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 .
DETAILED ACTION
1.A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on July 27,2026 has been entered.
Status of the Application
2. Claims 1, 3-4, 7-13 and 21-23 are pending under examination. Claims 14-17 and 19 are withdrawn from further consideration as being drawn to non-elected group. Claims 2, 5-6, 18 and 20 are canceled. The Applicant’s arguments have been fully considered and found persuasive for the following reasons.
Response to Arguments:
3. With reference to the rejection of claims 1, 3-4, 7-13 and 21-23 under 35 USC 103 as being obvious over Reuter et al. in view of Kaper et al. has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 112
4. 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 1, 3-4, 7-13 and 21-23 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. The claim 1 recites ‘wherein the product nucleic acid composition comprises product fragmented RNA and a product fragmented genomic DNA that can be amplified by the same set of primers’. The limitation is unclear and indefinite because step b) recites cDNA synthesis to produce a product via reverse transcription reaction, which would produce cDNA product. It is not clear how said product comprises a product fragmented genomic DNA. Further, it is not clear how product genomic DNA is produced in said reverse transcription reaction. In addition, the method steps only recite fragmenting genomic DNA and the recitation of product fragmented genomic DNA is unclear and indefinite because it is not clear whether the product fragmented genomic DNA is referring to fragmented genomic DNA or any other product that comprises fragmented genomic DNA.
Claim Rejections - 35 USC § 103
5. 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.
Claims 1, 3-4, 7-13 and 21-23 are rejected under 35 U.S.C. 103 as being unpatentable over Soumillon et al. (WO 2018/064640) in view of Weitz et al. (WO 2017/184707).
Soumillon et al. teach a method of claims 1, 22, for amplifying nucleic acids in a sample, comprising: a) fragmenting nucleic acids in a sample to produce a fragmented nucleic acid sample comprising fragmented RNA and fragmented genomic DNA, wherein the fragmenting comprises tagmenting the genomic DNA by a transposase and fragmenting RNA by enzymatic shearing (lysis) (para 0020, 00262-00264, 0015-0017);
b) contacting a fragmented nucleic acid sample comprising fragmented nucleic acid sample with a cDNA deoxyribonucleic acid synthesis primer comprising an RNA originating domain (barcode), and a template switch oligonucleotide (TSO) wherein the cDNA deoxyribonucleic acid synthesis primer does not relay on hybridization to a poly(A) tail under cDNA synthesis conditions to produce a product nucleic acid composition (para 0020, 00250, 00497); and c) amplifying the product nucleic acid composition (para 0020-0023, 00250).
With reference to claim 3-4, Soumillon et al. teach that the transposase attaches adaptors to the genomic DNA during tagmenting and the adaptors comprise DNA origination domain (barcode) (para 0016, 00250, 00135).
With reference to claims 7-10, Soumillon et al. teach that the TSO comprises an RNA origination domain, wherein the RNA origination domain of cDNA synthesis primer and TSO differ from each other by at least one nucleotide or comprise same sequence and said cDNA synthesis primer and TSO are combined to generate a single RNA origination domain (para 00249, 00294, 00497).
With reference to claim 11-12, Soumillon et al. teach that the method further comprises sequencing the nucleic acids of the product nucleic acid composition and determining whether a nucleic acid of the product nucleic acid composition originated from RNA or DNA depending on the presence of the RNA origination domain (para 0022-0023, 00113-00115).
With reference to claim 13, Soumillon et al. teach that the sample is from a single cell (para 00115, 00253).
With reference to claim 21, Soumillon et al. teach the product nucleic acid composition comprises a product nucleic acid comprising an RNA origination domain and a product nucleic acid that does not comprise an RNA origination domain (para 00250, 0020-0023).
With reference to claim 22-23, Soumillon et al. teach that the fragmenting RNA comprises chemical, enzymatic or acoustic shearing (para 00250-00252, 0020, 00446, 00496, 00473).
However, Soumillon et al. did not specifically teach same primer pair can amplify fragmented RNA and fragmented DNA.
Weitz et al. teach a method for simultaneous amplification and sequencing target RNA and genomic DNA, wherein the method comprises amplification of barcoded gDNA and barcoded target RNA with the same set of primers (example 2 on page 41-42, page 17, line 3-15- indicating use of forward and universal adapter primers to amplify both gDNA and target RNA).
It would be primarily obvious to an ordinary person skilled in the art before the effective filing date of the invention to modify the method as taught by Soumillon et al. with a primer set to amplify gDNA and RNA as taught by Weitz et al. to develop an improved method for amplifying nucleic acids in a sample. The ordinary person skilled in the art would have motivated to modify the method of Soumillon et al with the teachings of Weitz et al. and have a reasonable expectation of success that the combination would result in an improved sensitive method for amplifying nucleic acids because Weitz et al. explicitly taught use of same primer set to amplify gDNA and RNA (Example 2 on page 41-42) that would reduce additional steps to amplify nucleic acids in a droplet and such a modification is considered obvious over the cited prior art.
Conclusion
No claims are allowed.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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