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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 2/27/2025 has been entered.
Claim Status and Formal Matters
The instant response is not compliant with 37 CFR 1.121 as claim 2 is listed as both currently amended and canceled. However to promote compact prosecution and customer service the instant response will be examined. However further amendments that are non-compliant with 37 CFR 1.121 may not be entered or examined. Claim 2 should be presented as claim 41 in all future responses.
This action is in response to papers filed 2/27/2025
Claims 1-2, 24, 26, 28-40 are pending.
Claims 1-2, 29-30, 33-35 have been amended.
Claims 39-40 have been added by amendment.
Applicant’s election of group I, (1) immobilizing at least a portion of the plurality of first affinity agents to a surface (2) target molecule is a protein (3) contacting of (1) and/or (ii) is performed at a temperature of 4-37 °C (A) first affinity agents are immobilized to the surface of a solid-phase bead (5) label nucleic acid is linked to at least one fluorophore (6) (i) and (ii) occur simultaneously (7) each sample well is functionalized with positively-charged molecules o (8) delivered to and maintained in the sample wells by electrostatic interactions with positively-charged molecules at the interior base of each sample well in the reply filed on 5/3/2023 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 21-23 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 5/32023.
Claims 1-2, 24, 26, 28-40 are being examined.
Priority
The instant application was filed 12/15/2021 and claims priority from provisional application 63125634 , filed 12/15/2020.
Information Disclosure Statement
The information disclosure statement filed 2/27/2025 fails to comply with the provisions of 37 CFR 1.98(a)(4) because it lacks the appropriate size fee assertion. It has been placed in the application file, but the information referred to therein has not been considered as to the merits.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-2, 24, 26, 28-40 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1 and 2 have been amended to recite, ”comprises using a sensor.” The response asserts, “Support for the claim amendments and new claims may be found throughout the specification as filed including p. 3, lines 24-26, p. 14, lines 3-13 and lines 19-31, p. 3, lines 15-19 and Examples 1- 3.” The cited portions do not recite,”sensor.” Review and searching of the specification reveal the recitation of biosensor 10 times, which is of different in scope than merely reciting a sensor. Further the claims recites, “CMOS sensor” twice which is of different scope than “comprising a sensor.” Thus the claim as amended appears to be new matter.
Response to Arguments
This is a new grounds of rejection necessitated by amendment.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-2, 24, 26, 28-40 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.
Claim 1 has been amended to recite, “combining the segments of the label molecules with a known concentration of reference molecules in a detection chip comprising an ordered array of sample wells, wherein each reference molecule is linked to at least one fluorophore.” The claim is confusing and unclear as the claim encompasses a single sample, but then step (v) requires a detection chip comprising an ordered array of sample wells. Thus it is unclear if the claim requires a single sample is combined in a single well of the ordered array of sample wells or if the claim requires the sample is placed in multiple wells of the ordered array of the sample wells. If the later it is unclear how the segments from a sample is divided to be in multiple wells.
Claim 1 recites, “(vi) measuring ratio of detection events of label molecules relative to detection events of reference molecules.” The specification provides no limiting definition of “detection events”. While the claim has been amended to require a sensor, it is unclear what is required of an detection event. IT is unclear if merely determining fluorescence from the segment is enough or if the recitation of events requires some other detection or measuring event.
Claim 1 concludes with, “ (vii measuringthe concentration of target molecules in the sample by measuring the ratio of detection events of label molecules relative to detection events of reference molecules, wherein measuring the ratio of detection events comprises using a sensor to measure is on the dwell time of label molecules and reference molecules in the sample wells and wherein the first affinity agents are antibodies..” The metes and bounds of the claim are unclear how determining the concentration in the sample is done as the claim provides no specific guidance. Further it is unclear if it is “in part based on dwell time” what the rest of the concentration is based upon. Further it is unclear what is required of “dwell time.” The claim does not define dwell time. Review and searching of the specification did not reveal a definition or standard of what is required of dwell time. The specification on page 15 states, “fluorescence measurements (e.g., dwell time) are analyzed using pulse calling.” Searching and review of the art for “pulse calling” and “dwell time” only revealed the instant application and the WO document. Cambridge dictionary (https://dictionary.cambridge.org/us/dictionary/english/dwell-time, downloaded 8/24/2024) defines dwell time as, “how long people are likely to spend looking at an advertisement, buying goods, etc., especially while they are waiting somewhere such as an airport or train station.” Thus the metes and bounds are unclear. Further the claim has been amended to recite, “comprising using a sensor.” The specification provides no specific guidance what is required of a sensor. Thus it is unclear if the claim requires a specific structure or merely encompasses anything that can be used to sense or detect the fluorescent labels.
