DETAILED ACTION
Status of the Claims
Claims 54-73 are currently pending and are examined herein.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 05/31/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 112(b) -- Indefiniteness
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 62 and 68 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 pre-AIA the applicant regards as the invention.
Claims 62 and 68 each recites limitations as being “preferably”. As per MPEP 2173.05(c)-(d), “[i]f stated in a single claim, examples and preferences lead to confusion over the intended scope of the claim. In those instances where it is not clear whether the claimed narrower range is a limitation, a rejection under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph should be made.”
As per MPEP 2173: It is of utmost importance that patents issue with definite claims that clearly and precisely inform persons skilled in the art of the boundaries of protected subject matter. Therefore, claims that do not meet this standard must be rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph as indefinite. Further, as per MPEP 2173.02: If the language of the claim is such that a person of ordinary skill in the art could not interpret the metes and bounds of the claim so as to understand how to avoid infringement, a rejection of the claim under 35 U.S.C. 112, second paragraph, would be appropriate. As currently written, the metes and bounds of the rejected claims are unascertainable for the reasons set forth above, thus the above claim(s) and all dependent claims are rejected under 35 USC 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph.
Claim Rejections – 35 U.S.C. 102
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 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Lance et al.
Claims 54-63, 65-66, 68-69, and 72-73 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Lance et al. (U.S. PGPub 2020/049575 A1, cited in IDS of 05/31/2024).
Regarding claim 54, Lance discloses a method for sequentially attaching a plurality of oligonucleotides to nucleic acids to produce barcoded nucleic acids, wherein the nucleic acids are obtained from a plurality of cells (e.g., as per para 00183-0191), wherein the plurality of cells are in a plurality of microcapsules (e.g., “may be encapsulated within a microcapsule” as per para 00203), each microcapsule comprising a semi-permeable shell and a core (e.g., the “polymer or gel may be diffusely permeable to chemical or biochemical reagents” as per para 00208 and/or have a “tunable pore size” as per para 00209), wherein each cell is in a separate microcapsule, the method comprising:
(a) lysing the cells within the microcapsules to release DNA and RNA inside the microcapsules (e.g., lysed as per para 00178 and/or 00180);
(b) optionally in the microcapsule:
(i) converting released cellular RNA to cDNA by reverse transcription (e.g., using reverse transcriptase as per para 00161-00162); and/or
(ii) fragmenting the released cellular DNA to produce fragmented DNA (e.g., fragmenting as per para 00304); and/or
(iii) amplifying fragmented DNA and/or cDNA (e.g., as per para 00304),
(c) applying a combinatorial indexing strategy to attach the plurality of oligonucleotides one at a time to the released cellular DNA, the released cellular RNA, the cDNA, and/or the fragmented DNA and/or amplified DNA and/or cDNA in each microcapsule to produce barcoded nucleic acids (e.g., combinatorial barcoding of the nucleic acids as per para 0063 and/or 0074);
wherein the barcoded nucleic acids produced in each microcapsule comprise a sequence of oligonucleotides that is specific to that microcapsule (e.g., identifiable individually as per para 0074).
Regarding claim 55, Lance discloses the above method, wherein the combinatorial indexing strategy of (c) comprises:
(i) randomly distributing the plurality of microcapsules into a plurality of compartments, wherein each compartment comprises more than one microcapsule;
(ii) processing the microcapsules in each compartment to attach an oligonucleotide to the nucleic acid in the microcapsules, wherein a different oligonucleotide is utilized in each compartment;
(iii) pooling and randomly re-distributing the plurality of microcapsules into a further plurality of compartments, wherein each further compartment comprises more than one microcapsule, and processing the microcapsules in each compartment to attach a further oligonucleotide to the nucleic acid in the microcapsules, wherein a different oligonucleotide is utilized in each of the further compartments; and
optionally repeating step (iii) one or more times (e.g., split-and-pool combinatorial barcoding as per para 0074 and/or 00137-00141).
Regarding claim 56, Lance discloses the above method, comprising attaching a unique molecular identifier and/or an adapter to the released cellular RNA, the released cellular DNA or the barcoded nucleic acids (e.g., as per para 0085 and/or 00140), optionally wherein the adapter is a PCR adapter, and/or a sequencing adapter, and/or wherein the adapter comprises an endonuclease recognition sequence and/or a promoter sequence.
Regarding claim 57, Lance discloses the above method, wherein the attaching comprises ligating or attaching via a nucleic acid extension reaction (e.g., as per para 00142).
Regarding claim 58, Lance discloses the above method, comprising breaking the plurality of microcapsules to release the barcoded nucleic acids under conditions that do not damage the barcoded nucleic acids (e.g., as per para 00303).
Regarding claim 59, Lance discloses the above method, comprising purifying and/or amplifying the released barcoded nucleic acids (e.g., as per para 00304).
Regarding claim 60, Lance discloses the above method, comprising producing a DNA library with the barcoded nucleic acids within the microcapsules or with the released barcoded nucleic acids (e.g., as per para 00154 and/or 00287).
Regarding claim 61, Lance discloses the above method, comprising sequencing the barcoded nucleic acids (e.g., sequenced as per para 00232 and/or 00287).
