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.
Claim Status
Claims 1-2, 4-5, 7-8, and 10-18 are pending and being examined on the merits.
Information Disclosure Statement
Applicant’s submission of an IDS is acknowledged. Some references in the specification are still not represented in the submitted IDS.
The listing of references in the specification is not a proper information disclosure statement (see paragraphs [0036, 0037, and 0049] for example). 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, they have not been considered.
Drawings
Applicant’s amendments to the specification and drawings are acknowledged. All objections to the drawings are withdrawn in light of Applicant’s amendments and submission of substitute drawings.
Specification
The objection to the specification for minor informalities and inclusion of an embedded hyperlink are withdrawn in light of Applicant’s amendments to the specification.
Claim Interpretation
Claim 1 is directed to a method that comprises “a capture step” in which a bioparticle is captured on “an analysis substrate”. The specification does not provide a special definition of surface but provides a non-limiting example of an analysis substrate being a slide glass (paragraph [0030 and 0055]). In light of no special definition or limiting examples in the specification and employing the broadest reasonable interpretation of the claim language in light of the state of the art, “an analysis substrate” can be any solid substance to which the molecule is attached.
Claim 18 is drawn to a “system.” The specification recites a “system” wherein the “system” is defined in terms of structural limitations. In addition, the claims recite structural limitations of the “system.” Thus, the “system” is interpreted to encompass any collection of reagents and parts used together that are not necessarily part of a completely integrated single unitary device. Any further interpretation of the word is considered an “intended use” and does not impart any further structural limitation on the claimed subject matter.
Claim Rejections - 35 USC § 112b – Indefiniteness
Withdrawn 112b Rejections:
The rejection of claims 1-19 under 35 U.S.C. 12b as detailed in the previous Office Action of 7/14/2025 are withdrawn in light of Applicant’s amendment to claims and cancelation of claims 3, 6, 9, and 19.
New Rejections (Necessitated by Amendments):
Claims 1-2, 4-5, 7-8, and 10-17 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 target substance" in line 15. There is insufficient antecedent basis for this limitation in the claim.
Claims 2, 4-5, 7-8, and 10-17 depend from claim 1, inherit this deficiency, and are rejected on the same basis.
Claim 7 recites the limitation "the target substance" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 7 contains the limitation “wherein in the analysis step, the barcode sequence is associated with the target substance”. However, it is unclear how this association is accomplished. The barcode sequence could be associated with a target through fluorescence, through reverse transcription incorporating the barcode sequence into amplicons, or through hybridization-based capture of the target substance. The “analyzing” is not defined in claim 1, from which claim 7 depends, and therefore does not provide any further clarification as to how this association is accomplished. Further clarification is required.
Claim 8 recites the limitation "the target substance" in lines 1 and 3. There is insufficient antecedent basis for this limitation in the claim.
In the interest of compact prosecution and for the purposes of examination, the target substance of claim 1 is being interpreted as a target substance released from the bioparticle disruption, as defined in claim 5. However, clarification of the target substance and its origins in claim 1 is required.
Claim Rejections - 35 USC § 103
Withdrawn 103 Rejections:
The rejection of claims 1-8, 10-11, 13, and 14-19 under 35 U.S.C. 103 as being unpatentable over Stoeckius et al. (hereinafter “Stoeckius”, US 20180251825 A1; cited on IDS submitted on 12/22/2022) in view of Fan et al. (hereinafter “Fan”, US 10,466,243 B2) are withdrawn in light of Applicant’s amendments and cancellation of claims 3, 6, and 19.
The rejection of Claims 9 and 12 under 35 U.S.C. 103 as being unpatentable over Stoeckius et al. (hereinafter “Stoeckius”, US 20180251825 A1; cited on IDS submitted on 12/22/2022) in view of Fan et al. (hereinafter “Fan”, US 10,466,243 B2) as applied to claims 1-8, 10-11, 13, and 14-19 above, and further in view of Gaublomme et al. (hereinafter “Gaublomme”; US 2018/0320224 A1) are withdrawn in light of Applicant’s amendments and cancellation of claim 9.
