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 .
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-2 and 4-8 is/are rejected under 35 U.S.C. 102(a)(1) and (1)(2) as being anticipated by US 20120028342 (herein after “Ismagilov”).
Regarding claim 1, see Ismagilov in paragraph 0123 disclosing for example a microfabricated device [SlipChip]. The device can be used for immunoassays for example (para. 0126).
Analyte capture can be via functionalization of the surface of an area [in the device] (para. 0127).
Capture elements include antibodies, affinity proteins, etc. (para. 0128).
The disclosed approach can analyze samples with low concentrations of analytes of rare nucleic acids, proteins, biomarkers, etc. (para. 0130).
The sample may be a sweat sample (para. 0137).
The device may contain channels through which flow is desired as well as an array of capillary channels (para. 0146).
The Ismagilov device is a capillary with a surface comprising a capture (such as antibody). Examiner notes that the following show that the device is on a microscale and that the channels, including the main channel for analysis is considered a capillary, as it is capable of capillary action (see below, in particular paragraph 0146).
See paragraph 0126 disclosing movement of a substance through, into, and/or across at least one duct and/or area. For example movement of a substance can be used for washing steps in immunoassays, removal of products or byproducts, introduction of reagents, or dilutions.
See paragraph 0127 disclosing the following.
“…. Analytes can be essentially any discrete material which can be flowed through a microscale system. Analyte capture may be accomplished for example by preloading the areas of the device with capture elements that are trapped in the areas (such as particles, beads or gels, retained within areas via magnetic forces or by geometry or with relative sizes of beads and ducts or with a membrane), thus whatever absorbs, adsorbs, or reacts with these beads or gels is also trapped. These areas will then retain an amount or component or analyte of the substances they are exposed to. This can also be done by functionalization of the surface of an area, deposition of a material on an area, attaching a monomer in a polymerization reaction (such as peptide or DNA synthesis) to an area, etc.” Para. 0127 (emphasis added).
See paragraph 0128, disclosing the following.
“Other examples of capture elements include antibodies, affinity-proteins, aptamers, beads, particles and biological cells…Capture elements are optionally coupled to reagents, affinity matrix materials, or the like, e.g., nucleic acid synthesis reagents, peptide synthesis reagents, polymer synthesis reagents, nucleic acids, nucleotides, nucleobases, nucleosides, peptides, amino acids, monomers, cells, biological samples, synthetic molecules, or combinations thereof. Capture elements optionally serve many purposes within the device, including acting as blank particles, dummy particles, calibration particles, sample particles, reagent particles, test particles, and molecular capture particles, e.g., to capture a sample at low concentration. Additionally the capture elements may be used to provide particle retention elements. Capture elements are sized to pass or not pass through selected ducts or membranes (or other microscale elements). Accordingly, particles or beads will range in size depending on the application.” Para. 0128 (emphasis added).
“A substance may be introduced to fill the majority of reaction areas and ducts. Filling may be continued further to provide excess sample, larger than the volume of areas and ducts. Introducing a volume of substance which is greater than the volume of areas and ducts will increase the amount of analyte which may be captured within the capture. Introducing a wash fluid after the introduction of a substance may be performed to wash the capture elements and analytes which are bound to the capture elements. Subsequent further slipping may be performed to conduct reactions and analysis of the analytes.” Para. 0129 (emphasis added).
“… In another example of inducing movement of a substance, differential pressures due to surface tension and flow resistance can be used to drive flow after slipping, even without applying external pressure. In one instance, a device may contain one or more main channels through which flow is desired as well as an array of one or more capillary channels, which are smaller than the main channel and therefore have a higher capillary pressure than the main channel. The device can be slipped to bring the main channel(s) into fluidic communication with the array of capillary channels, thus creating a fluidic path that has higher pressure in the capillary channels than in the main channel, which drives flow into the main channel. The device and the slipping motion can be tuned to provide control over the rate and duration of flow. For example, reservoirs of fluid that are open to the atmosphere can be located at controlled distances the capillary and/or main channel, to control the pressure due to flow resistance. These reservoirs can optionally be connected via a duct to the capillary and/or main channel, to further decrease flow resistance and thus increase the flow rate. This could for example be used to drive flow through a washing channel, to wash during an immunoassay, or to drive slow flow over a perfusion culture of cells or a suspension of beads.” Para. 0146 (emphasis added).
