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 .
Claim Status
Claim(s) 1-8 are currently pending and under examination herein.
Claim(s) 1-8 is/are rejected.
Claim(s) 8 is objected to.
Priority
The instant application claims the benefit of priority to Provisional Application No. 63/328628, filed 07 April 2022. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.78. As such, the effective filing date of claims 1-8 is 07 April 2022.
Information Disclosure Statement
The Information Disclosure Statement(s) filed on 07 April 2023 is in compliance with the provisions of 37 CFR 1.97 and has been considered. A signed copy of list of references cited from the IDS is included with this Office Action.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see section [0122] of the Specification). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claim 2 is objected to because of the following informalities: “non-target gRNA sequence” is duplicated. Appropriate correction is required.
Claim 8 is objected to because of the following informalities: “gRNAS” should be corrected to “gRNA.” Appropriate correction is required.
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.
Claim 4 is rejected under 35 U.S.C. 112(b) as failing to set forth and distinctly claim the subject matter for which the inventor or a joint inventor regards as the invention. Claim 3 sets a specificity threshold range of 0 to about 4 nt, and Claim 4, which depends from Claim 3, broadens the threshold range to include at least 3 nt. Claims must particularly point out and distinctly define the metes and bounds of the subject matter that will be protected (see MPEP § 2171).
Claim Interpretation
The claims in this application are given their broadest reasonable interpretation 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. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-8 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more.
Step 2A, Prong 1 Considerations
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1 : YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea/law of nature/natural phenomenon:
Claim 1 describes identifying and selecting sequences using a computing device.
Claim 8 describes comparing target sequences using a computing device.
These limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. While claims 1 and 8 recite performing the analysis with a “computing device”, there are no additional limitations that indicate that this computing device requires anything other than carrying out the recited mental process or mathematical concept in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim 1 recites an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 1 : YES).
Step 2A, Prong 2 Considerations
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment. Specifically, the claims recite the following additional elements:
Claim 1 recites receiving at least one non-target strain genome sequence.
Claim 8 recites generating nucleotide sequence permutations.
There are no limitations that indicate that the claimed computing device or the formats of the provided data require anything other than generic computing systems. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. The steps for receiving or generating do not recite an improvement upon conventional functioning of a computer. Claims 1 and 8 merely invoke a computing device as a tool (see MPEP § 2106.05(d)(I)). As such, claims 1 and 8 are directed to an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 2 : NO).
Step 2B (MPEP 2106.05.A i-vi)
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment. The instant claims recite the following additional elements:
Claim 1 recites a computer-implemented method and use of a computing device.
Claim 8 recites use of a computing device.
As discussed above, there are no additional limitations to indicate that the claimed analysis engine requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. The limitation for use of a computer-implemented method, or use of a computing device amount to mere instructions to apply the judicial exception in a generic way because the executable steps are so generically recited. MPEP 2106.05(d) discloses that a claim to an abstract idea requiring no more than a generic computer to perform generic computer functions that are well-understood, routine and conventional activities previously known to the industry are not enough to qualify as “significantly more” when recited in a claim with a judicial exception. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B : No). As such, claims 1 and 8, and 2-8 as being dependent, or multiply dependent, on claim 1, are not patent eligible.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 1 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Reuter et al. (Nucleic Acids Research 2021 vol. 49 no. 6, pgs. 3584-3598, IDS entered on 07 Apr 2023). Regarding Claim 1 1st element, Reuter teaches a computer-implemented method of comparative analysis of CRISPR motifs across a wide range of bacterial genomes and plasmids to identify strain-specific gRNA (see Introduction 3rd paragraph and Materials and Methods subsection “CSTB Algorithm” 1st paragraph). Claim 1 2nd element teaches receiving, at a computing device, at least one non-target strain genome sequence, at least one target strain genome sequence, the PAM sequence, a PAM orientation, a specificity threshold, and a target length is taught by Reuter as considered motifs are NGG-anchored sequences of 18-23 bp long. NGG being the canonical PAM sequence (see Materials and Methods subsection “CSTB Algorithm” 1st paragraph). Claim 1 3rd element teaches identifying, using the computing device, a plurality of candidate gRNA sequences within the at least one target strain genome sequence, based on the PAM nucleotide sequence, the PAM orientation, and the target length, Reuter teaches indexing of CRIPSR motifs as integers, enabling computationally efficient comparison of the sets of motifs across several organisms. Motifs being broad specificity gRNA sequences contained within the target strain genome sequences. Claim 1 4th element teaches selecting, using the computing device, at least one broad-specificity gRNA sequence from the plurality of candidate gRNA sequences, wherein each broad-specificity gRNA sequence is contained within all of the at least one target strain genome sequences. Reuter teaches a selection tool which allows for the selection of species whose genomes feather identical/similar CRISPR motifs, which defines the targeted CRISPR motifs (see “CSTB algorithm” section 1st paragraph). Claim 1 5th element teaches identifying, using the computing device, a plurality of non-target gRNA sequences within the at least one non-target strain genome sequence, based on the PAM nucleotide sequence, the PAM orientation, and the target length. Reuter teaches a selection tool allowing for the election of ‘excluded,’ or non-target organisms, which must have no motif in common with targeted ones (see “CSTB algorithm” 1st paragraph). Finally, Claim 1 6th element teaches selecting, using the computing device, at least one strain-specific gRNA sequence from the at least one broad-specificity gRNA sequence based on the specificity threshold, wherein the at least one strain-specific gRNA sequence is not contained within any of the non-target strain gRNA sequences. Reuter teaches an interactive table of gRNA sequences and their occurrences in each selected organism, with sorting and filtering capabilities on motif counts and sequence composition, allowing for the easy selection of motifs of interest (see “CSTB algorithm” 2nd paragraph).Claim Rejections - 35 USC § 103
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 non-obviousness.
