DETAILED ACTION
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 .
Election/Restrictions
Applicant’s election without traverse of claims 1-3, 6, 9, 11, 13, 17-19, 21, 23-24, 30-31, 43, 46-47, 117, and 170 in the reply filed on 4 May 2026 is acknowledged.
Claim 134 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 4 May 2026.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Information Disclosure Statement
The information disclosure statement(s) (IDS) filed 26 February 2024, 6 November 2024, and 12 February 2026 are considered, initialed, and attached hereto.
The listing of references in the specification (on pages 79-81 of the specification filed on 27 November 2023) is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892 or in a proper IDS, they have not been considered.
Claim Status
Claims 1-3, 6, 9, 11, 13, 17-19, 21, 23-24, 30-31, 43, 46-47, 117, 134, and 170 are pending.
Claims 4-5, 7-8, 10, 12, 14-16, 20, 22, 25-29, 32-42, 44-45, 48-116, 118-133, 135-169, and 171-175 are canceled.
Claim 134 is withdrawn.
Claims 1-3, 6, 9, 11, 13, 17-19, 21, 23-24, 30-31, 43, 46-47, 117, and 170 are under examination.
Drawings
The drawings filed 27 November 2023 are objected to because text in FIG. 1E, FIG. 1F, FIG. 7K, and FIG. 9A is illegible. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The use of terms such as Tween and SUPERase-In, which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 6 is objected to because of the following informalities: "wherein cell" in line 1 should read "wherein the cell". Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 46 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 46 recites the limitation "The method of claim 46" in line 1. There is insufficient antecedent basis for this limitation in the claim. For the purpose of examination, claim 46 is interpreted as depending from the only prior independent claim, claim 1, instead of itself.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-3, 6, 9, 13, 17-19, 21, 23-24, 30-31, 43, 46-47, 117, and 170 are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (cited in IDS filed 26 February 2024)(WO 2019/199579, published 17 October 2019), herein Wang 1, in view of Nagendran et al. (US 2023/0126825, effectively filed 14 April 2021), herein Nagendran, and as evidenced by Eun (“Chapter 1 - Enzymes and Nucleic Acids: General Principles”, Enzymology Primer for Recombinant DNA Technology, Academic Press, pages 62-68 (1996)).
Regarding claim 117, Wang 1 teaches a plurality of oligonucleotide probes (a SNAIL probe and primer set) comprising a first oligonucleotide probe and a second oligonucleotide probe, wherein i) the first oligonucleotide probe comprises a portion that is complementary to the second oligonucleotide probe, a portion that is complementary to a nucleic acid of interest, and a first barcode sequence; and ii) the second oligonucleotide probe comprises a portion that is complementary to the nucleic acid of interest and a portion that is complementary to the first oligonucleotide probe (FIG 1A, in the box labeled ‘SNAIL probe’, the oligonucleotide on the right is the claimed first oligonucleotide probe, comprising a portion complementary to the mRNA target and a gene-unique identifier, equivalent to a barcode, and the oligonucleotide on the left is the claimed second oligonucleotide probe, comprising a portion complementary to the mRNA target and the first and second oligonucleotides comprise portions complementary to each other; see also [0004] where the first oligonucleotide taught is equivalent to the claimed second oligonucleotide probe and the second oligonucleotide taught is equivalent to the claimed first oligonucleotide probe).
Regarding claim 117, however, Wang 1 does not teach that the first oligonucleotide probe also comprises a second barcode sequence and that the second oligonucleotide probe also comprises a barcode sequence, wherein the barcode sequence of the second oligonucleotide probe is complementary to the second barcode sequence of the first oligonucleotide probe. This deficiency is made up for in the teachings of Nagendran.
