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 .
Claims Summary
Claim 1 is directed to a method for characterizing genome integrity comprising:
Incubating at least one biomolecule comprising nucleic acid with a chaotropic agent; the biomolecule is viral vector (claim 3) that is a genome, plasmid fragment contamination, and/or DNA fragment contamination from a host cell DNA (claim 4), or a retrovirus (claim 5), specifically a lentivirus (claim 6), or a recombinant lentivirus (claim 7); the chaotropic agent is a denaturing agent (such as guanidium thiocyanate, among others (claim 15)), or lysis buffer (claim 14);
Extracting the nucleic acids from the biomolecule, using spin column-based purification for solid phase extraction (claim 17);
Diluting the nucleic acids; the nucleic acids are diluted using water and/or sample solution (claim 19), wherein the sample solution is sample loading solution or formamide (claim 20);
Heating the nucleic acids to denature the nucleic acids;
Loading the denatured nucleic acids onto a capillary electrophoresis (CE) capillary, wherein the capillary is filled with a buffer comprising a polymer matrix; the polymer matrix is crosslinked polymer, among others (claim 28); the polymer matrix comprises a fluorescent dye (claim 29);
Applying a separation voltage to the capillary to separate the denatured nucleic acids; and
Detecting at least one nucleic acid genome separated from the denatured nucleic acids with a detector
The method further comprises incubating the biomolecule with a carrier molecule (claim 9), such as a carrier RNA, among others (claim 10). Prior to that, the biomolecule is treated with an enzyme (claim 11), such as ribonuclease, among others (claim 12).
Claims 35, 36 and 39 are directed to intended uses of the claims. Claims 35 and 36 are directed to the intended use of the method in a multi-capillary electrophoresis system workflow. Claim 39 is directed to the intended use of the method for titer determination of a viral product, and/or determination of percent of full capsids in viral product or complete lentiviral particles.
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.
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, 3, 4, 11, 12, 14, 15, 19, 20, 28, 35, 38 and 39 are rejected under 35 U.S.C. 103 as being unpatentable over Skeidsvoll et al. (Electrophoresis, 1996, 17:1512-1517, “Skeidsvoll”) in view of Hadd and Jovanovich (WO 01/09389 A2, “Hadd”, of record in the IDS filed 5/31/2024) and Azizi et al. (Anal. Chem., 2012, 84(21):9585-9591, “Azizi”). The claims are summarized above and correlated with the teachings of the prior art in bold font below.
Skeidsvoll discloses analysis of RNA (100-2000 bases) by capillary electrophoresis (CE). The human glioma cell line, GaMg, is exposed to TRIzol™ (which comprises guanidinium thiocyanate) to extract total RNA (see page 1513, left column, top paragraph, last sentence) (claim 1, aspects of chaotropic agent and nucleic acid extraction, claim 14 and 15). The RNA is dissolved in EDTA buffer, diluted in formamide and heated to completely denature the nucleic acids (see page 1513, left column, top paragraph, last sentence) (claim 1, aspect of dilution and heating, claims 19 and 20). Samples are then injected into the capillary which is filled with separation buffer comprising urea and HPMC (hydroxypropylmethylcellulose, a linear polymer matrix) (see section 2.4) (claim 1, aspect of capillary filled with polymer matrix, claim 28). The samples are then subjected to electroseparation under separation voltage and RNA detected using a UV absorbance detector (see section 2.4 and Figure 1) (claim 1, aspects of separation and detection).
