DETAILED ACTION
Response to Amendment
Applicant’s response to the office action filed on November 3, 2025 has been entered. The claims pending in this application are claims 46-50, 52-63, 68, and 69 wherein claims 56-60 have been withdrawn due to the restriction requirement in the office action mailed on December 9, 2021. Claims 46-50, 52-63, 68, and 69 will be examined.
Claim Objections
Claim 68 or 69 is objected to because of the following informality: “SEQ ID NO:1-4” should be “SEQ ID NOs: 1-4”.
Appropriate correction is required.
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 68 and 69 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.
Claim 68 or 69 recites the limitation “the amplified product nucleic acid” in the claim. There is insufficient antecedent basis for this limitation in the claim because claim 46 or 61 does not have a phrase “an amplified product nucleic acid”. Furthermore, since claim 46 or 61 does not indicate which components in steps (a) to (d) contain SEQ ID Nos:1-4, it is unclear why the amplified product nucleic acid produced in step d) can comprise SEQ NOs: 1-4 or complements thereof. Please clarify.
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.
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 46, 48-50, and 52-55 are rejected under 35 U.S.C. 103 as being unpatentable over Zhu et al., (BioTechniques, 30, 892-897, 2001) or Chenchik et al., (US Patent No. 5,962,272, published on October 5, 1999) in view of Chiang et al., (US 2009/0220969 A1, published on September 3, 2009) and Salimullah et al., (Cold Spring Harb. Protoc., doi:10.1101/pdb.prot5559 (pages 96-11), 2011).
Regarding claims 46, and 53-55, Zhu et al., or Chenchik et al., teach a method comprising: c) combining: i) the template RNA (ie., mRNA); ii) a template switch
oligonucleotide (TSO) comprising a first nucleotide sequence domain; iii) a polymerase having terminal transferase activity (ie., a reverse transcriptase); iv) a first strand primer (ie., the cDNA synthesis (CDS) primer) comprising a first domain (ie., the poly T domain of the cDNA synthesis primer which does not include an anchor nucleotide V) that hybridizes only to the template RNA and a second domain having a nucleotide sequence that is different from said first nucleotide sequence domain present in the TSO wherein the first domain comprises only a single type of nucleotide (ie., Poly T) and is 3’ of the second domain; and dNTPs; in a reaction mixture under conditions sufficient to produce a product nucleic acid (eg., first strand cDNA-RNA hybrid) comprising the template RNA and the TSO hybridized to adjacent regions of a single product nucleic acid (eg., first strand cDNA) comprising the first strand primer and a region polymerized from the dNTPs by the polymerase; and d) amplifying the product nucleic acid with a forward primer and a reverse primer, wherein each of the forward primer (ie., 5’ anchor primer or 5’ PCR primer) and the reverse primer (ie., the CDS primer) comprises a sequencing platform adapter construct comprising at least a portion of a capture sequence that is utilized by a sequencing platform (ie., some portion of each of the 5’ anchor primer or 5’ PCR primer and the CDS primer has an ability to hybridize to a surface-attached sequencing platform oligonucleotide on a sequencing platform), wherein the sequencing platform adapter constructs of the forward primer and the reverse primer are different, wherein the capture sequence specifically hybridizes to a surface-attached sequencing platform oligonucleotide on the sequencing platform, and wherein the forward primer specifically hybridizes to a sequence in the product nucleic acid which is complementary to a region of the template switch oligonucleotide that is not in the first nucleotide sequence domain and the reverse primer includes a sequence that is identical to a sequence in the product nucleic acid which is a region of the first strand primer (ie., the CDS primer) that is not the first domain (ie., a domain having poly T) of the first strand primer as recited in claim 46, wherein the polymerase is a reverse transcriptase as recited in clam 53, and the template switch oligonucleotide, the first strand primer, or both the template switch oligonucleotide and the first strand primer comprise a sequencing platform adapter construct that is utilized by a sequencing platform (eg., 5’ region of the template switch oligonucleotide in Figure 1 of Zhu et al., or Figure 3 of is capable of serving as a sequencing primer binding domain) as recited in claim 54, the sequencing platform adapter construct comprises a sequencing primer binding domain as recited in claim 55 (for Zhu et al., see pages 893 and 894, and Figure 1 or For Chenchik et al., see Examples 1 and 2 in columns 13-17 and Figure 3).
