DETAILED ACTION
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 .
Office Action: Notice
Any objection or rejection of record in the previous Office Action, mailed 1/9/2026,
which is not addressed in this action has been withdrawn in light of Applicants' amendments
and/or arguments. This action is a second NON-FINAL.
Claim Status
No claim has been amended (7/9/2026). No new matter was added. Claims 1-5, 8-10, 12-13 and 15 are under examination on the merits.
Rejections Withdrawn
Claim Rejections - 35 USC § 102
The 35 U.S.C. 102 (a)(1) and (a)(2) rejection for claims 1-3, 8-10, 12-13 and 15 as being anticipated by Bostick et al., (WO 2017/048993 A1, published 3/23/2017, from IDS 4/13/2021) is withdrawn. Specifically, upon review of the Applicant’s Arguments (7/9/2026), Bostick does not disclose each limitation of claim 1 arranged as claimed in the specified workflow. In particular, Bostick does not teach the claimed in vitro transcription/amplified RNA (aRNA) workflow as claimed as part of end-repair of fragmented RNA prior to polyadenylation.
New Rejections
Claim Rejections - 35 USC § 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 (i.e., changing from AIA to pre-AIA ) 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 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, 8-10, 12-13 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Bostick et al., (WO 2017/048993 A1, published 3/23/2017, from IDS 4/13/2021), in view of Kobayashi et al. (“Non-cloning synthesis of cRNA probe and its application to in situ hybridization analysis of formalin-fixed paraffin embedded tissue”, J. Toxicol. Pathol.; published 2003) and Allen et al. (PGPub US 2020/0102586 A1, published 4/2/2020, filed 9/28/2018). This rejection is modified, as necessitated by Applicants' arguments.
Regarding claim 1 Bostick teaches a library preparation and analysis (Figure 1; Abstract).
Regarding claim 1 step a, Bostick teaches an RNA sample (pg. 2).
Regarding claim 1 step b, Bostick teaches fragmenting RNA (pg. 12). Specifically, Bostick teaches chemical fragmentation (pg.12, line 16).
Regarding claim 1 step c Bostick teaches adenylating fragmented RNA (pg. 12), specifically Bostick teaches (poly)adenylating precursor RNA using any convenient approach (pg. 12, line 29).
Regarding claim 1 step d, Bostick teaches a cDNA primer may include a domain that hybridizes to the template RNA. Bostick teaches the sequence of the first and second domains may be independently defined or arbitrary (pgs. 14 and 15).
Regarding claim 1 step e, Bostick teaches the first strand cDNA primer includes a barcode domain for identification of the sample. In certain aspects the cDNA primer may include a unique molecular identifier (UMI) or other barcode to mark each RNA molecule converted to cDNA individually (pg. 15, lines 22-24). After first strand synthesis the cDNA is amplified via PCR to generate product double strand cDNA to produce a second strand DNA complementary to the first strand cDNA (pg.19, line 19, Bostick further teaches a unique molecular identifier (UMI) on Oligo dT primers (pg. 14 and 15). Additionally, Bostick teaches that solid phase amplification of these polynucleotides is typically performed by first ligating known adapter sequences or a template switch oligonucleotide under first strand cDNA synthesis conditions, as previously described, to each end of a targeted polynucleotide (i.e., aRNA) (p. 1, lines 1-15; p. 2, lines 1-5; p. 8 lines 10-20). Bostick also teaches that synthesis of cDNA from template nucleic acid mRNA in the methods described above are performed directly on cell lysates allowing purification or depletion of RNA via release from cells, to reduce mitochondrial and ribosomal contamination (p. 32, lines 10-15).
Regarding claim 2 Bostick teaches sample RNA is isolated from a single cell (pg.11 line 10).
Regarding claim 3 Bostick teaches RNA may be microRNA, small nucleolar RNA, and small nuclear RNA (pg.10).
Regarding claim 8, step k Bostick teaches PCR amplification conditions, sufficient to produce a product double stranded cDNA (pg. 20 line 27- 33). Bostick teaches primer binding sites (domains) which may be on the end of double stranded cDNA. Bostick teaches amplification primer binding site can be randomly attached to fragment ends of double-stranded cDNA library (pg. 8 line 25).
