in [0028], which recites “a plurality of dual barcode oligonucleotide capture beads, each capture bead comprising a first and a second plurality of oligonucleotide sequences separately attached to an outer surface of the capture bead, wherein the first plurality is an oligonucleotide sequence comprising: (a) a PCR handle attached to each capture bead, wherein the PCR handle is identical in each oligonucleotide sequence on each capture bead; (b) a first barcode attached to the PCR handle, wherein the first barcode is identical for all oligonucleotide sequences attached to the same capture bead, and wherein the first barcode differs for each capture bead; (c) a unique molecular identifier (UMI) of length 6 to 16 nucleotides (nt) attached to the barcode, wherein the UMI may differ between oligonucleotide sequences on the capture bead, wherein the UMI may differ between different capture beads”);
wherein each cellular well is configured to align with a unique species of one of said barcoded solid phase PCR probes (regarding “align”, the barcoded solid phase PCR probes are attached to a respective co-localized capture bead residing in the same well as the cell as described in [0144], which recites “cells in different microwells to be captured by their respective co-localized beads…. linking between each cell's imaging phenotype and optical barcode sequence of the bead that resides in the same well with the cell”) (regarding “unique species”, Sims discloses that the first barcode is identical for the oligonucleotide sequences attached to a particular capture bead and differs for each capture bead, see [0028], which recites “the first barcode differs for each capture bead”); and
wherein each cellular well is further configured to allow for cellular observation (see [0144], which recites “full single-cell RNA sequencing and imaging work flow … a microwell array device is filled … single-cell suspension is then loaded into the device. The device is scanned under a microscope to obtain imaging phenotype and location of each individual cell in the device”) (see [0166], which recites “the microscope automatically scanned and imaged the entire microwell array and identifies the beads in each microwell”) (see [0204], which recites “the cell-loaded device was then scanned”), cellular lysing (see [0207], which recites “the cell/bead loaded device was then connected to the system for the automated cell lysis”), and genetic sequencing therein (see [0144], which recites “full single-cell RNA sequencing”) to provide barcoded complementary DNA (cDNA) sequences (see [0144], which recites “barcoding of cDNA”) with mapped cellular observations for each cell within said one or more cellular wells (see [0144], which recites “the look-up table generated in the bead synthesis step are then used to further link each cell's imaging phenotype to sequencing barcode sequence of the bead that resided in the same well with the cell and the associated mRNA expression profile”).
With respect to claim 10, Sims teaches the system of claim 1, wherein the system is scalable such that said cellular observations are mapped to said barcoded cDNA sequences massively in parallel (see [0002], which recites “The instant disclosure addresses this issue by combining a highly scalable microfluidic platform for single cell RNA-Seq and imaging with associated methodologies that allow for the association of sequence barcodes for inexpensive pooled library preparation with optical barcodes in devices described herein”) (see [0003], which recites “The devices, systems, and methods described herein address the scalability problem of parallel preparation of low-input single cell libraries for RNA sequencing”) (see also [0144], which recites “ full single-cell RNA sequencing and imaging work flow … Optically barcoded mRNA capture beads are then loaded into the device. …, and optical demultiplexing are performed on the device which allows the linking between each cell's imaging phenotype and optical barcode sequence of the bead that resides in the same well with the cell. After the optical demultiplexing step, all beads are extracted from the device. Tube-based PCR reactions are used to pre-amplify bead-bound cDNA molecules. In the case where the number of cells in the device is greater than the optical barcoding capacity enabled by the current 4096 unique optical sequences, the microwell array is cut into multiple pieces before the beads were extracted and processed in separate tubes in parallel”).