Zhu et al., or Chenchik et al., do not disclose that a) providing a non-polyadenylated ribonucleic acid (RNA) and (b) adding a plurality of non-templated nucleotides to an end of the non-polyadenylated RNA to produce a template RNA wherein the forward primer and the first strand primer comprise sequencing platform adaptor constructs which are not present in the first strand primer or the template switch oligonucleotide and their method does not include a ligation method as recited in claim 46 wherein the non-templated nucleotides are added to the 3’ end of the non-polyadenylated RNA as recited in claim 48, the non-templated nucleotides are added in an enzymatic reaction as recited in claim 49, the non-templated nucleotides form a polyadenylation (poly A) sequence as recited in claim 50, and the non-polyadenylated RNA is a microRNA as recited in claim 52. However. Zhu et al., or Chenchik et al., teach that the forward primer (ie., the CDS primer) and the first strand primer (ie., the CDS primer) are identical (for Zhu et al., see Figure 1 or For Chenchik et al., see Figure 3).
Chiang et al., teach a) providing a non-polyadenylated ribonucleic acid (RNA) (siRNA) and (b) adding a plurality of non-templated nucleotides to an end of the non-polyadenylated RNA to produce a template RNA (ie., siRNA having a polyA sequence) and their method (ie., adding step) does not include a ligation step (ie., step (b) using E. coli poly (A) polymerase, not a RNA ligase) as recited in claim 46 wherein the non-templated nucleotides are added to the 3’ end of the non-polyadenylated RNA as recited in claim 48, the non-templated nucleotides are added in an enzymatic reaction (ie., using a poly(A) polymerase) as recited in claim 49, the non-templated nucleotides form a polyadenylation (poly A) sequence as recited in claim 50, and the non-polyadenylated RNA is a microRNA as recited in claim 52 (see paragraphs [0007] to [0013] and [0022], Figure 1, and claims 1-25).
Since Salimullah et al., teach to synthesize a first strand of a cDNA using a reverse transcription primer, synthesize a second strand of the cDNA using a PCR and amplifying the cDNA using library PCR in the presence of a forward primer having a region which is not complementary to the cDNA and a reverse primer having a region which is not complementary to the cDNA (see Figure 1 and pages 97 and 98), the forward and reverse primers in the library PCR taught by Salimullah et al., comprise sequencing platform adaptor constructs (ie., the regions in the forward and reverse primers in the library PCR which are not complementary to the cDNA) which are not present in the first strand primer or the template switch oligonucleotide as recited in claim 46.
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have performed the methods recited in claims 46, 48-50, and 52 by providing a non-polyadenylated ribonucleic acid (RNA) (ie., microRNA or miRNA), adding a plurality of non-templated nucleotides to an end of the non-polyadenylated RNA to produce a template RNA (ie., microRNA or miRNA having a polyA sequence) wherein their method (ie., the adding step) does not include a ligation method (ie., step (b) using E. coli poly (A) polymerase, not a RNA ligase), the non-templated nucleotides are added to the 3’ end of the non-polyadenylated RNA, the non-templated nucleotides are added in an enzymatic reaction (ie., using a poly(A) polymerase), the non-templated nucleotides form a polyadenylation (poly A) sequence, and the non-polyadenylated RNA is a microRNA, and the forward and reverse primers comprise sequencing platform adaptor constructs which are not present in the first strand primer or the template switch oligonucleotide in view of the prior arts of Zhu et al., or Chenchik et al., and Chiang et al., and Salimullah et al.. One having ordinary skill in the art would have been motivated to do so because Chiang et al., have taught providing a non-polyadenylated ribonucleic acid (RNA) (ie., microRNA or miRNA) and adding a plurality of non-templated nucleotides to an end of the non-polyadenylated RNA to produce a template RNA (ie., microRNA or miRNA having a polyA sequence) and the adding step does not include a ligation step (ie., step (b) using E. coli poly (A) polymerase, not a RNA ligase) as recited in claim 46 wherein the non-templated nucleotides are added to the 3’ end of the non-polyadenylated RNA as recited in claim 48, the non-templated nucleotides are added in an enzymatic reaction (ie., using a poly(A) polymerase) as recited in claim 49, the non-templated nucleotides form a polyadenylation (poly A) sequence as recited in claim 50, and the non-polyadenylated RNA is a microRNA as recited in claim 52 (see paragraphs [0007] to [0013] and [0022], Figure 1, and claims 1-25), Salimullah et al., teach to synthesize a first strand of a cDNA using a reverse transcription primer, synthesize a second strand of the cDNA using a PCR, and amplifying the cDNA using library PCR in the presence of a forward primer having a region which is not complementary to the cDNA and a reverse primer having a region which is not complementary to the cDNA (see Figure 1 and pages 97 and 98), and the simple substitution of one kind of template RNA sample (ie., the template RNA sample containing mRNA taught by Zhu et al., or Chenchik et al.,) from another kind of template RNA sample (ie., the template RNA sample containing miRNA comprising a 3’ polyadenine sequence taught by Chiang et al.,) during the process for performing the method recited in claim 46, in the absence of convincing evidence to the contrary, would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made since the template RNA sample containing mRNA taught by Zhu et al., or Chenchik et al., and the template RNA sample containing miRNA comprising a 3’ polyadenine sequence taught by Chiang et al., are used for the same purpose (ie., serving as a template RNA for synthesizing a cDNA). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to perform steps (a) and (b) of the method recited in claim 46 and the methods recited in claims 48-50 and 52 using the RNA synthesis method taught by Chiang et al., and perform step (d) of claim 46 using a forward primer having a region which is not complementary to the cDNA and a reverse primer having a region which is not complementary to the cDNA wherein the forward primer and the reverse primer have the same structure designs of the forward and reverse primers of the library PCR taught by Salimullah et al., in view of the prior arts of Zhu et al., or Chenchik et al., Chiang et al., and Salimullah et al., in order to produce a template RNA for the method recited in claim 46.