Regarding claim 9, it is noted that step (h) remains optional, and thus, the teachings of Bostick anticipate claim 9 for the same reasons they anticipate claim 8. Further, Bostick teaches the sequencing platform adapter may include adapter sequences, indexing sequences, sources barcode sequences, and UMI (unique molecular identification sequences) (pg.35, line 29).
Claim 10 further limits claim 8 optional step m, but does not require the practice of optional step m, therefore by meeting step k, claim 10 is also anticipated.
Regarding claim 12 Bostick teaches preparing a sequencing library, pooling one or more sequencing libraires (pg. 25, line 33), furthermore Bostick teaches deep sequencing the sequencing library (pgs. 32-34).
Regarding claim 13 Bostick teaches cDNA library and first strand cDNA primers include a unique molecular identifier or other barcode to mark each RNA molecule converted to cDNA individually (pg. 15 lines 21-24 and pg. 32-33).
Regarding claim 15, Bostick teaches PCR amplification conditions, sufficient to produce a product double stranded cDNA (pg. 20 line 27- 33). Bostick teaches primer binding sites (domains) which may be on the end of double stranded cDNA, and are randomly attached to fragment ends of double-stranded cDNA library (pg. 8 line 25). Specifically, Bostik teaches that following ligation of adapter sequences, unused adapter molecules must be separated from the ligated polynucleotides before proceeding to the amplification, so as to avoid unwanted amplification of adapters that have not been attached to the target polynucleotides (p.1, lines 20-25).
Bostick does not teach or suggest performing in vitro transcription of the cDNA obtained by reverse transcription to produce amplified RNA (aRNA). Bostick does not teach or suggest fragmentation by exposure to a divalent metal-cation at a temperature between 55-110 °C. Bostick does not teach or suggest that the metal cation is Mg2+.
Regarding claim 1, Kobayshi teaches generating cRNA by in vitro transcription of a cDNA template (Abstract). Further, Kobayshi teaches ligating a T7 promoter adapter to an RT-PCR-generated cDNA product, amplifying the T7 promoter-containing cDNA by PCR, and using the resulting cDNA as a template for in vitro transcription with T7 RNA polymerase to produce cRNA (Figure 1; In vitro transcription: p. 248).
Allen teaches a method to create a cDNA library, Allen teaches fragmenting mRNA, polyadenylating RNA fragments followed by oligo-dt primed reverse transcription.
Regarding claim(s) 4 and 5, Allen teaches fragmenting mRNA at 60 °C in the presence of a divalent cation e.g., Mg2+ (pg. 4 col. 2).
It would have been obvious to have modified Bostick’s method of fragmenting mRNA for reverse transcription to include Allen’s step of treatment (end repair) under suitable conditions. One would have been motivated to do so because as stated by Allen treatment of the 5’ Hydroxyl and 3’ Phosphate may be required before moving on to the polyadenylation step.
It would have been obvious to have modified Bostick’s method to include in vitro transcription of the resulting cDNA to produce aRNA, as taught by Kobayashi. Kobayashi teaches ligating a T7 promoter adapter to an RT-PCR generated cDNA product, amplifying the T7 promoter-containing cDNA, and using the resulting cDNA as a template for in vitro transcription with T7 RNA polymerase to produce cRNA, as highlighted above. One of ordinary skill in the art would have been motivated to employ Kobayashi’s known T7-based in vitro transcription technique in Bostick’s RNA analysis workflow to provide an RNA amplification product from the cDNA intermediate for subsequent analysis and processing. One of ordinary skill would have had a reasonable expectation of success because Kobayashi demonstrates successful production of cRNA by in vitro transcription from a T7-promoter containing cDNA template.