With respect to claim 12, Sims (US20210254143) teaches a method of single-cell observation and sequencing (see claim 46, which recites “method for single cell RNA capture and sequencing library preparation, for linking sequence data acquired from the library to cell imaging data”) comprising:
providing a platform (microwell device in [0117]) defining one or more cellular wells (plurality of microwells in [0004]), each cellular well configured to capture a single cell of a target of interest (see [0074], which recites “the device described herein is a solid state device that allows for single cell isolation”) (see [0049], which recites “single cell lysates (green) are trapped in individual microwells);
providing a sequencing element (a plurality of dual barcode oligonucleotide capture beads in [0028]) comprising a barcoded solid phase PCR probe (a first plurality of oligonucleotide sequences in [0028], which recites “a plurality of dual barcode oligonucleotide capture beads, each capture bead comprising a first and a second plurality of oligonucleotide sequences separately attached to an outer surface of the capture bead, wherein the first plurality is an oligonucleotide sequence comprising: (a) a PCR handle attached to each capture bead, wherein the PCR handle is identical in each oligonucleotide sequence on each capture bead; (b) a first barcode attached to the PCR handle, wherein the first barcode is identical for all oligonucleotide sequences attached to the same capture bead, and wherein the first barcode differs for each capture bead; (c) a unique molecular identifier (UMI) of length 6 to 16 nucleotides (nt) attached to the barcode, wherein the UMI may differ between oligonucleotide sequences on the capture bead, wherein the UMI may differ between different capture beads”); wherein
each cellular well is configured to align with a unique species of said barcoded solid phase PCR probe (regarding “align”, the barcoded solid phase PCR probes are attached to a respective co-localized capture bead residing in the same well as the cell as described in [0144], which recites “cells in different microwells to be captured by their respective co-localized beads…. linking between each cell's imaging phenotype and optical barcode sequence of the bead that resides in the same well with the cell”) (regarding “unique species”, Sims discloses that the first barcode is identical for the oligonucleotide sequences attached to a particular capture bead and differs for each capture bead, see [0028], which recites “the first barcode differs for each capture bead”);
capturing individual cells of a target of interest within said one or more cellular wells (see [0046] which recites “Cells are first deposited in the microwell array”), one single cell of said target of interest per each cellular well (see [0021], which recites “introducing at least one cell into a microwell”)(see also [0131], which recites “cells are loaded in individual microwells randomly, according to Poisson statistics, such that the majority of cell-containing wells contain one cell”);
recording cellular observation data in association with each said single cell of said target of interest within each cellular well (see [0144], which recites “the device is scanned under a microscope to obtain imaging phenotype and location of each individual cell in the device”);
lysing each said single cell of said target of interest within each cellular well (see [0144], which recites “lysis buffer and oil are flowed into the device sequentially to trigger cell lysis”);
sequencing genetic material of said lysed cell within each cellular well, creating barcoded cDNA sequences (see [0144] which recites “full single-cell RNA sequencing and imaging work flow … Lysis buffer and oil are flowed into the device sequentially to trigger cell lysis and physically isolate the microwells from each other allowing mRNA from cells in different microwells to be captured by their respective co-localized beads. After the mRNA capture step, captured mRNA molecules are reverse transcribed which coverts mRNA into double-stranded DNA-RNA duplex resulting in the barcoding of cDNA. …The amplified cDNA copies are released into the liquid phase and further amplified into sequencing library”); and
mapping cellular observations for each cell of said target of interest within said one or more cellular wells to said barcoded cDNA sequences (see [0144], which recites “the look-up table generated in the bead synthesis step are then used to further link each cell's imaging phenotype to sequencing barcode sequence of the bead that resided in the same well with the cell and the associated mRNA expression profile”).
With respect to claim 18, Sims teaches the method of claim 12, wherein said target of interest comprises cancer cells, cells associated with autoimmune diseases, or cells associated with allergies (see [0108], which recites “cells analyzed are cancer cells”); and said cellular observations are selected from the group consisting of: interactions with drugs, interactions with proteins, interactions with other cells, interactions with biological materials, binding kinetics, affinity, and combinations thereof (see [0003] which recites “systems, and methods described herein allow for parallel RNA profiling of individual cells in a device that is compatible with short term cell culture, drug stimulation experiments, and high-content fluorescence imaging”).
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 2 and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Daridon (US20160236195) in view of Fowler (US20130295602).
With respect to claim 2, Sims teaches the system of claim 1.