Furthermore, the motivation to make the substitution cited above arises from the expectation that the prior art elements will perform their expected functions to achieve their expected results when combined for their common known purpose. Support for making the obviousness rejection comes from the M.P.E.P. at 2144.06, 2144.07 and 2144.09.
Also note that there is no invention involved in combining old elements is such a manner that these elements perform in combination the same function as set forth in the prior art without giving unobvious or unexpected results. In re Rose 220 F.2d. 459, 105 USPQ 237 (CCPA 1955).
Response to Arguments
In page 7, fourth paragraph bridging to page 12, first paragraph of applicant’s remarks, applicant argues that “[A]pplicant submits that the skilled artisan would not be motivated to
modify the references as asserted by the Office because 1) the library PCR primers of
Salimullah would serve no use in the methods of Zhu and Chenchik, and 2) the skilled artisan would not be motivated to combine the methods of Zhu or Chenchik with the polyadenylation
methods of Chiang. With regard to 1), the skilled artisan would not modify the methods of Zhu or Chenchik to replace the forward and reverse primers of Zhu or Chenchik with the library PCR primers of Salimullah because the library PCR primers of Salimullah would serve no purpose in the methods of Zhu or Chenchik. Zhu and Chenchik employ restriction digest for downstream library preparation which would remove the sequences added by the library PCR primers. Specifically, the methods of Zhu and Chenchik are directed to using template switching on mRNA targets in order to generate full-length cDNA libraries. The methods of Zhu and Chenchik also employ the usage of restriction digests to generate sticky ends to be used for
vector integration. Both Zhu and Chenchik introduce the restriction sites for digest during the first-strand synthesis stage. For instance, Zhu states ‘Briefly, first-strand synthesis is carried out in the presence of two oligonucleotides: a ‘lock-docking’ CDS primer (5) that contains an SfiIB site and primes reverse transcriptase and a TS-oligonucleotide that contains an SfilA site.’ (pg. 894 2ⁿᵈ column last paragraph). With regard to Chenchik, following the description of second-strand synthesis and/or PCR amplification, Chenchik states ‘When an oligonucleotide CDS primer is used, the ds cDNA prepared in the second step by PCR or by mRNA replacement technology can be ligated with adaptor or digested with restriction enzyme(s) in sequences corresponding to CDS and CAPSwitch oligonucleotide banking portions, thus generating ds cDNA molecules which will be ligated to any conventional cloning vector’ (Column 11 5th paragraph). Thus, Chenchick discloses that when an adaptor ligation step is not used, as is specified in the amended claims of the present application, the ds cDNA is digested using restriction sites in the sequences contained in the CDS and CAPSwitch oligonucleotides. The above reading of Chenchik is further supported by Example 2 which states ‘For example, instead of the adaptor ligation step (step 3), ds cDNA generated by PCR can be digested by rare cutting restriction endonuclease(s) in sequences corresponding CDS and CAPswitch oligonucleotide flanking portions and cloned directly into vector’ (Column 15 3rd paragraph).