Regarding claim 117, Nagendran teaches a SNAIL probe and primer set, wherein the SNAIL probe, equivalent to the claimed first oligonucleotide probe, comprises a barcode sequence and the primer, equivalent to the claimed second oligonucleotide probe, includes a sequence that is complementary to the barcode sequence (“a backbone sequence of a padlock probe or snail probe includes a sequence that is substantially complementary to an amplification primer […] In some embodiments, the backbone sequence includes a unique molecule identifier (UMI) or barcode sequence (e.g., any of the exemplary barcode sequences described herein). In some embodiments, the barcode sequence includes a sequence that is substantially complementary to an amplification primer” [0144]). Nagendran also teaches that the barcode sequence can be specific to the SNAIL probe (“In some instances, the backbone UMI or backbone barcode sequence comprises a sequence (e.g., n=5-50 nucleotides) that is specific to the padlock probe or snail probe” [0144]). Since longstanding evidence such as that of Eun teaching that mismatches reduce annealing of the mismatched strands and even single base pair mismatches can be distinguished for short sequences (Eun page 66, paragraph titled “ii. Mismatching bases”), one of ordinary skill in the art would understand that using barcodes unique to the probe+primer pair in the region of complementary between the probe and primer, as taught by Nagendran, will cause there to be mismatches if, for example, a probe targeting gene X tries to hybridize to a primer targeting gene Y, and these mismatches would reduce the ability of the mismatched probe and primer to amplify and create a non-specific amplification product, thereby biasing amplification products to ones created when a probe and primer targeting the same gene hybridize as they would not have any mismatch. By reducing non-specific amplification, the specificity of detection is increased. Therefore, the combination of Wang 1 and Nagendran would have the first oligonucleotide probe comprise both a first barcode sequence that is a gene-unique identifier (as taught by Wang 1) and a second barcode sequence that is complementary to a barcode sequence on the second oligonucleotide probe (as taught by Nagendran) to increase the specificity of their reaction.
Regarding claim 170, the combination of Wang 1 and Nagendran teach a system comprising one or more pairs of the oligonucleotide probes of claim 117 (see 35 U.S.C. 103 rejection of claim 117 above; step b) of claim 170 recites pairs of oligonucleotide probes identical to those of claim 117), and Wang 1 further teaches the oligonucleotide probes in a system with a cell (FIG 1A, note the mRNA the SNAIL probe and primer set binds to is in a cell).
Regarding claim 1, the combination of Wang 1 and Nagendran teach one or more pairs of oligonucleotide probes of the oligonucleotide probes of claim 117 (see 35 U.S.C. 103 rejection of claim 117 above; step a) recites pairs of oligonucleotide probes identical to those of claim 117). Wang 1 further teaches a method for mapping gene and protein expression in a cell, the method comprising: a) contacting the cell with the one or more pairs of oligonucleotide probes (“contacting a fixed and permeabilized intact tissue with at least a pair of oligonucleotide primers under conditions to allow for specific hybridization, wherein the pair of primers comprise a first oligonucleotide and a second oligonucleotide [0004], the second oligonucleotide of Wang 1 is equivalent to the claimed first oligonucleotide probe/snail probe and the first oligonucleotide of Wang 1 is equivalent to the claimed second oligonucleotide probe/primer, these are modified by Nagendran as discussed in the 35 U.S.C. 103 rejection of claim 117 above for the snail probe to further comprise a second barcode sequence complementary to a barcode sequence on the primer; FIG. 1A); b) ligating the 5’ end and the 3’ end of the first oligonucleotide probe together to produce a circular oligonucleotide (“adding ligase to ligate the second oligonucleotide and generate a closed nucleic acid circle” [0004]; FIG. 1A); c) performing rolling circle amplification to amplify the circular oligonucleotide using the second oligonucleotide probe as a primer to produce one or more concatenated amplicons (“performing rolling circle amplification in the presence of a nucleic acid molecule, wherein the performing comprises using the second oligonucleotide as a template and the first oligonucleotide as a primer for a polymerase to form one or more amplicons” [0004]; FIG. 1A); d) contacting the cell with one or more detecting agents, wherein each detecting agent binds to a protein of interest (“In some embodiments, the methods disclosed herein may be adapted to image DNA-conjugated antibodies for highly multiplexed protein detection” [0130], one of ordinary skill in the art would understand this to teach that