DETAILED ACTION
Preliminary Amendment
The preliminary amendment filed on April 26, 2023 has been entered. The claims pending in this application are claims 1022-1041.
Election/Restrictions
This application contains claims directed to the following patentably distinct species:
(1) the partition is in a well (claim 1034)
(2) the partition is in a droplet (claim 1034)
The species are independent or distinct because these species are directed to different partition methods which have different properties. In addition, these species are not obvious variants of each other based on the current record.
Applicant is required under 35 U.S.C. 121 to elect a single disclosed species, or a single grouping of patentably indistinct species, for prosecution on the merits to which the claims shall be restricted if no generic claim is finally held to be allowable. Currently, generic claims are claims 1022-1033 and 1035-1041.
There is a serious search and/or examination burden for the patentably distinct species as set forth above because the searches for species (1) and (2) are not overlap.
Applicant is advised that the reply to this requirement to be complete must include (i) an election of a species to be examined even though the requirement may be traversed (37 CFR 1.143) and (ii) identification of the claims encompassing the elected species or grouping of patentably indistinct species, including any claims subsequently added. An argument that a claim is allowable or that all claims are generic is considered nonresponsive unless accompanied by an election.
The election may be made with or without traverse. To preserve a right to petition, the election must be made with traverse. If the reply does not distinctly and specifically point out supposed errors in the election of species requirement, the election shall be treated as an election without traverse. Traversal must be presented at the time of election in order to be considered timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are added after the election, applicant must indicate which of these claims are readable on the elected species or grouping of patentably indistinct species.
Should applicant traverse on the ground that the species, or groupings of patentably indistinct species from which election is required, are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing them to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the species unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other species.
Upon the allowance of a generic claim, applicant will be entitled to consideration of claims to additional species which depend from or otherwise require all the limitations of an allowable generic claim as provided by 37 CFR 1.141.
During a telephone conversation with Dr. Jing Liu (Reg. No. 62,377) on April 23, 2026, a provisional election was made without traverse to prosecute species (1) of claim 1034 (see above). Affirmation of this election must be made by applicant in replying to this Office action. Species (2) of claim 1034 has been withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to a non-elected invention.
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
Information disclosure statements (IDS) filed on November 29, 2022, April 26, 2025, September 26, 2025, and April 11, 2026 contain 176 pages and 3862 patent and non-patent literatures. However, most of these patent and non-patent literatures are not related to this instant application and applicant should only file patent and non-patent literatures which are related to this instant application such that the valuable time of the examiner will not be wasted.
Drawings
Some words in Figure 18 cannot be recognized. Applicant is required to submit new Figure 18 in response to this office action. No new matter may be introduced in the required drawing. The 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).
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiency – Figure 18 contains 7 nucleotide sequences having more than 10 nucleotides. However, Figure 18 only labels these nucleotide sequences as SEQ ID Nos: 3 and 4. Other nucleotide sequences appearing in Figure 18 are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide sequences must appear either in Figure 18 or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities: (1) since cases 16/789,358 and 15/715,028 have been patented, applicant is required to update these information in paragraph [0001] of the specification; and (2) there is a default control having more than 10 nucleotides in each of pages 239 and 241. However, there is no SEQ ID NO. for this default control in each of pages 239 and 241.
Appropriate correction is required.
Claim Objections
Claim 1022 is objected to because of the following informalities: (1) “the cellular component binding reagent is” in lines 7 and 8 should be “the cellular component binding reagents are”; (2) “associated” in line 1o should be “bound”; (3) “in the partition comprising the single cell” in the partitioning step should be “in the partitions comprising the single cell”; (4) “each labeled nucleic acid” in extending step should be “each of the labeled nucleic acids”; and (5) “a molecular label sequence” in extending step should be “the molecular label sequence”.
Claim 1025 is objected to because of the following informality: “the cellular component binding reagent comprises” should be “each of the plurality of cellular component binding reagents further comprises” in view of claim 1022.
Claim 1026 is objected to because of the following informality: “each of the oligonucleotide probes comprises” should be “each of the plurality of oligonucleotide probes further comprises” in view of claim 1022.
