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 .
Status of the Claims
Claims 1-2, 4-5, and 8-10, 12-14, and 21-30 are pending. Claims 1-2, 4-5, 8-10, 12-14, and 21-30 are the subject of this Final Office Action. Claims 23-30 are new. Claims 6, 11, and 15-20 have been cancelled. Applicant’s amendments to the claims necessitate a new grounds of rejection.
Claim Interpretation
Amended claim 1 recites the limitation “flowing a continuous encapsulation layer spanning all open surfaces of the set of wells, thereby sealing the set of wells and preventing egress of nucleic acid molecules from the plurality of wells of the set of wells.”
The claim is interpreted as encompassing any solution or material which is flowed over the open surfaces of the set of wells, which would result in the nucleic acid molecules remaining within the wells.
New Grounds - Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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.
Claims 1-2, 4-6, 8-10, 12-14, 21 and 30 are rejected under 35 U.S.C. 103 as being unpatentable over McNeely et al. (US-20040109793, previously cited) in view of Collins (US20130244906, previously cited) and Gong et al. (WO 2014/065758 A1).
Regarding claim 1, McNeely teaches a microfluidic device for performing PCR ([0065], Example 1, claims 50-51):
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which corresponds to the instant claim as follows
A method comprising:
providing a microfluidic device comprising a substrate having a surface (Fig. 1 – 100/101/102/103), an inlet (Fig. 1 - 122), an outlet (Fig. 1 – 131; claim 68: “an outlet channel”) and a set of wells recessed below the surface of the substrate (Fig. 1 - 127) and in fluid communication with the inlet and outlet, the set of wells coupled by a channel (Fig. 1 – 124/126/127/128/129/130/131; [0065])
Regarding claim 1’s language of:
wherein the channel is coupled at a first end to the inlet and at a second end to the outlet,
McNeely teaches channels coupled at a first end to an inlet (Fig. 1 – 122/124/126/127/128/129/130/131; [0065]). McNeely teaches an outlet channel downstream of the junction between channels (claim 68).
Additionally, Collins teaches channels coupled at a first end to the inlet and coupled at a second end to an outlet (Fig. 1, [0054]). Collins teaches that droplets can be collected at an outlet for further processing ([0070]). It would have been obvious to one of ordinary skill in the art to couple the channels at the inlet and the outlet, as it would have been a simple combination of the channels coupled at the outlet as taught by Collins with the channels of McNeely; additionally, it would allow one of ordinary skill in the art to collect the droplets for further processing, with no evidence of unexpected results.
Regarding claim 1’s language of:
delivering a sample comprising nucleic acid molecules of interest and a process reagent for polymerase chain reaction (PCR) to the inlet and into a plurality of wells of the set of wells
McNeely teaches ([0065]: “A PCR cocktail containing DNA sample of interest, but without primers, is pumped (with the use of a syringe pump, for example) into inlet 122”); .
McNeely teaches delivering reagents and sample into the set of wells via the inlet ([0065]; claim 59).
Regarding claim 1’s language of :
flowing a continuous encapsulation layer spanning all open surfaces of the set of wells, thereby sealing the set of wells and preventing egress of nucleic acid molecules from the plurality of wells of the set of wells,
Collins teaches flowing oil after trapping cells for the encapsulation of cells (par. 0028, 0052). Collins does not teach that this a continuous encapsulation layer spanning all open surfaces of the set of cells.
Gong teaches a method of isolating nucleic acids in an aqueous sample using a microfluidic device (Abstract).
Gong teaches flowing mineral oil over an array of wells which acts as a sealant. Gong further teaches that this allows for applications such as flowing a PCR reaction mixture, then sealing with the oil to allow for the assay to be performed (pg. 5, lines 33-35, pg. 18, lines 15-21, pg. 22, lines 13-15; pg. 40, line 1; Fig. 2, Fig. 5).
It would have been obvious to one of ordinary skill in the art to flow a continuous encapsulation layer as taught by Gong, as Gong teaches that this acts as a sealant and allows for reaction mixtures to be sealed in the wells to enable additional analysis and assays to occur, and it would be a simple substitution of one encapsulation method for another, with no evidence of unexpected results.
Regarding claim 1, McNeely further teaches
performing an assay with nucleic acid content within the set of wells ([0065]: “The microfluidic circuitry shown in FIG. 1 is designed for performing polymerase chain reaction (PCR) with a DNA sample to detect sequences of interest, but could be used to implement various biochemical reactions, and particularly those which require that sample be subject to one or more heating steps. Such reactions include, but are not limited, to various reactions used in DNA processing, for example, PCR, which requires multiple heating steps (thermal cycling), or ligase chain reaction (LCR) or rolling circle amplification (RCA) for DNA amplification, or cycle sequencing, all of which use a single isothermal heating step.”).
