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
The amended claims 1-19, 23 were filed on 4/15/2022 and are under consideration. Claims 20-22 and 24-26 were cancelled.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/15/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDSs are being considered by the examiner.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Drawings
The drawings are objected to because Fig 3, 7,9, 11 need SEQ ID Nos.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
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.
Claims 1-18 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 1 is indefinite over the ambiguity in the phraseology regarding “using a region in the non-targeted nucleic acid in which the nucleotide sequence or modification state differs from that of the target nucleic acid as a target region, using a region in the target nucleic acid in which the nucleotide sequence or modification state differs from that of the non-target nucleic acid as a corresponding target region” since it is not clear whether these regions are intended to be at the same relative nucleotide positions as one another on the two different nucleic acid sequences, or whether the corresponding target region of the target nucleic acid could be somewhere different, or in any sequence site positions on this nucleic acid, and not only or not the in the equivalent site positions in the target region of the non target nucleic acid sequence. Thus, the metes and bounds of the claim cannot be determined. Claims 2-18 depend from claim 1 and are indefinite for the same reason.
Claim 1 is indefinite over the use of a parenthetical phrase “(excluding molecules composed solely of a nucleic acid)” since it is unclear whether this is a requirement or an optional limitation in the claim. Claims 2-18 depend from claim 1 and are indefinite for the same reason.
Claim 8 and 11 are indefinite over the use of 1) a “molecule” as being considered “a complex of a DNA strand cleavage activity deficient Cas9 protein and a RNA” (claim 8) or as being considered, “a complex of an RNA strand cleavage activity deficient Cas13a protein and a gRNA” (claim 11), since it is unclear whether two ordinary artisans would consider these complexes to be a molecule. Claim 9, 15, and 17 depend directly or indirectly from, and are indefinite in claim 8. Claims 12 and 18 depend from, and are indefinite in claim 11.
Claim 14 is indefinite over the use of the molecule as being a CpG methylated DNA-binding protein” for the same reasons as above. Claim 16 depends from, and is indefinite in claim 14.
Claim Rejections - 35 USC § 112 - Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-18 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the full scope of the claimed invention. In particular, the specification fails to demonstrate possession of the full scope of the claimed invention. In particular the specification fails to demonstrate possession of “a molecule”.
The Federal Circuit has explained that a specification cannot always support expansive claim language and satisfy the requirements of 35 U.S.C. 112 "merely by clearly describing one embodiment of the thing claimed." LizardTech v. Earth Resource Mapping, Inc., 424 F.3d 1336, 1346, 76 USPQ2d 1731, 1733 (Fed. Cir. 2005). The issue is whether a person skilled in the art would understand applicant to have invented, and been in possession of, the invention as broadly claimed. In LizardTech, claims to a generic method of making a seamless discrete wavelet transformation (DWT) were held invalid under 35 U.S.C. 112, first paragraph, because the specification taught only one particular method for making a seamless DWT and there was no evidence that the specification contemplated a more generic method. Id.; see also Tronzo v. Biomet, 156 F.3d at 1159, 47 USPQ2d at 1833 (Fed. Cir. 1998)(holding that the disclosure of a species in a parent application did not provide adequate written description support for claims to a genus in a child application where the specification taught against other species).
MPEP § 2164(II)(A)(3)(a)(ii). “Whenever the issue arises, the fundamental factual inquiry is whether the specification conveys with reasonable clarity to those skilled in the art that, as of the filing date sought, applicant was in possession of the invention as now claimed.” MPEP § 2163.02.
The specification does not have a explicit definition of “a molecule”. In this case, the term is exceptionally broad. Webster dictionary defines molecule as the smallest particle of a substance that retains all of the properties of the substance and is composed of one or more atoms, for example a molecule of water or a molecule of oxygen.
