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 .
DETAILED ACTION
Status of Claims
Claims 1-19, 21, 28-30, 33-36 and 38-41 are pending. Claims 19, 21, 28-30 and 33-35 are the subject of this FINAL Office Action. Claims 1-18 and 36-41 are withdrawn.
Priority
The claims receive a priority date of 05/03/2020 because this is the first priority date with support for cell lysis at 90-98°C for 2-10 minutes without NA isolation (which is the use of the Quick Extract™ DNA Extraction Solution (QE09050) as explained in paragraph 0456 of the instant specification). See also US20240052436, para. 0227 (“Each sample analyzed in the automated process disclosed herein was plated in duplicate in a 384 well plate. 7 μL of lysis solution (e.g., proteinase K or Quick Extract) was added to each well of the 384 well plate. Subsequently, 7 μL of sample was added to each well of the 384 well plate. The plate was incubated at 55° C. for 15 min followed by a 3 minute incubation at 98° C.”); para. 0229 (“Briefly proteinase K (PK) or Quick Extract (QE) we added to the sample and heated at 65° C. for 6 min and 98° C. for 3 min”).
Claim Notes
The claims are directed to the well-known SHERLOCK assay composition. The intended use or method of using the claimed composition does not distinguish the composition.
Oddly, Applicants removed the structural features of the claim found in the previous “extraction-free polynucleotide isolation solution.” Thus, the claims now read on any composition with Cas protein, guide polynucleotide, “isothermal amplification reagents,” and “detection construct.” This is a lot of prior art.
New Grounds of 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 –
(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.
Claims 19, 21, 28-30 and 34 are rejected under 35 U.S.C. § 102(a)(1) as being anticipated by WO2019011022.
As to claim 19 and 30, WO2019011022 teaches teaches SHERLOCK using LAMP, in a single reaction (e.g. Figs. 19-20, Example 11, Claims). Specifically, the claims, for example, state
A method for detecting the presence of a target nucleic acid molecule in a sample, which comprises the following steps: (i) Provide a detection system, which includes: (a) a Cas12b protein, which is a Cas12b or a Cas protein having similar bypass single-stranded DNA cleavage activity to Cas12b; (b) a guide RNA that guides Cas12b protein to specifically bind to a target nucleic acid molecule; (c) a nucleic acid probe, which is a single-stranded DNA; Wherein, the target nucleic acid molecule is target DNA; (d) a buffer; (e1) a polymerase for amplifying a target DNA; (e2) an optional reverse transcriptase for reverse transcription; (e3) dNTPs for amplification reactions and / or reverse transcription reactions; and (f) test samples to be tested; (ii) performing a reverse transcription and / or amplification reaction on the detection system to obtain a reverse transcription and / or amplification detection system; (iii) detecting whether the nucleic acid probe in the detection system in the previous step is cleaved by the Cas12b protein, and the cleavage is a trans cleavage that bypasses the single-stranded DNA
[ . . . ]
wherein the method of amplification is selected from the group consisting of PCR amplification, LAMP amplification, RPA amplification, ligase chain reaction, branched DNA amplification, NASBA, SDA, Transcription-mediated amplification, rolling circle amplification, HDA, SPIA, NEAR, TMA, and SMAP2
Thus, SHERLOCK with LAMP reagents in a single reaction, or Cas12b detection after LAMP to yield a composition with both LAMP reagents and Cas12b detection reagents, was clearly taught in WO2019011022.
It is also noted that claim 19 merely states “isothermal amplification reagents,” which encompasses any reagents capable of being used in isothermal amplification, such as any generic buffer, water, dNTPs, etc. This, too is taught in WO2019011022, and shown above (e.g. dNTPs, buffer, etc.). Thus, under both a narrow construction and a broad construction of claim 19, WO2019011022 anticipates.
As to the specific Cas12b of claim 19, WO2019011022 teaches that well-known Cas12b option “is selected from the group consisting of AacCas12b (Alicyclobacillus acidoterrestris), Aac2Cas12b (Alicyclobacillus acidiphilus), AkCas12b (Alicyclobacillus kakegawensis), AmCas12b (Alicyclobacillus macrosporangiidus), AhCas12b (Alicyclobacillus herbarius), AcCas12b (Alicyclobacillus) Contaminans).”