New 103 Rejections (Necessitated by Amendments):
Claims 1-2, 4-5, 7-8, and 10-18 are rejected under 35 U.S.C. 103 as being unpatentable over Stoeckius et al. (hereinafter “Stoeckius”, US 20180251825 A1; cited on IDS submitted on 12/22/2022) in view of Fan et al. (hereinafter “Fan”, US 10,466,243 B2; cited on PTO-892 of 7/14/2025), Gaublomme et al. (hereinafter “Gaublomme”; US 2018/0320224 A1; cited on PTO-892 of 7/14/2025), and Zhang et al. (hereinafter “Zhang”, Royal Society of Chemistry, 1/9/2020).
Regarding claims 1, 10-11, and 16-17: Stoeckius teaches a bioparticle analysis method in which cells (bioparticles) are labeled with oligo-antibody conjugates (which reads on a molecule; Fig. 1A). The antibody reads on a bioparticle capturing part and is conjugated to an oligonucleotide which contains a barcode sequence (Fig. 1A). After the cell is bound by the molecule, Stoeckius teaches an isolation step in which the cell is isolated into an emulsion droplet (which reads on a microspace) using a microfluidic device (Fig. 1C). Stoeckius teaches disrupting the bioparticle in the microspace (claim 1; “cell lysis in droplet”, Fig 1C step 5). Stoeckius teaches an analysis step of analyzing the target substance after the disruption step. Stoeckius teaches that the barcode sequence is associated with the target substance and that the target substance (mRNA in this case) has a base sequence that is analyzed via sequencing processing (claim 1; paragraphs [0013, 0038, 0121, and 0438]).
Stoeckius does not teach capturing the bioparticle with a molecule with a cleavable linker that is immobilized on an analysis substrate and subsequently cleaving the linker to release the bioparticle (claim 1), how the linker is cleaved (claims 10 and 11), or how the bioparticle and bioparticle capturing part are bound to each other (claims 16 and 17). However, capturing bioparticles using molecules immobilized on a surface is known in the art, as taught by Fan.
Fan teaches a method in which antibodies are immobilized to the surface of a microfluidic device and are used to specifically bind target cells (claims 1 and 16; col 2, ln 15-38 and col 9, ln 54-58). Fan teaches that the molecules for binding the target cells are attached to an analysis substrate (the channels of the microfluidic device; this reads on a preparation step of preparing an alysis substrate; col 5, ln 61-67). The antibodies can be attached to the surface via a “spacer” which is a DNA linker that is cleavable by “chemical means” (chemical stimulation) or by light (photic stimulation, claims 1 and 10; col 8, ln 59-63). Fan teaches separate steps of first dissociating the antibody from the surface and then dissociating the antibody from the target particle. This implies that once cleavages is achieved, the captured state of the bioparticle is maintained by the bioparticle capturing part (claim 11; col 7, ln 30-35). Fan teaches an incubation step in which the fluid containing target cells are passed through the microfluidic channel with immobilized antibodies at a constant flow rate (claim 17; col 11, ln 11-13 and col 16, ln 47-60). Fan teaches, after capturing the target cells, cleaving the linker then releasing and collecting the captured target cells (col 12, ln 35-37 and col 13, ln 29-34).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Stoeckius with the method of Fan. One would be motivated to first capture target cells from a population of heterogeneous cells on a surface before isolation given the assertion by Fan that this enables “high capture efficiency and high capture purity of the target cells” (col 6, ln 1-2). One would have a reasonable expectation of success given that Fan demonstrates successful capture and release of target cells by immobilized antibody-oligo conjugates.
Stoeckius in view of Fan do not teach that the bioparticle to be released from the surface is selected on a basis of a label of the bioparticle or a label of the molecule (claim 1) or that only a selected bioparticle is released from the surface (claim 12). However, selective release of a bioparticle from a surface based on a label of the bioparticle or molecule is known in the art, as taught by Gaublomme.
