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
The instant application having Application No. 17/947,445 has claims 1-9 and 11-20 pending filed on 09/19/2022; there are 3 independent claims and 16 dependent claims, all of which are ready for examination by the examiner. The applicant canceled the original claim 10 (dated 12/09/2025).
Acknowledgement Of References Cited By Applicant
As required by M.P.E.P. 609(C), the applicant’s submission of the Information Disclosure Statement dated December 9, 2025 is acknowledged by the examiner and the cited references have been considered in the examination of the claims now pending. As required by M.P.E.P 609 C (2), a copy of the PTOL-1449 initialed and dated by the examiner is attached to the instant office action.
Response to Arguments
This Office Action is in response to applicant’s communication filed on December 9, 2025 in response to PTO Office Action dated September 11, 2025. The Applicant’s remarks and amendments to the claims and/or specification were considered with the results that follow.
Claim Interpretation - 35 USC § 112(f)
After considering the applicant’s comments for the claims 9 and 11-15 (dated 12/09/2025), the Claim Interpretation under 35 U.S.C. 112(f) is maintained as the claim limitations meets the three-prong test (MPEP § 2181). The claim limitation(s) for the independent claim 9 “the system comprising: a memory storing instructions; a user interface; and a processor configured to execute the instructions causing the system to” does not modify the term “means” or “step” or the generic placeholder by sufficient structure, material, or acts for performing the claimed function. Refer MPEP § 2181 II (B) “To claim a means for performing a specific computer-implemented function and then to disclose only a general-purpose computer as the structure designed to perform that function amounts to pure functional claiming. Aristocrat, 521 F.3d 1328 at 1333, 86 USPQ2d at 1239.”
Claim Rejections
Claim Rejections - 35 USC § 103
35 USC § 103 Rejection of claims 1-20
Applicant's arguments filed on 12/09/2025 with respect to the claims 1-9 and 11-20 have been fully considered but are moot because the arguments do not apply to any of the references being used in the current rejection.
CLAIM INTERPRETATION
The following is a quotation of 35 U.S.C. 112(f):
(f) ELEMENT IN CLAIM FOR A COMBINATION. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as "configured to" or "so that"; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are: component in 9 and 11-15.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 103
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 1-4, 6, 9, 11,13 and 16-19 are rejected under 35 U.S.C. 103 as being unpatentable over Dube et al (US PGPUB 20090239308) in view of Subramaniam et al (US PGPUB 20160063181) and in further view of Ismagilov et al (US PGPUB 20150247190) and Janaway et al (US PGPUB 20110252353).
As per claim 1:
Dube teaches:
“A computer-implemented method for generating a data visualization, the method comprising” (Paragraph [0008] and Paragraph [0026] (provides a method for computing copy number variation (CNV) in a DNA sample using digital PCR and a chart (data visualization) showing data from a CNV study (Fig. 9b)))
“receiving fluorescent emission data obtained by a detector, the fluorescent emission data i) comprising a plurality of data points corresponding to fluorescence emission values from a plurality of reaction sites” (Paragraph [0013] (the system also includes a second optical system configured to receive optical radiation emitted from the nanofluidic chip (a plurality of data points corresponding to fluorescence emission) where a nanofluidic chip support is configured to receive a nanofluidic chip having a plurality of reaction chambers (a plurality of reaction sites of a substrate)))
“and (ii) indicative of a presence or absence of one or more dyes at the plurality of reaction sites” (Paragraph [0046] and Paragraph [0105]( microfluidic analyses are utilized herein, including devices that can be utilized to conduct thermal cycling reactions such as nucleic acid amplification reactions and after the reaction is completed, the Digital PCR Analysis is used to process the data and count the numbers of both FAM-positive chambers (target gene) and VIC-positive chambers (RNase P) (presence or absence of one or more dyes) in each panel)).
