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 Objections
Claim 1 is objected to because of the following informalities:
In line 4, “a main channel” should read “the main channel” if referring to the same “main channel” established in line 3.
In line 6, it is suggested to recite “at least one pad” as “at least one pad of the plurality of pads”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 1-14, 16, 19-21, 25, and 29-31 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.
Regarding claim 1, claim 1 recites “the pad” in line 9. It is unclear if “the pad” is referring to only one pad of the “plurality of pads” or the “at least one pad”, or if “the pad” is referring to each pad of the plurality of pads. Claims 2-14, 16, 19-21, 25, and 29-31 are rejected by virtue of their dependency on claim 1.
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.
Claims 1-6, 8-9, and 29-31 are rejected under 35 U.S.C. 102(a)(1) or 102(a)(2) as being anticipated by Pamula et al. (US 20070243634 A1; cited in the IDS filed 08/29/2023).
Regarding claim 1, Pamula teaches a system for executing chemical reactions (abstract and paragraphs [0003],[0055] teaches systems employing a droplet microactuator for chemical reactions such as PCR; Fig. 3), the system comprising:
a source reservoir (Fig. 3, DNA input reservoir 302);
an input channel in fluid communication with the source reservoir and a main channel (Fig. 3, interpreted as the channel between and in fluid communication with DNA input reservoir 302, i.e. source reservoir, and the central channel comprising an array of electrodes, i.e. main channel), the input channel being configured to distribute a reaction volume from the source reservoir into a main channel (interpreted as a functional limitation, see MPEP 2114; Fig. 3 and [0143] teaches the DNA input reservoir 302 fluidically connected to the central channel comprising an array of electrodes, therefore the arrangement is configured to distribute a reaction volume from the DNA input reservoir to the central chamber; [0374] teaches the droplet actuator loading fluids on the droplet microactuator from input reservoirs), the main channel comprising a plurality of pads inner surface of the main chamber (Fig. 3 shows the electrodes of the droplet microactuator are arranged in an array on the inner surface; Figs. 11-16 teaches cross-sectional views of the electrodes on an inner surface of a channel or chamber) configured to convey the reaction volume as a plurality of droplets via electrowetting (interpreted as a functional limitation, see MPEP 2114; [0022],[0054] teaches transport of droplets by the microactuator; [0375] teaches the droplet actuator includes electrodes to employ electrowetting to effect droplet operations; [0375] teaches the electrodes allow for dispensing of droplets; [0438] teaches dispensing from a source during droplet dispensing is by electrowetting forces; therefore, the electrodes are capable of conveying a reaction volume as droplets via electrowetting), at least one pad configured to capture an enzyme (interpreted as a functional limitation, see MPEP 2114; [0154] teaches the droplet microactuator includes a magnet or electromagnet such that magnetically responsive beads can be immobilized, released, or moved on the microactuator using magnetic fields; [0347] teaches [0386],[0389] teaches the droplet microactuator can include magnetic field generating elements; [0544] teaches applying/removing magnetic field to/from the droplet microactuator; therefore, the microactuator comprising electrodes that can have magnetic fields applied to/from the surface is structurally capable of capturing an enzyme at a later time, such as an enzyme on a magnetic bead; note that “an enzyme” is not positively recited structurally);
wherein each droplet of the plurality of droplets contains a magnetic bead, wherein the enzyme is attached to the magnetic bead (interpreted as a functional limitation of the pad, see MPEP 2114; note that the plurality of droplets, magnetic bead, and enzyme attached to the magnetic bead is not positively recited structurally; as discussed above, [0375],[0438] teaches the droplet actuator includes electrodes that employ electrowetting to effect or dispense droplets, and [0154],[0386], [0389], [0544] teaches the microactuator comprising electrodes that can have magnetic fields applied to/from the surface; therefore, the electrodes of the microactuator are structurally capable of conveying each droplet and capturing the enzyme attached to the magnetic bead as claimed at a later time), and wherein the pad comprises an electromagnet ([0154] teaches the droplet microactuator includes an electromagnet) configured to capture the magnetic bead to which the enzyme is attached (interpreted as a functional limitation, see MPEP 2114; note that “magnetic bead to which the enzyme” is not positively recited structurally; [0154],[0386], [0389], [0544] teaches the microactuator comprising electrodes that can have an electromagnet or magnetic fields applied to/from the surface; therefore, the electrodes of the microactuator are structurally capable of capturing a magnetic bead to which an enzyme is attached at a later time); and
a destination reservoir (Fig. 3, waste area 314) configured to receive the plurality of droplets from the main channel into a pool (Fig. 3 and [0143] teaches a waste area 314 as a pool is provided, which is structurally capable of receiving droplets from the central chamber via the electrodes of droplet microactuator).
