DETAILED ACTION
Notice 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 .
Election/Restrictions
Applicant’s election without traverse Group I, claims 21-35, on 13 January 2026 is acknowledged. The requirement is deemed proper and therefore made Final.
Status of Application
Claims 21-38 are pending; claims 36-38 are withdrawn as being directed to non-elected subject matter. Thus, claims 21-35 are subject to examination on the merits.
Priority
The instant application is a CON of US 17/209,043 (now US Patent 11891633) which is a CON of US application 17/207,387 which is a DIV of US application 16/806,763 (now US Patent 11034942), which was filed 27 February 2020.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 13 January 2026, 16 July 2025 and 05 April 2024 has been considered by the examiner. See initialed and signed PTO/SB/08’s.
Claim Interpretation
In claims 34 and 35, each set of mutations, identified by an indent and all starting with “M129A” will be interpreted as requiring all of the recited substitutions. For example, these two different sets of substitutions as first presented in claim 34, require all 11 substitutions in the first two lines; or require all 10 substitutions in lines 3-4; and so on. This is consistent with that presented in Table 6 of the specification. This could be made clearer in the claims, however, by annotating each different set of substitutions with different markers such as (a), (b)…. Or (i), (ii)…. etc.
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Claim Rejections - 35 USC § 112(b)
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.
Claim 34 is 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 34 recites the limitation "M129A; D141A; E143A; T144A; L409A; Y410G; P411I; A486V; T515S; T591I; G153E; K713E; L479S" AND “M129A; D141A; E143A; T144A; L409A; Y410G; P411I; A486V; T515S; T591I; G153E; K713E; A640L” (which are the third to last and the last set of substitutions listed in claim 34) in reference to claim 21. There is insufficient antecedent basis for these limitations/substitutions in the claim because the recited substitutions do not require A486V + T515S, and at least one or more selected from: D215A, D315A, K477W, K477A, K478A, K603A, R714A, E719A, or N736A.
Claim Rejections - 35 USC § 102
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.
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)(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) 21-35 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Fuller et al. (US 2020/0080065 – cited on IDS; with an effectively filed date of 11 September 2018).
The applied reference has a common inventor and assignee with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
N.B. Applicant’s should note, MPEP 717.02(a)(I) states, regarding any 102(b)(2)(C) statement - “The statement should either be on or begin on a separate sheet and must not be directed to other matters (37 CFR 1.4(c)).”
Regarding claims 21-35, Fuller et al. teach Family B, 9o DNA polymerases including Pyrococcus abyssi which has 93.6% sequence identity with instant SEQ ID NO: 1 (Pyrococcus horikoshii) – See Supplemental Content, file 20260324_145817_us-18-540-158-1.rapbm, Duplicates for Result #12, wherein it is specifically recited:
[0305] The aim of the general experimental plan was to produce an optimized polymerase for nucleic acid sequencing methods. A total of 488 variants of P. abyssi were engineered. All variants were profiled against a variety of reverse terminators. Some of the better performing enzymes have between 7 and 12 mutations relative to the wild-type. Included herein are 202 sequences of the P. abyssi based enzymes that appear useful for nucleic acid sequencing. The motif A region having mutations SAP, SAV, SGI, AGP, and AGI are among the better performing enzymes in terms of incorporation rate.
Wherein motif A is defined as the LYP amino acids at positions 409-411 (See paragraph 0189).
Specific substitutions are recited in claim 1 and are of a polymerase comprising at least 80% identity to SEQ ID NO: 1 (as noted above from Pyrococcus abyssi which has 93.6% sequence identity with instant SEQ ID NO: 1), and an L409A/S/H + Y410G/A + P411V/I/P + A486L/V (claim 14) + T515S (claim 15) – this is in regards to instant claims 21-25, 28, 31-32.
Specific substitutions are recited in claim 17 and Table 7 and encompass (regarding instant claims 26 and 34-35):
M129A, D141A, T144A, E143A, L409A, Y410G, P411I, A486V, T515S, and K477W;
M129A, D141A, E143A, D215A, D315A, L409A, Y410A, P411I, A486V, T515S, and T590I;
M129A, D141A, T144A, E143A, L409A, Y410G, P411I, A486V, T515S, T590I, G153E, K478A;
This is to name but a few overlapping substitutions as taught in Table 7 compared to the instant claims 26 and 34-35.
