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 .
Amendments
This action is in response to papers filed 6th July 2026 in which claim 1 was amended and no claims canceled, or added. All of the amendments have been thoroughly reviewed and entered.
Any rejection or objection not reiterated herein has been overcome by amendment.
Applicant's remarks with respect to §103 rejections have been fully considered but they are not persuasive for the reasons discussed in this Office Action. The §103 rejection is maintained.
Status of the Claims
Accordingly, claims 1-10 and 12-15 are being examined.
Withdrawn Claim Rejections - 35 USC § 101
Applicants amended claim 1 to recite in the last line, delivering the pgRNA sequence to a patient to treat coronavirus infection of the patient .
This limitation is an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, that makes the claim eligible under Step 2A.
Therefore, the limitation overcomes the JE that raised the § 101 rejection. See MPEP 2106.04(d)(2).
Therefore, the § 101 rejection is withdrawn.
Maintained 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.
Claim(s) 1-4, 8-10, 12-13, and 14-15 remain rejected under 35 U.S.C. 103 as being unpatentable over Sabeti (U.S. PG Pub 2021/0102197A1) with an effective filing date of 10/7/2019 from a listed provisional (62/912021) in view of Chuai (Chuai et al., Genome Biology 19: article 80, pp. 1-18; published 6/26/2018), as discussed in the Non-Final rejection of 3/27/2026 and reiterated below.
Discussion regarding the new amendment are made in bold below.
Claim 1 recites: A method to determine a pgRNA sequence comprising:
identifying two or more target sequences in a viral genome for recognition by a Cas effector;
for each target sequence of the two or more target sequences, calculating a homology score comprising aligning said target sequence with each other target sequence of the two or more target sequences;
determining one or more target pairs based at least in part on the homology score, wherein each target pair comprises a first target sequence and a second target sequence of the two or more target sequences having the homology score calculated as greater than or equal to 60% sequence identity;
generating a pgRNA template for at least one of the one or more target pairs, wherein the pgRNA template has a complementary sequence to the first target sequence, the second target sequence, or a convergent sequence.
generating a relative activity score for each of one or more pgRNA templates by determining a first sequence identity for the pgRNA template to a complementary sequence to the first target sequence and a second sequence identity for the pgRNA template to a complementary sequence to a second nucleotide sequence present in a different viral genome, a mutant viral genome, or both, wherein each pgRNA template comprises a sequence of nucleotides; thus the relative activity score is based at least in part on the first sequence identity and the second sequence identity.
calculating an off-target score only for each pgRNA template having calculated the first sequence identity as greater than 60% and the second sequence identity as greater than 60%; i.e., a threshold activity score and
determining the pgRNA sequence based at least in part on the relative activity score for each pgRNA template, the off-target score, or both; and
delivering the pgRNA sequence to a patient to treat a coronavirus infection of the patient.
As per the claim interpretation above, the limitation “60% sequence identity” in claim 1c will be given the broadest reasonable interpretation to mean “60% sequence homology/complementarity”.
Regarding claim 1, Sabeti teaches: A method to determine diagnostic/binding molecules to be sensitive across sequence diversity for a set of target sequences ([0007], the binding molecule is an amplification primer, hybridization probe, toehold switch, or guide molecule [0013]), i.e., pgRNA, comprising:
identifying all known sequences within a region (claim 21), wherein the nucleic acid detection system comprises a target molecule for a virus, e.g., SARS-CoV-2 [0014] for detection by Cas [0015], i.e., identifying two or more target sequences in a viral genome for recognition by a Cas effector;
constructing a ground set of possible binding molecules by finding representative subsequences across the set using locality sensitive hashing, identifying a function that quantifies detection activity between a binding molecule and a targeting sequence, (claim 21, Fig. 9, [0172], In a typical case, there are a small number of clusters owing to sequence homology across the alignment, [0708]), i.e., for each target sequence of the two or more target sequences, calculating a homology score comprising aligning said target sequence with each other target sequence of the two or more target sequences;
identifying a set of binding molecules within the ground set that maximizes a function of the expected activity (claim 21; In some embodiments, the degree of complementarity, when optimally aligned using a suitable alignment algorithm, can be about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more [0264]), i.e., determining one or more target pairs based at least in part on the homology score, wherein each target pair comprises a first target sequence and a second target sequence of the two or more target sequences having the homology score calculated as greater than or equal to 60% sequence identity;
determining unique guide-target pairs having sequence composition representative of viral genomes (claim 21; [0127]; Fig. 3; The molecules can be designed to provide an optimal guide to: bind one target, bind across a set of targets, differentiate mismatches between targets, and differentiate SNPs with one mismatch between targets [0169]; two strategies: (1) the consensus probe, computed at every site within the window, that detects the most number of sequences (' consensus'); and (2) the most common probe sequence, determined at every site within the window, that detects the most number of sequences, middle of [0651] comprising lines 2-5, Pg. 217), i.e., generating a pgRNA template for at least one of the one or more target pairs, wherein the pgRNA template has a complementary sequence to the first target sequence, the second target sequence, or a convergent sequence.
