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 .
Please note: The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Response to Amendment
The amendment to the claims filed on 12/9/2025 does not comply with the requirements of 37 CFR 1.121(c) because the claims do not contain all necessary markings to indicate all deleted/changed subject matter (claim 6 does not indicate that “(Ilf)” was changed to “(Il(f)”). Amendments to the claims filed on or after July 30, 2003 must comply with 37 CFR 1.121(c) which states:
(c) Claims. Amendments to a claim must be made by rewriting the entire claim with all changes (e.g., additions and deletions) as indicated in this subsection, except when the claim is being canceled. Each amendment document that includes a change to an existing claim, cancellation of an existing claim or addition of a new claim, must include a complete listing of all claims ever presented, including the text of all pending and withdrawn claims, in the application. The claim listing, including the text of the claims, in the amendment document will serve to replace all prior versions of the claims, in the application. In the claim listing, the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered).
(1) Claim listing. All of the claims presented in a claim listing shall be presented in ascending numerical order. Consecutive claims having the same status of “canceled” or “not entered” may be aggregated into one statement (e.g., Claims 1–5 (canceled)). The claim listing shall commence on a separate sheet of the amendment document and the sheet(s) that contain the text of any part of the claims shall not contain any other part of the amendment.
(2) When claim text with markings is required. All claims being currently amended in an amendment paper shall be presented in the claim listing, indicate a status of “currently amended,” and be submitted with markings to indicate the changes that have been made relative to the immediate prior version of the claims. The text of any added subject matter must be shown by underlining the added text. The text of any deleted matter must be shown by strike-through except that double brackets placed before and after the deleted characters may be used to show deletion of five or fewer consecutive characters. The text of any deleted subject matter must be shown by being placed within double brackets if strike-through cannot be easily perceived. Only claims having the status of “currently amended,” or “withdrawn” if also being amended, shall include markings. If a withdrawn claim is currently amended, its status in the claim listing may be identified as “withdrawn—currently amended.”
(3) When claim text in clean version is required. The text of all pending claims not being currently amended shall be presented in the claim listing in clean version, i.e., without any markings in the presentation of text. The presentation of a clean version of any claim having the status of “original,” “withdrawn” or “previously presented” will constitute an assertion that it has not been changed relative to the immediate prior version, except to omit markings that may have been present in the immediate prior version of the claims of the status of “withdrawn” or “previously presented.” Any claim added by amendment must be indicated with the status of “new” and presented in clean version, i.e., without any underlining.
(4) When claim text shall not be presented; canceling a claim.
(i) No claim text shall be presented for any claim in the claim listing with the status of “canceled” or “not entered.”
(ii) Cancellation of a claim shall be effected by an instruction to cancel a particular claim number. Identifying the status of a claim in the claim listing as “canceled” will constitute an instruction to cancel the claim.
(5) Reinstatement of previously canceled claim. A claim which was previously canceled may be reinstated only by adding the claim as a “new” claim with a new claim number.
As noted above, the amendment under consideration herin fails to comply with 37 CFR 1.121 because the claims do not contain all necessary markings to indicate all changed subject matter. Thus, the amendment could be considered non-responsive. In the interest of compact prosecution the amendment at issue will not be considered non-responsive. However, any future responses failing to comply with 37 CFR 1.121 will be held non-responsive, and will not be considered. Applicants are encouraged to thoroughly review all subsequent amendments to ensure they are compliant.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 12/9/2025 has been entered.
Claim Status
Claims 1-10 are pending and being examined on the merits.
Claim Objections
Withdrawn Claim Objections:
The objections to claims 1-4, 6, and 8, as detailed in the Office Action of 8/20/2025, are withdrawn in light of Applicant’s amendments to the claims.
New Claim Objections (Necessitated by Amendments):
Claims 5, 6, and 9 are objected to because of the following informalities:
Claim 5 reads “BR (binding region): oligonucleotide comprising 3 to 30 nucleotide residues n : integer => 1”. There should be a comma between “residues” and “n” to make it clear that this is defining a new term (“n”) and not a continuation of the definition of BR.
