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 .
Priority
This application is a DIV of 17/377,279 filed 07/15/2021 now PAT 11,535,892 which claims benefit of 638/212,059 filed 06/17/2021.
Drawings
The drawings were received on 11/22/2022. These drawings are found acceptable by the examiner.
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 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 11,535,892 {US Patent ‘892}.
An obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but an examined application claim is not patentably distinct from the reference claim(s) because the examined 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).
Although the claims at issue are not identical, they are not patentably distinct from each other because both the claims 1-19 of the instant invention and the claims 1-2 of US Patent ‘892 are directed to a method for pairwise sequencing, comprising: a) providing a plurality of single stranded nucleic acid concatemer template molecules immobilized to a support; b) sequencing the plurality of immobilized concatemer template molecules with a first plurality of sequencing polymerases, a plurality of soluble forward sequencing primers and a first plurality of multivalent molecules, thereby generating a plurality of extended forward sequencing primer strands; c) retaining the plurality of immobilized concatemer template molecules and replacing the plurality of extended forward sequencing primer strands with a plurality of forward extension strands that are hybridized to the retained immobilized concatemer template molecules by conducting a primer extension reaction; d) removing the retained immobilized concatemer template molecules while retaining the plurality of forward extension strands and retaining the plurality of immobilized surface primers; and e) sequencing the plurality of retained forward extension strands with a second plurality of sequencing polymerases, a plurality of soluble reverse sequencing primers and a second plurality of multivalent molecules, wherein individual multivalent molecules in the first plurality of multivalent molecules of step (b) and in the second plurality of multivalent molecules of step (e) comprise (i) a core; and (ii) a plurality of nucleotide arms which comprise a core attachment moiety, a spacer, a linker, and a nucleotide unit, wherein the core is attached to the plurality of nucleotide arms via their core attachment moiety, wherein the spacer is attached to the linker, wherein the linker is attached to the nucleotide unit. (Claim 1 of instant invention and claim 1 of US Patent ‘892).
The limitations of the claims 2-19 of the instant invention are embodied by the limitations of the claims 1-12 of US Patent ‘892.
The claims 1-19 of the instant invention differ from the claims 1-12 of US Patent ‘892 in that they are broader in scope with slight variations in wording and method steps. Thus, the claims 1-19 of the instant invention falls entirely within the scope of the claims 1-12 of US patent ‘892. As the court stated in In re Goodman, 29 USPQ2d 2010 (CAFC 1993), “a second application-- "containing a broader claim, more generical in its character than the specific claim in the prior patent"--typically cannot support an independent valid patent. Miller, 151, U.S. at 198; See Stanley, 214 F.2d at 153. Thus, the generic invention, as noted above is "anticipated" by the species of the patented invention. Cf., Titanium metal corp. v. Banner, 778 F.2d 775, 227 USPQ 773 (Fed. Cir. 1985) (holding that an earlier species disclosure in the prior art defeats any generic claims). This court's predecessor has held that, without a terminal disclaimer, the species claims preclude issuance of the generical application. "In re Van Ornum, 686 F.2d 937, 944, 214 USPQ 761, 767 (CCPA 1982); Schneller, 397 F.2d at 354".
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 4, 6-10, 12, 14, 15, 17-25 of U.S. Patent No. 11,859,241 {US Patent ‘241}.
An obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but an examined application claim is not patentably distinct from the reference claim(s) because the examined 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).
Although the claims at issue are not identical, they are not patentably distinct from each other because both the claims 1-19 of the instant invention and the claims 1 of US Patent ‘241 are directed to a method for pairwise sequencing, comprising: a) providing a plurality of single stranded nucleic acid concatemer template molecules immobilized to a support; b) sequencing the plurality of immobilized concatemer template molecules with a first plurality of sequencing polymerases, a plurality of soluble forward sequencing primers and a first plurality of multivalent molecules, thereby generating a plurality of extended forward sequencing primer strands; c) retaining the plurality of immobilized concatemer template molecules and replacing the plurality of extended forward sequencing primer strands with a plurality of forward extension strands that are hybridized to the retained immobilized concatemer template molecules by conducting a primer extension reaction; d) removing the retained immobilized concatemer template molecules while retaining the plurality of forward extension strands and retaining the plurality of immobilized surface primers; and e) sequencing the plurality of retained forward extension strands with a second plurality of sequencing polymerases, a plurality of soluble reverse sequencing primers and a second plurality of multivalent molecules, wherein individual multivalent molecules in the first plurality of multivalent molecules of step (b) and in the second plurality of multivalent molecules of step (e) comprise (i) a core; and (ii) a plurality of nucleotide arms which comprise a core attachment moiety, a spacer, a linker, and a nucleotide unit, wherein the core is attached to the plurality of nucleotide arms via their core attachment moiety, wherein the spacer is attached to the linker, wherein the linker is attached to the nucleotide unit. (Claim 1 of instant invention and claim 1 of US Patent ‘241).