the DNA-conjugated antibodies are a detecting agent that binds to a protein of interest and further that a probe set can comprise pairs of probes for nucleic acids of interest as well as other pairs of probes for the DNA conjugated to antibodies since multiplexing works by using the gene-unique identifier/barcode to distinguish targets); e) embedding the one or more concatenated amplicons and the one or more detecting agents in a polymeric matrix (“embedding the one or more amplicons in the presence of hydrogel subunits to form one or more hydrogel- embedded amplicons” [0004], note that the detecting agent would also be embedded since an amplicon would be made by the pair of probes targeting the DNA conjugated to the antibody and the primer the amplicon extends from would still be hybridized to the DNA-conjugated antibody, thereby connecting the detecting agent to the matrix via the amplicon when the amplicon is embedded; FIG. 1A); f) contacting the one or more concatenated amplicons embedded in the polymeric matrix with a third oligonucleotide probe comprising a sequence that is complementary to the first barcode sequence of the first oligonucleotide probe (“contacting the one or more hydrogel-embedded amplicons having the barcode sequence with a pair of primers under conditions to allow for ligation, wherein the pair of primers comprise a third oligonucleotide and a fourth oligonucleotide, wherein the ligation only occurs when both the third oligonucleotide and the fourth oligonucleotide ligate to the same amplicon” [0004]; FIG. 1A, note in the SEDAL sequencing ‘Readout’ frame that the third and fourth oligonucleotides are binding based on complementarity with the gene-unique identifier/barcode); and g) imaging the one or more concatenated amplicons embedded in the polymeric matrix and the one or more detecting agents embedded in the polymeric matrix to determine the location of the nucleic acids of interest and the proteins of interest in the cell (“imaging the one or more hydrogel-embedded amplicons to determine in situ gene sequencing of the target nucleic acid in the cell” [0004]; FIG. 1A; “In some aspects, a non-transitory computer readable medium transforms raw images acquired through microscopy of multiple rounds of in situ sequencing first into decoded gene identities and spatial locations” [0081]).
Regarding steps d)-g) of claim 1 above, particularly step d), examiner discussed that the combination of Wang 1 and Nagendran teach a method assaying both a nucleic acid of interest and a protein of interest. However, it is noted that the claim as written reads on not just the detection of separate nucleic acids and proteins of interest, but also reads on the detection of a single protein using the DNA-conjugated antibody taught by Wang 1 using the oligonucleotide probe pair taught by the combination of Wang 1 and Nagendran to detect the DNA conjugated to the antibody as the nucleic acid of interest. MPEP §2111.01 II. recites: “Altiris Inc. v. Symantec Corp., 318 F.3d 1363, 1371, 65 USPQ2d 1865, 1869-70 (Fed. Cir. 2003) (Although the specification discussed only a single embodiment, the court held that it was improper to read a specific order of steps into method claims where, as a matter of logic or grammar, the language of the method claims did not impose a specific order on the performance of the method steps, and the specification did not directly or implicitly require a particular order)”. Since no logic or grammar of the claim requires that step d) be performed after steps a) through c), the broadest reasonable interpretation of the claim encompasses a method comprising contacting the cell with a DNA-conjugated antibody that binds a protein of interest, and then proceeding with the steps a) through c) and e) through g) treating the DNA conjugated to the antibody as the nucleic acid of interest, all of which is taught in the combination of Wang 1 and Nagendran as discussed above.
Regarding claims 2-3, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method wherein gene and protein expression are profiled in multiple cells and wherein the cells comprise a plurality of cell types (FIG. 1; FIG. 13; “The spatial cell-typing of mouse primary visual cortex was extended to more than 30,000 cells across volumes spanning all six layers and the corpus callosum” [00200] and rest of [00200]).
Regarding claim 6, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method wherein the cell is present within an intact tissue (“a target nucleic acid in a cell in an intact tissue” [0004]).
Regarding claim 9, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method wherein the nucleic acid of interest is RNA (FIG. 1A, note that the panel labeled ‘SNAIL probe’ shows the primer and snail probe hybridizing to mRNA; “As used herein, the term “target nucleic acid” is any polynucleotide nucleic acid molecule (e.g., DNA molecule; RNA molecule, modified nucleic acid, etc.)” [0035]).
