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 .
Withdrawn Rejections
The rejection of claims 37 and 65 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, has been withdrawn in view of applicant’s amendments to the claims.
Claim Rejections - 35 USC § 112
New Rejection – Necessitated by Amendment
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.
Claim 69 is 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 69 recites that the sample/composition mixture “is used directly in a downstream process without replacing the composition”. It is not clear what is meant by this phrase. It is not clear how one can replace the “composition” once it is mixed with the sample.
The phrase "optionally" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(h).
The term optionally means “not required or mandatory”. For example, a composition comprising A, B, C, and optionally D means that component D can or cannot be present (D is not required to be present). In the rejected claims, however, it appears the use of “optionally” is an attempt to define “preferred” embodiments or limitations. For example, claim 37 states that the temperature is between “between about 4°C and about 100°C, optionally about 4°C, about 10°C, about 15°C, about 20°C, about 25°C, about 30°C, about 37°C, about 42°C, about 65°C, about 72°C, about 95°C, or about 100°C”. Further, claim 69 states that the composition is used in a downstream process, optionally nucleic acid extraction. In these instances, the term “optionally” does not make sense given the definition of optionally (not required or mandatory).
Claim Rejections - 35 USC § 102
New Rejection – Necessitated by Amendment
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 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 –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 32, 33, 35, 59 and 66-67 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Haydock et al. (U.S. Patent Application No. 2013/0122496; published May 16, 2013) and as evidenced by www.merriam-webster.com/dictionary/room temperature.
The instant claims are directed to a method of inactivating pathogens and stabilizing nucleic acids and/or proteins thereof contained within a sample suspected of containing a pathogen, the method comprising:
a) obtaining a sample suspected of containing a pathogen;
b) contacting the sample with a composition; and
c) incubating the sample contacted with the composition under conditions to allow for inactivation of pathogens and stabilization of nucleic acids and/or proteins,
wherein the composition in b) has a pH between about 6 and about 7 at about 20°C, and comprises:
i) about 2-6M of a chaotropic agent,
ii) about 0.01-0.1 M of a chelator,
iii) about 0.5%-3.0% of a detergent,
iv) about 0.02-0.1 M of a buffer, and
v) about 5%-40% of an alcohol,
wherein the composition does not comprise a reducing agent and wherein the composition does not comprise a mucolytic agent.
Haydock et al. teaches lysing a biological sample with a lysis buffer. In this regard, Haydock et al. states:
when cells are present within the biological sample they are lysed to provide a cell lysate from which the nucleic acid is extracted. A variety of methods of cell lysis are known in the art and are suitable for use within the invention. Examples of cell lysis methods include enzymatic treatment (using, for example, proteinase K, pronase, or Subtilisin), mechanical disruption (e.g., by Sonication, application of high pressure, use of a piezobuzzer device, or bead beating), or chemical treatment. (see paragraph [0032])
Suitable sources of biological samples include nasal swabs (see paragraph [0031]) [claim 33].
Haydock et al. further states that:
Lysing cells in the sample by treating them with a chaotropic salt solution is particularly advantageous. Methods and reagents for lysing cells using chaotropic salts are known in the art, and reagents can be purchased from commercial suppliers. Lysis is generally carried out between room temperature1 and about 95°C., depending on the cell type. (emphasis added) (see paragraph [0032])
The methods of Haydock et al. can be employed within point-of-care diagnostic assays to identify disease pathogens, and can be utilized in genetic screening (see paragraph [0046]).
Haydock et al. teaches a lysis/binding buffer is a solution of 6M Guanidine hydrochloride, 50 mM sodium citrate pH 6.0, 20 mM EDTA, 3% Triton X-100, and 10% Tween-20, which is combined at a ratio of one part buffer, one part sample, and one part ethanol to yield final concentrations of 2M Guanidine hydrochloride, 16.5 mM sodium citrate pH 6.0, 6.6 mM EDTA, 1% Triton X-100, 3.3% Tween-20, and 33% ethanol. This buffer is preferred for use with blood products and viral samples (see paragraph [0035]) [claims 35, 59].
Haydock et al. does not recite that the buffer contains a reducing agent or a mucolytic agent.
For claim 66, because the composition of Haydock et al. falls within the scope of the composition recited in claim 32, the method of Haydock et al. would stabilize the nucleic acids in the sample when the sample is stored at about 40C for up to about 270 days.