Sims fails to teach one or more cellular traps; and
wherein each cellular trap is aligned with one of said one or more cellular wells.
In the analogous art of fluidic devices, Daridon (US20160236195) teaches one or more cellular traps (trap 266 in [0360]); and
wherein each cellular trap (trap 266) is aligned with one of one or more cellular wells (capture chamber 270 in [0360]) and is configured to trap said single cell of a target of interest (see [0362], which recites “trapped cells in chamber 270”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the system disclosed by Sims by incorporating the one or more cellular traps as disclosed by Daridon with a reasonable expectation of success for the benefit of precise positioning and retention of a single cell for observation in real time (see [0337] of Daridon, which recites “cell analyses that benefit from or require the precise positioning and retention of a single cell or a small group of cells. In particular, positioned and retained cells may be treated and observed in real time”).
Sims in view of Daridon fails to teach the cellular trap is configured to bind to said single cell of a target of interest.
In the analogous art of fluidic devices, Fowler (US20130295602) teaches one or more cellular traps (a capture compartment in [0011]) configured to bind to said single cell of a target of interest (see [0011], which recites “a capture compartment; and/or a binding partner covering a discrete region of the capture compartment, where the discrete portion is sized so that only a single cell binds to the discrete region”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the system disclosed by Sims in view of Daridon by configuring the one or more cellular traps to bind to said single cell of a target of interest as disclosed by Fowler with a reasonable expectation of success for the benefit of selectively capturing and retaining an individual cell at the predetermined region for subsequent observation and processing.
With respect to claim 13, Sims teaches the method of claim 12.
Sims fails to teach providing one or more cellular traps, wherein each cellular trap is aligned with one of said one or more cellular wells and is configured to bind to said single cell of a target of interest.
In the analogous art of fluidic devices, Daridon (US20160236195) teaches providing one or more cellular traps (trap 266 in [0360]); and
wherein each cellular trap (trap 266) is aligned with one of one or more cellular wells (capture chamber 270 in [0360]) and is configured to trap said single cell of a target of interest (see [0362], which recites “trapped cells in chamber 270”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method disclosed by Sims by incorporating the one or more cellular traps as disclosed by Daridon with a reasonable expectation of success for the benefit of precise positioning and retention of a single cell for observation in real time (see [0337] of Daridon, which recites “cell analyses that benefit from or require the precise positioning and retention of a single cell or a small group of cells. In particular, positioned and retained cells may be treated and observed in real time”).
Sims in view of Daridon fails to teach the cellular trap is configured to bind to said single cell of a target of interest.
In the analogous art of fluidic devices, Fowler (US20130295602) teaches one or more cellular traps (a capture compartment in [0011]) is configured to bind to said single cell of a target of interest (see [0011], which recites “a capture compartment; and/or a binding partner covering a discrete region of the capture compartment, where the discrete portion is sized so that only a single cell binds to the discrete region”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method disclosed by Sims in view of Daridon by configuring the one or more cellular traps to bind to said single cell of a target of interest as disclosed by Fowler with a reasonable expectation of success for the benefit of selectively capturing and retaining an individual cell at the predetermined region for subsequent observation and processing.
Claims 4 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Vision (US20030148284).
With respect to claim 4, Sims teaches the system of claim 1, wherein:
said sequencing element (plurality of dual barcode oligonucleotide capture beads) further comprises:
a shared primer sequence (PCR handle in [0029]);
a molecular barcode (first barcode in [0030]); and
an adapter sequence (oligo(dT) in [0032]).
Sims fails to teach a molecular spacer.
In the analogous art of analytical devices, Vision (US20030148284) teaches a molecular spacer (see [0041], which recites “ linking agent includes a spacer between the amino modifier and the oligonucleotide solid phase primer. Spacer molecules are used to maximize the sensitivity and efficiency of the detection assay”) (see also [0077], which recites “5′ HEG Spacer”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the system disclosed by Sims by incorporating the molecular spacer (5′ HEG Spacer) as disclosed by Vision with a reasonable expectation of success for the benefit of maximizing sensitivity and efficiency of a detection assay (see [0041] of Vision, which recites “spacer molecules are used to maximize the sensitivity and efficiency of the detection assay”).