It would further have been obvious to have modified Bostick’s method of attaching adapters to RNA to include Allen’s step of ligating an adapter to RNA because Bostick teaches ligation-based strategies as an alterative method for adding nucleotides to precursor RNA (p. 13, lines 6-8), and Allen teaches ligating adapters to RNA. One of ordinary skill in the art would have been motivated to employ Allen’s adapter ligation in the modified Bostick/Kobayashi method because Allen teaches that adapter ligation can be used for quantitative determination of specified sequences within an RNA or DNA sample (p. 8, col. 2).
Applicant’s Arguments: The Applicant argues that Bostick in view of Allen fails to teach or suggest the claimed sequence of end-repair immediately following RNA fragmentation and prior to polyadenylation and further fails to teach the claimed IVT/aRNA workflow, including generating aRNA by in vitro transcription of CDNA and subsequently processing that aRNA. Applicant further asserts that the claimed sequence produces unexpected results and therefore would not have been obvious.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully considered and are found partially persuasive, as discussed below. Applicant is persuasive that Bostick alone does not expressly disclose the claimed in vitro transcription/aRNA workflow. Accordingly, the prior rejection has been modified to further rely upon Kobayashi.
However, the arguments do not overcome the rejection under 35 SUC 103 as presently set forth. Allen teaches treatment of fragmented RNA ends prior to polyadenylation and therefore addresses the claimed end-repair sequence. Kobayashi further teaches using a T7-promoter containing cDNA as a template for in vitro transcription with T7 RNA polymerase to produce cRNA, thereby demonstrating that production of an RNA product from a cDNA intermediate by IVT was known in the art. As discussed in the rejection above, one of ordinary skill would have reason to incorporate Kobayashi’s known IVT technique into the Bostick/Allen method to provide an amplified RNA product from the cDNA intermediate for subsequent processing, with reasonable expectation of success based on Kobayashi’s successful production of cRNA by this technique. Further, Allen teaches adapter ligation to RNA, and Bostick teaches reverse transcription and subsequent processing of RNA/cDNA products. Thus, when the teachings of the references are considered as a whole, rather than requiring any single reference to disclose the entire claimed sequence would have been obvious for the reasons set forth above.
Applicant’s assertion of unexpected results has also been considered. However, absent sufficient evidence demonstrating results that are unexpected relative to the closest prior art and commensurate in scope with the claims, the assertion does not outweigh the evidence of obviousness presented by the combined teachings of Bostick, Allen and Kobayashi. Accordingly, Applicant’s arguments are not persuasive of patentability over the newly modified rejection.
Rejections Maintained
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 2, 9 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1, 2, and 33 of copending Application No. 18020391 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because Claim 1 is anticipated by copending claim 2.
Regarding claim 2 in application 18020391 teaches fragmenting RNA (claim 1a, 33).
Regarding claim 1 step c, 18020391 teaches polyadenylation of RNA (claim 2).
Regarding step d, 18020391teaches cDNA synthesis with a poly-T primer hybridized to a polyA tag of RNA (claim 2). 391 further teaches reverse transcription to obtain cDNA sequencing library (claim1g).
Regarding step e, 18020391 teaches poly-T primer further comprising a UMI and/or barcode (claims 2,33).
Regarding claim 2, copending application teaches RNA from a single cell (claim 1).
Regarding claim 9, copending application teaches each cDNA in the cDNA sequencing library comprises a barcode and optionally a UMI (claim 33).
Claim(s) 1, 2, 3, 8, 9, 10, 12-13 and 15 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 1, 2, 15, and 33 of copending Application No. 18020391 in view of Bostick et al., (WO 2017/048993 A1, published 3/23/2017, from IDS 4/13/2021).
Regarding claim 2 copending application 18020391 teaches fragmenting RNA (claim 1a).
Regarding claim 1 step c, copending application teaches polyadenylation of RNA (claim 2).
Regarding step d, copending application teaches cDNA synthesis with a poly-T primer hybridized to a polyA tag of RNA (claim 2). 18020391 further teaches reverse transcription to obtain cDNA sequencing library (claim1g).
Regarding step e, copending application teaches poly-T primer further comprising a UMI and/or barcode (claims 2,33).
Regarding claim 2, copending application teaches RNA from a single cell (claim 1).
