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 .
The preliminary amendment filed October 13, 2023, canceling claims 1-25 and adding new claims 26-54 is acknowledged.
Claims 26-54 are pending and will be examined.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on October 11, 2022 and April 6, 2023 was filed in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered 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 26-54 are rejected on the ground of nonstatutory double patenting as
being unpatentable over claims 1, 6-7, 9, 13, 16 of U.S. Patent No. 10246744 (‘744 patent herein). Although the claims at issue are not identical they are not patentably distinct from each other because while the claims are not identical they are not sufficiently distinct that the claimed methods do not include overlapping subject matter for the reasons detailed below.
The claim limitations are very similar regarding the dependent claims (compare claim 28, 32, 36, 41 to claim 8 of the ‘744 patent; compare claim 28, 33, 37 to claim 9 of the ‘744 patent; compare claim 33, 37 to claim 13 of the ‘744 patent). The same type of comparison could be carried out over many of the claims in both claim sets. The difference lies in comparing claim 1 of the ‘744 patent and claim 26 of the instant application. While the claims are not the same, both methods are drawn to the same technique which examines nucleotide incorporation into a ternary complex, precluding incorporation of a test nucleotide and identifying the next base to be primed on the template. While there are differences they are not significant. Therefore, the claims are not patentably distinct.
Claims 26-54, are rejected on the ground of nonstatutory double patenting as being
unpatentable over claims 1-2, 5, 7-9, 12-13, 16-18, 21-22, 32-33, 43, 45, 53-54, 69 of (U.S.
Patent No. 10077470; September 2018; '470 patent herein). Although the claims at issue are not
identical they are not patentably distinct from each other because while the claims are not
identical they are not sufficiently distinct that the claimed methods do not include overlapping
subject matter for the reasons detailed below.
The claim limitations are very similar regarding the dependent claims (compare claim 5-6
to claims 21-22 of '470 patent; compare claim 31 to claim 16 of '470 patent; compare claim 32 to
claim 17 of '470 patent). The same type of comparison could be carried out over many of the
claims in both claim sets. The difference lies in comparing claim 1 of the '470 patent and claim
26 of the instant application. While the claims are not the same, both methods are drawn to the
same technique which examines nucleotide incorporation into a ternary complex, precluding
incorporation of a test nucleotide and identifying the next base to be primed on the template.
While there are differences between the claims, the differences are not significant. Therefore, the claims are not patentably distinct.
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.
Claim(s) 26-54 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Vander Horn et al. (US PgPub 20100330570; December 2010.
With regard to claim 26, Vander Horn teaches a method of identifying a base in a primed template nucleic acid, comprising:
I. performing an examination step wherein chemical incorporation of a nucleotide to the primed template nucleic acid is disabled or severely inhibited, the examination step comprising:
(a) providing a ternary complex comprising a polymerase, primed template nucleic acid comprising a primer, and a nucleotide complementary to the next base of the primed template nucleic acid under conditions that (paragraph 10, for example, where the method is described; paragraph 293-298, for example)
(i) stabilize the ternary complex and
(ii) destabilize binary complex formed between the primed template nucleic acid and the polymerase when the nucleotide is not complementary to the next base of the primed template nucleic acid;
(b) washing to remove any unbound polymerase and unbound nucleotides, wherein the washing occurs under conditions that stabilize the ternary complex and destabilize the binary complex (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted; see also Example 7, 8 and 12);
(c) detecting the ternary complex while precluding incorporation of the nucleotide into the primer (Exanple 7, which includes transient binding steps; paragraph 577-584; see also Example 8); and
(d) identifying the next base of the primed template nucleic acid from the detected ternary complex (see Figure 11 for example, where order of correct or incorrect incorporation and washing steps are depicted).
With regard to claim 27, Vander Horn teaches the method of claim 26, wherein the washing comprises contacting the ternary complex with a ternary complex stabilizing agent (see Figure 11 for example, where order of correct or incorrect incorporation and washing steps are depicted; see also see paragraph 91-95, where stabilizing the ternary complex is discussed).
With regard to claim 28, Vander Horn teaches the method of claim 26, wherein the primer comprises a reversible terminator moiety at the 3' end and wherein the method further comprises removing the reversible terminator moiety prior to incorporating a nucleotide comprising an unlabeled reversible terminator moiety (paragraph 10, for example, where the
method is described; paragraph 293-298, for exarnple, where reversible terminators are included).
With regard to claim 29, Vander Horn teaches the method of claim 26, wherein the method is performed in the absence of detectably labeled nucleotides or in the presence of detectibly labeled nucleotides wherein the labels of the detectably labeled nucleotides are not detected (paragraph 7, for example).
With regard to claim 30, Vander Horn teaches the method of claim 26, further comprising an incorporation step, the incorporation step comprising incorporating into the primer a nucleotide that is complementary to the next base (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted; see also Example 12).