Dube does not EXPLICITLY disclose: determining, based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level; displaying on a user interface a data visualization; wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites; the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication; adjusting the quality threshold to an adjusted quality threshold; and displaying on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Subramaniam teaches:
“determining, based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level” (Paragraph [0038], Paragraph [0056] and Paragraph [0096] (to improve the quality of information being processed, sequence data analysis computer further utilizes one or more quality control (QC) metrics to flag and filter gene expression data taken both from the plate documents and the studies, the QC metrics may be set up to operate using a continuous measure of results and threshold values to indicate when to flag a results and when to both flag and filter a result from the data and this QC metric sequences through each data point (a first set of data points and a second set of data points ) taken during each cycle looking for multiple low-valued data points (a first set of data points and a second set of data points)))
“displaying on a user interface a data visualization” (Paragraph [0063] (a collection of GUI tools to view flag and filtering as performed in accordance with various implementations))
“the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication” (Paragraph [0064] (each QC metric is capable of independently flagging a well and therefore it is possible that a single well may contain multiple or many different flags and also multiple numeric values (the first set of data points and the second set of data points) could be displayed for each element and well in the plate)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Subramniam and apply them on teachings of Dube for the computer implemented method “based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level; displaying on a user interface a data visualization; the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication”. One would be motivated as this process of quality-control or QC is an important aspect of the experiment as it eliminates non-usable data points and improves the reliability of the overall experiment or associated study (Subramaniam, Paragraph [0002]).
Dube and Subramaniam do not EXPLICITLY disclose: wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites; adjusting the quality threshold to an adjusted quality threshold; and displaying on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Ismagilov teaches:
“wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites” (Paragraph [0202] and Paragraph [0228] (a device can comprise a plurality of spatially-distinct analysis regions (each data point is displayed at a relative spatial location), wherein each analysis region holds a portion of the sample and a graphical user interface may be generated so that the result of processed data can be displayed in the interface)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Ismagilov and apply them on teachings of Dube and Subramaniam for the computer implemented method “wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites”. One would be motivated as the data associated with the sample comprises measurements from greater than one spatially-isolated compartment each of the compartments comprising a portion of the sample (Ismagilov, Paragraph [0024]).
Dube, Subramaniam and Ismagilov do not EXPLICITLY disclose: adjusting the quality threshold to an adjusted quality threshold; and displaying on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Janaway teaches:
“adjusting the quality threshold to an adjusted quality threshold” (Paragraph [0022] (in response to input from an end user (adjusting the quality threshold), a processor may generate a first plot of first probe intensity versus a second probe intensity (an adjusted quality threshold) using the first data set))
“and displaying on the user interface, an adjusted data visualization” (Paragraph [0022] (a processor may display the first plot and the second plot in response to input from an end user))
“wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points” (Paragraph [0089] (a visualization tool presented in response to input from an end user (the adjusted data visualization displays) may provide for a step-wise display of genotyping data (an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points), or it may provide for the display run and such a visualization tool may provide an end user a dynamic review of all data as a function of time as an aid to analysis of genotyping data))
“wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication” (Paragraph [0025] (a visualization tool may assist an end user in the displaying of various aspects of genotyping data sets, thereby facilitating in the analysis of genotyping data, wherein a processor may display on the first plot quality values for the first data set and displays on the second plot quality values for the second data set)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Janaway and apply them on teachings of Dube, Subramaniam and Ismagilov for the computer implemented method “adjusting the quality threshold to an adjusted quality threshold; and displaying on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication”. One would be motivated as using such a visualization tool, an end user may dynamically understand the impact of a variety of experimental conditions on the outcome of a genotyping experiment including troubleshoot ambiguous end-point data, make manual calls, enhance genotype assignment, optimize assay and analysis conditions etc. (Janaway, Paragraph [0018]).
As per claim 2:
Dube, Subramaniam, Ismagilov and Janaway teach the method as specified in the parent claim 1 above.
Subramaniam further teaches:
“wherein the first and second indications differ in color” (Paragraph [0067] (a color system may be implemented to identify an outcome of each QC metric and the corresponding element of matrix)).
As per claim 3:
Dube, Subramaniam, Ismagilov and Janaway teach the method as specified in the parent claim 1 above.
Ismagilov further teaches:
“wherein the reaction sites are spatially disposed in a two-dimensional array” (Paragraph [0024] and Paragraph [0040] (the data associated with the sample comprises measurements from greater than one spatially-isolated compartment each of the compartments comprising a portion of the sample and at least a portion of the sample is partitioned into an array comprising at least 2 or more containers).
As per claim 4:
Dube, Subramaniam, Ismagilov and Janaway teach the method as specified in the parent claim 1 above.