Accordingly, if the skilled artisan were to employ the library PCR primers of Salimullah, which
contain sequencing platform adaptor constructs in the region of the primers that are not complementary to the CDR, then following the restriction digest step of Zhu or Chenchik methods, the sequencing platform adapter constructs would be removed from the cDNA and would serve no purpose. Zhu requires the step of restriction digest because restriction digest sites allow for the identification of correct amplification products for library preparation. This teaching of Zhu is evidenced by the fact that Zhu states ‘The observed enrichment for full-length cDNA clones in the SMART library is likely the result of three principal factors... Consequently, template switching is unlikely in first-strand synthesis events in which reverse transcriptase prematurely aborts polymerization after encountering strong mRNA secondary structure. Thus, the truncated cDNAs lack SfilA anchors and are eliminated during the cloning process’ (pg. 896 2ⁿᵈ column 2ⁿᵈ paragraph). Chenchik also requires the step of restriction digest because
all of the embodiments that are directed to generating cDNA libraries involve the incorporation of the cDNA into vectors, i.e., the embodiments disclosed in FIG. 3 and FIG. 4 and described in Examples 2 and 3. The embodiments disclosed in Example 1 and 4 do not apply to the claimed methods as the methods of Example 1 require the use of gene-specific primers (See column 14 last paragraph) and the methods of Example 4 use a single primer as the forward and reverse primer (See step 2 of Example 4 in column 20.) As discussed above, the section of Chenchik referring to cloning into vectors states ‘When an oligonucleotide CDS primer is used, the ds cDNA prepared in the second step by PCR or by mRNA replacement technology can be ligated with adaptor or digested with restriction enzyme(s) in sequences corresponding to CDS and CAPSwitch oligonucleotide banking portions, thus generating ds cDNA molecules which will be ligated to any conventional cloning vector’ (Column 11 5th paragraph). Thus, both Zhu and Chenchik require the use of restriction digests for downstream library generation and thus
would have no use for the library PCR primers of Salimullah. As Chiang is cited merely for the
polyadenylation of RNA and Salimullah is cited merely for the library PCR primers, Chiang and
Salimullah fail to remedy the deficiencies of Zhu or Chenchik. With regard to 2), Applicant submits that the skilled artisan would not be motivated to combine the references as asserted by the Office in order to generate a cDNA library from all RNA species in a cell. Numerous instances within the specification state that ‘The methods of the present disclosure find use in
generating sequencing-ready libraries corresponding to any RNA starting material of interest (e.g., mRNA) and are not limited to polyadenylated RNAs. For example, the subject methods may be used to generate sequencing-ready cDNA libraries from non-polyadenylated RNAs, including microRNAs, small RNAs, siRNAs, and/or any other type of non-polyadenylated RNAs of interest.’ (pg. 31 lines 9-14; see also pg. 8 lines 6-22 and pg. 25 line 9 to pg. 26 line 17) Accordingly, the methods as claimed allow for the generation of a sequencing-ready library from all RNA species in a cell because the methods as claimed utilize a first strand primer that hybridizes to the non-templated nucleotides in the template RNA and thus would hybridize not only to the template RNA produced from the non-polyadenylated RNA but also to polyadenylated RNA to which non-templated nucleotides were not added experimentally (i.e. mRNA). None of the references would lead the skilled artisan to combine the template switching methods of Zhu or Chenchik with the polyadenylation methods of Chiang. The methods of Zhu and Chenchik are directed to methods of generating full-length cDNA libraries from mRNA and not non-polyadenylated RNA. In Zhu, the above teaching of Zhu is exemplified by the fact that Zhu only ever makes reference to mRNA. For instance, the abstract of Zhu states ‘cDNA
libraries generated using this method will be useful for accelerating the collection of mRNA 5’ end sequence information, which is currently very limited in GenBank.’ Additionally, the beginning of the results section of Zhu states ‘When reverse transcriptase reaches the 5’ end of the mRNA, the enzyme’s terminal transferase activity adds additional nucleotides’ (pg. 894 2ⁿᵈ column last paragraph). Thus, the methods of Zhu only ever contemplate the usage of mRNA. With regard to Chenchik, Chenchik also only ever contemplates using mRNA in their methods. This teaching of Chenchik is evidenced by the fact that the abstract of Chenchik states ‘The present invention pertains to methods for the Synthesis and cloning of full-length cDNA, or cDNA fragments, that correspond to the complete sequence of 5’-ends of mRNA molecules.’ The field of invention of Chenchik also states ‘The present invention relates to improved