Given the high level of skill in the art as evidenced by McNeely and Collins (claim 1 – microfluidic chip based PCR assay), one of ordinary skill in the art of microfluidics would have reasonably considered variations on the design of a system to analyze biological samples as was routine in the art and arrive at the claimed invention.
Regarding claim 2, McNeely teaches wherein delivering the sample into the inlet and into the set of wells comprises capturing nucleic acid material of the sample within the set of wells ([0065]).
Regarding claim 4, McNeely teaches wherein delivering the sample comprises delivering the sample into the inlet and toward the outlet of the substrate, with a pressure differential between the inlet and the outlet ([0065]: “While fluid is injected into device 100, valves 106 a-106 d are in the open position, to allow air within the circuit to move through the circuit ahead of the sample, and escape through air vent 135”).
Regarding claim 5, wherein the substrate defines the set of wells at a region having a total surface area of at least 144 square millimeters,
McNeely teaches that the microfluidic device comprises one or more wells (i.e., [0069], [0081], Fig. 3A) but does not specifically teach at least 144 square millimeters. One of ordinary skill in the art would have considered Collins’ teaching of ~10000 sites in a 10mm x 10mm area ([0052]-[0054]) and reasonably consider using larger areas to accommodate more wells/sites on the surface and arrive at the claimed limitation.
Regarding claim 6, McNeely teaches further comprising delivering a set of reagents into the inlet, into the fluid layer adjacent to the set of wells, and into the set of wells by diffusive transport ([0065] Fig 1 – 124). Regarding the diffusive transport language, one of ordinary skill in the art would reasonably consider such a process as it is routinely used in the art for fluidics and taught by McNeely and Collins ([0022], [0057]: “PCR reagents and the single cells in both plates are mixed by diffusion.”).
Regarding claim 8, McNeely teaches wherein performing the assay comprises performing an in-situ hybridization assay for nucleic acid contents captured within the set of wells ([0097]; claim 59).
Regarding claim 9, McNeely teaches wherein transmitting heat through the substrate comprises providing a thermal control module comprising the heating plate arranged near a surface of the substrate (Fig. 1, 105; [0029]; [0064]-[0065]).
Regarding claim 10, McNeely teaches wherein transmitting heat comprises transmitting heat for at least one of PCR and an immunoassay with nucleic acid content captured within the set of wells ([0065]).
Regarding claim 12, McNeely teaches further comprising imaging contents of the set of wells, thereby enabling identification and assessment of contents of the set of wells during performance of the assay ([0065]: “The device is disassembled to permit dye in wells 131 a- 131 d to be read to quantify the amount of reaction products, or, if the device is formed at least in part of transparent material (i.e., transparent to the detected wavelengths), it may be possible to detect reaction products”) such that one of ordinary skill in the art would have considered imaging the contents of the wells and arrive at the claimed invention.
Regarding claim 13, further comprising returning a result characterizing a cancer cell phenotype represented in the sample, although McNeely teaches detecting analytes of interest for diagnostics ([0102]-[0104]) McNeely does not specifically teach cancer cell phenotype. However, one of ordinary skill in the art following McNeely would have considered the teaching of Collins regarding cancer diagnostics in similar microfluidic device ([0077]) and arrive at the claimed invention.
Regarding claim 14, McNeely teaches performing PCR with primers and probes ([0065]: “For example, pico green dye can be used for to label amplified DNA sequences produced by PCR to produce a fluorescent signal that can be detected to determine the presence or quantity or reaction product.”; [0097]) which one of ordinary skill in the art would reasonably considered and arrive at the claimed wherein the process reagent comprises PCR primers, polymerase, one or more probes, and a set of fluorophores for detection of biomarkers of the sample.
Regarding claim 21, as McNeely, Collins, and Deutsch teach the same method of claim 1, the results would necessarily be the same, and therefore the method taught by McNeely, Collins, and Deutsch would achieve a 90% capture efficiency.
Regarding claim 30, McNeely teaches the use of capillary action (par. 0022, 0068, 0082). Gong further teaches the use of capillary action (pg. 5, lines 1-13; pg .43, lines 10-12).
Claims 22-29 are rejected under 35 U.S.C. 103 as being unpatentable over McNeely et al. (US-20040109793, previously cited) in view of Collins (US20130244906, previously cited), Deutsch et al. (WO 2004/113492 A1, previously cited) and Gong et al. (WO 2014/065758 A1).
Regarding claim 22, McNeely teaches a microfluidic device for performing PCR ([0065], Example 1, claims 50-51):
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which corresponds to the instant claim as follows
A method comprising:
delivering a nucleic acid into at least one well of a substrate ( [0065]: “A PCR cocktail containing DNA sample of interest, but without primers, is pumped (with the use of a syringe pump, for example) into inlet 122”); McNeely teaches delivering reagents and sample into the set of wells via the inlet ([0065]; claim 59).