Claim 1028 is objected to because of the following informality: “a partition of the plurality of partitions comprises a single solid support” should be “a partition of the plurality of partitions is on a single solid support”.
Claim 1030 is objected to because of the following informality: “determining the copy number of the at least one cellular component target in one or more of the plurality of cells” should be “said determining the copy number of the at least one cellular component target in one or more of the plurality of cells”.
Claim 1031 is objected to because of the following informality: “cellular component binding reagents that are not associated with the plurality of cells” should be “the cellular component binding reagents that are not bound with the plurality of cells”.
Claim 1032 is objected to because of the following informality: “the cellular component binding reagent” should be “the cellular component binding reagents”.
Claim 1032 is objected to because of the following informality: “the partition is a well or a droplet” should be “each of the plurality of partitions is formed in a well or as a droplet”.
Claim 1035 is objected to because of the following informality: “obtaining sequencing information of the plurality of labeled nucleic acids, or products thereof” should be “said obtaining sequencing information of the plurality of labeled nucleic acids, or products thereof”.
Claim 1037 is objected to because of the following informality: “the universal primer sequence” should be “the universal sequence” in view of claim 1022.
Claim 1038 or 1039 is objected to because of the following informality: “associated” should be “bound”.
Claim 1041 is objected to because of the following informality: “at least 10 of the plurality of cellular component binding reagents each” should be “each of at least 10 of the plurality of cellular component binding reagents”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
Scope of Enablement
Claims 1022-1041 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for contacting a plurality of cellular component binding reagents with a plurality of cells comprising a plurality of cellular component targets, does not reasonably provide enablement for determining the copy number of at least one cellular component target of the plurality of cellular component targets in one or more of the plurality of cells based on only sequence information of the plurality of labeled nucleic acids or products thereof using the method recited in claims 1022-1041. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Wands states at page 1404,
“Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”
The Nature of The Invention
The claims are drawn to a method for measurement of cellular component target expression in cells. The invention is a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
The Breadth of The Claims
Claims 1022-1041 encompass a method for measurement of cellular component target expression in cells, comprising: contacting a plurality of cellular component binding reagents with a plurality of cells comprising a plurality of cellular component targets, wherein each of the plurality of cellular component binding reagents comprises a cellular component binding reagent specific oligonucleotide comprising a target region, a universal sequence, and a unique identifier for the cellular component binding reagent, and wherein the cellular component binding reagent is capable of specifically binding to at least one of the plurality of cellular component targets;
partitioning the plurality of cells associated with the plurality of cellular component binding reagents to a plurality of partitions, wherein a partition of the plurality of partitions comprises a single cell from the plurality of cells associated with the cellular component binding reagents; in the partition comprising the single cell, contacting a plurality of oligonucleotide probes with the cellular component-binding reagent specific oligonucleotides, wherein each of the plurality of oligonucleotide probes comprises a molecular label sequence and a target binding region capable of binding to a target region, and wherein the molecular label sequence is from a diverse set of unique molecular label sequences; extending the oligonucleotide probes hybridized to the cellular component- binding reagent specific oligonucleotides to generate a plurality of labeled nucleic acids, wherein each labeled nucleic acid comprises a unique identifier, or a complementary sequence thereof, and a molecular label sequence; and obtaining sequence information of the plurality of labeled nucleic acids, or products thereof, to determine the copy number of at least one cellular component target of the plurality of cellular component targets in one or more of the plurality of cells.
Working Examples
The specification provides 6 examples (see pages 99-105 of US 2024/0019434 A1, which is US publication of this instant case). However, the specification provides no working example for determining the copy number of at least one cellular component target of the plurality of cellular component targets in one or more of the plurality of cells based on only sequence information of the plurality of labeled nucleic acids or products thereof using the method as recited in claims 1022-1041.
