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 .
DETAILED ACTION
1. The Applicant’s response to the office action filed on December 11, 2025 is acknowledged.
Status of the Application
2. Claims 1, 5-7, 9-10, 13, 24, 26, 29-31, 33-36, 38-39, 43-44, 46-53, 56-68, 70-79 are pending under examination. Claims 2-4, 8, 11-12, 14-23, 25, 27-28, 32, 37, 40-42, 45, 54-55, 69 were canceled. The Applicant’s arguments and the amendment have been fully considered and found persuasive for following reasons.
Claim Rejections - 35 USC § 103-maintained
3. 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.
Claims 1, 5-7, 9-10, 13, 24, 26, 29-31, 33-36, 38-39, 43-44, 46-53, 56-68 and 70-79 are rejected under 35 U.S.C. 103 as being unpatentable over Williams et al. (US 2009/0155123) in view of Cracauer et al. (US 2008/0261220) and Catanzariti et al. (US 5,786,182).
Williams et al. teach a method of claim 1, 79, performing a plurality of nucleic acid amplification assays in an automated analyzer, the method comprising the steps of: (a) and (b) loading the analyzer (automated liquid dispenser) with a plurality of sample-containing receptacles (holders, tubes, racks) and loading said analyzer with at least one container containing a first set of oligomers (primers) and at least one second container containing a second set of amplification oligomers, wherein first and second amplification each comprises PCR (para 0095-0132, 0140-0141, para 0166-0218, 0240-0251);
(c and d) assigning first and second amplification assays to be performed on a first set
of samples contained in one of the plurality of samples containing receptacles, the first amplification assay and a second amplification assay being lab developed test (molecular diagnostic assays) to be performed by the auto analyzer in accordance with a first set of assay parameters installed on the analyzer changeable by a user (para 0037-0038, 0094-0132, 0139, 0170-0174, 0240-0251);
(e) producing purified forms of the first and second samples by exposing each of the first and second samples to reagents and conditions adapted to isolate and purify a first analyte and a second analyte which may be present in the first and second samples, respectively (para 0144-0150, para 0175-0199);
(f) dissolving a first amplification reagent containing a polymerase and the first set of amplification oligomers, wherein the first amplification reagent is dissolved with a first solvent and wherein the first solvent does not contain an amplification oligomer or a polymerase (para 0050, 0151-0174, 0100-0124, 0084-0089, 0095-0096, 0213-0218);
(g) forming a first amplification reaction mixture with the purified form of the first sample and the first amplification reagent dissolved in step (f) wherein the first amplification reaction mixture contains a first set of amplification oligomers for amplifying a first region of the first analyte or a nucleic acid bound to the first analyte in a first nucleic acid amplification reaction of the first nucleic acid amplification assay (para 0050, 0151-0174, 0100-0124, 0084-0089, 0095-0096, 0213-0218);
(h) dissolving a second amplification reagent containing polymerase with a second solvent containing a set of amplification oligomers (para 0050, 0151-0174, 0100-0124, 0084-0089, 0095-0096, 0213-0218);
(i) forming a second reaction mixture with the purified for of the second sample and the second amplification reagent dissolved in step (h), wherein the second amplification reaction mixture contains a second set of amplification oligomers (primers) for amplifying a second region of the second analyte or a nucleic acid bound to the second analyte in a second nucleic acid amplification reaction of the second nucleic acid amplification assay (para 0151-0152, para 0200);
(j) exposing the first and second amplification reaction mixtures to thermal conditions for amplifying the first and second regions, respectively (para 0153, 0201); and (k) determining the presence or absence of the first and second analytes in the first and second amplification reaction mixtures, respectively wherein the method comprises one or more steps performed by the automated analyzer on at least one first sample and at least one second sample (para 0153-0157, 0201);
With reference to claims 5-6, 9, 48-49, Williams et al. teach that the method comprises identifying the assays to be performed using a touch screen or a keyboard and wherein one or more of the user-defined parameters are communicated to a controller of the analyzer using a touch screen or a keyboard; and wherein the user-defined parameters are used to process raw data generated by the analyzer during step (g) (para 0037-0052, 0139).