Claim 2 recites, “ (v) combining the isolated segments of the label molecules with a known concentration of reference molecules in a detection chip comprising an ordered array of sample wells, wherein each reference molecule is linked to at least one fluorophore.” The claim is confusing and unclear as the claim encompasses a single sample, but then step (v) requires a detection chip comprising an ordered array of sample wells. Thus it is unclear if the claim requires a single sample is combined in a single well of the ordered array of sample wells or if the claim requires the sample is placed in multiple wells of the ordered array of the sample wells. If the later it is unclear how the segments from a sample is divided to be in multiple wells.
Claim 2 recites, “((vi) detecting the label molecules and the reference molecules, thereby measuring the a ratio of detection events of label molecules relative to detection events of reference molecules.” The specification provides no limiting definition of “detection events”. While the claim has been amended to require a sensor, it is unclear what is required of an detection event. It is unclear if merely determining fluorescence from the segment is enough or if the recitation of events requires some other detection or measuring event.
Claim 2 recites, “ measuring the concentration of target molecules in the sample by measuring based on the ratio of detection events of label molecules relative to detection events of reference molecules, wherein [[the ]]measuring the ratio of detection events comprises using a sensor to measureis determined in part based on the dwell time of label molecules and reference molecules in the sample wells and wherein the first affinity agents are antibodies,.” The metes and bounds of the claim are unclear how determining the concentration in the sample is done as the claim provides no specific guidance. Further it is unclear if it is “in part based on dwell time” what the rest of the concentration is based upon. Further it is unclear what is required of “dwell time.” The claim does not define dwell time. Review and searching of the specification did not reveal a definition or standard of what is required of dwell time. The specification on page 15 states, “fluorescence measurements (e.g., dwell time) are analyzed using pulse calling.” Searching and review of the art for “pulse calling” and “dwell time” only revealed the instant application and the WO document. Cambridge dictionary (https://dictionary.cambridge.org/us/dictionary/english/dwell-time, downloaded 8/24/2024) defines dwell time as, “how long people are likely to spend looking at an advertisement, buying goods, etc., especially while they are waiting somewhere such as an airport or train station.” Thus the metes and bounds are unclear. urther the claim has been amended to recite, “comprising using a sensor.” The specification provides no specific guidance what is required of a sensor. Thus it is unclear if the claim requires a specific structure or merely encompasses anything that can be used to sense or detect the fluorescent labels.
Response to Arguments
The response traverses the rejection in view of the amendments to the claims. This argument has been thoroughly reviewed but is not considered persuasive as the amendment does not address all of the issues.
The response traverses the rejection of dwell time by asserting WO20200102741A1 which is incorporated by reference in its entirety provides what is required for dwell time. This argument has been thoroughly reviewed but is not considered persuasive as USC 37 CFR 1.57 (d) states:
(d) "Essential material" may be incorporated by reference, but only by way of an incorporation by reference to a U.S. patent or U.S. patent application publication, which patent or patent application publication does not itself incorporate such essential material by reference. "Essential material" is material that is necessary to:
(1) Provide a written description of the claimed invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and set forth the best mode contemplated by the inventor of carrying out the invention as required by 35 U.S.C. 112(a);
(2) Describe the claimed invention in terms that particularly point out and distinctly claim the invention as required by 35 U.S.C. 112(b); or
(3) Describe the structure, material, or acts that correspond to a claimed means or step for performing a specified function as required by 35 U.S.C. 112(f).
Thus incorporation by reference to a WO document is not a US patent or US patent publication. Thus the argument is not persuasive.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-2, 24, 26, 28-40 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a abstract idea or mental step without significantly more. The claim(s) recite(s) the abstract idea or mental step of determining. This judicial exception is not integrated into a practical application because if there no additional steps which rely upon or integrate the determining. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims require no specific reagents.