With respect to claim 7, Sims in view of Vision teaches the system of claim 4, wherein:
said sequencing element (plurality of dual barcode oligonucleotide capture beads) further comprises a unique molecular identifier (UMI) site (unique molecular identifier (UMI) in [0031] of Sims) positioned downstream of said shared primer sequence (PCR handle) and upstream of said adapter sequence (Oligo(dT) (see Figs 15B of Sims).
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Vision (US20030148284) in view of Peter (US20090036664).
With respect to claim 5, Sims in view of Vision teaches the system of claim 4.
Sims in view of Vision fails to teach or reasonably suggest that said sequencing element further comprises first and second potential cleavage sites positioned downstream of said molecular spacer and upstream of said shared primer sequence.
In the analogous art of analytical methods and systems, Peter (US20090036664) teaches a sequencing element (oligonucleotide in [0037]) further comprises first and second potential cleavage sites (see [0037], which recites “An oligonucleotide of a complex mixture can include one, or more than one cleavage sites. …, the oligonucleotide comprises two, … cleavage site(s). A cleavage site can separate at least two different subsequences on the same oligonucleotide. Each oligonucleotide and/or subsequence can be used as a primer or probe. In one step, each oligonucleotide can be cleaved from a substrate and optionally, within the sequence of the oligonucleotide at one or more cleavage sites. When more than one cleavage sequences is present, each cleavage sequence can be the same or different. In an embodiment, when more than one cleavage sequence is present, the cleavage sequences are all the same…. Primers or probes can be utilized in assays such as FISH, M-FISH, PCR, Southern blotting”) (see [0038], which recites “photocleavable moiety is linked to the oligonucleotide sequence by a spacer or linker”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the system disclosed by Sims in view of Vision by incorporating the first and second potential cleavage sites as disclosed by Peter with the first and second potential cleavage sites positioned downstream of said molecular spacer and upstream of said shared primer sequence with a reasonable expectation of success for the benefit of enabling selective cleavage and release, and subsequent processing of, the primer and/or probe.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Daridon (US20160236195) in view of Fowler (US20130295602) in view of Sing (US20150147821).
With respect to claim 8, Sims in view of Daridon in view of Fowler teaches the system of claim 2.
Sims in view of Daridon in view of Fowler fails to teach that each cellular trap is configured so as to allow for testing said single cell of said target of interest for affinity data using one or more magnetic field.
In the analogous art of analytical systems, Sing (US20150147821) teaches allowing for testing a single cell (cell 222 in [0028]) of a target of interest (see [0028], which recites “the cell 222 may be fixed on a cell substrate 224”) for affinity data (see [0029], which recites “quantification of the binding affinity can also be performed using label-based modalities to determine the binding constant”) using one or more magnetic field (magnetic field in [0038], which recites “Systems for measuring the binding affinity of different compositions are also provided. Such systems generally include a magnetic field source configured to apply a rotating magnetic field to magnetic beads in contact with a substrate”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify each cellular trap as disclosed by Sims in view of Daridon in view of Fowler so as to allow for a single cell of a target of interest to be tested for affinity data using one or more magnetic field as disclosed by Sing with a reasonable expectation of success for the benefit of detecting and quantifying binding affinity between different compositions (see [0026] of Sing, which recites “allow for detection and quantification of the binding affinity between different compositions”).
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Daridon (US20160236195) in view of Fowler (US20130295602) in view of Fontaine (US20110171746) in view of Casagrande (US20030022370).
With respect to claim 9, Sims in view of Daridon in view of Fowler teaches the system of claim 2, further comprising a light source (laser light source in [0143] of Sims and light source 2012 in [0602] of Daridon).
Sims in view of Daridon in view of Fowler fails to teach that each cellular trap further comprises a light source configured so as to allow for testing said single cell of said target of interest for affinity data with plasmin resonance.