As to claim 21, this states an inherent property of the claimed Cas1b, which is taught in WO2019011022 as explained above.
As to claim 28-29, the gRNA is capable of binding to any target such as pathogenic microorganism virus targets (“The detection method of the present invention can detect nucleic acid molecules of different species, such as nucleic acid molecules of mammals, plants, or microorganisms and viruses. The method of the present invention is particularly suitable for detecting pathogenic microorganisms, gene mutations or specific target DNA or RNA.”).
As to claim 34, “additives to increase reaction specificity or kinetics” is an intended use; thus, any additive will meet this limitation.
New Grounds of 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.
Claim(s) 19, 21, 28-30 and 33-35 is/are rejected under 35 U.S.C. 103 as being unpatentable over WO2019011022, in view of ABUDAYYEH (US 20180340219), in further view of CN 111763768, CN 104328208 A and CN 109825647 A.
The prior art as a whole demonstrates that it would have been obvious to a skilled artisan at the time of filing to apply SHERLOCK-LAMP to familiar targets such as SARS-CoV-2, extracted using either familiar Quick Extract technique or familiar nucleic acid binding beads, and to use familiar LAMP primers with a reasonable expectation of success.
WO2019011022, clearly teaches SHERLOCK using LAMP, in a single reaction (e.g. Figs. 19-20, Example 11, claims). Specifically, the claims, for example, state
A method for detecting the presence of a target nucleic acid molecule in a sample, which comprises the following steps: (i) Provide a detection system, which includes: (a) a Cas12b protein, which is a Cas12b or a Cas protein having similar bypass single-stranded DNA cleavage activity to Cas12b; (b) a guide RNA that guides Cas12b protein to specifically bind to a target nucleic acid molecule; (c) a nucleic acid probe, which is a single-stranded DNA; Wherein, the target nucleic acid molecule is target DNA; (d) a buffer; (e1) a polymerase for amplifying a target DNA; (e2) an optional reverse transcriptase for reverse transcription; (e3) dNTPs for amplification reactions and / or reverse transcription reactions; and (f) test samples to be tested; (ii) performing a reverse transcription and / or amplification reaction on the detection system to obtain a reverse transcription and / or amplification detection system; (iii) detecting whether the nucleic acid probe in the detection system in the previous step is cleaved by the Cas12b protein, and the cleavage is a trans cleavage that bypasses the single-stranded DNA
[ . . . ]
wherein the method of amplification is selected from the group consisting of PCR amplification, LAMP amplification, RPA amplification, ligase chain reaction, branched DNA amplification, NASBA, SDA, Transcription-mediated amplification, rolling circle amplification, HDA, SPIA, NEAR, TMA, and SMAP2
ABUDAYYEH demonstrates familiar SHERLOCK assay with LAMP, along with heat samples such as saliva to 95° C for 2-5 minutes without any further extraction, which was well-known before effective filing as demonstrated therein. As to claim 19-23, 28-30 and 34-35, ABUDAYYEH teaches LAMP SHERLOCK assay with Cas12b for viral detection (Abstract; paras. 0248, 0517, 0621; claim 14). Any addition of Cas12b detection into the LAMP reaction yields a composition with both LAMP reagents plus Cas12b detection reagents.
In fact, as to the intended use in claim 19, ABUDAYYEH even discloses to heat samples such as saliva to 95° C for 2-5 minutes without any further extraction (paras. 0094-97, 0503, 0505, 0535).
Thus, SHERLOCK with LAMP in a single reaction, or Cas12b detection after LAMP to yield a composition with both LAMP reagents and Cas12b detection reagents, was routine.
Although WO2019011022 does not explicitly teach Quick Extract, yet this, too was a familiar technique used with LAMP reactions. For example, all of CN 104328208 A (“Adopt DNA rapid fractionation method, boil by sample diluting liquid, supernatant liquor is as the DNA profiling of loop-mediated isothermal amplification”) and CN 109825647 A (“application by quick coarse extraction DNA” using “NaOH and Tris-HCl, wherein NaOH concentration 0.5M, Tris-HCl PH value be 8.0”) teach to use methods that do not require nucleic acid isolation to quickly extract nucleic acids in the field. Thus, SHERLOCK LAMP with various quick extraction techniques was routine.