The specification provides minimal guidance on the structural definition of the molecule and depicts a few examples of the use of “a molecule” in the reactions, which are a small fraction of all possible molecules, which is seemingly an unlimited type, scope and structure of a molecule that could be considered. dCas9 and dCas13 have support in the specification for use, and particular gRNAs are described. Adequate written description to demonstrate full possession of “a molecule” in the claims, is insufficient, given the very expansive nature of the term used and that point that most reactions involve “a molecule”, which for example could include water, but as such may not meet the intention of the applicant with the claims.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, the claims will be given their broadest reasonable interpretation, in view of the specification, and as set forth at MPEP§ 2111 and using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. Here, regarding claim 1 and the above comments, the two regions discussed above, will be considered to be regions that differ from one another.
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.
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.
Claims 1-8 are rejected under 35 U.S.C. 103 as being unpatentable over SHIN et al. (US20190203280 A1, filed 9/6/17) in view of Zuo (Modern Path 2009 22:1023-1031).
Claim 1 is a method for detecting nucleic acids by conducting amplification,
using [a ‘target region, in] non-target nucleic acid (NA), differs from target NA with a “corresponding target region”, using a nucleic acid test sample as a template,
a primer to both target/non-target NA, amplification reaction in presence of molecule that can bind to target of non-target, under a temperature where the molecule binds to the non target NA and detecting the target NA based on the presence/absence of amplification product.
Regarding claims 1-8, SHIN disclosed applying methods and “identifying mutations” of biomarkers that cause cancer [0006], as well as detecting specificity in [newly emerging] viruses and bacteria that are “new variant” diseases [0005]. SHIN disclosed binding of, and improving detecting of NA target ([0007], e.g. virus, ‘280, Claim 4). SHIN disclosed providing a target NA template, a molecule that is not a NA, which is using the dCas9 protein, and gRNA (guide RNA) which binds to a target NA sequence ([0007][0009][0035];also meeting instant claim 8), where the protein and gRNA bind as complex of dCas9 to non-target, improving specific detection of the novel target [0005], or improving detection of that which is amplified [0028] [0034] e.g. a novel variant (mutant) of a viral disease [0005], or other DNA, RNA, [0031]-[0033], and guide RNA with a template where a molecule is the dCas9 protein, are also provided and bound ([0023-0030][0055-0063],[0064-0066]).
Shin disclosed a method of particular and specific detection of target amplification due to amplification with the addition of dCas9protein and gRNA where there is amplification of target over the non-target, where amplification of non-target is prevented and specificity of detection of target is improved [0011-0013]. The sample contained the target nucleic acid [0011] (also meeting instant claim 2). Shen disclosed detecting new variants of pathogenic virus (or bacteria) [0005], as well as “identifying mutations of biomarkers that cause cancer” [0006], where the target region and corresponding target regions would differ with novel variant mutation. Shin also disclosed detecting diseases with similar physical symptoms. Shin’s goal was to amplify desired target or novel mutants with specificity and to use the dCas9 on the non-target (non mutant) to improve specific detection of target over non-target.
Re claim 5, SHIN further disclosed an amplification primer to a target infectious disease ([0031], ‘280, claim 5) and detecting the amplification product ([0007],[0011],[0037]-[0039]; meeting claim 2), and that the dCas9 and gRNA binding to the target NA sequence are in a composition with a NA polymerase, a primer for amplification of the target and a buffer [0032]. SHIN indicated that the amplifying could occur via isothermal NA amplification ([0037], meeting instant claim 4), where RPA was used [0055] at 38 degrees C for DNA, and 43 degrees C for RNA (meeting instant claims 3-5).
Shin disclosed the importance of identifying novel variation in virus/bacteria, as well as mutation associated with cancer in biomarkers.