Regarding claims 29-30, said altered polymerases display increased rate of incorporation of modified nucleotides, relative to wild-type (paragraph 0414).
Regarding 33, said polymerase is capable of incorporating modified nucleic acids at a reaction temperature across the range of 55o to 80oC.
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 §§ 706.02(l)(1) - 706.02(l)(3) 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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
Claims 21-35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of US patent 11136565. Although the claims at issue are not identical, they are not patentably distinct from each other because they overlap to such an extent to be obvious variations of one another.
The instant claims in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: a valine at amino acid position 486 (A486V) or at an amino acid position functionally equivalent to amino acid position 486; a serine at amino acid position 515 (T515S) or at an amino acid position functionally equivalent to amino acid position 515; AND at least one of the following amino acids: an alanine at amino acid position 215 (D215A) or at an amino acid position functionally equivalent to amino acid position 215;
an alanine at amino acid position 315 (D215A) or at an amino acid position functionally equivalent to amino acid position 315; an alanine at amino acid position 477 (K477A) or at an amino acid position functionally equivalent to amino acid position 477; a tryptophan at amino acid position 477 (K477W) or at an amino acid position functionally equivalent to amino acid position 477; an alanine at amino acid position 478 (K478A) or at an amino acid position functionally equivalent to amino acid position 478; an alanine at amino acid position 603 (K603A) or at an amino acid position functionally equivalent to amino acid position 603; an alanine at amino acid position 714 (R714A) or at an amino acid position functionally equivalent to amino acid position 714; an alanine at amino acid position 719 (E719A) or at an amino acid position functionally equivalent to amino acid position 719; or an alanine at amino acid position 736 (N736A) or at an amino acid position functionally equivalent to amino acid position 736. Additional substitutions are at positions 409, 410, 411, 153, 129, 141, 143, 144, 522, 591, 479, 640, 713 and 720 (claims 22-27).
The claims to the ‘565 patent in their broadest are drawn to a polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: an alanine at an amino acid position corresponding to amino acid position 409; a at an amino acid position corresponding to amino acid position 410; and a proline at an amino acid position corresponding to amino acid position 411 (claim 1). Dependent claim 11 recites specific substitutions:
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; and K477A;
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; and K478A;
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; and D215A;
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; and D315A;
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; D215A; and D315A;
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; K712E; and K477A;
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; K712E; and K478A
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; K712E; K477A; K478A; and L479S;
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; K712E; and D215A;
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; K712E; and D315A; or
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T590I; G153E; K712E; D215A; and D315A
The difference between the two sets of claims is instant SEQ ID NO: 1 is from Pyrococcus horikoshii whereas SEQ ID NO: 1 of the ‘565 patent is drawn to Pyrococcus abysii. However, it is noted that percent identity between the two sequences are 93.6%, so each set of claims encompass one another based upon the limitation of having greater than 80% identity to SEQ ID NO: 1 as recited in both sets of claims.
Thus, given the overlap in sequences and specific substitutions, the claims are deemed obvious variations of one another.
Claims 21-35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of US patent 11851687. Although the claims at issue are not identical, they are not patentably distinct from each other because they overlap to such an extent to be obvious variations of one another.
The instant claims in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: a valine at amino acid position 486 (A486V) or at an amino acid position functionally equivalent to amino acid position 486; a serine at amino acid position 515 (T515S) or at an amino acid position functionally equivalent to amino acid position 515; AND at least one of the following amino acids: an alanine at amino acid position 215 (D215A) or at an amino acid position functionally equivalent to amino acid position 215; an alanine at amino acid position 315 (D215A) or at an amino acid position functionally equivalent to amino acid position 315; an alanine at amino acid position 477 (K477A) or at an amino acid position functionally equivalent to amino acid position 477; a tryptophan at amino acid position 477 (K477W) or at an amino acid position functionally equivalent to amino acid position 477; an alanine at amino acid position 478 (K478A) or at an amino acid position functionally equivalent to amino acid position 478; an alanine at amino acid position 603 (K603A) or at an amino acid position functionally equivalent to amino acid position 603; an alanine at amino acid position 714 (R714A) or at an amino acid position functionally equivalent to amino acid position 714; an alanine at amino acid position 719 (E719A) or at an amino acid position functionally equivalent to amino acid position 719; or an alanine at amino acid position 736 (N736A) or at an amino acid position functionally equivalent to amino acid position 736. Additional substitutions are at positions 409, 410, 411, 153, 129, 141, 143, 144, 522, 591, 479, 640, 713 and 720 (claims 22-27). Dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 28), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 29), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 32) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 33).
