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 .
Election/Restrictions
Applicant’s election without traverse of Group I (claims 1-11) and the species of single-stranded DNA and recombinant adeno-associated virus in the reply filed on 11/5/2025 is acknowledged.
Claim Status
Claims 1-11 and 18-26 are pending.
Claims 18-26 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 11/5/2025.
Claims 1-11 are being examined on the merits.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement (see paragraphs [0055, 0079, and 0084] for examples). 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The use of the terms “QIAquick” (paragraph [0048]), “FAM” and “Texas Red” (paragraph [0106]), and “SYBR” (paragraph [0154]), which are trade names or marks used in commerce, have been noted in this application. These terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The examples above are not an exhaustive list of unmarked trade names or marks used in commerce throughout the specification. Please carefully read through and properly notate each instance.
Claim Objections
Claims 4 and 6 are objected to because of the following informalities:
Claim 4 reads “using information about a total number of particles in the fluid sample without assaying the particle protein in the sample” and should read “using information about a total number of particles in the fluid sample without assaying the particle protein in the fluid sample”. This maintains consistency of the claim terms (fluid sample vs. sample) throughout the claim.
Claim 6, line 10, reads “whereby the labeled extracted proteins are separated according to size by flowing the extracted proteins” and should read “whereby the labeled extracted proteins are separated according to size by flowing the labeled extracted proteins” to maintain claim term consistency.
Claim 6, line 17, reads “thereby determining an amount of protein in the sample” and should read “thereby determining an amount of protein in the fluid sample” to maintain claim term consistency.
Appropriate correction is required.
Claim Rejections - 35 USC § 112b - Indefiniteness
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 1-11 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 1 recites the limitation "the detectable nucleic acid label" in line 11-12 and “the detectable label” in lines 16 and 20. There is insufficient antecedent basis for this limitation in the claim. Lines 7-8 recite “labeling the extracted recombinant nucleic acids, producing labeled extracted recombinant nucleic acids”, but does not state what the nucleic acids are labeled with. To clear up this lack of antecedent basis, the labeling step could be amended to read “labeling the extracted recombinant nucleic acids with a detectable nucleic acid label, producing labeled extracted recombinant nucleic acids”. Additionally, “the detectable label” should be amended to specify “the detectable nucleic acid label” to avoid confusion with the detectable label used in claim 6 for detecting proteins.
Claim 1 recites the limitation “comparing a) to a reference standard representative of full particles and, based on the comparison, determining a ratio of full particles to partially full particles, producing a first assay result and/or comparing b) to a reference standard representative of full particles and, based on the comparison, determining a ratio of full particles to empty particles in the fluid sample, producing a first assay result”. It is unclear if the “first assay result” generated would be a combination of the comparisons of both a) and b), or if the comparison performed in a) would be the first assay result, and if the comparison b) is also performed if this would technically be a “second” assay result. For purposes of examination “a first assay result” encompasses: comparison of a), OR comparison of b), OR comparison of a) AND comparison of b) both. However, clarification on the record is required.
Claims 2-11 depend from claim 1, inherit these deficiencies, and are rejected on the same basis.
Claim 2 recites the limitation “introducing the extracted recombinant nucleic acids into a well and/or microchannel of a microfluidic device”. It is unclear how a feature of a microfluidic device could be both a well AND a microchannel. Clarification is required.
Claim 6 recites the limitation "the detectable label" in lines 8-9, 12, and 14. There is insufficient antecedent basis for this limitation in the claim. Lines 4-5 recite “labeling the extracted proteins of the particles, producing labeled extracted proteins of the particles”, but does not state what the proteins are labeled with. To clear up this lack of antecedent basis, the labeling step could be amended to read “labeling the extracted proteins of the particles with a detectable protein label, producing labeled extracted proteins of the particles”. Additionally, “the detectable label” should be amended to specify “the detectable protein label” to avoid confusion with the detectable nucleic acid label used in claim 1 for detecting nucleic acids.
Claim 6 recites the limitation “comparing the first assay result and the second assay result”, however it is unclear which first assay result would be used to compare to the second assay result. As discussed in the rejection of claim 1 above, the scope of what constitutes a “first assay result” is unclear and therefore needs to be defined. As such, it is unclear in this claim what the “first assay result” is that is being compared to the second assay result. Clarification is required.
