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 .
DETAILED ACTION
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Status of Claims
Claims 14-16, 18-27 and 29-31 are currently pending. Claims 14, 16, 18-27 and 29-31 have been amended by Applicants’ amendment filed 06-09-2026. Claims 17 and 28 have been canceled by Applicants’ amendment filed 06-09-2026. No claims have been added by Applicants’ amendment filed 06-09-2026.
A complete reply to the final rejection must include cancellation of nonelected claims or other appropriate action (37 CFR 1.144) See MPEP § 821.01.
Therefore, claims 14-16, 18-27 and 29-31 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed July 27, 2023, is a 35 U.S.C. 371 national stage filing of International Application PCT/CN2021/141391, filed December 25, 2021, which claims the benefit of Chinese Patent Application CN202011568787.3, filed December 25, 2020.
Acknowledgment is made of applicant's claim for foreign priority based on Chinese Patent Application CN202011568787.3, filed in China on December 25, 2020.
Should applicant desire to obtain the benefit of foreign priority under 35 U.S.C. 119(a)-(d) prior to declaration of an interference, a certified English translation of the foreign application must be submitted in reply to this action. 37 CFR 41.154(b) and 41.202(e).
Failure to provide a certified translation may result in no benefit being accorded for the non-English application.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed June 9, 2026 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection
not specifically addressed below are herein withdrawn.
Claim Rejections - 35 USC § 101
The rejection of claims 14-31 is withdrawn under 35 U.S.C. 101 because the claims are directed to neither a “process” nor a “machine,” but rather embraces or overlaps two different statutory classes of invention set forth in 35 U.S.C. 101 which is drafted so as to set forth the statutory classes of invention in the alternative only. Id. at 1551 due to Applicant’s amendment to the claims, filed June 9, 2026.
In view of the withdrawn rejection, Applicant’s arguments are rendered moot.
Claim Rejections - 35 USC § 102
The rejection of claims 14-31 is withdrawn under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Yin et al. (hereinafter “Yin”) (US Patent No. 11649485, issued May 16, 2023; WO2020123305, filed December 6, 2019; effective filing date January 6, 2019) as evidenced by Fan et al. (hereinafter “Fan”) (US Patent Application Publication 20210095331, published April 1, 2021; filed September 29, 2020; effective filing date September 30, 2019).
Yin does not specifically exemplify parallel microfluidic channels.
In view of the withdrawn rejection, Applicant’s arguments are rendered moot.
Maintained Objections/Rejections
Claim Interpretation: the term “one kind of first barcode nucleic acid” in claim 14 is interpreted to refer to any “kind” of first barcode nucleic acid (e.g., <10 nucleotides, >8 nucleotides, DNA, RNA, synthetic, random, cell-specific, origin-specific, etc.).
The term “a chemical bonding means” in claim 14 is interpreted to fall under 35 USC 112(f) as a means-plus-function.
The terms “a first direction” and “a second direction” in claim 14 can refer to any direction including the same direction, opposite directions, parallel directions, east, north, parallel, etc.
The term “joining the second barcode nucleic acid to the first barcode nucleic acid” is interpreted to refer to the joining the second barcode nucleic acid to the first barcode nucleic acid either directly (e.g., hybridization, etc.) or indirectly through some other component (e.g., the surface, a target nucleic acid, the tissue, a linker/spacer, etc.).
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1, 4, 5, 7, 26, 27, 32, 41 and 42 is maintained under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claims 14 and 16 are indefinite for the recitation of the term “the nucleic acid” such as recited in claim 14, line 13. There is insufficient antecedent basis for the term “the nucleic acid” in the claim because claim 14, lines 6 and 8-9 recites the term “a first set of barcode nucleic acids” and “a plurality of first barcode nucleic acids.”
Claims 14, 19, 22, 23 and 25 are indefinite for the recitation of the terms “has” and/or “having” such as recited in claim 14, lines 11 and 20 because the transitional phase “has” is unclear as to whether the term ‘comprises’ a different barcode sequence, ‘consists of’ a different barcode sequence, ‘consists essentially of’ a different barcode sequence, or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
The rejection of claims 14 and 19 is maintained, and claim 24 is newly rejected as indefinite for the recitation of the term “the surface” such as recited in claim 14, lines 15, 25, 33 and 35. There is insufficient antecedent basis for the term “the surface” in the claim.
Claim 14 is indefinite for the recitation of the term “a joining reaction” such as recited in claim 14, line 24 because the term “a joining reaction” is unclear. There are no chemical reactions called “joining reactions”, such that it is unclear whether a bond is formed and/or what reactions are encompassed by the term “a joining reaction” including whether the reaction involves ligation, annealing, condensation, covalent bond formation, non-covalent bond formation, etc. and, thus, the metes and bounds of the claim cannot be determined.
Claim 14 is indefinite for the recitation of the term “intersect the plurality of second barcode strips” such as recited in claim 14, lines 26-27 because it is unclear how applying first barcodes to form a first barcode strip, and applying second barcodes to form a second barcode strip, which form an array of dots are recited to “intersect.” Moreover, claim 14, line 35 recites a plurality of microfluidic channels that are in parallel, such that it is unclear how the barcode strips (e.g., separate spots forming an array) “intersect” and, thus, the metes and bounds of the claim cannot be determined.
Claim 14 is indefinite for the recitation of the term “the tissue” such as recited in claim 14, line 30. There is insufficient antecedent basis for the term “the tissue” in the claim because claim 14, line 3 recites the term “a biological tissue sample.” The Examiner suggests that Applicant amend the claim to recite, for example, “cells in the biological tissue sample.”
Claim 14 is indefinite for the recitation of the term “each microfluidic channel” such as recited in claim 14, line 38. There is insufficient antecedent basis for the term “each microfluidic channel” in the claim because claim 14, lines 33-34 recites the term “a plurality of microfluidic channels.” The Examiner suggests that Applicant amend the claim to recite, for example, “each channel of the plurality of microfluidic channels.”