Regarding the claim 22 language, “having a plurality of wells in a hexagonal configuration, wherein the wells of the plurality of wells comprise a hexagonal cross-section and are interconnected with each other by a common channel,”
McNeely teaches a plurality of wells interconnected with each other by a common channel with vertical walls extending from a base surface to an open surface (Fig. 1 – 124/126/127/128/129/130/131; [0064, 0065]).
Neither McNeely nor Collins teaches the wells comprise a hexagonal cross-section or a hexagonal configuration.
Deutsch teaches a chip-device for holding living cells in a plurality of wells (Abstract). Deutsch teaches that to increase loading of cells per unit area, the wells can be round or hexagonal and be hexagonally packed (pg. 30, lines 3-5).
It would have been obvious to one of ordinary skill in the art to use hexagonal cells and be hexagonally packed. Deutsch teaches that hexagonal wells are a known well shape, and teaches that a hexagonally packed configuration increases loading of cells per unit area. A hexagonal well would therefore be a simple substitution of one well shape for another, and a person of ordinary skill in the art would be motivated to use a hexagonal packed configuration as Deutsch teaches that this configuration increases loading of cells per unit area, with no evidence of unexpected results.
Regarding claim 22’s language of :
flowing an immiscible fluid through the common channel to form a continuous encapsulation layer in the common channel spanning open surfaces of the wells of the plurality of wells of wells,
Collins teaches flowing oil after trapping cells for the encapsulation of cells (par. 0028, 0052). Collins does not teach that this a continuous encapsulation layer spanning all open surfaces of the set of cells.
Gong teaches a method of isolating nucleic acids in an aqueous sample using a microfluidic device (Abstract).
Gong teaches flowing mineral oil over an array of wells which acts as a sealant. Gong further teaches that this allows for applications such as flowing a PCR reaction mixture, then sealing with the oil to allow for the assay to be performed (pg. 5, lines 33-35, pg. 18, lines 15-21, pg. 22, lines 13-15; pg. 40, line 1; Fig. 2, Fig. 5). Gong further teaches the wells connected by a common channel (Fig. 17; pg. 36, lines 14-34).
It would have been obvious to one of ordinary skill in the art to flow a continuous encapsulation layer as taught by Gong, as Gong teaches that this acts as a sealant and allows for reaction mixtures to be sealed in the wells to enable additional analysis and assays to occur, and it would be a simple substitution of one encapsulation method for another, with no evidence of unexpected results.
Regarding claim 22, McNeely further teaches
performing PCR within the at least one well ([0065]: “The microfluidic circuitry shown in FIG. 1 is designed for performing polymerase chain reaction (PCR) with a DNA sample to detect sequences of interest, but could be used to implement various biochemical reactions, and particularly those which require that sample be subject to one or more heating steps. Such reactions include, but are not limited, to various reactions used in DNA processing, for example, PCR, which requires multiple heating steps (thermal cycling), or ligase chain reaction (LCR) or rolling circle amplification (RCA) for DNA amplification, or cycle sequencing, all of which use a single isothermal heating step.”).
Given the high level of skill in the art as evidenced by McNeely, Gong, and Collins (claim 1 – microfluidic chip based PCR assay), one of ordinary skill in the art of microfluidics would have reasonably considered variations on the design of a system to analyze biological samples as was routine in the art and arrive at the claimed invention.
Regarding claim 23, McNeely teaches ([0065]: “A PCR cocktail containing DNA sample of interest, but without primers, is pumped (with the use of a syringe pump, for example) into inlet 122”); McNeely teaches delivering reagents and sample into the set of wells via the inlet ([0065]; claim 59).
Regarding claim 24, McNeely teaches further comprising imaging contents of the set of wells, thereby enabling identification and assessment of contents of the set of wells during performance of the assay ([0065]: “The device is disassembled to permit dye in wells 131 a- 131 d to be read to quantify the amount of reaction products, or, if the device is formed at least in part of transparent material (i.e., transparent to the detected wavelengths), it may be possible to detect reaction products”) such that one of ordinary skill in the art would have considered imaging the contents of the wells and arrive at the claimed invention.
Regarding claim 25, McNeely teaches wherein transmitting heat through the substrate comprises providing a thermal control module comprising the heating plate arranged near a surface of the substrate (Fig. 1, 105; [0029]; [0064]-[0065]).
Regarding claim 26, further comprising returning a result characterizing a cancer cell phenotype represented in the sample, although McNeely teaches detecting analytes of interest for diagnostics ([0102]-[0104]) McNeely does not specifically teach cancer cell phenotype. However, one of ordinary skill in the art following McNeely would have considered the teaching of Collins regarding cancer diagnostics in similar microfluidic device ([0077]) and arrive at the claimed invention.