technology for selectively synthesizing full-length cDNA having complete sequence information of full-length mRNA.’ (Column 1 2ⁿᵈ paragraph) Chenchik does recite performing the methods with total RNA, however, in these instances Chenchik states that the first-strand primer, i.e., CDS primer, binds to mRNA and does not indicate that the primer binds to any other type of RNA (See column 3 5th paragraph). Thus, the teachings of Zhu and Chenchik are specifically focused on generating cDNA libraries from mRNA and not all RNA species within a cell. Nowhere within Zhu or Chenchik is there any discussion of generating a library from any RNA other than mRNA, and thus does not contemplate a method of generating a library from all RNAs in a cell. The teachings of Chiang would also not lead the skilled artisan to the claimed invention. The methods of Chiang are directed to the use of RT-PCR to identify specific small RNAs in a cell because the first strand synthesis primer contains nucleotides that hybridize both to the specific small RNA targets in addition to the artificially added polyA sequence on the 3’ end of the RNA. Specifically, Chiang discloses ‘Thus, in various embodiments, the present teachings provide a method for detecting and/or quantifying a small RNA…a first primer of not more than 40 nucleotides in length having complementarity to at least two 3' terminal end nucleotides of the small RNA and the sequence of contiguous A residues of the polyadenylated small RNA so as to hybridize therewith and initiate synthesis of a cDNA complementary to the polyadenylated small RNA;’ (paragraph [0008]; emphasis added). Chiang does not contemplate a method for generating a sequencing-ready library from all RNA species present in a cell because the first strand primers of Chiang are ‘specific for the particular small RNA being detected by virtue of having at least two 3' terminal nucleotides that are complementary to at least two 3' terminal nucleotides of the small RNA.’ (paragraph [0028]) Accordingly, the skilled artisan would not be motivated to combine the teachings of Zhu or Chenchik, Chiang, and Salimullah to generate a library of all RNA species of a cell from the work of Chiang. A skilled artisan looking to Salimullah would also not be motivated to combine the references as asserted by the Office to arrive at the claimed invention. Salimullah is directed to Cap analysis gene expression (CAGE) which is a method to identify the 5’ ends of transcripts. Specifically, Salimullah discloses ‘Instead of the cap-trapper method (Carninci et al. 1996, 1997), the nanoCAGE protocol uses a template-switching method based on the reverse transcription of the cap of the messenger RNA (mRNA) to enrich for 5’ ends (Chenchik et al. 1998), as well as a semisuppressive polymerase chain reaction (PCR) approach (Plessy et al. 2010) to minimize short PCR artifacts (Fig. 1).’ (pg. 1 2ⁿᵈ paragraph; emphasis added) Accordingly, the methods of Salimullah are focused on generating libraries from mRNA
and not generating libraries of all RNA species of a cell. Overall, all of the cited references are either directed to generating a sequencing-ready library from a specific type of RNA (mRNA; Zhu, Chenchik, and Salimullah) or directed to quantifying or sequencing specific target RNAs (i.e. Chiang). The methods disclosed herein are not ‘the simple substitution of one kind of template RNA sample (ie., the template RNA sample containing mRNA taught by Zhu et al., or
Chenchik et al.,) from another kind of template RNA sample (ie., the template RNA sample containing siRNA comprising a 3’ polyadenine sequence taught by Chiang et al.,)’ (OA pg. 7) as asserted by the Office, but an entirely new method for generating a sequencing-ready library from all RNA species within a cell as evidenced by the fact that such a method had not been previously contemplated within the art. As such, claims 46, 48-50, 52-55, and 68 are not obvious over Zhu or Chenchik, in view of Chiang and Salimullah at least because the skilled artisan would not be motivated to combine the references as asserted by the Office. The skilled artisan would not be motivated to combine the reference as asserted by the Office because 1) the library PCR primers of Salimullah would serve no use in the methods of Zhu and Chenchik, and 2) the skilled artisan would not be motivated to combine the methods of Zhu or Chenchik with the polyadenylation methods of Chiang. Applicant respectfully requests that this rejection be withdrawn” .
These arguments have been fully considered but they are not persuasive toward the withdrawal of the rejection.