The claims to the ‘687 patent in their broadest are drawn to a method of sequencing a nucleic acid sequence comprising: a) hybridizing a nucleic acid template with a primer to form a primer-template hybridization complex; b) contacting the primer-template hybridization complex with a DNA polymerase and nucleotides, wherein each of the nucleotides comprises a detectable label; c) subjecting the primer-template hybridization complex to conditions which enable the polymerase to incorporate a nucleotide into the primer-template hybridization complex to form a modified primer-template hybridization complex; d) detecting the detectable label; thereby sequencing a nucleic acid sequence; wherein the DNA polymerase comprises an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: an alanine or serine at amino acid position 409 or at an amino acid position functionally equivalent to amino acid position 409; a glycine or alanine at amino acid position 410 or at an amino acid position functionally equivalent to amino acid position 410; a proline, valine, glycine, isoleucine, or serine at amino acid position 411 or at an amino acid position functionally equivalent to amino acid position 411 (claim 1). Dependent claim 14 recites: wherein the DNA polymerase comprises the following amino acids: an alanine at amino acid position 129, 141, 143, 144, and 409 or at an amino acid position functionally equivalent to amino acid position 129, 141, 143, 144, and 409, a glycine at amino acid position 410 or at an amino acid position functionally equivalent to amino acid position 410, a tryptophan at amino acid position 477 or at an amino acid position functionally equivalent to amino acid position 477, an alanine at amino acid position 478 or at an amino acid position functionally equivalent to amino acid position 478, a valine at amino acid position 486 or at an amino acid position functionally equivalent to amino acid position 486, a serine at amino acid position 515 or at an amino acid position functionally equivalent to amino acid position 515, an isoleucine at amino acid position 591 or at an amino acid position functionally equivalent to amino acid position 591, and a leucine at amino acid position 640 or at an amino acid position functionally equivalent to amino acid position 640. Dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 9), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 10), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 12) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 13). Specific substitutions recited in claim 17 are:
b) M129A, 141A, E143A, T144A, L409A, Y410G, A486V, T515S, T591I, K477W, K478A, A640L; or
c) M129A, D141A, E143A, T144A, L409A, Y410G, A486V, T515S, T591I, K603A, A640L.
The sequences of both sets of claims, e.g. SEQ ID NO: 1, have 100% identity to one another – see Supplemental content, 20260324_145816_us-18-540-158-1.rai, Duplicates for Result #1. Thus, the main difference between the claims is the claims to the ‘687 patent teaching the same polymerases but utilized the in a method of nucleic acid sequencing. However, the polymerases as utilized in said method would still anticipate the instant polymerases as claimed.
Thus, given the overlap in sequences and specific substitutions, the claims are deemed obvious variations of one another.
Claims 21-35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of US patent 11845923. Although the claims at issue are not identical, they are not patentably distinct from each other because they overlap to such an extent to be obvious variations of one another.
The instant claims in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: a valine at amino acid position 486 (A486V) or at an amino acid position functionally equivalent to amino acid position 486; a serine at amino acid position 515 (T515S) or at an amino acid position functionally equivalent to amino acid position 515; AND at least one of the following amino acids: an alanine at amino acid position 215 (D215A) or at an amino acid position functionally equivalent to amino acid position 215; an alanine at amino acid position 315 (D215A) or at an amino acid position functionally equivalent to amino acid position 315; an alanine at amino acid position 477 (K477A) or at an amino acid position functionally equivalent to amino acid position 477; a tryptophan at amino acid position 477 (K477W) or at an amino acid position functionally equivalent to amino acid position 477; an alanine at amino acid position 478 (K478A) or at an amino acid position functionally equivalent to amino acid position 478; an alanine at amino acid position 603 (K603A) or at an amino acid position functionally equivalent to amino acid position 603; an alanine at amino acid position 714 (R714A) or at an amino acid position functionally equivalent to amino acid position 714; an alanine at amino acid position 719 (E719A) or at an amino acid position functionally equivalent to amino acid position 719; or an alanine at amino acid position 736 (N736A) or at an amino acid position functionally equivalent to amino acid position 736. Additional substitutions are at positions 409, 410, 411, 153, 129, 141, 143, 144, 522, 591, 479, 640, 713 and 720 (claims 22-27). Dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 28), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 29), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 32) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 33).