Regarding claim 62, Lance discloses the above method, comprising labelling (hashing) the plurality of cells in the plurality of microcapsules prior to (a), preferably with DNA-antibody conjugates (e.g., as per para 0074 and/or 0095).
Regarding claim 63, Lance discloses the above method, wherein (b) comprises converting the released cellular RNA to cDNA by reverse transcription (e.g., as per para 00158 and/or 00161).
Regarding claim 65, Lance discloses the above method, wherein (b) comprises fragmenting the released cellular DNA (e.g., as per para 00302 and/or 00304 and/or 00349).
Regarding claim 66, Lance discloses the above method, comprising fragmenting the released cellular DNA by physical, chemical or enzymatic means (e.g., as per para 00302 and/or 00304 and/or 00349).
Regarding claim 68, Lance discloses the above method, comprising fragmenting the released cellular DNA using enzymatic means, preferably a nuclease(s) and/or transposase and/or an enzyme fused to antibody (e.g., as per para 00302 and/or 00304 and/or 00349).
Regarding claim 69, Lance discloses the above method, wherein the semi-permeable shell allows diffusion of a reagent, an enzyme and/or a substrate for the method steps through the shell, while retaining the nucleic acids, optionally wherein the substrate is a barcoding oligonucleotide, or a PCR primer (e.g., the “polymer or gel may be diffusely permeable to chemical or biochemical reagents” as per para 00208 and/or have a “tunable pore size” as per para 00209).
Regarding claim 72, Lance discloses the above method, wherein the semi-permeable shell comprises a gel formed from a polymer, wherein the polymer in the gel is covalently cross-linked (e.g., as per para 00205-00210).
Regarding claim 73, Lance discloses the above method, wherein the polymer is a polyampholyte and/or a polyelectrolyte or a synthetic polymer (e.g., as per para 00205-00210).
Claim Rejections – 35 U.S.C. 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 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
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.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Lance et al.
Claims 54-63, 65-66, and 68-73 are rejected under 35 U.S.C. 103 as being unpatentable over Lance et al. (U.S. PGPub 2020/049575 A1, cited in IDS of 05/31/2024).
Lance is relied on as above, however, it is noted that the reference is silent as to the explicit numerical limitations as recited in claims 70-71 regarding the specific molecular weights.
Regarding claims 70-71, Lance generally discloses microcapsules in terms such as the “polymer or gel may be diffusely permeable to chemical or biochemical reagents” as per para 00208 and/or having a “tunable pore size” as per para 00209.
In accordance with MPEP 2144.05, which states “where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation” citing In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). See also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 (“The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages”). In the instant case, the specific limitations of wherein the semi-permeable shell allows for diffusion of smaller molecular weight compounds of approximately MW 200,000 or less through the shell, while retaining larger molecular weight compounds of approximately MW 300,000 and above, and/or wherein the semi-permeable shell is permeable to compounds having a molecular weight of 120 ± 80 kDa or lower would have been obvious during the course of routine optimization, absent unexpected results.
Lance et al. and Shore et al.
Claims 54-66 and 68-73 are rejected under 35 U.S.C. 103 as being unpatentable over Lance et al. (U.S. PGPub 2020/049575 A1, cited in IDS of 05/31/2024) in view of Shore et al. (PLoS, 2016, 11(11): e0167009).
Lance is relied on as above, however, it is noted that the reference is silent as to the limitation of ligating an oligonucleotide sequence to the released cellular RNA before reverse transcription, as set forth in claim 64.
Shore discloses methods for ligating adapters to RNAs prior to reverse transcription (e.g., as per the Abstract).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to ligate the adapters to the RNAs of Lance prior to reverse transcription as per Shore. One of ordinary skill in the art would have been motivated to do so since Shore discloses the benefits of doing so, particularly for shorter RNAs (e.g., as per the Introduction section).
Given the teachings of the prior art and the level of the ordinary skilled artisan at the time of the application’s effective filing date, it must be considered, absent evidence to the contrary, that said skilled artisan would have had a reasonable expectation of success in practicing the claimed invention.
Lance et al. and Vitomirov et al.
Claims 54-63 and 65-73 are rejected under 35 U.S.C. 103 as being unpatentable over Lance et al. (U.S. PGPub 2020/049575 A1, cited in IDS of 05/31/2024) in view of Vitomirov et al. (Mitochondrion, 2017, 32:16-18).
Lance is relied on as above, however, it is noted that the reference is silent as to the limitation of fragmenting the released cellular DNA using ultrasound or using complexes that generate hydroxyl radicals, as set forth in claim 67.
Vitomirov discloses fragmenting cellular DNA using ultrasound in oil-in-water droplets (e.g., Abstract and Methods section).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to sonicate the cellular DNA of Lance using the methods of Vitomirov. One of ordinary skill in the art would have been motivated to do so since Vitomirov teaches that this has shorter processing times than enzymatic digestion and does not require inactivation of DNases (e.g., as per the Abstract).
Given the teachings of the prior art and the level of the ordinary skilled artisan at the time of the application’s effective filing date, it must be considered, absent evidence to the contrary, that said skilled artisan would have had a reasonable expectation of success in practicing the claimed invention.
Conclusion
No claims are allowed.
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/JEREMY C FLINDERS/
Primary Examiner, Art Unit 1684
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