With reference to claim 7, 50-51, 57-59, Williams et al. teach that the plurality of sample-containing receptacles are supported by one or more receptacle-holding racks during step (a), and wherein the steps comprise reading machine-readable indicia (sample identification verifier) on the sample-containing receptacles or the receptacle-holding racks, the machine-readable indicia identifying which assays to perform (para 0077-0094-0138).
With reference to claim 10, 52, Williams et al. teach that the user-defined parameters each include a thermal profile, and wherein the thermal profiles of the first and second nucleic acid amplification reactions are the same or differ by at least one of number of cycles, time to completion, a denaturation temperature, an annealing temperature, and an extension temperature (para 0095-0096).
With reference to claim 13, 53, Williams et al. teach that the step (d) comprises immobilizing the first and second analytes on solid supports (para 0077, 0176-0200).
With reference to claims 23, 26, 29-31, 33, 57-61, Williams et al. teach that the first amplification reagent contains all oligomers necessary for performing the first nucleic acid amplification reaction, wherein the first and second amplification reagents, first and second solvents are stored and reconstituted in mixing wells (reaction chambers, vials or containers) of the same or different reagent packs, each reagent pack including multiple mixing wells which comprise one or more additional vials containing a solvent that contains a set of amplification oligomers, wherein the first solvent is a universal reagent, and container or reaction receptacles (wells) is fluidically connected to a sealed
fluid reservoir and access chamber (para 0151-0174, 0100-0124, 0084-0089, 0095-0096, 0213-0218).
With reference to claims 24, 56, Williams et al. teach that the first amplification reagent and the second amplification reagent each contain a detection probe (para 0151-0157).
With reference to claims 34-35, 62-63, Williams et al. teach that further comprising dispensing an oil into each of the first and second reaction receptacles prior to step (f) the step of closing each of the first and second reaction receptacles with a cap prior to step (f), the cap engaging the corresponding first or second receptacle in a frictional or interference fit (para 0220-0238, 0202-0218).
With reference to claims 36, 38, 64-65, 71, Williams et al. teach that the method further comprising the step of contacting the purified forms of the first and second samples with an elution buffer prior to step (e), such that the purified forms of the first and second samples are contained in first and second eluates, respectively, when forming the first and second amplification reaction mixtures and a step of centrifuging the closed first and second reaction receptacles prior to step (f), (para 0175-0200, 0124-0130, para 0229-0231).
With reference to claims 39, 43, 66-68, Williams et al. teach that the method further comprising the steps of: transferring an aliquot of at least one of the first and second eluates to a storage receptacle prior to step (e); closing the storage receptacle with a cap, the cap engaging the corresponding storage receptacle in a frictional or interference fit; retaining the storage receptacle within the analyzer at least until the completion of step (g); a third nucleic acid amplification assay to be performed on the aliquot in the storage sample, the third nucleic acid amplification assay to be performed in accordance with a third set of assay parameters, the third set of assay parameters being different than the first and second sets of assay parameters; forming a third amplification reaction mixture with the aliquot in the storage receptacle after step (g), wherein the third amplification reaction mixture contains a third set of amplification oligomers for amplifying a third region of a third analyte (additional analyte) or a nucleic acid bound to the third analyte (additional analyte) in a third nucleic acid amplification reaction; exposing the third amplification reaction mixture to thermal conditions for amplifying the third region; and determining the presence or absence of the third analyte in the third amplification reaction mixture wherein the third nucleic acid amplification assay (para 0094-0132, 0060-0085).
With reference to claims 44-46, Williams et al. teach that the step (f) is initiated at different times for the first and second amplification reaction mixtures, wherein the first and second amplifications configured to perform molecular diagnostic assays (para 0095-0096, para 0250, 0048-0052).
With reference to claims 47, Williams et al. teach that the first and second amplification reaction mixtures are simultaneously exposed to thermal conditions in step (f) (para 0095-0096).
With reference to claims 72-76, Williams et al. teach displaying one or more graphical user interfaces configured to enable user inputs to select or modify at least one parameter and communicating user-defined parameters to the controller (processor) using touchscreen or keyboard (para 0036-0046).
With reference to Claim 77-78, Williams et al. teach the first and second solvent containers are carried in a container compartment configured to slide out from a main body of the automated analyzer wherein the container comprises a main body with two or more recesses configured to hold vials (para 0043-0046, 0078-0079).