Finally, the elected primers are five known LAMP oligos with one obvious variant.
As to claim 33, CN 111763768 teaches primers and probes directed to SARS-CoV-2:
“the sequence of F3 is: 5'-GCTGCTGAGGCTTCTAAG-3', respectively;
the sequence of B3 is: 5'-GCGTCAATATGCTTATTCAGC-3', respectively;
the FIP sequence is: 5'-GCGGCCAATGTTTGTAATCAGTAGACGTGGTCCAGAACAA-3', respectively;
the BIP sequence is: 5'-TCAGCGTTCTTCGGAATGTCGCTGTGTAGGTCAACCACG-3', respectively;
the LoopF sequence is: 5'-CCTTGTCTGATTAGTTCCTGGT-3', respectively;
the loopR sequence is: 5'-CAGCGCTTCAGCGTTCTTCG-3' are provided.”
The bolded are the same as instant SEQ ID NOS: 62115-62119. “LoopR sequence,” above, is equivalent in function to SEQ ID NO: 62120. Although their sequences differ, yet SEQ ID NO: 62120 is an obvious option based on known N gene sequence and known LAMP primer design (see e.g. CN 111763768). Applicants merely moved the loopR primer over a few bases versus CN 111763768:
CN 111763768 vs N gene (NCBI MT503099)
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64
356
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SEQ ID NO: 62120 vs N gene (NCBI MT503099)
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68
344
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It is obvious to optimize a primer based on a known gene sequence using known primer design.
In sum, the claims amount to the obvious combination of familiar LAMP SHERLOCK methods to achieve familiar detection results.
As to Applicants’ arguments that none of the cited prior art teaches “wherein the sample undergoes cell lysis at 90-98°C for 2-10 minutes without requiring nucleic acid isolation prior to amplification,” this is an intended use of the claimed composition and does not change the compositional mixture. Even if the intended use changed the scope of the claimed composition, yet as explained above, ABUDAYYEH discloses to heat samples such as saliva to 95° C for 2-5 minutes without any further extraction (paras. 0094-97, 0503, 0505, 0535).
New Grounds of Rejection - Double Patenting- Obvious Type
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 obviousness-type 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); and 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 a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Instant claims 19-23, 28-30 and 33-35 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over conflicting claims 1-13 of US 11453907.
The instant claims are obvious over the conflicting claims because the conflicting claims teach the same SHERLOCK LAMP technique with the same primers. More specifically, the conflicting claims teach:
1. A single reaction composition for detecting the presence of a target polynucleotide in a crude or unprocessed sample, comprising:
a DNA isolation solution capable of isolating target RNA from the crude or unprocessed sample comprising a cell or virus containing a target RNA;
one or more thermostable Cas proteins possessing collateral activity;
at least one guide polynucleotide comprising a sequence capable of binding the target RNA and designed to form a CRISPR-Cas complex with the one or more Cas proteins;
isothermal amplification reagents comprising optimized loop-mediated isothermal amplification (LAMP) primers and amplification reagents; and
a detection construct comprising a polynucleotide component, wherein the one or more Cas proteins exhibit collateral nuclease activity and cleave the polynucleotide component of the detection construct once activated by the target RNA, thereby generating a detectable signal.
2. The composition of claim 1, wherein at least one of the one or more Cas proteins is a Type V Cas.
3. The composition of claim 2, wherein the at least one of the one or more Cas proteins is a Cas12b is selected from the group consisting of SEQ ID NOs: 61644-61954.
4. The composition of claim 3, wherein the Cas12b is Brevibacillus sp. SYSU G02855 (Br) Cas12b or Alicyclobacillus acidiphilus (Aap) Cas 12b.
5. The composition of claim 4, wherein the at least one guide polynucleotide comprises a sequence selected from SEQ ID NOs: 61957-61961 and 61970-61972.