Claim 6 reads “(Il(f)” in line 3 and should read “(Ilf)”.
Claim 9 recites “wherein the nucleic acids of the target cell to be identified are single-stranded” and “the single stranded nucleic acid”. It should read “wherein the nucleic acids of the target cell to be identified are [[single-stranded]]single stranded” and “the [[single stranded]]single-stranded nucleic acid”.
Withdrawn Claim Rejections
35 USC § 112b: The rejections of claims 9 and 10, as detailed in the Office Action of 8/20/2025, are withdrawn in light of Applicant’s amendments to the claims.
35 USC § 102: The rejection of claims 1-4 and 7-9 under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Bharadwaj and Onov (hereinafter referred to as Bharadwaj; WO2019099908A1, published May 23, 2019, priority November 17, 2017; cited in IDS submitted 4/25/2022) is withdrawn in light of Applicant’s amendments.
35 USC § 102/103: The rejection of claims 5 and 6 under 35 U.S.C. 102(a)(1) and 102(a)(2) as anticipated by or, in the alternative, under 35 U.S.C. 103 as obvious over Bharadwaj and Onov (hereinafter referred to as Bharadwaj; WO2019099908A1, published May 23, 2019, priority November 17, 2017; cited in IDS submitted 4/25/2022) in view of Macosko et al. (Cell, 2015; cited on PTO-892 of 4/7/2025) is withdrawn in light of Applicant’s amendments.
35 USC § 103: The rejection of claim 10 under 35 U.S.C. 103 as being unpatentable over Bharadwaj and Onov (hereinafter referred to as Bharadwaj; WO2019099908A1, published May 23, 2019, priority November 17, 2017; cited in IDS submitted 4/25/2022) in view of Gerver et al. (hereinafter “Gerver”; Lab on a Chip, 2012) is withdrawn in light of Applicant’s amendments of the claims.
New Claim Rejections
Claim Rejections - 35 USC § 112a – New Matter
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new matter rejection.
Claim 1 has been amended to contain the limitation “this combined assessment of two pre-selected physical properties being done at the same time”. There is no support for this limitation in the original disclosure. There is support for the pre-selected physical property of the cell and the pre-selected physical property of the color-coded composition being combined for the decision of the isolation of the two together throughout the specification (paragraphs [0009-0011, 0051, and 0053]). However, there is no support for the assessment of the physical property occurring “at the same time”. The working examples provided by the specification indicate that the sorting of the cells and the color-coded compositions (beads) occurs sequentially rather than at the same time (e.g., step 14 of Case 2 (paragraph [0053]): “cell is first sort event, bead is second event”).
Claims 2-10 depend from claim 1, inherit this deficiency, and are rejected on the same basis.
Claim Rejections - 35 USC § 112b - Indefiniteness
Claims 1-10 are 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 1 recites the limitation "the at least one pre-selected physical property of the target cell" in line 12-13. There is insufficient antecedent basis for this limitation in the claim. This indefiniteness could be overcome by removing “the” between “assessing” and “at least on pre-selected physical property of the target cell”. This removes ambiguity as to whether there should have been a pre-selected physical property of the target cell earlier in the claim.
Additionally, claim 1 contains the limitation that the combined assessment of the pre-selected physical properties of the target cell and the color-coded composition occurs “at the same time”. As stated in the 112a New Matter rejection above, there is no support/definition as to what is meant by “at the same time” in the specification. The specification contains a working example in which the cells and beads are mixed and are sequentially sorted. It is unclear whether “at the same time” means that the cells and beads are both being imaged and sorted at the same time or if the cells are imaged and sorted followed by the beads being imaged and sorted with a particular sorted cell. Clarification is required.
Claims 2-10 depend from claim 1, inherit these deficiencies, and are rejected on the same basis.