Claim 15 and 21 are indefinite for the recitation of the term “mRNA” such as recited in claim 15, line 2 because claim 15 depends from claim 14, wherein claim 14 does not recite the presence of mRNA and, thus, the metes and bounds of the claim cannot be determined. The Examiner suggests that Applicant amend the claim to recite, for example, wherein the probes of the array are capable of recognizing and binding nucleic acids in the biological tissue sample.”
Claim 16 is indefinite for the recitation of the term “further analyze the nucleic acids” such as recited in claim 16, line 3 because claim 16 depends from instant claim 14, wherein claim 14 does not recite a step of analyzing nucleic acids and, thus, the metes and bounds of the claim cannot be determined.
Claim 18 is indefinite for the recitation of the term “amplification reaction” such as recited in claim 18, lines 3-4 because claim 18 depends from instant claim 14, wherein claim 14 does not recite an amplification reaction and, thus, the metes and bounds of the claim cannot be determined.
Claim 20 is indefinite for the recitation of the term “a first probe fragment” such as recited in claim 20, lines 2-3 because it is unclear whether the term refers to the first barcode nucleic acid, a portion of the first barcode nucleic acid, to an additional barcode in the first barcode nucleic acid, the a portion of an additional first barcode, or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claims 20 and 24 are indefinite for the recitation of the term “a target nucleic acid” such as recited in claim 20, line 3 because claim 20 depends from instant claim 14, wherein claim 14 does not recite the presence of target nucleic acids and, thus, the metes and bounds of the claim cannot be determined.
Claim 20 is indefinite for the recitation of the term “a second barcode fragment” such as recited in claim 20, line 4 because the purpose of the second barcode fragment is unclear. More specifically, it is unclear whether the second barcode nucleic acid comprises a second barcode fragment; or whether the first probe fragment recognizes and binds a second barcode fragment and, thus, the metes and bounds of the claim cannot be determined.
Claim 21 is indefinite for the recitation of the term “a second probe fragment” such as recited in claim 20, lines 2-3 because it is unclear whether the term refers to the second barcode nucleic acid, a portion of the second barcode nucleic acid, to an additional barcode in the second barcode nucleic acid, the a portion of an additional second barcode, or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claim 23 is indefinite for the recitation of the terms “single-stranded linking nucleic acid” and “a sequence at each end of the single-stranded linking nucleic acid” in claim 23, lines 3 and 5-6 because claim 23 depends from instant claim 14, wherein claim 14 does not recite the presence of “single-stranded linking nucleic acid” and/or “a sequence at each end of the single-stranded linking nucleic acid” and, thus, the metes and bounds of the claim cannot be determined.
Claim 24 is indefinite for the recitation of the term “joining” such as recited in claim 24, line 2. There is insufficient antecedent basis for the term “joining” in the claim because claim 14, line 24 recites the term “a joining reaction”. The Examiner suggests that Applicant amend the claim to recite, for example, “probes generated in the joining reaction.”
Claim 24 is indefinite for the recitation of the term “a capture fragment” in claim 24, line 3 because claim 24 depends from instant claim 14, wherein claim 14 does not recite that the first barcode nucleic acid, the second barcode nucleic acids, and/or the probes comprise a capture fragment and, thus, the metes and bounds of the claim cannot be determined.
Claim 26 is indefinite for the recitation of the term “a barcode sequence” such as recited in claim 26, lines 1 and 3. There is insufficient antecedent basis for the term “a barcode sequence” in the claim because claim 14, lines 11-12 and 20-21 recite the term “a different barcode sequence.”
Claim 26 is indefinite for the recitation of the terms “a barcode sequence”; “a first barcode fragment”; and “a second barcode fragment” in claim 26, lines 1-4 because claim 26 depends from instant claim 14, wherein claim 14 does not recite the presence of “a barcode sequence”; “a first barcode fragment”; and “a second barcode fragment” and, thus, the metes and bounds of the claim cannot be determined.
Claim 26 is indefinite for the recitation of the terms “the first barcode nucleic acids” and “the second barcode nucleic acids” such as recited in claim 26, lines 2 and 4. There is insufficient antecedent basis for the terms “the first barcode nucleic acids” and “the second barcode nucleic acids” in the claim because claim 14, lined 7-8 and 17-18 recite the terms “a plurality of first barcode nucleic acids” and “a plurality of second barcode nucleic acids.”
Claim 26 is indefinite for the recitation of the term “is identified” such as recited in claim 26, line 5 because no step is recited that could lead to the identification of barcode nucleic acids such that it is completely unclear how barcode nucleic acids are identified and, thus, the metes and bounds of the claim cannot be determined.
Claim 27 is indefinite for the recitation of the term “concentration” such as recited in claim 27, line 1 because a concentration requires something in which to dissolved, be miscible with and/or suspend something else (e.g., liquid, solvent, water, etc.), such that claim 27 depends from instant claim 14, wherein claim 14 does not recite any liquid or solvent and, thus, the metes and bounds of the claim cannot be determined.
Claim 27 is indefinite for the recitation of the term “a flow channel” in claim 27, line 2 because claim 27 depends from instant claim 14, wherein claim 14 does not recite that the presence of a flow channel and, thus, the metes and bounds of the claim cannot be determined.
Claim 29 is indefinite for the recitation of the term “an amino-aldehyde group reaction” in claim 29, lines 2-3 because Applicant has not particularly pointed out and distinctly claimed the subject matter which the applicant regards as his invention. It is completely unclear what reactions are encompassed by the term “an amino-aldehyde group reaction”. Moreover, it is unclear whether the term is referring to a type of reaction, to a reaction between an amino group and an aldehyde, or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claim 30 is indefinite for the recitation of the term “each channel” in claim 30, lines 1-2. There is insufficient antecedent basis for the term “each channel” in the claim because claim 14, lines 15-16 recites the term “a plurality of microfluidic channels.”
