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 .
Status of the Claims
It is acknowledged that Applicant amended claims 42, 47, 60, and 65 and cancelled claims 61, 64, 66, and 67 in the response filed July 24, 2026.
Claims 42-45, 47, 48, 52-60, 62, 63, and 65 are currently pending and herein examined.
Summary of Response to Arguments
This action is in response to the papers filed July 24, 2026. Applicant's remarks and amendments have been fully and carefully considered and have been responded to in this office. Any new grounds of rejection presented in this Office Action are necessitated by Applicant's amendments. Any rejections or objections not reiterated herein have been withdrawn. This action is made FINAL.
As a result of amendments to and cancellation of the appropriate claims, the rejections under 35 U.S.C. 112(a) and 35 U.S.C. 112(b) and the duplicate claim warnings have been withdrawn.
Regarding claim interpretation under 35 U.S.C. 112(f), Applicant persuasively argued that the term ‘amplification oligomer,’ as read in light of the specification (par. 141, 146), would be understood a person with ordinary skill in the art to provide structure necessary for the function “to amplify a target region of the nucleic acid.” Therefore, the notice of claim interpretation under 35 U.S.C. 112(f) has been withdrawn.
Regarding rejections under 35 U.S.C. 103, amendments to the claims have necessitated new grounds of rejection, which are set forth below. A detailed response to Applicant’s arguments concerning these rejections are set forth on pg. 10-14 of this office action.
Priority
It is acknowledged that the instant application is a 371 of international PCT Application No. PCT/US2022/035456, filed June 29, 2022, and that it claims benefit of provisional 63/217,560, filed July 1, 2021. The effective filing date is considered to be July 1, 2021.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 42-45, 47, 48, 52-57, 59, 60, 62, 63, and 65 are rejected under 35 U.S.C. 103 as being unpatentable over Beckers et al. (published Oct 20, 2011; Patent Application Publication US 2011/0256592), in view of Lundin et al. (published Jan 6, 1998; US Patent No. 5,705,345), Mhlanga et al. (published Dec 2001; Mhlanga et al. Methods. 2001 Dec;25(4):463-71), and Mauch et al. (published Sept. 19, 2019; Patent Application Publication US 20190284604 A1).
These rejections have been revised and updated in response to claim amendments filed July 24, 2026.
Regarding claim 42, Beckers recites providing a sample containing or suspected of containing a target nucleic acid (par. 25). Beckers recites contacting the sample with an aqueous mixture comprising at least one polymerase (par. 29), α-cyclodextrin (par. 26, 29, 43), polysorbate 20 (par. 78), at least one buffering agent (par. 29), nucleotide triphosphates (par. 29), at least one cofactor (par. 78), and at least one amplification oligomer configured to amplify a target region of the target nucleic acid (par. 29: “primers”). Beckers teaches using the reaction mixture to perform an in vitro nucleic acid amplification reaction, wherein the target nucleic acid, if present in the sample, is used as a template for generating one or more amplicons corresponding to the target region (par. 28-31, 56).
Regarding the concentrations required in claim 42, Beckers teaches that α-cyclodextrin is present at a concentration of 0.1 mM to 50 mM in the reaction mixture (par. 40). Given an approximate molar mass of α-cyclodextrin of 972.84 g/mol, the concentration of α-cyclodextrin is recited at a concentration of between 0.1 mg/mL and 50 mg/mL, which overlaps the range of “from about 5 mg/mL to about 20 mg/mL” with sufficient specificity that the limitation is considered to have been met. Beckers recites that polysorbate 20 (or Tween-20) is present in 10xPCR buffer at 0.1% (par. 79), meaning that polysorbate 20 would be present at 0.01% in the reaction mixture, which falls within the range of from about 0.001% to 0.025% required by the claim.
Regarding claims 43 and 45, Beckers recites detecting one or more amplicons and detecting performed in real time (par. 56). In this case, Beckers recites that the method of nucleic acid amplification can include real-time PCR, which is by definition a method of detecting nucleic acid amplification products (amplicons) throughout the amplification reaction (in real time).