Dube further teaches:
“wherein the one or more dyes comprise a first fluorescent dye and a second fluorescent dye, the plurality of data points correspond to fluorescence emission values from the first fluorescent dye and the second fluorescent dye and the method further comprises: displaying on the user interface a second data visualization” (Paragraph [0052] and Paragraph [0147] (the digital PCR Analysis is used to count the number of positive chambers in each panel, when two assays with two fluorescent dyes are used in a multiplex digital PCR reaction, two genes can be independently quantitated, the CCD is used as an array of photodetectors wherein each pixel or group of pixels corresponds to a reaction chamber and the optics may be designed or altered such that image quality is reduced or the image is blurred at the detector in order to increase the useable depth of field of the optical system to collect more light from each reaction chamber))).
Also, Subramaniam further teaches:
“wherein: the second data visualization displays a scatter plot containing the first and second sets of data points, wherein: a first axis of the scatter plot represents fluorescence emission values associated with the first fluorescent dye, and a second axis of the scatter plot represents fluorescence emission values associated the second fluorescent dye” (Paragraph [0100]] (the QC metric receives a measured composite signal response emitted from the probe dyes and passive reference in each well of the plate, using Multicomponent analysis, the QC metric generates a multicomponent plot (data visualization displays a scatter plot) of each expected dye component as derived from the composite signal response where the dye component breakdown depends on the configuration settings in the instrument that identifies the set of dyes being used in the particular assay)).
As per claim 6:
Dube, Subramaniam, Ismagilov and Janaway teach the method as specified in the parent claim 4 above.
Dube further teaches:
“wherein the fluorescent emission data corresponding to fluorescence emission values associated with the first fluorescent dye is indicative of presence or absence of a first target nucleotide sequence at the plurality of reaction sites” (Paragraph [0137], Paragraph [0139] and Paragraph [0147] (a first section of the emission filter wheel is adapted to pass fluorescent emissions produced by a first fluorescent dye, certain intercalation dyes that have dramatic fluorescent enhancement upon binding to double-stranded DNA, and/or show strong chemical affinity for double-stranded DNA, can be used to detect double-stranded amplified DNA and an array of photodetectors to maximize the amount of light collected from each reaction chamber wherein each pixel or group of pixels corresponds to a reaction chamber rather than being used to produce an image of the array))
“and the fluorescent emission data corresponding to fluorescence emission values associated with the second fluorescent dye is indicative of a present or absence of a second target nucleotide sequence which is different from the first target nucleotide sequence” (Paragraph [0137], Paragraph [0139] and Paragraph [0147] (a second section of the emission filter wheel is adapted to pass fluorescent emissions produced by a second fluorescent dye, certain intercalation dyes that have dramatic fluorescent enhancement upon binding to double-stranded DNA, and/or show strong chemical affinity for double-stranded DNA, can be used to detect double-stranded amplified DNA and an array of photodetectors to maximize the amount of light collected from each reaction chamber wherein each pixel or group of pixels corresponds to a reaction chamber rather than being used to produce an image of the array)).
As per claim 9:
Dubey teaches:
“A system for data visualization, the system cornprising”
(Paragraph [0008] and Paragraph [0026] (provides a system for computing copy number variation (CNV) in a DNA sample using digital PCR (dPCR) and a chart (data visualization) showing data from a CNV study (Fig. 9b)))
“a memory storing instructions” (Paragraph [0013] (a computer comprising a
data processor and a computer-readable medium or memory storing a plurality of instructions))
“a user interface” (Paragraph [0103] (a chart showing data from a CNV study
to distinguish between samples with varying numbers of copies of a target gene))
“and a processor configured to execute the instructions causing the system to”
(Paragraph [0013] (the plurality of instructions includes instructions that cause the data processor to determine a number of the plurality of reaction chambers characterized by a presence of one or more of the DNA molecules))
“receive fluorescent emission data obtained by a detector, the fluorescent emission data i) comprising a plurality of data points corresponding to fluorescence emission values from a plurality of reaction sites” (Paragraph [0013] (the system also includes a second optical system configured to receive optical radiation emitted from the nanofluidic chip (a plurality of data points corresponding to fluorescence emission) where a nanofluidic chip support is configured to receive a nanofluidic chip having a plurality of reaction chambers (a plurality of reaction sites of a substrate)))
“and (ii) indicative of a presence or absence of one or more dyes at the plurality of reaction sites” (Paragraph [0046] and Paragraph [0105]( microfluidic analyses are utilized herein, including devices that can be utilized to conduct thermal cycling reactions such as nucleic acid amplification reactions and after the reaction is completed, the Digital PCR Analysis is used to process the data and count the numbers of both FAM-positive chambers (target gene) and VIC-positive chambers (RNase P) in each panel)).