The claims to the ‘923 patent in their broadest are drawn to a method of incorporating a modified nucleotide into a nucleic acid sequence by allowing the following components to interact: (i) a DNA template, (ii) a nucleotide solution, and (iii) a polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: an alanine, serine or histidine at amino acid position 409 or at an amino acid position functionally equivalent to amino acid position 409; a glycine or alanine at amino acid position 410 or at an amino acid position functionally equivalent to amino acid position 410; a proline, valine or isoleucine at amino acid position 411 or at an amino acid position functionally equivalent to amino acid position 411. Additional dependent claims 9 and 10 recite wherein there is a valine at position 486 and a serine at position 515. Specific substitutions for said
The sequences of both sets of claims, e.g. SEQ ID NO: 1, have 93.6% identity to one another – See Supplemental Content, 20260324_145816_us-18-540-158-1.rai, Duplicates for Result #11. Thus, the main difference between the claims is the claims to the ‘923 patent teaching the same polymerases but utilized the in a method of nucleic acid sequencing. However, the polymerases as utilized in said method would render obvious the instant polymerases as claimed when the dependent claims 31-31 and 33 and 36-37 are combined.
Thus, given the overlap in sequences and specific substitutions, the claims are deemed obvious variations of one another.
Claims 21-35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of US patent 12454683. Although the claims at issue are not identical, they are not patentably distinct from each other because they overlap to such an extent to be obvious variations of one another.
The instant claims in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: a valine at amino acid position 486 (A486V) or at an amino acid position functionally equivalent to amino acid position 486; a serine at amino acid position 515 (T515S) or at an amino acid position functionally equivalent to amino acid position 515; AND at least one of the following amino acids: an alanine at amino acid position 215 (D215A) or at an amino acid position functionally equivalent to amino acid position 215; an alanine at amino acid position 315 (D215A) or at an amino acid position functionally equivalent to amino acid position 315; an alanine at amino acid position 477 (K477A) or at an amino acid position functionally equivalent to amino acid position 477; a tryptophan at amino acid position 477 (K477W) or at an amino acid position functionally equivalent to amino acid position 477; an alanine at amino acid position 478 (K478A) or at an amino acid position functionally equivalent to amino acid position 478; an alanine at amino acid position 603 (K603A) or at an amino acid position functionally equivalent to amino acid position 603; an alanine at amino acid position 714 (R714A) or at an amino acid position functionally equivalent to amino acid position 714; an alanine at amino acid position 719 (E719A) or at an amino acid position functionally equivalent to amino acid position 719; or an alanine at amino acid position 736 (N736A) or at an amino acid position functionally equivalent to amino acid position 736. Additional substitutions are at positions 409, 410, 411, 153, 129, 141, 143, 144, 522, 591, 479, 640, 713 and 720 (claims 22-27). Dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 28), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 29), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 32) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 33).
The claims to the ‘683 patent in their broadest are drawn A polymerase comprising an amino acid sequence that is at least 85% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids:
an alanine at amino acid position 409 or at a position corresponding to amino acid position 409; a glycine at amino acid position 410 or at a position corresponding to amino acid position 410; an alanine at amino acid position 144 or at a position corresponding to amino acid position 144; and a serine at amino acid position 515 or at a position corresponding to amino acid position 515. Additional dependent claim 6 recites wherein there is a valine at position 486. Specific substitutions such as those in claim 18 are as follows:
d) M129A, D141A, T144A, E143A, L409A, Y410G, P411I, A486V, T515S, and K477W
The sequences of both sets of claims, e.g. SEQ ID NO: 1, have 93.6% identity to one another – See Supplemental Content, 20260324_145816_us-18-540-158-1.rai, Duplicates for Result #11. Thus, the main difference between the claims is the claims to the ‘683 patent teaching the same polymerases but utilized the in a method of nucleic acid sequencing. However, the polymerases as utilized in said method would render obvious the instant polymerases as claimed when the dependent claims 31-31 and 33 and 36-37 are combined.