Gaublomme teaches a single cell analysis method in which a surface with immobilized oligonucleotides with either a poly T sequence or an aptamer sequence are used to capture target particles such as mRNA and proteins, respectively (paragraphs [0007, 0010 and 0011]). Gaublomme teaches that the oligonucleotides are immobilized to the solid support via a cleavable linker (paragraph [0011]). Gaublomme teaches that the cleavable linker can be different between the first oligonucleotides that contain aptamers against proteins and the second oligonucleotides that contain sequences for capturing mRNAs (paragraph [0011]). Gaublomme teaches that because the linkers are cleavable by different mechanisms, the oligonucleotides can be selectively released based on whether it’s an aptamer or mRNA capturing oligo, which reads on the label of the molecule being the basis for releasing the captured particle from the surface (claim 1). Gaublomme teaches that the selected particles can then be released at different times via different cleavage mechanisms, which reads on “a selected bioparticle is released from the surface” (claim 12; paragraph [0011]). The claim language “a selected bioparticle” is singular, however the method from which claim 12 depends is a method “comprising”, therefore claim 12 is interpreted to mean that multiple selected bioparticles can be released from the surface.
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Stoeckius in view of Fan with the method of Gaublomme. One would be motivated to selectively cleave linkers based on the bioparticle associated with said linker given the assertion by Gaublomme that this allows for cleavage at different times and thus isolation of different types of particles in the same experiment from the same source (paragraph [0011]). One would have a reasonable expectation of success given the many different way through which cleavage of a linker can be achieved (as taught by Gaublomme) and that design of said linker can be associated with a particular label on the molecule itself (such as the capture sequence, also taught by Gaublomme).
While Stoeckius in view of Fan and Gaublomme teach selective release of a particular bioparticle based on the label of the molecule, they do not teach that the label of the molecule or bioparticle is a fluorochrome or a nucleic-acid bound antibody (claim 1). However, use of a fluorochrome to select cells (bioparticles) for release is known in the art, as taught by Zhang.
Zhang teaches a method of selected release of circulating tumor cells using capture probes (Abstract). Zhang teaches capture of two different types of CTCs using aptamers targeting each type on the same slide (Abstract). Zhang teaches “CCRF-CEM cells were pre-dyed with calcein AM for 10 min and Ramos cells were pre-dyed with DiI for 30 min”, both of which are fluorochromes (Capture and selective release of multiple CTCs). Zhang teaches imaging the capture cells prior to release to confirm efficient capture and then addition of either one releasing agent or the other depending on the desired cell to be released (Capture and selective release of multiple CTCs).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Stoeckius in view of Fan and Gaublomme with that of Zhang. One would be motivated to do so given the assertion by Zhang that visualizing the bioparticles by a label before selective release allows for confirmation of capture before release, as well as determination that selective release was achieved with specificity after release (Capture and selective release of multiple CTCs). One would have a reasonable expectation of success given that dying of cells with fluorescent materials for imaging is routinely practiced in the art.
Regarding claim 2: Stoeckius teaches that multiple identical constructs (which reads on plurality of molecules) bound to the bioparticle have the same barcode (paragraph [0104]).
Regarding claim 4: Stoeckius teaches disrupting the bioparticle in the microspace (claim 1; “cell lysis in droplet”, Fig 1C step 5) which in turn dissociates the molecule from the bioparticle (claim 4; “antibody-oligo release”, Fig 1C step 5).
Regarding claim 5: Stoeckius teaches that the molecule further includes a target substance capturing part (“an Anchor sequence comprises or consists of a poly-T sequence”, paragraph [0089]). Stoeckius does not explicitly teach capturing mRNA (a target substance) with the poly-T anchor sequence, however it would have been obvious to one skilled in the art to replace the poly-A sequence at the end of the nucleic acid tagged antibody with the poly-T sequence, as taught by Stoeckius et al. (paragraph [0089]). This would have yielded the predictable result of allowing hybridization between the poly-A tail of an mRNA and the nucleic acid poly-T anchor sequence (paragraph [0015 and 0438]). mRNA reads on a target substance constituting the bioparticle that would be available in the disruption step for binding by the target substance capturing part (the poly-T sequence).
