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 claims
Claims 1-19 as amended on September 1, 2023 are pending and have been examined.
Specification
The disclosure is objected to because of the following informalities:
On page 4, line 10, Figure 2 is referenced. However, Figures 2A-2E were supplied as part of the disclosure. MPEP 608.01(f) and 37 CFR 1.74 require a description of all figures.
Throughout the specification (pages 2, 3, 8, 9, and 12) SEQ ID NOs 1-6 are described as “an amino acid sequence”, when they are nucleic acid sequences.
On page 2, line 11, polymerase chain reaction is incorrectly abbreviated as “PCT”.
On page 2, line 17, the word generated is misspelled as “geernated”.
Appropriate correction is required.
Claim Objections
Claims 2, 3, 6, 8, 11, 13, and 14 are objected to because of the following informalities:
In claims 2, 3, 13, and 14 SEQ ID NOs 1-6 are referred to as “an amino acid sequence” when they are nucleic acid sequences.
In claim 6, polymerase chain reaction is incorrectly abbreviated as “PCT”.
Claim 8 does not end with a period. As per MPEP 608.01(m), each claim must begin with a capital letter and end with a period.
In claim 11, ATAC is misspelled as “ATACT”.
Appropriate correction is required.
Claim Interpretation
The claims describe SEQ ID NOs 1-6 as amino acid sequences. However, the corresponding sequences disclose nucleic acid sequences. For the purposes of examination, these claims will be interpreted as referring to nucleic acid sequences.
The preamble of claims 12-19 recite a “kit.” The specification, however, does not define this term, and so it is being interpreted to encompass any collection of reagents that includes all of the elements of the claims. Any further interpretation of the word is considered an “intended use” and does not impart any further structural limitation of on the claimed subject matter.
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation is:
"a stabilizing agent configured to stabilize a target" in claim 12. Here, “a stabilizing agent” acts as a generic placeholder and is modified by its function of stabilizing a target. This generic placeholder does not impart sufficient structure to the limitation and is therefore being interpreted under 35 U.S.C. 112(f).
Because this claim limitation is being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it is being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. Such corresponding structure is:
an RNase inhibitor (as identified in the specification on page 3, lines 21-22: “In non-limiting embodiments, the stabilizing agent can be configured to stabilize the target by irreversibly inactivating RNases”) and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
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 2, 3, 13, 14, and 19 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.
Claims 2, 3, 13, and 14 recite the term "the adapter". There is insufficient antecedent basis for this limitation in the claim because claims 1 and 12 recite both “an adapter” and “an adapter sequence” as two distinct entities and it is unclear which of these the claims at issue are referring to. For the purposes of examination, “the adapter” will be interpreted as referring to “an adapter” of claims 1 or 12, where “an adapter” is loaded onto the Tn5 transposome complex/reagent. To rectify this rejection, it is suggested that Applicant rephrase “an adapter sequence” of claims 1 and 12 to clearly delineate between the two aforementioned entities and thereby remove the lack of antecedent basis for claims 2, 3, 13, and 14. Other solutions are possible.
Claims 2, 3, 13, and 14 recite “the amino acid sequence set forth in” and then list multiple separate sequence ID NOs. This is indefinite because the use of the word “the” implies a singular sequence is being claimed, which is in contradiction to the plural sequence ID NOs provided. For the purposes of examination, these claims will be interpreted as being directed to a Markush grouping (see MPEP 2117) constituting the sequences enumerated. These claims may be amended to say “a sequence selected from the group consisting of…” to rectify this rejection. Other solutions are also possible.
Claim 19 recites the limitation "the kit of claim 1". There is insufficient antecedent basis for this limitation in the claim because there is no kit recited in claim 1. In light of the previous claims, claim 19 will be interpreted as being dependent on the kit of claim 12.
Claim Rejections - 35 USC § 102
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.
Claims 12-14 and 16-19, are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhu et al. (Nat Struct Mol Biol, 2019, 26:1063-1070).
Regarding claim 12, Zhu teaches a stabilizing agent (“RNase Inhibitor Mix” – Methods, col. 1, line 63), a tagmentation agent (“Tn5 transposomes” – Methods pg. 1, col. 1, line 33), an adapter (“DNA adaptor oligos” – Methods pg. 1, col. 1, line 34), wherein the Tn5 transposome complex/reagent is loaded with the adapter (“loaded transposases” – Methods pg. 1, col. 1, line 41), and a reverse transcriptase enzyme (“Maxima Reverse Transcriptase” – Methods pg. 1, col. 1, line 67).