First, although applicant argues that “the skilled artisan would not modify the methods of Zhu or Chenchik to replace the forward and reverse primers of Zhu or Chenchik with the library PCR primers of Salimullah because the library PCR primers of Salimullah would serve no purpose in the methods of Zhu or Chenchik. Zhu and Chenchik employ restriction digest for downstream library preparation which would remove the sequences added by the library PCR primers” and “[B]oth Zhu and Chenchik introduce the restriction sites for digest during the first-strand synthesis stage”, since the purpose for synthesizing a first stranded cDNA or a mRNA:cDNA hybrid using a template-switch oligonucleotide comprising a restriction enzyme cleavage site and a cDNA synthesis primer comprising the restriction enzyme cleavage site in the prior art of Zhu et al., or Chenchik et al., is to incorporate a restriction enzyme cleavage site to a synthesized double stranded cDNA such that the synthesized double stranded cDNA can be digested by a restriction enzyme and then can be cloned to a vector (see Figure 1 from Zhu et al., or Figures 3-1 and 3-2 from Chenchik et al.,), claim 46 does not require to clone a synthesized double stranded cDNA to a vector, the 5’ anchor primer and CDS primer taught by Zhu et al., or the 5’ PCR primer and CDS primer taught by Chenchik et al., and the forward and reverse primers of the library PCR taught by Salimullah et al., are used for the same purpose (ie., synthesizing a second stranded cDNA), in view of the prior arts of Zhu et al., or Chenchik et al., Chiang et al., and Salimullah et al., one having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to perform step (d) of claim 46 using a forward primer having a region which is not complementary to the cDNA and a reverse primer having a region which is not complementary to the cDNA wherein the forward primer and the reverse primer have the same structure designs of the forward and reverse primers of the library PCR taught by Salimullah et al., in order to produce a template RNA for the method recited in claim 46.
Second, although applicant argues that “[A]pplicant submits that the skilled artisan would not be motivated to combine the references as asserted by the Office in order to generate a cDNA library from all RNA species in a cell”, “the teachings of Zhu and Chenchik are specifically focused on generating cDNA libraries from mRNA and not all RNA species within a cell”, “[C]hiang does not contemplate a method for generating a sequencing-ready library from all RNA species present in a cell because the first strand primers of Chiang are ‘specific for the particular small RNA being detected by virtue of having at least two 3' terminal nucleotides that are complementary to at least two 3' terminal nucleotides of the small RNA.’ (paragraph [0028])”, “[A] skilled artisan looking to Salimullah would also not be motivated to combine the references as asserted by the Office to arrive at the claimed invention”, and “all of the cited references are either directed to generating a sequencing-ready library from a specific type of RNA (mRNA; Zhu, Chenchik, and Salimullah) or directed to quantifying or sequencing specific target RNAs (i.e. Chiang). The methods disclosed herein are not ‘the simple substitution of one kind of template RNA sample (ie., the template RNA sample containing mRNA taught by Zhu et al., or Chenchik et al.,) from another kind of template RNA sample (ie., the template RNA sample containing siRNA comprising a 3’ polyadenine sequence taught by Chiang et al.,)’ (OA pg. 7) as asserted by the Office, but an entirely new method for generating a sequencing-ready library from all RNA species within a cell as evidenced by the fact that such a method had not been previously contemplated within the art”, the rejection is not dependent on either Zhu et al., or Chenchik et al., Chiang et al., or Salimullah et al., alone and is based on a combination of Zhu et al., or Chenchik et al., Chiang et al., and Salimullah et al.. Furthermore, miRNA taught by Chiang et al., can be reasonably considered as a non-polyadenylated ribonucleic acid (RNA) recited in claim 46. Since Chiang et al., have taught providing a non-polyadenylated ribonucleic acid (RNA) (micro RNA or miRNA) and adding a plurality of non-templated nucleotides to an end of the non-polyadenylated RNA to produce a template RNA (ie., microRNA or miRNA having a polyA sequence) and the template RNA sample containing mRNA taught by Zhu et al., or Chenchik et al., and the template RNA sample containing miRNA comprising a 3’ polyadenine sequence taught by Chiang et al., are used for the same purpose (ie., serving as a template RNA for synthesizing a cDNA), the simple substitution of one kind of template RNA sample (ie., the template RNA sample containing mRNA taught by Zhu et al., or Chenchik et al.,) from another kind of template RNA sample (ie., the template RNA sample containing miRNA comprising a 3’ polyadenine sequence taught by Chiang et al.,), in the absence of convincing evidence to the contrary, would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made. In addition, applicant has not indicated why one having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to substituting one kind of template RNA sample (ie., the template RNA sample containing mRNA taught by Zhu et al., or Chenchik et al.,) from another kind of template RNA sample (ie., the template RNA sample containing miRNA comprising a 3’ polyadenine sequence taught by Chiang et al.,) during the process of performing the method recited in claim 46.
