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 .
Priority
This application is a CON of 16/412,346 (05/14/2019, now US 11725205)
and claims foreign priority to UNITED KINGDOM 1807793.3 (05/14/2018).
Claim Rejections - 35 USC § 102
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 4-7, 11, 12, 15-22 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by White et al. (WO2016059363).
Regarding claim 1, White teaches A method of amplifying a target polynucleotide, comprising:
a) providing a template polynucleotide comprising a 5' hairpin, a target polynucleotide and a 3' hairpin, wherein the 5' hairpin comprises one or more non-canonical nucleotides (Fig. 8: first polynucleotide including a 5’ hairpin and 3’ hairpin; p. 5; p. 15, “The hairpin loop is preferably formed from nucleotides which result in the hairpin loop having a lower melting temperature (Tm) than the double stranded portion”)”; p. 14 “Each substrate may comprise two hairpin loops, i.e. one in both strands of each substrate or one at both ends of each substrate”; Fig. 7(h)) ;
b) contacting the template polynucleotide with a polymerase and canonical nucleotides, (Fig. 8: step 4; p. 17: non-canonical nucleotides, “polymerase is provided with a population of free nucleotides”) wherein:
(i) the polymerase extends, using the canonical nucleotides, the template polynucleotide from its 3' end to form a first extended polynucleotide comprising the 5' hairpin at its 5' end and the complement of the 5' hairpin at its 3' end, wherein the complement of the 5' hairpin forms a 3' hairpin (Fig. 8: step 4-5: first extended polynucleotide complement comprises a 3’ hairpin); and
(ii)the polymerase extends the first extended polynucleotide from its 3' end to form a second extended polynucleotide comprising the 5' hairpin at its 5' end and the complement of the 5' hairpin at its 3' end, wherein the complement of the 5' hairpin forms a 3' hairpin (Fig. 8: step 7).
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White Fig. 8 (caption from p. 5):
Figure 8 shows a cartoon representation of a preferred method of the invention. Steps 1 to 4 were the same as in Figure 1. Step 5 involved adding a hairpin loop to the construct formed in Figure 1. Step 6 involved heat treatment of the modified double-stranded polynucleotide so that the strands were denatured into single-stranded construct. Finally, step 7 involved a DNA polymerase forming the complementary strand.
Regarding claim 4, White teaches wherein the polymerase is a strand displacing polymerase (p. 2 line 12-13, 27-30; p. 17).
Regarding claim 5, White teaches wherein the method is carried out at a constant temperature (p. 32 line 30-33; p. 17 line 21-22).
Regarding claim 6, White teaches further comprising the initial step of preparing the template polynucleotide (claim 1, Fig. 7, p. 2 line 7; p. 11 line 31 – p. 12 line 4; p. 18 line 31).
Regarding claim 7, White teaches further comprising the initial step of preparing the template polynucleotide by ligating an adaptor comprising a 5' hairpin to the 5' end(s) of a target polynucleotide (claim 1, Fig. 7, p. 2 line 7; p. 11 line 31 – p. 12 line 4; p. 18 line 31).
Regarding claim 11, White teaches further comprising the initial step of preparing the template polynucleotide by primer hybridization and extension (Fig. 1; p. 20, lines 13-16).
Regarding claim 12, White teaches wherein a target polynucleotide is amplified using: (i) a first primer comprising a 5' hairpin and a sequence at its 3' end that is complementary to a sequence in the 3' end of the first strand of the target polynucleotide; and (ii) a second primer comprising a 5' hairpin and a sequence at its 3' end that is complementary to a sequence in the 3' end of the second strand of the target polynucleotide (Fig. 1, step 2).
Regarding claim 15, White teaches a method of amplifying a target polynucleotide,
comprising: (a) providing a primer pair, wherein each primer comprises a 5' hairpin that
comprises one or more non-canonical nucleotides; (b) contacting a sample comprising a target
polynucleotide with the primer pair, a polymerase and canonical nucleotides under conditions
suitable for polymerase activity (Fig. 7; p. 45, Example 2).
Regarding claim 16, White teaches a method of amplifying a target polynucleotide, comprising:(a) ligating an adaptor comprising a 5' hairpin that comprises one or more non-canonical nucleotides to the target polynucleotide to produce a template polynucleotide; (b) contacting the template polynucleotide with a polymerase and canonical nucleotides under conditions suitable for polymerase activity (Fig. 7; p. 45, Example 2: “Figure 7 shows a cartoon representation of the sample preparation steps described in steps 2.1 and 2.2 below. This example shows that MuA transposase was able to insert MuA substrates which contained a hairpin loop which contained analogues of dG and dC in the hairpin loop of the MuA adapter (dG was replaced with deoxyinosine and dC was replaced deoxyzebularine).”; instant specification at p. 24-25: ligation includes via transposase “In one embodiment, the double stranded adaptor may be a MuA substrate and a MuA transposase may be used to (i) fragment a polynucleotide to produce the target polynucleotide and (ii) ligate the MuA substrate to the target polynucleotide.”).
Regarding claim 17, White teaches further comprising adding sequencing adaptors to one or both ends of the extended polynucleotide (claim 10, p. 25).
Regarding claim 18, White teaches an extended polynucleotide obtainable by a method according to claim 1 (Fig. 8: bottom polynucleotide).