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 2 is rejected under 35 U.S.C. 103 as being unpatentable over Reuter et al. as applied to claim 1 above and further in view of Shmakov et al. (Molecular Cell 2015 vol. 60 pgs. 385-397).
Claim 2 is directed to the PAM nucleotide sequence and the target sequence arranged according to the PAM orientation selected from 5'-(PAM nucleotide sequence)-(target nucleotide sequence)-3' or 5'-(target nucleotide sequence)- PAM nucleotide sequence)-3'.
Reuter teaches the PAM nucleotide sequence and target sequence arranged according to the PAM orientation 5'-(target nucleotide sequence)- PAM nucleotide sequence)-3'.
Reuter does not teach a target sequence arranged according to the PAM orientation 5'-(PAM nucleotide sequence)-(target nucleotide sequence)-3'.
However, Shmakov teaches a target sequence arranged according to the PAM orientation 5'-(PAM nucleotide sequence)-(target nucleotide sequence)-3' (see Fig 4(A) and Fig 4(F)).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Reuter and Shmakov to include a target sequence arranged according to the PAM orientation at the 5’ end in order to enhance the range of gRNAs to include a diverse range of CRISPR-Cas systems.
Claims 3, 4 and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Reuter et al. as applied to claim 1 above, and in further view of Hsu et al. (Nature Biotechnology Letters 2013 vol. 31 no.9 pgs. 827-834, IDS entered 07 Apr 2023).
Claims 3, 4 and 5 are all dependent, or multiply dependent, on Claim 2, which is anticipated by Reuter et al. and Shmakov et al. as described above.
Claims 3, 4 and 5 all teach specificity thresholds. Claim 3 does not disclose a specific value, while claim 3 discloses a specificity threshold from 0 to 4 nt, and claim 5 discloses a specificity threshold of at least 3 nt.
Reuter does not explicitly teach a range for a specificity threshold.
However, Hsu teaches a specificity threshold of 3, 4 and 5 consecutive or multiple mismatches, which falls in the range disclosed in both Claims 4 and 5 (see Figure 3(a)).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Reuter and Hsu to account for a range of mismatches in the computer-implemented method of producing gRNAs in order to integrate and quantify the contributions of mismatch location on Cas cleavage.
Claims 6 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Reuter et al. and Shmakov as applied to claim 2 above and further in view of Reuter et al.
Claim 6 teaches a target length range from about 10 to 20 nt,
Claim 7 teaches a target length of 20 nt.
Shmakov does not teach a specific target length range.
Reuter teaches a target length range of 18-23 nt, which falls in the range disclosed in both Claims 6 and 7 (see Materials and Methods Subsection “CSTB algorithm” 1st paragraph).
Taken together, it would have been obvious to one of ordinary skill in the art before the effective filing date of the invention to combine Reuter and Shmakov to use the disclosed target length ranges in order to account for the general length range of gRNA target sequences.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Reuter as applied to claim 1 above, and in further view of Altschul and Erickson (Molecular Biology and Evolution 1985 vol. 2 no.6, pgs. 526-538).
Claim 8 teaches nucleotide sequence permutations within the target region of non-target gRNA sequences, comparing the broad-specificity gRNA targets sequences to the nucleotide permutations, and discarding those broad-specificity gRNA sequences that match the permutations.
Reuter does not teach nucleotide sequence permutations.
However, Althschul and Erickson teach nucleotide sequence permutations.
Taken together, it would have been obvious to one of ordinary skill in the art to combine Reuter and Altschul to utilize nucleic acid permutations to find broad-specificity gRNA sequences that match any of the nucleotide sequence permutations and delete them in order to further reach a desired degree of gRNA specificity.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARANDA CANTRELL whose telephone number is (571) 270-5651. The examiner can normally be reached Monday - Thursday 7:30-4:30 pm.
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/M.S.C./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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