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
It is noted that the present claims are seen to be entitled to a priority date of 12/21/23, the date the present 3’-allyl blocking groups attached to the 3’-oxygen atom were 1st introduced.
Double Patenting - Statutory
A rejection based on double patenting of the “same invention” type finds its support in the language of 35 U.S.C. 101 which states that “whoever invents or discovers any new and useful process... may obtain a patent therefor...” (Emphasis added). Thus, the term “same invention,” in this context, means an invention drawn to identical subject matter. See Miller v. Eagle Mfg. Co., 151 U.S. 186 (1894); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Ockert, 245 F.2d 467, 114 USPQ 330 (CCPA 1957).
A statutory type (35 U.S.C. 101) double patenting rejection can be overcome by canceling or amending the claims that are directed to the same invention so they are no longer coextensive in scope. The filing of a terminal disclaimer cannot overcome a double patenting rejection based upon 35 U.S.C. 101.
Claim 90 is provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 88 of copending Application No. 18/392,975 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Claim 90 is provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 78 of copending Application No. 18/393,291 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Claim 90 is provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 38 of copending Application No. 18/392,547 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Claim 122 is provisionally rejected under 35 U.S.C. 101 as claiming the same invention as that of claim 70 of copending Application No. 18/392,547 (reference application). This is a provisional statutory double patenting rejection since the claims directed to the same invention have not in fact been patented.
Double Patenting – Non-statutory
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 67-73, 76-77, 79-80, 82-83, 88-90, 112-113, 116, 119, and 121-122 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8, 20-21, 23-25, 27-28, 30-31, 36-38, 60-61, 65, 67, and 69-70 of copending Application No. 18/392,547 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both applications are substantially overlapping in being drawn to methods of sequencing nucleic acids with the same 3’-O-allyl reversible terminator nucleotides and kits comprising the same. It appears the method set forth in ‘547 would anticipate those claimed herein as they are drawn to the same methods.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 67-73, 76-77, 79-80, 82-83, 88-90, 112-113, 116, 119, and 121-122 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 41, 78-86, 88-89, 91-92, 94-95, 97, 100-101, 107, 109-110, and 121-123 of copending Application No. 18/393,291 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both applications are substantially overlapping in being drawn to methods of sequencing nucleic acids with the same 3’-O-allyl reversible terminator nucleotides and kits comprising the same. It appears the method set forth in ‘291 would anticipate those claimed herein as they are drawn to the same methods.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 67-73, 76-77, 79-80, 82-83, 88-90, 112-113, 116, 119, and 121-122 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 61-62, 70-72, 74-83, 84-88, 110-112, 114, 117, and 119-120 of copending Application No. 18/392,975 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both applications are substantially overlapping in being drawn to methods of sequencing nucleic acids with the same 3’-O-allyl reversible terminator nucleotides. It appears the method set forth in ‘975 would anticipate those claimed herein as they are drawn to the same methods.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 67-73, 76-77, 79-80, 82-83, 88-90, 112-113, 116, 119, and 121-122 is/are rejected under 35 U.S.C. 103 as being unpatentable over US 2020/0216891 (‘891) in view of 2009/0263791 (‘791).
‘891 discloses methods of determining the sequence of a plurality of different a target polynucleotide ([0022]), comprising incorporating a nucleotide comprising a 3'-OH blocking group into a copy polynucleotide that is complementary to at least a portion of the target polynucleotide (i.e., a sequencing primer; [0023]), a solid support comprising at least 5,000,000
features/cm² ([0210]) wherein multiple copies of a polynucleotide are present at each site and multiple target nucleic acids are manipulated simultaneously (i.e., multiplexing; [0209]). ‘891 teaches that all four nucleotide types are delivered to an array simultaneously with a DNA polymerase ([0200] and [0201]), that the solid support is imaged to determine the identity of incorporated nucleotides ([0201]), that the 3' blocking group of incorporated reversibly terminated nucleotides is cleaved by a palladium catalyst ([0121]) that is soluble in water
(i.e., in aqueous solution) and the solution comprises tris(hydroxypropyl)phosphine ([0124]). ‘891 teaches washing unincorporated nucleotides and chemically removed byproducts from the copy polynucleotide strand, and that this sequential incorporation is repeated at least 50 - at least
250 times ([0026]). ‘891 teaches that the 3'-OH blocked nucleotide comprises a detectable label ([0134]) conjugated by a cleavable linker ([0140]). The detectable label is a fluorescent dye ([0134]), and that the cleavable linker has various structures ([0150]). ‘891 teaches sequencing on clustered arrays (i.e., distinct features on the array comprise multiple polynucleotide template molecules; [0216]) and that the solid support comprises at least 5,000,000 features/cm² ([0210]).
The various bases claimed herein are taught in ‘891 such as: the purine bases are 7-deaza
purines ([0136] and [0141]); the T nucleotide has the disclosed structures ([0161] and [0264]); the A nucleotide has the disclosed structures ([0161] and [0256]); the C nucleotide has
the disclosed structure ([0161] and [0252]); and that the G nucleotide (i.e., at least one type of nucleotide) has the disclosed structure ([0262]). Regarding claim 112, ‘891 teaches that the sequencing cycles are repeated 50, 100 or 150 times for example ([0184]) wherein the phasing value is less than 0.25 or 0.18 after 150 or 50 cycles of sequencing ([0184]). The deblocking solution comprises ethanolamine (i.e., a primary amine; [0244]). ‘891 also teaches using DNA Pol 1901 (i.e., an altered archaeal family B polymerase comprising the modifications Leu408Ala, Tyr409Ala and Pro410lle (i.e., the first, second and third amino acids of the 3-amino acid region 408-410 contain amino acids as required by instant claim121 – see [0171] and [0278]). It appears applicants novelty is drawn to the use of the 3’-deoxy-2’-allyl protecting groups for use in determining the sequence of target polynucleotides, however, these compounds are known to be used for the same purpose, and modifying the process conditions as set forth above would be prima facia obvious. ‘891 teaches that allyl protecting groups are used as caps for 3'-OH
groups ([0008]), but does not specifically teach that these allyl protecting groups are chemically removed under the conditions disclosed.
However, ‘791 teaches 2’-deoxy nucleotides with 3' allyl blocking groups for use in methods of sequencing/detecting nucleotides (see figure 5 for example). ‘791 teaches that their allyl blocking group is removed by Pd-catalyzed (i.e., palladium) deallylation in aqueous buffer and "allows the re-initiation of the polymerase reaction," i.e., exposes a 3'-OH group for further
nucleotide incorporation ([0080]).
It would have been obvious to one having ordinary skill in the art to have simply substituted with 3' AOM protecting group taught by ‘891 with the 3'-allyl protecting group taught by ‘791 to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have recognized that the 3' allyl blocking group taught by ‘791 is removed under essentially the same conditions as those taught by ‘891 for the removal of
the 3' AOM protecting group (aqueous Na₂PdCl₄ with P(PhSO₃Na)₃; ‘791- [0093] and ‘891 [0124]) and that one of these known elements could have been substituted for the other with predictable results.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TRAVISS C MCINTOSH III whose telephone number is (571)272-0657. The examiner can normally be reached Monday-Friday 9AM-5:30PM EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Scarlett Goon can be reached at 571-270-5241. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/TRAVISS C MCINTOSH III/Primary Examiner, Art Unit 1693
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