Claim 31 is indefinite for the recitation of the terms “spacing” and “adjacent microfluidic channels” such as recited in claim 31, lines 1-2 because claim 31 depends from instant claim 14, wherein claim 14 does not recite any spacing and/or adjacent microfluidic channels and, thus, the metes and bounds of the claim cannot be determined.
Claim 31 is indefinite for the recitation of the term “the microfluidic channels” in claim 31, line 2. There is insufficient antecedent basis for the term “the microfluidic channels” in the claim because claim 14, lines 15-16 recites the term “a plurality of microfluidic channels.”
Claim Rejections - 35 USC § 112(d)
The rejection of claims 16, 20, 24 and 27 is maintained, and claims 15, 18, 21, 23 and 26 are newly rejected, under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 15 and 21 recite (in part): “recognize and bind mRNA” in claim 15, line 2 because claims 15 and 21 depend from instant claim 14, wherein claim 14 does not recite recognizing and/or binding mRNA. Thus, claim 15 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 16 recites (in part): “wherein further comprises high throughput next generation sequencing or synthetic sequencing to further analyze the nucleic acids” in lines 1-2 because claim 16 depends from instant claim 14, wherein claim 16 does not recite an initial analyzing of nucleic acids. Thus, claim 16 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 20 recites (in part): “for recognizing and binding a target nucleic acid in the biological tissue sample” in lines 3-4 because claim 20 depends from instant claim 14, wherein claim 20 does not recite the presence of a target nucleic acid. Thus, claim 20 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 23 recites (in part): “wherein the first barcode nucleic acid has a first linking fragment at 3' end for linking to the second barcode nucleic acid via a single-stranded linking nucleic acid…the single-stranded linking nucleic acid” in lines 1-7 because claim 23 depends from instant claim 14, wherein claim 23 does not recite the presence of a single-stranded linking nucleic acid and/or a sequence at each end of the single-stranded linking nucleic acid. Thus, claim 23 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 24 recites (in part): “wherein the a probe of the probes generated in joining the second barcode nucleic acid…and a second barcode fragment” in lines 1-5 because claim 24 depends from instant claim 14, wherein claim 24 does not recite that the first barcode nucleic acid, the second barcode nucleic acids, and/or the probes comprise a capture fragment. Thus, claim 24 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 26 recites (in part): “wherein a barcode sequence of a first barcode fragment of each of the first barcode nucleic acids…is identified” in lines 1-5 because claim 26 depends from instant claim 14, wherein claim 14 does not recite any step that can lead to the identification of barcode nucleic acids. Thus, claim 26 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 27 recites (in part): “wherein a concentration of nucleic acid in a flow channel in A or B” in lines 1-2 because claim 7 depends from instant claim 14, wherein claim 14 does not recite the presence of a flow channel and/or the presence of any solvent or solution for which a concentration is determined. Thus, claim 26 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies
with the statutory requirements.
New Objections/Rejections
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 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 14-16, 18-27 and 29-31 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Fan et al. (hereinafter “Fan”) (US Patent No. 12157912, issued December 3, 2024; also as US20210095331, published April 1, 2021; filed September 29, 2020; effective filing date September 30, 2019). This is a new rejection necessitated by amendment of the claims in the response filed 06-09-2026.
Regarding claim 14, Fan teaches compositions and methods for producing a molecular expression map of a biological sample using Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq) (Abstract). Fan teaches downstream spatial reconstruction is enabled by confining reagents labelled with different polynucleotide barcodes to specific spatial regions of the tissue to be mapped (interpreted as different barcode sequences, claim 14) (col 1, lines 41-44). Fan teaches that the high throughput, high-spatial resolution (HSR) technology of the present disclosure matches the profiling capability of non-spatial techniques, which routinely profile tens of thousands of cells per run; and can be used to target an entire class of coding RNA molecules, such as messenger RNA (mRNA), and not merely a targeted panel of RNA molecules, which is particularly useful generating transcriptomic maps, wherein parallel microfluidic channels (10 μm, 25 μm, or 50 μm in width) are used to deliver molecular barcodes to the surface of a fixed (e.g., formaldehyde or formalin fixed) tissue slide in a spatially confined manner, such that cross-flow of two sets of barcodes A1-A50 and B1-B50 followed by ligation in situ yields a 2D mosaic of tissue pixels, each containing a unique combination of full barcode AiBj (i = 1-50, j = 1-50) to permit the simultaneous barcoding of mRNAs, proteins, or even other omics on a fixed tissue slide, enabling the construction of a high-spatial-resolution multi-omics atlas by next generation sequencing (NGS) (interpreted as microfluidic channels in parallel; joining a second barcode to a first barcode on the surface of a biochip; unique barcodes; and interpreting pixel tissues as spots, claim 14A-C) (col 1, lines 49-67; and col 2, lines 1-2). Fan teaches a method, comprising: (a) delivering to a region of interest in a fixed section of a mammalian tissue mounted on a substrate binder-DNA tag conjugates (interpreted as a biochip comprising a surface; a tissue sample; and barcodes) that comprises: (i) a binder molecule that specifically binds to a protein of interest and (ii) a DNA tag, wherein the DNA tag comprises a binder barcode and a polyadenylation (poly A) sequence; (b) delivering to the region of interest a first set of barcoded polynucleotides that bind to nucleic acids of the fixed tissue section, wherein the first set of barcoded polynucleotides is delivered through a first microfluidic device clamped to the region of interest, optionally wherein the first microfluidic device comprises 5-50 variable width microchannels, each having (i) an inlet port and an outlet port, (ii) a width of 50-150 μm at the inlet port and at the outlet port, and (iii) a width of 10-50 μm at the region of interest; (c) delivering to the region