Note that “chemical reactions”, “reaction volume”, “plurality of droplets”, “enzyme”, “magnetic bead”, and “the enzyme is attached to the magnetic bead” are not positively recited structurally and is interpreted as a functional limitation of the claimed system. A claim is only limited by positively recited elements; thus, inclusion of the material or article (“chemical reactions”, “reaction volume”, “plurality of droplets”, “enzyme”, “magnetic bead”, and “the enzyme is attached to the magnetic bead”) worked upon by a structure (system) being claimed does not impart patentability to the claims (see MPEP 2115).
Note that the limitations of the input channel, pads, electromagnet, and destination reservoir are interpreted as functional limitations. A functional recitation of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the functional limitations, then it meets the claim. See MPEP 2114. The apparatus of Pamula is identical to the presently claimed structure. Pamula discloses the claimed input channel, main channel, pads, electromagnet, and destination reservoir as claimed and therefore, would have the ability to perform the functional limitations recited in the claim. See MPEP 2112.01 (I). Moreover, Pamula teaches the droplet actuator includes electrodes that employ electrowetting to effect or dispense droplets ([0375],[0438]), and teaches the microactuator comprising electrodes that can have electromagnets and magnetic fields applied to/from the surface ([0154],[0386], [0389], [0544]). Additionally, Pamula teaches immobilizing, releasing, and moving magnetically responsive beads with a magnetic field of the droplet microactuator ([0154],[0182]); and polymerase is used on a bead ([0135]). Therefore, the electrodes of the microactuator are structurally capable of conveying each droplet via electrowetting and capturing the enzyme attached to the magnetic bead as claimed at a later time.
Regarding claim 2, Pamula further teaches wherein each pad of the plurality of pads comprises an electrode, a dielectric material, and a hydrophobic surface ([0377] teaches the droplet microactuator includes an array of electrodes that includes materials such as a dielectric component, i.e. dielectric material, and a hydrophobic coating, i.e. hydrophobic surface).
Regarding claim 3, Pamula further teaches wherein the plurality of pads is arranged as an array on the inner surface (Fig. 3 shows the electrodes of the droplet microactuator are arranged in an array on the inner surface; Figs. 11-16 teaches cross-sectional views of the array of electrodes on an inner surface of a channel or chamber), the array configured to convey an individual droplet of the plurality of droplets along a pad column of the array (interpreted as a functional limitation, see MPEP 2114; [0022],[0054] teaches transport of droplets by the microactuator; [0375] teaches the droplet actuator includes electrodes to employ electrowetting to effect droplet operations; Fig. 3 teaches electrodes includes columns of electrodes; therefore, the electrodes of the microactuator are capable of conveying individual droplets along a pad column of the array), wherein the array comprises a plurality of pad columns and each pad column extends along a length of the main channel (Fig. 3 teaches columns of electrodes, e.g. the electrodes from element 302 to the central row of electrodes, that extend along a length of the central chamber that includes element 316).
Regarding claim 4, Pamula further teaches wherein the plurality of pad columns is configured to convey multiple droplets in parallel (interpreted as a functional limitation, see MPEP 2114; [0121] teaches multiple droplet sets may be tested in parallel; [0476] teaches droplets can be manipulated in parallel; therefore, the pad columns in Fig. 3 are structurally capable of conveying multiple droplets in parallel).
Regarding claim 5, Pamula further teaches the system of claim 1, further comprising a cover plate positioned at a height h above the inner surface of the main channel, wherein the height h delimits the main channel in one dimension (note that Fig. 3 shows a top view of the system, but does not explicitly show a cover plate; however, Figs. 6, 9,10-16 and [0394] teaches a top plate, i.e. cover plate, that is encloses the interior space of the droplet microactuator and is positioned at a height above the inner surface of a main channel of the microactuator, which delimits the height of the main channel; therefore, the system that includes the droplet microactuator system, such as Fig. 3, includes the cover plate as claimed).
