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 .
Status of the Claims
Claim 1 is cancelled. Claims 2-21 are under examination.
Claim Rejections - 35 USC § 112
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.
Claims 2-21 are 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 2 recites “where the first probe and the second probe are capable of forming an invasive cleavage structure in the presence of the target nucleic acid” without any corresponding structure. The capability to form an invasive structure is not a positive structural limitation and optional since it is not required. Additionally, in order for it to be capable of forming the invasive cleavage structure, specific structural elements are required of the target nucleic acid sequence, the first probe, the second probe, and the type of endonuclease as recited in the specification. The specification also teaches that the elements in the probe must be in a specific orientation that is not recited in the claim. Therefore, the claim is indefinite because it does not recite the corresponding structural features for the above clause.
Claims 3-21 are included as they do not recite the required structural elements.
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) 2-12 and 14-21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Allawi et al. (US 7,759,062 B2) in view of Frisen et al. (US 2014/0066318 A1).
Allawi et al. teach invasive cleavage assays. Allawi et al. teach a first probe that that is substantially complementary to a target sequence and a second probe that is substantially complementary to the target sequence. (Figure 5). The second probe comprises a flap that is not complementary to the target and acts as a detection method. (Figure 5). The probes overlap by one nucleotide and are cleaved with an endonuclease at the overlap resulting in the flap being cleaved. (see Figure 5 and column 53 “i. Invasive Cleavage Assays). Once cleaved, the overlap binds to a FRET cassette resulting in detection. (Figure 5). Figure 5 reproduced below.
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Allawi et al. teach a method of detecting the cleaved flap; however, they do not teach wherein the flap has a barcode with a capture binding domain or an array comprising a plurality of capture probes with a spatial barcode.
Frisen et al. teach a spatial array with capture probes immobilized on the array. (Claim 1). Frisen et al. teach the capture probes comprise a capture region and a positional domain that corresponds to the position of the capture probe on the array. (claim 1). Frisen et al. teach the position domain comprises a barcode. (claim 6).
Frisen et al. teach the array allows high throughput analysis and sequencing. [0003]. Therefore, one of ordinary skill in the art would be motivated to utilize the capture probe with a barcode sequence taught by Frisen et al. with the method taught by Allawi et al. allowing one of skill in the art to use the method taught by Allawi et al. in a high throughput fashion. By coupling the cleavage and detection method taught by Allawi et al. with an array, one of skill in the art could analysis and detect multiple samples in the same assay.
Regarding claim 3, Allawi et al. teach wherein the first probe and the second probe are complementary to adjacent sequences of the target nucleic acid. (Figure 5).
Regarding claim 4, Allawi et al. teach that the probes may or may not form an invasive cleavage structure when they do not bind the target next to each other. (See Figure 5B). Figure 5B does not show an overlap.
Regarding claim 5 and 6, Allawi et al. shows in Figure 5 that the first probe is complementary to the WT and the second probe can be complementary to the WT or the mutation.
Regarding claim 7, Allawi et al. teach the use of FEN-1. (col 24 lines 16-29).
Regarding claims 8 and 9, Allawi et al. teach that samples can be obtained through the action of a reverse transcriptase. (col. 43 lines 41-50). Frisen et al. teach a desired reverse transcriptase: MuLV. [0191].
Regarding claim 10. Allawi et al. teach an amplification step using ligase. (col 24 lines 40-67).
Regarding claim 11, Allawi et al. teach that a ligase is specific to the type of nucleic acid and contemplate T4 DNA ligase. (col 24 lines 52-67).
Regarding claim 12, Frisen et al. teach a mixture with T4 DNA ligase with 1mM ATP. [0200].
Regarding claims 14 and 15, Allawi et al. teach the use of primers that are also the INVADER sequence (first probe). (See figure 5 and Example 2).
Regarding claims 16, 17, and 18, Frisen et al. teach the inclusion on RNase H for RNA removal. [0157].
Regarding claims 19 and 20, Frisen et al. teach the inclusion of Proteinase K for removal of residual tissue. [0462].
Regarding claim 21, Allawi et al. in view of Frisen et al. teach the kit of claim 2. Where the only difference between a prior art product and a claimed product is printed matter that is not functionally related to the product, the content of the printed matter will not distinguish the claimed product from the prior art. In re Ngai, 367 F.3d 1336, 1339, 70 USPQ2d 1862, 1864 (Fed. Cir. 2004). (Claim at issue was a kit requiring instructions and a buffer agent. The Federal Circuit held that the claim was anticipated by a prior art reference that taught a kit that included instructions and a buffer agent, even though the content of the instructions differed.) See also In re Gulack, 703 F.2d
1381, 1385-86, 217 USPQ 401, 404 (Fed. Cir. 1983). (“Where the printed matter is not functionally related to the substrate, the printed matter will not distinguish the invention from the prior art in terms of patentability…[T]he critical question is whether there exists any new and unobvious functional relationship between the printed matter and the substrate.”)
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Allawi et al. (US 7,759,062 B2) in view of Frisen et al. (US 2014/0066318 A1) as applied to claims 2-12 and 14-21 above, and further in view of Patel et al. (Bioorganic Chemistry, 2008) and Samanta et al. (Nucleic Acids Research, 2018).
The teachings of Allawi et al. in view of Frisen et al. are applied to claim 13 as they were applied to claims 2-12 and 14-21. Allwai et al. in view of Frisen et al. do not teach a second probe with a preadenylated phosphate group on at its 5’ end and a first probe with at least two RNA bases at the 3’ end.
Patel et al. teach a method of using T4 DNA ligase to preadenylate DNA which creates an activated form of DNA that is useful for in vitro selection experiments. (abstract, see document in general).
Samanta et al. teach a method of modifying a 3’ end by incorporating a variety of functionalized nucleotide analogs. (abstract). These nucleotides can contain, for example, biotin or a fluorophore enabling detection or capture. (abstract).
Therefore, one of skill in the art would have been motivated to include these two modifications to the kit taught by Allawi et al. in view of Frisen et al. because the kit is an array that can be used to detect a target nucleic acid. The 5’ modification will make the kit more efficient because the DNA probe is active and the 3’ modification will allow further detection options.
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 2-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 11,959,130 B2. The instant claims are drawn to kit that recites components used in the method of the 130 patent. Therefore, the kit would have been obvious to one of skill in the art to make based on the method and recited elements to perform the method of the 130 patent.
Claims 2-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-29 of U.S. Patent No. 11,608,520 B2. The instant claims are drawn to kit that recites components used in the method of the 520 patent. Therefore, the kit would have been obvious to one of skill in the art to make based on the method and recited elements to perform the method of the 520 patent.
Conclusion
No claims are allowed.
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/MINDY G BROWN/Patent Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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