Claim 6 recites the limitation "the population of recombinant viral particles" in line 23. There is insufficient antecedent basis for this limitation in the claim. Claim 6 depends from claim 1, which only defines “a population of particles”. No structure of the particles has been defined as “viral” or otherwise. Therefore, this limitation lacks antecedent basis and the scope of the claim is unclear.
Claim 7 depends from claim 6, inherits these deficiencies, and is rejected on the same basis.
Claim 7 recites the limitation “introducing the extracted proteins of the particles into a well and/or microchannel of a microfluidic device”. It is unclear how a feature of a microfluidic device could be both a well AND a microchannel. Clarification is required.
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.
Claims 1-3, 5, and 8-10 are rejected under 35 U.S.C. 103 as being unpatentable over Wu (Wu et al., US 2023/0126263 A1; EFD of 9/3/2021) in view of Hutanu (Hutanu et al., Electrophoresis 2021) and Park (Park et al., WO 2005/068993 A1; cited on IDS of 10/3/2023).
Regarding claim 1: Wu teaches a method of characterizing fluid samples containing particles to determine a ratio of full particles to empty particles in the fluid sample (Abstract). Wu teaches applying a sample containing particles to a capillary containing a separation matrix, labeling the target component (such as nucleic acid) with a selective binding agent (which can be added before or after separation (paragraph [0056]), detecting a signal and determining the quantity/characteristic of the nucleic acid based on the migration through the separation matrix (paragraphs [0005-0006, 0025]). Wu teaches that the nucleic acid can be recombinant nucleic acid within a viral particle such as adeno-associated virus (paragraphs [0022 and 0023]). Wu teaches comparing the data obtained from a test sample of particles to data obtained from a sample with known proportions of full/empty particles (Abstract). This allows for the establishment of a relationship between nucleic acid content and proportions of particles in a “full” state which allows for prediction of proportions of particles in full, partial, and empty states in particles of an unknown state (Abstract, paragraph [0019]). Comparison of the test sample to a reference standard representative of full particles allows for determining of the ration of full particles to partially full particles to produce a first assay result and characterize the population of particles in the fluid sample. Wu teaches that multiple aliquots can be obtained from the same sample to run samples through two different analyses, one targeting nucleic acid and the other protein (paragraph [0054]).
Wu does not teach extracting the recombinant nucleic acids from the first aliquot of the sample or flowing the sample through a polymeric separation medium within the microchannel to separate the labeled nucleic acids by size and characterizing the nucleic acids by the time it takes to flow through the polymeric separation channel. However, extraction of recombinant nucleic acids from viral particles to characterize the nucleic acid sizes by time it takes to travel through a polymeric separation medium is known in the art, as taught by Hutanu.
Hutanu teaches using capillary gel electrophoresis to characterize nucleic acids from viral particle samples (3.3 Capillary gel electrophoresis). Hutanu teaches application of nucleic acids from viral particles to a separation matrix comprised of 1% PVP (a polymeric separation medium) and SYBR-Green II (for labeling the nucleic acid; 3.3 Capillary gel electrophoresis). Hutanu teaches that for proper size distinction by gel electrophoresis, the nucleic acid needs to be released from the virus (3 Results and discussion) and could be achieved using the QIAquick PCR purification kit (2 Materials and methods – CGE). Hutanu teaches determining the size of the nucleic acids by the time it takes to travel through the separation medium and comparison to known size standards (Figure 3).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Wu with the size separation medium as taught by Hutanu. One would be motivated to characterize nucleic acids according to size given the assertion by Hutanu that with CGE “is possible to separate all DNA size species, depending on their sequence length and conformation” and “quantify by signal intensity using an appropriate reference standard” (3.3 Capillary gel electrophoresis). Additionally, Hutanu demonstrates that the resolution that can be achieved with CGE allows for determination of improperly filled viral particles as well (fragments or over fill), which may not be possible with other methods (3.3 Capillary gel electrophoresis). One would have a reasonable expectation of success in using this methodology given that Wu teaches that their method can also be applied to information obtained from systems that employ capillaries with a separation matrix that separates nucleic acids by size based on voltage application (paragraph [0090]).
Wu in view of Hutanu does not teach flowing the labeled extracted recombinant nucleic acids from a polymeric separation medium in a microchannel into a detection region that is in fluid communication with said microchannel and which comprises a sensor capable of detecting a signal. However, microfluidic devices that allow for separation of nucleic acids through a separation medium in a microchannel that is in fluid communication with a detection region and a sensor is known in the art, as taught by Park.