of interest reverse transcription reagents to produce cDNAs linked to barcoded polynucleotides of the first set; (d) delivering to the region of interest a second set of barcoded polynucleotides, wherein the second set of barcoded polynucleotides is delivered through a second microfluidic device clamped to the region of interest (interpreted as parallel microchannels; applying a first set of barcodes and applying a second set of barcodes in a first and second direction), optionally wherein the second microfluidic device comprises 5-50 variable width microchannels, each having (i) an inlet port and an outlet port; (e) delivering to the region of interest ligation reagents to join barcoded polynucleotides of the first set to 15 barcoded polynucleotides of the second set; (f) imaging the region of interest to produce a sample image; (g) delivering to the region of interest lysis buffer or denaturation reagents to produce a lysed or denatured tissue sample; and (h) extracting cDNA from the lysed or denatured tissue sample (interpreted as fixing a first set of barcodes on a surface through parallel microchannels in a first direction; and applying a second set of barcode in a second direction through parallel microchannels, wherein the barcodes undergo a joining reaction, claim 14A-C) (col 2, lines 51-67; and col 3, lines 1-8 and 13-20). Fan teaches Figure 1 below, which illustrates parallel microfluidic channels, and applying barcodes from two (2) directions (interpreted to form barcode strips; and flow channels, claim 14) (Figure 1):
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Figure 1
Fan teaches that different barcode reagents are pipetted to these inlets and drawn into the microchannels by vacuum applied to the roof cap of the outlets situated on the other side of the PDMS chip (Figure 7B), where validation of spatial barcoding using fluorescent DNA probes, such that the images show parallel lines of Cy3-labelled barcode A (left panel) on the tissue slide defined by the first flow, the square pixels of FITC-labeled barcode B (right panel) corresponding to the intersection of the first and the second flows, and the overlay of both fluorescence colors (middle); and because barcode B is ligated to the immobilized barcode A in an orthogonal direction, it is detectable only at the intersection of the first set (A1-A50) and the second set (B1-B50) of microchannels (interpreted as loading microfluidic channels with different barcodes sequences; intersecting; joining by ligation; and forming probe spots, claim 14) (col 6, lines 43-55).
Regarding claim 15, Fan teaches a custom-designed PDMS microfluidic device with 50 parallel microchannels in the center of the chip is aligned and placed on the tissue slide to introduce the 1st set of barcodes A1 to A50, wherein each barcode is tethered with a ligation linker and an oligo-dT sequence (interpreted as a 5’ end primer) for binding the poly-A tail of mRNAs or ADTs (interpreted as probes recognize and bind mRNA, claim 15) (col 5, lines 11-16).
Regarding claim 16, Fan teaches single-cell deterministic barcoding, wherein Figure 15 depicts the experimental procedure to perform deterministic barcoding in cells (DBIC) to detect and eventually sequence single-cell transcriptome in a massively parallel and deterministic manner, which means each cell to be analyzed by sequencing has a known combination barcode AiBj (i=1-50, j=1-50) and known location on the substrate (interpreted as NGS sequence or synthetic sequencing, claim 16) (col 10, lines 4-10; and Figure 15).
Regarding claim 18, Fan teaches a custom-designed PDMS microfluidic device with 50 parallel microchannels in the center of the chip is aligned and placed on the tissue slide to introduce the 1st set of barcodes A1 to A50, wherein each barcode is tethered with a ligation linker and an oligo-dT sequence (interpreted as a 5’ end primer) for binding the poly-A tail of mRNAs or ADTs (interpreted as probes recognize and bind mRNA; and first barcode comprises a 5’ end primer, claim 15) (col 5, lines 11-16). Fan teaches that parallel microfluidic channels (10 μm, 25 μm, or 50 μm in width) are used to deliver molecular barcodes to the surface of a fixed (e.g., formaldehyde or formalin fixed) tissue slide in a spatially confined manner, such that cross-flow of two sets of barcodes A1-A50 and B1-B50 followed by ligation in situ yields a 2D mosaic of tissue pixels, each containing a unique combination of full barcode AiBj (i = 1-50, j = 1-50) to permit the simultaneous barcoding of mRNAs, proteins, or even other omics on a fixed tissue slide, enabling the construction of a high-spatial-resolution multi-omics atlas by next generation sequencing (NGS) (interpreted as microfluidic channels in parallel; joining a second barcode to a first barcode on the surface of a biochip; unique barcodes; and interpreting pixel tissues as spots, claim 14A-C) (col 1, lines 58-67; and col 2, lines 1-2).
Regarding claims 19-25, Fan teaches in Figures 5A-C, a non-limiting example of the barcoded polynucleotide (e.g., barcoded DNA) of the present disclosure is shown in Figure 5B, wherein barcoded polynucleotides (e.g., of a first set of barcoded polynucleotides) include a ligation linker sequence, a spatial barcode sequence, and a polyT sequence, such that barcoded polynucleotides (e.g., of a second set of barcoded polynucleotides) include a ligation linker sequence, a spatial barcode sequence, a unique molecular identifier (UMI) sequence, and a first PCR handle end sequence, wherein the PCR handle end sequence can be terminally functionalized with biotin, which facilitates the purification in the later steps using streptavidin-coated magnetic beads (interpreted as comprising fragments for binding; comprising a UMI; and linker fragment, claims 19-24) (col 5, lines 62-63; col 21, lines 7-18; and Figures 5A-C). Fan teaches in Figure 5 that DNA barcode A consist of a poly T region, a barcode region, and a ligation region (interpreted as the first/second barcode nucleic acid), wherein the polyT region will recognize the poly A tail of mRNA and ADTs, while DNA barcode B consists of a ligation region, a barcode region, and UMI region, and a PCR primer handle region (interpreted as the first/second barcode nucleic acids comprising ligation regions, UMI, and primer fragments, claims 19-22) (col 6, lines 22-26; and Figure 5). Figures 5A-C (in part) are shown below:
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Figure 5A Figure 5B Figure 5C
Regarding claim 27, Fan teaches that for immunofluorescence staining a mixture of three antibodies was used at a final concentration of 25 mg/mL in 1% BSA, PBS (interpreted to encompass 0.1-100 mM, claim 27) (col 45, lines 51-52).
