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 Group I in the reply filed on June 22, 2026 is acknowledged.
Claim 80 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 June 22, 2026.
Information Disclosure Statement
The IDS received on August 15, 2024, October 27, 2025, and June 22, 2026 are proper and are being considered by the Examiner.
NPL references 949-951 of the IDS received on August 15, 2024 have been lined through as the citation does not have at least a publication year.
Drawings
The drawings received on February 26, 2024 are acceptable.
Claim Rejections - 35 USC § 112
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.
Claims 4, 6-17, 19, 20, 27, 41, 42, and 65 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 4 is indefinite for reciting the below phrase:
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The phrase appears to be circular in description and makes no sense.
For the purpose of prosecution, each intracellular target-binding reagent comprises an oligonucleotide comprising a unique identifier sequence for the target-binding reagent.
Claim 4 recites the phrase, “the cell surface target-binding reagent”. There is an insufficient antecedent basis for this limitation in the claim.
Claim 8 recites the phrase, “the decoy oligonucleotide”. It is unclear to which of the plurality of decoy oligonucleotides, “the decoy oligonucleotide” is referring to.
For the purpose of prosecution, the phrase has been construed to mean, “the decoy oligonucleotides”.
Claims 9, 11-17, 19, and 20 are indefinite for the same reason as claim 8 and the same claim construction has been made.
Claim 10 recites the phrase, “the sequence”. It is unclear which sequence this phrase is referring to as the parent claim contains many oligonucleotides such as decoy oligonucleotides, intracellular target-binding reagent specific oligonucleotide, oligonucleotide barcodes.
Claim 41 recites the phrase, “the lysis buffer”. There is an insufficient antecedent basis for this limitation in the claim. No interpretation could be made for this claim as there is a complete lack of such a step occurring in any of the preceding claims. The claim has not been further treated on its merit therefore.
Claim 42 is indefinite for the same reason as claim 41 and also has not been further treated on its merit.
Claims 6-17, 19, 20, 27, 41, 42, and 65 are indefinite by way of their dependency on claim 4.
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.
Claims 4, 6-17, 19, 20, and 65 are rejected under 35 U.S.C. 103 as being unpatentable over Fan et al. (US 2018/0088112 A1, published March 29, 2018) in view of Nazarenko et al. (US 2006/0051809 A1, published March 9, 2006).
With regard to claim 4, Fan et al. teach a multiomic detection that allows the detection of protein and gene expression (“present disclosure relates generally to molecular biology, and more particular to simultaneous measurement of protein expressions and gene expression”, section [0003]), wherein the artisans teach the steps of:
fixing a plurality of cells each comprising a plurality of intracellular targets (i.e., proteins), copies of a nucleic acid target (i.e., genes, mRNA, etc.), and one or more non-target nucleic acid (see “method comprises ‘fixating the cell prior to contacting the cell with a first pair of interaction determination compositions”, section [0169]);
permeabilizing the plurality of cells (“[s]ingle cells … permeabilized … were sorted”, section [0899]);
contacting the plurality of intracellular target-binding reagents with the plurality of cells, wherein each of the plurality of intracellular target-binding reagent comprises an intracellular target-binding reagent specific oligonucleotide comprising a unique identifier1 (see below, from Figure 4, antibody specific oligo sequence);
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partitioning the plurality of cells associated with the intracellular target-binding reagents to a plurality of partitions, wherein a partition of the plurality of partitions comprise a single cell from the plurality of cells (“[i]ndividual cells and beads may be compartmentalized using alternatives to microwells, for example, a single solid support and single cell could be confined within a single droplet in an emulsion”, section [0407]);
in the partition, comprising the single cell, contacting a plurality of oligonucleotide barcodes with the copies of the nucleic acid target and the intracellular target-binding reagent specific oligonucleotides for hybridization wherein the oligonucleotide barcode each comprises a first molecular label (see Fig. 2, reproduced below):
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As seen, the bead comprises a sequence that hybridizes with nucleic acid target and the intracellular target-binding reagent specific oligonucleotides (via the dT region), wherein the oligonucleotide barcode comprises a first molecular label;
extending the plurality of oligonucleotide barcodes hybridized to the intracellular target-binding reagent specific oligonucleotides to generate a plurality of barcoded intracellular target-binding reagent specific oligonucleotides each comprising a sequence complementary to at least a portion of the unique intracellular target identifier sequence and the first molecular label (see above, where the polyA tail anneals to the polydT region of the bead-immobilized barcode, and its extension results in the requisite structure, see also “analysis of simultaneous quantitative analysis of a plurality of protein targes and a plurality of nucleic acid target molecules in a sample … extend the oligonucleotide probes hybridized to … the oligonucleotide 525”, section [0508], the oligonucleotide 525 is conjugated to the antibody, id.);
extending the plurality of oligonucleotide barcodes hybridized to the copies of the nucleic acid target to generate a plurality of barcoded nucleic acid molecules each comprising complementary to at least a portion of the nucleic acid target and the first molecular label (see above, also section [0508]); and
obtaining a sequence information of the plurality of barcoded nucleic acid molecules to determine the copy number of the nucleic acid target and obtaining sequence information of the plurality of barcoded intracellular target-binding reagent specific oligonucleotides or products thereof to determine the number of copies of at least one intracellular target in one or more of the plurality of cells (“obtaining the sequencing data comprises obtaining sequencing data of the plurality of amplicons”, section [0096]), see also, “extending the oligonucleotide probes hybridized to the oligonucleotides and nucleic acid target molecules to produce a plurality of labeled nucleic acids, wherein each of the labeled nucleic acid comprises a unique identifier or a nucleic acid target molecule, and a barcode sequence; and determining the number of unique barcode sequences for each unique identifier and each nucleic acid target molecule, whereby the quantity of each protein target and each nucleic acid target molecule in the sample is determined”, section [0008]).