Claim analysis
The instant claim 1 is directed towards method of determining the concentration of target molecules in a sample, the method comprising:(i) contacting the sample comprising the target molecules with a plurality of first affinity agents having a binding affinity for the target molecules to produce a plurality of first complexes comprising a target molecule bound to a first affinity agent, wherein at least a portion of the plurality of first affinity agents are immobilized to a surface, wherein the target molecules are proteins;(ii) contacting the plurality of first complexes with a plurality of second affinity agents having a binding affinity for the first complexes to produce a plurality of second complexes comprising a second affinity agent bound to a first complex, wherein at least a portion of the second affinity agents are linked to label molecules, and wherein each of the label molecules is linked to at least one fluorophore;(iii) removing unbound second affinity agents and/or isolating the plurality of second complexes;(iv) isolating at least a segment of each of the label molecules from the bound second affinity agents of the plurality of second complexes;(v) combining the segments of the label molecules with a known concentration of reference molecules in a detection chip comprising an ordered array of sample wells, wherein each reference molecule is linked to at least one fluorophore;(vi) detecting the label molecules and the reference molecules, thereby measuring[[the]]a ratio of detection events of label molecules relative to detection events of reference molecules; and(vii) measuring the concentration of target molecules in the sample by measuring based on the ratio of detection events of label molecules relative to detection events of reference molecules, wherein [[the ]]measuring the ratio of detection events comprises using a sensor to measure i the dwell time of label molecules and reference molecules in the sample wells and wherein the first affinity agents are antibodies, the first affinity agents specifically bind to an epitope of the target molecules, and the second affinity agents are antibodies..
The measuring steps are mental step or abstract idea.
The instant claim 2 is directed towards a method of determining the concentration of target molecules in a sample, the method comprising:(i)(a) contacting the sample comprising the target molecules with a plurality of first affinity agents having a binding affinity for the target molecules to produce a plurality of first complexes comprising a target molecule bound to a first affinity agent, wherein the target molecules are proteins,(i)(b) immobilizing at least a portion of the plurality of first affinity agents to a surface;(ii) contacting the plurality of first complexes with a plurality of second affinity agents having a binding affinity for the first complexes to produce a plurality of second complexes comprising a second affinity agent bound to a first complex, wherein at least a portion of the second affinity agents are linked to label molecules and wherein each of the label molecules is linked to at least one fluorophore;(iii) removing unbound second affinity agents and/or isolating the plurality of second complexes;(iv) isolating at least a segment of each of the label molecules from the bound second affinity agents of the plurality of second complexes;(v) combining the isolated segments of the label molecules with a known concentration of reference molecules in a detection chip comprising an ordered array of sample wells, wherein each reference molecule is linked to at least one fluorophore;(vi) detecting the label molecules and the reference molecules, thereby measuring the a ratio of detection events of label molecules relative to detection events of reference molecules; and(vii) measuring the concentration of target molecules in the sample by measuring based on the ratio of detection events of label molecules relative to detection events of reference molecules, wherein measuring the ratio of detection events comprises using a sensor to measure is the dwell time of label molecules and reference molecules in the sample wells and wherein the first affinity agents are antibodies, the first affinity agents specifically bind to an epitope of the target molecules, and the second affinity agents are antibodies..
The measure steps are mental step or abstract idea.
Steps (i) to (ii) and (v) of claim 1 are required active steps.
Steps (i)(a), (i)(b) to(ii) and (v) of claim 2 are required active steps.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, abstract idea mental step.
With regards to claim 1, the claim recites, “, measuring the concentration of target molecules in the sample by measuring based on the ratio of detection events of label molecules relative to detection events of reference molecules, wherein [[the ]]measuring the ratio of detection events comprises using a sensor to measure i the dwell time of label molecules and reference molecules in the sample wells..” This is an abstract idea or mental step as it requires determining a ratio.
With regards to claim 2, the claim recites, “measuring the concentration of target molecules in the sample by measuring based on the ratio of detection events of label molecules relative to detection events of reference molecules, wherein [[the ]]measuring the ratio of detection events comprises using a sensor to measure i the dwell time of label molecules and reference molecules in the sample wells..” This is an abstract idea or mental step as it requires determining a ratio.
