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 Status
Claim 1 filed on 08/21/2026 are pending. Claims 4 & 5 are withdrawn from consideration as being drawn to a non-elected invention. The cancellation of claim 2 in the reply filed on 08/21/2026 is acknowledged. All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 112
Claim 1 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.
Regarding amended claim 1, the recitation of “measuring a light emission intensity at each of the spots of the microarray at each of a plurality of time points” in lines 12-13 of the claim is unclear what is precisely comprised by “at each of a plurality of time points”. If recitation is to comprise measuring each of the spots of the microarray at a plurality of times it is suggested the claim be amended to recite “measuring a light emission intensity at each of the spots of the microarray at a plurality of timepoints”. In addition, the recitation of “calculating the amount of microorganisms in the test sample based on the estimated amount of the extracted nucleic acid” in lines 18-19 of the claim is unclear what the relationship is between the amount of microorganisms and the estimated amount of extracted nucleic acids. How does an estimated amount to extracted nucleic acid relate back to an amount of microorganisms. In addition, the recitation of “concentration of the extracted nucleic acid in the test sample is based on luminance values of spots for a reference nucleic acid of known concentrations obtained in advance after an arbitrary hybridization reaction time and a calibration curve of nucleic acid concentration” in lines 20-23 of the claim is unclear what the relationship is between concentration of extracted nucleic acid and luminance values. How does a concentration of extracted nucleic acid relate back to luminance values.
Response to Arguments
The response traverses the rejection. The response asserts that the claims have been amended to be in proper format under US practice and to correct any antecedent basis issues. This argument has been thoroughly reviewed but was not found persuasive as, as discussed previously, the recitation of “calculating the amount of microorganisms in the test sample based on the estimated amount of the extracted nucleic acid” in lines 18-19 of the claim is unclear what the relationship is between the amount of microorganisms and the estimated amount of extracted nucleic acids. How does an estimated amount to extracted nucleic acid relate back to an amount of microorganisms.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Claim Rejections - 35 USC § 102
Claim(s) 1 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Andersen (United States Application Publication US 2018/0223339 A1, August 2018), as cited on the IDS dated 01/06/2025.
Regarding amended claim 1, it is noted, as discussed above, the recitation of “concentration of the extracted nucleic acid in the test sample is based on luminance values of spots for a reference nucleic acid of known concentrations obtained in advance after an arbitrary hybridization reaction time and a calibration curve of nucleic acid concentration” in lines 20-23 of the claim is unclear what the relationship is between concentration of extracted nucleic acid and luminance values. How does a concentration of extracted nucleic acid relate back to luminance values. Therefore, this recitation is given its broadest reasonable interpretation to encompass a calibration curve with reference controls to estimate the concentration of the extracted nucleic acid.
Andersen teaches a method of detecting the presence, relative abundance, and quantity of microorganisms with operational taxon unit (OTU) specific probes that are attached to a substrate forming a microarray comprising collecting a sample and concentrating and filtering (purifying) microorganisms in the sample (concentrating and purifying the microorganisms in the test sample), detecting microorganisms in the sample based on the selective hybridization of a plurality of probes hybridized with fluorescent molecules to nucleic acids isolated from the microorganisms to be detected (extracting a nucleic acid from the concentrated and purified microorganisms and hybridizing the extracted nucleic acid with probes fixed at spots of a microarray), and after hybridization of isolated (extracted) nucleic acids to fluorescent probes on a microarray measuring fluorescent emission signal (light emission intensity) to detect and quantify isolated (extracted) nucleic acids in the sample enabling detection and quantification of microorganisms in the sample (measuring light emission intensity at each of the spots of the microarray of the hybridized nucleic acid, estimating an amount of extracted nucleic acid based on the estimated amount of hybridized nucleic acid, and calculating the amount of the microorganism in the test sample based on the