To construct an activity function, the system develops a dataset and training models to predict activity. The system creates a database of unique guide-target pairs having sequence composition representative of viral genomes. The system then classifies all guide-target pairs as inactive or active and trains a classifier on all pairs. The system creates a regressing model for active pairs with a convolutional neural network to create a model that predicts the activity of active guide-target pairs and classifies the pairs based on activity (claim 21; [0009]). The following recitations from Sabeti disclose how activity scores depend not only on 1 target sequence but target sequences across the diversity of viral genomes:
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Thus Sabeti’s method step reads on: generating a relative activity score for each of one or more pgRNA templates by comparing the pgRNA template to a complementary sequence to the first target sequence and a complementary sequence to a second nucleotide sequence present in a different viral genome, a mutant viral genome, or both, wherein each pgRNA template comprises a sequence of nucleotides;
f. developing an exact query algorithm to enforce specificity (claim 21; identifying off-target hits, [0010],[0666]; The result finds any non-specificity of a query and thus identifies binding molecules with high specificity to the target set, [0010]; Fig. 5). Following identification of binding molecules with maximal activity, processing the binding molecules with the maximal activity by (Sabeti claim 1):
1. computing non-specificity across the diverse set of genomes with an exact query algorithm, and
2. generating the binding molecules with minimal non-specificity across the diverse set of genomes;
i.e., determining an off-target score for each pgRNA template based at least in part on a threshold relative activity score generated for said pgRNA template;
g. performing a branch and bound search to identify a ranked list of binding molecules (claim 21, [0011]; Fig. 6), i.e., determining the pgRNA sequence based at least in part on the relative activity score for each pgRNA template, the off-target score, or both.
h. utilizing the pgRNA sequence for treatment of a viral infection (In certain embodiments, the guide molecules are designed with CRISPR-Cas systems designed to modify a target sequence for therapeutic purposes, last line of para [0193]; a method of treating a subject [0301-0302, 0355-0356]; prevention or treatment of disease in an individual [0331]).
Sabeti continue to teach the development of therapy to treat coronaviruses. See Sabeti claims 42-50 and 52. Claim 42 and 52 are reproduced below:
42. A method for developing or designing a therapy or therapeutic, comprising optimizing a binding molecule for the therapy or therapeutic according to claim 1,… 52. The composition of claim 50, wherein the target is associated with a disease, virus, is expressed in cancer cells, or is expressed in pathogen-infected cells,. optionally wherein the target is associated with SARS-CoV-2.
SARS-CoV-2 is a coronavirus.
See recitation from Sabeti below that summarizes Sabeti’s method. Note, as per definitions provided by Sabeti, diagnostic/binding molecule is interpreted as pgRNA.
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Regarding claim 2, Sabeti teaches wherein the binding molecules are (target) sequence specific molecules, typically a polypeptide or nucleic acid [0171]. With respect to guide sequence, a nucleic acid-targeting guide may be selected to target any target nucleic acid sequence. The target sequence may be DNA. The target sequence may be any RNA sequence, [0265]. i.e., wherein the two or more target sequences are RNA, DNA or both.
Regarding claim 3, Sabeti further teaches wherein the two or more target sequences are RNA ([0265]; claim 22).
Regarding claim 4, Sabeti further teaches, wherein identifying the target sequences in the viral genome comprises: determining a target sequence that is associated with a PAM (protospacer adjacent motif) or PFS (protospacer flanking sequence or site); Depending on the nature of the CRISPR-Cas protein, the target sequence should be selected, such that its complementary sequence in the DNA duplex is upstream or downstream of the PAM. In the embodiments, the complementary sequence of the target sequence is downstream or 3' of the PAM or upstream or 5' of the PAM. CRISPR-Cas systems that target RNA do not typically rely on PAM sequences. Instead such systems typically recognize protospacer flanking sites (PFSs) instead of PAMs ([0333]; Fig. 40, Figs. 46-49, Fig. 52, [0338]) i.e., determining a sequence position for each of one or more protospacer motifs present in the viral genome based at least in part on the Cas effector, wherein each of the one or more protospacer motifs comprise an adjacent sequence of nucleotides; and
assigning at least one sequence position as a protospacer position; and
identifying the two or more target sequences as a sequence of nucleotides immediately downstream of the protospacer position.