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as no additional steps integrate or otherwise depend from the judicial exception.
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No, as the claims provide no specific limitation which are significantly more than steps or reagents set forth with a high degree of generality.
The art of Gildor (USPGPUB 20190094214) and Cao (USPGPUB 20180223361) demonstrate the active steps required of the claims are routine and conventional.
Response to Arguments
The response traverses the rejection in view of the amendments to the claims. The response further alleges the claim integrates the judicial exception but does not identify how the judicial exception is integrated. Thus the rejection is maintained.
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 (i.e., changing from AIA to pre-AIA ) 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.
Claim(s) 1-2, 24, 26, 28-33, 35-40 is/are rejected under 35 U.S.C. 103 as being unpatentable Gildor (USPGPUB 20190094214) and Cao (USPGPUB 20180223361)
Claims 1 and 2 have been amended to recite,” measuring the concentration of target molecules in the sample by measuring the ratio of detection events of label molecules relative to detection events of reference molecules, wherein ]measuring the ratio of detection events comprises using a sensor to measureis determined on the dwell time of label molecules and reference molecules in the sample wells and wherein the first affinity agents are antibodies, the first affinity agents specifically bind to an epitope of the target molecules, and the second affinity agents are antibodies..” The specification does not provide a standard or definition of what is required or encompassed by a dwell time. It is unclear what is required of “dwell time.” The claim does not define dwell time. Review and searching of the specification did not reveal a definition or standard of what is required of dwell time. The specification on page 15 states, “fluorescence measurements (e.g., dwell time) are analyzed using pulse calling.” Searching and review of the art for “pulse calling” and “dwell time” only revealed the instant application and the WO document. Cambridge dictionary (https://dictionary.cambridge.org/us/dictionary/english/dwell-time, downloaded 8/24/2024) defines dwell time as, “how long people are likely to spend looking at an advertisement, buying goods, etc., especially while they are waiting somewhere such as an airport or train station.” Thus the metes and bounds are unclear. The dwell time appear to merely require fluorescence measurement.
Further the claims have been amended to recite, “comprising using a sensor.” The specification provides no specific guidance on what is require of a sensor. Thus it is unclear if the claim requires a specific structure or anything which can sense of detect fluorescence.
Gildor teaches a method of determining the concentration of target molecules in a sample (para [0026], Described herein are methods of detecting a target in a sample. Digital affinity linkage assay methods have been discovered in which the concentration of a target is determined on a solid support; and para [0014], the target comprises a protein; and para [0016], the target is a plurality of different targets; Proteins are molecules), the method comprising: (i) contacting the sample comprising the target molecules with a plurality of first affinity agents having a binding affinity for the target molecules to produce a plurality of first complexes comprising a target molecule bound to a first affinity agent (para (0004], a method of detecting a target in a sample comprises contacting the sample with a first affinity agent linked to a solid support, wherein the first affinity agent specifically binds to the target, if present, thereby forming a target bound to the first affinity agent; and para (0016], the target is a plurality of different targets, the first affinity agent is a plurality of different first affinity agents; and para (0014], the target is a complex; If the first affinity agents specifically bind to the target, it is reasonably understood that the plurality of first affinity agents have a binding affinity for the target molecules; Further, if· the target is a complex and the first affinity agents bind to the complex, the resulting structure is a complex), wherein at least a portion of the plurality of first affinity agents are immobilized to a surface (para [0004], a method of detecting a target in a sample comprises contacting the sample with a first affinity agent linked to a solid support; and para (0013], the solid support or the plurality of solid supports is/are a magnetic bead (s), a nonmagnetic bead (s), or a surface_ (s) of a reaction vessel (s)); (ii) contacting the plurality of first complexes with a plurality of second affinity agents having a binding affinity for the first complexes to produce a plurality of second complexes comprising a second affinity agent bound to a first complex (para [0004], a method of detecting a target in a sample comprises ... contacting the separated sample with a second affinity agent comprising a first label and a third affinity agent comprising a second label, wherein the second and third affinity agents specifically bind to the target, thereby forming a target labeled affinity agent complex; and para [0016], the second affinity agent is a plurality of different second affinity agents comprising a plurality of first labels; If the second affinity agents specifically bind to the target, it is reasonably understood that the plurality of second affinity agents have a binding affinity for the first complexes), wherein at least a