6. The composition of claim 1, wherein the optimized LAMP primers are selected from SEQ ID NOs: 1-40, 499 and 61,983-61,988.
7. The composition of claim 1, wherein the at least one guide polynucleotide is selected from SEQ ID NOs: 40,500-61,643 and SEQ ID NO: 61,989.
8. The composition of claim 7, wherein the at least one guide polynucleotide comprises a spacer specific for the N gene or S gene of SARS-CoV-2.
9. The composition of claim 1, further comprising one or more additional additives selected from the group consisting of glycine, taurine, histidine, and combinations thereof.
10. The composition of claim 1, further comprising RNA binding beads.
11. The composition of claim 1, wherein the at least one guide polynucleotide is an optimized guide polynucleotide.
12. The composition of claim 1, further comprising reverse transcriptase.
13. A method for detecting coronavirus in a sample, the method comprising;
distributing a crude or unprocessed sample comprising a cell or virus containing a target RNA or set of said samples into individual discrete volumes, each individual discrete volume comprising the composition of claim 1;
incubating the crude or unprocessed sample or set of said samples in the composition of claim 1 at conditions sufficient to isolate the target RNA of the cell or virus via reagents of the DNA isolation solution;
amplifying the isolated target RNA using isothermal amplification, wherein, optionally, isolation of the target RNA from the composition of claim 1 between the incubating and amplifying steps is omitted; and
detecting amplified target RNA by binding of the CRISPR-Cas complex to the amplified target RNA, wherein binding of the amplified target RNA activates cleavage of the detection construct thereby generating a detectable signal.
Claim 4 very clearly states that “the Cas12b is Brevibacillus sp. SYSU G02855 (Br) Cas12b or Alicyclobacillus acidiphilus (Aap) Cas 12b.” Thus, the conflicting claims render obvious the instant claims.
Instant claims 19-23, 28-30 and 33-35 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over conflicting claims 1-14 of US 11639523.
The instant claims are obvious over the conflicting claims because the conflicting claims teach the same SHERLOCK LAMP technique with the same primers. More specifically, the conflicting claims teach:
1. A non-naturally occurring or engineered composition comprising
a Cas12b protein from Alicyclobacillus acidiphilus; and
a guide molecule that does not impede the Cas12b's activity at elevated temperatures above 55° C., comprising a guide sequence with at least 95% or more sequence similarity to a direct repeat and tracrRNA sequence from the Alicyclobacillus acidoterrestris CRISPR-Cas12b system and capable of forming a complex with the Cas12b protein and directing the complex to bind to a target polynucleotide.
2. The composition of claim 1, wherein the guide sequence comprises one of SEQ ID NOs: 61957-61961.
3. The composition of claim 1, wherein the Cas12b protein is fused to one or more localization signals.
4. The composition of claim 1, further comprising a detection construct comprising a non-target polynucleotide, wherein the Cas protein exhibits collateral activity and cleaves the non-target polynucleotide component once activated by the target polynucleotide.
5. The composition of claim 4, further comprising one or more isothermal amplification reagents.
6. The composition of claim 5, wherein the isothermal amplification reagents are loop-mediated isothermal amplification (LAMP) reagents, wherein the LAMP reagents are primers selected from SEQ ID NOs: 61983-61988.
7. The composition of claim 6, wherein the guide molecule is designed to bind to a polynucleotide sequence of SARS-CoV-2, wherein the guide molecule is SEQ ID NO: 61989.
8. A vector composition comprising one or more polynucleotide sequences encoding the Cas12b protein and the guide molecule in the composition of claim 1.
9. A non-naturally occurring or engineered prokaryotic or eukaryotic isolated host cell comprising the composition of claim 1, or progeny thereof.
10. A method of targeting one or more target polynucleotides, the method comprising contacting the one or more target polynucleotides with a non-naturally occurring or engineered composition of claim 1, wherein targeting comprises modifying the one or more target polynucleotides comprises increasing or decreasing expression of the one or more genes in the one or more target polynucleotides, insertion of a recombination template or a portion thereof to the one or more target polynucleotides.