Regarding claim 6, Pamula further teaches wherein at least one of the height h of the main channel, a width w of the main channel, a droplet speed v of the plurality of droplets through the main channel, and an average fractional volume o of the main channel occupied by the plurality of droplets, is configured such that an effective flow rate of the system, equal to h*w*v*o, is sufficient for moving an initial reaction volume in the source reservoir through the main channel in a target amount of time (Figs. 3, 6-11 teaches the main channel having structural dimensions including height and width; [0022],[0054] teaches transport of droplets by the microactuator; therefore, the main channel is structurally capable of having an effective flow rate that is sufficient for moving an initial reaction volume in input reservoir 302 through the central channel in an amount of time; note that “plurality of droplets” are not positively recited structurally).
Note that “reaction volume” and “plurality of droplets” are not positively recited structurally and is interpreted as a functional limitation of the claimed system. A claim is only limited by positively recited elements; thus, inclusion of the material or article “reaction volume”, “plurality of droplets”) worked upon by a structure (system) being claimed does not impart patentability to the claims (see MPEP 2115).
Note that the limitations of the main channel are interpreted as functional limitations. A functional recitation of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the functional limitations, then it meets the claim. See MPEP 2114. The apparatus and main channel of Pamula is identical to the presently claimed structure. Pamula discloses the claimed input channel, main channel, pads, electromagnet, and destination reservoir as claimed and therefore, would have the ability to perform the functional limitations recited in the claim. See MPEP 2112.01 (I).
Regarding claim 8, Pamula further teaches wherein the droplet speed v is determined by a pad length x and a pad switching frequency f such that the droplet speed is equal to x*f (interpreted as an intended use of the system, see MPEP 2114; [0022],[0054] teaches transport of droplets by the microactuator; [0222] teaches transport of the droplets at high speed; [0376] teaches electrodes are controlled by switches and a controller; therefore, the system is structurally capable of conveying the droplets at a droplet speed and the pad is capable of switching, thus allowing for determination of the droplet speed).
Regarding claim 9, Pamula further teaches wherein the plurality of pads comprises a pad row set to a target temperature (Fig. 3 teaches a thermal cycling area 316 with a row of electrodes; [0102],[0107] teaches thermal cycling involves heating and cooling the droplet microactuator; therefore, the row of electrodes of the thermal cycling area 316 is interpreted as set to a target temperature for thermal cycling).
Regarding claim 29 , note that “reaction volume” and “the reaction volume comprises a library of DNA molecules that encode digital information” are not positively recited structurally and is interpreted as a functional limitation of the claimed system. A claim is only limited by positively recited elements; thus, inclusion of the material or article (“reaction volume”; “the reaction volume comprises a library of DNA molecules that encode digital information”) worked upon by a structure (system) being claimed does not impart patentability to the claims (see MPEP 2115).
Note that the limitations of the input channel, pads, electromagnet, and destination reservoir are interpreted as functional limitations. A functional recitation of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the functional limitations, then it meets the claim. See MPEP 2114. The apparatus of Pamula is identical to the presently claimed structure. Pamula discloses the claimed input channel, main channel, pads, electromagnet, and destination reservoir as claimed and therefore, would have the ability to perform the functional limitations recited in the claim (i.e. distributing and conveying a reaction volume as droplets, wherein the reaction volume comprises a library of DNA molecules that encode digital information). See MPEP 2112.01 (I).
Regarding claim 30, note that “reaction volume” and “the reaction volume comprises a library of genomic DNA” are not positively recited structurally and is interpreted as a functional limitation of the claimed system. A claim is only limited by positively recited elements; thus, inclusion of the material or article (“reaction volume”; “the reaction volume comprises a library of genomic DNA”) worked upon by a structure (system) being claimed does not impart patentability to the claims (see MPEP 2115).
Note that the limitations of the input channel, pads, electromagnet, and destination reservoir are interpreted as functional limitations. A functional recitation of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the functional limitations, then it meets the claim. See MPEP 2114. The apparatus of Pamula is identical to the presently claimed structure. Pamula discloses the claimed input channel, main channel, pads, electromagnet, and destination reservoir as claimed and therefore, would have the ability to perform the functional limitations recited in the claim (i.e. distributing and conveying a reaction volume as droplets, wherein the reaction volume comprises a library of genomic DNA). See MPEP 2112.01 (I).
Regarding claim 31, note that “reaction volume” and “the reaction volume comprises a library of DNA variants for screening” are not positively recited structurally and is interpreted as a functional limitation of the claimed system. A claim is only limited by positively recited elements; thus, inclusion of the material or article (“reaction volume”; “the reaction volume comprises a library of DNA variants for screening”) worked upon by a structure (system) being claimed does not impart patentability to the claims (see MPEP 2115).