Regarding claims 8 and 9, Sabeti further teaches wherein the different viral genome and the viral genome are included in a viral family wherein the viral family is coronaviruses [0345].
Regarding claim 10, Sabeti further teaches an embodiment of their binding molecule wherein the binding molecule is a guide RNA. The guide RNA has sufficient complementarity with a target nucleic acid sequence to hybridize with the target nucleic acid sequence and direct sequence-specific binding of a nucleic acid-targeting complex to the target nucleic acid sequence. In some embodiments, the degree of complementarity, when optimally aligned using a suitable alignment algorithm, can be 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences [0264]. Sabeti further teaches sequences specific to each pathogen of interest may be identified or selected by comparing the coding sequences from the pathogen of interest to all coding sequences in other organisms by BLAST software ([0468]; Among other goals for this work, planned evaluation includes: (2) specificity at both the species and subspecies levels against highly related viruses, [0552]). i.e., The method of claim 1, wherein comparing the pgRNA to different viral genome, the mutant viral genome, or both is calculated based on a BLAST alignment.
Regarding claim 14, Sabeti further teaches identifying the target sequences in the viral genome comprises: determining a target sequence that is associated with a PAM (protospacer adjacent motif) or PFS (protospacer flanking sequence or site), [0333]; i.e., wherein determining the pgRNA sequence is based at least in part on a region of interest present in the viral genome.
Regarding claim 15, Sabeti further teaches identifying a set of binding molecules within the ground set that maximizes a function of the expected activity (claim 21; In some embodiments, the degree of complementarity, when optimally aligned using a suitable alignment algorithm, can be about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more [0264]). Thus, if each binding molecule is x% complementary to its target, then that binding molecule is also x% complementary to another binding molecule within the set of binding molecules chosen with x% complementarity as the cut-off, i.e., each target pair comprises a first target sequence and a second target sequence of the two or more target sequences having the homology score calculated as greater than or equal to 75% sequence identity.
Sabeti does not specifically teach wherein calculating the off-target score is associated with a threshold first sequence identity as greater than 60% and the second sequence identity as greater than 60% (claim 1) or pgRNA templates having calculated the first sequence identity as greater than 90% and the second sequence identity as greater than 90% (claim 12) or wherein calculating the off-target score is based at least in part on comparing each of the one or more pgRNA templates to a human genome sequence or a human transcriptome sequence (claim 13); rather Sabeti teaches the threshold for calculating sequence identity to be: maximal activity.
However, before the effective filing date of instant application, Chuai teaches the importance of determining off-target scores for sgRNA templates from established human datasets (Fig.3).
Chuai further discusses “effective application of CRISPR systems… [and] CRISPR-based gene knockout” (pg. 1, Abstract and l. column) and teaches that “In this system, a single-guide RNA (sgRNA) guides Cas9 proteins to specific genomic targets. Recognition and cleavage occur via complementarity of a 20-nucleotide (nt) sequence within the sgRNA to the genomic target, i.e., the on-target, upstream of a protospacer adjacent motif (PAM)… a major challenge for its effective application is to accurately predict the sgRNA on-target knockout efficacy and off-target (OT) profile beforehand. Accurate prediction would facilitate the optimized design of sgRNAs by maximizing their on-target efficacy (high sensitivity) and minimizing their off-target effects (high sensitivity)” (pg. 1, l. column). Chuai evaluate the ability of their algorithm (DeepCRISPR) to predict off-target sites (For this purpose, we curated the human sgRNA whole-genome off-target profile data, pg. 8, l. column, 3rd paragraph).
Chuai further teaches that “improvement in off-target prediction… is very important since near-zero off-targeting is the ultimate goal for all CRISPR-based gene therapies” (pg. 8, r. column). In this way, Chuai teaches design of guide molecules that bind to target sequences, with high specificity and sensitivity, to enable effective delivery of CRISPR systems comprising Cas proteins for therapeutic purposes.
It would have been prima facie obvious to one of ordinary skill in the art before the filing date of the instant application to modify Sabeti’s method to perform the off-target score calculation specifically when the calculated pgRNA templates have 60% or 90% activity scores.
One of ordinary skill in the art would have been motivated by Chuai’s assertion that minimizing off-target activity is very important and Sabeti’s method resulting in high activity score molecules only, and proceeded to utilize a certain threshold number in an exact query algorithm to enforce a threshold activity score before calculating an off-target score. The ordinary skilled artisan, would have been motivated to use these figures (60% or 90%) as their threshold criteria as a matter of design choice and further motivated to do so because of Chuai’s assertion that minimizing off-target scores to near-zero should be a goal of CRISPR therapy. The combination of prior art elements according to known methods to yield predictable results supports a conclusion of obviousness. Given the teachings of the cited references and the level of skill of the ordinary skilled artisan, it must be considered, absent evidence to the contrary, that the ordinary skilled artisan would have had a reasonable expectation of success in practicing the claimed invention reached when combining the cited references because Sabeti and Chuai both discuss computer-implemented, algorithmic methods of designing binding molecules. See MPEP 2144 II and 2143 I.(A).
