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 .
Application Status
Applicant’s remarks, including Exhibit A (hereinafter referred to as the “Kati Statement”), and amendments to the claims filed November 24, 2025 are acknowledged. Claim 12 was amended. Claims 1-2, 9, 11-12, 16, 21-26, 64, and 66-74 are pending and under examination herein.
Priority
Applicant’s priority claims to provisional Application No. 62/669,715 and PCT/US2019/031724 are acknowledged. Claims 1-2, 9, 11-12, 16, 21-26, 64, and 66-74 find support in Application No. 62/669,715, filed May 10, 2018. The effective filing date of all claims currently under examination is May 10, 2018.
Withdrawn Rejections
Applicant’s remarks, the Kati Statement, and amendments to the claims have been thoroughly reviewed. The Kati Statement provides that the full text of Ashur, while deposited to the Carolina Digital Repository on April 19, 2016, was not made publicly available until June 1, 2018. The Kati Statement provides that on April 19, 2016, “only the abstract was visible to the public.” The § 103 rejections over Barrett and Ashur raised in the prior action rely on the full text disclosure of Ashur. Because the full text of Ashur is no longer available as prior art in view of the Kati Statement, the § 103 rejections made over Barrett and Ashur, and Barrett and Ashur in further view of Martelotto are withdrawn. Applicant’s amendments to the claims resolve the objection to claim 12, which is also withdrawn.
Applicant’s remarks and amendments to the claims have been thoroughly considered, but are not persuasive to place the claims in condition for allowance for the reasons that follow. Any objection or rejection not reiterated herein has been overcome by amendment.
Claim Rejections - 35 USC § 112(b)
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 9, 16, 21-23, 26, and 67-69 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. The following rejections are maintained from the prior action.
Claims 9, 21-23, 26, and 67-69 recite the term “about,” which is a relative term. MPEP 2173.05(b) states that “The use of relative terminology… does not automatically render the claim indefinite.” However, MPEP 2173.05(b)(III)(A) states that “In determining the range encompassed by the term “about,” one must consider the context of the term as it is used in the specification and claims of the application.” The specification describes “about” as “encompass[ing] variations in one example ± 20% or ± 10%, in another example ± 5%... from the specified amount, as such variations are appropriate to perform the disclosed methods” (pg. 9, lines 29-33). While the specification provides a standard for “about,” and the frequencies, fragment sizes, temperatures, and hours recited in the claims can be measured using tools in the art, this standard does not provide sufficient guidance to determine which variation (i.e., ± 20%, ± 10%, ± 5%, etc.) of the recited frequencies, peak fragment sizes, temperatures, and hours is “appropriate” to perform the disclosed methods. For the purposes of compact prosecution, the claims will be examined under the interpretation that the term “about” is ± 20% from the specified amount.
Claim 16 recites “below room temperature.” The specification states that room temperature is “about 20-25°C” (pg. 15, line 7). As stated above, while the specification provides a standard for “about,” and temperature can be measured using tools in the art, this standard does not provide sufficient guidance to determine which variation of the temperature (i.e., ± 20%, ± 10%, ± 5%, etc.) is “appropriate” to perform the disclosed method. For the purposes of compact prosecution, the claim will be examined under the interpretation that the term “about” is ± 20% from the specified amount.
Response to Remarks - 35 USC § 112(b)
Applicant’s remarks regarding the § 112(b) rejections raised in the prior action have been reviewed. Applicant asserts that the specification “provides a clear definition of the term “about”, indicating that the recited amount encompasses a maximum range of ± 20%,” and therefore, the skilled artisan would understand the metes and bounds of the claims. Examiner respectfully disagrees with Applicant’s characterization of the specification’s definition of the term “about.” The specification describes “about” as “encompass[ing] variations in one example ± 20% or ± 10%, in another example ± 5%... from the specified amount, as such variations are appropriate to perform the disclosed methods” (pg. 9, lines 29-33). There is insufficient guidance to determine which variation (i.e., ± 20%, ± 10%, ± 5%, etc.) of the recited frequencies, peak fragment sizes, temperatures, and hours is “appropriate” to perform the disclosed methods, and therefore, the metes and bounds of the claims remain unclear.
Notice to Joint Inventors
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 Rejections - 35 USC § 103 – Barrett and Janzen
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.
Claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74 are rejected under 35 U.S.C. 103 as being unpatentable over Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record). The rejections that follow are maintained from the prior action.
Regarding claim 1, Barrett teaches a method of extracting DNA from FFPE tissue samples (pg. 3-4). Barrett teaches that FFPE tissue samples are a vast resource of clinically annotated samples, with patient follow-up data, including diagnostic and therapeutic outcomes (pg. 1). Barrett teaches that FFPE tissues contain “highly desirable and informative materials for the application of high definition genomics that could improve patient management and provide a molecular basis for the selection of personalized therapeutics” for individuals with cancer, for example (pg. 1). However, Barrett teaches that the variable quality of DNA extracted from FFPE tissue samples is a major barrier to using genomic profiling of FFPE tissue samples to advance treatment and diagnosis (pg. 1).
Barrett teaches a method of obtaining DNA from FFPE tissue (“a method of identifying aberrations in a variable cancer cell genome derived from FFPE tissue sample… the method typically includes the steps of: dewaxing a FFPE tissue sample; rehydrating the tissue sample; treating the tissue sample to obtain a suspension of de-agglomerated nucleic suitable for flow sorting (e.g., processing the tissue with EDTA, collagenase, and hyaluronidase)… extracting the genetic material from at least a portion of the sorted nucleic,” pg. 4-5; “FFPE sample preparation and flow sorting”, pg. 16-17; EXAMPLE 1”, pg. 21).