The limitations of the claims 2-19 of the instant invention are embodied by the limitations of the claims 1, 3, 4, 6-10, 12, 14, 15, 17-25 of US Patent ‘241.
The claims 1-19 of the instant invention differ from the claims 1, 3, 4, 6-10, 12, 14, 15, 17-25 of US Patent ‘241 in that they are broader in scope with slight variations in wording and method steps. Thus, the claims 1-19 of the instant invention falls entirely within the scope of the claims 1, 3, 4, 6-10, 12, 14, 15, 17-25 of US patent ‘241. As the court stated in In re Goodman, 29 USPQ2d 2010 (CAFC 1993), “a second application-- "containing a broader claim, more generical in its character than the specific claim in the prior patent"--typically cannot support an independent valid patent. Miller, 151, U.S. at 198; See Stanley, 214 F.2d at 153. Thus, the generic invention, as noted above is "anticipated" by the species of the patented invention. Cf., Titanium metal corp. v. Banner, 778 F.2d 775, 227 USPQ 773 (Fed. Cir. 1985) (holding that an earlier species disclosure in the prior art defeats any generic claims). This court's predecessor has held that, without a terminal disclaimer, the species claims preclude issuance of the generical application. "In re Van Ornum, 686 F.2d 937, 944, 214 USPQ 761, 767 (CCPA 1982); Schneller, 397 F.2d at 354".
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-22 of U.S. Patent No. 11,220,707 {US Patent ‘707}.
An obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but an examined application claim is not patentably distinct from the reference claim(s) because the examined 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).
Although the claims at issue are not identical, they are not patentably distinct from each other because both the claims 1-19 of the instant invention and the claims 1 of US Patent ‘707 are directed to a method for pairwise sequencing, comprising: a) providing a plurality of single stranded nucleic acid concatemer template molecules immobilized to a support; b) sequencing the plurality of immobilized concatemer template molecules with a first plurality of sequencing polymerases, a plurality of soluble forward sequencing primers and a first plurality of multivalent molecules, thereby generating a plurality of extended forward sequencing primer strands; c) retaining the plurality of immobilized concatemer template molecules and replacing the plurality of extended forward sequencing primer strands with a plurality of forward extension strands that are hybridized to the retained immobilized concatemer template molecules by conducting a primer extension reaction; d) removing the retained immobilized concatemer template molecules while retaining the plurality of forward extension strands and retaining the plurality of immobilized surface primers; and e) sequencing the plurality of retained forward extension strands with a second plurality of sequencing polymerases, a plurality of soluble reverse sequencing primers and a second plurality of multivalent molecules, wherein individual multivalent molecules in the first plurality of multivalent molecules of step (b) and in the second plurality of multivalent molecules of step (e) comprise (i) a core; and (ii) a plurality of nucleotide arms which comprise a core attachment moiety, a spacer, a linker, and a nucleotide unit, wherein the core is attached to the plurality of nucleotide arms via their core attachment moiety, wherein the spacer is attached to the linker, wherein the linker is attached to the nucleotide unit. (Claim 1 of instant invention and claim 1 of US Patent ‘707).
The limitations of the claims 2-19 of the instant invention are embodied by the limitations of the claims 1-22 of US Patent ‘707.