With regard to claim 31, Vander Horn teaches the method of claim 30, wherein step I. is repeated at least once using a different type of nucleotide prior to the incorporation step (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted: see also Example 12).
With regard to claim 32, Vander Horn teaches the method of claim 30, wherein the nucleotide that is incorporated comprises a reversible terminator moiety (paragraph 293-298, for example).
With regard to claim 33, Vander Horn teaches the method of claim 32, wherein the nucleotide that is incorporated is unlabeled (paragraph 7, for example).
With regard to claim 34, Vander Horn teaches the method of claim 30, wherein the incorporation step further comprises replacing the polymerase with a different type of polymerase that catalyzes the incorporation (see Example 10, for example, where a mutated polymerase is tested in the method).
With regard to claim 35, Vander Horn teaches the method of claim 26, further comprising an incorporation step, the incorporation step comprising replacing the nucleotide with a second nucleotide and incorporating the second nucleotide into the primer (see Figure 11 for example, where order of correct or incorrect incorporation and washing steps are depicted; see also Example 12).
With regard to claim 36, Vander Horn teaches the method of claim 35, wherein the second nucleotide comprises a reversible terminator moiety (paragraph 293-298, for example).
With regard to claim 37, Vander Horn teaches the method of claim 36, wherein the second nucleotide is unlabeled (paragraph 7, for example).
With regard to claim 38, Vander Horn teaches the method of claim 35, wherein the incorporation step further comprises replacing the polymerase with a different type of polymerase that catalyzes the incorporation (see Example 10, for example, where a mutated polymerase is tested in the method).
With regard to claim 39, Vander Horn teaches the method of claim 26, wherein the conditions comprise presence of a polymerase inhibitor that precludes incorporation of the nucleotide into the primer (paragraph 293-298, for example).
With regard to claim 40, Vander Horn teaches the method of claim 26, wherein the conditions comprise an amino acid mutation in the polymerase that precludes incorporation of the nucleotide into the primer (see Example 10, for example, where a mutated polymerase is tested in the method).
With regard to claim 41, Vander Horn teaches the method of claim 26, wherein the conditions comprise presence of a reversible terminator on the 3' end of the primer that precludes incorporation of the nucleotide into the primer (paragraph 293-298, for example).
With regard to claim 42, Vander Horn teaches the method of claim 26, wherein the nucleotide comprises a label moiety (paragraph 121, where labels are described).
With regard to claim 43, Vander Horn teaches the method of claim 26, further comprising repeating step I. at least once using a second nucleotide that is different from the nucleotide (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted; see also Example 12).
With regard to claim 44, Vander Horn teaches the method of claim 26, wherein the primed template nucleic acid is attached to a surface (paragraph 123, for example, where the complex is immobilized).
With regard to claim 45, Vander Horn teaches the method of claim 44, wherein the surface is attached to a clonally amplified population of the primed template nucleic acid (Example 11 for example where clonal beads are used).
With regard to claim 46, Vander Horn teaches the method of claim 44, wherein the surface comprises a plurality of different template nucleic acids (paragraph 206-207, where multiple ternplates can be used).
With regard to claim 47, Vander Horn teaches the method of claim 26, wherein step (a) of providing the ternary complex comprises contacting the primed template nucleic acid with a reaction mixture comprising the polymerase and the nucleotide (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted: see also Example 12).
With regard to claim 48, Vander Horn teaches the method of claim 47, wherein the reaction mixture comprises 1 type of nucleotide (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted: see also Example 12).
With regard to claim 49, Vander Horn teaches the method of claim 47, wherein the reaction mixture comprises 2 types of nucleotides (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted: see also Example 12).
With regard to claim 50, Vander Horn teaches the method of claim 47, wherein the reaction mixture comprises 4 types of nucleotides (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted: see also Example 12).
With regard to claim 51, Vander Horn teaches the method of claim 47, wherein the reaction mixture comprises salt at a concentration in the range of 50 to 1500 mM (paragraph 211 for example).
With regard to claim 52, Vander Horn teaches the method of claim 51, wherein the reaction mixture comprises a MgCl2 salt (paragraph 211 for example).
With regard to claim 53, Vander Horn teaches the method of claim 47, wherein the reaction mixture comprises a pH from 7.4 to 9.0 (see Figure 11, for example, where order of correct or incorrect incorporation and washing steps are depicted: see also Example 12).
With regard to claim 54, Vander Horn teaches the method of claim 26, wherein the detecting comprises detecting a change in refractive index, a light scattering signal or a detectable tag (paragraph 12L where labels are described).
Conclusion
No claims are allowed. All claims stand rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE KANE MUMMERT whose telephone number is (571)272-8503. The examiner can normally be reached M-F 9:00-5:30.
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/STEPHANIE K MUMMERT/Primary Examiner, Art Unit 1681