Skeidsvoll does not disclose genome characterization from a viral vector, such as a nucleic acid genome, plasmid fragment contamination and/or DNA fragment contamination from a host cell DNA. Skeidsvoll’s method is a proof-of-principle exemplification, thus one would have been motivated to apply the method to other sources of RNA, for example, such as viral RNA, with a reasonable expectation of success. Hadd’s CE method comprises obtaining nucleic acid from a DNA or RNA virus, for example, and mixing it with a chaotropic agent to denature the nucleic acid, such as guanidine thiocyanate, among other options (see page 24, line 12 through page 25, line 30, and page 26, lines 19-31) (claims 14 and 15). Azizi discloses viral quantitative capillary electrophoresis (CE) with laser-induced fluorescent detection to separate intact virus particles from DNA (residual host cell DNA) and RNA impurities, and for counting and quality control of RNA viruses (see abstract) (claim 1, aspect of genome integrity, claims 3 and 4). Azizi exemplifies the method using vesicular stomatitis virus (VSV, negative strand RNA virus), chosen because of its therapeutic oncolytic capabilities as well as its use as a shuttle vector (see page 9586, left column, last full paragraph). VSV is propagated in Vero cells which are then lysed via incubation with RNase A (endoribonuclease) and heated. Fluorescent dye is diluted in buffer and then added to the samples (see page 9586, “Chemicals and Materials”, and “Preparation of rRNA and DNA Standards, Virus Lysis, RNase A, and NaOH Treatments”) (claims 11 and 12).
As outlined above, it would have been obvious to have applied Skeidsvoll’s proof-of-principle method to other sources of RNA, such as RNA from viruses (viral genomes), residual host cell DNA and RNA impurities, as is taught by Hadd and Azizi in their CE methods, respectively.
With regard to claims 35, 38 and 39, these methods are directed to intended uses of the method. Claims 35 and 36 are directed to the intended use of the method in a multi-capillary electrophoresis system workflow. Claim 39 is directed to the intended use of the method for titer determination of a viral product, and/or determination of percent of full capsids in viral product or complete lentiviral particles. Claims 35 and 36 are directed to the intended use of the method in a multi-capillary electrophoresis system workflow. Claim 39 is directed to the intended use of the method for titer determination of a viral product, and/or determination of percent of full capsids in viral product or complete lentiviral particles. According to the MPEP 2111.02(II), intended uses in the preamble of the claims must be evaluated to determine whether or not the recited intended use results in a manipulative difference between the claimed invention and the prior art. In this case, since the prior art is useful for CE methods, and the intended uses are for CE methods (Skeidsvoll, Hadd and Azizi) and titer determination of a viral product (Azizi), then there is no manipulative difference between the claimed invention and the prior art.
Therefore, the claimed embodiments would have been obvious to one of ordinary skill in the art before the filing date of the claimed invention.
Claims 5-7 are rejected under 35 U.S.C. 103 as being unpatentable over Skeidsvoll et al. (Electrophoresis, 1996, 17:1512-1517, “Skeidsvoll”) in view of Hadd and Jovanovich (WO 01/09389 A2, “Hadd”, of record in the IDS filed 5/31/2024) and Azizi et al. (Anal. Chem., 2012, 84(21):9585-9591, “Azizi”), as applied to claim 1 above, and further in view of Poeschla et al. (US 2001/0016347 A1, “Poeschla”). Claim 5-7 are directed to embodiments wherein the viral vector is a retrovirus, specifically a lentivirus.
Skeidsvoll discloses RNA viruses generally, but does not teach retroviruses, specifically lentiviruses. However, it would have been obvious to have applied Skeidsvoll’s method to lentiviral vectors, such as those taught by Poeschla. One would have been motivated by Poeschla’s teaching that non-primate lentiviral recombinant vectors are a safer alternative to murine retroviral vectors (see paragraph [0004]). One would have had a reasonable expectation of success since lentiviruses are RNA viruses. Therefore, the claimed embodiments would have been obvious to one of ordinary skill in the art before the filing date of the claimed invention.
Claims 9 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Skeidsvoll et al. (Electrophoresis, 1996, 17:1512-1517, “Skeidsvoll”) in view of Hadd and Jovanovich (WO 01/09389 A2, “Hadd”, of record in the IDS filed 5/31/2024) and Azizi et al. (Anal. Chem., 2012, 84(21):9585-9591, “Azizi”), as applied to claim 1 above, and further in view of Ginsberg et al. (US 2003/0186237 A1, “Ginsberg”). Claims 9 and 10 are directed to embodiments wherein the nucleic acid is incubated with a carrier molecule, such as glycogen.
