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 .
Response to Arguments
Applicant respectfully submits that the prior art is silent on how it determines whether a spot is considered reacted or not. Applicants concedes that the prior art teaches that the reacted spots may be detected by analyzing an image obtained from the fluorescent signal, and the light intensity of the fluorescent signal may be digitized and expressed in numerals. Applicants also concedes that the prior art teach that “the light intensity of the fluorescent signal represents the degree of hybridization caused by the reactions between the probe materials and the target material” and “the greater the light intensity of the fluorescent signal is, the greater the degree of the complementarity between the probe materials and the target material is”. But Applicant argues that the prior art is silent as to the mechanism by which the light intensity is used to make a determination or to what degree a particular spot has reacted. Examiner respectfully disagrees. The prior art clearly teaches that the light intensity is directly proportional to the degree of reaction. One skilled in the art can determine the exact thresholds to use to classify the degree of reaction by comparing the pixel values or intensity values to predefined thresholds. These thresholds may be determined through routine experimentation and/or through trial and error.
Moreover, the claim language only stipulates that “criterion, threshold or range is indicative of a different degree of reaction”. D1 clearly teaches the criteria, i.e., the light intensity of the fluorescent signal represents the degree of hybridization caused by the reactions between the probe materials and the target material” and “the greater the light intensity of the fluorescent signal is, the greater the degree of the complementarity between the probe materials and the target material is.
Applicant respectfully submits that the prior art does not teach a look up table. Examiner noted in the Office Action that the prior art does not explicitly teach a look up table. However, Examiner explained that the prior art teaches that a reference file is stored in the database containing information about the different probe materials at each spot and also information about the light intensity that is generated from each position after a reaction between the probe material and the target material. D1 does not explicitly recite that the measured light intensity is compared with the stored light intensity information to determine the degree of reaction, however D1 does suggest that the measured light information maybe be evaluated using the information stored in the reference file to identify the target material and the degree of hybridization using the reference information. In other words, it would have been obvious for one skilled in the art based on the disclosure to determine the degree of hybridization or reaction by comparing the measured light intensity from the captured image with the information stored in the reference file to determine the type of reaction that has occurred.
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 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, 3-4, 6-10, 12-14 and 16 are rejected under 35 U.S.C. 103 as being unpatentable over D1.1
With regard to claim 1, D1 teach method of analyzing assays performed at respective assay sites of an array or microarray that comprises a plurality of assay sites arranged in a plurality rows and columns, each assay site comprising a well or spot forming a reaction site, the computer being comprised in an assay analysis system that further comprises at least one camera for collecting one or more images of the array or microarray and an output device (see fig. 1, abstract, ¶ 30: image of microarray with plurality of assay sites, each site is a spot forming a reaction), the method comprising: receiving, at the computer, at least one image collected by the at least one camera, the at least one image collectively or individually imaging the plurality of assay sites of the array or microarray, processing the at least one image to determine at least one image metric representative of the degree of reaction at that assay site (see fig. 1-2: image of microarray with plurality of assay sites; ¶¶ 31-32: light intensity measurement representative of degree of hybridization);
for each of the assay sites, determining, by the computer, one or more parameters for that assay site, wherein the one or more parameters are predetermined for a given assay type, sample type, location, location in the array or site, and the one or more parameters for at least one of the assay sites of the array or microarray are different from the one or more parameters for at least one other of the assay sites of the array or microarray (see ¶¶ 41-42: reference file stored in storage containing information about the probe material at each of the spot and information about light intensity of a fluorescent signal at each position after a reaction between the probe and the target material, parameters at each spot is different); and
for each of the assay sites, determining, by the computer, an extent of the reaction at that assay site from the at least one image metric for that assay site and the one or more parameters for that assay site and outputting the determined extent of the reaction at that assay site on the output device (see ¶¶ 31-32, 41-42: a reference file with information about the probe material at each of the spots and information about light intensity or parameter that is generated from the position of the probe material after a reaction between the probe material and target material, the extent of reaction being proportional to the light intensity at the spot)
wherein:
the parameters comprise one or more criteria, thresholds or ranges (see ¶¶ 41-42: reference file containing criteria for a reaction such as information about light intensity or other properties of each of the spot);
each criterion, threshold or range is indicative of a different degree of reaction (see ¶¶ 41-42, 31-42: light intensity indicative of different degrees of reaction)
the determining of the extent of the reaction at an assay site by the computer comprises determining whether or not the at least one image metric for that site is above or below the one or more thresholds or within or out with the one or more ranges or does or doesn’t meet at least one of the criteria to determine the degree of reaction (see ¶¶ 31-32, 41-42: light intensity at the spot is maybe evaluated to determine the degree of hybridization by comparing with information from the reference file);
and the identifying of the one or more different parameters that comprise one or more criteria, thresholds or ranges by the computer comprises, for each site, looking up or determining the value of the one or more parameters for that site from a look-up table, database, data store, or function that associates parameters with assay types, sample types and/or sites or from an input device (see ¶¶ 41-42: site parameters such as information about the probe material, light intensity or other properties of the spot is stored in a reference file).
