DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Priority
This application claims benefit of priority to Provisional Application 61/081,930 filed on 07/18/2008 and Provisional Application 61/492,602 filed on 06/02/2011. This application is also a Continuation of Application 13/487,030 filed on 06/01/2012 and a Continuation In Part of Application 12/504,764 filed on 07/17/2009. The Earliest Effective Filing date of the instant Application for purposes of applying prior art is 7/17/2009. Support for claims 35-40 is found in Application 13/487,030. Therefore, for examination purposes, the effective filing date for claims 21-30 and 33-34 is 7/17/2009 and the effective filing date for claims 35-40 is 06/01/2012.
Amendment and Claim Status
In the reply filed on 11/13/2025, Applicant amended claims 21, 23 and 36-37. Claims 1-20 and 31-32 are cancelled.
Claims 21-30 and 33-40 are currently pending and under examination.
Withdrawn Rejections
The 35 USC § 112(a) rejection over claims 21-30 and 33-40 is withdrawn due to Applicant’s amendments and persuasive arguments.
The 35 USC § 112(b) rejection over claims 21-30 and 33-40 is withdrawn due to Applicant’s amendments and persuasive arguments.
The 35 USC § 101 rejection over claims 21-30 and 33-40 is withdrawn due to Applicant’s amendments and persuasive arguments.
Maintained Rejections (With modification due to amendment)
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of pre-AIA 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
Claims 21-22, 25-30 and 33-40 are rejected under pre-AIA 35 U.S.C. 102(a) as being anticipated by Monforte (US 20080124726 A1, 05/29/2008).
Regarding claims 21 and 26, Monforte discloses a method for single cell biochemical analysis, wherein the invention provides method and instruments for high-throughput biochemical analysis of large numbers of single cells (Abstract), reading on in vitro. This is beneficial because it enables the determination of a distribution of a particular characteristic in a population of individual cells, not just the population average of a specific trait (Paragraph [0093]). This analysis includes:
a) Providing i) a plurality of cells in an aqueous first solution that further contains at least one reagent for detecting the presence or absence of the biomolecule, where the reagent is capable of generating or participating in generating an amplified signal corresponding to the presence or absence of the biomolecule; ii) a second solution that is immiscible with said first solution and capable of forming vesicles when admixed with the first solution;
b) combining the first and second solutions under conditions that result in the formation of a plurality of reaction vesicles, where each reaction vesicle formed contains one cell from the plurality of cells and a reagent for detecting the presence or absence of the biomolecule;
c) subjecting the reaction vesicles to conditions suitable for detecting the biomolecule, wherein the reagent generates or participates in generating an amplified signal corresponding to the presence or absence of the biomolecule associated with the one cell in each reaction vesicle;
d) detecting the amplified signal from the plurality of vesicles;
e) correlating the signal with the presence or absence of the biomolecule associated with said cells, thereby detecting the presence or absence of the biomolecule associated with said cells and generating a detecting result; and
f) displaying the detection result for said plurality of cells (Paragraph [0018]).
Regarding the admixing of step a) part ii), a Poisson distribution of compartmentalized cells is achieved with proper mixing (Paragraph [0100]). Further, the term ‘reagent’ refers to any component not endogenous to a cell that is involved in the assay of a biomolecule associated with a cell, including antibodies, antibody-enzyme fusion proteins, secondary antibodies to detect a primary antibody, substrates for enzymes that generate signals for detecting and labels (Paragraph [0067]). The amplified signal that is generated can be an enzymatic reaction product (Paragraph [0028]), reading on a chemical reaction.
Fluorescence levels are recorded during each PCR cycle and are proportional to the amount of product amplified, the fluorescence signal is recorded as statistically significant, or where the fluorescence signal is above an ambiguous level (Paragraph [0208]). Recording fluorescence levels of the amplified product reads on identifying the fluid partitions that contain released detectable label as the detectable label is what is fluorescing.