Dubey does not EXPLICITLY disclose: determine, based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level; display on a user interface a data visualization; wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites; the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication; receive an adjusted quality threshold; and display on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Subramaniam teaches:
“determine, based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level” (Paragraph [0038], Paragraph [0056] and Paragraph [0096] (to improve the quality of information being processed, sequence data analysis computer further utilizes one or more quality control (QC) metrics to flag and filter gene expression data taken both from the plate documents and the studies, the QC metrics may be set up to operate using a continuous measure of results and threshold values to indicate when to flag a results and when to both flag and filter a result from the data and this QC metric sequences through each data point (a first set of data points and a second set of data points ) taken during each cycle looking for multiple low-valued data points (a first set of data points and a second set of data points)))
“display on a user interface a data visualization” (Paragraph [0063] (a collection of GUI tools to view flag and filtering as performed in accordance with various implementations))
“the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication” (Paragraph [0064] (each QC metric is capable of independently flagging a well and therefore it is possible that a single well may contain multiple or many different flags and also multiple numeric values (the first set of data points and the second set of data points) could be displayed for each element and well in the plate)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Subramniam and apply them on teachings of Dube for the system “determine, based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level; display on a user interface a data visualization; the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication”. One would be motivated as this process of quality-control or QC is an important aspect of the experiment as it eliminates non-usable data points and improves the reliability of the overall experiment or associated study (Subramaniam, Paragraph [0002]).
Dube and Subramaniam do not EXPLICITLY disclose: wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites; receive an adjusted quality threshold; and display on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Ismagilov teaches:
“wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites;” (Paragraph [0202] and Paragraph [0228] (a device can comprise a plurality of spatially-distinct analysis regions (each data point is displayed at a relative spatial location), wherein each analysis region holds a portion of the sample and a graphical user interface may be generated so that the result of processed data can be displayed in the interface)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Ismagilov and apply them on teachings of Dube and Subramaniam for the system “wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites;”. One would be motivated as the data associated with the sample comprises measurements from greater than one spatially-isolated compartment each of the compartments comprising a portion of the sample (Ismagilov, Paragraph [0024]).
Dube, Subramaniam and Ismagilov do not EXPLICITLY disclose: receive an adjusted quality threshold; and display on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Janaway teaches:
“receive an adjusted quality threshold” (Paragraph [0022] (in response to input from an end user (receive an adjusted quality threshold), a processor may generate a first plot of first probe intensity versus a second probe intensity (an adjusted quality threshold) using the first data set))
“and display on the user interface, an adjusted data visualization” (Paragraph [0022] (a processor may display the first plot and the second plot in response to input from an end user))
“wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points” (Paragraph [0089] (a visualization tool presented in response to input from an end user (the adjusted data visualization displays) may provide for a step-wise display of genotyping data (an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points), or it may provide for the display run and such a visualization tool may provide an end user a dynamic review of all data as a function of time as an aid to analysis of genotyping data))
“wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication” (Paragraph [0025] (a visualization tool may assist an end user in the displaying of various aspects of genotyping data sets, thereby facilitating in the analysis of genotyping data, wherein a processor may display on the first plot quality values for the first data set and displays on the second plot quality values for the second data set)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Janaway and apply them on teachings of Dube, Subramaniam and Ismagilov for the system “receive an adjusted quality threshold; and display on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication”. One would be motivated as using such a visualization tool, an end user may dynamically understand the impact of a variety of experimental conditions on the outcome of a genotyping experiment including troubleshoot ambiguous end-point data, make manual calls, enhance genotype assignment, optimize assay and analysis conditions etc. (Janaway, Paragraph [0018]).
As per claim 11, the claim is rejected based upon the same rationale given for the parent claim 9 and the claim 4 above.
As per claim 13, the claim is rejected based upon the same rationale given for the parent claim 11 and the claim 6 above.