Regarding claims 44 and 62-63, Beckers recites that the method of nucleic acid amplification can include real-time PCR using labeled probes such as molecular beacons (par. 56). Real-time PCR is a method of detecting amplicons in real-time, as discussed for claim 43. As evidenced by Mhlanga, molecular beacons are detection probe oligomers configured to specifically hybridize to a target sequence contained in one or more amplicons, and which comprise a fluorescent label and a non-fluorescent quencher (Mhlanga: pg. 464 – Description of Method). Therefore, the limitations of claims 44 and 62-63 are considered to have been met.
Regarding claims 48 and 59, Beckers recites that the aqueous mixture further comprises a lyoprotectant (par. 78: “trehalose”), and that the aqueous mixture is reconstituted from a lyophilized formulation (par. 77).
Regarding claim 52, Beckers recites that the α-cyclodextrin is present in the reaction mixture at a concentration of between 0.1 mg/mL and 50 mg/mL, as discussed for claim 42. This overlaps the claimed range of from about 8 mg/mL to about 15 mg/mL with sufficient specificity that the limitation is considered to have been met.
Regarding claim 53, Beckers recites that the polysorbate 20 is present in the reaction mixture at a concentration of 0.01% (par. 79), as discussed for claim 42. This falls within the range of from about 0.0015% to 0.015% required by the claim.
Regarding claim 54, Beckers teaches at least two amplification oligomers configured to amplify the target region of the nucleic acid (par. 29). Here, a broad reasonable interpretation of “at least two amplification oligomers configured to amplify the target region of the nucleic acid” includes the embodiment of a plurality of “primers”, as recited in Beckers.
Regarding claim 55, Beckers recites that the at least one polymerase is a DNA polymerase (par. 29).
Regarding claim 56, Beckers recites that the aqueous mixture comprises a reverse transcriptase and a DNA-dependent DNA polymerase (par. 50, 55). In an embodiment of Beckers invention where RNA is the target nucleic acid sequence (par. 55-56), the reverse transcriptase would be used to obtain the DNA template, and the DNA polymerase would be used to amplify the obtained DNA.
Regarding claim 57, Beckers recites the buffering agent Tris (par. 78) in the reaction mixture at a concentration of between 15 mM and 75 mM (par. 79). Note that Tris is recited in the 10x PCR buffer at a concentration between 150 mM and 750 mM, and would be present at 1x in the reaction mixture. The disclosed range overlaps the required concentration of from about 5mM to about 50 mM with sufficient specificity that the limitation is considered to have been met.
Regarding claim 59, Beckers recites that the aqueous mixture comprises trehalose (par. 78), which is a lyoprotectant as required by the claim.
Regarding claims 42, 47, and 65, Beckers does not explicitly teach whether the sample is extracted or containing at least one detergent which is anionic or SDS or LLS. However, Beckers does disclose the use of anionic detergents such as SDS for use as extractants before DNA amplification reactions (par. 13 – discussing the findings of Lundin et al. 1998).
Lundin teaches providing extracted samples containing at least one detergent, wherein the detergent is anionic, and wherein the detergent is SDS (col. 16-17: Example 4). These samples were subsequently neutralized with α-cyclodextrin and analyzed via PCR.
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Beckers and Lundin. One would have been motivated to do so in order to lyse cells and release nucleic acids for analysis (col. 20, claims 1-4), with a reagent which can be neutralized by α-cyclodextrin to prevent inhibition of amplification reactions (col 7, ln. 15-24).
Regarding claim 42, neither Beckers nor Lundin recites that the sample containing or suspected of containing the target nucleic acid constitutes at least 40% of the reaction mixture.
Mauch teaches that the relative volumes of reconstituted dried nucleic acid amplification components to sample may be from about 9.9/0.1 to 5/5 (par. 84). This would be the equivalent to samples volumes of approximately 0.01% to 50%.
It would have been obvious to a person with ordinary skill in the art, with reasonable expectation of success, to try optimizing the proportion of sample containing or suspected of containing the target nucleic acid to be at least 40% of the total reaction mixture. One would have been motivated to do so because the relative proportion of sample in amplification reactions is a known results effective variable, as demonstrated by Mauch. One would have had reasonable expectation of success because Mauch, Lundin, and Beckers all describe nucleic acid amplification reactions containing overlapping elements, such as detergents (Mauch: par. 79; Beckers: par. 13, 78; Lundin: col. 16, ln. 53-55) and lyophilized reagents (Beckers: par. 78, 129; Lundin: col. 4, ln 25-30).