With regard to claim 65, the intracellular target comprises protein target (“binding target of the cellular component can comprise … intracellular protein” section [0078]).
Fan et al. do not teach that the method employ blocking reagent comprising decoy oligonucleotides (claim 4, in-part).
Consequently, Fan et al. do not teach that the blocking reagent is contacted with the plurality of cells at the same time or after fixing/permeabilizing of the cells (claim 6), or that the decoy oligonucleotides are capable of hybridizing to at least a portion of a non-target nucleic acid (claim 7), wherein the decoy oligonucleotides comprise a sequence complementary to at least a portion of a non-target nucleic acid (claim 8), comprise a sequence identical or substantially similar to a sequence of the intracellular target-binding reagent specific oligonucleotide (claim 9), having a sequence of 3-40 bases in length (claim 10), or that the at most, has 50% identity to the intracellular target-binding reagent specific oligonucleotides (claim 11), does not comprise a UMI (claim 12), has a random sequence (claim 13), with no more than 4-7 consecutive Ts or As (claim 14), at least one G or C in every 4-7 bases (claim 15), has at least one modified nucleotides (claim 16), at 5’ and/or 3’ (claim 17), which prevents a polymerase extension reaction (claim 19), the modification recited in claim 20.
Nazarenko et al. teach a well-known means of utilizing a blocker oligonucleotide to prevent cross-hybridization of target nucleic acid to target-specific probes (“method employes probes in addition to the CSP [capture specific probe] … blocker probe comprises sequences that are substantially complementary to the sequence of the CSP … addition of blocker probes to the hybridization reaction mixture prevents non-hybridized CSPs from hybridizing to cross-reactive nucleic acid sequences present in the target and therefore increases the specificity of the detection”, section [0064]).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Fan et al. with the advantage well-known in the art, as taught by Nazarenko et al., thereby arriving at the invention as claimed for the following reasons.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
One of ordinary skill in the art would have been motivated to employ blocker oligonucleotides having a sequence that is similar to the antibody-conjugated oligonucleotide sequence of Fan et al. for the same purpose of preventing the antibody-oligonucleotide conjugate to anneal to non-specific target nucleic acids within the permeabilized cell instead of the protein target for which it is designed.
Doing so would have realized the same predictable outcome of ensuring that only the antibody-oligonucleotide conjugates bound via the respective protein are detected instead of antibody-oligonucleotide conjugates which are non-specifically bound to the permeabilized cell through the non-specific binding via its oligonucleotide.
As to the determination of the actual sequence of such blocker oligonucleotides (or decoy oligonucleotides), including but not limited to its length, its sequence and base compositions, such would have been well-within the purview of the ordinarily skilled artisan to design that which provides an optimal result at reducing non-specific interaction between the antibody-oligonucleotide conjugate and non-target nucleic acids present within the permeabilized cell.
As to the blocker oligonucleotides comprising a modification at its 5’ and/or 3’ end(s), doing so would also have been obvious so that the blocker oligonucleotide non-specifically annealed to non-targets are not extended in the extension reaction of Fan et al., in order to reduce non-specific detectable products.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Claim 27 is rejected under 35 U.S.C. 103 as being unpatentable over Fan et al. (US 2018/0088112 A1, published March 29, 2018) in view of Nazarenko et al. (US 2006/0051809 A1, published March 9, 2006) as applied to claims 4, 6-17, 20, and 65 above, and further in view of Xiang et al. (Nucleic Acids Research, 2004, vol. 32. No. 22, e185, pages 1-8).
The teachings of Fan et al. and Nazarenko et al. have already been discussed above.
While Fan et al. expressly suggest that the cell are fixed and permeabilized, the artisans do not explicitly suggest all types of reagents which can be utilized in the fixation.
Consequently, Fan et al. (nor Nazarenko et al.) teach a cleavable cross-linking reagent, DSP.
Xiang et al. teach the use of a reverse cross-linker, DSP for expression profiling and immunostaining:
“the RNA that is extracted is chemically modified and it cannot be reverse-transcribed readily … we looked for an alternative fixative that would penetrate cell readily … protect RNA from degradation and permit us to extract unmodified RNA with ease … obvious candidates were reverse cross-linkers …the most attractive was dithio-bis(succinimidyl propionate) (DSP)” (page 1)
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Fan et al. and Nazarenko et al. with the teachings of Xiang et al., thereby arriving at the invention as claimed for the following reasons.
One of ordinary skill in the art would have realized that utilizing a reversible fixation reagent such as DSP in the fixing and permeabilization step of Fan et al. that has been shown to, “yield RNA that could be amplified efficiently … resembling those seen with unfixed/unstained samples” would have been advantageous, allowing access to the mRNA for Fan et al.’s subsequent step of hybridization/extension reaction as well as amplification steps.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 September 5, 2026
/YJK/
1 see above claim interpretation surrounding this phrase.
Prosecution Insights