The claims 1-19 of the instant invention differ from the claims 1-22 of US Patent ‘707 in that they are broader in scope with slight variations in wording and method steps. Thus, the claims 1-19 of the instant invention falls entirely within the scope of the claims 1-22 of US patent ‘707. As the court stated in In re Goodman, 29 USPQ2d 2010 (CAFC 1993), “a second application-- "containing a broader claim, more generical in its character than the specific claim in the prior patent"--typically cannot support an independent valid patent. Miller, 151, U.S. at 198; See Stanley, 214 F.2d at 153. Thus, the generic invention, as noted above is "anticipated" by the species of the patented invention. Cf., Titanium metal corp. v. Banner, 778 F.2d 775, 227 USPQ 773 (Fed. Cir. 1985) (holding that an earlier species disclosure in the prior art defeats any generic claims). This court's predecessor has held that, without a terminal disclaimer, the species claims preclude issuance of the generical application. "In re Van Ornum, 686 F.2d 937, 944, 214 USPQ 761, 767 (CCPA 1982); Schneller, 397 F.2d at 354".
Closest prior art
8. The claims 1-19 appear to be free of the prior art. The independent claim 1 of the instant invention is drawn to a method for pairwise sequencing, comprising: a) providing a plurality of single stranded nucleic acid concatemer template molecules immobilized to a support; b) sequencing the plurality of immobilized concatemer template molecules with a first plurality of sequencing polymerases, a plurality of soluble forward sequencing primers and a first plurality of multivalent molecules, thereby generating a plurality of extended forward sequencing primer strands; c) retaining the plurality of immobilized concatemer template molecules and replacing the plurality of extended forward sequencing primer strands with a plurality of forward extension strands that are hybridized to the retained immobilized concatemer template molecules by conducting a primer extension reaction; d) removing the retained immobilized concatemer template molecules while retaining the plurality of forward extension strands and retaining the plurality of immobilized surface primers; and e) sequencing the plurality of retained forward extension strands with a second plurality of sequencing polymerases, a plurality of soluble reverse sequencing primers and a second plurality of multivalent molecules, wherein individual multivalent molecules in the first plurality of multivalent molecules of step (b) and in the second plurality of multivalent molecules of step (e) comprise (i) a core; and (ii) a plurality of nucleotide arms which comprise a core attachment moiety, a spacer, a linker, and a nucleotide unit, wherein the core is attached to the plurality of nucleotide arms via their core attachment moiety, wherein the spacer is attached to the linker, wherein the linker is attached to the nucleotide unit.
The closest prior art, Rigatti et al. (US 2011/0223601) teach a method for pairwise sequencing of first and second regions of target polynucleotides, wherein each target polynucleotide comprises a first and second strand, the method comprising: (a) providing a solid support comprising immobilized first strands of the target polynucleotides; (b) sequencing the first region of the first strands of the target polynucleotides; (c) copying the first strands of the target polynucleotides thereby generating the second strands of the target polynucleotides; and (d) sequencing the second region of the second strands of the target polynucleotides, wherein determining the sequence of the first and second regions of the target polynucleotides achieves pairwise sequencing of the first and second regions of the target polynucleotides. Rigatti discloses methods of solid-phase pairwise sequencing as indicated above, including an embodiment which uses a uracil primer, but these methods do not involve the use of a concatemer.
Drmanac et al (US 2021/0189483) teach a paired-end sequencing method comprising: (a) providing a DNA array comprising a surface with at least 1,000 DNA concatemers immobilized thereon, (b) for each of a plurality of DNA concatemers on the array, (i) annealing first read primers to primer binding sites on the DNA concatemer, (ii) extending at least some of the first read primers to incorporate dNTPs or dNTP analogs, thereby producing first read strands, wherein each of the dNTPs or dNTP analogs being incorporated is identified to produce first reads, (c) performing controlled MDA by (i) extending at least some of the first read strands with a polymerase having strand-displacement activity to generate a plurality of second strands, each second strand comprising a portion that is hybridized to the DNA concatemer, and an unhybridized, single-stranded branch, or (ii) removing the first read strands and extending a plurality of MDA primers that are hybridized to the DNA concatemers with a polymerase having strand-displacement activity to generate a plurality of second strands, each comprising a sequence that is hybridized to one of the plurality of single strand DNA concatemers, and an unhybridized, single-stranded branch; and (d) annealing second read primers to the single-stranded branches of the plurality of second strands, (e) extending the second read primers to generate the second reads.
Drmanac et al disclose a method of solid-phase pairwise sequencing using concatemers and uridine, but uridine is incorporated into extended first read strands, and is not provided in concatemers.
Conclusion
9. No claims are allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681