Substances are mixed (see for example para. 0158-160).
Use of the device includes protein activity assay and protein binding assay, for example (para. 0162).
“The devices of the present invention can be analyzed using a variety of known detection methods (optical, x-ray, MALDI, FP/FCS, FCS, fluorometric, colorimetric, chemiluminescence, bioluminescence, scattering, Surface Plasmon Resonance, electrochemical, electrophoresis, lasers, mass spectrometry, Raman spectrometry, FLIPR.TM. (Molecular Devices), etc.). The device can be analyzed directly when suitable materials are used (i.e., optically transparent materials used for optical detection methods). For those detection methods, such as optical absorption, in which the signal is a function of pathlength, multiple areas can be formed on the device such that they contain identical contents, but differ only in pathlength. In this way, the chances are increased that the signal obtained from at least one of the areas will be within the dynamic range of the detector. A computer system configured to account for the differing pathlengths could be used to obtain the final desired result, for example an analyte concentration. The device alternatively can be opened and individual areas analyzed or designed to allow slippage into a further position that allows for access to individual areas (e.g., through access holes). In some embodiments, amplification of the reaction areas may be conducted (e.g. silver-based amplification, microphage amplification, etc.).” Para. 0171 (emphasis added).
The device can contain areas that are used as positive or negative controls. To make positive controls, the analyte that is being tested for in other areas on the device can be preloaded in the control areas, such that when the device parts are moved as described herein, the pre-loaded analyte is exposed to reactions and detected using the same method as the sample to be measured. When a positive control does not give the expected result, it can be sign of improper storage or usage of the device. Similarly, negative control areas can be prepared that contain no analyte, which would be expected to give no signal when exposed to the reagents for analysis. Para. 0175.
“In some embodiments, the device can contain areas that are used as positive or negative controls. To make positive controls, the analyte that is being tested for in other areas on the device can be preloaded in the control areas, such that when the device parts are moved as described herein, the pre-loaded analyte is exposed to reactions and detected using the same method as the sample to be measured. When a positive control does not give the expected result, it can be sign of improper storage or usage of the device. Similarly, negative control areas can be prepared that contain no analyte, which would be expected to give no signal when exposed to the reagents for analysis. Additive verification controls can also be used to determine integrity of the assay. Using the techniques of the present invention, a known amount, X, of analyte can be added to the sample containing the unknown amount of analyte, and then both the sample containing additional material and the original sample containing the unknown amount are assayed for analyte concentration using the same method, preferably on the same device to give results Y, for the unknown sample, and Z, for the unknown sample with added amounts of analyte. The difference between Z and Y should be X, and any deviation from X indicates a problem with the assay, such as degradation of the assay reagents.” Para. 0175 (emphasis added).
[Examiner notes that, aAs exemplified above, the difference between results from an unknown amount and a known amount is determined. This is the same as a comparison, and it is also well-known in the art.]
The capture area contains a substance capable of capturing an amount of the analyte and the capturing substance could be surface bound antibodies, or other molecules selective for the analyte (para. 0180).
Measuring concentration can be done by measuring intensity or time to reach intensity (para. 0181).
“In some embodiments, measuring concentration can be done by measuring intensity or time to reach intensity. Time resolution can be automatic or manual. For visual or photometric detection, the device may include a computer with a timer to control or signal at what time or times an image should be acquired or a test area observed.” Para. 0181 (emphasis added).