portion of the second affinity agents are linked to label molecules (para [0004], a method of detecting a target in a sample comprises ... contacting the separated sample with ·a second affinity agent comprising a first label and a third affinity agent comprising a second label, wherein the second and third affinity agents specifically bind to the target, thereby forming a target labeled affinity agent complex; and para (0016], the second affinity agent is a plurality of different second affinity agents comprising a plurality of first labels); (iii) optionally removing unbound second affinity agents and/or isolating the plurality of second complexes (para [0004], a method of detecting a target in a sample comprises ... separating the target-labeled affinity agent complex from uncomplexed second and third affinity agents based on the presence or absence of the solid support); but does not teach the method comprising (iv) optionally isolating at least a segment of each of the label molecules from the bound second affinity agents of the plurality of second complexes; (v) combining the segments of the label molecules with a known concentration of reference molecules; (vi) determining the ratio of detection events of label molecules relative to detection events of reference molecules; and (vii) determining the concentration of target molecules in the sample based at least in part on the ratio of detection events of label molecules relative to detection events of reference molecules. “
Gildor teaches partitioning into microchannels or microwells which are broadly encompassed by ordered array.
Gildor teaches, “[0065] In some embodiments, the first affinity agent is cleaved from the solid support prior to the next (partitioning) step, thereby releasing the target-labeled affinity agent complex from the solid support. In some embodiments, an amino acid tag linking the target-labeled affinity agent complex to the solid support is cleaved by a sequence-specific protease (e.g., TEV, factor Xa, or thrombin). In certain embodiments, a photo-cleavable linker between the solid surface and the first affinity agent is cleaved by exposing the linker to light. In some embodiments, the target-labeled affinity agent complex is cross-linked prior to partitioning the separated target-labeled affinity agent complex into a plurality of partitions. [0066] In exemplary step 150, a plurality of partitions are formed from the separated target-labeled affinity agent complex such that a subset of the partitions contains the target-labeled affinity agent complex. The partitions can include any of a number of types of partitions, including solid partitions (e.g., wells or tubes) and fluid partitions (e.g., aqueous phase or droplet within an oil phase). In some embodiments, the partitions are droplets. In some embodiments, the partitions are microchannels or microwells. Methods and compositions for partitioning a solution are described, for example, in published patent applications WO 2012/135259, WO 2014/117088, WO 2010/036352, and U.S. Pat. No. 9,156,010, the entire content of each of which is incorporated by reference herein.”
Gildor teaches, “[0080] In certain embodiments, a method of detecting a target in a sample comprises contacting the sample with a first affinity agent linked to a solid support, a second affinity agent comprising a first label, and a third affinity agent comprising a second label. The first, second and third affinity agents specifically bind to the target, if present, thereby forming a target-labeled affinity agent complex. In some embodiments, the first, second, and third affinity agents specifically bind to different epitopes on the target. The next step comprises separating the target-labeled affinity agent complex from uncomplexed components in the sample based on the presence or absence of the solid support, thereby generating a separated target-labeled affinity agent complex. Next, the separated target-labeled affinity agent complex is partitioned into a plurality of partitions. The presence of the target is detected in the sample by detecting the presence of the first and second labels in at least one same partition.”
Gildor teaches use of a detector (sensor )(0089).