In the analogous art of analytical systems, Fontaine (US20110171746) teaches a light source (light source 10 in [0076]) configured so as to allow for testing said single cell of said target of interest for affinity data with plasmin resonance (see [0070], which recites “cell-based receptor/ligand interactions, …, and antibody and small molecule affinity analysis. Various SPR sensors”) (see [0033]-[0034]), which recites “a surface plasmon resonance (SPR) sensor system comprising: … a light source”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify each cellular trap as disclosed by Sims in view of Daridon in view of Fowler by incorporating the light source configured so as to allow for testing said single cell of said target of interest for affinity data with plasmin resonance as disclosed by Fontaine with a reasonable expectation of success for the benefit of providing label-free measurement of cell-based receptor/ligand interactions and affinity (see [0109] of Fontaine).
Sims in view of Daridon in view of Fowler in view of Fontaine fails to teach that each cellular trap is configured so as to allow for removal of surrounding cells using one or more magnetic field.
In the analogous art of analytical systems, Casagrande (US20030022370) teaches allowing for removal of surrounding cells using one or more magnetic field (see [0068], which recites “the present invention's ability to immobilize and/or array cells allows the device to be used for filtration or enrichment of the cell-containing fluid for a particular cell-type. For example, this may be accomplished by negative selection of cells associated with magnetic material. In this method, a cellular subset of a cell containing fluid is purified by removing all other cell types from the fluid by using a bioaffinity ligand that is specific for all cell types other than the desired cellular subset. An advantage of this technique is that members of the desired cellular subset are not directly contacted. In another example, a desired subset of cells is positively selected by immobilization and/or arraying on the substrate”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify each cellular trap as disclosed by Sims in view of Daridon in view of Fowler in view of Fontaine by configuring so as to allow for removal of surrounding cells using one or more magnetic field as disclosed by Casagrande with a reasonable expectation of success for the benefit of isolating a desired cell from undesired cells (see [0068] of Casagrande).
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Xiong (US20210396647).
With respect to claim 11, Sims teaches the system of claim 1, further comprising: a microscope (microscope in [0166]).
Sims fails to teach a lensless microscope configured to allow a user to view all of said one or more cellular wells at once.
In the analogous art of analytical systems, Xiong (US20210396647) teaches a lensless microscope configured to allow a user to view all of one or more cellular wells at once (see [0007], which recites “Lens-free holographic microscopy (LFHM) can be used to image objects such as viruses and cells, as well as non-biological structures. It provides an ultra-large field-of-view (>20 mm2) with sub-micron resolution, which are key enablers of high dynamic range and extreme multiplexing. Furthermore, LFHM is amendable to compact and cost-effective field-portable devices”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the system disclosed by Sims by incorporating the lensless microscope as disclosed by Xiong with a reasonable expectation of success for the benefit of enabling high dynamic range and extreme multiplexing compactly and cost effectively (see [0007], which recites “Lens-free holographic microscopy (LFHM) can be used to image objects such as viruses and cells, as well as non-biological structures. It provides an ultra-large field-of-view (>20 mm2) with sub-micron resolution, which are key enablers of high dynamic range and extreme multiplexing. Furthermore, LFHM is amendable to compact and cost-effective field-portable devices”).
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Daridon (US20160236195) in view of Fowler (US20130295602) in view of Fontaine (US20110171746).
With respect to claim 16, Sims in view of Daridon in view of Fowler teaches the method of claim 13 further comprising a light source (laser light source in [0143] of Sims and light source 2012 in [0602] of Daridon).
Sims in view of Daridon in view of Fowler fails to teach applying one or more light source to each single cell of said target of interest within said one or more cellular wells to test for affinity data with plasmin resonance; and calculating binding kinetics.