Note that the limitations of the input channel, pads, electromagnet, and destination reservoir are interpreted as functional limitations. A functional recitation of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the functional limitations, then it meets the claim. See MPEP 2114. The apparatus of Pamula is identical to the presently claimed structure. Pamula discloses the claimed input channel, main channel, pads, electromagnet, and destination reservoir as claimed and therefore, would have the ability to perform the functional limitations recited in the claim (i.e. distributing and conveying a reaction volume as droplets, wherein the reaction volume comprises a library of DNA variants for screening). See MPEP 2112.01 (I).
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 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 the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Pamula as applied to claim 6 above, and further in view of Jovanovich et al. (US 8476063 B2) and Du et al. (US 20170253914 A1).
Regarding claim 7, Pamula fails to teach: wherein the initial reaction volume is greater than or equal to about 1 liter and the target amount of time is less than or equal to about 2 hours.
Jovanovich teaches microfluidic devices for DNA sequencing and genotyping, proteomics, pathogen detection, diagnostics and biodefense (abstract). Jovanovich teaches a need for the art of modular microfluidic components that can interface preparative modules, or methods, that operate at larger scale with microfluidic preparative and/or analytical components (column 1, lines 45-53). Jovanovich teaches target analytes in a sample can be concentrated prior to introduction into a microfluidic device, wherein the target analytes can be processed through devices that can hold macroscale volumes, such as liter volumes, to concentrate the target analytes into a small surface, such as a microbead (column 6, lines 44-50). Jovanovich teaches a flowthrough device that can process up to liter sample volumes (column 31, lines 38-40). Jovanovich teaches an instrument to perform analysis on a cell containing sample comprising a reservoir dimensioned to receive a liquid having an initial sample volume of a milliliter to a liter (claim 1). Jovanovich teaches the use of large diameter channels to yield appropriate flow rates (column 9, lines 35-37). Jovanovich teaches a variety of flow rates can be achieved by the timing of the actuation sequence, diaphragm size, altering channel widths, and other on-chip dimensions (column 12, lines 20-22).
Du teaches an apparatus for dispersing or mixing micro-quantity of liquid (abstract). Du teaches the apparatus generates droplets of fluid ([0026]). Du teaches a container can be a PCR microplate or PCR tube ([0129]). Du teaches the apparatus or system are simple, inexpensive, and easy to operate, a high-throughput liquid dispensing can be achieved, and the dispensing volume of the first liquid can be easily adjusted with a high accuracy; and the apparatus or system can have broad application in the field of genome sequencing and digital PCR quantitative nucleic acid amplification analysis ([0156]). Du teaches a fluid driving speed can be about 10 mL/min ([0084]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Pamula to incorporate Jovanovich’s teachings of a microfluidic device for DNA sequencing and performing analysis and processing of liter sample volumes (column 6, lines 44-50; column 31, lines 38-40; claim 1) and adjusting parameters to achieve desired flow rates (column 9, lines 35-37; column 12, lines 20-22) and Du’s teachings of an apparatus for fluid processing of droplets of samples, such as for PCR (abstract; [0026], [0129],[0156]) with a fluid driving speed of 10mL/min ([0084]) to provide: wherein the initial reaction volume is greater than or equal to about 1 liter and the target amount of time is less than or equal to about 2 hours (e.g. a flow rate of 10mL/min would process 1 liter in 100 minutes or less than 2 hours). Doing so would have a reasonable expectation of successfully improving interfacing and operation at a larger scale (Jovanovich, column 1, lines 45-53; column 6, lines 44-50) while ensuring appropriate flow rates to achieve desired timing and high-throughput of the reaction volume through the system (Jovanovich, column 9, lines 35-37, column 12, lines 20-22, column 31, lines 38-40; Du, [0084],[0156]).
Claims 10-14 are rejected under 35 U.S.C. 103 as being unpatentable over Pamula as applied to claim 9 above.
Regarding claim 10, Pamula fails to teach: wherein the array comprises multiple pad rows set to multiple target temperatures, and wherein each pad column comprises a pad from each pad row of the multiple pad rows set to multiple target temperatures, such that a droplet is exposed to the multiple target temperatures as it is conveyed along an individual pad column of the array.