Regarding claim 60, neither Beckers nor Lundin explicitly teach a concentration of trehalose within the range of about 0.1 M to about 0.2 M.
Mauch teaches the addition of trehalose to dried reaction mixtures at concentrations ranging between 0.04 M to 0.40 M (par. 58, 77).
It would have been obvious to a person with ordinary skill in the art, with reasonable expectation of success, to try optimizing the concentration of trehalose present in the reaction mixture to be within a range of about 0.01 M to about 0.2 M. One would have been motivated to do so because the concentration of trehalose in nucleic acid amplification reactions is a known results effective variable, as demonstrated by Mauch. One would have had reasonable expectation of success because Mauch’s range of concentrations overlaps with the claimed range.
Claim 58 is rejected under 35 U.S.C. 103 as being unpatentable over Beckers et al. (published Oct 20, 2011; Patent Application Publication US 2011/0256592), in view of Lundin et al. (published Jan 6, 1998; US Patent No. 5,705,345), Mhlanga et al. (published Dec 2001; Mhlanga et al. Methods. 2001 Dec;25(4):463-71), and Mauch et al. (published Sept. 19, 2019; Patent Application Publication US 20190284604 A1), as applied to claim 42 above, and further in view of Huggett et al. (published Aug 28, 2008; Huggett et al. BMC Res Notes. 2008 Aug 28;1:70).
These rejections have been revised and updated in response to claim amendments filed July 24, 2026.
Beckers, Mhlanga, Lundin, and Mauch teach the limitations of claim 42, as discussed above.
Regarding claim 58, Beckers, Lundin, and Mauch teach that the aqueous mixture comprises EDTA (Beckers: par. 78, 81; Lundin: Example 4; Mauch: par. 15). However, none of the combined references explicitly teaches a concentration of EDTA within the required range.
Huggett teaches concentrations of EDTA in nucleic acid amplification including 1.0, 1.25, 1.5, 2.0, 2.5, and 4.0 mM (pg. 3, col. 1: “Inhibitory samples”). While 4 mM EDTA was completely inhibitory to qPCR, lower concentrations produced varying degrees of inhibition in qPCR reactions (pg. 3-4: “Inhibition by ethylenediaminetetraacetic acid (EDTA)”; Figure 4).
It would have been obvious to a person with ordinary skill in the art, with reasonable expectation of success, to try optimizing the concentration of EDTA present in the reaction mixture to be within a range of about 0.025 mM to about 0.25 mM. One would have been motivated to do so because the concentration of EDTA in nucleic acid amplification reactions is a known results effective variable, as demonstrated by Huggett. One would have had reasonable expectation of success because Huggett shows that this range of EDTA concentrations has minimal adverse effect on PCR (Figure 4).
Response to Arguments
In the response mailed July 24, 2026, Applicant argued that neither Beckers nor Lundin taught the amended limitations of claim 42 (“wherein the sample containing or suspected of containing the target nucleic acid constitutes at least 40% of the reaction mixture.”) and that Lorenz teaches away from the claimed invention.
These arguments have been fully considered. However, as a result of the amendments to the claims, the modified rejections are based a different combination of references. These combined references teach all the limitations of claim 42. As Lorenz is no longer relied upon, arguments concerning that reference are considered to be moot.
Applicant argued that there is no motivation or suggestion in Beckers or Lundin that α-cyclodextrin could be used to mitigate the inhibitory effects of a detergent in an amplification reaction containing a substantially high volume of detergent-extracted sample (at least 40%, as recited in the claims).
This argument has been considered but is not found persuasive. In the modified rejections set forth above, Mauch teaches high volumes samples (>40% of the reaction volume) while explicitly contemplating the presence of detergents in the reaction mixture (including anionic detergents – see par. 79). Lundin teaches various relative concentrations of SDS and α-cyclodextrin in an extracted sample, holding sample proportion constant in the reaction mixture. As the claims do not specify any particular concentration of detergent in the extracted sample, and the combination teaches appropriately high proportions of sample in reaction mixtures with varying ratios of SDS to α-cyclodextrin/polysorbate-20, the Applicant has not demonstrated that a person with ordinary skill in the art would NOT be motivated arrive at the claimed invention.