As per claim 16:
Dubey teaches:
“a non-transitory computer-readable storage medium encoded with instructions”
(Paragraph [0013] (a computer comprising a data processor and a computer-readable medium storing a plurality of instructions))
“executable by a processor” (Paragraph [0013] (The plurality of instructions
includes instructions that cause the data processor to estimate the concentration of the DNA molecule in the biological sample))
“for generating a data visualization, the instructions configured, upon execution, io cause the processor io carry out a method of” (Paragraph [0008], Paragraph [0013] and Paragraph [0026] provides a system for computing copy number variation (CNV) in a DNA sample using digital PCR (dPCR), a chart (data visualization) showing data from a CNV study to distinguish between samples with varying numbers of copies of a target gene and includes instructions that cause the data processor to determine a number of the plurality of reaction chambers characterized by a presence of one or more of the DNA molecules))
“receiving fluorescent emission data obtained by a detector, the fluorescent emission data i) comprising a plurality of data points corresponding to fluorescence emission values from a plurality of reaction sites” (Paragraph [0013] (the system also includes a second optical system configured to receive optical radiation emitted from the nanofluidic chip (a plurality of data points corresponding to fluorescence emission) where a nanofluidic chip support is configured to receive a nanofluidic chip having a plurality of reaction chambers (a plurality of reaction sites of a substrate)))
“and (ii) indicative of a presence or absence of one or more dyes at the plurality of reaction sites” (Paragraph [0046] and Paragraph [0105]( microfluidic analyses are utilized herein, including devices that can be utilized to conduct thermal cycling reactions such as nucleic acid amplification reactions and after the reaction is completed, the Digital PCR Analysis is used to process the data and count the numbers of both FAM-positive chambers (target gene) and VIC-positive chambers (RNase P) in each panel)).
Dubey does not EXPLICITLY disclose: determining, based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level; displaying on a user interface a data visualization; wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites; the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication; adjusting the quality threshold to an adjusted quality threshold; and displaying on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Subramaniam teaches:
“determining, based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level” (Paragraph [0038], Paragraph [0056] and Paragraph [0096] (to improve the quality of information being processed, sequence data analysis computer further utilizes one or more quality control (QC) metrics to flag and filter gene expression data taken both from the plate documents and the studies, the QC metrics may be set up to operate using a continuous measure of results and threshold values to indicate when to flag a results and when to both flag and filter a result from the data and this QC metric sequences through each data point (a first set of data points and a second set of data points ) taken during each cycle looking for multiple low-valued data points (a first set of data points and a second set of data points)))
“displaying on a user interface a data visualization” (Paragraph [0063] (a collection of GUI tools to view flag and filtering as performed in accordance with various implementations))
“the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication” (Paragraph [0064] (each QC metric is capable of independently flagging a well and therefore it is possible that a single well may contain multiple or many different flags and also multiple numeric values (the first set of data points and the second set of data points) could be displayed for each element and well in the plate)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Subramniam and apply them on teachings of Dube for the non-transitory computer-readable storage medium “based on a quality threshold, a first set of data points of the plurality of data points is of a first data quality level, and a second set of data points of the plurality of data points is of a second data quality level; displaying on a user interface a data visualization; the first set of data points being displayed with a first indication and the second set of data points being displayed with a second indication differing from the first indication”. One would be motivated as this process of quality-control or QC is an important aspect of the experiment as it eliminates non-usable data points and improves the reliability of the overall experiment or associated study (Subramaniam, Paragraph [0002]).
Dube and Subramaniam do not EXPLICITLY disclose: wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites; adjusting the quality threshold to an adjusted quality threshold; and displaying on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Ismagilov teaches:
“wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites” (Paragraph [0202] and Paragraph [0228] (a device can comprise a plurality of spatially-distinct analysis regions (each data point is displayed at a relative spatial location), wherein each analysis region holds a portion of the sample and a graphical user interface may be generated so that the result of processed data can be displayed in the interface)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Ismagilov and apply them on teachings of Dube and Subramaniam for the non-transitory computer-readable storage medium “wherein: the data visualization displays the first set of data points and the second set of data points in a spatial representation such that each data point is displayed at a relative spatial location of its corresponding reaction site of the plurality of reaction sites”. One would be motivated as the data associated with the sample comprises measurements from greater than one spatially-isolated compartment each of the compartments comprising a portion of the sample (Ismagilov, Paragraph [0024]).