Regarding claim 13, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 and Nagendran both further teach that the barcode sequences on the first and second oligonucleotide probes are 5-15 nucleotides in length (“A 5-base barcode (library size of 1,024) was designed and built into each padlock probe as a gene-unique identifier to be sequenced, thus enabling multiplexed gene detection (FIG. 1A)” Wang 1 [00179]; “the backbone UMI or backbone barcode sequence comprises a sequence (e.g., n=5-50 nucleotides)” Nagendran [0144], the taught range of 5-50 nucleotides overlaps the claimed range of 5-15 nucleotides, so there is a prima facie case of obviousness, see MPEP §2144.05 I.). Note that the recitation “the barcodes sequences on the first and second oligonucleotide probes” in claim 13 is interpreted to include all of the first and second barcode sequence on the first oligonucleotide probe and the barcode sequence on the second oligonucleotide probe.
Regarding claim 17, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). As can be seen in FIG. 1A of Wang 1, Wang 1 teaches a first oligonucleotide probe (the padlock oligonucleotide/snail probe on the right of the box labeled “SNAIL probe”) comprising the structure: 5’-[first portion complementary to the second probe]-[portion complementary to nucleic acid of interest]-[first barcode sequence (the gene-unique identifier)]-[second portion complementary to the second probe]-3’. Since in the combination of Wang 1 and Nagendran the second barcode taught by Nagendran is added to a portion of the snail probe that is complementary to the second probe/primer, the only options in this structure to place the second barcode sequence are either the first portion complementary to the second probe or the second portion complementary to the second probe. As there are only 2 options, in the course of routine optimization it would be obvious for one of ordinary skill to try both options from the limited set of options. Therefore, the first oligonucleotide comprising the structure 5’-[first portion complementary to the second probe]-[portion complementary to nucleic acid of interest]-[first barcode sequence (the gene-unique identifier)]-[second barcode sequence]-3’ is prima facie obvious in view of the teachings of Wang 1 and Nagendran.
Regarding claim 18, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). As can be seen in FIG. 1A of Wang 1, Wang 1 teaches a second oligonucleotide probe (the primer oligonucleotide probe on the left of the box labeled “SNAIL probe”) comprising the structure: 5’-[portion complementary to nucleic acid of interest]-[first portion complementary to the first probe]-[second portion complementary to the first probe]-3’. Since in the combination of Wang 1 and Nagendran the complement of the barcode taught by Nagendran is added to a portion of the primer that is complementary to the first probe/snail probe, the only options in this structure to place the second barcode sequence are either the first portion complementary to the first probe or the second portion complementary to the first probe. As there are only 2 options, in the course of routine optimization it would be obvious for one of ordinary skill to try both options from the limited set of options. Therefore, the second oligonucleotide comprising the structure 5’-[portion complementary to nucleic acid of interest]-[first portion complementary to the first probe]-[barcode sequence]-3’ is prima facie obvious in view of the teachings of Wang 1 and Nagendran.
Regarding claim 19, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). As taught by Nagendran and evidenced by Eun, the second barcode sequence of the first oligonucleotide probe increases the specificity of the detection of the nucleic acid and reduces non-specific amplification (see 35 U.S.C. 103 rejection of claim 117 above in the paragraph regarding Nagendran).
Regarding claim 21, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method wherein the third oligonucleotide probe comprises a detectable label (FIG. 1A and 1E, “the decoding probes (line with star-symbol label) were labeled by fluorophores” [00174] and the rest of [00174] discussing FIG. 1).
Regarding claim 23, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method wherein the one or more detecting agents are antibodies that each comprise a detectable label (“DNA-conjugated antibodies for highly multiplexed protein detection” [0130], the DNA conjugated to the antibody is considered to be encompassed by the broadest reasonable interpretation of label since, though no limiting definition of detectable label is present in the instant specification, it does provide an example “i.e., any label that can be used to visualize the location” [0070], and the DNA-conjugated antibody can be used to visualize the location indirectly by using the DNA as a nucleic acid of interest for steps a)-c) and e)-g) of the method as taught by the combination of Wang 1 and Nagendran).