Regarding claim 19, White teaches a method of characterising a polynucleotide, comprising: ( a) contacting the polynucleotide of claim 18 with a nanopore such that the
polynucleotide translocates through the nanopore; and (b) taking one or more measurements as the polynucleotide moves with respect to the nanopore, wherein the measurements are
indicative of one or more characteristics of the polynucleotide and thereby characterising the
polynucleotide (Fig. 7; p. 45, Example 2; p. 34-35; claims 1, 9, 10, 14, 15).
Regarding claims 20-22, White teaches the adaptor, primer pair, and kit as with claims 15 and 16.
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.
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, 15-22 are rejected under 35 U.S.C. 103 as being unpatentable over White et al. (WO2016059363).
White teaches as detailed in the 35 USC 102 rejection of claims 1, 4-7, 11, 12, 15-22 supra and is incorporated herein. Any differences in teaching among the claims and White would have been obvious to one of ordinary skill in the art because one of ordinary skill in the art would have been motivated at the relevant time to amplify the target nucleotides of White using the techniques disclosed therein and arrive at the claimed invention.
Regarding claim 2 wherein the polymerase extends the second extended polynucleotide from its 3' end to form a third extended polynucleotide comprising the 5' hairpin at its 5' end and the complement of the 5' hairpin at its 3' end, wherein the complement of the 5' hairpin forms a 3' hairpin, White teaches an “Additional polymerase step” (p. 24-25) but does not specifically teach forming a third polynucleotide by extending the second polynucleotide using polymerase, however one of ordinary skill in the art would have recognized that the additional polymerase step could be repeated to increase the amount of information in the polynucleotides to facilitate characterization as taught by White (p. 24: “the amount of information in the modified double stranded polynucleotides is doubled to facilitate characterisation of the template polynucleotide.”) and would result in forming a third polynucleotide and would arrive at the claimed invention.
Regarding claim 3 wherein the polymerase extends the third extended polynucleotide, and optionally any further extended polynucleotides produced by extending the third extended polynucleotide and/or by subsequent extensions, to produce further extended polynucleotides comprising the 5' hairpin at their 5' ends and the complement of the 5' hairpin at their 3' ends, wherein the complement of the 5' hairpin forms a 3' hairpin as with claim 3, White does not specifically extending the third polynucleotide with polymerase, however one of ordinary skill in the art would have recognized that the extension could be repeated to increase the amount of information as taught by White (p. 24) and would result in forming a further extended polynucleotides and would arrive at the claimed invention.
Regarding claim 8 wherein the target polynucleotide is a double stranded polynucleotide and the method comprises ligating a double stranded adaptor comprising a 5' hairpin and a 3' hairpin to each end of the target polynucleotide, White does not specifically teach ligating said adapter comprising a 5’ and 3’ hairpin adapter, however based on the teaching of White regarding the 5’ hairpin adapter and extension to form a complementary 3’ hairpin, one of ordinary skill in the art would have recognized that an alternative would have been to simply ligate such structures and arrive at the claimed invention with a reasonable expectation of success.
Regarding claim 9 depending from claim 8, wherein the target polynucleotide is a double stranded polynucleotide and the method comprises ligating a double stranded adaptor comprising a 5' hairpin to each end of the target polynucleotide, and extending the 3' end of each strand of the target polynucleotide using a polymerase to produce a 3' hairpin that is complementary to the 5' hairpin although White teaches ligating an adaptor comprising a 5’ hairpin and extension, White does not specifically teach ligating said adapter comprising a 5’ and 3’ hairpin adapter, however based on the teaching of White regarding the 5’ hairpin adapter and extension to form a complementary 3’ hairpin, one of ordinary skill in the art would have recognized that an alternative would have been to simply ligate such structures and arrive at the claimed invention with a reasonable expectation of success..
Regarding claim 10 depending from claim 9, wherein the double stranded adaptor is a MuA substrate and a MuA transposase is used to (i) fragment a polynucleotide to produce the target polynucleotide and (ii) ligate the MuA substrate to the target polynucleotide, White renders claim 9 obvious and White further teaches the use of MuA substrate and transposase to fragment and ligate to the target (claims 1, 13; p. 2; Fig. 7; Example 2) which one of ordinary skill in the art would have considered and arrive at the claimed invention.
With each of the claims, the level of skill in the art is very high such that one of ordinary skill in the art would consider routine the combination of elements from the teaching of the art. One of ordinary skill in the art would have recognized that the results of the combination would be predictable due to the well-known nature and optimizations routinely performed in the art. Thus, one of ordinary skill in the art would have arrived at the invention as claimed before the effective filing date with a reasonable expectation of success.
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 1-11, 15-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of U.S. Patent No. 11725205. Although the claims at issue are not identical, they are not patentably distinct from each other because the patent claims anticipate the instant claims.
Claims 1-11, 15-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 11390904. Although the claims at issue are not identical, they are not patentably distinct from each other because the patent claims anticipate and render obvious the instant claims in the same manner as in the 35 USC 102 and 103 rejections supra as the patent shares a disclosure with White et al. (WO2016059363).
Claims 1-11, 15-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 10579449. Although the claims at issue are not identical, they are not patentably distinct from each other because the patent claims anticipate and render obvious the instant claims in the same manner as in the 35 USC 102 and 103 rejections supra as the patent shares a disclosure with White et al. (WO2016059363).
Conclusion
No claims allowed.
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/ROBERT H HAVLIN/Primary Patent Examiner, Art Unit 1626