Pamula teaches an embodiment of an array of electrodes having multiple rows and columns (Figs. 2A-2B, 20). Pamula teaches the droplet microactuator may include 2, 3 or more thermal zones, each of which may be heated to a different specified temperature ([0116]; Fig. 2B). Pamula teaches including a series of independently adjustable heating elements to provide for an appropriate heating ramp as droplets pass form one target temperature zone to another; which provides flexibility in working with a variety of protocols each requiring different target temperature zones and ramp profiles; for example, in a matrix of heating elements, target temperature zones may be at adjacent heating elements and/or separated by heating elements ([0119]). Pamula teaches a temperature optimization step or protocol using multiple independently heated thermal zones for optimizing temperatures and/or times for denaturation, annealing, and/or extension ([0121]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the array of Pamula to incorporate Pamula’s teachings of droplet microactuator electrodes arranged in multiple rows and columns or a matrix (Figs. 2A-2B, 20; [0119]), wherein the droplet microactuator includes multiple thermal zones having different temperatures ([0116],[0119],[0121]) to provide: wherein the array comprises multiple pad rows set to multiple target temperatures, and wherein each pad column comprises a pad from each pad row of the multiple pad rows set to multiple target temperatures, such that a droplet is exposed to the multiple target temperatures as it is conveyed along an individual pad column of the array. Doing so would have a reasonable expectation of successfully improving and optimizing control of temperature between different rows and columns of the system, therefore improving flexibility and adjustability for a variety of protocols that require different target temperature zones and ramp profiles.
Regarding claim 11, Pamula further teaches a pattern of pad rows along the length of the main channel (Fig. 3 shows a row of electrodes in the central chamber including a thermal cycling area 316). Pamula fails to explicitly teach: wherein the array comprises a pattern of pad rows having a cyclical temperature pattern along the length of the main channel.
Pamula teaches a row of electrodes in a thermal cycling area which employ a variety of heater configurations (Fig. 3 and [0143], area 316). Pamula teaches an embodiment of an array of electrodes having multiple rows and columns (Figs. 2A-2B, 20). Pamula teaches the droplet microactuator may include 2, 3 or more thermal zones, each of which may be heated to a different specified temperature ([0116]; Fig. 2B). Pamula teaches including a series of independently adjustable heating elements to provide for an appropriate heating ramp as droplets pass form one target temperature zone to another; which provides flexibility in working with a variety of protocols each requiring different target temperature zones and ramp profiles; for example, in a matrix of heating elements, target temperature zones may be at adjacent heating elements and/or separated by heating elements ([0119]). Pamula teaches a temperature optimization step or protocol using multiple independently heated thermal zones for optimizing temperatures and/or times for denaturation, annealing, and/or extension ([0121]). Pamula teaches multiple distinct thermal zones for thermal cycling requiring different temperatures to be performed on different portions of the droplet microactuator; where droplets can be transported or shuffled between zones of different fixed temperatures to perform the thermal cycling, which can produce faster reactions and offer greater operational flexibility ([0454]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the pads and main channel of modified Pamula to incorporate Pamula’s teachings of the droplet microactuator includes multiple thermal zones having different temperatures ([0116],[0119],[0121]) and transporting or shuffling droplets between zones of different temperatures for thermal cycling ([0454]) to provide: wherein the array comprises a pattern of pad rows having a cyclical temperature pattern along the length of the main channel. Doing so would have a reasonable expectation of successfully improving and optimizing control of temperature between pads along a row, therefore improving flexibility and adjustability for a variety of protocols that require different target temperature zones and ramp profiles (Pamula, [0119],[0121]), such as for thermal cycling, and thus improving reaction speeds and flexibility (Pamula, [0454]).
Regarding claim 12, modified Pamula fails to teach: wherein the pattern defines a temperature cycle, and wherein the array includes a plurality of instances of the pattern.
Pamula teaches the droplet microactuator may include 2, 3 or more thermal zones, each of which may be heated to a different specified temperature ([0116]; Fig. 2B). Pamula teaches including a series of independently adjustable heating elements to provide for an appropriate heating ramp as droplets pass form one target temperature zone to another; which provides flexibility in working with a variety of protocols each requiring different target temperature zones and ramp profiles; for example, in a matrix of heating elements, target temperature zones may be at adjacent heating elements and/or separated by heating elements ([0119]). Pamula teaches a temperature optimization step or protocol using multiple independently heated thermal zones for optimizing temperatures and/or times for denaturation, annealing, and/or extension ([0121]). Pamula teaches multiple distinct thermal zones for thermal cycling requiring different temperatures to be performed on different portions of the droplet microactuator; where droplets can be transported or shuffled between zones of different fixed temperatures to perform the thermal cycling, which can produce faster reactions and offer greater operational flexibility ([0454]). Pamula teaches additional thermal cycling steps may also be incorporated in various protocols of the invention ([0098]). Pamula teaches multiple droplets can be thermal cycled in parallel ([0099]). Pamula teaches an embodiment with parallel rows of electrodes for thermal cycling between a lower temperature heating area and an upper temperature heating area (Fig. 1; [0056]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the array of modified Pamula to incorporate Pamula’s teachings of including additional thermal cycling steps ([0098]) and multiple droplets being thermally cycled in parallel ([0056], [0099]; Fig. 1) to provide: wherein the pattern defines a temperature cycle, and wherein the array includes a plurality of instances of the pattern. Doing so would have a reasonable expectation of successfully improving parallel thermal cycling of multiple droplets and improving flexibility of protocols that require additional thermal cycling steps.