In the analogous art of analytical systems, Fontaine (US20110171746) teaches applying one or more light source (light source 10 in [0076]) to each single cell of said target of interest within said one or more cellular wells to test for affinity data with plasmin resonance (see [0070], which recites “cell-based receptor/ligand interactions, …, and antibody and small molecule affinity analysis. Various SPR sensors”) (see [0033]-[0034]), which recites “a surface plasmon resonance (SPR) sensor system comprising: … a light source”) (see [0143], which recites “The disclosed DRCA cell assay system uses a sensor chip SPR system to monitor and characterize, in real-time, modulator-induced dynamic cellular events at different penetration depths. Confluent cells are selected to cover the bottom of the gold coated surface of the wells”); and calculating binding kinetics (see [0121], which recites “measure the kinetic interaction or the end-point readouts using optical sensors such as the DRCA instrument”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method disclosed by Sims in view of Daridon in view of Fowler by incorporating applying one or more light source as disclosed by Fontaine with a reasonable expectation of success for the benefit of providing label-free measurement of cell-based receptor/ligand interactions and affinity (see [0109], of Fontaine).
Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of DuVall (WO2020264387).
With respect to claim 17, Sims teaches the method of claim 12, further comprising:
mapping said cellular observations to said barcoded cDNA sequences massively in parallel (see [0002]-[0003]) and [0144]).
Sims fails to teach storing said massively parallel barcoded cDNA sequences and mapped cellular observations to a cellular database.
In the analogous art of analytical methods and systems, DuVall (WO2020264387) teaches storing barcoded cDNA sequences and mapped cellular observations to a cellular database (memory 122 and controller 124 in Fig 1B) (see claim 6, which recites “receiving, for each cell identifying optical barcode, nucleic acid sequencing data; and storing a data association between the nucleic acid sequencing data, the cell identifying optical barcode, and the first image associated with the cell identifying optical barcode”) (see pages 11-12, which recite “the controller 124 is programmed for causing the system 100 to automate the SCOPESeq process as described below with reference to Figures 6A-6B. For example, the controller 124 can be programmed to store a record for each microwell in the array 130 and to associate, with each microwell record, one or more images of the microwell and identifying features of the microwell contents such as a phenotypic information of the cell and optical barcode readout (e.g., a fluorescent signal) associated with a microbead residing in the microwell in the presence of the complementary optical hybridization probe”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method disclosed by Sims by incorporating storing barcoded cDNA sequences and mapped cellular observations to a cellular database as disclosed by DuVall with a reasonable expectation of success for the benefit of preserving and retrieving the correspondence between each cell’s phenotype/image and the associated sequencing information.
Claim 19 is rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Glanville (WO2022217116A1).
With respect to claim 19, Sims teaches the method of claim 12.
Sims fails to teach said target of interest comprises venom from a species or subspecies of interest in development of fully humanized antivenom.
In the analogous art of analytical devices, Glanville (WO2022217116A1) teaches a target of interest comprises venom from a species or subspecies of interest (see [0004], which recites “snake venom from more than one species of snake”) in development of fully humanized antivenom (see [0004], which recites “broadly-neutralizing, fully human universal antivenom antibodies and cocktails of antibodies that exhibit(s) vastly superior properties than those currently available. Reference to an antibody herein may be interchanged with an antigen-binding fragment. Disclosed are an antivenom antibody and an antibody cocktail capable of neutralizing venom from multiple snake species with reduced potential for negative side effects”) (see also [0295], which recites “the technology described herein enabled the generation of an immune library using unique Next Generation Sequencing (NGS) to guide amplification and tracking of antibody variable domain repertoires from blood draws before and 28 days post venom immunization of the male subject, followed by deep sequencing and antibody phage display, enabling downstream venom binders to be traced back to the source blood draw”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method as disclosed by Sims such that the target of interest comprises venom from a species or subspecies of interest in development of fully humanized antivenom as disclosed by Glanville with a reasonable expectation of success for the benefit of identifying and characterizing antibodies for neutralizing venom toxins from medically relevant species.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Sims (US20210254143) in view of Juncker (US20200319173).
With respect to claim 20, Sims teaches method of claim 12.
Sims fails to teach that said method is utilized to minimize cross-reactivity.