Zhu does not explicitly disclose that the reverse transcriptase enzyme is configured to transcribe DNA from both a DNA and an RNA template and perform a terminal transferase activity by template switching and an introduction of an adapter sequence into a cDNA and a transposed chromatin of the target. However, the properties recited (DNA- and RNA-dependent DNA-synthesis, terminal transferase activity via template switching) are inherent properties of Maxima Reverse Transcriptase (an MMLV reverse transcriptase). As stated in the instant specification, “RAM-seq was performed using the inherent terminal transferase and template switching capability of a Moloney Murine Leukemia Virus (MMLV) reverse transcriptase.” Additionally, DNA- and RNA- dependent DNA-synthesis is a recognized inherent ability of MMLV reverse transcriptases, as evidenced in Oscorbin et al. (Computational and Structural Biology Journal, 2021, 19: 6315-6327) which states, “the reverse transcriptase of Moloney MuLV is a typical RT… possessing 3 catalytic activities: RNA- and DNA- dependent DNA polymerase, and RNAse H” (pg. 6316, “Properties”, lines 1-4). Because the claimed properties are inherent to the Maxima Reverse Transcriptase, Zhu also anticipates these properties (see MPEP § 2112).
Regarding claim 13, Zhu further teaches that the adapter comprises a nucleic acid sequence at least 80% identical to the sequence set forth in SEQ ID NOs: 1-3 (Supplementary Table 1: SEQ ID NO 1 – AdapterA; SEQ ID NO 3 – pMENTs).
Regarding claim 14, Zhu teaches that the adapter comprises a nucleic acid sequence at least 80% identical to the sequence set forth in SEQ ID NOs: 4-6 (Supplementary Table 1: SEQ ID NO 3 – pMENTs).
Regarding claim 16, Zhu further teaches the reverse transcriptase enzyme comprises a Moloney Murine Leukemia Virus (MMLV) reverse transcriptase (“Maxima Reverse Transcriptase” – Methods pg. 1, col. 1, line 67).
Regarding claim 17, Zhu further teaches that the target comprises a nucleus, a whole cell, or a combination thereof (“nuclei” – Methods pg. 1, col. 1, line 52).
Regarding claim 18, Zhu teaches that the stabilizing agent is configured to stabilize the target by irreversibly inactivating RNases (see claim 12).
Regarding claim 19, Zhu teaches that the library simultaneously includes profiles of transcriptome and chromatin accessibility with the target (pg. 1063, col. 2, lines 8-10).
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.
The factual inquiries 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.
Claims 1-5, 8-9 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Zhu, in view of Ohtsubo et al. (Sci Rep, 2017, 7: 41769).
Regarding claim 1, Zhu teaches a method comprising stabilizing a target (“RNase Inhibitor Mix” – Methods pg. 1, col. 1, line 63), performing a tagmentation on the target using a Tn5 transposase reagent, wherein the Tn5 transposase reagent is loaded with an adapter (pg. 1063, col. 2, lines 36-38), and generating a library using a reverse transcriptase enzyme (“Maxima Reverse Transcriptase” – Methods pg. 1, col. 1, line 67). Zhu additionally teaches performing a terminal transferase activity (Zhu Figure 1a-1, annotated below; pg. 1064, col. 1, lines 11-13) and an introduction of an adapter sequence (“anchor oligo” – Methods pg. 1, col. 2, line 31) into a cDNA and a transposed chromatin of the target (Zhu Figure 1a). However, Zhu does not teach template switching and that the reverse transcriptase enzyme is configured to perform the terminal transferase activity nor introduce the adapter sequence.
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Zhu Figure 1a-1, annotated
Ohtsubo teaches that a reverse transcriptase can be configured to perform a template switching on both a cDNA (pg. 1, Introduction, paragraph 3) and blunt-end DNA, such as a transposed chromatin (pg. 7, Discussion, lines 1-2). Additionally, Ohtsubo teaches that the use of a reverse transcriptase for terminal transferase activity by template switching is preferable to that of other enzymes with terminal transferase activity due to its strong tailing activity, small tail length, and ability to append any nucleotide (pg. 7 and 9). Specifically, Ohtsubo writes, “the use of strong tailing activity reduces the amount of DNA needed for analysis, which will be useful for single-cell or ancient DNA analyzes” (pg. 9, lines 23-24). Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success in using a reverse transcriptase to perform a terminal transferase activity on both a cDNA and a transposed chromatin because reverse transcriptases are routinely used in similar contexts (pg. 1, Introduction, paragraph 3).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to apply the reverse transcriptase configured to perform a terminal transferase activity by a template switching from Ohtsubo to the method of Zhu with a reasonable expectation of success, based on the motivation taught in Ohtsubo.
Regarding claim 2, Zhu further teaches that the adapter comprises a nucleic acid sequence at least 80% identical to the sequence set forth in SEQ ID NOs: 1-3 (Supplementary Table 1: SEQ ID NO 1 – AdapterA; SEQ ID NO 3 – pMENTs).
Regarding claim 3, Zhu also teaches that the adapter comprises a nucleic acid sequence at least 80% identical to the sequence set forth in SEQ ID NOs: 4-6 (Supplementary Table 1: SEQ ID NO 3 – pMENTs).