Regarding claim 13, modified Pamula further teaches: wherein the reaction volume is a polymerase chain reaction (PCR) formulation (interpreted as a functional limitation of the system, see MPEP 2114; note that “reaction volume” is not positively recited structurally; Pamula, [0055]-[0056],[0068],[0070] teaches the system is capable of being used for PCR with PCR reagents, i.e. PCR formulation), and wherein the multiple target temperatures of an individual cycle are configured for melting double stranded DNA, annealing primers, and extending primers ([0116],[0119],[0121],[0454] teach independently adjusting the temperature and optimizing temperatures for denaturing, annealing, and extension; [0076] teaches melting temperature for primers are selected to permit annealing; therefore, the system of modified Pamula is structurally capable of adjusting/optimizing temperature for melting double stranded DNA, annealing primers, and extending primers; note that “double stranded DNA” and “primers” are not positively recited structurally).
Regarding claim 14, modified Pamula fails to teach: wherein a pad switching frequency and a number of pad rows for an individual temperature of the temperature cycle are set such that an individual droplet spends a target period of time at the individual temperature.
Pamula teaches a row of electrodes in a thermal cycling area which employ a variety of heater configurations (Fig. 3 and [0143], area 316). Pamula teaches an embodiment of an array of electrodes having multiple rows and columns (Figs. 2A-2B, 20). Pamula teaches the droplet microactuator may include 2, 3 or more thermal zones, each of which may be heated to a different specified temperature ([0116]; Fig. 2B). Pamula teaches including a series of independently adjustable heating elements to provide for an appropriate heating ramp as droplets pass form one target temperature zone to another; which provides flexibility in working with a variety of protocols each requiring different target temperature zones and ramp profiles; for example, in a matrix of heating elements, target temperature zones may be at adjacent heating elements and/or separated by heating elements ([0119]). Pamula teaches multiple droplets can be thermal cycled in parallel ([0099]). Pamula teaches an embodiment with parallel rows of electrodes for thermal cycling between a lower temperature heating area and an upper temperature heating area (Fig. 1; [0056]). Pamula teaches droplets may be cycled through temperatures for different periods of time, and protocols are executed for optimizing temperature and time periods for denaturation and/or extension steps ([0101]). Pamula teaches thermal cycling using optimized time periods ([0120]). Pamula teaches a temperature optimization step or protocol using multiple independently heated thermal zones for optimizing temperatures and/or times for denaturation, annealing, and/or extension ([0121]). Pamula teaches multiple distinct thermal zones for thermal cycling requiring different temperatures to be performed on different portions of the droplet microactuator; where droplets can be transported or shuffled between zones of different fixed temperatures to perform the thermal cycling, which can produce faster reactions and offer greater operational flexibility ([0454]). Pamula teaches electrodes are controlled by switches and a controller ([0376]). Pamula teaches droplets may be manipulated at a frequency ([0384]), and the system includes a program with instructions to set the frequency or rate at which the steps of executed, such as timing of electrode activation/deactivation ([0504]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the array of modified Pamula to incorporate Pamula’s teachings of multiple droplets being thermally cycled in parallel ([0056], [0099]; Fig. 1), controlling the electrodes by switches and a controller ([0376]), manipulating droplets at a frequency ([0384],[0504]), and optimizing time period for thermal cycling ([0101],[0120],[0121]) to provide: wherein a pad switching frequency and a number of pad rows for an individual temperature of the temperature cycle are set such that an individual droplet spends a target period of time at the individual temperature. Doing so would have a reasonable expectation of successfully improving parallel thermal cycling of multiple droplets for optimized time periods.
Claims 16 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Pamula as applied to claim 1 above, and further in view of Mandell et al. (US 20180237850 A1).