In the analogous art of analytical methods, Juncker (US20200319173) teaches a method is utilized to minimize cross-reactivity (see [0015], which recites “cross-reactivity between reagents in multiplexed assays is minimized or eliminated by minimizing or eliminating interactions between non-cognate affinity binders”) (see also [0009] which recites “Cross-reactivity also hinders other types of multiplexed assays”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method disclosed by Sims such that the method is utilized to minimize cross-reactivity as disclosed by Juncker with a reasonable expectation of success for the benefit of improving specificity of multiplexed analysis by reducing undesired interactions between non-cognate affinity binders (see [0015] of Juncker, which recites “cross-reactivity between reagents in multiplexed assays is minimized or eliminated by minimizing or eliminating interactions between non-cognate affinity binders”) (see also [0009] of Juncker, which recites “cross-reactivity also hinders other types of multiplexed assays”).
Allowable Subject Matter
Claims 3, 6 and 14-15 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
With respect to claim 3, the cited prior fails to teach that each cellular trap comprises a microfluidic valve configured to open and close over a respective center hole via a microfluidic pump.
With respect to claim 6, the cited prior art fails to teach or reasonably suggest that each said solid phase PCR probe further comprises a run ID segment; and said first potential cleavage site comprises a cleavage site on said run ID segment allowing for reusability of said solid phase PCR probe.
With respect to claim 14, the cited prior art fails to teach each cellular trap comprises a microfluidic valve configured to open and close over a respective center hole, the method further comprising:
for each cellular well, engaging a microfluidic pump to open said microfluidic valve and allow said single cell of said target of interest through said cellular trap and into said cellular well.
With respect to claim 15, the cited prior art fails to teach or reasonably suggest applying one or more micro electromagnets to each single cell of said target of interest within said one or more cellular wells; and calculating binding kinetics.
Citation of Relevant Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure: With respect to claim 1, Vigneault (US20190025304) teaches a single-cell observation and sequencing system (composition in the abstract) comprising:
a platform (microtiter plate in [0339]) defining one or more cellular wells (see [0339], which recites “a well of a microtiter plate”), each cellular well (the scope of the claims includes one cellular well) configured to capture a single cell of a target of interest (see [0032], which recites “each vessel of the plurality of vessels comprises a single cell … the vessel is a well”);
a sequencing element (solid support in [0032]) comprising one or more barcoded solid phase polynucleotide polymerase chain reaction (PCR) probes (template vessel barcoded polynucleotide in [0032], which recites “the template vessel barcoded polynucleotide is bound to a solid support”) (see also [0034], which recites “amplifying a template vessel barcoded polynucleotide”) (see also [0229], which recites “oligonucleotides can be amplified and amplified products of the reaction can be recovered from the vessels. Amplified products can be PCR enriched to add next-generation sequencing (NGS) tags”);
wherein each cellular well is configured to align with a unique species of one of said barcoded solid phase polymerase (see [0020], which recites “the vessel barcode sequence of a vessel barcoded polynucleotide or amplicon thereof in a first vessel of the plurality of vessels is a different than the vessel barcode sequence of a vessel barcoded polynucleotide or amplicon thereof in a second vessel of the plurality of vessels”) (see also [0228], which recites “a polynucleotide harboring a vessel barcode can also be introduced during formation of the vessels. These vessel barcoded polynucleotides can carry degenerate barcodes such that each oligonucleotide containing a vessel barcode contains a unique identity code corresponding to the vessel they are in”); and
wherein each cellular well is further configured to allow (the broadest reasonably interpretation for ‘configured to allow for’ is ‘capable of permitting’) for cellular observation (see [0422]-[0424]), cellular lysing (see [0018], which recites “lysing the single cell … the lysing is after the single cell is isolated in the vessel”) and genetic sequencing (see [0007], which recites “sequencing polynucleotide molecules from the vessels”) (see also [0229] and [0232]) therein to provide barcoded complementary DNA (cDNA) sequences (see [0423], which recites “mRNA were reverse transcribed to cDNA”) with mapped cellular observations for each cell within said one or more cellular wells (see [0425], which recites “next generation sequencing, the dual barcoding strategy allows clustering of sequence reads into both their molecules and cells of origin”).
Conclusion
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/JONATHAN BORTOLI/Examiner, Art Unit 1797
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