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 .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 7/15/26 is being considered by the examiner.
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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
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.
Claims 1, 4, 9, 10, 15, 16, 17, 18, 19, 20, 52, and 53 are rejected under 35 U.S.C. 103 as being unpatentable over Burg (US Pub 2014/0263059; previously cited), in view of Dohale (US Pub 2017/0327867; previously cited), and further in view of Dothie (US Pub 2015/0044696).
Regarding Claim 1, Burg teaches a device for preparing a sample for analyte detection (separation device 100, Fig. 2) comprising:
a processing module comprising a filter configured to remove solid particulate from the sample ([0026] a filtration membrane 80), and
Burg is silent to a fluid routing network comprised of a plurality of fluid pathways and a plurality of processing modules, a second processing module comprising an enricher downstream from the filter and configured to increase a quantity of target analytes in the sample, a fluid supply comprising one or more reagents, and one or more pumps that moves the one or more reagents and the same through the device.
Dohale teaches in the related art of fluidic devices. [0153] In another embodiment, the lysis chamber can be split into at least two portions 1105 and 1142 that are connected to a branched channel 1145. During initial sample filtering, an instrument pump can be connected to a first port P1 1143 and applies negative pressure to pull the sample through a first filter 1138 in the lysis chamber. [0231] Device 3002 has a controller and single processor 3055 which is in communication with each of a first heating unit 3056, a second heating unit 3057, detection unit 3058, fluidic unit 3059 and a graphical user interface (GUI) 3060. [0232] as shown in FIG. 31, there is provided a system controller 3155 which is in communication with a GUI 3160. The system controller 3155 is additionally in communication with a fluidic unit 3159, a first heating unit 3156, a second heating unit 3157 and a detection unit 3158. In one embodiment, fluidic unit 3159 comprises and is in communication with pump 3151, pressure sensing unit 3161, at least one valve 3162 and linear actuation unit 3163. [0186] Therefore, in one embodiment there is an aliquoting module comprising a reaction chamber in fluid communication with a supply channel, and, a fluidic inlet in fluidic communication with the reaction chamber. [0173] In the bottom panel of FIG. 17, reaction chamber outlet 1711 and waste chamber outlet 1709 are opened while pump 1751 builds a positive pressure in the entire channel network of the cartridge including the reaction chamber(s) 1710. [0098] The present disclosure provides a sample to answer system and methods of use for analyzing a sample for the presence of one or more targets of interest. In one embodiment, as provided in FIG. 1A, the sample to answer system comprises the steps of providing a sample, enriching the sample for one or more targets of interest, amplifying and detecting the target(s) of interest, and providing as a result a determination of the presence or absence of the target(s) of interest in the sample.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have added a processing module (processor), an enricher downstream from the filter and configured to increase a quantity of target analytes in the sample, a fluid supply comprising a reagent and a pump that move the reagents from the fluid supply and move the sample to the enricher; and a fluid routing network comprised of fluid pathway and valve to direct flow of the sample and the reagents to the enricher, one or more pumps that moves the one or more reagents and the same through the device, as taught by Dohale, to the device, as taught by Burg, to allow for a fluid pathway for a sample to flow through before and after separation for detecting the presence of microorganisms in a sample, cartridges, devices and systems for same, as taught by Dohale, in [0010].
Modified Burger is silent to a rotary valve to direct flow of the sample and the one or more reagents to the enricher through a channel of the rotary valve, wherein the channel of the rotary valve fluidically couples the first processing module or the second processing module and the one or more reagents of the fluid supply.
Dothie teaches in the related art of processing a sample. [0016] By rotating the rotating valve, sequentially connectable fluidic conduits and/or chambers can be brought into communication with each other via the internal channel in the rotating valve. For example, the rotating valve can be positioned to connect a first fluidic conduit and/or chamber and a second fluidic conduit and/or chamber in the housing together via the internal channel in the rotating valve. The rotating valve can then be rotated so that the second fluidic conduit and/or chamber can be brought into communication with a third fluidic conduit and/or chamber in the housing via the internal channel within the rotating valve, and so on for the n fluidic conduits in the housing. [0018] The advantages of one or more embodiments of the invention include: [0019] The ability to meter a defined volume of fluid within the at least one internal channel within the rotating valve.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have added a rotary valve to direct flow of the sample and the one or more reagents to the enricher through the rotary valve, wherein the rotary valve fluidically couples the first processing module or the second processing module and the one or more reagents of the fluid supply, as taught by Dothie, in the device as taught by Burger, to meter a small volume of fluid, as taught by Dothie, in [0002].
Regarding Claim 4, modified Burg teaches the device of claim 1, further comprising electronics ([0343] supporting electronics) and software subsystem that controls the one or more pumps and the rotary valve ([0233] In one embodiment, a controller 3055 can be used to coordinate the process and interface with the other various unit. The controller 3055 can comprise one or more computing units (e.g., single board computer, processor, microcontroller, etc.). In one embodiment, the controller can store and execute a script. In another embodiment, the controller comprises retrievable memory.).