The statistical functions can be incorporated into system software where the software performs one or more statistical or probabilistic analysis of signals received from one or more of the aliquots subjected to amplification, wherein this analysis can include Poisson analysis (Paragraph [0358]), reading on determining if the complexes are in a Poisson distribution or not.
The detection of variance in the distribution of a particular biomolecule in a collection of individual cells from a population provides insight into rare events that give rise to particular phenotypes, and in turn to a disease state, such as cancer, inflammation and neurological disease (Paragraph [0121]).
Regarding the new limitations to instant claim 21, Monforte discloses microfluidics technology for partitioning (Paragraph [0112]) and a computer being operably coupled to a detector that is able to receive and store signals from a detector (Paragraph [0069]). The detector detects a signal generated by a reagent corresponding to the presence or absence of the biomolecule (Paragraph [0144]).
Regarding claims 22 and 25, Monforte discloses a probe is associated with a suitable label or reporter moiety so that the probe and its target can be detected. Detection systems include detection of fluorescence, enzymatic activity and binding properties that permit specific binding of the reporter (Paragraph [0203]).
Regarding claims 27 and 28, Monforte discloses a first antibody can be detected by a secondary antibody specific for the first that has been conjugated to a signal producing enzyme, such as horseradish peroxidase enzyme. A colorimetric substrate can be added so the horseradish peroxidase produces a detectable product after catalysis of the colorimetric substrate (Paragraph [0152]).
Regarding claim 29, Monforte discloses the detecting step includes quantitating the amplified signal (Paragraph [0028]).
Regarding claim 30, Monforte discloses quantitating refers to assigning a numerical value to the signal measured, wherein the quantitation can be correlated to the concentration of a biomolecule, such as the number of protein molecules present or absolute concentration of a protein that is present (Paragraph [0081]).
Regarding claim 33, Monforte discloses partitioning the cells into separate physical locations or aqueous droplets (Paragraph [0117]).
Regarding claim 34, Monforte discloses the use of two liquid phases, a first phase that is aqueous and a second phase that is immiscible with the aqueous phase (Paragraph [0094]).
Regarding claims 35 and 36, Monforte discloses detectors for monitoring the signals from a single aqueous volume (Paragraph [0342]), wherein the detector is photo multiplier tubes (Paragraph [0344]). The detector can include or be operably linked to a computer that has software for converting detector signal information, like applied voltages (Paragraph [0356]), into assay result information (Paragraph [0345]), and further correlates an expression level of a gene in one cell with the expression level of that same gene in a plurality of other cells, and displays the data to the user (Paragraph [0357]). Considering a scaling factor is simply a number used as a multiplier to represent a number on a different scale, the disclosure of converting signal information into assay result information and correlating that to an expression level of a gene in cell, reads on converting volts to a number of molecules using a scaling factor.
Regarding claim 37, Monforte discloses with proper mixing, a Poisson distribution of compartmentalized cells is achieved, wherein the mean distribution will be chosen to be less than one cell per partition to increase the number of partitions that only have one cell (Paragraph [0100]). If it is predicted each partition only contains one cell, there is a small probability each partition will contain no cells or more than one cell, but it is statistically likely to contain one cell (Paragraph [0100]). Thus, if there is a deviation from the expected Poisson distribution, whereby one is expected, but more than one protein is present, there would naturally be an aggregation of protein.
Regarding claim 38, Monforte discloses a first antibody can be detected by a secondary antibody specific for the first that has been conjugated to a signal producing enzyme, such as horseradish peroxidase enzyme (Paragraph [0152]). A further characteristics of the invention is the one or more biochemical reagents being linked to a solid phase (Paragraph [0261]), such as a magnetic bead (Paragraph [0266]). The beads are coupled to a second molecule that provides a capture function, more specifically, a bead coupled to an antibody (Paragraph [0268]).
Regarding claim 39, Monforte discloses integration of solid phase capture allows the vesicles that contain cells to be disrupted and the beads to be washed and purified, to enable the detection of one or more captured detectable probes (Paragraph [0260]). Further, magnetic beads can be manipulated by applying a magnetic field to rapidly isolate the beads from a liquid phase (Paragraph [0270]).