If color change or other detectable difference occurs when the analyte is bound to capture sites, measuring the length or size of the capture zone directly gives a measure of the amount of analyte. Alternatively, a competitive strategy in which a complex of a capture molecule and a labeled analyte is pre-formed in the volume, then added analyte displaces the labeled analyte, and finally the labeled analyte is detected as will be apparent to one skilled in the art. Para. 0183.
The detection antibody is chosen to bind strongly to the analyte, or the detection antibody may be labeled such as with a fluorescent tag, or may be unlabeled, depending on the specific immunoassay configuration. The device can be configured to perform a single immunoassay on a single sample or a plurality of samples, or many different such immunoassays on a single sample or a plurality of samples. Para. 0187.
Areas of the device may constitute a separation area. Separation may be carried out by methods known in the art, such as capillary electrophoresis. Para. 0191.
In some embodiments, a user-loaded SlipChip can be used to perform multiplexed nanoliter-scale experiments by combining a sample with multiple different reagents, each at multiple mixing ratios. The mixing ratios, characterized, for example, by diluting a fluorescent dye, can be controlled by the volume of each of the combined areas. Para. 0195.
The device can be used to combine a sample with many different reagents to perform multiplexed experiments in a user-loaded fashion. Para. 0196.
The device can include continuous fluidic path formed by a reagent inlet, reagent areas, and outlet. Para. 0200.
The [SlipChip] device is compatible with a wide range of visual detection chemistries. In SlipChip experiments in a 55 nL volume at 5 pM analyte (about 165,000 molecules) this chemistry produced a visible signal that was clearly distinguishable from background. The signal was generated within 10 minutes. Para. 0446.
Multistep processing of, for example, thousands of, for example, nanoliter, picoliter or femtoliter volumes can be achieved by using the SlipChip. Sophisticated fluid manipulation on a SlipChip can be used to perform the multi-step heterogeneous immunoassays and other chemistries that are preferred for detection of TBI biomarkers at the single-molecule level. The SlipChip is a microfluidic platform that can be used to encode a complex program for parallel manipulation of thousands of small volumes. Heterogeneous immunoassays can be performed quantitatively with amplification on certain embodiments of the SlipChip. To detect low levels of protein biomarkers in TBI, heterogeneous immunoassays are useful because a large excess of capture antibody can be used to drive binding. For these assays, multi-step processing is preferred, including washing steps and addition of reagents for signal amplification. The inventors have demonstrated a bead-based immunoassay with pM-level sensitivity for the metabolic marker insulin, using nanoliter volumes on SlipChip. Stochastic confinement on the SlipChip can be used for the counting of single DNA molecules after amplification by digital PCR. The inventors demonstrated that single molecules of DNA can be detected and their concentration quantified by counting the number of positive areas out of 1,280 total areas, each 2.6 nL in volume. Para. 0460.
Certain embodiments of the SlipChip can be used to quantify a range of about 0.02-200 pM concentrations, or down to 0.001 pM with coincidence detection. Para. 462.
Thus as to Applicant’s claims 1, measuring fluorescence in a fluidic path such as a channel or capillary is equivalent to Applicant’s measuring luminescence in a test capillary. The assay format may be competitive (para. 0183). Measuring can occur within 30 minutes [e.g., 10 minutes, para. 0446]. The device can contain areas that are used as negative control areas that are prepared that contain no analyte, which would be expected to give no signal when exposed to the reagents for analysis (para. 0175.) Areas for positive or negative controls are disclosed (para. 0175). It is understood by one skilled in the art that a comparison between the area where the assay is performed on the sample and the negative control area is made, as is well known in the art to make use of the negative control. The concentration or amount of analyte is determined (para. 0181), as is well known in the art. The sample may be a sweat sample (para. 0137).
As to claim 2, substances are mixed (see for example para. 0158-160).
As to claim 4, a plurality of reagents can be used for multiplexed experiments (see for example para. 0195). Competitive format assays can be performed (para. 0183).