estimated amount of the extracted nucleic acid) (abstract lines 1-14; paragraph [0006] lines 1-23; paragraph [0010] lines 1-14; paragraph [0030] lines 1-13; paragraph [00159] lines 1-5; paragraph [0163] lines 1-18; paragraph [0166] lines 1-8; paragraph [0170] lines 1-18; paragraph [0171] lines 1-20; paragraph [0173] lines 1-17; paragraph [0174] lines 1-26; paragraph [0175] lines 1-18; paragraph [0176] lines 1-15; paragraph [0301] lines 1-11; paragraph [0399] lines 1-8). Andersen also teaches that the array fluorescent emission signals (light emission intensity) are normalized to allow for comparison of replicate experiments (measuring a light emission intensity at each of the spots of the microarray at each of a plurality of time points) and that this method can be used for testing samples at various timepoints (plurality of timepoints) (paragraph [0179] lines 1-3; paragraph [0209] lines 15-24). In addition, Andersen teaches the hybridization reaction comprises use of MES hybridization buffer (hybridization reaction solution containing salts and surfactant necessary for the hybridization reaction of the extracted nucleic acids) (paragraph [0356] lines 15-24). Andersen also teaches that amount of hybridized extracted nucleic acid comprises use of a receiver operating curve (calibration curve) through use of reference controls of known concentrations to determine concentration of the extracted nucleic acid (a calibration curve with reference controls to estimate the concentration of the extracted nucleic acid) (paragraph [0456] lines 1-14; paragraph [0457] lines 1-9; paragraph [0458] lines 1-24).
Response to Arguments
The response traverses the rejection. The response asserts that amended claim 1 requires measuring a light emission intensity at each of the spots of the microarray at each of a plurality of timepoints to estimate an amount of hybridized nucleic acid and estimating an amount of the extracted nucleic acid based on the estimated amount of the hybridized nucleic acid at each of the plurality of timepoints. Further, the response asserts that Andersen describes measuring a fluorescent emission signal after hybridization, that is a measurement taken at a single, post-hybridization endpoint (see, e.g., paragraphs [0006], [0010], and [0163]-[0176]) and that Andersen does not disclose acquiring light emission intensity at a plurality of timepoints during the hybridization reaction, nor estimating the amount of nucleic acid from such time-resolved measurements. Further, the response asserts that because this limitation is absent from Andersen, Andersen does not anticipate claim 1 and the present invention is novel over Andersen. This argument has been thoroughly reviewed but was not found persuasive. First, as discussed further above, Andersen teaches that the array fluorescent emission signals (light emission intensity) are normalized to allow for comparison of replicate experiments (measuring a light emission intensity at each of the spots of the microarray at each of a plurality of time points) and that this method can be used for testing samples at various timepoints (plurality of timepoints) (paragraph [0179] lines 1-3; paragraph [0209] lines 15-24). Further, Andersen teaches measuring fluorescent emission signal (light emission intensity) to detect and quantify isolated (extracted) nucleic acids in the sample enabling detection and quantification of microorganisms in the sample (measuring light emission intensity at each of the spots of the microarray of the hybridized nucleic acid, estimating an amount of extracted nucleic acid based on the estimated amount of hybridized nucleic acid, and calculating the amount of the microorganism in the test sample based on the estimated amount of the extracted nucleic acid) (abstract lines 1-14; paragraph [0006] lines 1-23; paragraph [0010] lines 1-14; paragraph [0030] lines 1-13; paragraph [00159] lines 1-5; paragraph [0163] lines 1-18; paragraph [0166] lines 1-8; paragraph [0170] lines 1-18; paragraph [0171] lines 1-20; paragraph [0173] lines 1-17; paragraph [0174] lines 1-26; paragraph [0175] lines 1-18; paragraph [0176] lines 1-15; paragraph [0301] lines 1-11; paragraph [0399] lines 1-8). Therefore, Andersen teaches acquiring light emission intensity at a plurality of timepoints during the hybridization reaction and estimating an amount of nucleic acid from such time-resolved measurements. Therefore, as discussed further above, Andersen teaches each and every element of claim 1 as currently amended.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claim 1 is rejected.
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 BAILEY C BUCHANAN whose telephone number is (703)756-1315. The examiner can normally be reached Monday-Friday 8:00am-5:00pm ET.
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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/Primary Examiner, Art Unit 1682