Regarding claim 16, Pamula fails to teach: wherein a pad of the plurality of pads is conjugated with an enzyme.
Pamula teaches the system allows for PCR ([0055]); and PCR reagents include polymerase to facilitate amplification of a target nucleic acid ([0070], [0072],[0075],[0080]). Pamula teaches polymerase containing droplets on a droplet microactuator to provide conditions sufficient to facilitate amplification of a target nucleic acid ([0085]). Pamula teaches biotin incorporated with DNA polymerase to capture amplicon on a streptavidin bead ([0135]). Pamula teaches the droplet microactuator can include a magnet or electromagnet for immobilizing, releasing, or moving magnetically responsive beads ([0154]); where the beads can be maintained in place and transported from place to place in droplets ([0182]). Pamula teaches magnetically responsive beads can be used to move the beads and attached materials on a droplet microactuator ([0430]).
Mandell teaches a detection apparatus for sequencing by synthesis method (abstract). Mandell teaches the method can include reagents including polymerase where the polymerase can have magnetic particles attached ([0004]). Mandell teaches polymerase immobilized, i.e. conjugated, to designated areas, the polymerase configured to capture a corresponding template strand ([0018]). Mandell teaches target nucleic acids can be bound by binding to a polymerase that is attached to a surface, wherein copies can be produced by PCR ([0326]). Mandell teaches polymerase may be immobilized to a surface of a flow cell using known linkers, i.e. conjugated ([0341]-[0342]). Mandell teaches a droplet actuator with electrodes can be used for droplet manipulation via electrowetting ([0331]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the pad of Pamula to incorporate Pamula’s teachings of the use of polymerase and magnetic beads that can be immobilized, released, or moved on the droplet microactuator ([0085], [0154],[0182], [0430]) and Mandell’s teachings of conjugating polymerase to designated areas, such as a surface of a flow cell ([0014], [0018], [0326],[0341]-[0342]) and droplet manipulation via electrowetting ([0331]) to provide: wherein a pad of the plurality of pads is conjugated with an enzyme (i.e. polymerase). Doing so would have a reasonable expectation of successfully improving control of positioning (e.g. conjugation) of polymerase at desired areas of the main channel, such as a pad, therefore optimizing sample processing protocols at desired locations of the system.
Regarding claim 19, modified Pamula further teaches wherein the enzyme is a polymerase (see above claim 16).
Claims 20-21 are rejected under 35 U.S.C. 103 as being unpatentable over Pamula as applied to claim 1 above, and further in view of Kinney et al. (US 20190331638 A1).
Regarding claim 20, Pamula fails to explicitly teach: the system of claim 1, further comprising an input pump configured to convey the plurality of droplets from the source reservoir into the main channel via the input channel.
Pamula teaches the droplet microactuator may be complemented or supplemented with micropumping ([0386]). Pamula teaches the droplet microactuator includes input ports for samples that can be loaded using conventional robotics; and an embodiment where droplets are routed on the droplet microactuator as they are pumped out of the capillary into the input port (paragraph [0432]). Pamula teaches an embodiment (Fig. 10) including a syringe pump to provide fluid to a main channel via an input channel (Fig. 10; [0314]).
Kinney teaches a cartridge for use in an electrowetting sample processing system having inlet ports for introducing an input liquid (abstract). Kinney teaches a processing zone for processing a PCR process ([0040]). Kinney teaches ports are individually connected to a control element, such as a valve and individual pump ([0115]). Kinney teaches an input pump to introduce liquids and a further pump or waste pump to remove liquid ([0126],[0127]). Kinney teaches the flow through the cartridge having flow based on pressure characteristics ([0010]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Pamula to incorporate Pamula’s teachings of complementing or supplementing the system with micropumping ([0386]) and pumping droplets into and out of the system ([0314],[0432]) and Kinney’s teachings of a cartridge for an electrowetting sample processing system that includes pumps for introducing and removing liquids ([0010], [0115],[0126],[0127]) to provide: the system of claim 1, further comprising an input pump configured to convey the plurality of droplets from the source reservoir into the main channel via the input channel. Doing so would have a reasonable expectation of successfully improving control of fluid introduction to the main channel.
Regarding claim 21, Pamula fails to teach: the system of claim 1, further comprising an output pump configured to aspirate droplets from the main channel to the destination reservoir.