Regarding claim 29, Fan teaches that a biological sample is fixed by chemically preserving the natural state of a biological sample, for example, for subsequent histological analysis, where fixation agents include, for example, formalin (e.g., formalin fixed paraffin embedded (FFPE) tissue), formaldehyde, paraformaldehyde and glutaraldehyde (interpreted as an aldehyde group, claim 29) (col 20, lines 13-21). Fan teaches that the biological sample is a tissue or a cell that is sectioned and mounted on a surface, such as the surface of a glass microscope slide including a polylysine-coated glass microscope slide (interpreted as an amino-aldehyde group reaction, claim 29) (col 20, lines 24-29).
Regarding claim 30, Fan teaches the first set of barcoded polynucleotides and the second set of barcoded polynucleotides are delivered through a first microfluidic device clamped to the region of interest, wherein the first microfluidic device comprises 5-50 mm variable width microchannels (interpreted as encompassing microfluidic channel width of 2-200 mm, claim 30) (col 2, lines 24-28 and 34-39).
Regarding claim 31, Fan teaches that the pitch is the distance between microchannels of a microfluidic device (e.g., chip), wherein the pitch of a microfluidic device is at least 10 μm (e.g., at least 15 μm, at least 20 μm, at least 25 μm, at least 30 μm, at least 35 μm, at least 40 μm, or at least 50 μm); and/or 10 μm to 150 μm (e.g., 10-125 μm, 10-100 μm, 25-150 μm, 25-125 μm, 25-100 μm, 50-150 μm, 50-125 μm, or 50-100 μm) (interpreted as encompassing a distance of 5-400 mm, claim 31) (col 15, lines 1-3).
Fan meets all the limitations of the claims and, therefore, anticipates the claimed invention.
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 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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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 14-16, 18-27 and 29-31 are rejected under 35 U.S.C. 103 as being unpatentable over Yin et al. (hereinafter “Yin”) (US Patent No. 11649485, issued May 16, 2023; WO2020123305, filed December 6, 2019; effective filing date January 6, 2019; of record) in view of Fan et al. (hereinafter “Fan”) (US Patent No. 12157912, issued December 3, 2024; also as US20210095331, published April 1, 2021; filed September 29, 2020; effective filing date September 30, 2019) as evidenced by Guermonprez et al. (hereinafter “Guermonprez”) (Biomicrofluidics, 2015, 9, 1-13); and Chee et al. (hereinafter “Chee”) (US Patent No. 9868979, issued January 16, 2018); and Boutet et al. (hereinafter “Boutet”) (International Application WO2019113533, published December 7, 2019). This is a new rejection necessitated by amendment of the claims in the response filed 06-09-2026.
Regarding claims 14 and 23, Yin teaches compositions and methods for generating capture probes on a substrate for identifying the location of analytes in a biological sample (interpreted as probes; and biological samples, claim 14) (Abstract). Yin teaches that in some embodiments of methods of generating an array, one or more physical barriers are printed on the substrate, wherein the one or more physical barriers form one or more chambers including one or more chamber walls, which can include a hydrophobic surface; as well as, a tapered end in contact with the substrate, wherein the second oligonucleotide is delivered using a microfluidic device (interpreted as delivering barcode nucleic acids using a microfluidic device, claim 17) (col 7, lines 3-14). Yin teaches that a substrate can generally have any suitable form or format such as, for example, a substrate can be flat, curved, e.g., convexly or concavely curved towards the area where the interaction between a biological sample, e.g., tissue sample, and a substrate takes place; and a substrate can be planar, chip, or slide; and a substrate can contain one or more patterned surfaces within the substrate, such that the substrate can have any desired shape (e.g., channels, wells, projections, ridges, divots, etc.) (interpreted as a surface; encompassing parallel channels; a chip; and spots, claim 14) (col 93, lines 5-13). teaches generating an array including: (a) providing a substrate including a plurality of features immobilized on the substrate, where a feature of the plurality of features includes a first oligonucleotide, and where the first oligonucleotide includes a first spatial barcode, (b) delivering a second oligonucleotide to the first oligonucleotide, where the second oligonucleotide includes a second spatial barcode and a capture domain, and (c) attaching the first oligonucleotide and the second oligonucleotide, thereby generating a capture probe including the first spatial barcode, the second spatial barcode, and the capture domain (col 5, lines 58-67; and col 6, lines 1-2). Yin teaches that each feature can be printed or deposited at a specific location on the substrate (e.g., inkjet printing); and each feature can have a unique oligonucleotide that functions as a spatial barcode, and capture probes for multiplexing ( e.g., capturing multiple analytes or multiple types of analytes, e.g., proteins and nucleic acids), wherein a feature can contain a photo-crosslinkable polymer precursor and an oligonucleotide, and/or a photo-crosslinkable polymer precursor can be deposited into a patterned feature on the substrate (e.g., well) (interpreted as being fixed to a chip surface by chemical bonding, including crosslinking, claims 28 and 29) (col 100, lines 65-67; and col 101, lines 1-8). Yin teaches microfluidic channel networks such as on a chip can be utilized to generate partitions (interpreted as a chip; microfluidic device; flow channels, claim 14) (col 194, lines 43-45). Yin teaches that methods of generating a spatial array including: (a) providing an array including a plurality of oligonucleotides, where the 3' end of an oligonucleotide of the plurality of oligonucleotides is attached to a substrate; (b) providing a plurality of primers, where a primer of the plurality of primers is substantially complementary to a portion of the oligonucleotide; (c) extending the primer using the oligonucleotide as a template, thereby generating a first oligonucleotide with a free 3' end, (d) extending the first oligonucleotide to produce a 3' overhang, (e) providing a splint oligonucleotide that hybridizes to the 3' end of