For claim 67, Haydock et al. teaches that lysis is generally carried out between room temperature2 and about 95°C., depending on the cell type.
Claim Rejections - 35 USC § 103
New Rejection – Necessitated by Amendment
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.
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.
Claim(s) 37, 60 and 61 are rejected under 35 U.S.C. 103 as being unpatentable over Haydock et al. (U.S. Patent Application No. 2013/0122496; published May 16, 2013) as applied to claims 32, 33, 35, 59 and 66-67 above.
The instant claims are directed to the method of claim 32 where the sample is incubated with the composition for specified times and at specified temperatures.
The teachings of Haydock et al. are outline above and incorporated herein. Haydock et al. teaches that lysis is generally carried out between room temperature and about 95°C. Regarding incubation times, in Example 5, Haydock et al. teaches lysing bacteriophage MS2 with the disclosed lysis buffer. In this example, the sample and lysis buffer were incubated for 20 minutes.
Given the state of the art, given the knowledge of one of ordinary skill in the art and given the teachings of Haydock et al., it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods taught by Haydock et al. and use any of the disclosed incubation times in the examples. One would have been motivated to do so and there would have been a reasonable expectation of success (to achieve maximum or efficient lysis of the cells to release nucleic acid).
For claims 60 and 61, Haydock et al. teaches a composition comprising each component except isopropanol. However, Haydock et al. further teaches that a C1 to C4 aliphatic alcohol, such as methanol, ethanol, isopropanol, or tert-butyl alcohol, can be included. Based on this teaching, it would be routine and well within the purview of one of ordinary skill in the art to use any of the recited alcohols (methanol, ethanol, isopropanol, or tert-butyl alcohol) as the alcohol in the lysis composition of Haydock et al. and the result would be predictable (lysis of the sample). Applicant has not demonstrated unexpected results for the recited alcohols.
As for the amounts in claim 61, determining effective dosages of each component in the lysis buffer is routine experimentation. Haydock et al. teaches the use of specific amounts of each component, including an alcohol. It is obvious and routine to determine the necessary amount of an agent that needs to be administered to achieve a desired effect. Further, applicant has not demonstrated unexpected results for the claimed amounts.
Furthermore, according to section 2144.05 of the MPEP, 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 re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). See also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 (“The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages.”)
Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claim(s) 65 and 68 are rejected under 35 U.S.C. 103 as being unpatentable over Haydock et al. (U.S. Patent Application No. 2013/0122496; published May 16, 2013) as applied to claims 32, 33, 35, 59 and 66-67 above, and further in view of Hearn et al. (Biochemistry And Molecular Biology Education, 2010, 38(3): 161–166), Panda et al. (J Parasit Dis, July-Sept 2019, 43(3):337–342) and Miltenyi Biotec (Homogenization of tissue for mRNA isolation, 2011).
The instant claim is directed to the method of claim 32 where the composition further comprises a foam suppressor (claim 65) such as Antifoam A (claim 68).
The teachings of Haydock et al. are outline above and incorporated herein. Haydock et al. does not teach including a foam suppressor in the lysis composition. However, Hearn et al. teaches that during DNA extraction higher concentrations of detergent such as SDS causes the lysis solution to foam and this causes problems when transferring the solution as DNA is left behind (see page 164, right column). Panda et al. teaches that during DNA extraction the addition of isoamyl alcohol removes any foam produced during lysis. Miltenyi Biotec teaches the use of Antifoam A to prevent excessive foam formation during sample homogenization for mRNA isolation.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods taught by Haydock et al. and include a foam suppressor, e.g., isoamyl alcohol or any other known anti-foaming agent such as Antifoam A, in the lysis composition, particularly since a detergent is present. One would have been motivated to do so and there would have been a reasonable expectation of success given the teachings of Hearn et al. [the presence of foam causes problems when transferring the lysed solution as DNA is left behind] and given the teachings of Panda et al. [Isoamyl alcohol is used to remove any foam] and Miltenyi Biotec [Antifoam A to prevent excessive foam formation during sample homogenization for mRNA isolation].
Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Response to Arguments
In the reply dated 5/15/2026, applicant argues that the amounts taught by Haydock et al. for sodium citrate and EDTA are below the claimed lower bounds of “about 0.02-0.1M” buffer and “about 0.01-0.1M” chelator, respectively. Applicant’s arguments have been fully considered and not found persuasive.