Claim Rejections - 35 USC § 102
Claims 1, 4, and 7 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang (Zhang et al., bioRxiv September 12, 2019; cited on IDS of 7/7/2025).
Zhang teaches a method in which target cells from a cell population are controllably isolated into distinct entities with at least one color-coded bead to enable identification of nucleic acids of interest (single-cell RNA sequencing; Abstract and pg 3, paragraph 3).
Claim 1 is directed to a method for identifying nucleic acids of a target cell from a cell population through isolating at least one target cell from the cell population and at least one color-coded composition comprising a solid particle conjugated to an oligonucleotide into one compartment. Zhang teaches isolated a specific target cells based on a pre-selected physical property (color, red or green) into a compartment with a specific color-coded composition comprising a solid particle conjugated to an oligonucleotide which is also isolated based on a pre-selected physical property (color, blue). Zhang teaches that the combined assessment of the two pre-selected physical properties is done at the same time (pg 3, paragraph 2: “To enable scRNA-seq of the printed cells, Drop-Seq beads must also be printed, which requires that they be detectable in the print head; this is accomplished by labeling them with 4-MU, a blue dye that does not overlap with the cell stains (Fig. 2B, lower left). This signal allows bead-loaded droplets to be discerned from bead-empty droplets (Fig. 2B, lower right). To print cells and beads in defined combinations, we generate a “print file” containing gating and location instructions that we input into the printer software; the printer reads this file, printing cells and beads to the nanoplate according to the instructions in the file (Fig. 2C, left).”). Zhang teaches, after isolation of the selected cell with the selected bead, lysing the at least one isolated target cell and coupling the nucleic acid molecules of the lysed isolated target cells with the oligonucleotide of the color-coded composition, forming a first conjugate and then determining the sequence of the first conjugate, thereby identifying the target cell (Figure 1).
Claim 4 is directed to the pre-selected physical properties of the color-coded composition in which the physical property is defined by the solid particle. Zhang teaches that the physical property of the beads (the solid particle) are the color (pg 3, paragraph 2: “To enable scRNA-seq of the printed cells, Drop-Seq beads must also be printed, which requires that they be detectable in the print head; this is accomplished by labeling them with 4-MU, a blue dye that does not overlap with the cell stains”).
Claim 7 is directed to the type of compartment that the target cell and color-coded composition are placed into, which consists of one aqueous droplet surrounded by a fluid immiscible with water. Zhang teaches a device which suspends the target cell and the color-coded composition into separate droplets, which are then merged in defined combinations to create merged droplets within a nanowell plate. The emulsions/droplets are aqueous droplets surrounded by a fluid immiscible with water (oil; Materials and Methods - Cell and bead encapsulation within monodisperse droplet emulsions).
Claim Rejections - 35 USC § 103
Claims 2 and 3 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang (Zhang et al., bioRxiv September 12, 2019; cited on IDS of 7/7/2025) in view of Siltanen (Siltanen et al., WO 2020232072 A1, EFD of 5/14/2019).
The teachings of Zhang are detailed above. Relevant to the instantly rejected claims, Zhang teaches deterministic droplet creation through sorting of cells and oligonucleotide-adorned beads based on pre-selected physical properties of each and performing sequencing on nucleic acids released from said cells.
Zhang does not teach that the pre-selected physical property of the target cell is based on protein composition. However, use of protein composition to deterministically sort cells into isolated droplets is known in the art, as taught by Siltanen.
Siltanen teaches a method of selectively combining distinct entities (cells and beads) by detecting an optical quality and then selectively combining them based upon this assessment of a pre-determined physical property (Abstract). Siltanen teaches that cells can be labeled with fluorescent antibodies to facilitate cell sorting from a mixed population of cells (paragraph [0463]). Labelling of cells with fluorescent antibodies reads on the pre-selected physical property being a protein composition, wherein at least one intracellular or extracellular protein is marked by fluorescence staining.