Dube, Subramaniam and Ismagilov do not EXPLICITLY disclose: adjusting the quality threshold to an adjusted quality threshold; and displaying on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication.
However, in an analogous art, Janaway teaches:
“adjusting the quality threshold to an adjusted quality threshold” (Paragraph [0022] (in response to input from an end user (adjusting the quality threshold), a processor may generate a first plot of first probe intensity versus a second probe intensity (an adjusted quality threshold) using the first data set))
“and displaying on the user interface, an adjusted data visualization” (Paragraph [0022] (a processor may display the first plot and the second plot in response to input from an end user))
“wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points” (Paragraph [0089] (a visualization tool presented in response to input from an end user (the adjusted data visualization displays) may provide for a step-wise display of genotyping data (an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points), or it may provide for the display run and such a visualization tool may provide an end user a dynamic review of all data as a function of time as an aid to analysis of genotyping data))
“wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication” (Paragraph [0025] (a visualization tool may assist an end user in the displaying of various aspects of genotyping data sets, thereby facilitating in the analysis of genotyping data, wherein a processor may display on the first plot quality values for the first data set and displays on the second plot quality values for the second data set)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Janaway and apply them on teachings of Dube, Subramaniam and Ismagilov for the non-transitory computer-readable storage medium “adjusting the quality threshold to an adjusted quality threshold; and displaying on the user interface, an adjusted data visualization; wherein the adjusted data visualization displays, in the spatial representation, an adjusted first set of data points of the plurality of data points and an adjusted second set of data points of the plurality of data points; wherein the adjusted first set of data points meets the first quality level based on the adjusted quality threshold and is displayed with the first indication, and wherein the adjusted second set of data points meets the second quality level based on the adjusted quality threshold and is displayed with the second indication”. One would be motivated as using such a visualization tool, an end user may dynamically understand the impact of a variety of experimental conditions on the outcome of a genotyping experiment including troubleshoot ambiguous end-point data, make manual calls, enhance genotype assignment, optimize assay and analysis conditions etc. (Janaway, Paragraph [0018]).
As per claim 17, the claim is rejected based upon the same rationale given for the parent claim 16 and the claim 2 above.
As per claim 18, the claim is rejected based upon the same rationale given for the parent claim 16 and the claim 4 above.
As per claim 19, the claim is rejected based upon the same rationale given for the parent claim 18 and the claim 6 above.
Claims 5 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Dube et al (US PGPUB 20090239308) in view of Subramaniam et al (US PGPUB 20160063181) and in further view of Ismagilov et al (US PGPUB 20150247190), Janaway et al (US PGPUB 20110252353) and Chiu et al (US PGPUB 20140087386).
As per claim 5:
Dube, Subramaniam, Ismagilov and Janaway teach the method as specified in the parent claim 4 above.
Dube, Subramaniam, Ismagilov and Janaway do not EXPLICITLY teach: wherein the second data visualization is displayed alongside the data visualization on the user interface.
However, in an analogous art, Chiu teaches:
“wherein the second data visualization is displayed alongside the data visualization on the user interface” (Paragraph [0021], Paragraph [0095] and Paragraph [0135] (user interface output devices may include a display subsystem, where it can include producing a first plurality of droplets having a first volume distribution and analyzing a second plurality of droplets having a second volume distribution to determine individual volumes of the droplets in the second plurality, and also display a cumulative histogram)).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Chiu and apply them on teachings of Dube, Subramaniam, Ismagilov and Janaway for the computer implemented method “wherein the second data visualization is displayed alongside the data visualization on the user interface”. One would be motivated as by integrating dPCR with on-chip gradient generation, or by using digitized volumes of varying sizes, the invention effectively increases the dynamic range of dPCR chip from 1 order to 6 orders magnitude (Chiu, Paragraph [0077]).
As per claim 12, the claim is rejected based upon the same rationale given for the parent claim 11 and the claim 5 above.
Claims 7, 8, 14, 15 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Dube et al (US PGPUB 20090239308) in view of Subramaniam et al (US PGPUB 20160063181) and in further view of Ismagilov et al (US PGPUB 20150247190), Janaway et al (US PGPUB 20110252353) and Larson et al (US PGPUB 20240132939).