Thus, Sabeti in view of Chuai make obvious instant claims 1-4, 8-10, 12-13, and 14-15.
Claim(s) 5-7 are rejected under 35 U.S.C. 103 as being unpatentable over Sabeti (U.S. PG Pub 2021/0102197A1) with an effective filing date of 10/7/2019 from a listed provisional (62/912021) in view of Chuai (Chuai et al., Genome Biology 19: article 80, pp. 1-18; published 6/26/2018) as applied to claims 1-4, 8-10, 12-13, and 14-15 above, and further in view of Kleinstiver (Kleinstiver BP et al., Nat Biotechnol. 2019 Mar;37(3):276-282).
The teachings of Sabeti and Chuai with respect to the method of claim 1 have been taught above. Sabeti further teaches wherein the DNA-targeting effector protein may be any of the Type V system Cas proteins such as a Cas12 [0210].
Sabeti does not teach wherein the Cas12 is enAsCas12a (claim 5) or wherein the one or more protospacer motifs are from the group consisting of: TTYN, CTTV, RTTC, TATM, CTCC, TCCC, TACA, RTTS, TATA, TGTV, ANCC, CVCC, TGCC, GTCC, TTAC, or combinations thereof (claim 6) or wherein the one or more protospacer motifs are from the group consisting of: TTYN, CTTV, RTTC, TATM, CTCC, TCCC, TACA, or combinations thereof (claim 7).
However, before the effective filing date, Kleinstiver teaches an engineered Cas12a variant called enAsCas12a that has remarkably better properties than the wild-type protein; i.e. substantially expanded targeting range and two-fold higher genome editing activity (title, abstract). This variant of Cas12 is also able to recognize PAMs such as CTTV (Fig. 3g).
It would have been prima facie obvious to one of ordinary skill in the art before the filing date of the instant application to have utilized the Cas12a and corresponding PAM of Kleinstiver in the method of Sabeti for the advantage of a better Cas12a. The ordinary skilled artisan, would have been motivated to make this combination because of 1) the known benefit of the engineered Cas12 as taught by Kleinstiver and further 2) the reduction to practice of such an engineered Cas with novel PAMs as taught by Kleinstiver. The combination of prior art elements according to known methods to yield predictable results supports a conclusion of obviousness. Given the teachings of the cited references and the level of skill of the ordinary skilled artisan, and Sabeti’s assertion that various Cas proteins are within the scope of the ordinary artisan at the time of applicants’ invention, it must be considered, absent evidence to the contrary, that the ordinary skilled artisan would have had a reasonable expectation of success in practicing the claimed invention reached when combining the cited references because Sabeti and Kleinstiver both discuss diagnostic molecules to use with Cas effectors. See MPEP 2144 II and 2143 I.(A).
Thus, Sabeti and Chuai in view of Kleinstiver make obvious instant claims 5-7.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
Response to Applicant’s Remarks:
On Pgs. 8-9 of the Remarks, Applicant alleges particular points of distinction with respect to the cited prior art.
A. Applicant alleges that Sabeti does not teach the amended limitation of independent claim 1; i.e., delivering the pg RNA sequence to a patient to treat a coronavirus infection of the patient.
Instead, Sabeti in [0193] teaches design of guide molecules for use with CRISPR-Cas systems for "diagnostic and therapeutic purposes" and that the designed molecules may "modify a target sequence for therapeutic purposes."
This argument of distinction is found unpersuasive.
As discussed in instant rejection, see Sabeti’s teachings addressing this limitation in bold in above OA, do include treating a coronavirus infection of a patient.
B. Applicant continues to allege dependent claims and secondary references do not cure the deficiencies of the primary reference, and cite case law. This is not persuasive, as the primary reference has not been argued persuasively to be deficient and Applicants have not presented any arguments re the secondary references on their merits.
Applicants arguments are not dispositive. The §103 rejection is maintained.
Conclusion
No claims are allowed.
Correspondence
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHABANA MEYERING, Ph.D. whose telephone number is (703)756-4603. The examiner can normally be reached M - F: 9am to 5pm EST.
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SHABANA S. MEYERING, Ph.D.
Examiner
Art Unit 1635
/SHABANA S MEYERING/ Examiner, Art Unit 1635
/RAM R SHUKLA/ Supervisory Patent Examiner, Art Unit 1635
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