However, Williams et al. did not specifically teach system defined parameters not changeable by a user. Although Williams et al. teach dissolving first amplification reagent comprising amplification oligomers with a solvent that does not comprise an amplification oligomer or polymerase, Williams et al. does not specifically teach dissolving a second amplification reagent comprising a polymerase with a solvent comprising a set of amplification oligomers.
Cracauer et al. teach automated nucleic acid detection assays comprising user-defined parameter based in-vitro diagnostic assays that are changeable by a user and system-defined parameters or lab-developed tests comprising analyte-specific reagent assays that are integrated in automated system that are not changeable by the user (para 1237-1241, 1268-1272, 205-0213, 1169). Cracauer et al. also teach multiple PCR amplifications having different thermal cycling parameters (para 0616-0620, 0639-0642, 0608).
Catanzariti et al. teach an automated amplification method comprising automated processing of amplification reaction in disposable dual chambered reaction vessels, wherein a disposable dual chamber reaction vessel comprises a single or unit dose of reagents for an amplification reaction, wherein the two chambers of the dual chamber vessel contain stored amplification reagents, wherein the amplification reagent in the first chamber contains primers, deoxynucleotides, MgCl2 and other salts and buffer components, and the second chamber contains amplification enzyme, wherein dissolving the first amplification reagent comprising amplification oligomers (primers) with a test sample solution (first solvent), which upon heating, test sample nucleic acid undergoes denaturation and anneals to the primers, then the solution comprising said nucleic acid and amplification primers from the first chamber is flown into the second chamber and mixes with the amplification reagent containing amplification enzyme (col.6, line 40-67, col. 7, line 1-67, col. 8, line 1-11).
It would have been prima facie obvious to one of the ordinary people skilled in the art before the effective filling date of the invention to combine the method of Williams et al. with nucleic acid detection assays comprising in-vitro assays and lab developed tests as taught by Cracauer et al. and dissolving or reconstituting amplification reagents as taught by Catanzariti et al to improve the sensitivity of the automated method for analyzing biological sample. The ordinary person skilled in the art would have motivated to combine the references and have a reasonable expectation of success that the combination would improve the sensitivity of the assays because Cracauer et al. explicitly taught use automated assays, wherein lab-developed analyte specific reagent parameters were set to validate invitro diagnostic assays (para 1237-172) and Catanzariti et al. explicitly taught dual chamber disposable reaction vessel containing amplification reagents and reconstituting or dissolving lyophilized or stored amplification reagents in the disposable dual chamber reaction vessels (col. 6, line 40-67, col. 2, line
17-34) and such a modification of the method of Williams et al. with the method as taught by Cracauer et al. and Catanzariti et al. is considered obvious over the cited prior art.
Response to Arguments:
With reference to the rejection of claims under 35 USC 103 as being unpatentable over Williams et al. in view of Cracauer et al. and Catanzariti et al., the Applicant’s arguments and the amendment have been fully considered and found unpersuasive. With reference to the arguments drawn to no teaching of dissolving amplification reagents by Williams et al. and no reason to modify the method with the teachings of Cracauer et al., the arguments were found unpersuasive. Further, the Applicant argues that inclusion of Catanzariti et al. would not remedy the deficiencies of Williams et al. and Cracauer et al. because Catanzariti et al. does not teach each of the first and second amplification comprising polymerase chain reaction (PCR). The arguments were found unpersuasive. The amendment incorporating the limitations of claim 10 in to claim 1 did not change the scope of the claims. As discussed in the rejection, Williams et al. teach first and second amplifications each comprising PCR. As discussed in the rejection it would be obvious to modify the method of Williams et al. with system defined parameters as taught by Cracauer et al. to perform lab-developed tests installed in automated system. Further, it would be obvious to modify the automated method with automated processing of amplification reaction comprising dissolving amplification reagents as taught by Catanzariti et al. to improve the automated process of amplification, which minimizes manual processing and reduce contamination of reagents during the automated amplification process. With reference to no teaching of PCR by Catanzariti et al., the arguments were found unpersuasive because Catanzariti et al. teach amplification comprising thermal cycles of denaturation, annealing temperatures which are within the scope of PCR and the amplification reaction components are not restricted to only isothermal amplification. For all the above, the rejection has been maintained and restated to address the amendment.
Conclusion
No claims are allowable.
THIS ACTION IS MADE FINAL. 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.
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/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681