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 .
Status of the Claims
Claims 1-10 are pending. Claims 1-5 are the subject of this NON-FINAL Office Action. Claims 6-10 have been withdrawn. This is the first action on the merits.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-5, in the reply filed on 08/29/2025 is acknowledged. Claims 6-10 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. The requirement is still deemed proper and is therefore made FINAL.
Drawings
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they do not include the following reference sign(s) mentioned in the description:
Par. 0022 describes Fig. 2 and refers to “the microfluidic device 10.” The reference sign “10” is not in Fig. 2.
The reference sign “10” is in Fig. 10.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description:
Fig. 7 includes reference character “20,” which is not mentioned in the description of Fig. 7 in par. 0033 or par. 0035.
The reference character “20” is described in par. 0038 in reference to Fig. 9, which does not include the reference character “20” in the drawing.
Corrected drawing sheets in compliance with 37 CFR 1.121(d), and/or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) 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. 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.
Claim Objections
Claim 1 and 4 are objected to because of the following informalities:
Claim 1 refers to “the plurality of microwell” in line 13 and line 15. Claim 1 refers to “the plurality of capture oligonucleotide” in line 15. “Microwell” and “oligonucleotide” should be plural (e.g. microwells and oligonucleotides) to match the previously recited terminology.
Claim 4 similarly recites “the plurality of capture oligonucleotide” and should be corrected to “the plurality of capture oligonucleotides.”
Appropriate correction is required.
Claim Interpretation
Claim 1 recites the limitation “recording the morphological characteristics of the cell.” Claim 1 does not require a particular method of recording the morphological characteristics of a cell. The claim will be interpreted as encompassing any method of recording morphological characteristics of a cell.
Claim 1 recites the limitation “and the morphological characteristics and gene expression of the cell are integrated together.” The claim does not recite a particular method or structure for the integration of the morphological characteristics and gene expression of the cell. The claim will be interpreted as not requiring any additional method steps or structures to achieve the integration of the morphological characteristics and gene expression of the cell.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1-3 and 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Brower et al. (WO 2020/243160 A1) in view of Kim et al.(Electroactive microwell arrays for highly efficient single-cell trapping and analysis. Small. 7, 2011, 3105-3247).
Regarding claim 1, Brower teaches a method for associating data from phenotypic analysis of a single cell with sequencing data from the single-cell using spectrally-encoded microbeads (Abstract).
Brower teaches generating an arrayed configuration comprising a plurality of single-cell analysis compartments, wherein each single cell analysis compartment comprises a single cell or nucleus and a single microbead with a plurality of capture oligonucleotides immobilized on the bead (par. 0009).
Brower teaches the arrayed configuration can comprise a microfluidic device comprising a microwell array (par. 0011, 0100). Brower further teaches the microwell device may further comprise an electrode slide (par. 0011).
Brower teaches the capture oligonucleotides comprises a nucleic acid sequence that is substantially complementary to a sequence of one or more target polynucleotides from the cell or nucleus (par. 0009). Brower further teaches the capture oligonucleotide may comprise a unique molecular identifier sequence (par. 0009, 0010, 0070).
Brower teaches the capture oligonucleotides comprises a spectral identifier sequence (par. 0007), which is a barcode sequence unique to a single bead and thus unique to a microwell (par. 0007, 0009, 0089, 0091, 0097).
Brower teaches the target polynucleotide can be mRNA (par. 0007).
Brower teaches imaging the arrayed configuration to determine spatial position of the single cell or nucleus and the microbead contained in each single-cell analysis compartment (par. 0009, 0010).
Brower teaches that single cells in the compartments are permeabilized or lysed and the nucleic acids are hybridized with the capture oligonucleotides immobilized on the beads (par. 0071). Brower teaches this step occurs after the phenotyping step (par. 0087).
Brower further teaches processing the polynucleotides bound to the microbead by methods such as an RT-PCR reaction, or by the use of a reverse transcriptase so that cDNA is attached to the bead surface and followed by a PCR reaction to generate amplicons which can be pooled for sequencing (par. 0009, 0010), and the sequencing data was analyzed to couple spectral bead codes (corresponding to barcodes) to gene expression data such that transcriptomic bead data is directly matched to each single cell classified phenotypes via 1:1 linkage with the spectral bead code and identifier linkage (par. 0090-0092).
Brower teaches an electrode (DEP ITO) slide for electrical lysis (par. 0082; Fig. 1), but does not specifically teach using an interdigital electrode to capture a single cell above each of the plurality of microwells.
Kim teaches a method for arraying an analyzing large populations of single cells in the form of a microfluidic device (Abstract). Kim teaches the device uses interdigitated electrodes for the dielectrophoresis (DEP) (pg. 3241, right col., par. 1, par. 3). Kim teaches the interdigitated ITO electrodes attract cells (pg. 3241, right col., par. 1; Fig. 1a).
It would have been obvious to one of ordinary skill in the art to substitute the DEP ITO electrode slide as taught by Brower for the interdigital electrode slide of Kim, as it would be a simple substitution of one type of DEP ITO electrode slide for another, with no evidence of unexpected results.
Regarding claim 2, Brower teaches the barcode sequence is 9 bases (par. 0097).
Regarding claim 3, Brower teaches the unique molecular identifier sequence comprises 8 bases (Tables 2 and 3; pg. 43-51).
Regarding claim 5, Brower teaches the cell morphology is imaged using bright-field and fluorescent images (par. 0086, 0089; Fig. 2B).
Claim(s) 4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Brower and Kim as applied to claim 1 above, and further in view of ThermoFisher Scientific (Behind the Bench Staff. PCR Primer Design Tips. ThermoFisher Scientific, Published 09/25/2019).
Regarding claim 4, Brower teaches the capture oligonucleotide can comprise a PCR handle sequence (par. 0070; Fig. 2A). Brower teaches the PCR handle sequence comprises 25 bases (Fig. 2A).
ThermoFisher Scientific teaches that a good length for PCR primers is generally around 18-30 bases (What makes a good primer, #1). It would have been obvious to one of ordinary skill in the art to modify the PCR handle sequence of Brower to include 30 bases, as ThermoFisher Scientific teaches that 30 bases is a good length for PCR primers; thus, the primer binding site would be at least 30 bases to accommodate the length of the PCR primer, with no evidence of unexpected results. Furthermore, modifying the length of a primer and thus a primer binding site would be routine optimization of PCR, with no evidence of unexpected results.
Conclusion
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/R.L.B./Examiner, Art Unit 1684 /AARON A PRIEST/Primary Examiner, Art Unit 1681