Claim 47 is rejected under 35 U.S.C. 103 as being unpatentable over Zhu et al., or Chenchik et al., in view of Chiang et al., and Salimullah et al., as applied to claims 46, 48-50, and 52-55 above, and further in view of Seligmann et al., (US 2014/0087954 A1, priority date: May 4, 2011).
The teachings of Zhu et al., Chenchik et al., Chiang et al., and Salimullah et al., have been summarized previously, supra.
Zhu et al., Chenchik et al., Chiang et al., and Salimullah et al., do not disclose sequencing the amplified product nucleic acid by the sequencing platform that comprises the surface-attached sequencing platform oligonucleotide that captures the at least portion of the capture sequence of the sequencing platform adapter construct as recited in claim 47.
Seligmann et al., teach sequencing the amplified product nucleic acids by the sequencing platform that comprises the surface-attached sequencing platform oligonucleotide that captures the at least portion of the capture sequence of the sequencing platform adapter construct as recited in claim 47 (see paragraphs [0009], [0044], [0047], and [0210] and claims 1, 8, and 10).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have performed the method recited in claim 47 by designing a surface-attached sequencing platform oligonucleotide that captures the at least portion of the capture sequence of the sequencing platform adapter construct based on the nucleotide sequence of the forward primer and nucleotide sequence of the reverse primer in the library PCR taught by Salimullah et al., attaching the surface-attached sequencing platform oligonucleotide to a sequencing platform, and sequencing the amplified product nucleic acids by the sequencing platform that comprises the surface-attached sequencing platform oligonucleotide in view of the prior arts of Zhu et al., or Chenchik et al., Chiang et al., Salimullah et al., and Seligmann et al.. One having ordinary skill in the art would have been motivated to do so because Seligmann et al., teach sequencing the amplified product nucleic acids by the sequencing platform that comprises the surface-attached sequencing platform oligonucleotide that captures the at least portion of the capture sequence of the sequencing platform adapter construct as recited in claim 47 (see paragraphs [0009], [0044], [0047], and [0210] and claims 1, 8, and 10). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to perform the method recited in claim 47 by designing a surface-attached sequencing platform oligonucleotide that captures the at least portion of the capture sequence of the sequencing platform adapter construct based on the nucleotide sequence of the forward primer and nucleotide sequence of the reverse primer in the library PCR taught by Salimullah et al., attaching the surface-attached sequencing platform oligonucleotide to a sequencing platform, and sequencing the amplified product nucleic acids by the sequencing platform that comprises the surface-attached sequencing platform oligonucleotide in view of the prior arts of Zhu et al., or Chenchik et al., Chiang et al., Salimullah et al., and Seligmann et al..
Response to Arguments
In page 12, second and third paragraphs of applicant’s remarks, applicant argues that “[A]s discussed above, the skilled artisan would not be motivated to combine the references as asserted by the Office. As Seligmann is cited solely for the element of ‘sequencing the amplified product nucleic acids by the sequencing platform that comprises the surface-attached sequencing platform oligonucleotide that captures the at least portion of the capture sequence of the sequencing platform adapter construct’ (OA pg. 12-13), Seligmann fails to remedy the deficiency of Zhu or Chenchik in view of Chiang and Salimullah”.
These arguments have been fully considered but they are not persuasive toward the withdrawal of the rejection because Chenchik et al., Chiang et al., and Salimullah et al., teach all limitations recited in claim 46 (see Response to Arguments related to the Rejection Item No.7) and Seligmann et al., is used for combining with Zhu et al., or Chenchik et al., Chiang et al., Salimullah et al., for rejecting claim 47.
Claims 61-63 are rejected under 35 U.S.C. 103 as being unpatentable over Chenchik et al., in view of Chiang et al., and Salimullah et al., as applied to claims 46, 48-50, and 52-55 above, and further in view of Linnarson (US 2012/0010091 A1, published on January 12, 2012) and Sooknanan (US 2009/0227009 A1, published on September 10, 2009).
The teachings of Chenchik et al., Chiang et al., and Salimullah et al., have been summarized previously, supra.
Chenchik et al., Chiang et al., and Salimullah et al., teach all limitations recited in claim 61 except a randomized tag of at least 4 nucleotide as recited in claim 61 wherein the randomized tag comprises at least 6 nucleotides as recited in claim 62. However, Chenchik et al., teach that the randomized tag (ie., the arbitrary sequence) is positioned 5’ of the first nucleotide sequence domain as recited in claim 63 (see columns 7 and 15).