Cao teaches a method of characterizing a sample (para [0002], According to some embodiments herein, a method of characterizing a sample is provided) comprising labeling a plurality of sample molecules with at least a first label (para [0002], The method can comprise labeling a plurality of sample molecules with at least a first label) (v) combining the segments c;if the label molecules with reference molecules (para (0002], The method can comprise providing a plurality of labeled reference molecules ... The method can comprise translocating the plurality of labeled sample molecules and the plurality of labeled reference molecules though a fluidic channel); (vi) determining the ratio of detection events of label molecules relative to detection events of reference molecules (para (0002], The method can comprise detecting signals from the labeled sample molecules so as to ascertain at least a first pattern or plurality of patterns characteristic of the first genomic fragment or fragments of interest; and a second pattern or plurality of patterns characteristic of the reference genomic fragment or fragments. The method can comprise correlating signals ascertaining the first pattern or plurality of patterns to signals ascertaining the second pattern or plurality of patterns ... In some embodiments, correlating signals comprises using the ratio (K) between the signal arising from a plurality of labeled sample molecules or portions thereof (S1, S2 ... Sn) and the signal arising from the reference).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to apply the method taught by Cao to determine the concentration of the labelled second complexes taught by Gildor because both methods are used to characterize a protein target from a blood sample (Cao, para [0006], the sample of any of the methods herein is selected from the group consisting of a bacteria, a virion, a DNA molecule, an RNA molecule, a nucleic acid polymer, a protein ... ln some embodiments, the sample of any of the methods herein is derived from maternal blood; and Gildor, para [0014], the target comprises a protein; and para [0057], the sample is a biological sample ... A biological sample can be any tissue or bodily fluid obtained from the biological organism, e. g., blood). Further, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to determine the concentration of the reference molecules prior to combining the label molecules and reference molecules in order to be able to determine the concentration of the label molecules from the ratio of detection events using a detector (or sensor) . The artisan would have a reasonable expectation of success as the artisan is merely using known methods.
Further, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to (vii) determine the concentration of target molecules in the sample based at least in part on the ratio of detection events of label molecules relative to detection events of reference molecules because the method can be used to detect an amount of the labelled molecules or the reference molecules (para [0025], FIG. 2 is a schematic diagram illustrating an embodiment of an imaging setup to detect signals emitted from labeled molecules or particles to tabulate the amount, intensity, and configuration of the sample and reference molecule or particles). The artisan would have a reasonable expectation of success as the artisan is merely combining art accepted methods.
With regards to claim 2, Gildor teaches a method of determining the concentration of target molecules in a sample (para [0026], Described herein are methods of detecting a target in a sample. Digital affinity linkage assay methods have been discovered in which the concentration of a target is determined on a solid support; and para [0014], the target comprises a protein; and para [0016], the target is a plurality of different targets; Proteins are molecules), the method comprising: (i) contacting the sample comprising the target molecules with a plurality of first affinity agents having a binding affinity for the target molecules to produce a plurality of first complexes comprising a target molecule bound to a first affinity agent (para (0004], a method of detecting a target in a sample comprises contacting the sample with a first affinity agent linked to a solid support, wherein the first affinity agent specifically binds to the target, if present, thereby forming a target bound to the first affinity agent; and para (0016], the target is a plurality of different targets, the first affinity agent is a plurality of different first affinity agents; and para (0014], the target is a complex; If the first affinity agents specifically bind to the target, it is reasonably understood that the plurality of first affinity agents have a binding affinity for the target molecules; Further, if· the target is a complex and the first affinity agents bind to the complex, the resulting structure is a complex), wherein at least a portion of the plurality of first affinity agents are immobilized to a surface (para [0004], a method of detecting a target in a sample comprises contacting the sample with a first affinity agent linked to a solid support; and para (0013], the solid support or the plurality of solid supports is/are a magnetic bead (s), a nonmagnetic bead (s), or a surface_ (s) of a reaction vessel (s)); (ii) contacting the plurality of first complexes with a plurality of second affinity agents having a binding affinity for the first complexes to produce a plurality of second complexes comprising a second affinity agent bound to a first complex (para [0004], a method of detecting a target in a sample comprises ... contacting the separated sample with a second affinity agent comprising a first label and a third affinity agent comprising a second label, wherein the second and third affinity agents specifically bind to the target, thereby forming a target labeled affinity agent complex; and para [0016], the second affinity agent is a plurality of different second affinity agents comprising a plurality of first labels; If the second affinity agents specifically bind to the target, it is reasonably understood that the plurality of second affinity agents have a binding affinity for the first complexes), wherein at least a
portion of the second affinity agents are linked to label molecules (para [0004], a method of detecting a target in a sample comprises ... contacting the separated sample with ·a second affinity agent comprising a first label and a third affinity agent comprising a second label, wherein the second and third affinity agents specifically bind to the target, thereby forming a target labeled affinity agent complex; and para (0016], the second affinity agent is a plurality of different second affinity agents comprising a plurality of first labels); (iii) optionally removing unbound second affinity agents and/or isolating the plurality of second complexes (para [0004], a method of detecting a target in a sample comprises ... separating the target-labeled affinity agent complex from uncomplexed second and third affinity agents based on the presence or absence of the solid support); but does not teach the method comprising (iv) optionally isolating at least a segment of each of the label molecules from the bound second affinity agents of the plurality of second complexes; (v) combining the segments of the label molecules with a known concentration of reference molecules; (vi) determining the ratio of detection events of label molecules relative to detection events of reference molecules; and (vii) determining the concentration of target molecules in the sample based at least in part on the ratio of detection events of label molecules relative to detection events of reference molecules. “
Gildor teaches partitioning into microchannels or microwells which are broadly encompassed by ordered array.