It would have been prima facie obvious to one having ordinary skill in the art, as of the effective filing date of the instant application, to have modified the method of Zhang to use the fluorescently labeled antibodies of Siltanen for the pre-selected physical property of cells. One would be motivated to do so given the assertion by Siltanen that this elminatees the need for oversampling of more abundant cell types in a mixed cell sample, which reduces sequencing costs (paragraph [0463]). One would have a reasonable expectation of success given that Zhang labels cells prior to sorting with fluorescent dyes, and labeling of cells with fluorescent antibodies would yield the predictable result of successful sorting based on the fluorescence of the antibodies rather than the fluorescence of the dyes.
Claims 5, 6, 8, and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang (Zhang et al., bioRxiv September 12, 2019; cited on IDS of 7/7/2025) in view of Macosko (Macosko et al., Cell 2015; cited on PTO-892 of 4/7/2025).
The teachings of Zhang are detailed above. Relevant to the instantly rejected claims, Zhang teaches deterministic droplet creation through sorting of cells and oligonucleotide-adorned beads based on pre-selected physical properties of each and performing sequencing on nucleic acids released from said cells. Zhang teaches that the color-coded composition, the bead, is a solid particle (X) attached to a PCR handle, a color specific barcode, a bead specific barcode, a UMI, and a binding region.
Claims 5 and 6 are directed to the composition of the color-coded composition which consists of a solid particle (X) attached to an oligonucleotide comprised of a PCRhandle (P, 4-30 nucleotides), a color specific barcode (C, 1-8 nucleotides), a bead specific barcode (B, 8-30 nucleotides), and a binding region (BR, 3-30 nucleotides). The specification of the instant application describes the color specific barcode as a sequence which “allows identification of the cell or cell type” and the bead specific barcode as the sequence which “serves as cell specific barcodes allowing to assign sequencing information to the origin cell” (page 5 of the instant specification, paragraphs [0026-0027]). The descriptions, while slightly different, both allow association of the sequence with the identity of the target cell and are barcoding sequences. Claim 6 further includes a unique molecular identifier sequence (U) in the composition. Additionally, the specification refers to each as a “barcode” as “they allow identifying a single target by their unique sequence” and may be composed of “same or different nucleotide sequences” (paragraphs [0021-0022]). Zhang teaches a barcoded oligonucleotide attached to a bead (Figure 1B). This barcoded oligonucleotide comprises a PCR handle and a binding region (poly T sequence; Figure 1B). Zhang further teaches a barcode on the oligonucleotide attached to the bead which can “be traced back to a well on the array…and associated with the previously recorded optical data”, which reads on bead specific barcode and color specific barcode given that association of a particle physical property with a cellular physical property when isolating into a compartment enables identification of the cell of origin upon sequencing (pg 2, paragraph 3). Zhang teaches that the oligonucleotide also include a UMI sequence (Figure 1B). The composition, as taught by Zhang, has these particular regions contiguously attached (0 nucleotide residue spacers).
Zhang does not teach the particular lengths of the PCR handle, barcodes, binding region, or UMI. However, specific ranges of functional regions in oligonucleotides used for single cell barcoded sequencing is known in the art, as taught by Macosko.
Macosko teaches a method called Drop-Seq, which enables single cell mRNA profiling using barcoded oligos attached to beads. The oligonucleotides contain a PCR handle that is 23 nucleotides long (reads on 4 to 30 nucleotide residues), a barcode sequence that is 12 nucleotides long (reads on bead specific barcode of 8 to 30 nucleotide residues), a UMI that is 8 nucleotides long (reads on 5 to 15 nucleotide residues), and a binding region (poly-T) that is 30 nucleotides long (reads on 3 to 30 nucleotide residues; Figure 1B-D and Table S6).