the first oligonucleotide, and (f) ligating a second oligonucleotide to the 3' end of the first oligonucleotide (interpreted as an array comprising a surface; first barcode has a 5’ end for attachment to the chip; a plurality of joined first barcodes and second barcodes; probe fragment at the 3’ end for linking or binding a target; and a primer at the 5’ end of the first barcode, claims 14, 18-21, 23 and 24) (col 2, lines 18-30). Yin teaches that the second oligonucleotide further includes a constant sequence substantially complementary to a portion of the splint oligonucleotide; a unique molecular identifier; and/or a spatial barcode (interpreted as comprising a second barcode or joined barcode; and a UMI, claim 14) (col 2, lines 46-53). Yin teaches that in some embodiments of methods of generating an array, one or more physical barriers are printed on the substrate, wherein the one or more physical barriers form one or more chambers including one or more chamber walls, which can include a hydrophobic surface; as well as, a tapered end in contact with the substrate, wherein the second oligonucleotide is delivered using a microfluidic device (interpreted as including microfluidic channels, claim 14) (col 7, lines 3-14). Yin teaches that the capture probe can include a UMI sequence that can uniquely identify a given transcript, and a spatial barcode sequence and a capture domain that is capable of specifically hybridizing with an analyte capture agent, which can includes an oligonucleotide that includes an analyte capture sequence that interacts with the capture domain coupled to the feature (interpreted as unique barcodes, claim 14) (col 258, lines 21-28). Yin teaches isothermal nucleic acid amplification, which is helicase-dependent nucleic acid amplification on a substrate (e.g., on-chip) is described in EMBO Rep., 795-800 (2004); US Patent 7282328; Andresen, et. al., Helicase-dependent amplification: use in OnChip amplification and potential for point of care diagnostics, Expert Rev Mal Diagn., 9, 645-650, doi: 10.1586/erm.09.46 (2009), which are incorporated herein by reference in their entirety (interpreted as a biochip, claim 14) (col 62, lines 6-18). Yin teaches that a substrate can contain one or more capture probes designed to capture mRNA from one organism (e.g., a human), and one or more capture probes designed to capture DNA from a second organism (e.g., a bacterium), wherein the relative abundance of each analyte in the biological sample; and since an array can contain thousands or millions of capture probes (or more), an array can interrogate many analytes in parallel (interpreted as channels set in parallel, claim 14) (col 102, lines 29-39). Yin teaches methods for sequencing genetic material include, but are not limited to, DNA hybridization methods (e.g., Southern blotting), restriction enzyme digestion methods, Sanger sequencing methods, next-generation sequencing methods (e.g., single-molecule real-time sequencing, nanopore sequencing, and Polony sequencing), ligation methods, microarray methods, targeted sequencing, single molecule real-time sequencing, exon sequencing, electron microscopy-based sequencing, panel sequencing, transistor-mediated sequencing, direct sequencing, random shotgun sequencing, Sanger dideoxy termination sequencing, whole-genome sequencing, sequencing by hybridization, pyrosequencing, etc. (interpreted as NGS and synthetic sequencing, claims 14 and 16) (col 209, lines 15-28). Yin teaches in Figure 25, a diagram showing a method of capturing an analyte with a capture domain and performing reverse transcription to obtain a complementary cDNA sequence (interpreted as reverse transcription, claim 14) (col 20, lines 22-25; and Figure 25). Yin teaches that examples of substrates that can be used in the methods and systems described herein include, but are not limited to, slides (e.g., slides formed from various glasses, slides formed from various polymers), hydrogels, layers and/or films, membranes (e.g., porous membranes), flow cells, cuvettes wafers, plates, or combinations thereof, wherein substrates can optionally include functional elements such as recesses, protruding structures, microfluidic elements (e.g., channels, reservoirs, electrodes, valves, seals, and various markings (col 92, lines 59-67; and col 93, lines 1-2), where it is known that microfluidic devices and flow cells can comprise parallel microfluidic channels as evidenced by Guermonprez (Abstract; and pg. 3, Figure 1); and Chee (col 5, lines 45-48). Yin teaches that the bead array contains microfluidic channels to direct reagents to the spots or beads on the array (col 139, lines 48-50). Yin teaches that features within an array are positioned regularly with respect to one another to form a pattern including a wide variety of different patterns of features can be implemented in arrays, such as but are not limited to, square arrays of features, rectangular arrays of features, hexagonal arrays of features (including hexagonal close-packed arrays), radial arrays of features, spiral arrays of features, triangular arrays of features, and more generally, any array in which adjacent features in the array are reached from one another by regular increments in linear and/or angular coordinate dimensions (interpreted as parallel channels, claim 14) (col 141, 23-33). Yin teaches that a nucleic acid molecule can include a functional domain used in subsequent processing including a sequencer specific flow cell attachment sequence such as for a P5 sequence for Illumina sequencing systems, and a sequencing primer sequence (e.g., an R1 primer for Illumina sequencing systems), wherein flow cells and microfluidic channels on a chip can be substantially parallel as evidenced by Boutet (paragraphs [00159]; and [00265]; and Figure 5).
Regarding claims 15 and 24, Yin teaches that arrays can be designed with pluralities of capture probes that can be designed to capture a substantial population of analytes such as mRNA, or to capture specific (e.g., gene specific) analytes (interpreted as probes for binding a target; for binding mRNA; and capture fragments, claims 14, 15 and 24) (col 2, lines 55-57). Yin teaches that the capture domain includes a poly-T sequence or gene-specific sequence (interpreted as a probe for binding a target; for binding mRNA; capture fragment, claims 14, 15 and 24 ) (col 2, lines 55-57).