Linnarson teaches that “[T]he structure of a typical TSO is shown in FIG. 3. In this particular TSO, the 3’ template switching sequence includes three riboguanines (rG). The cell-tag is shown as ‘XXXXX’ and can in general have any length or nucleotide composition. Arbitrary sequence can be inserted at the 5’ end of the TSO, after the 5’APS, or after the cell-tag, but not at the 3’ end” (see paragraph [0090] and Figure 3).
Sooknanan teaches that each of oligonucleotide sequence tags comprises a randomized portion such as 6 randomized nucleotides (ie., a randomized tag of 6 nucleotides) (see paragraph [0351]).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have performed the methods recited in claims 61 and 62 using a template switch oligonucleotide (TSO) comprising a first nucleotide sequence domain (ie., three riboguanines (rG)) and a randomized tag of at least 6 nucleotides (ie., an arbitrary sequence comprising at least 6 nucleotides) in view of the prior arts of Chenchik et al., Chiang et al., Salimullah et al., Linnarson and Sooknanan. One having ordinary skill in the art would have been motivated to do so because Linnarson teaches that in this particular TSO, the 3’ template switching sequence includes three riboguanines (rG) and the cell-tag of the template switching sequence is shown as “XXXXX”, can in general have any length or nucleotide composition, and is located on 5’ of the three riboguanines (rG) (see paragraph [0090] and Figure 3) while Sooknanan teaches that each of oligonucleotide sequence tags comprises a randomized portion such as 6 randomized nucleotides (ie., a randomized tag of 6 nucleotides) (see paragraph [0351]). One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to make a template switch oligonucleotide (TSO) comprising a first nucleotide sequence domain (ie., three riboguanines (rG)) and a randomized tag of 6 nucleotides (ie., an arbitrary sequence comprising at least 6 nucleotides) and perform the methods recited in claims 61 and 62 using this template switch oligonucleotide in view of the prior arts of Chenchik et al., Chiang et al., Salimullah et al., Linnarson and Sooknanan.
Response to Arguments
In page 12, fourth paragraph bridging to page 13, first paragraph of applicant’s remarks, applicant argues that “[A]s discussed above, the skilled artisan would not be motivated to combine the reference as asserted by the Office at least because 1) the library PCR primers of Salimullah would serve no use in the methods of Chenchik, and 2) the skilled artisan would not be motivated to combine the methods of Chenchik with the polyadenylation methods of Chiang. As Linnarson and Sooknanan are cited merely for teaching randomized tags, Linnarson and Sooknanan fail to remedy the deficiencies of Chenchik and Chiang. As such, claims 61-63 and 69 are not obvious over Chenchik in view of Chiang, Salimullah, Linnarson, and Sooknanan at least because the skilled artisan would not be motivated to combine the references as asserted by the Office”.
These arguments have been fully considered but they are not persuasive toward the withdrawal of the rejection. Since Chenchik et al., Chiang et al., and Salimullah et al., teach all limitations recited in claim 46 (see Response to Arguments related to the Rejection Item No.7) and all limitations recited in claim 61 except a randomized tag of at least 4 nucleotide as recited in claim 61 wherein the randomized tag comprises at least 6 nucleotides as recited in claim 62, Chenchik et al., teach that the randomized tag (ie., the arbitrary sequence) is positioned 5’ of the first nucleotide sequence domain as recited in claim 63 (see columns 7 and 15), Linnarson teaches that “[T]he structure of a typical TSO is shown in FIG. 3. In this particular TSO, the 3’ template switching sequence includes three riboguanines (rG). The cell-tag is shown as ‘XXXXX’ and can in general have any length or nucleotide composition. Arbitrary sequence can be inserted at the 5’ end of the TSO, after the 5’APS, or after the cell-tag, but not at the 3’ end” (see paragraph [0090] and Figure 3), and Sooknanan teaches that each of oligonucleotide sequence tags comprises a randomized portion such as 6 randomized nucleotides (ie., a randomized tag of 6 nucleotides) (see paragraph [0351]), one having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to make a template switch oligonucleotide (TSO) comprising a first nucleotide sequence domain (ie., three riboguanines (rG)) and a randomized tag of 6 nucleotides (ie., an arbitrary sequence comprising at least 6 nucleotides) and perform the methods recited in claims 61 and 62 using this template switch oligonucleotide in view of the prior arts of Chenchik et al., Chiang et al., Salimullah et al., Linnarson and Sooknanan.
Conclusion
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.
No claim is allowed.
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/FRANK W LU/
Primary Examiner, Art Unit 1683
December 12, 2025