Regarding claim 9, copending application teaches each cDNA in the cDNA sequencing library comprises a barcode and optionally a UMI (claim 33).
The copending application does not teach the steps of claim(s) 3, 8, 10, 12-13 and 15.
Bostick teaches a method of preparing a sequencing library (Figure 1; Abstract).
Regarding claim 3 Bostick teaches RNA may be microRNA, small nucleolar RNA, and small nuclear RNA (pg.10).
Regarding claim 8, step k Bostick teaches PCR amplification conditions, sufficient to produce a product double stranded cDNA (pg. 20 line 27- 33). Bostick teaches primer binding sites (domains) which may be on the end of double stranded cDNA. Bostick teaches amplification primer binding site can be randomly attached to fragment ends of double-stranded cDNA library (pg. 8 line 25).
Claim 10 further limits claim 8 optional step m, but does not require the practice of optional step m, therefore by meeting step k, I am rejecting claim 10.
Regarding claim 12, Bostick teaches preparing a sequencing library, pooling one or more sequencing libraires (pg. 25, line 33), furthermore Bostick teaches deep sequencing the sequencing library (pgs. 32-34).
Regarding claim 13, Bostick teaches cDNA library and first strand cDNA primers include a unique molecular identifier or other barcode to mark each RNA molecule converted to cDNA individually (pg. 15 lines 21-24 and pg.32-33).
Regarding claim 15, Bostik teaches that following ligation of adapter sequences, unused adapter molecules must be separated from the ligated polynucleotides before proceeding to the amplification, so as to avoid unwanted amplification of adapters that have not been attached to the target polynucleotides (p.1, lines 20-25).
It would have been obvious to modify the method taught in the claims of copending application 18020391 to include Bostick’s method of creating a cDNA library. One would have been motivated to do so because this will create a cDNA library from RNA, wherein a next generation sequencing library are produced (Bostick pg.33).
This is a provisional nonstatutory double patenting rejection.
Claim(s) 1 and 4-6 is/are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 1, 2, 15, 17, 18 and 33 of copending Application No. 18020391 in view of Allen et al. (PGPub US 2020/0102586 A1, published 4/2/2020, filed 9/28/2018).
Regarding claim 1, copending application teaches the limitations of claim 1 as described above and is incorporated herein.
The copending application fails to teach the limitation of claim(s) 4-6 of the instant application.
Regarding claim(s) 4 and 5, Allen teaches fragmenting mRNA at 60 °C in the presence of a divalent cation e.g., Mg2+ (pg. 4 col. 2).
Regarding claim 6, Allen teaches some methods produce fragments that have 5’ Hydroxyl or 3’Phosphate and shall require treatment by phosphatase and/or kinase treatment before polyadenylation step (Allen pg. 10, col. 2).
It would have been obvious to have modified the copending application method of fragmenting to include Allen’s step of treatment (end repair) under suitable conditions. One would have been motivated to do so because as stated by Allen treatment of the 5’ Hydroxyl and 3’ Phosphate may be required before moving on to the polyadenylation step.
This is a provisional nonstatutory double patenting rejection.
Applicant’s Arguments: The Applicant argues that the provisional nonstatuatory double patenting rejection should be withdrawn because the instant application has an earlier effective filing date (10/29/2019) than the cited copending application (8/18/2021), and therefore the claims are not obvious over the copending claims. Applicant further contends that, pursuant to MPEP 1490 (VI)(D)(2)(a), where a provisional nonstatuatory double patenting rejection is the only remaining rejection in an application having the earlier patent term filing date, the rejection should be withdrawn and the application permitted to issue.
Examiner’s Response to Traversal: The Applicant’s arguments regarding withdrawal of the provisional nonstatuatory double patenting rejection have been fully considered, but are not persuasive at this time. As a rejection under USC 103 remains outstanding, the provisional nonstatuatory double patenting rejection is maintained. Applicant’s arguments will be reconsidered if and when double patenting is the sole remaining issue. therefore, these rejections are maintained, as set forth above.
Conclusions
No claim is allowed.
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/ELIZABETH ROSE LAFAVE/
Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