Regarding claim 24, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method further comprising contacting the one or more detecting agents with a secondary detecting agent (“the methods disclosed herein may be adapted to image DNA-conjugated antibodies for highly multiplexed protein detection” [0130]; “contacting a fixed and permeabilized intact tissue with at least a pair of oligonucleotide primers […], wherein the pair of primers comprise a first oligonucleotide […]; wherein each of the first oligonucleotide […] comprises a first complementarity region […]; wherein the first complementarity region of the first oligonucleotide is complementary to a first portion of the target nucleic acid” [0004]; treating the DNA conjugated to the antibody from [0130] as a target nucleic acid to be sequenced in the method of [0004], the oligonucleotides such of the method of [0004] such as the first oligonucleotide are secondary detecting agents).
Regarding claim 30, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method wherein the one or more detecting agents are antibodies that are each conjugated to an oligonucleotide sequence, and that each bind to a protein of interest (“the methods disclosed herein may be adapted to image DNA-conjugated antibodies for highly multiplexed protein detection” [0130]).
Regarding claim 31, the combination of Wang 1 and Nagendran teach the method of claim 30 (see 35 U.S.C. 103 rejection of claim 30 above). Wang 1 further teaches the method further comprising contacting each of the one or more antibodies that bind to a protein of interest with an oligonucleotide conjugated to a detectable label, wherein the oligonucleotide conjugated to a detectable label is complementary to the oligonucleotide sequence conjugated to the one or more antibodies (“the methods disclosed herein may be adapted to image DNA-conjugated antibodies for highly multiplexed protein detection” [0130]; treating the DNA conjugated to the antibody from [0130] as a target nucleic acid to be sequenced in the method of [0004] as discussed with regard to claim 1 above, the second oligonucleotide of [0004] is the claimed oligonucleotide conjugated to a detectable since it is complementary to a target nucleic acid, which is the DNA conjugated to the antibody, and is conjugated to a detectable label, which is the barcode sequence that is used to visualize the location of the target nucleic acid in step (g) of the method of [0004]).
Regarding claim 43, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method wherein the first barcode sequence of the first oligonucleotide probe is a gene-specific sequence used to identify the nucleic acid of interest (FIG. 1A, “gene-unique identifier”).
Regarding claim 46, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). Wang 1 further teaches the method wherein the method is performed at a subcellular resolution of 200 nm (“The methods disclosed include imaging the one or more hydrogel-embedded amplicons using any of a number of different types of microscopy, e.g., confocal microscopy, two- photon microscopy, light-field microscopy, intact tissue expansion microscopy, and/or CLARITY™-optimized light sheet microscopy (COLM)” [0099]; “ordinary, non-confocal light microscopes are limited by diffraction to about 200 nm resolution” [00111]; “Intact tissue expansion microscopy (exM) enables imaging of thick preserve specimens with roughly 70nm lateral resolution” [00113], since the claimed subcellular resolution of 200 nm falls within the taught range of microscopy techniques used in the method wherein some techniques are limited to 200+ nm resolution and expansion microscopy can increase the resolution to as low as 70 nm resolution, the claimed resolution is within a taught range and therefore prima facie obvious.
In view of the advantage of increased specificity of detection by reducing non-specific amplification that SNAIL probes with a barcode sequence complementary to a barcode sequence in the primer possess as taught by Nagendran and as evidenced by Eun, it would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to combine the method using SNAIL probes taught by Wang 1 with Nagendran in order to increase the specificity of detection (MPEP §2143 I. G.). One of ordinary skill in the art would have a reasonable expectation of success in this combination because both teach methods using SNAIL probes and the inclusion of a second barcode in the SNAIL probe and a complementary barcode in the primer of the method of Wang 1 would not prevent the SNAIL probe and primer from functioning to target nucleic acids of interest and generate an amplicon. Therefore, the invention as a whole of claims 1-3, 6, 9, 13, 17-19, 21, 23-24, 30-31, 43, 46-47, 117, and 170 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (cited in IDS filed 26 February 2024)(WO 2019/199579, published 17 October 2019), herein Wang 1, in view of Nagendran et al. (US 2023/0126825, effectively filed 14 April 2021), herein Nagendran, as evidenced by Eun (“Chapter 1 - Enzymes and Nucleic Acids: General Principles”, Enzymology Primer for Recombinant DNA Technology, Academic Press, pages 62-68 (1996)), as applied to claims 1-3, 6, 9, 13, 17-19, 21, 23-24, 30-31, 43, 46-47, 117, and 170 above, and further in view of Wang et al. (cited in IDS filed 26 February 2024)(“Three-dimensional intact-tissue sequencing of single-cell transcriptional states” Science 361(6400), eaat5691 (2018)), herein Wang 2.