11. A method for detecting a target polynucleotide in a sample, comprising
contacting the sample with the composition of claim 4, wherein the Cas protein exhibits collateral activity and cleaves the detection construct once activated by the target polynucleotide, and the cleaved detection construct generate a signal; and
detecting the signal thereby determining presence of the target polynucleotide in the sample.
12. A kit for modifying or detecting a target polynucleotide in a sample, comprising the composition of claim 1.
13. The composition of claim 1, wherein the guide molecule comprises a sequence with at least 95% or more sequence similarity to one of SEQ ID NOs: 61957-61961.
14. The vector composition of claim 8, wherein the polynucleotide sequences are codon optimized for expression in a eukaryotic cell.
Claim 1 clearly states “a Cas12b protein from Alicyclobacillus acidiphilus.” Thus, the conflicting claims render obvious the instant claims.
Instant claims 19-23, 28-30 and 33-35 are rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over conflicting claims 1-14 of US 11851702.
The instant claims are obvious over the conflicting claims because the conflicting claims teach the same SHERLOCK LAMP technique with the same primers. More specifically, the conflicting claims teach:
1. A cartridge comprising at least a first and second ampoule, a lysis chamber, an amplification chamber, and a sample receiving chamber, wherein the first ampoule comprises DNA isolation solution capable of isolating a target RNA from a crude or unprocessed sample comprising a cell or virus containing the target RNA and the second ampoule comprises a loop-mediated isothermal amplification (LAMP) composition for detecting the presence of the target RNA in a sample, comprising optimized LAMP primers consisting of SEQ ID NOs: 61983-61988 and amplification reagents for single amplification and glycine or taurine, or a combination thereof for amplifying the target RNA in less than one hour.
2. The cartridge of claim 1, configured to fit in a system comprising a heating means, an optic means, a means for releasing reagents on the cartridge, and a means for readout of assay result.
3. The cartridge of claim 1, wherein the contents of the first ampoule and/or second ampoule are lyophilized.
4. A device designed to receive one or more cartridges of claim 2 and further comprising one or more motors connected to a plunger for rupturing of the first and second ampoule of the cartridge and configured within the device to align with the first and second ampoule of the inserted cartridge, a heating element configured to align with the amplification chamber of the inserted cartridge, an optical detector configured to align with the amplification chamber of the inserted cartridge, and a display.
5. The device of claim 4, further comprising a graphical user interface for programming the device and/or readout of the results of the assay.
6. A system comprising a docking station and two or more devices of claim 5, wherein the docking station is configured to receive the two or more devices.
7. The cartridge of claim 1, wherein the second ampoule comprises isothermal amplification reagents and a CRISPR-Cas collateral detection system for amplifying and detecting a target RNA.
8. The cartridge of claim 7, wherein the target RNA is a coronavirus.
9. The cartridge of claim 1, wherein the DNA isolation solution and/or the lysis well comprises RNA binding beads.
10. The cartridge of claim 1, wherein the DNA isolation solution comprises a protease.
11. The cartridge of claim 10, wherein the protease is proteinase K.
12. The cartridge of claim 1, wherein the amplification reagents comprise reverse transcriptase.
13. The cartridge of claim 1, wherein the first ampoule comprises isolation solution in an amount to provide a ratio from 2:1 to 1:2 isolation solution:crude or unprocessed sample.
14. The cartridge of claim 1, wherein the LAMP composition further comprises colorimetric or fluorescent detection reagents.
As to the “CRISPR-Cas collateral detection system for amplifying and detecting a target RNA,” the specification discloses that the species of this genus include “Cas12b is Alicyclobacillus acidiphilus (AapCas12b)” and “[i]n certain other example embodiments, the Cas12b protein is Brevibacillus sp. SYSU G02855 (BrCas12b).” Thus, the conflicting claims render obvious the instant claims.
Prior Art
The prior art is replete with SHERLOCK or HOLMES assays: US 20180340219; WO 2019011022; WO 2019233385.
Conclusion
No claims are allowed.
All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Aaron Priest whose telephone number is (571)270-1095. The examiner can normally be reached 8am-6pm.
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/AARON A PRIEST/Primary Examiner, Art Unit 1681