As to claim 5, an array of capillaries may be used (para. 0146.)
As to claim 6, any portion of the Ismagilov device is considered to be disposable [i.e., capable of being disposed of].
As to claim 7, measuring can occur within 20 minutes [e.g., 10 minutes, para. 0446].
As to claim 8, Ismagilov discloses that the SlipChip can be used to separate and detect small molecules such as drugs and their metabolites and complexes, hormones, environmental pollutants, antibiotics, nicotine and its metabolites, drugs of abuse, stress hormones, other molecules associated with chronic and acute stress (para. 0321).
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.
Claim(s) 3 and 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over US 20120028342 (herein after “Ismagilov”).
Ismagilov has been discussed above.
Regarding claim 3, while Ismagilov is silent as to the sample of sweat having a total volume of less than or equal to about 4 uL, given the small volume disclosed by Ismagilov (para. 0446, 0460), it would have been obvious to one skilled in the art that the invention allows for detection of analyte in a sample provided in a volume of less than or equal to 4 uL, as a workable range.
Regarding claim 9, Ismagilov is silent as to the detection limit of the device for the target analyte being less than or equal to about 150 pg/mL. However, Ismagilov discloses that certain embodiments can be used to quantify a range of about range of about 0.02-200 pM concentrations, or down to 0.001 pM with coincidence detection (para. 0462). Thus detecting target analyte of less than or equal to about 10 pg/mL appears to fall within a workable range of the Ismagilov device.
Response to Arguments
Applicant's arguments have been fully considered but they are not persuasive.
Applicant asserts that Ismagilov’s paragraph 0146 describes that its device can include an array of capillary channels that can be brought into communication with the main channel to drive flow into the main channel. Applicant argues that there is no mention in paragraph 0146 of a test capillary with a surface comprising at least one antibody or introducing a test sample into a test capillary to contact the test sample with the surface of the test capillary, as required by claim 1.
Applicant states that Ismagilov also fails to disclose measuring a first luminescence value of a test sample comprising (i) the sample of sweat that optionally comprising a target analyte capable of binding with the at least one antibody and (ii) one or more competitive conjugates comprising a luminescent moiety and an analyte capable of binding with the at least one antibody.
Applicant states the following. Ismagilov’s paragraph 0137 relied on by the Office provides an open-ended laundry list of various types of biological and nonbiological samples of which sweat is one example but no further guidance or embodiment toward selecting sweat as a sample. Also, Ismagilov fails to disclosure measuring a first luminescence value comprising one or more competitive conjgates comprising a luminescent moiety and an analyte capable of binding with the at least one antibody. Instead, Ismagilov’s paragraph 0171 generically reports an open-ended list of at least 17 detection methods of which chemiluminescence is one, but provides nothing further regarding the actual steps performed for measuring luminescence, measuring a first luminescence value of the claimed test sample comprising one ore more competitive conjugates comprising a luminescent moiety and an analyte capable of binding with the at least one antibody.
Applicant further states that the Office [p. 6 of previous action] “measuring fluorescence in a fluidic path such as a channel or capillary is equivalent to Applicant’s measuring luminescence in a test capillary.” Applicant states however that Ismagilov provides no disclosure regarding any type of measuring occurring in or within a capillary, as claimed. Applicant asserts that, rather, Ismagilov reports an array of capillary channels for purposes of driving fluid flow into the main channel.
These arguments are not persuasive. In short, paragraph 0146 of Ismagilov shows that even the main channel is a capillary (as “capillary pressure occurs there too, though less than in what is called “capillary channel”). Also, regarding luminescence, it is understood to occur within the main channel [capillary]. Luminescence detection, including on a sample of sweat, is known in the art, as discussed by Ismagilov, and thus details of such detection is understood by one skilled in the art.
The following disclosures by Ismagilov (as elaborated above in the grounds for rejection) is provided below to show disclosures by Ismagilov for the claimed limitations.