Thus, given the overlap in sequences and specific substitutions, the claims are deemed obvious variations of one another.
Claims 21-35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of US patent 11884943. Although the claims at issue are not identical, they are not patentably distinct from each other because they overlap to such an extent to be obvious variations of one another.
The instant claims in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: a valine at amino acid position 486 (A486V) or at an amino acid position functionally equivalent to amino acid position 486; a serine at amino acid position 515 (T515S) or at an amino acid position functionally equivalent to amino acid position 515; AND at least one of the following amino acids: an alanine at amino acid position 215 (D215A) or at an amino acid position functionally equivalent to amino acid position 215; an alanine at amino acid position 315 (D215A) or at an amino acid position functionally equivalent to amino acid position 315; an alanine at amino acid position 477 (K477A) or at an amino acid position functionally equivalent to amino acid position 477; a tryptophan at amino acid position 477 (K477W) or at an amino acid position functionally equivalent to amino acid position 477; an alanine at amino acid position 478 (K478A) or at an amino acid position functionally equivalent to amino acid position 478; an alanine at amino acid position 603 (K603A) or at an amino acid position functionally equivalent to amino acid position 603; an alanine at amino acid position 714 (R714A) or at an amino acid position functionally equivalent to amino acid position 714; an alanine at amino acid position 719 (E719A) or at an amino acid position functionally equivalent to amino acid position 719; or an alanine at amino acid position 736 (N736A) or at an amino acid position functionally equivalent to amino acid position 736. Additional substitutions are at positions 409, 410, 411, 153, 129, 141, 143, 144, 522, 591, 479, 640, 713 and 720 (claims 22-27). Dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 28), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 29), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 32) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 33).
The claims to the ‘943 patent in their broadest are drawn to a polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: an alanine or serine at amino acid position 409 or at an amino acid position functionally equivalent to amino acid position 409; a glycine or alanine at amino acid position 410 or at an amino acid position functionally equivalent to amino acid position 410; a proline, valine, glycine, isoleucine, or serine at amino acid position 411 or at an amino acid position functionally equivalent to amino acid position 411; and a glutamine, valine, arginine or alanine at position 93 or a position functionally equivalent thereto (claim 1). Additional dependent claims recite serine at 515 (See claim 2); and specific substitutions further comprising an alanine at amino acid position 129, 141, 143, and 144 or an amino acid position functionally equivalent to amino acid position 129, 141, 143, and 144, functionally equivalent to amino acid position 411, a valine at amino acid position 486 or an amino acid position functionally equivalent to amino acid position 486, a serine at amino acid position 515 or an amino acid position functionally equivalent to amino acid position 515, an isoleucine at amino acid position 591 or an amino acid position functionally equivalent to amino acid position 591, a tryptophan at amino acid position 477 or an amino acid position functionally equivalent to amino acid position 477; and an alanine at amino acid position 478 or an amino acid position functionally equivalent to amino acid position 478 (Claim 7); or in dependent claim 9:
a) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K477W; K478A; A640L; V93A;
b) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K603A; A640L; V93R
c) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K477W; K478A; A640L; V93Q;
d) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K603A; A640L; V93A; or
e) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K603A; A640L; and V93Q.
Dependent claims further recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 3), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 4), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 5) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 6)
The sequences of both sets of claims, e.g. SEQ ID NO: 1, have 100% identity to one another –See Supplemental Content, 20260324_145816_us-18-540-158-1.rai file, Duplicates for Result #1.
Thus, the difference between the two sets of claims is that the ‘943 patent further recites a mutation in position 93 of SEQ ID NO: 1. However, the limitations as encompassed claims 1-7 of the ‘943 patent would readily anticipate the instant claims.
Claims 21-35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of US patent 11891633. Although the claims at issue are not identical, they are not patentably distinct from each other because they overlap to such an extent to be obvious variations of one another.