The recited amounts in claim 32 are preceded by the word “about”. The instant specification defines “about” as “a reasonable amount of deviation of the modified term such that the end result is not significantly changed. These terms of degree should be construed as including a deviation of at least ±5% of the modified term if this deviation would not negate the meaning of the word it modifies” (see paragraph [0041]).
It is the Office’s position that the amounts taught by Haydock et al. fall within the claimed amounts of “about 0.02-0.1M” buffer and “about 0.01-0.1M” chelator in view of the definition of “about” in the instant specification. The same argument applies to the ethanol concentration.
Applicant next argues that Haydock et al. does not teach a stand-alone aqueous molecular transport medium for directly contacting a sample. Applicant’s arguments have been considered and not found persuasive.
The claims are not directed to a stand-alone aqueous molecular transport medium for directly contacting a sample. The claims are directed to a method of inactivating a pathogen and stabilizing nucleic acid by contacting a sample with a composition comprising i) about 2-6M of a chaotropic agent, ii) about 0.01-0.1M of a chelator, iii) about 0.5%-3.0% of a detergent, iv) about 0.02-0.1M of a buffer, and v) about 5%-40% of an alcohol. The cited prior art teaches the claimed method.
For applicant’s arguments regarding claims 60 an 61, as outlined above, Haydock et al. teaches a composition comprising each component except isopropanol. However, Haydock et al. further teaches that a C1 to C4 aliphatic alcohol, such as methanol, ethanol, isopropanol, or tert-butyl alcohol, can be included. Based on this teaching, it would be routine and well within the purview of one of ordinary skill in the art to use any of the recited alcohols (methanol, ethanol, isopropanol, or tert-butyl alcohol) as the alcohol in the lysis composition of Haydock et al. and the result would be predictable (lysis of the sample). Applicant has not demonstrated unexpected results for the recited alcohols.
For the amounts recited in claim 61, determining effective dosages of each component in the lysis buffer is routine experimentation. Haydock et al. teaches the use of specific amounts of each component, including an alcohol, which were sufficient to lyse pathogens in the sample. It is obvious and routine to determine other workable or optimal amounts of an agent that needs to be administered to achieve a desired effect. Further, applicant has not demonstrated unexpected results for the claimed amounts.
Applicant next argues, for claim 65, that neither Hearn et al. nor Panda et al. teach or suggest adding a foam suppressor to the composition of Haydock et al. Hearn et al. teaches that teaches that during DNA extraction detergents such as SDS cause the lysis solution to foam and this causes problems when transferring the solution as DNA is left behind. Panda et al. teaches that isoamyl alcohol can reduce/suppress foaming, and the newly added reference Miltenyi Biotec teaches the use of Antifoam A to prevent excessive foam formation during sample homogenization for mRNA isolation. Thus, the combined teachings of these references provide motivation to add an antifoaming agent to the lysis composition of Haydock et al. with a reasonable expectation of success.
As for applicant’s hindsight arguments, MPEP § 2145(X)(A) states that “[a]ny judgement on obviousness is in a sense necessarily a reconstruction based on hindsight reasoning, but so long as it takes into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention was made and does not include knowledge gleaned only from applicant’s disclosure, such a reconstruction is proper.” In re McLaughlin 443 F.2d 1392, 1395, 170 USPQ 209, 212 (CCPA 1971). Here, the obviousness rejections take into account only knowledge which was within the level of ordinary skill in the art at the time the claimed invention was made and does not include knowledge gleaned only from applicant’s disclosure.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 Nicole Kinsey White whose telephone number is (571)272-9943. The examiner can normally be reached M to Th 6:30 am to 6:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Thomas Visone can be reached at 571-270-0684. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/NICOLE KINSEY WHITE/Primary Examiner, Art Unit 1672
1 Room temperature in Celsius is defined as a temperature of from 59° to 77°F (15-25°C) that is suitable for human occupancy and at which laboratory experiments are usually performed (see www.merriam-webster.com/dictionary/room temperature).
2 Room temperature in Celsius is defined as a temperature of from 59° to 77°F (15-25°C) that is suitable for human occupancy and at which laboratory experiments are usually performed (see www.merriam-webster.com/dictionary/room temperature).
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