DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
2. Claim 58 is objected to because of the following informalities: “(ii) an anti-sense strand comprising a sequence comprising a sequence” in line 5 should be changed to “(ii) an anti-sense strand comprising a sequence . Appropriate correction is required.
Claim Rejections - 35 USC § 112
3. 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.
4. Claim 72 is rejected 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 72 recites “wherein a concentration of template DNA in (a) is between 0.1 ng and 100 ng” (emphasis provided). Since “0.1 ng” or “100 ng” specifies amount (or weight) rather than concentration, claim 72 is 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.
In the interest of compact prosecution and for purposes of current examination, the wherein clause in claim 72 is being interpreted as “wherein an amount of template DNA in (a) is between 0.1 ng and 100 ng, inclusive of the endpoints”.
Double Patenting
5. 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.
6. Claims 58-62, 64, 67-70, 72 and 171 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 22-32 of U.S. Patent No. 11,427,846. Although the claims at issue are not identical, they are not patentably distinct from each other because claims 22-32 of U.S. Patent No. 11,427,846 teach or render obvious all the features as recited in instant claims 58-62, 64, 67-70, 72 and 171. Specifically, claim 22 of U.S. Patent No. 11,427,846 teaches all the steps and elements recited in instant claim 58. In addition, the other features as recited in instant claims 59-62, 64, 67-70, 72 and 171 are also taught or rendered obvious by claims 22-32 of U.S. Patent No. 11,427,846.
Claim Rejections - 35 USC § 102
7. 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 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.
8. 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.
9. Claims 58-59, 61-62, 64, 67-68, 72 and 171 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Turchinovich et al. (RNA Biol. 2014, 11(7):817-828).
Regarding claim 58
Turchinovich et al. teach, throughout the whole document, a method of making a composition, wherein the composition comprises a double-stranded deoxyribonucleic acid (dsDNA) sequence comprising: (i) a sense strand comprising, from 5’ to 3’, a sequence comprising a first adaptor sequence, a template sequence, and a second adaptor sequence, and (ii) an anti-sense strand comprising a sequence complementary to the sequence of the sense strand (i), wherein the second adaptor sequence comprises a hybridization site (e.g., “CCC”) for a template switching oligonucleotide (TSO); wherein the method comprises the following steps: (a) contacting a template sequence and a polymerase (e.g., reverse transcriptase) under conditions sufficient to allow for terminal transferase activity, to produce an intermediate double-stranded deoxyribonucleic acid (dsDNA) sequence, wherein the intermediate dsDNA comprises the adaptor sequence at the 3’ end of the sense strand and the antisense strand; (b) contacting the intermediate dsDNA, the polymerase and at least one template switching oligonucleotide (TSO) under conditions sufficient to allow for DNA-dependent DNA polymerase activity, to produce the composition (see Figure 1; page 818, paragraph spanning columns 1-2).
Regarding claim 59
The method according to Turchinovich et al., wherein the adaptor sequence at the 3’ end of the sense strand and the antisense strand comprises a poly(C) sequence (e.g., “CCC”) (see Figure 1).
Regarding claim 61
The method according to Turchinovich et al., wherein the conditions sufficient to allow for terminal transferase activity or DNA-dependent DNA polymerase activity comprise a plurality of deoxynucleotides (dNTPs) (see Figure 1; page 826, paragraph spanning columns 1-2).
Regarding claim 62
The method according to Turchinovich et al., wherein the conditions sufficient to allow for terminal transferase activity comprise a plurality of dCTPs (see page 818, paragraph spanning columns 1-2).
Regarding claim 64
The method according to Turchinovich et al., wherein the conditions sufficient to allow for DNA-dependent DNA polymerase activity comprise an incubation at temperatures from between 27°C and 50°C, inclusive of the endpoints, for a period of between 2 and 20 minutes (e.g., “15 min at 42 °C”. See page 826, column 2, paragraph 1).
Regarding claims 67-68
The method according to Turchinovich et al., wherein the polymerase comprises a reverse transcriptase, wherein the reverse transcriptase is a Moloney Murine Leukemia Virus Reverse Transcriptase (MMLV) reverse transcriptase (see Figure 1 caption).