Shin did not explicitly say to amplify with primer that hybridizes to both target and non-target NA, or disclose amplification and a molecule binding to the target region of the non-target that corresponds to the corresponding target region in the target that differ,
Zuo disclosed the use of primers that amplify KRAS, specifically wild-type and mutants at two codons (e.g. Table 2), including more than one mutation associated with cancer. Patients diagnosed with cancer were being re-screened in a lab where KRAS testing had been routinely conducted with a given primer set (Pg 1024, right col, para 2) and primers for codon 12 and 13 were being used (Pg 1024, right col, para 2). A heterozygous sample with a ratio of mutant:WT DNA was used, here demonstrating that cold PCR was more sensitive for detection than PCR (Fig 2a, b; Pg 1027 left col, para 1). Next different KRAS mutations from clinical bone-marrow samples were detected (Pg 1027, right col final para; Table 2) and samples negative for these mutations were also detected (Pg 1028, left col para 1), demonstrating use of the same primer to detect samples with and without nucleotide changes and the value of these primers, since bone-marrow tests are used for detecting cancer recurrence, and since some specimens have smalls fraction of tumor cells, and mutations may be heterozygous (e.g. 20%, Pg 1027, right col, final para).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for the ordinary artisan to have incorporated the methodology of Zuo into the method of Shin, having recognized that multiple target nucleotide sequences with a mutation, or base pair difference (e.g. mutant and wildtype, or polymorphic sites) had been successfully amplified with the same set of primers used for detection of mutant and heterozygous genotypes by Zuo. The ordinary artisan would have had a reasonable expectation for success given Zuo’s success using these in cold PCR, and the motivation to use this method would be high having been provided by both Zou and Shin, since Zou detected new mutations in previously diagnosed cancer patients, and since Shin indicated the value of detecting cancer biomarker mutations, and pointed to the milieu of sample contents sometimes found in a sample, where for cancer detection this can include healthy and mutated cells, and the motivation to use one primer for wildtype and mutant sequences would be high.
Claim 6, 7 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over SHIN et al. (US20190203280 A1, filed 9/6/17) in view of ZUO (Modern Path 2009 22:1023-1031), and further in view of LIU et al (Sci Reports 6: 19675; 27 Jan 2016). The contributions of Shin and Zuo as relevant to the prior claims has been discussed.
Regarding claim 6: detecting target NA where “corresponding target region” in target NA and “target region in non-target NA” differ, claim 7: target region is a mutation site or polymorphism, and claim 9: gRNA specifically recognizes and binds DNA with sequence complementary to target in nontarget
Shin disclosed gRNA and detection of target, and of non-target, based on amplification product but did not say molecule binds to target in non-target NA and corresponding target region in target. Shin did disclose new variants in diseases, and distinguishing mutations in biomarkers of cancer [0006]
Shin did not explicitly address the two regions (target and corresponding target) differences.
LIU discussed targeting guide RNA (sgRNA) specificity, noting the value of the fewest off target mismatches for improved on-target efficiency (Pg 2, para 1). On-target efficiency is highly dependent on the sgRNA, and relevant sgRNA sequence determinants include nucleotide composition at specific positions, particularly e.g. adjacent to PAM, impacting sgRNA functionality (Pg 2 para2). The targeted region and sequence features of sgRNAs can impact their effects (Pg 2 para 2). Here, position-dependent nucleotides impact sgRNA performance (Pg 5, para 1), particularly proximity to PAM, which was correlated with on-target efficiency, including single base pair differences, critical for sgRNA: DNA recognition (Pg 5 third full para). Relevant to the instant case, guide RNA: DNA recognition is impacted by single base pair differences, similarly explicated on Pg 56 [0104] of the instant application as relevant here.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious to one of ordinary skill in the art to use the well-established principles of primer design combined with routine optimization to amplify target sequences for similar diseases of interest using similar primers, and to additionally incorporate the relevant knowledge of Shin to further to use a gRNA(s) that specifically and precisely amplified just the novel mutant in infectious disease or cancer biomarker based upon the principles of DNA hybridization and the gRNA knowledge provided by Liu. The motivation to do so would arise from a desire to identify the presence of a disease and emerging novel mutants (or difference cancer biomarker mutants), of significant interest to Shin, with their focus on an urgent need for sensitive, specific of detection of global (pandemic) associated viruses/bacterial pathogens that require quick, early diagnosis and treatment, including for example infectious diseases like tuberculosis or MERS (Shin [0005], [0031],[0069]). Infectious disease strains (or cancer biomarker mutants) that differed by perhaps single mutants would be expected to have target and corresponding target that were the same or very similar. LIUs methods allow for control in amplification allowing for amplification product desired.