As per claim 7:
Dube, Subramaniam, Ismagilov and Janaway teach the method as specified in the parent claim 6 above.
Subramaniam further teaches:
“wherein the scatter plot contains clusters of data points, the clusters of data points comprising” (Paragraph [0117] (a QC metric may first determine a number of clusters of samples on the allelic discrimination plot including)).
Dube, Subramaniam, Ismagilov and Janaway do not EXPLICITLY teach: a first cluster of data points indicative of the absence of both the first and second target nucleotide sequence; a second cluster of data points indicative of the presence of the first target nucleotide sequence and the absence of the second target nucleotide sequence; a third cluster of data points indicative of the absence of the first target nucleotide sequence and the presence of the second target nucleotide sequence; and a fourth cluster of data points indicative of the presence of both the first and the second target nucleotide sequences.
However, in an analogous art, Larson teaches:
“a first cluster of data points indicative of the absence of both the first and second target nucleotide sequence” (Paragraph [0127] the bottom left cluster includes microdroplets not containing any sequence))
“a second cluster of data points indicative of the presence of the first target nucleotide sequence and the absence of the second target nucleotide sequence” (Paragraph [0127] (the bottom middle cluster includes microdroplets containing sequence for SMN1))
“a third cluster of data points indicative of the absence of the first target nucleotide sequence and the presence of the second target nucleotide sequence” (Paragraph [0127] (the bottom right cluster includes microdroplets containing sequence for SMN2))
“and a fourth cluster of data points indicative of the presence of both the first and the second target nucleotide sequences” (Paragraph [0127] (the top left cluster includes microdroplets containing the reference sequence (SMARCC1))).
It would have been obvious to one of ordinary skill in the art before the effective filing date to take the teachings of Larson and apply them on teachings of Dube, Subramaniam, Ismagilov and Janaway for the computer implemented method “a first cluster of data points indicative of the absence of both the first and second target nucleotide sequence; a second cluster of data points indicative of the presence of the first target nucleotide sequence and the absence of the second target nucleotide sequence; a third cluster of data points indicative of the absence of the first target nucleotide sequence and the presence of the second target nucleotide sequence; and a fourth cluster of data points indicative of the presence of both the first and the second target nucleotide sequences”. One would be motivated as the fluorescence emission from each droplet is determined and plotted on a scattered plot based on its wavelength and intensity, clusters, each representing droplets having the corresponding fluorescence wavelength and intensity are shown for different dyes like the VIC dye and the FAM dye at different intensities (Larson, Paragraph [0117]).
As per claim 8:
Dube, Subramaniam, Ismagilov, Janaway and Larson teach the method as specified in the parent claim 7 above.
Subramaniam further teaches:
“wherein the data points in each cluster are displayed with a different color” (Paragraph [0067] (a color system may be implemented to identify an outcome of each QC metric and the corresponding element of matrix)).
As per claim 14, the claim is rejected based upon the same rationale given for the parent claim 13 and the claim 7 above.
As per claim 15, the claim is rejected based upon the same rationale given for the parent claim 14 and the claim 8 above.
As per claim 20, the claim is rejected based upon the same rationale given for the parent claim 19 and the claim 7 above.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Kurnik Ronald, (US PGPUB 20070073489), systems and methods for determining the elbow or Ct value in a real-time, or kinetic, PCR amplification curve data set. The PCR data set may be visualized in a two-dimensional plot of fluorescence intensity (y-axis) vs. cycle number (x-axis). The data set is transformed to produce a partition table of data points with one column including the fluorescence at cycle (n) and a second column including the fluorescence at cycle (n+i), where i is typically 1 or greater. A cluster analysis process is applied to the partition table data set to determine a plurality of clusters in the partition table data set.
Parks et al, (US PGPUB 20060015291), it provides methods of analyzing and/or displaying data. In one aspect, the invention provides methods for visualizing or displaying high dynamic range data obtained from flow cytometry analyses. Related systems and computer programs products are also provided.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. 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).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAMAL K DEWAN whose telephone number is (571) 272-2196. The examiner can normally be reached on Mon-Fri 8:00 AM – 5:00 PM (EST). If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, TONY MAHMOUDI can be reached on 571-272-4078. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Kamal K Dewan/
Examiner, Art Unit 2163
/ALEX GOFMAN/Primary Examiner, Art Unit 2163
Prosecution Insights