Regarding claim 72
The method according to Turchinovich et al., wherein an amount of template DNA in (a) is between 0.1 ng and 100 ng (e.g., 1 ng) (see page 819, column 1, last paragraph: “We have used either 1 ng or 5 pg of … DNA as inputs for the DNA library preparation”. Also see page 826, paragraph spanning columns 1-2).
Regarding claim 171
The method according to Turchinovich et al., wherein the conditions sufficient to allow for terminal transferase activity or DNA-dependent DNA polymerase activity comprise three dNTP (see Figure 1; page 826, paragraph spanning columns 1-2).
Claim Rejections - 35 USC § 103
10. 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 of this title, 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.
11. 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.
12. Claim 60 is rejected under 35 U.S.C. 103 as being unpatentable over Turchinovich et al. (RNA Biol. 2014, 11(7):817-828) as applied to claims 58-59 above, and further in view of Betts et al. (WO 2014/066179 A1).
Turchinovich et al. teach the method of claims 58-59 as discussed above, wherein the adaptor sequence at the 3’ end of the sense strand and the antisense strand comprises a poly(C) sequence. Turchinovich et al. do not disclose that the adaptor sequence at the 3’ end of the sense strand and the antisense strand may, alternatively, comprise a poly(G) sequence.
However, the same field of endeavor (i.e., template switch-based methods for producing product nucleic acids), Betts et al. teach the homonucleotide stretch of 3 or more of the same nucleotides that are added by the terminal transferase activity of the polymerase may be all dGTP (i.e., a poly(G) sequence) instead of all dCTP (i.e., a poly(C) sequence) (see paragraph bridging pages 10-11).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to, alternatively, use the terminal transferase activity of the polymerase to add a poly(G) sequence (that would be comprised in the adaptor sequence at the 3’ end of the sense strand and the antisense strand), as taught by Betts et al., in the method of Turchinovich et al. thus arriving at the instantly claimed invention, because substituting equivalents known for the same purpose is considered prima facie obvious (see MPEP 2144.06(II)). Given the teachings of the prior art and the level of the ordinary skilled artisan at the effective filing date of the claimed invention, it must be considered, absent evidence to the contrary, that said skilled artisan would have had a reasonable expectation of success in practicing the claimed invention.
13. Claims 69-70 are rejected under 35 U.S.C. 103 as being unpatentable over Turchinovich et al. (RNA Biol. 2014, 11(7):817-828) as applied to claims 58 and 67-68 above, and further in view of Zhu et al. (BioTechniques 2001, 30(4):892-897).
Turchinovich et al. teach the method of claims 58 and 67-68 as discussed above. Although Turchinovich et al. indicate that the conditions sufficient to allow for DNA-dependent DNA polymerase activity (i.e., reverse transcriptase activity) include the use of RT buffer supplied by Clontech (see page 826, column 2, paragraph 1), Turchinovich et al. do not describe the details about the buffer.
However, Zhu et al., from Clontech, teach that such RT buffer (for use with reverse transcriptase) comprises 30 mM MgCl2 (i.e., co-factor Mg2+ at a concentration of 30 mM) (see page 893, column 2, the paragraph under “First-Strand cDNA Synthesis and Template Switching”).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use the RT buffer comprising 30 mM MgCl2 (i.e., co-factor Mg2+ at a concentration of 30 mM), as disclosed by Zhu et al., in the method of Turchinovich et al. thus arriving at the instantly claimed invention, because such RT buffer was recognized in the art as suitable for using with reverse transcriptase for cDNA synthesis. In addition, combining prior art elements according to known methods to yield predictable results is considered prima facie obvious (see MPEP 2143.I.A). Given the teachings of the prior art and the level of the ordinary skilled artisan at the effective filing date of the claimed invention, it must be considered, absent evidence to the contrary, that said skilled artisan would have had a reasonable expectation of success in practicing the claimed invention.
Conclusion
14. No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAIJIANG ZHANG whose telephone number is (571)272-5207. The examiner can normally be reached Monday - Friday, 8:30 am - 5 pm.
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/KAIJIANG ZHANG/Primary Examiner, Art Unit 1684