Regarding claim 40, Monforte discloses the use of microfluidic devices (Paragraph [0068]).
USC § 102 – Response to Arguments
Applicant's arguments filed 11/13/2025 have been fully considered but they are not persuasive.
Applicant argued on Page 14 that Monforte does not disclose determining that reaction products are present in partitions at a non-Poisson distribution or determining whether reaction products conform to a Poisson distribution in partitions after being partitioned in a digital laboratory assay.
It is the Examiner’s position that Monforte does meet these limitations. As discussed above, Monforte discloses utilizing statistical functions, including Poisson analysis (Paragraph [0358]). Thus, as the Poisson analysis was completed, it would necessarily determine if reaction products are or are not present in the partitions at a non-Poisson distribution. Additionally, Monforte does disclose the products were partitioned in a digital laboratory assay, the microfluidic device. Thus, Applicant’s arguments are not persuasive.
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) 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.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 21-30 and 33-40 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Monforte (US 20080124726 A1, 05/29/2008) as applied to claims 21-22, 25-30 and 33-40 above, and further in view of Greferath et al. (CA 2632822 A1, 06/21/2007).
The teachings of Monforte are disclosed above.
Regarding claims 23 and 24, Monforte does not disclose wherein the protein is beta amyloid protein or wherein the distribution is measured as an aggregate of beta amyloid protein.
However, Greferath et al. disclose a method for detecting amyloid-associated diseases or conditions, including immunological methods commonly used for detecting or quantifying substances in biological samples or in an in situ condition (Page 73, Paragraph 1). More specifically,
Diagnosis of an amyloid-associated disease or condition in a patient may be achieved by detecting the immunospecific binding of a monoclonal antibody to an epitope of the amyloid protein in a sample or in situ, which includes bringing the sample or a specific body part or body area suspected to contain the amyloid antigen into contact with an antibody which binds an epitope of the amyloid protein, allowing the antibody to bind to the amyloid antigen to form an immunological complex, detecting the formation of the immunological complex and correlating the presence or absence of the immunological complex with the presence or absence of amyloid antigen in the sample and comparing the amount of said immunological complex to a normal control value, wherein an increase in the amount of said aggregate compared to a normal control value indicates that said patient is suffering from an amyloid-associated condition (Page 73, Paragraph 2).
Greferath et al. further disclose the use of labeled antibodies for detection. Specifically, the antibody can be labeled with an enzyme, wherein enzyme-conjugated labels are particularly useful for quick results (Page 75, Paragraph 2). Detecting involves a double antibody method wherein a first antibody is labeled indirectly by reactivity with a second antibody that has been labeled with a detectable label, such as a fluorescent substance (Page 76, Paragraph 2). Greferath et al. further disclose the use of a 96-well plate (Page 100, Paragraph 1), reading on a fluid partition.
Exemplary rationales that may support a conclusion of obviousness include combining prior art elements according to known methods to yield predictable results. See MPEP 2143(I)(A). As such, it would have been prima facie obvious to one of ordinary skill in the art to utilize beta amyloid as the protein and measure the distribution of each partition by the aggregation of beta amyloid protein in the method of Monforte as the two methods are very similar, both being drawn to evaluation of proteins within a single partition via fluorescence, and detecting the amount of aggregation of beta amyloid protein was a known and effective means for detecting a condition in a human as taught by Greferath et al. as it amounts to combining prior art elements according to known methods to yield predictable results.
USC § 103 – Response to Arguments
Applicant's arguments filed 11/13/2025 have been fully considered but they are not persuasive.
Applicant argued on Page 15 that Geferath et al. do not teach or suggest any method that involves forming fluid partitions, a distribution of any reaction products among partitions or determining whether reaction products conform to a Poisson distribution in partitions.
The Examiner agrees, however, Geferath et al. was not utilized for the limitations argued. Geferath et al. was utilized specifically for the limitations of claims 23 and 24. See rejection above. The primary reference, Monforte, was utilized to teach the argued limitations.
Conclusion
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.
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/A.T.W./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653