Regarding claim 11, the combination of Wang 1 and Nagendran teach the method of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). However, though Wang 1 teaches the method wherein gene expression of up to 1000 nucleic acids of interest is mapped (“advantages of the methods described herein include […] highly multiplexed (up to 1000 genes)” [00129]), neither Wang 1 nor Nagendran teach the method wherein gene expression of more than 2000 nucleic acids of interest is mapped. This deficiency is made up for in the teachings of Wang 2.
Regarding claim 11, Wang 2 teaches the STARmap technique that Wang 1 is based upon (“Design and validation of STARmap principles” Wang 2 page 1; Fig. 1 of both Wang 1 and Wang 2; “The methods disclosed herein include an image-based in situ nucleic acid (DNA and/or RNA) sequencing technology by an improved sequencing-by-ligation process, specific signal amplification, hydrogel-tissue chemistry to turn biological tissue into a transparent sequencing chip, and associated data analysis pipelines, collectively termed Spatially-resolved Transcript Amplicon Readout Mapping (STARmap)” Wang 1 [0044]). Wang 2 further teaches doing the STARmap technique wherein gene expression for more than 2000 nucleic acids of interest is mapped (“although the STARmap scheme can encode and decode more than 1 million codes and the physical volume of mammalian cells is not limiting for amplification of more than 1000 genes (fig. S15), the 1020-gene experiments approached the upper limit of the optical volume of cells (fig. S15E); for those cases in which more genes are needed, STARmap may cover the whole transcriptome with more sequencing rounds of serial 1000-gene detection, or via optical resolution enhanced with superresolution microscopy or the physical swelling typical of the hydrogel-tissue chemistries” Wang 2 page 7 third paragraph; both doing the full 1020-gene in two serial sequencing rounds or using any of the described methods to cover the whole transcriptome would map gene expression of more than 2000 nucleic acids of interest).
In view of the advantage of being able to map more targets, including the whole transcriptome, by using serial sequencing rounds or methods of enhancing optical resolution as taught by Wang 2, it would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to combine the method based on STARmap taught by the combination of Wang 1 and Nagendran with Wang 2 in order to increase the number of targets that can be detected in a sample (MPEP §2143 I. G.). One of ordinary skill in the art would have a reasonable expectation of success in this combination because both teach methods using SNAIL probes to accomplish STARmap and are in the same field of endeavor. Therefore, the invention as a whole of claim 11 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 117 and 170 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 117 and 176 of copending Application No. 18/575,255, herein ‘255. Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding instant claim 117, claim 117 of ‘255 claims a set of probes comprising a first probe possessing all the limitations of the first oligonucleotide probe of instant claim 117 (with differing naming, see double patenting rejection of instant claim 1 above) and a third probe possessing all the limitations of the second oligonucleotide probe of instant claim 117 (with different naming, see double patenting rejection of instant claim 1 above). Note that this double patenting rejection is anticipation-type since the further limitations of claim 117 of ‘255 make it a species of the instant claim 117.
Regarding instant claim 170, claim 176 of ‘255 claims a system comprising a cell, a first probe possessing all the limitations of the first oligonucleotide probe of instant claim 117 (with differing naming, see double patenting rejection of instant claim 1 above) and a third probe possessing all the limitations of the second oligonucleotide probe of instant claim 117 (with different naming, see double patenting rejection of instant claim 1 above). Note that this double patenting rejection is anticipation-type since the further limitations of claim 176 of ‘255 make it a species of the instant claim 170.