Regarding claim 16, Yin teaches methods for sequencing genetic material include, but are not limited to, DNA hybridization methods (e.g., Southern blotting), restriction enzyme digestion methods, Sanger sequencing methods, next-generation sequencing methods (e.g., single-molecule real-time sequencing, nanopore sequencing, and Polony sequencing), ligation methods, microarray methods, targeted sequencing, single molecule real-time sequencing, exon sequencing, electron microscopy-based sequencing, panel sequencing, transistor-mediated sequencing, direct sequencing, random shotgun sequencing, Sanger dideoxy termination sequencing, whole-genome sequencing, sequencing by hybridization, pyrosequencing, etc. (interpreted as NGS and synthetic sequencing, claim 16) (col 209, lines 15-28). Yin teaches that Figure 17A shows an example of microfluidic channel structure 1700 for delivering spatial barcode carrying beads to droplets (interpreted as channels carrying nucleic acids, claim 31) (col 19, lines 22-24; and Figure 17A).
Regarding claim 18, Yin teaches in Figure 39 the immobilization of oligos comprising primers (interpreted as a first barcode comprising a primer fragment, claim 18) (Figure 39). Figure 39 (in part) is shown below:
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Regarding claim 19, Yin teaches a method for generating a spatial array, comprising: (a) providing a substrate including a plurality of first oligonucleotides, where a first oligonucleotide of the plurality of first oligonucleotides is attached to a region of the substrate through its 3'-end or its 5'-end, (b) attaching a second oligonucleotide to an unattached end of the first oligonucleotide, where the second oligonucleotide includes a spatial barcode (interpreted as attaching via the 5’ end, claim 19) (col 9, lines 1-8).
Regarding claims 20 and 21, Yin teaches in Figure 27, wherein the second oligonucleotide comprises a poly(dT) sequence, wherein a 3' polyadenylated tail of an mRNA transcript that hybridizes to a poly (dT) sequence (e.g., capture domain) can be used as a template for single strand synthesis of a corresponding cDNA molecule (col 27, lines 32-35; and Figure 27). Figure 27 (in part), is shown below:
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Figure 27
Regarding claim 22, Yin teaches that the second oligonucleotide further includes a constant sequence substantially complementary to a portion of the splint oligonucleotide; a unique molecular identifier; and/or a spatial barcode (interpreted as comprising a second barcode or joined barcode; and a UMI, claims 14 and 22) (col 2, lines 46-53).
Regarding claims 25 and 26, Yin teaches an example of a capture probe in Figure 6, where the capture probe 602 is optionally coupled to a feature 601 by a cleavage domain 603, such as a disulfide linker, wherein the capture probe can include functional sequences that are useful for subsequent processing, such as functional sequence 604, which can include a sequencer-specific flow cell attachment sequence, such as a P5 sequence, as well as functional sequence 606, which can include sequencing primer sequences, such as a R1 primer binding site, such that sequence 604 can be a P7 sequence and sequence 606 is a R2 primer binding site, wherein spatial barcode 605 can be included within the capture probe for use in barcoding the target analyte, such that the functional sequences can generally be selected for compatibility with any of a variety of different sequencing systems, e.g., 454 Sequencing, Ion Torrent Proton or PGM, Illumina X10, PacBio, Nanopore, etc.; and the spatial barcode 605, functional sequences 604 (e.g., flow cell attachment sequence) and 606 (e.g., sequencing primer sequences) can be common to all of the probes attached to a given feature, wherein the spatial barcode can also include a capture domain 607 to facilitate capture of a target analyte (interpreted as a flow cell for NGS sequencing comprising microfluidic channels; joined barcodes; feature 601 as a spot; capture domain 607 for binding targets or mRNA; and comprising primer sequences; primer fragment at the 5’ end; and designated barcode sequences, claims 14, 25 and 26) (col 65, lines 5-21 and 33-38). Figure 6 is shown below:
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Yin teaches that each feature can be printed or deposited at a specific location on the substrate (e.g., inkjet printing); and each feature can have a unique oligonucleotide that functions as a spatial barcode, and capture probes for multiplexing ( e.g., capturing multiple analytes or multiple types of analytes, e.g., proteins and nucleic acids), wherein a feature can contain a photo-crosslinkable polymer precursor and an oligonucleotide, and/or a photo-crosslinkable polymer precursor can be deposited into a patterned feature on the substrate (e.g., well) (interpreted as being fixed to a chip surface by chemical bonding, including crosslinking, claims 28 and 29) (col 100, lines 65-67; and col 101, lines 1-8).
Regarding claim 27, Yin teaches that any suitable number of species (e.g., primer, barcoded oligonucleotide) can be associated with a bead such that, upon release from the bead, the species (e.g., primer, e.g., barcoded oligonucleotide) are present in the partition at a pre-defined concentration, wherein such pre-defined concentration can be selected to facilitate certain reactions for generating a sequencing library, e.g., amplification, within the partition, wherein the pre-defined concentration of the primer can be limited by the process of producing nucleic acid molecule (e.g., oligonucleotide) bearing beads (interpreted as a concentration including 0.1-100 mM, claim 27) (col 247, lines 19-28).
Regarding claim 29, Yin teaches that functional groups that can be introduced on a substrate that allow for attachment of a first oligonucleotide (e.g., a 5’-amine modified oligonucleotide) to a substrate include linkers with available carboxy aldehyde or epoxy groups (interpreted as an amino-aldehyde group reaction, claim 29) (col 300, lines 42-46).
Regarding claim 30, Yin teaches that the channels can direct the migration of a cell such that it does not contact another cell on the array (e.g., the channels do not overlap with each other), and in some embodiments, the channels are about the same width as or wider than a cell, such that for a mammalian cell, a channel can have a width of about 2 μm to about 10 μm) (interpreted as encompassing 2-200 μm, claim 30) (col 215, lines 50-55).
Regarding claim 31, Yin teaches that arrays of different feature densities can be prepared by adjusting the spacing between adjacent features in the array, wherein the geometric center-to-center (e.g., pitch) spacing between adjacent features in an array is between 100 nm to 10 μm, 500 nm to 2 μm, 1 μm to 5 μm, and 20 μm to 200 μm (interpreted as encompassing 5-400 μm, claim 31) (col 141, lines 63-67; and col 142, line 1).
Yin does not specifically exemplify parallel microfluidic channels (instant claims 14, 30 and 31, all in part).