The Amount of Direction or Guidance Provided and The State of The Prior Art
Although the specification provides 6 examples (see pages 99-105 of US 2024/0019434 A1, which is US publication of this instant case), the specification provides no working example for determining the copy number of at least one cellular component target of the plurality of cellular component targets in one or more of the plurality of cells based on only sequence information of the plurality of labeled nucleic acids or products thereof using the method as recited in claims 1022-1041. Furthermore, there is no experimental condition and/or experimental data in the specification to support the claimed invention. During the process of the prior art search, the examiner has not found any prior art which is related to determine the copy number of at least one cellular component target of the plurality of cellular component targets in one or more of the plurality of cells based on only sequence information of the plurality of labeled nucleic acids or products thereof using the method as recited in claims 1022-1041
Level of Skill in The Art, The Unpredictability of The Art, and The Quantity of Experimentation Necessary
While the relative skill in the art is very high (the Ph.D. degree with laboratory experience), there is no predictability whether the copy number of at least one cellular component target of the plurality of cellular component targets in one or more of the plurality of cells can be determined based on only sequence information of the plurality of labeled nucleic acids or products thereof using the method as recited in claims 1022-1041.
Since the specification teaches that “[S]ome embodiments disclosed herein provide a plurality of compositions each comprising a cellular component binding regent (e.g., a protein binding reagent) conjugated with an oligonucleotide, wherein the oligonucleotide comprises a unique identifier for the cellular component binding reagent that it is conjugated with. A binding target of the cellular component binding reagent can be, or comprise, a carbohydrate, a lipid, a protein, an extracellular protein, a cell-surface protein, a cell marker, a B-cell receptor, a T-cell receptor, a major histocompatibility complex, a tumor antigen, a receptor, an integrin, an intracellular protein, or any combination thereof. In some embodiments, the cellular component binding reagent (e.g., the protein binding reagent) is capable of specifically binding to a protein target. In some embodiments, each of the oligonucleotides can comprise a barcode, such as a stochastic barcode. A barcode can comprise a barcode sequence (e.g., a molecular label), a cell label, a sample label, or any combination thereof. In some embodiments, each of the oligonucleotides can comprise a linker. In some embodiments, each of the oligonucleotides can comprise a binding site for an oligonucleotide probe, such as a poly(A) tail. For example, the poly(A) tail can be, e.g., unanchored to a solid support or anchored to a solid support. The poly(A) tail can be from about 10 to 50 nucleotides in length. In some embodiments, the poly(A) tail can be 18 nucleotides in length. The oligonucleotides can comprise deoxyribonucleotides, ribonucleotides, or both”, “[F]IG. 4 shows a schematic illustration of an exemplary protein binding reagent, e.g., an antibody, that is conjugated with an oligonucleotide comprising a unique identifier sequence for the antibody. An oligonucleotide-conjugated with an antibody, an oligonucleotide for conjugation with an antibody, or an oligonucleotide previously conjugated with an antibody can be referred to herein as an antibody oligonucleotide (abbreviated as ‘AbOligo’ or ‘AbO’). The oligonucleotide can also comprise additional components, including but not limited to, one or more linker, one or more unique identifier for the antibody, optionally one or more barcode sequences (e.g., molecular labels), and a poly(A) tail. In some embodiments, the oligonucleotide can comprise, from 5’ to 3’, a linker, a unique identifier, a barcode sequence (e.g., a molecular label), and a poly(A) tail”, “[I]n some embodiments, the plurality of cellular component binding reagents are capable of specifically binding to a plurality of cellular component targets in a sample, such as a single cell, a plurality of cells, a tissue sample, a tumor sample, a blood sample, or the like. In some embodiments, the cellular component binding reagents are protein binding reagents, and the plurality of protein targets comprises a cell-surface protein, a cell marker, a B-cell receptor, a T-cell receptor, an antibody, a major histocompatibility complex, a tumor antigen, a receptor, or any combination thereof. In some embodiments, the plurality of protein targets can comprise intracellular proteins. In some embodiments, the plurality of protein targets can comprise intracellular proteins”, [F]IG. 5 shows a schematic illustration of an exemplary method of simultaneous quantitative analysis of both protein and nucleic acid targets in single cells. In some embodiments, a plurality of compositions 505, 505b, 505c, etc., each comprising a protein binding reagent, such as an antibody, is provided. Different protein binding reagents, such as antibodies, which bind to different protein targets are conjugated