Note that D1 describes that light intensity of the fluorescent signal represents the degree of hybridization cause by the reaction between the probe materials and the target material at a given spot (see ¶ 32). D1 further teaches that a reference file is stored in the database containing information about the different probe materials at each spot and also information about the light intensity that is generated from each position after a reaction between the probe material and the target material. D1 does not explicitly recite that the measured light intensity is compared with the stored light intensity information to determine the degree of reaction, however D1 does suggest that the measured light information maybe be evaluated using the information stored in the reference file to identify the target material and the degree of hybridization using the reference information. In other words, it would have been obvious for one skilled in the art based on the disclosure to determine the degree of hybridization or reaction by comparing the measured light intensity from the captured image with the information stored in the reference file to determine the type of reaction that has occurred.
D1 teach that “the light intensity of the fluorescent signal represents the degree of hybridization caused by the reactions between the probe materials and the target material” and “the greater the light intensity of the fluorescent signal is, the greater the degree of the complementarity between the probe materials and the target material is” and therefore explicitly teach a criteria is indicative of a different degree of reaction, but D1 fails to explicitly teach a threshold or range. However, one skilled in the art can determine the exact thresholds to use to classify the degree of reaction by comparing the pixel values or intensity values to predefined thresholds. These thresholds may be determined through routine experimentation and/or through trial and error.
With regard to claim 3, D1 teach wherein the parameters for a site depend on one or more of: an assay type performed at the site, a location of the site on the array or microarray, and/or a targeted assay type (see ¶¶ 41-42: parameters stored in the reference file depend on the properties of each of the site or spot).
With regard to claim 4, D1 teach wherein the at least one metric for a site comprises or is representative of pixel intensities for an area of the image representing [[a]] the spot at that site, the spot being formed by reaction of an analyte and having a property indicative of the degree of reaction (see ¶¶ 31-32, 38: intensity representative of the image spot).
With regard to claim 6, D1 teach cropping the image around the array of sites; and/or gridding the image into segments wherein each segment encloses a spot and/or assay site (see fig. 1, ¶ 41: grid pattern image, implicit that the image is processed to segment each of the spots).
With regard to claim 7, D1 teach the cropping, gridding and/or the determining of the one or more metrics for the assay site uses common parameters that are shared with one or more or each or every other spot or site with the same assay type (see fig. 1, ¶ 41: grid pattern image, implicit that the image is processed to segment each of the spots).
With regard to claim 8, D1 teach wherein the parameters for metrics for determining an extent of the reaction at the assay site are unique for that site (see ¶¶ 41-42: reference file stores parameters that are unique for each of the spots).
With regard to claim 9, D1 teach detecting or identifying shapes in the image that comprise circles of a diameter within a predefined interval; and/or edge detection to determine the edges of the spots in the at least one image (see fig. 1: the grid patterns image inherently analyzed to detect the spots by performing edge detection).
With regard to claim 10, D1 teach comprising filtering out identified spots having a measure of pixel intensity less than a threshold; and/or outside a predefined geometric area corresponding to the location of the assay sites on the array or microarray and positioned based on at least one other identified spot, control spot, or reference point on the array or microarray (see ¶¶ 35, 38: control or fiducial spots are filtered out and analyzed).
With regard to claim 12, D1 fails to explicitly teach wherein the identifiers are obtained by an input device comprising at least one of a user input device for receiving user input, a barcode reader, a QR code reader or other machine readable code reader, an RFID tag reader, and/or an infra-red signal reader, however Examiner takes Official Notice to the fact that bar code readers or QR code readers are extremely well known in the field of micro array analysis and would have been particularly obvious to incorporate known teachings in to the configuration of D1 yielding predictable and enhanced processing of arrays.
With regard to claim 13, D1 teach wherein the determining of the extent of the reaction at the assay site comprises performing one or more logic tests to the at least one metric for that assay site and the one or more parameters for that assay site, where the result of the one or more logic tests is the extent of the reaction at the assay site comprising an indication of at least one of: whether or not there has been a reaction at that assay site; a degree of reaction at that assay site; whether or not there is activity at that assay site; a degree of activity at that assay site; and/or whether or not an analyte is present at that assay site (see ¶¶ 31-32, 41-42: light intensity analyzed to determine whether a reaction occurred and the degree of reaction).
With regard to claim 14, see discussion of claim 1.
With regard to claim 16, see discussion of claim 1.
Claim 5 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AVINASH YENTRAPATI whose telephone number is (571)270-7982. The examiner can normally be reached on 8AM-5PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sumati Lefkowitz can be reached on (571) 272-3638. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AVINASH YENTRAPATI/Primary Examiner, Art Unit 2672
1 US Publication No. 2010/0256002.
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