Therefore, instant claims 117 and 170 are not patentably distinct from claims 117 and 176 of ‘255.
Claims 1-3, 6, 18, and 43 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 18, 37, 39, 41, and 45 of copending Application No. 18/575,255, herein ‘255, in view of Wang et al. (cited in IDS filed 26 February 2024)(WO 2019/199579, published 17 October 2019), herein Wang 1.
This is a provisional nonstatutory double patenting rejection.
Regarding instant claim 1, claim 1 of ‘255 claims a method comprising contacting a cell in step a) with one or more sets of probes wherein the first probe is equivalent to the first oligonucleotide probe of instant claim 1 (note that the first oligonucleotide barcode sequence of ‘255 is the second barcode sequence and the second oligonucleotide barcode sequence of ‘255 is the first barcode sequence) and the third probe is equivalent to the second oligonucleotide probe of instant claim 1, an identical (apart from naming) steps b) and c), a step d) that embeds concatenated amplicons in a polymeric matrix like step e) of instant claim 1 without the embedding of detecting agents, and a sequencing step e) that is broader than the claimed steps f) and g) of contacting and imaging in instant claim 1. The differences are (1) that claim 1 of ‘255 possesses further limitations pertaining to a second probe that recognizes a ribosome, (2) steps d) and e) of claim 1 of ‘255 is broader than steps e), f), and g) of instant claim 1, and (3) claim 1 of ‘255 lacks step d) of instant claim 1 of contacting the cell with one or more detecting agents wherein each detecting agent binds to a protein of interest. Regarding difference (1), the addition of further limitations in claim 1 of ‘255 does not prevent it from reading on instant claim 1. The deficiencies (2) and (3) are made up for in the teachings of Wang 1.
Regarding instant claim 1, Wang 1 teaches a similar method using similar probes that includes all limitations of steps d), e), f), and g) of instant claim 1 (see 35 U.S.C. 103 rejection of claim 1 above).
Regarding instant claim 2, claim 37 of ‘255 claims the method wherein the method is performed in multiple cells (the difference in recitation “gene and protein expression are profiled” in instant claim 2 and “RNAs being translated are profiled” in claim 37 of ‘255 is strictly intended use and does not differentiate the scope of the claims).
Regarding instant claim 3, claim 39 of ‘255 claims the method wherein the cells comprise a plurality of cell types.
Regarding instant claim 6, claim 41 of ‘255 claims the method wherein the cell is present within an intact tissue.
Regarding instant claim 18, claim 18 of ‘255 claims the method wherein the third probe (equivalent to the claimed second oligonucleotide probe in the instant claims) comprises the structure: 5’-[portion complementary to RNA of interest, narrower than the nucleic acid of interest of instant claim 18]-[portion complementary to first probe]-[barcode sequence]-3’.
Regarding instant claim 43, claim 45 of ‘255 claims the method wherein the second oligonucleotide barcode sequence of the first probe (equivalent to the first barcode sequence of the first oligonucleotide probe in the instant claims) is a gene specific sequence used to identify an RNA of interest (narrower than the nucleic acid of interest of claim 45).
In view of Wang 1’s teaching of using probes like those in ‘255 claim 1 to not just detecting nucleic acid sequences of interest but also proteins of interest using DNA-conjugated oligonucleotides, one of ordinary skill in the art would be motivated to combine Wang 1 and ‘255 to improve claim 1 of ‘255 with the ability to detect proteins of interest. One of ordinary skill in the art would have a reasonable expectation of success because both Wang 1 and ‘255 use SNAIL probes and the inclusion of DNA-conjugated antibodies for protein detection would not be expected to prevent the specific binding and amplification of SNAIL probes. Therefore, the invention as a whole of claims 1-3, 6, 18, and 43 are prima facie obvious variants of claims 1, 18, 37, 39, 41, and 45 of ‘255.
Conclusion
Claims 1-3, 6, 9, 11, 13, 17-19, 21, 23-24, 30-31, 43, 46-47, 117, and 170 are rejected. Claim 134 is withdrawn.
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/JEFFREY BELLAH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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