See paragraph 0126 disclosing movement of a substance through, into, and/or across at least one duct and/or area. For example movement of a substance can be used for washing steps in immunoassays, removal of products or byproducts, introduction of reagents, or dilutions.
See paragraph 0127 disclosing the following.
“…. Analytes can be essentially any discrete material which can be flowed through a microscale system. Analyte capture may be accomplished for example by preloading the areas of the device with capture elements that are trapped in the areas (such as particles, beads or gels, retained within areas via magnetic forces or by geometry or with relative sizes of beads and ducts or with a membrane), thus whatever absorbs, adsorbs, or reacts with these beads or gels is also trapped. These areas will then retain an amount or component or analyte of the substances they are exposed to. This can also be done by functionalization of the surface of an area, deposition of a material on an area, attaching a monomer in a polymerization reaction (such as peptide or DNA synthesis) to an area, etc.” Para. 0127 (emphasis added).
See paragraph 0128, disclosing the following.
“Other examples of capture elements include antibodies, affinity-proteins, aptamers, beads, particles and biological cells…Capture elements are optionally coupled to reagents, affinity matrix materials, or the like, e.g., nucleic acid synthesis reagents, peptide synthesis reagents, polymer synthesis reagents, nucleic acids, nucleotides, nucleobases, nucleosides, peptides, amino acids, monomers, cells, biological samples, synthetic molecules, or combinations thereof. Capture elements optionally serve many purposes within the device, including acting as blank particles, dummy particles, calibration particles, sample particles, reagent particles, test particles, and molecular capture particles, e.g., to capture a sample at low concentration. Additionally the capture elements may be used to provide particle retention elements. Capture elements are sized to pass or not pass through selected ducts or membranes (or other microscale elements). Accordingly, particles or beads will range in size depending on the application.” Para. 0128 (emphasis added).
“A substance may be introduced to fill the majority of reaction areas and ducts. Filling may be continued further to provide excess sample, larger than the volume of areas and ducts. Introducing a volume of substance which is greater than the volume of areas and ducts will increase the amount of analyte which may be captured within the capture. Introducing a wash fluid after the introduction of a substance may be performed to wash the capture elements and analytes which are bound to the capture elements. Subsequent further slipping may be performed to conduct reactions and analysis of the analytes.” Para. 0129 (emphasis added).
“… In another example of inducing movement of a substance, differential pressures due to surface tension and flow resistance can be used to drive flow after slipping, even without applying external pressure. In one instance, a device may contain one or more main channels through which flow is desired as well as an array of one or more capillary channels, which are smaller than the main channel and therefore have a higher capillary pressure than the main channel. The device can be slipped to bring the main channel(s) into fluidic communication with the array of capillary channels, thus creating a fluidic path that has higher pressure in the capillary channels than in the main channel, which drives flow into the main channel. The device and the slipping motion can be tuned to provide control over the rate and duration of flow. For example, reservoirs of fluid that are open to the atmosphere can be located at controlled distances the capillary and/or main channel, to control the pressure due to flow resistance. These reservoirs can optionally be connected via a duct to the capillary and/or main channel, to further decrease flow resistance and thus increase the flow rate. This could for example be used to drive flow through a washing channel, to wash during an immunoassay, or to drive slow flow over a perfusion culture of cells or a suspension of beads.” Para. 0146 (emphasis added).
Substances are mixed (see for example para. 0158-160).
Use of the device includes protein activity assay and protein binding assay, for example (para. 0162).