Skeidsvoll does not disclose incubating the nucleic acid with a carrier molecule. However, it would have been obvious to have done so with a reasonable expectation of success. Ginsberg discloses treatment of RNA-containing cells with RNA extraction reagents, such as TRIzol™ (which comprises guanidinium thiocyanate), along with the use of an inert carrier, such as glycogen, to maximize RNA precipitation (see paragraph [0115]). In view of Ginsberg’s teachings, one would have been motivated to include glycogen in Skeidsvoll’s method in order to improve RNA precipitation, with a reasonable expectation of success. Therefore, the claimed embodiments would have been obvious to one of ordinary skill in the art before the filing date of the claimed invention.
Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Skeidsvoll et al. (Electrophoresis, 1996, 17:1512-1517, “Skeidsvoll”) in view of Hadd and Jovanovich (WO 01/09389 A2, “Hadd”, of record in the IDS filed 5/31/2024) and Azizi et al. (Anal. Chem., 2012, 84(21):9585-9591, “Azizi”), as applied to claim 1 above, and further in view of Conrad et al. (US 2005/0059054 A1). Claim 17 is directed to an embodiment wherein nucleic acid extraction is via spin column-based purification.
Skeidsvoll does not disclose solid phase extraction of nucleic acids via spin column-based purification prior to dilution. Hadd discloses processing of nucleic acids by spin filtration but does not disclose specifically column-based spin (see page 5, line 7 to page 6, line 2). It would have been obvious to have used any known method for spin filtration, including spin columns for RNA extraction from samples, as disclosed in Conrad (see paragraph [0072]). One would have been motivated to use column-based spin because it is a recognized method of extraction and purifying nucleic acid from samples. One would have had a reasonable expectation of success since Hadd suggests spin filtration. Therefore, the claimed embodiment would have been obvious to one of ordinary skill in the art before the filing date of the claimed invention.
Claim 29 is rejected under 35 U.S.C. 103 as being unpatentable over Skeidsvoll et al. (Electrophoresis, 1996, 17:1512-1517, “Skeidsvoll”) in view of Hadd and Jovanovich (WO 01/09389 A2, “Hadd”, of record in the IDS filed 5/31/2024) and Azizi et al. (Anal. Chem., 2012, 84(21):9585-9591, “Azizi”), as applied to claim 1 above, and further in view of Shen et al. (Biologicals, 2013, 41:201-208, “Shen”, of record in the IDS filed 5/31/2024). Claim 29 is directed to an embodiment wherein the polymer matrix comprises a fluorescent dye.
Khedival does not disclose the use of a fluorescent dye. It would have been obvious to have modified Skeidsvoll’s method to include laser-induced fluorescent detection, including adding a dye to the polymer matrix. One would have been motivated by Shen’s disclosure of the advantages of laser-induced fluorescent detection in combination with CE, including greater sensitivity and resolution, smaller samples, lower amounts of reagents, etc. (see Shen, page 201, right column, last paragraph). Azizi discloses the use of laser-induced fluorescent detection as well, using fluorescent dye (see abstract). In Shen’s method, fluorescent dye is added to the gel solution prior to addition of the nucleic acid sample (see page 202, section 2.3). One would have had a reasonable expectation of success given that laser-induced fluorescent detection and the use dyes added to the polymer matrix would work with Skeidsvoll’s method, which also uses CE. Therefore, the claimed embodiment would have been obvious to one of ordinary skill in the art before the filing date of the claimed invention.
Conclusion
No claim is allowed.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to Stacy B. Chen whose telephone number is 571-272-0896. The examiner can normally be reached on M-F (7:00-4:30). If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Thomas Visone, can be reached on 571-270-0684. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/STACY B CHEN/Primary Examiner, Art Unit 1672
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