Park teaches a method for spatially separating components in a sample using a microfluidic channel in a microfluidic device (Abstract). Park teaches applying analytes (such as nucleic acids or proteins) to a separation channel segment comprised of through separation media to affect migration of the analytes by size to resolve and identify/quantitate them (pg 3, ln 19; pg 4, ln 14-21). Separation channel segment reads on polymeric separation medium in a microchannel (pg 4, ln 14-21; pg 20, ln 19-21; pg 24, ln 15-25). Park teaches a detection region in fluid communication with the microchannel containing the polymeric separation medium (pg 37, ln 26-27) in which there is a sensor that can detect a signal from a nucleic acid or protein which has been labeled as they exit the polymeric separation medium (pg 4, ln 23-26; pg 8, ln 14-18; pg 22, ln 1-2; pg 37, ln 26-27). Park teaches determining an amount of time taken by the labelled nucleic acids to flow through the polymeric separation medium in the microchannel into the detection region, which is indicative of the size of the nucleic acids in the fluid sample (pg 24, ln 15-25 and pg 25, ln 18-25).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have performed the method of Wu in view of Hutanu with the microfluidic device as taught by Park. One would be motivated to do so given the assertion by Park that their system provides “highly repeatable analytical results with high sensitivity, speed and resolution” (pg 3, ln 9-10 and pg 11, ln 25-28). One would have a reasonable expectation of success given that Park teaches application of nucleic acids to a microfluidic channel that contains a separation medium such as polyvinylpyrrolidone (PVP, as used in Hutanu; pg 24, ln 22).
Regarding claim 2: Hutanu teaches that the polymeric separation medium comprises SYBR Green II, which binds to the nucleic acids upon introduction to the capillary (or microchannel) and produced labeled extracted nucleic acids (3.3 Capillary gel electrophoresis).
Regarding claim 3 and 5: Wu teaches determining amount of particle protein in a sample taken from a second aliquot by assaying the particle protein (paragraph [0054]).
Regarding claim 8 and 9: Wu teaches that the nucleic acid can be recombinant nucleic acid within a viral particle such as adeno-associated virus (paragraphs [0022 and 0023]). Wu teaches that recombinant AAVs contain plasmids up to 5kb in length (reads on single -stranded DNA genome in the range of 500-7000 nucleotides in length; paragraph [0023]).
Regarding claim 10: Hutanu teaches that there is good correlation in capillary electrophoretic methods between the fluorescence signal and the virus concentration when particles are in the range of 10^11 to 10^13 GC/mL and demonstrated results of an electropherogram of AAV samples at 10^13 viral particles per mL (Figure 4 and 3.4 Capillary zone electrophoresis).
Claims 4 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Wu (Wu et al., US 2023/0126263 A1; EFD of 9/3/2021) in view of Hutanu (Hutanu et al., Electrophoresis 2021) and Park (Park et al., WO 2005/068993 A1; cited on IDS of 10/3/2023) as applied to claims 1-3, 5, and 8-10 above, and further in view of Luo (Luo et al., LCGC Supplements, 2020).
The teachings of Wu in view of Hutanu and Park as they apply to claims 1 and 3, from which claims 4 and 11 depend, are detailed above. Relevant to the instantly rejected claims, Wu in view of Hutanu and Park teach a method of characterizing particles in a fluid sample through size separation polymeric medium within a microchannel of a microfluidic device. Wu in view of Hutanu and Park teach that the nucleic acid has to be extracted from the particles for accurate analysis in a polymeric separation medium.
Wu in view of Hutanu and Park do not teach determination of total number of particles in a fluid sample without assaying a particle protein in the fluid sample (claim 4) and they do not teach that the nucleic acid is extracted by contacting particles with a proteinase and a denaturing agent (claim 11). However, determination of a total number of particles in a fluid sample without assaying a particle protein in the fluid sample, and extraction of nucleic acid by proteinase and denaturing agents is known in the art, as taught by Luo.
