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 .
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
No IDS has been filed to date of the instant Office communication.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 3, 4, 5, 12-17 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 3 recites the phrase, “sample is diluted most 2.5 times”. This is grammatically unclear. The phrase has been construed to mean that the sample is diluted at most 2.5 times, meaning no more than 2.5 times.
Claim 4 is indefinite because it is unclear what is meant by the phrase, “complete digested sample,” as a sample that is completely digested would not have any “workable elements/molecules” therein. For the purpose of prosecution, the phrase has been construed to mean the digestion step has been completed.
Claims 5 and 17 are indefinite for the phrase, “method is performed at a temperature of at most 95oC except for the final elongation step of the digital droplet polymerase chain reaction” because it is unclear whether this means that the temperature does not exceed 95oC, or the assay is performed “mostly” at 95oC. These claims cannot be further interpreted for prior art analysis, however. This is because if the former interpretation is assumed, then the step elongation step of ddPCR must be grater than 95oC, which cannot occur; and if the latter interpretation is assumed, the claims recite steps that require incubation of protease/nuclease which occur outside of 95oC, and would not fall within the reasonable breath of all steps of the method being “mostly” at 95oC.
Claims 12, 14, and 15 recite the limitation, “Tris*HCl” which appears to be an unconventional usage of a well-known buffer, Tris-HCl. The well-known usage has been assumed.
Claim 13 is indefinite by way of its dependency on claim 12.
Claims 14 and 15 are also indefinite for the below reason.
Claims 14 and 15 depend from claim 12 (via claim 13).
Claim 12 recites a nuclease incubation step involving 40 mM Tris-HCl.
Claims 14 and 15 recite a proteinase K incubation step involving 20 mM Tris-HCl. Because the nuclease treatment step occurs prior to the proteinase K treatment, there appears to be a gap in the steps, that allow the two incubation steps to occur at different buffer concentrations. For the purpose of prosecution, the claims have been construed to involve at least a purification step of the digested sample prior to their incubation with proteinase K.
Claim 16 recites the phrase, “the protease”. There is an insufficient antecedent basis for this generic recitation of the species, “proteinase K”. The phrase has been construed to be referencing proteinase K.
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.
Claims 1-4, 6-11, and 16 are rejected under 35 U.S.C. 103 as being unpatentable over Dobnik et al. (Frontiers in Microbiology, 2019, vol. 10, pages 1-13) in view of Su et al. (Cold Spring Harb. Protoc., 2020, pages 158-161).
With regard to claims 1, 2, and 4, Dobnik et al. teach a well-known means of purifying Adeno-associated virus (AAV) for using them in gene therapy as vectors to transfer genes to human subject (see page 1, 1st paragraph), wherein the artisans teach the step of measuring the viral payload, comprising the steps of:
providing a sample that is free of non-encapsulated DNA (“AAVrh.10hCLN was purified from crude viral lysate by iodixanol gradient and QHP anion exchange chromatography … purified vectors were concentrated using 100 kDa MWCO Amicon Ultra-15 centrifugal filter units”, page 2, 2nd column); and
determining the viral DNA copy number by ddPCR (see “[a]bsolute quantification of vector genomes was performed using ddPCR”, page 4, 2nd column); also “[c]opy numbers were calculated per mL”, page 4, 2nd column), wherein the incubation of proteinase K is in the presence of SDS ([p]roteinase K reaction was composed of Proteinase K … 0.5 EDTA … 10% SDS … and nuclease free water”, page 3, 2nd column).
The incubation of the sample is performed in the presence of proteinase K and DNase I (“[t]wo different pre-treatments … DNase digestion with proteinase K … used”, page 6, 2nd column).
With regard to claim 9, the nuclease is DNase I (see page 6, 2nd column, 1st paragraph).
Donik et al. do not teach that the concentration of SDS is 0.05% (w/v) to 1.5% (w/v).
While Donik et al. expressly teach the combination of DNase I and Proteinase K treatment of AAV vector, wherein Proteinase K treatment is performed in the presence of SDS, as well as the DNA copy number analysis via ddPCR, Donik et al. do not particularly teach the concentration of SDS being at 0.05 to 1.5% (claim 1, in-part).
Donik et al. also do not particularly teach the assay conditions such as the amount used for proteinase K, and DNase I that are used to purify the AAV vector from non-encapsidated host DNA (via DNase I) and release the DNA of AAV (via proteinase K), or the total volume of the reaction (claims 3, 6-8, and 10-11).
Su et al. teach a method of titrating rAAV genome copy number, wherein the artisans treat the viral vector with DNase I to ensure removal of non-encapsidated DNA in the sample, wherein the DNase I is incubated with the sample for 30 minutes at 37oC (page 159) and heat inactivated by heating (“followed by a heat treatment to heat-inactivate DNase I”, page 158).
It would have been prima facie obvious one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Su et al., thereby arriving at the invention as claimed for the following reasons.
As taught by Donik et al., the motivation to analyze the titres of vectors (via determination of copy number) used in gene therapy via ddPCR had been known. As well, the motivation to ensure that the amount of contaminating host DNA (i.e., non-encapsidated DNA) from the copy number determination and the release of the vector DNA by treatment with proteinase K had been known, also expressly taught by Donik et al.
While Donik et al. did not explicitly teach all possible concentrations that the proteinase K and DNase I could be used in an optimized assay, or the amount of the reaction volume, such determination is not deemed to be outside that of the purview of the of an ordinarily skilled artisan because the reagent combinations, as well as the motivation for doing to have been expressly taught by Donk et al. and discovery of their optimal concentrations involving routine optimization would have been obvious to one of ordinary skill in the art.
Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In reAller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
Lastly, inactivation of enzymes, such as proteinase K and DNase I at temperatures of 95oC would have been an obvious application as Su et al. suggest that enzymes, such as DNase I is inactivated at high temperature and one of ordinary skill in the art would have recognized that such a temperature would also be applicable to other enzymes, such as proteinase K1.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
Claims 12-15 are free of prior art as the combination of the specific buffer combination with the concentration of SDS is not deemed to be an obvious combination of reagents and their concentration for an assessment of DNA copy number of viral genome from a viral vector via ddPCR.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
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/YOUNG J KIM/Primary Examiner
Art Unit 1637 October 14, 2026
/YJK/
1 See Peper et al., “[p]roteinase K (PK) … is a nonspecific aminopeptidase with a typical pH working range of 7.4-8 and a temperature optimum between 37 and 60oC …”, page 123); also “PK was inactivated by 10 min incubation at 95oC”, page 124, 1st column.
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