Regarding Claim 9, modified Burg teaches the device of claim 1, wherein the processing module further comprises a detector downstream from all components of the processing module, the detector configured to detect the target analytes in the eluate ([0106] A detector can be implemented using a conventional digital camera, such as the Canon 5D digital SLR camera, a CMOS sensor, a photodiode, optical fiber, or a digital video camera. In one embodiment, detector is implemented using an electron multiplying charge coupled device (EMCCD). The detector can be configured and arranged to detect emissions from the reaction chamber and to output image data corresponding to the detected emissions.).
Regarding Claim 10, modified Burg teaches the device of claim 9, wherein the detector produces an optically detectable signal ([0106] A detector can be implemented using a conventional digital camera, such as the Canon 5D digital SLR camera, a CMOS sensor, a photodiode, optical fiber, or a digital video camera. In one embodiment, detector is implemented using an electron multiplying charge coupled device (EMCCD). The detector can be configured and arranged to detect emissions from the reaction chamber and to output image data corresponding to the detected emissions.).
Regarding Claim 15, modified Burg teaches the device of claim 1, wherein the processing module further comprises a detector downstream from all components of the processing module, the detector configured to detect the target analytes in the sample ([0106] A detector can be implemented using a conventional digital camera, such as the Canon 5D digital SLR camera, a CMOS sensor, a photodiode, optical fiber, or a digital video camera. In one embodiment, detector is implemented using an electron multiplying charge coupled device (EMCCD). The detector can be configured and arranged to detect emissions from the reaction chamber and to output image data corresponding to the detected emissions.).
Regarding Claim 16, modified Burg teaches the device of claim 1, wherein the sample has a volume comprising at most or about 400 microliters (µl), 350 µl, 300 µl, 250 µl, 200 µl, 150 µl,100 µl,50 µl, 45 µl, 40 µl, 35 µl, 30 µl, or less (the sample would be capable of having a volume of 400µl or less).
Regarding Claim 17, modified Burg teaches the device of claim 1, wherein the sample is whole blood (See Abstract. The invention is directed to a method and a device for separating plasma from whole blood.).
Regarding Claim 18, modified Burg teaches the device of claim 1, wherein the target analytes comprise a target region of cell-free deoxyribonucleic acid (DNA) (the target analytes is directed to intended use of the device and is not part of the claimed device. The target analytes would be capable of comprising a target region of cell-free deoxyribonucleic acid (DNA)).
Regarding Claim 19, modified Burg teaches the device of claim 18, wherein the cell-free DNA is fragmented (the target analytes is directed to intended use of the device and is not part of the claimed device. The target analytes would be capable of comprising a target region of cell-free deoxyribonucleic acid (DNA) and the cf-DNA is capable of being fragmented).
Regarding Claim 20, modified Burg teaches the device of claim 18, wherein the sample comprises an amount of the target analytes comprising between or about 4pg to 100pg, 4pg to 150pg, 4pg to 200pg, 4pg to 250pg, 4pg to 300pg, 4pg to 350pg, 4pg to 400pg, 4pg to 450pg, 4pg to 500pg, 10pg to 100pg, 10pg to 150pg, 10pg to 200pg, 10pg to 250pg, 10pg to 300pg, 10pg to 350pg, 10pg to 400pg, 10pg to 450pg, 10pg to 500pg, 20pg to 100pg, 20pg to 150pg, 20pg to 200pg, 20pg to 250pg, 20pg to 300pg, 20pg to 350pg, 20pg to 400pg, 20pg to 450pg, 20pg to 500pg, 30pg to 100pg, 30pg to 150pg, 30pg to 200pg, 30pg to 250pg, 30pg to 300pg, 30pg to 350pg, 30pg to 400pg, 30pg to 450pg, or 30pg to 500pg (the sample and the target analytes within the sample are directed to intended use of the device and the target analytes are capable of having a weight within one of these ranges).
Regarding Claim 52, modified Burg teaches the device of claim 1, wherein the rotary valve fluidically couples the first processing module and the second processing module and the one or more reagents of the fluid supply ([0105] a means for the communication of fluids between sample preparation subsystem output ports or valves and the input port or ports of the fluidic or microfluidic components of the device. [0188] In other embodiments of the test cassette and docking unit, the sealing mechanism may comprise other means of mechanically sealing the chamber such as a rotating valve as illustrated in FIG. 22.).
Regarding Claim 53, modified Burg teaches the device of claim 19, wherein each fragment of the fragmented cell-free DNA comprises a methylation marker (the fragmented cell-free DNA is directed to intended use of the device and is not required as part of the device).