Gildor teaches, “[0065] In some embodiments, the first affinity agent is cleaved from the solid support prior to the next (partitioning) step, thereby releasing the target-labeled affinity agent complex from the solid support. In some embodiments, an amino acid tag linking the target-labeled affinity agent complex to the solid support is cleaved by a sequence-specific protease (e.g., TEV, factor Xa, or thrombin). In certain embodiments, a photo-cleavable linker between the solid surface and the first affinity agent is cleaved by exposing the linker to light. In some embodiments, the target-labeled affinity agent complex is cross-linked prior to partitioning the separated target-labeled affinity agent complex into a plurality of partitions. [0066] In exemplary step 150, a plurality of partitions are formed from the separated target-labeled affinity agent complex such that a subset of the partitions contains the target-labeled affinity agent complex. The partitions can include any of a number of types of partitions, including solid partitions (e.g., wells or tubes) and fluid partitions (e.g., aqueous phase or droplet within an oil phase). In some embodiments, the partitions are droplets. In some embodiments, the partitions are microchannels or microwells. Methods and compositions for partitioning a solution are described, for example, in published patent applications WO 2012/135259, WO 2014/117088, WO 2010/036352, and U.S. Pat. No. 9,156,010, the entire content of each of which is incorporated by reference herein.”
Gildor teaches, “[0080] In certain embodiments, a method of detecting a target in a sample comprises contacting the sample with a first affinity agent linked to a solid support, a second affinity agent comprising a first label, and a third affinity agent comprising a second label. The first, second and third affinity agents specifically bind to the target, if present, thereby forming a target-labeled affinity agent complex. In some embodiments, the first, second, and third affinity agents specifically bind to different epitopes on the target. The next step comprises separating the target-labeled affinity agent complex from uncomplexed components in the sample based on the presence or absence of the solid support, thereby generating a separated target-labeled affinity agent complex. Next, the separated target-labeled affinity agent complex is partitioned into a plurality of partitions. The presence of the target is detected in the sample by detecting the presence of the first and second labels in at least one same partition.”
Gildor teaches use of a detector (sensor )(0089).
Cao teaches a method of characterizing a sample (para [0002], According to some embodiments herein, a method of characterizing a sample is provided) comprising labeling a plurality of sample molecules with at least a first label (para [0002], The method can comprise labeling a plurality of sample molecules with at least a first label) (v) combining the segments c;if the label molecules with reference molecules (para (0002], The method can comprise providing a plurality of labeled reference molecules ... The method can comprise translocating the plurality of labeled sample molecules and the plurality of labeled reference molecules though a fluidic channel); (vi) determining the ratio of detection events of label molecules relative to detection events of reference molecules (para (0002], The method can comprise detecting signals from the labeled sample molecules so as to ascertain at least a first pattern or plurality of patterns characteristic of the first genomic fragment or fragments of interest; and a second pattern or plurality of patterns characteristic of the reference genomic fragment or fragments. The method can comprise correlating signals ascertaining the first pattern or plurality of patterns to signals ascertaining the second pattern or plurality of patterns ... In some embodiments, correlating signals comprises using the ratio (K) between the signal arising from a plurality of labeled sample molecules or portions thereof (S1, S2 ... Sn) and the signal arising from the reference).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to apply the method taught by Cao to determine the concentration of the labelled second complexes taught by Gildor because both methods are used to characterize a protein target from a blood sample (Cao, para [0006], the sample of any of the methods herein is selected from the group consisting of a bacteria, a virion, a DNA molecule, an RNA molecule, a nucleic acid polymer, a protein ... ln some embodiments, the sample of any of the methods herein is derived from maternal blood; and Gildor, para [0014], the target comprises a protein; and para [0057], the sample is a biological sample ... A biological sample can be any tissue or bodily fluid obtained from the biological organism, e. g., blood). Further, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to determine the concentration of the reference molecules prior to combining the label molecules and reference molecules in order to be able to determine the concentration of the label molecules from the ratio of detection events using a detector (or sensor) . The artisan would have a reasonable expectation of success as the artisan is merely using known methods.