with different unique identifiers. Next, the protein binding reagents can be incubates with a sample containing a plurality of cells 510. The different protein binding reagents can specifically bind to proteins on the cell surface, such as a cell marker, a B-cell receptor, a T-cell receptor, an antibody, a major histocompatibility complex, a tumor antigen, a receptor, or any combination thereof. Unbound protein binding reagents can be removed, e.g., by washing the cells with a buffer. The cells with the protein binding reagents can be then separated into a plurality of compartments, such as a microwell array, wherein a single compartment 515 is sized to fit a single cell and a single bead 520. Each bead can comprise a plurality of oligonucleotide probes, which can comprise a cell label that is common to all oligonucleotide probes on a bead, and barcode sequences (e.g., molecular label sequences). In some embodiments, each oligonucleotide probe can comprise a target binding region, for example, a poly(dT) sequence. The oligonucleotides 525 conjugated to the antibody can be detached from the antibody using chemical, optical or other means. The cell can be lysed 535 to release nucleic acids within the cell, such as genomic DNA or cellular mRNA 530. Cellular mRNA 530, oligonucleotides 525 or both can be captured by the oligonucleotide probes on bead 520, for example, by hybridizing to the poly(dT) sequence. A reverse transcriptase can be used to extend the oligonucleotide probes hybridized to the cellular mRNA 530 and the oligonucleotides 525 using the cellular mRNA 530 and the oligonucleotides 525 as templates. The extension products produced by the reverse transcriptase can be subject to amplification and sequencing. Sequencing reads can be subject to demultiplexing of a cell label, a barcode sequence (e.g., a molecular label), gene identity, antibody specific oligo identity, etc., which can give rise to a digital representation of protein and gene expression of each single cell in the sample”, “[I]n some embodiments, the methods disclosed herein comprise determining the number of unique barcode sequences (e.g., molecular label sequences) for each unique identifier and/or each nucleic acid target molecule. For example, the sequencing reads can be used to determine the number of unique barcode sequences for each unique identifier and/or each nucleic acid target molecule”, and “[I]n some embodiments, the number of unique barcode sequences for each unique identifier and/or each nucleic acid target molecule indicates the quantity of each protein target and/or each nucleic acid target molecule in the sample. In some embodiments, the quantity of a protein target and the quantity of its corresponding nucleic acid target molecules, e.g., mRNA molecules, can be compared to each other. In some embodiments, the ratio of the quantity of a protein target and the quantity of its corresponding nucleic acid target molecules, e.g., mRNA molecules, can be calculated. The protein targets can be, for example, cell surface protein markers. In some embodiments, the ratio between the protein level of a cell surface protein marker and the level of the mRNA of the cell surface protein marker is low” (see paragraphs [0239], [0240], [0461], [0468], [0469], and [0508] to [0510], and Figures 4 and 5 of US 2024/0019434 A1, which is US Publication of this instant case), the specification clearly indicates that a cellular component binding reagent is a protein binding reagent conjugated with an oligonucleotide which can bind the plurality of cellular component targets recited in claim 1023 and the scope of claims 1022-1041 is much broader than the scope of the specification since claims 1022-1041 does not limit the cellular component binding reagent to a protein binding reagent conjugated with an oligonucleotide. Although claim 1022 requires contacting a plurality of cellular component binding reagents with a plurality of cells comprising a plurality of cellular component targets wherein each of the plurality of cellular component binding reagents comprises a cellular component binding reagent specific oligonucleotide comprising a target region, a universal sequence, and a unique identifier for the cellular component binding reagent and wherein the cellular component binding reagent is capable of specifically binding to at least one of the plurality of cellular component targets and partitioning the plurality of cells associated with the plurality of cellular component binding reagents to a plurality of partitions wherein a partition of the plurality of partitions comprises a single cell from the plurality of cells associated with the cellular component binding reagents, since claim 1022 does not require that a plurality of cellular component targets is located on the surface of a cell and the plurality of cells is permeable cells or does not have a method step for delivering a cellular component binding reagent specific oligonucleotide to inside of the plurality of cells, if the plurality of cellular component targets is located inside of a cell and the plurality of cells has complete cell membranes, it is unpredictable how each of the plurality of cellular component binding reagents comprising a cellular component binding reagent specific oligonucleotide can bind to a plurality