The instant claims in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: a valine at amino acid position 486 (A486V) or at an amino acid position functionally equivalent to amino acid position 486; a serine at amino acid position 515 (T515S) or at an amino acid position functionally equivalent to amino acid position 515; AND at least one of the following amino acids: an alanine at amino acid position 215 (D215A) or at an amino acid position functionally equivalent to amino acid position 215; an alanine at amino acid position 315 (D215A) or at an amino acid position functionally equivalent to amino acid position 315; an alanine at amino acid position 477 (K477A) or at an amino acid position functionally equivalent to amino acid position 477; a tryptophan at amino acid position 477 (K477W) or at an amino acid position functionally equivalent to amino acid position 477; an alanine at amino acid position 478 (K478A) or at an amino acid position functionally equivalent to amino acid position 478; an alanine at amino acid position 603 (K603A) or at an amino acid position functionally equivalent to amino acid position 603; an alanine at amino acid position 714 (R714A) or at an amino acid position functionally equivalent to amino acid position 714; an alanine at amino acid position 719 (E719A) or at an amino acid position functionally equivalent to amino acid position 719; or an alanine at amino acid position 736 (N736A) or at an amino acid position functionally equivalent to amino acid position 736. Additional substitutions are at positions 409, 410, 411, 153, 129, 141, 143, 144, 522, 591, 479, 640, 713 and 720 (claims 22-27). Dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 28), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 29), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 32) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 33).
The claims to the ‘633 patent in their broadest are drawn to a polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids:
an alanine at amino acid position 409 or at an amino acid position functionally equivalent to amino acid position 409; a glycine at amino acid position 410 or at an amino acid position functionally equivalent to amino acid position 410; a proline at amino acid position 411 or at an amino acid position functionally equivalent to amino acid position 411; and valine at amino acid position 486 or at an amino acid position functionally equivalent to amino acid position 486; dependent claims 3-6 recite a further amino acid at selected positions including serine at position 515.
Additional dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 7), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 8), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 10) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 11). Specific substitutions as in claim 13 are:
b) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K477W; K478A; and A640L; or
c) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K603A; and A640L.
The sequences of both sets of claims, e.g. SEQ ID NO: 1, have 100% identity to one another –See Supplemental Content, 20260324_145816_us-18-540-158-1.rai file, Duplicates for Result #1.
Thus, claims as encompassed by claims 1-13 of the ‘633 patent would readily anticipate the instant claims.
Claims 21-35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-29 of US patent 11034942. Although the claims at issue are not identical, they are not patentably distinct from each other because they overlap to such an extent to be obvious variations of one another.
The instant claims in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: a valine at amino acid position 486 (A486V) or at an amino acid position functionally equivalent to amino acid position 486; a serine at amino acid position 515 (T515S) or at an amino acid position functionally equivalent to amino acid position 515; AND at least one of the following amino acids: an alanine at amino acid position 215 (D215A) or at an amino acid position functionally equivalent to amino acid position 215; an alanine at amino acid position 315 (D215A) or at an amino acid position functionally equivalent to amino acid position 315; an alanine at amino acid position 477 (K477A) or at an amino acid position functionally equivalent to amino acid position 477; a tryptophan at amino acid position 477 (K477W) or at an amino acid position functionally equivalent to amino acid position 477; an alanine at amino acid position 478 (K478A) or at an amino acid position functionally equivalent to amino acid position 478; an alanine at amino acid position 603 (K603A) or at an amino acid position functionally equivalent to amino acid position 603; an alanine at amino acid position 714 (R714A) or at an amino acid position functionally equivalent to amino acid position 714; an alanine at amino acid position 719 (E719A) or at an amino acid position functionally equivalent to amino acid position 719; or an alanine at amino acid position 736 (N736A) or at an amino acid position functionally equivalent to amino acid position 736. Additional substitutions are at positions 409, 410, 411, 153, 129, 141, 143, 144, 522, 591, 479, 640, 713 and 720 (claims 22-27). Dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 28), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 29), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 32) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 33).
The claims to the ‘942 patent in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids:
an alanine or serine at amino acid position 409 or at an amino acid position functionally equivalent to amino acid position 409; a glycine at amino acid position 410 or at an amino acid position functionally equivalent to amino acid position 410; a proline at amino acid position 411 or at an amino acid position functionally equivalent to amino acid position 411; an alanine at amino acid position 129 or at an amino acid position functionally equivalent to amino acid position 129; an alanine at amino acid position 141 or at an amino acid position functionally equivalent to amino acid position 141; an alanine at amino acid position 143 or at an amino acid position functionally equivalent to amino acid position 143; and an alanine or valine at amino acid position 486 or at an amino acid position functionally equivalent to amino acid position 486; dependent claims 6-8 recites a further amino acid at selected positions including serine at position 515.