Regarding claims 7-8: Stoeckius teaches an analysis step of analyzing the target substance after the disruption step. Stoeckius teaches that the barcode sequence is associated with the target substance and that the target substance (mRNA in this case) has a base sequence that is analyzed via sequencing processing (paragraphs [0013, 0038, 0121, and 0438]).
Regarding claim 13: Stoeckius teaches that the microspace is an emulsion particle (Fig. 1C and paragraph [0032]).
Regarding claims 14 and 15: Stoeckius in view of Fan teaches a molecule immobilized to a surface that comprises a bioparticle capturing part, a barcode sequence, and a cleavable linker (see details and citations above). Stoeckius teaches that prior to isolation of the cell, a determination step can be performed to sort cells into distinct pools, and then proceed to isolation (paragraph [0453]). Stoeckius teaches that the cells can be simultaneously labeled with the antibody-oligo conjugates and fluorophore-antibody conjugates which are subjected to fluorescence-activated cell sorting (FACS, which involves irradiating the bioparticle with light), to separate the cells into pools based on relative fluorescence prior to isolation into single-cell droplets (paragraph [0453]).
Regarding claim 18: Stoeckius teaches a bioparticle analysis method in which cells (bioparticles) are labeled with oligo-antibody conjugates (which reads on a molecule; Fig. 1A). The antibody reads on a bioparticle capturing part and is conjugated to an oligonucleotide which contains a barcode sequence (Fig. 1A). After the cell is bound by the molecule, Stoeckius teaches an isolation step in which the cell is isolated into an emulsion droplet (which reads on a microspace) using a microfluidic device (Fig. 1C). Stoeckius teaches inclusion of reagents necessary for performing a method of target particle barcoding and isolation in a kit (paragraph [0012]). Stoeckius also teaches an isolation device (such as a microfluidic chip for single cell encapsulation, paragraph [0032]). Stoeckius teaches sequencing of the target substance with systems such as the 10X Genomics single cell 3’ solution, which is a single cell analysis device (paragraph [0136]).
Stoeckius does not teach an analysis system capable of capturing the bioparticle with a molecule with a cleavable linker that is immobilized on a surface combined with a device to cleave the linker. However, a device capable of capturing bioparticles using molecules immobilized on a surface and cleaving said particle with a cleavage device is known in the art, as taught by Fan.
Fan teaches antibodies immobilized to the surface of a microfluidic device which are used to specifically bind target cells (col 2, ln 15-38 and col 9, ln 54-58). The antibodies can be attached to the surface via a “spacer” which is a DNA linker that is cleavable by “chemical means” or by light (col 8, ln 59-63). Fan teaches, after capturing the target cells, cleaving the linker with a cleavage device (such as UV light) then releasing and collecting the captured target cells (col 12, ln 35-37 and col 13, ln 29-34).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the devices and kit compositions of Stoeckius with the devices of Fan. One would be motivated to first capture target cells from a population of heterogeneous cells on a surface before isolation given the assertion by Fan that this enables “high capture efficiency and high capture purity of the target cells” (col 6, ln 1-2). One would have a reasonable expectation of success given that Fan demonstrates successful capture and release of target cells by immobilized antibody-oligo conjugates. Combining the devices taught by Stoeckius with the devices as taught by Fan into a system for performing a method would have the obvious advantage of streamlining the assay process and achieving greater capture efficiency (as taught by Fan) and single-cell analysis with barcoded analytes (as taught by Stoeckius).
Stoeckius in view of Fan do not teach that the bioparticle to be released from the surface is selected on a basis of a label of the bioparticle or a label of the. However, selective release of a bioparticle from a surface based on a label of the bioparticle or molecule is known in the art, as taught by Gaublomme.