It would have been prima facie obvious to one having ordinary skill in the art, as of the effective filing date of the instant application, to have modified the method Zhang to use typical lengths of PCR handles, UMIs, and binding regions in the barcoded oligos, as taught Macosko. One would be motivated to use these lengths given that is has been proven in the art to effectively allow single cell expression profiling and allows for use of downstream applications such as Illumina sequencing, as taught by Macosko. One would have a reasonable expectation of success since Macosko demonstrate that these oligo sequence lengths work for interrogation of single cells. Additionally, Zhang teaches that their scRNA-seq protocol is adapted from the validated “Drop-Seq” protocol of Macosko (page 2, paragraph 3).
Claim 8 is directed to the association of a color specific barcode (determined through sequencing) with the physical property of the target cells used for selection. Zhang teaches using a paired data set of Drop-Seq barcode and optical information of the cell to associate the two and thus identify the cell of origin via sequencing of the conjugate (Figure 1 and page 2, paragraph 3-page 3, paragraph 1-2).
Claim 9 is directed to the method of claim 5 wherein the nucleic acids of the target cell are single-stranded and a complementary strand to this single stranded nucleic acid is synthesized and hybridized to the BR units of the color-coded composition to form a second conjugate, and the second conjugate is then sequenced to identify the target cell. Zhang teaches that the nucleic acids to be identified are RNA (single stranded) and that a complementary strand is synthesized and hybridized to the binding region of the color-coded composition and sequenced to identify the target cell (Figure 1 and Materials and Methods - Sequencing library preparation).
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang (Zhang et al., bioRxiv September 12, 2019; cited on IDS of 7/7/2025) in view of Gerver (Gerver et al.; Lab on a Chip, 2012; cited on PTO-892 of 8/20/2025 (U)).
The teachings of Zhang are outlined above. Relevant to the instantly rejected claim, Zhang teaches isolating single cells and beads into partitions by pre-selected physical properties. Zhang teaches that the beads are dyed.
Zhang does not teach that the beads (solid particle X) comprise at least two dyes having different emission spectra with a difference in emission maxima of at least 10nm. However, the use of multiple fluorescent dyes on the same solid particle with different emission spectra and a difference in emission maxima of at least 10nm was known in the art, as taught by Gerver.
Gerver teaches “spectrally encoded fluorescent beads” comprised of at least two “lanthanide nanophosphors” (Abstract). According to the instant specification, “Useful dyes are for example…metallo-organic complexes, such as Ru, Eu, Pt complexes” (paragraph [0039]). Lanthanide nanophosphors are metallo-organic complexes, with Eu being one of the lanthanide metals used to construct the nanophosphors taught by Gerver (Figure 1 description). Gerver teaches using differing ratios of fluorophores to construct spectral barcodes using dyes that have different emission spectra and differences in emission maxima of at least 10nm (Figure 1a).
It would have been prima facie obvious to one having ordinary skill in the art, as of the effective filing date of the instant application, to have modified the method of Zhang with the combinations of lanthanide nanophosphors as taught by Gerver. One would be motivated to incorporate the at least two fluorescent dyes given the assertion by Gerver that this allows for the generation of “uniquely identifiable signatures” that can be employed for multiplex assays (Introduction, paragraphs 2 and 3). One would have a reasonable expectation of success given that Gerver teaches that spectral encoding schemes “are compatible with conventional bead synthesis procedures and standard detection optics” (Introduction, paragraph 3).
Response to Remarks
Applicant has traversed the rejection of claims 1-4 and 7-9 under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Bharadwaj and Onov (hereinafter referred to as Bharadwaj; WO2019099908A1, published May 23, 2019, priority November 17, 2017; cited in IDS submitted 4/25/2022) and the rejection of 5 and 6 under 35 USC 102(a)(1) and 102(a)(2) or in the alternative 35 USC 103 over Bharadwaj further in view of Macosko in the Remarks of 12/9/2025 (pages 7-9). The previous rejections over Bharadwaj have been withdrawn in light of Applicant’s amendments to the claims, and thus Applicant’s arguments regarding Bharadwaj are moot. New limitations introduced into the amendments have been addressed by the new rejections presented above.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
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/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683