Additional dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 10), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 11), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 13) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 14). Additional, specific substitutions are:
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K477W; and K478A (claim 19);
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K477A; K478A; and L479S (claim 21);
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K477W; K478A; and A640L (claim 25b);
M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K603A; and A640L (claim 25c).
The sequences of both sets of claims, e.g. SEQ ID NO: 1, have 100% identity to one another –See Supplemental Content, 20260324_145816_us-18-540-158-1.rai file, Duplicates for Result #1.
Thus, claims as encompassed by claims 1-29 of the ‘942 patent would readily anticipate the instant claims.
Claims 21-35 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of US patent 12344867. Although the claims at issue are not identical, they are not patentably distinct from each other because they overlap to such an extent to be obvious variations of one another.
The instant claims in their broadest are drawn to A polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: a valine at amino acid position 486 (A486V) or at an amino acid position functionally equivalent to amino acid position 486; a serine at amino acid position 515 (T515S) or at an amino acid position functionally equivalent to amino acid position 515; AND at least one of the following amino acids: an alanine at amino acid position 215 (D215A) or at an amino acid position functionally equivalent to amino acid position 215; an alanine at amino acid position 315 (D215A) or at an amino acid position functionally equivalent to amino acid position 315; an alanine at amino acid position 477 (K477A) or at an amino acid position functionally equivalent to amino acid position 477; a tryptophan at amino acid position 477 (K477W) or at an amino acid position functionally equivalent to amino acid position 477; an alanine at amino acid position 478 (K478A) or at an amino acid position functionally equivalent to amino acid position 478; an alanine at amino acid position 603 (K603A) or at an amino acid position functionally equivalent to amino acid position 603; an alanine at amino acid position 714 (R714A) or at an amino acid position functionally equivalent to amino acid position 714; an alanine at amino acid position 719 (E719A) or at an amino acid position functionally equivalent to amino acid position 719; or an alanine at amino acid position 736 (N736A) or at an amino acid position functionally equivalent to amino acid position 736. Additional substitutions are at positions 409, 410, 411, 153, 129, 141, 143, 144, 522, 591, 479, 640, 713 and 720 (claims 22-27). Dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 28), wherein the polymerase exhibits an increased rate of incorporation of modified nucleotides, relative to a control (claim 29), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 32) wherein the polymerase is capable of incorporating modified nucleotides at reaction temperatures across the range of 40°C to 80°C (claim 33).
The claims to the ‘867 patent in their broadest are drawn to a cell comprising a polymerase, wherein the polymerase comprising an amino acid sequence that is at least 80% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1; comprising the following amino acids: an alanine at amino acid position 409 or an amino acid position functionally equivalent to amino acid position 409; a glycine at amino acid position 410 or an amino acid position functionally equivalent to amino acid position 410; a proline, at amino acid position 411 or an amino acid position functionally equivalent to amino acid position 411; and a valine at amino acid position 93 or an amino acid position functionally equivalent to amino acid position 93. Dependent claims 5 recites a further amino acid at selected positions including serine at position 515. Specific substitutions in dependent claim 13 are: M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K477W; K478A; and A640L.
Additional dependent claims recite wherein the polymerase comprises an amino acid sequence that is at least 90% identical to a continuous 500 amino acid sequence within SEQ ID NO: 1 (claim 6), wherein the polymerase is a Pyrococcus abyssi or Pyrococcus horikoshii polymerase (claim 8). Specific substitutions are in claim 13 are:
g) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; K477W; and K478A;
i) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; and K603A;
j) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; and N736A;
l) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; and E719A;
m) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; and R714A;
n) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; and D215A;
o) M129A; D141A; E143A; T144A; L409A; Y410G; A486V; T515S; T591I; and D315A.
The difference between the sets of claims then is the ‘867 claims have the polymerases within a cell. However, this would still necessarily anticipate the instant claims because polymerases within the cells are the same. The sequences of both sets of claims, e.g. SEQ ID NO: 1, have 100% identity to one another –See Supplemental Content, 20260324_145816_us-18-540-158-1.rai file, Duplicates for Result #1.
Thus, claims as encompassed by claims 1-13 of the ‘867 patent would readily anticipate the instant claims.
Conclusion
No claim is allowed.
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/SUZANNE M NOAKES/Primary Examiner, Art Unit 1656 25 March 2026
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