Further, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to (vii) determine the concentration of target molecules in the sample based at least in part on the ratio of detection events of label molecules relative to detection events of reference molecules because the method can be used to detect an amount of the labelled molecules or the reference molecules (para [0025], FIG. 2 is a schematic diagram illustrating an embodiment of an imaging setup to detect signals emitted from labeled molecules or particles to tabulate the amount, intensity, and configuration of the sample and reference molecule or particles). The artisan would have a reasonable expectation of success as the artisan is merely combining art accepted methods.
Gildor teaches the target comprises a protein; and para [0016].
With regards to claim 24, Gildor teaches, “The beads and samples were incubated for 1.5 hours at room temperature” (105).
With regards to claim 26, Gildor teaches, “ 0018] In an embodiment, a kit for detecting a target in a sample comprises a first affinity agent linked to a solid support” Gildor teaches, “[0059] Exemplary solid supports include, but are not limited to, particles (e.g., magnetic beads, polymeric beads, or silica-based beads) or a solid surface the surface of a reaction vessel such as a tube or a well in a plate).”
With regards to claim 28-29, Gildor teaches, “the nucleic acid label is about 10, 15, 20, 25, 30, 35, 40, 45, 50.” (0083).
With regards to claim 30, Gildor teaches, “0083] In some embodiments, the first and second labels are nucleic acid (e.g., DNA) labels. Examples of suitable nucleic acid labels include, but are not limited to, oligonucleotide sequences, single-stranded DNA, double-stranded DNA.”
With regards to claim 31, Gildor teaches a washimg to remove unbound components (0021, figure 2).
With regards to claim 32, Gildor teaches heating to 95oC (0133), which is removing by altering temperature.
With regards to claim 33, Gildor teaches, “the first label is a first fluorophore and the second label is a second fluorophore.” (0010).
With regards to claim 37, Gildor teaches the sue of biotin-streptavidin linked solid support (0099).
With regards to claim 38, Gildor teaches hybridization of molecules (0083).
With regards to claims39-40, Cao teaches labeling with affinity reagents (0002)
Response to Arguments
The response begins traversing the rejection by asserting the amendments have overcome the rejections. This argument is not persuasive for the reasons set forth in the amended rejection.
The response continues by providing arguments with respect to dwell time as wet forth with respect to the 112(b) rejection. This argument has been thoroughly reviewed but is not considered persuasive as the WO document referenced is not a US patent application or US patent publication. Thus incorporating by reference of essential matter is not allowed as per USC 37 CFR 1.57 (d) states:
(d) "Essential material" may be incorporated by reference, but only by way of an incorporation by reference to a U.S. patent or U.S. patent application publication, which patent or patent application publication does not itself incorporate such essential material by reference. "Essential material" is material that is necessary to:
(1) Provide a written description of the claimed invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and set forth the best mode contemplated by the inventor of carrying out the invention as required by 35 U.S.C. 112(a);
(2) Describe the claimed invention in terms that particularly point out and distinctly claim the invention as required by 35 U.S.C. 112(b); or
(3) Describe the structure, material, or acts that correspond to a claimed means or step for performing a specified function as required by 35 U.S.C. 112(f).
Claim(s) 37 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gildor (USPGPUB 20190094214) and Cao (USPGPUB 20180223361) as applied to claims 1-2, 24, 26, 28-33, 35-40 above, and further in view of Brink (SG 10201607410T A) .
The teachings of Gildor and Cao are set forth above.
Gildor and Cao do not specifically teach the use of positively charged molecules in sample wells.
However, Brink teaches