Applicant argued that the claimed combination of α-cyclodextrin and polysorbate within an amplification reaction mixture show an unexpectedly superior and synergistic effect in mitigating the inhibition of polymerase activity observed in the presence of an extracting detergent. Applicant stated that Becker’s working examples were performed with β-cyclodextrin, treated polysorbate 20 as an optional component, and that Lundin’s Example 4 did not utilize a PCR containing Tween-20 (i.e. polysorbate-20). Thus, Applicant argued Beckers and Lundin do NOT demonstrate the benefit or combined effect of α-cyclodextrin and polysorbate-20 in mitigating the inhibitory effect of a detergent in an amplification reaction.
These arguments have been fully considered but are not found persuasive.
According to MPEP 716.02(b), the burden of establishing that results are unexpected and significant falls on the applicant. Applicants have to show unexpected results are in fact unexpected, unobvious, and of statistical and practical significance. According to MPEP 716.02(d), the objective evidence of non-obviousness must be commensurate in scope with claims. To establish unexpected results over a claimed range, applicants should compare a sufficient number of tests both inside and outside the claimed range to show the criticality of the claimed range. In re Hill, 284 F.2d 955, 128 USPQ 197 (CCPA 1960).
Applicant pointed to Example 1 of the specification (par. 182-185), where the following master mixes were used:
PNG
media_image1.png
278
464
media_image1.png
Greyscale
In this experiment, each of the master mixes were combined with sample eluate which had either been spiked with 100 mg/mL of SDS or not. The reactions consisted of 20µL master mix and 10µL sample (‘eluate’) for a total volume of 30µL. The results of the experiment are shown in Table 1 of the specification (par. 184-185). To summarize the results (see below): all tested master mix conditions were capable of supporting amplification when no SDS had been spiked into the sample eluate, and all master mixes EXCEPT the mix which lacked both α-cyclodextrin and polysorbate-20 (condition A) were similarly capable of supporting amplification in the presence of SDS. The results do not indicate the results of conditions D-F in the absence of SDS.
PNG
media_image2.png
136
670
media_image2.png
Greyscale
PNG
media_image3.png
164
673
media_image3.png
Greyscale
In this case, Applicant has not provided enough evidence to show that any unexpected results occurred over the whole range of α-cyclodextrin: 5-20 mg/mL and polysorbate-20: 0.001-0.025% (v/v). The Applicant has not provided a representative number of examples where concentrations below and above the claimed ranges were tested and compared to show that the results are of statistical and practical significance. Only one concentration of polysorbate-20 (0.025% v/v – at the top of the claimed range) was assessed in combination with α-cyclodextrin. Comparing conditions B and C, this concentration of polysorbate-20 produced similar results to those produced by compositions having concentrations of polysorbate-20 above the claimed range (holding α-cyclodextrin constant). Only one concentration of α-cyclodextrin within the claimed range (12.5 mg/mL) was used in combination with polysorbate-20. No valid comparisons of α-cyclodextrin concentrations within and outside of the claimed range are shown, as the other assessed concentration of α-cyclodextrin (50 mg/mL) was assessed in the absence of polysorbate-20. There are also no comparisons between β-cyclodextrin (as used in the working examples of Beckers) and the claimed α-cyclodextrin. Furthermore, regarding whether Beckers and Lundin supported the combination of α-cyclodextrin and polysorbate-20 (vs. optional polysorbate-20), please note that the instant specification also indicates that EITHER α-cyclodextrin or polysorbate-20 (conditions D-F) will allow for amplification in the presence of SDS. While the average Ct values of conditions D-F reported in Table 1 do appear to be larger than those of conditions B and C, it is not clear whether these differences are significant.
Thus, the results in the instant specification do not support the unexpected benefit of:
the use of α-cyclodextrin and polysorbate-20 at the claimed ranges (vs. the concentrations disclosed in Lundin and Beckers),
the use of α-cyclodextrin and polysorbate-20 (vs. polysorbate-20 and β-cyclodextrin), or
the use of α-cyclodextrin and polysorbate-20 in combination (vs. separately).
Modified rejections are set forth above.
Conclusion
No claims are 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 Christine M Jones whose telephone number is (571)272-2585. The examiner can normally be reached Monday - Friday, 8AM - 4PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at (571)272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