Luo teaches determination of AAV viral integrity through analysis of nucleic acids within the AAV particles using capillary gel electrophoresis methods (Abstract). Luo teaches contacting the samples with proteinase K (a proteinase) and a denaturing agent (Abstract guanidine-hydrochloride; guanidinium chloride is identified as a denaturing agent in paragraph [0097] of the instant specification). Luo teaches using capillary gel electrophoresis to determine the amounts and purities of nucleic acids in viral samples (Abstract). Luo teaches that the measuring of peak area differences between known “full” and known “empty” capsid samples may offer a titer determination perspective (thus not requiring measurement of protein amounts in the sample to determine the total number of particles in the sample (Analysis of the Origin of Impurities, paragraph 2 and Conclusions).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Wu in view of Hutanu and Park with that of Luo. One would be motivated to perform proteinase and denaturing treatment on the particles to extract nucleic acids given the assertion by Luo that this method is recommended for “in-depth impurity analysis” (Conclusion). Additionally, one would be motivated to determine the total number of particles in the fluid sample without assaying particle protein through the measurement of signal intensities under peaks of nucleic acid sizes and comparing to known samples with known concentrations given that this would obviate the need for an extra step of protein measurement in the sample (Analysis of the Origin of Impurities). One would have a reasonable expectation of success given that Luo demonstrates the successful size separation of extracted nucleic acids from viral particles in a capillary gel electrophoresis method.
Claims 6 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Wu (Wu et al., US 2023/0126263 A1; EFD of 9/3/2021) in view of Hutanu (Hutanu et al., Electrophoresis 2021) and Park (Park et al., WO 2005/068993 A1; cited on IDS of 10/3/2023) as applied to claims 1-3, 5, and 8-10 above, and further in view of Zhang (Zhang et al., Human Gene Therapy 2021).
The teachings of Wu in view of Hutanu and Park as they apply to claims 1-3, 5, and 8-10 are detailed above. Relevant to the instantly rejected claims, Wu in view of Hutanu and Park teach a method of characterizing particles in a fluid sample through size separation polymeric medium within a microchannel of a microfluidic device. Wu in view of Hutanu and Park teach methodologies for size dependent separation of labeled proteins for characterization of protein compositions of samples (and specifically protein compositions of particle samples in Wu; Wu: paragraphs [0025, 0027, and 0054]; Park: pg 3, ln 19, pg 24, ln 15-25).
Regarding claim 6: Wu in view of Hutanu and Park teaches a second aliquot of fluid sample in which proteins of particles are analyzed by flowing through a polymeric separation medium in a microchannel into a detection region with a sensor capable of detecting a signal from labeled protein that are separated according to size (Wu: paragraphs [0006, 0025, 0027, and 0054] Park: pg 4, ln 14-21, pg 8, ln 21, pg 20, ln 19-21, pg 25, ln 18-25). Park teaches determining an amount of time taken by the labelled proteins to flow through the polymeric separation medium in the microchannel into the detection region, which is indicative of the size of the proteins in the fluid sample (pg 24, ln 15-25 and pg 25, ln 18-25). Wu teaches quantitating the amount of protein in the sample by analyzing the area under the curve associated with signal to quantitate amounts of protein in the sample (paragraph [0054]). Wu teaches comparing measurements to known references standards to determine the amount of protein in the sample to produce a second assay result (paragraph [0088]). Wu teaches comparing the first assay result (nucleic acid) to the second assay result (protein), to determine a ratio of full viral particles to empty viral particles in the fluid sample, thus characterizing the population of recombinant viral particles in the fluid sample (paragraph [0088]).
Wu in view of Hutanu and Park do not explicitly teach extracting the proteins from the population of particles. However, extracting proteins from a population of particles in order to perform size separation analysis is known in the art, as taught by Zhang.
Zhang teaches extracting proteins from AAV fluid samples for analysis via capillary gel electrophoresis in order to determine the size separation (composition of proteins in the viral particles) and the relative peak sizes for protein abundance (Abstract and Experimental - CE-SDS LIF sample preparation; Figure 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Wu in view of Hutanu and Park with that of Zhang. One would be motivated to do so given the assertion by Zhang that the practice of extracting the proteins from the sample is well-known and routinely practiced in the art (Introduction, paragraph 2). One would have a reasonable expectation of success given that Zhang successfully extracts proteins from fluid particle samples for separation via capillary gel electrophoresis.
Regarding claim 7: Wu teaches binding of detectable labels to proteins in the separation channel (paragraphs [0006, 0056]).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
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/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683