“The devices of the present invention can be analyzed using a variety of known detection methods (optical, x-ray, MALDI, FP/FCS, FCS, fluorometric, colorimetric, chemiluminescence, bioluminescence, scattering, Surface Plasmon Resonance, electrochemical, electrophoresis, lasers, mass spectrometry, Raman spectrometry, FLIPR.TM. (Molecular Devices), etc.). The device can be analyzed directly when suitable materials are used (i.e., optically transparent materials used for optical detection methods). For those detection methods, such as optical absorption, in which the signal is a function of pathlength, multiple areas can be formed on the device such that they contain identical contents, but differ only in pathlength. In this way, the chances are increased that the signal obtained from at least one of the areas will be within the dynamic range of the detector. A computer system configured to account for the differing pathlengths could be used to obtain the final desired result, for example an analyte concentration. The device alternatively can be opened and individual areas analyzed or designed to allow slippage into a further position that allows for access to individual areas (e.g., through access holes). In some embodiments, amplification of the reaction areas may be conducted (e.g. silver-based amplification, microphage amplification, etc.).” Para. 0171 (emphasis added).
Applicant also argues the following. Ismagilov fails to disclose the claimed comparing step of comparing the first luminescence value with a second luminescence value of a comparative capillary in the bioreactor microfluidic deice having a comparative surface comprising the at least one antibody contacted with a comparative sample having the one or more competitive conjugates, but lacking the target analyte, to determine an amount of the target analyte present in the test sample. Applicant states that the Office appears to rely on Ismagilov’s paragraph 0175 and “well known” knowledge in the art as allegedly teaching the claimed comparing step. However, Ismagilov’s paragraph 0175 reports that its device can include areas that are used as positive and negative controls. A negative control area can be prepared that contains no analyte, which would be expected to give no signal when exposed to th reagents for analysis. This disclosure in Ismagilov’s paragraph 0175 and even the Office’s reliance on “well known” knowledge merely provides a generic concept of negative and positive controls and comparison between an assay and a negative control. Other than this generic disclosure and “well known” knowledge in the art, the Office has not actually accounted for the specified requirements recited in the claimed comparing step. Ismagilov makes no mention of measuring a first luminescence value nor does Ismagilov make any mention of a second luminescence value, and thus, it necessarily follows that Ismagilov provides no guidance toward comparing those two values. Ismagilov fails to disclose a comparative capillary in the bioreactor microfluidic device having a comparative surface comprising the at least one antibody contacted with a comparative sample having the one or more competitive conjugates, but lacking the target analyte. Furthermore, given this broad and generic disclosure in Ismagilov, a person of ordinary skill in the art would not have “at one envisage[d]” the claimed arrangement or combination of the claimed method.
These arguments are not persuasive. As noted in the grounds for rejection, areas for positive or negative controls are disclosed (para. 0175). It is understood by one skilled in the art that a comparison between the area where the assay is performed on the sample and the negative control area is made, as is well known in the art to make use of the negative control.
“In some embodiments, the device can contain areas that are used as positive or negative controls. To make positive controls, the analyte that is being tested for in other areas on the device can be preloaded in the control areas, such that when the device parts are moved as described herein, the pre-loaded analyte is exposed to reactions and detected using the same method as the sample to be measured. When a positive control does not give the expected result, it can be sign of improper storage or usage of the device. Similarly, negative control areas can be prepared that contain no analyte, which would be expected to give no signal when exposed to the reagents for analysis. Additive verification controls can also be used to determine integrity of the assay. Using the techniques of the present invention, a known amount, X, of analyte can be added to the sample containing the unknown amount of analyte, and then both the sample containing additional material and the original sample containing the unknown amount are assayed for analyte concentration using the same method, preferably on the same device to give results Y, for the unknown sample, and Z, for the unknown sample with added amounts of analyte. The difference between Z and Y should be X, and any deviation from X indicates a problem with the assay, such as degradation of the assay reagents.” Para. 0175 (emphasis added).
As exemplified above, the difference between results from an unknown amount and a known amount is determined. This is the same as a comparison, and it is also well-known in the art.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Ann Montgomery whose telephone number is (571)272-0894. The examiner can normally be reached Mon-Fri, 9-5:30 PM PST.
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/Ann Montgomery/Primary Examiner, Art Unit 1678