Regarding claims 14, 30 and 31 (all in part), Fan teaches compositions and methods for producing a molecular expression map of a biological sample using Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq) (Abstract). Fan teaches downstream spatial reconstruction is enabled by confining reagents labelled with different polynucleotide barcodes to specific spatial regions of the tissue to be mapped (interpreted as different barcode sequences, claim 14) (col 1, lines 41-44). Fan teaches that the high throughput, high-spatial resolution (HSR) technology of the present disclosure matches the profiling capability of non-spatial techniques, which routinely profile tens of thousands of cells per run; and can be used to target an entire class of coding RNA molecules, such as messenger RNA (mRNA), and not merely a targeted panel of RNA molecules, which is particularly useful generating transcriptomic maps, wherein parallel microfluidic channels (10 μm, 25 μm, or 50 μm in width) are used to deliver molecular barcodes to the surface of a fixed (e.g., formaldehyde or formalin fixed) tissue slide in a spatially confined manner, such that cross-flow of two sets of barcodes A1-A50 and B1-B50 followed by ligation in situ yields a 2D mosaic of tissue pixels, each containing a unique combination of full barcode AiBj (i = 1-50, j = 1-50) to permit the simultaneous barcoding of mRNAs, proteins, or even other omics on a fixed tissue slide, enabling the construction of a high-spatial-resolution multi-omics atlas by next generation sequencing (NGS) (interpreted as microfluidic channels in parallel; joining a second barcode to a first barcode on the surface of a biochip; unique barcodes; and interpreting pixel tissues as spots, claim 14A-C) (col 1, lines 49-67; and col 2, lines 1-2). Fan teaches a method, comprising: (a) delivering to a region of interest in a fixed section of a mammalian tissue mounted on a substrate binder-DNA tag conjugates (interpreted as a biochip comprising a surface; a tissue sample; and barcodes) that comprises: (i) a binder molecule that specifically binds to a protein of interest and (ii) a DNA tag, wherein the DNA tag comprises a binder barcode and a polyadenylation (poly A) sequence; (b) delivering to the region of interest a first set of barcoded polynucleotides that bind to nucleic acids of the fixed tissue section, wherein the first set of barcoded polynucleotides is delivered through a first microfluidic device clamped to the region of interest, optionally wherein the first microfluidic device comprises 5-50 variable width microchannels, each having (i) an inlet port and an outlet port, (ii) a width of 50-150 μm at the inlet port and at the outlet port, and (iii) a width of 10-50 μm at the region of interest; (c) delivering to the region of interest reverse transcription reagents to produce cDNAs linked to barcoded polynucleotides of the first set; (d) delivering to the region of interest a second set of barcoded polynucleotides, wherein the second set of barcoded polynucleotides is delivered through a second microfluidic device clamped to the region of interest (interpreted as parallel microchannels; applying a first set of barcodes and applying a second set of barcodes in a first and second direction), optionally wherein the second microfluidic device comprises 5-50 variable width microchannels, each having (i) an inlet port and an outlet port; (e) delivering to the region of interest ligation reagents to join barcoded polynucleotides of the first set to 15 barcoded polynucleotides of the second set; (f) imaging the region of interest to produce a sample image; (g) delivering to the region of interest lysis buffer or denaturation reagents to produce a lysed or denatured tissue sample; and (h) extracting cDNA from the lysed or denatured tissue sample (interpreted as fixing a first set of barcodes on a surface through parallel microchannels in a first direction; and applying a second set of barcode in a second direction through parallel microchannels, wherein the barcodes undergo a joining reaction, claim 14A-C) (col 2, lines 51-67; and col 3, lines 1-8 and 13-20). Fan teaches Figure 1 below, which illustrates parallel microfluidic channels, and applying barcodes from two (2) directions (interpreted to form barcode strips; and flow channels, claim 14) (Figure 1):
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Figure 1
Fan teaches that different barcode reagents are pipetted to these inlets and drawn into the microchannels by vacuum applied to the roof cap of the outlets situated on the other side of the PDMS chip (Figure 7B), where validation of spatial barcoding using fluorescent DNA probes, such that the images show parallel lines of Cy3-labelled barcode A (left panel) on the tissue slide defined by the first flow, the square pixels of FITC-labeled barcode B (right panel) corresponding to the intersection of the first and the second flows, and the overlay of both fluorescence colors (middle); and because barcode B is ligated to the immobilized barcode A in an orthogonal direction, it is detectable only at the intersection of the first set (A1-A50) and the second set (B1-B50) of microchannels (interpreted as loading microfluidic channels with different barcodes sequences; intersecting; joining by ligation; and forming probe spots, claim 14) (col 6, lines 43-55).
It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of producing a molecular expression map of a biological sample using Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-Seq) as exemplified by Fan, it would have been prima facie obvious for one of ordinary skill in the art at the time the invention was made to modify the method of generating capture probes on a substrate for identifying the location of analytes in a biological sample including producing a spatial array of immobilized oligonucleotides, each comprising a first barcode sequence, a second barcode sequence, UMI, primer sequence, and/or a capture sequence as disclosed by Yin to include the microfluidic delivery of a first set of barcoded polynucleotides and the delivery of a second set of barcoded polynucleotides to a substrate surface using parallel microfluidic channels aligned perpendicular one to the other, and joining the second barcoded polynucleotide to the first barcoded polynucleotide as taught by Fan with a reasonable expectation of success in creating arrays that capture spatial information of analytes within a biological sample including a tissue sample; in using the arrays to generate transcriptomic maps and/or to generate three-dimensional maps of analyte levels in a tissue sample; and/or in capturing and identifying gene specific analytes at specific locations within the biological sample, such that differences in analyte levels within different cells in a tissue can provide information on the presence or absence of disease in a mammal.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly
rejected under 35 USC §103(a) as obvious over the art.
Conclusion
Claims 14-16, 18-27 and 29-31 are rejected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
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