of cellular component targets inside of the plurality of cells such that the methods recited in claims 1022-1041 cannot be performed. Furthermore, although claim 1022 requires in the partition comprising the single cell, contacting a plurality of oligonucleotide probes with the cellular component-binding reagent specific oligonucleotides wherein each of the plurality of oligonucleotide probes comprises a molecular label sequence and a target binding region capable of binding to a target region and wherein the molecular label sequence is from a diverse set of unique molecular label sequences, extending the oligonucleotide probes hybridized to the cellular component-binding reagent specific oligonucleotides to generate a plurality of labeled nucleic acids, wherein each labeled nucleic acid comprises a unique identifier, or a complementary sequence thereof, and a molecular label sequence, and obtaining sequence information of the plurality of labeled nucleic acids, or products thereof, since claim 1022 does not require quantitate amounts of the plurality of labeled nucleic acids, without quantitating amounts of the plurality of labeled nucleic acids, it is unpredictable how the copy number of at least one cellular component target of the plurality of cellular component targets in one or more of the plurality of cells can be determined based on only sequence information of the plurality of labeled nucleic acids or products thereof such that the methods recited in claims 1022-1041 cannot be performed. In addition, since a carbohydrate does not have a direct, sequence-specific, high-affinity binding to nucleic acids and claim 1022 does not indicate that a plurality of cellular component targets is not carbohydrates, if the plurality of cellular component targets is carbohydrates, it is unpredictable how a cellular component binding reagent specific oligonucleotide of each of the plurality of cellular component binding reagents can bind to a plurality of cellular component targets such as carbohydrates such that the copy number of at least one cellular component target of the plurality of cellular component targets such as carbohydrates in one or more of the plurality of cells cannot be determined using the methods recited in claims 1022-1041.
Case law has established that “(t)o be enabling, the specification of a patent must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation’.” In re Wright 990 F.2d 1557, 1561. In re Fisher, 427 F.2d 833, 839, 166 USPQ 18, 24 (CCPA 1970) it was determined that “[T]he scope of the claims must bear a reasonable correlation to the scope of enablement provided by the specification to persons of ordinary skill in the art”. The amount of guidance needed to enable the invention is related to the amount of knowledge in the art as well as the predictability in the art. Furthermore, the Court in Genentech Inc. v Novo Nordisk 42 USPQ2d 1001 held that “[I]t is the specification, not the knowledge of one skilled in the art that must supply the novel aspects of the invention in order to constitute adequate enablement”.
In view of above discussions, the skilled artisan will have no way to predict the experimental results. Accordingly, it is concluded that undue experimentation is required to make the invention as it is claimed. These undue experimentation at least includes to test whether the copy number of at least one cellular component target of the plurality of cellular component targets in one or more of the plurality of cells can be determined based on only sequence information of the plurality of labeled nucleic acids or products thereof using the method as recited in claims 1022-1041.
Conclusion
In the instant case, as discussed above, the level of unpredictability in the art is high, the specification provides one with no guidance that leads one to claimed methods. One of skill in the art cannot readily anticipate the effect of a change within the subject matter to which the claimed invention pertains. Thus given the broad claims in an art whose nature is identified as unpredictable, the unpredictability of that art, the large quantity of research required to define these unpredictable variables, the lack of guidance provided in the specification, the absence of any working example related to claimed invention and the no teaching in the prior art balanced only against the high skill level in the art, it is the position of the examiner that it would require undue experimentation for one of skill in the art to perform the method of the claim as broadly written.
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 1022-1041 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 1022 is rejected as vague and indefinite in view of the extending step because it is unclear whether a unique identifier in each of the labeled nucleic acids is identical to a unique identifier of the cellular component binding reagent specific oligonucleotide in the contacting step or not. Please clarify.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Frank Lu, Ph. D., whose telephone number is (571)272-0746. The examiner can normally be reached Monday to Friday, 9 AM to 5 PM.
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/FRANK W LU/
Primary Examiner, Art Unit 1683
May 1, 2026
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