Pamula teaches the droplet microactuator may be complemented or supplemented with micropumping ([0386]). Pamula teaches the droplet microactuator includes input ports for samples that can be loaded using conventional robotics; and an embodiment where droplets are routed on the droplet microactuator as they are pumped out of the capillary into the input port (paragraph [0432]). Pamula teaches an embodiment (Fig. 10) including a syringe pump to provide fluid to a main channel via an input channel (Fig. 10; [0314]).
Kinney teaches a cartridge for use in an electrowetting sample processing system having inlet ports for introducing an input liquid (abstract). Kinney teaches a processing zone for processing a PCR process ([0040]). Kinney teaches ports are individually connected to a control element, such as a valve and individual pump ([0115]). Kinney teaches an input pump to introduce liquids and a further pump or waste pump to remove liquid ([0126],[0127]). Kinney teaches the flow through the cartridge having flow based on pressure characteristics ([0010]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the system of Pamula to incorporate Pamula’s teachings of complementing or supplementing the system with micropumping ([0386]) and pumping droplets into and out of the system ([0314],[0432]) and Kinney’s teachings of a cartridge for an electrowetting sample processing system that includes pumps for introducing and removing liquids ([0010], [0115],[0126],[0127]) to provide: the system of claim 1, further comprising an output pump configured to aspirate droplets from the main channel to the destination reservoir. Doing so would have a reasonable expectation of successfully improving control of fluid removal from the main channel.
Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Pamula as applied to claim 1 above, and further in view of Pollack et al. (US 20110097763 A1).
Regarding claim 25, Pamula fails to teach: wherein the destination reservoir further comprises a reagent configured to inhibit a reaction.
Pamula teaches a waste area ([0143]) and droplets may be transported away for further processing, analysis, and/or waste disposal ([0144]). Pamula teaches a waste or collection well can exist to allow droplets to be delivered to a target destination ([0418]).
Pollack teaches a system including droplet actuators for performing PCR (abstract). Pollack teaches droplets may be moved in directions, and amplification in the reactions in the droplets may be stopped in a region or transported away ([0141]). Pollack teaches reagents for quenching reactions in the droplets; wherein the droplets that are quenched may be subject to further assay steps and/or detection ([0186]). Pollack teaches a desire to quench or stop a reaction by known reagents ([0234]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the destination reservoir of Pamula to incorporate Pamula’s teachings of droplets transported way for processing, analysis, or waste disposal and/or collection at a target destination ([0143]-[0144],[0418]) and Pollack’s teachings of reagents for quenching and stopping reactions in droplets that may be in a region or transported away for further assay steps and/or detection ([0141], [0186], [0234]) to provide: wherein the destination reservoir further comprises a reagent configured to inhibit a reaction. Doing so would have a reasonable expectation of successfully improving sample processing of the droplets by providing quenching or stopping of reactions of desired droplets that are received in the destination reservoir, thus allowing for further processing, analysis, or waste disposal, and/or collection of the droplets.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Sista et al. (US 20150107995 A1) teaches droplet actuators for capturing, trapping, restraining, or manipulating magnetic beads on a droplet actuator (abstract). Sista teaches the system (Fig. 16) includes an array of pads or electrodes (1605,1610) having rows and columns (Fig. 16).
Pollack et al. (US 20130288254 A1) teaches droplet actuated molecular techniques for DNA sequencing using digital microfluidics including droplet actuator-based sample preparation and PCR amplification (abstract). Pollack teaches the droplet actuator (Fig. 5) includes an array of pads including electrodes (516). Pollack teaches embodiments that that uses DNA polymerase immobilized on magnetically responsive beads, which is included in a reagent droplet ([0196]-[0199]); wherein a magnet is used in a temperature control zone for retaining the magnetically responsive beads during operation ([0196]); and wherein the reaction droplet with magnetically responsive beads is transported by a magnetic field to be held by the magnetic field ([0199]).
Luo et al. (Luo, et al., "Design and Optimization of a Cyberphysical Digital-Microfluidic Biochip for the Polymerase Chain Reaction", IEEE Transactions on Computer- Aided Design of Integrated Circuits and Systems, Vol. 34, No.1 29-42; (January 2015); cited in the IDS filed 08/29/2023) teaches a microfluidic biochip for PCR (abstract; Fig. 1) including columns and rows of electrodes (Fig. 1), an inlet channel (incoming flow channel) and destination reservoir (waste); wherein the electrodes includes regions with different temperatures (Fig. 1).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to HENRY H NGUYEN whose telephone number is (571)272-2338. The examiner can normally be reached M-F 7:30A-5:00P.
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/HENRY H NGUYEN/Primary Examiner, Art Unit 1758
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