Claims 5, 6, 7, 8, 11, 12, 13, and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Burg (US Pub 2014/0263059; previously cited), in view of Dohale (US Pub 2017/0327867; previously cited), and further in view of Dothie (US Pub 2015/0044696) as applied to claim 1 above, and further in view of Thomas (US Pub 2018/0304260; previously cited).
Regarding Claims 5, 6, 7, 8, 11, 12, 13, and 14, modified Burg teaches the device of claim 1.
Modified Burg is silent to the plurality of processing modules further comprises a washer downstream from the filter and upstream from the enricher and configured to separate the target analytes from other substances within the sample, a hybridizer downstream from the filter and upstream from the enricher, the hybridizer configured to bind the target analytes to one or more antibodies of high affinity, an eluter downstream from the hybridizer and upstream from the enricher, the eluter configured to isolate analytes to be detected from the sample in an eluate, a diluter downstream from the enricher, the diluter configured to dilute the eluate in an aqueous buffer, a chromatography device, wherein the chromatography device is a lateral flow assay, at least one of the hybridizer, the eluter, the enricher, or the diluter comprise an air vent, a diluter downstream from the enricher, the diluter configured to dilute the sample in an aqueous buffer.
Thomas teaches in the related art of fluidic cassette for detecting. ([0059] FIG. 22 is a drawing of an embodiment of the cassette sealing mechanism wherein a drive gear is employed to mediate seal closure using a rotating valve. In other embodiments of the test cassette and docking unit, the sealing mechanism may comprise other means of mechanically sealing the chamber such as a rotating valve as illustrated in FIG. 22). ([0168] Solution compartmentalization component 1303 also preferably comprises reservoir 1314 containing a first wash buffer and reservoir 1315 containing a second wash buffer.) ([0010] The present invention is also a cassette for detecting a target nucleic acid, the cassette comprising a vertically oriented detection chamber, a lateral flow detection strip disposed in the detection chamber oriented such that a sample receiving end of the detection strip is at the bottom end of the detection strip, and a space in the detection chamber below the lateral flow detection strip for receiving fluid comprising amplified target nucleic acids, the space comprising sufficient capacity.) ([0170] Movement of the sample preparation subsystem components occurring during the sample preparation process are shown in FIG. 14, which depicts the sample preparation subsystem embodiment in cross-section before and after sample processing. Elution is preceded by displacement of binding matrix 1306 out of the capillary flow path and through seal component 1316 by the action of an actuator in the associated reusable test instrument. Seal component 1316 forms a seal with a portion of elution buffer conduit 1318 to allow the injection of elution buffer through binding matrix 1306 and into sample cup 1402. The cassette has numerous features to ensure correct operation of the device under gravity, such as vent pockets for enabling the flow of sample fluid from one chamber to the next when the vent pocket is unsealed. The cassette also can have a gasket to ensure free air movement between open vent pockets.)
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have added a rotary valve as the valve, a washer downstream from the filter and upstream from the enricher and configured to separate the target analytes from other substances within the sample, a hybridizer downstream from the filter and upstream from the enricher, the hybridizer configured to bind the target analytes to one or more antibodies of high affinity, an eluter downstream from the hybridizer and upstream from the enricher, the eluter configured to isolate analytes to be detected from the sample in an eluate, a diluter downstream from the enricher, the diluter configured to dilute the eluate in an aqueous buffer, a chromatography device, wherein the chromatography device is a lateral flow assay, at least one of the hybridizer, the eluter, the enricher, or the diluter comprise an air vent, a diluter downstream from the enricher, the diluter configured to dilute the sample in an aqueous buffer, to the device of modified Burg, to allow for an integrated device and related methods for detecting and identifying nucleic acids, as taught by Thomas, in [0002].
Response to Arguments
Applicant’s arguments with respect to claim 1 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
First, Applicant argues the rotating valve as taught by Thomas is for sealing a cassette and does not have a channel.
In response, the examiner notes a new reference (the prior art of Dothie, US Pub 2015/0044696) is cited in light of the amendment.
Second, Applicant argues the Office’s reason for combining the rotating valve of Thomas with Burg is not supported by the description of Thomas.
In response, the examiner notes a new reference is cited in light of the amendment.
Third, Thomas teaches away from using a valve to move fluid between chambers.
In response, the examiner notes a new reference is cited in light of the amendment.
Fourth, Applicant argues the proposed modification of Burg with the sealing rotary valve of Thomas would render Burg unsatisfactory for Burg’s intended purpose.
In response, the examiner notes a new reference is cited in light of the amendment.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JACQUELINE BRAZIN whose telephone number is (571)270-1457. The examiner can normally be reached M-F 8-5.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Charles Capozzi can be reached at 571-270-3638. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JB/
/CHARLES CAPOZZI/Supervisory Patent Examiner, Art Unit 1798
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