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. The Applicant’s response to the office action filed on December 09, 2025 is acknowledged.
Status of the Application
2. Claims 1-12 and 19 are pending under examination. Claims 13-18 and 20 were canceled. The Applicant’s arguments and the amendment have been fully considered and found persuasive for the following reasons.
Response to Arguments:
3. The objection to the specification has been withdrawn in view of the amendment.
4. The rejection of claims under 35 USC 102(a)(1) as being anticipated by Betts et al. has been withdrawn in view of the amendment. However, Betts et al. teach use of uracil DNA glycosylase and TSO having one or more ribonucleotides. The reference is used in a new combination in the following rejection to address the amendment.
New Rejections Necessitated by the Amendment
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 1-12 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Betts et al. (US 2017/0327882) in view Kuball et al. (WO 2017/212074).
Betts et al. teach a method of claim 1, for preparing DNA complementary to poly(A)-minus RNA comprising the steps of: i) treating the poly(A)-minus RNA with (a) poly(A) polymerase (PAP) to add a 3’ poly(A) tail to the poly(A)- minus RNA, thereby producing poly(A)-plus RNA, or (b) polynucleotide transferase to add a homopolynucleotide poly(N), where poly(N) is selected from poly(A), poly(C), poly(G) and poly(U), thereby producing poly(N)-plus RNA (para 0036-0037);
ii) annealing a cDNA synthesis primer comprising oligo(dT) to the poly(A)-plus RNA produced in (1)(a), or annealing a cDNA synthesis primer comprising oligo(dN’) to the poly(N)-plus RNA produced in (i)(b), wherein N’ is a nucleotide that base pairs with N, and synthesizing a first cDNA strand, thereby producing an RNA-cDNA intermediate (para 0038-0055);
iii) conducting a template switching reaction by contacting the RNA-cDNA intermediate with a template switching oligonucleotide (TSO) under conditions suitable for extension of the first cDNA strand, rendering the first cDNA strand additionally complementary to the TSO, wherein the TSO is 30-50 nucleotides in length and comprises one or more or two or more ribonucleotides (para 0038-0069, 0080);
iv) degrading the TSO, wherein degrading TSO comprises treatment of the TSO with uracil DNA glycosylase (UDG) (para 0080, 0065-0069, 0008).
With reference to claims 2, 11, Betts et al. teach that the method further comprising (v) amplifying sequence from the first cDNA strand to produce a pool of amplicons, further comprising sequencing amplicons produced in step (v) (para 0066-0077).
With reference to claims 3-4, Betts et al. teach that the method further comprising (vi) depleting high- abundance RNA species from the pool of amplicons and wherein the high-abundance RNA species comprises ribosomal RNA (para 0028-0029, 0084).
With reference to claims 5, Betts et al. teach that in step (iv) the TSO is degraded by treatment with uracil DNA glycosylase (UDG) or with a combination of UDG and endonuclease VIII (para 0080, 0065).
With reference to claims 6, Betts et al. teach that in step (i)(a) a mixture comprising poly(A)-minus RNA and polyadenylated RNA is treated with poly(A) polymerase (PAP) to add a 3’ poly(A) tail to the poly(A)-minus RNA and to the polyadenylated RNA, thereby producing the poly(A)-plus RNA (para 0037).
With reference to claims 7-9, Betts et al. teach that the mixture comprises RNA from one single cell, wherein the mixture comprises total RNA from a single cell and wherein the mixture comprises RNA from human cells (para 0029-0032).
With reference to claims 10, Betts et al. teach that the step of amplifying comprises associating the sequence from the first cDNA strand with one or more sequence elements selected from adaptors, indexing sequences, oligonucleotide binding sequences and barcodes (para 0073).
With reference to claims 12, 19, Betts et al. teach that the steps are carried out in the same compartment and wherein cell lysis prior to step (1) is carried out in the same compartment (para 0085-0088, 0031).
However, Betts et al. did not specifically teach TSO comprising 3-10 deoxyuridine (dU) nucleotides spaced or positioned in TSO such that the remaining fragment of TSO after degradation is no more than 10 nucleotides.
Kuball et al. each a method for preparing DNA complementary to poly(A)-minus RNA, wherein the method comprises 3 to 10 deoxyuridine nucleotides in a TSO oligonucleotides positioned in TSO such that the remaining fragments of TSO after degradation is no more than 10 nucleotides (page 61, line 21 to line 19 on page 62, table 2 and page 68, line 30 to line 23 on page 69, table 5: indicating template switch adapter in table 2 and 5 comprising more than 3 dU residues positioned at different positions so that after degradation no remaining fragments would be longer than 10 nucleotides).
It would have been prima facie obvious to one skilled in the art before the effective filing date of the invention to modify the method of Betts et al. with TSO comprising 3 to 10 deoxyuridine nucleotides as taught by Kuball et al. to develop an improved method for preparing cDNA. The ordinary person skilled in the art would have motivated to combine the method of Betts et al. with TSO comprising 3 to 10 dU nucleotides positioned in TSO as taught by Kuball et al. and have a reasonable expectation of success that the combination would improve the method for preparing cDNA because Kuball et al. explicitly taught use of TSO comprising 3-10 dU residues positioned at different positions so that after degradation no remaining fragments would be longer than 10 nucleotides that minimizes PCR bias during the cDNA preparation (page 61, line 30-34, page 62, line 1, table 2 and table 5) and such a modification of the method is considered obvious over the cited prior art.
Conclusion
No claims are allowable.
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.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681