Gaublomme teaches a single cell analysis system in which a surface with immobilized oligonucleotides with either a poly T sequence or an aptamer sequence are used to capture target particles such as mRNA and proteins, respectively (paragraphs [0007, 0010 and 0011]). Gaublomme teaches that the oligonucleotides are immobilized to the solid support via a cleavable linker (paragraph [0011]). Gaublomme teaches that the cleavable linker can be different between the first oligonucleotides that contain aptamers against proteins and the second oligonucleotides that contain sequences for capturing mRNAs (paragraph [0011]). Gaublomme teaches that because the linkers are cleavable by different mechanisms, the oligonucleotides can be selectively released based on whether it’s an aptamer or mRNA capturing oligo, which reads on the label of the molecule being the basis for releasing the captured particle from the surface.
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the devices and kit compositions of Stoeckius in view of Fan with the device of Gaublomme. One would be motivated to selectively cleave linkers based on the bioparticle associated with said linker given the assertion by Gaublomme that this allows for cleavage at different times and thus isolation of different types of particles in the same experiment from the same source (paragraph [0011]). One would have a reasonable expectation of success given the many different way through which cleavage of a linker can be achieved (as taught by Gaublomme) and that design of said linker can be associated with a particular label on the molecule itself (such as the capture sequence, also taught by Gaublomme).
While Stoeckius in view of Fan and Gaublomme teach selective release of a particular bioparticle based on the label of the molecule, they do not teach that the label of the molecule or bioparticle is a fluorochrome or a nucleic-acid bound antibody. However, use of a fluorochrome to select cells (bioparticles) for release is known in the art, as taught by Zhang.
Zhang teaches a method of selected release of circulating tumor cells using capture probes (Abstract). Zhang teaches capture of two different types of CTCs using aptamers targeting each type on the same slide (Abstract). Zhang teaches “CCRF-CEM cells were pre-dyed with calcein AM for 10 min and Ramos cells were pre-dyed with DiI for 30 min”, both of which are fluorochromes (Capture and selective release of multiple CTCs). Zhang teaches imaging the capture cells prior to release to confirm efficient capture and then addition of either one releasing agent or the other depending on the desired cell to be released (Capture and selective release of multiple CTCs).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the devices and kit compositions of Stoeckius in view of Fan and Gaublomme with that of Zhang. One would be motivated to do so given the assertion by Zhang that visualizing the bioparticles by a label before selective release allows for confirmation of capture before release, as well as determination that selective release was achieved with specificity after release (Capture and selective release of multiple CTCs). One would have a reasonable expectation of success given that dying of cells with fluorescent materials for imaging is routinely practiced in the art.
Response to Remarks
Applicant has traversed the rejection of claims 1-8, 10-11, 13, and 14-19 under 35 USC 103 as being obvious over Stoeckius in view of Fan, and claims 9 and 12 as being obvious over Stoeckius in view of Fan and further in view of Gaublomme (pg 28-33 of Remarks of 10/10/2025).
Applicant has argued that:
“Stoeckius in view of Fan does not teach that the bioparticle to be released from the surface is selected on a basis of a label of the bioparticle or a label of the molecule or that only a selected bioparticle is released from the surface. Gaublomme does not teach selective release of a bioparticle from a surface based on fluorescent labeling or a nucleic acid-bound antibody. No combination of the cited art teaches or suggests "a cleavage step of cleaving the cleavable linker to release the bioparticle from the analysis substrate, wherein in the cleavage step, a bioparticle to be released from the analysis substrate is selected on a basis of a label of the bioparticle or a label of the molecule, wherein the label of the bioparticle is a fluorochrome or a nucleic acid bound antibody, wherein the label of the molecule is a fluorochrome" in combination with the other limitations recited in the ordered combination of claim 1.” (pg 31-32 of Remarks).
These arguments are moot in light of the cancellation of the rejections of claims 1-8, 10-11, 13, and 14-19 under 35 USC 103 as being obvious over Stoeckius in view of Fan, and claims 9 and 12 as being obvious over Stoeckius in view of Fan and further in view of Gaublomme. The limitations that were added to claim 1 in the most recent version of the amended claims submitted on 10/10/2025 have been addressed in the new grounds of rejection presented above, necessitated by said amendments.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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