Regarding claim 4, Zhu additionally discloses placing the target on a solution, wherein the solution comprises an effective amount of phosphate-buffered saline (Methods pg. 1, col. 1, line 63).
Regarding claim 5, Zhu additionally discloses freezing the target before generating the library (p. 1069, col. 1, line 20).
Regarding claim 8, Zhu further teaches the reverse transcriptase enzyme comprises a Moloney Murine Leukemia Virus (MMLV) reverse transcriptase (“Maxima Reverse Transcriptase” – Methods pg. 1, col. 1, line 67).
Regarding claim 9, Zhu further teaches that the target comprises a nucleus, a whole cell, or a combination thereof (“nuclei” – Methods pg. 1, col. 1, line 52).
Regarding claim 11, Zhu teaches that the library simultaneously includes profiles of transcriptome and chromatin accessibility with the target (Introduction, col. 2, lines 8-10).
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Zhu in view of Nichols et al. (Current Protocols in Molecular Biology, 2008, 84:3.13.1-3.13.8).
See the previous section for prior art analysis of the limitations of claim 1. Additionally, Zhu discloses lysing the target (pg. 1064, col. 1, lines 13-17) and stabilizing the target using a solution that irreversibly inactivates RNases (“RNase Inhibitor Mix” – Methods pg. 1, col. 1, line 52). The distinction between Zhu and the instant application is Zhu used a restriction enzyme digestion step while the instant application specifies the use of RNases. However, the result of both steps is still the lysing of the target, indicating that the only difference is in the agent used.
Furthermore, Nichols teaches that RNases are commonly used to hydrolyze RNA to remove it from DNA preparations. Therefore, one of ordinary skill in the art before the time of the effective filing date of the claimed invention could have substituted the restriction enzyme digestion step of Zhu with a lysing using RNases, yielding the predictable result of lysing the target.
Claims 6, 7, and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Zhu in view of Picelli et al. (Nature Protocols, 2014, 9:171-181, cited in IDS of 6/22/2023).
Regarding claim 15, as discussed previously Zhu teaches all limitations of claim 12. In addition, Zhu discloses a primer for amplification of cDNA of the target (Supplemental Table 1: PA-R), wherein the primer is configured to be introduced at the 3’ end of a first strand of the cDNA and a 3’ end of a chromatin of the target (Zhu Figure 1a-2, annotated below). However, Zhu does not disclose the primer being configured to be introduced at the 5’ end of a first strand of the cDNA.
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Zhu Figure 1a-2, annotated
Picelli teaches a primer configured to be introduced at both 5’ and 3’ ends of a first strand of DNA (Picelli Figure 1, annotated below). Picelli specifies that “every full-length cDNA carries … an additional artificial sequence, which in this case is the same as the one located at the 5′ end of the oligo-dT primer (i.e., the 3′-end of the mRNA)” (page 2, col. 2, lines 11-15).
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Picelli Figure 1, annotated
Together, this indicates that the difference between the claimed invention and the prior art is the lack of actual combination of the elements taught by Zhu and Picelli. Additionally, adapter and primer design are routine tasks and therefore a person of ordinary skill in the art could have used known methods to combine the elements from Zhu and Picelli. Finally, each element merely performs the same function as it does separately, specifically PCR amplification. Based on this, it is clear that a person of ordinary skill in the art would have recognized that the results of the combination of a primer configured to be introduced at the 3’ ends of a cDNA and a chromatin from Zhu with a primer configured to be introduced at both 5’ and 3’ ends of a cDNA from Picelli would predictably result in a single primer configured to be introduced at all three locations for amplification of cDNA.
Regarding claim 6, see the previous discussion of claim 1. Additionally, Zhu discloses performing reverse transcription on the target (pg. 1063, col. 2, lines 15-16) and performing PCR amplification on the cDNA and the chromatin of the target at a predetermined cycle (pg. 1063, col. 2, lines 16-19). A primer for amplification introduced at both 5’ and 3’ ends of a first strand of the cDNA and a 3’ end of the chromatin of the target is discussed in view of Zhu and Picelli in the previous section regarding claim 15. Furthermore, Zhu discloses splitting the amplified cDNA and chromatin into a first group for an RNA library and a second group for an ATAC library (pg. 1064, col. 1, lines 13-17).
Regarding claim 7, Zhu further discloses generating the library comprises generating the RNA library by performing an RNA sequencing on the first group (Methods pg. 1, col. 2, lines 61-63), wherein the first group for the RNA library comprises a cell-specific barcode introduced through an RT primer (“barcoded RT primers” – Methods pg. 1, col. 1, line 65) and generating the ATAC library by performing an ATAC sequencing on the second group (Methods pg. 1, col. 2, lines 61-63), wherein the second group for the ATAC library comprises a cell-specific barcode introduced through an indexing primer (“Indexing PCR” – Methods, col. 2, lines 55-61).
Conclusion
No claims are allowed.
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/ALEXANDRA OLSON/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684