Regarding claim 27, McNeely teaches ([0065]: “A PCR cocktail containing DNA sample of interest, but without primers, is pumped (with the use of a syringe pump, for example) into inlet 122”); . McNeely teaches delivering reagents and sample into the set of wells via the inlet ([0065]; claim 59).
Regarding claim 28, McNeely teaches performing PCR with primers and probes ([0065]: “For example, pico green dye can be used for to label amplified DNA sequences produced by PCR to produce a fluorescent signal that can be detected to determine the presence or quantity or reaction product.”; [0097]) which one of ordinary skill in the art would reasonably considered and arrive at the claimed wherein the process reagent comprises PCR primers, polymerase, one or more probes, and a set of fluorophores for detection of biomarkers of the sample.
Regarding claim 29, McNeely teaches wherein performing the assay comprises performing an in-situ hybridization assay for nucleic acid contents captured within the set of wells ([0097]; claim 59).
Thus, the claims are rejected as prima facie obvious.
Response to Arguments
Applicant's arguments filed 0 have been fully considered but they are not persuasive. Applicant’s arguments regarding the continuous encapsulation layer are moot in light of the new grounds of rejection. As described above, McNeely in view of Collins and Gong render the claims obvious.
Applicant requests that the Office holds the double patenting rejection in abeyance. The Office is not persuaded of error by Applicants’ arguments because only “objections or requirements as to form not necessary to further consideration of the claims” may be held in abeyance. MPEP § 714.02.
New Grounds - Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
Claims 1-2, 4-6, 8-10, 12-14, and 21-30 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 14-18 of U.S. Patent No. US 10851426 in view of McNeely et al. (US-20040109793, previously cited), Collins (US20130244906, previously cited), Deutsch et al. (WO 2004/113492 A1, previously cited) and Gong et al. (WO 2014/065758 A1). The patent is to a method of analyzing a population of particles which one of ordinary skill in the art would have considered in view of McNeely, Collins, and Deutsch to arrive at the claimed invention for the reasoning detailed supra.
Claims 1-2, 4-6, 8-10, 12-14, and 21-30 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. US 10449543 in view of McNeely et al. (US-20040109793, previously cited), Collins (US20130244906, previously cited), Deutsch et al. (WO 2004/113492 A1, previously cited) and Gong et al. (WO 2014/065758 A1). The patent is to a method of analyzing a population of particles which one of ordinary skill in the art would have considered in view of McNeely, Collins, and Deutsch to arrive at the claimed invention for the reasoning detailed supra.
Claims 1-2, 4-6, 8-10, 12-14, and 21-30 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 12-20 of U.S. Patent No. US 10782226 in view of McNeely et al. (US-20040109793, previously cited), Collins (US20130244906, previously cited), Deutsch et al. (WO 2004/113492 A1, previously cited) and Gong et al. (WO 2014/065758 A1). The patent is to a method of analyzing a population of particles which one of ordinary skill in the art would have considered in view of McNeely, Collins, and Deutsch to arrive at the claimed invention for the reasoning detailed supra.
Claims 1-2, 4-6, 8-10, 12-14, and 21-30 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 11-20 of U.S. Patent No. US 11073468 in view of McNeely et al. (US-20040109793, previously cited), Collins (US20130244906, previously cited), Deutsch et al. (WO 2004/113492 A1, previously cited) and Gong et al. (WO 2014/065758 A1). The patent is to a method of analyzing a population of particles which one of ordinary skill in the art would have considered in view of McNeely, Collins, and Deutsch to arrive at the claimed invention for the reasoning detailed supra.
Claims 1-2, 4-6, 8-10, 12-14, and 21-30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11, 15-20 of U.S. Patent No. 11345951 in view of McNeely et al. (US-20040109793, previously cited), Collins (US20130244906, previously cited), Deutsch et al. (WO 2004/113492 A1, previously cited) and Gong et al. (WO 2014/065758 A1). The application is to a method of analyzing a population of cells which one of ordinary skill in the art would have considered in view of McNeely, Collins, and Deutsch to arrive at the claimed invention for the reasoning detailed supra.
Claims 1-2, 4-6, 8-10, 12-14, and 21-30 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10, 12-14 of copending Application No. 17/728789 in view of McNeely et al. (US-20040109793, previously cited), Collins (US20130244906, previously cited), Deutsch et al. (WO 2004/113492 A1, previously cited) and Gong et al. (WO 2014/065758 A1). The application is to a method of analyzing a population of particles which one of ordinary skill in the art would have considered in view of McNeely, Collins, and Deutsch to arrive at the claimed invention for the reasoning detailed supra.
This is a provisional nonstatutory double patenting rejection.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/R.L.B./Examiner, Art Unit 1684 /HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684