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)(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 19 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Gersbach
(US20180320197 A1; published 11/8/2018).
Claim 19, detecting NA binding molecule, by conducting NA amplification using test sample, NA and primer that hybridizes with NA, when the NA-binding molecule is contained within the test sample, no amplification product not obtained from amplification; when NA-binding molecule not in test sample, amplification product is obtained.
Gersbach disclose the use of dCas9/gRNA to alter gene expression in test samples (cells) ((Abstract), [0009]-[0011][0016]-[0019],[0021]).
Gersbach disclose detecting NA binding molecule by using a test sample (e.g. sample is gDNA from cells [0335], with DNA target system comprising dCas9 delivery with one or more gRNA [0036].
Conducting amplification with sample, NA, and primer to NA: ([0335], gDNA, NA=loci with translocations at sgRNA target sites were amplified by PCR of genomic DNA, with primer [0335][0336]).
When NA binding molecule is in test sample, product is not obtained ([0036] demonstrates no IL1RN mRNA expression for iCas9 plus gRNA (Fig 1C) but not the result of an amplification product when the dCas9 does not bind [0036]. However, also disclosed are RNA-seq results for samples treated [0041] with gRNA and an empty vector (control), or with iCas9-VP64 plus gRNAs. Gene expression between treatments with iCas9 and gRNAs decreased significantly (-4fold on a log2 expression scale of log10 of mean normalized RNA read counts) in IL32 (Fig 6), thus when iCas9 and gRNA are not bound, product is obtained.
Further [0048] disclosed use of dCas9 gRNA for DMD repair in cells, and PCR results disclosing the DMD mutant band is 817 bp but with the introduction of dCas9 and guide this band is gone (instead this results in a band of 630 bp, not the same 817 bp product). Thus, when the molecule is within the amplification, the reaction product of 817 bp is not obtained and when the molecule is not in the sample the 817 bp product is obtained
Claim 23 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Boyle (PNAS, 114:5461-546; May 2017).
Regarding claim 23, Boyle disclosed a method for evaluating nucleic-acid binding ability to a nucleic acid of a test substance (Pg 5461, para 1). A nucleic acid amplification reaction included primers, and target nucleic acids, here a library of λ mutant target nucleic acids, that hybridized with the test substance, here loaded dCas9 fluorescently labelled sgRNA:DNA, under a temperature where the methods tested the binding ability of a test substance to the λ mutant targets (Pg 5461, para 1; Pg 5462 left col, first full para, Fig 1). Association was evaluated by fluorescence detection and no signal was detected with tight dCas9 binding ( λ mutants in these cases had, e.g. fewer novel GG dinucleotides, or other, different particular mutations), and tight dCas9 binding would impede amplification (Pg. 5462 para 5). High green fluorescent signal was detected without tight dCas9 binding (e.g. mismatches in 7bp seed regions result in rapid rejection of the mutated targets, by dCas9), and the absence of dCas9 binding would not impede amplification (Pg 5463 left col para 1,2, Fig2B). As well, in general, single mismatches in PAM-d bases did not really impact association rate and had little effect on dCas9 binding but a second basepair mismatch greatly impacted dCas9 binding (Pg 5463 right col para 2).
Conclusion
All claims rejected. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Lisa Horth whose telephone number is (703)756-4557. The examiner can normally be reached Monday-Friday 8-4 EST.
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/LISA HORTH/ Examiner, Art Unit 1681
/GARY BENZION/ Supervisory Patent Examiner, Art Unit 1681