Regarding steps (a)-(b) of the claimed method, Barrett teaches initially processing the FFPE tissue, comprising contacting the FFPE tissue with xylene (an aromatic hydrocarbon) to remove paraffin, and contacting the sample with an enzymatic solution that comprises one or more enzymes that digest one or more extracellular matrix components, wherein the enzymatic solution comprises collagenase and hyaluronidase (“FFPE samples are… washed, for example, 3 times, with Xylene… to remove remaining paraffin… each sample is digested overnight (e.g., 6-17 hours) in 1 mL of a freshly prepared enzymatic cocktail containing… collagenase…,… and hyaluronidase in PBS”, pg. 16). Thus, Barrett teaches each limitation required of steps (a)-(b) of instant claim 1.
Regarding step (c) of the claimed method, Barrett teaches extracting DNA from the sample using a series of buffered, enzymatic incubation steps (“DNA extraction”, pg. 17). Barrett teaches exposing the extracted DNA to ultrasound energy, thereby providing processed DNA comprising fragments that have been extracted from the biological tissue (“high quality genomic DNA with a 260/280 ratio between 1.8 and 2.1 are fragmented to a target size of 150 to 200 bp, for example, on the Covaris E210 system”, pg. 19; “high quality genomic DNA with a 260/280 ratio between 1.8 and 2.1 is fragmented to a target size of 300-400bp on, for example, the Covaris E210 System”, pg. 20). However, Barrett does not teach exposing the sample itself (i.e., prior to any DNA extraction steps) to ultrasound energy.
Janzen, like Barrett, teaches that genomic profiling is likely to become standard in oncological medicine, but routine implementation “will require overcoming a number of hurdles including streamlining of sample processing” ([0003]). Specifically, Janzen teaches that “current DNA fragmentation methods are a bottleneck for diagnostic assays such as NGS and ChIP” ([0005]). Janzen teaches that DNA fragmentation for ChIP from FFPE tissue is challenging due to the rigidity and lysis-resistance caused by formaldehyde crosslinking ([0004]-[0005]). Janzen teaches that conventional sonication-based methods of DNA fragmentation “produces inconsistent results and is time consuming” ([0006]). Janzen teaches that “consistent DNA fragmentation is required for quality NGS data” ([0004]). Janzen teaches a method of obtaining consistently fragmented DNA from biological samples, including FFPE samples, which seeks to overcome the “disadvantages associated with conventional techniques for DNA shearing” ([0008]; (“the biological sample may include DNA or DNA that has been cross-linked to protein… The method may be successfully applied to… fixed and paraffin embedded tissue”, [0027]; “The same techniques may be applied in extraction and fragmentation of DNA from formalin fixed paraffin embedded (FFPE) tissue slices”, [0057]).
Regarding step (c) of the instantly claimed method, Janzen’s method utilizes lipid-coated phase-change micro- and nano-droplets comprising a liquid perfluorocarbon core which converts to gas upon the addition of ultrasound conversion energy ([0032-0036]). Janzen teaches that ultrasound sonication in the 10 kilohertz (“0.01 MHz”) to 10 megahertz range is sufficient to convert the precursor droplets to a microbubble that enhances tissue dispersion and DNA fragmentation (“The addition of controlled sized lipid microbubbles to an acoustic sonication process significantly improves the efficiency and consistency of DNA fragmentation… may also be used to enhance other sample processes, such as to effect cell lysis, to perform tissue dispersion”, [0022]; [0028]; [0032]-[0036]). Janzen teaches the method comprises mixing the sample with phase-change droplets, exposing the mixture to ultrasound energy, to thereby provide a processed sample comprising DNA fragments directly from the tissue ([0029]-[0039]; [Fig. 1-4]). Janzen teaches the phase-change droplet-based approach reduces the sonication time required to fragment DNA, which could greatly improve sample quality, and increase processing efficiency and robustness ([0057]). Janzen demonstrates that the method “significantly improve[s] the consistency of DNA fragmentation by producing fragments within a narrow size distribution,” and “does not interfere with downstream fluorescent based analyses” ([0055]-[0056]; Fig. 8).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have substituted the conventional DNA extraction and fragmentation steps in the method of processing FFPE tissue taught by Barrett, with the phase-change droplet-based approach taught by Janzen, to arrive at the method of instant claim 1. It would have amount to a simple substitution of known steps to extract and fragment DNA from FFPE tissue, by known means to yield predictable results. The skilled artisan would have had a reasonable expectation of success in extracting chromatin from FFPE tissue following the substitution because Janzen provides a working example of the phase-change droplet-based step, and teaches that “the same techniques may be applied to extraction and fragmentation of DNA from formalin fixed paraffin embedded (FFPE) tissue.” Barrett and Janzen both teach that genomic profiles obtained from FFPE samples are valuable resources for understanding the molecular basis of cancer, and advancing oncological treatment and diagnosis. However, Barrett and Janzen also emphasize that obtaining genomic profiles from FFPE samples is limited at least by time-consuming processing steps and variable DNA quality. The skilled artisan, recognizing that Janzen teaches a DNA extraction and fragmentation step applicable to FFPE tissue, that overcomes the “disadvantages associated with conventional techniques” would have been motivated to substitute the step of Barrett, in an effort to facilitate ease in processing and using FFPE tissue to advance oncological treatment and diagnosis.
Regarding claim 2, the organic solvent taught by Barrett – xylene – is an aromatic hydrocarbon (“FFPE samples are… washed, for example, 3 times, with Xylene… to remove remaining paraffin”, pg. 16).
Regarding claim 9, Janzen teaches that the ultrasound sonication is between 10 kilohertz (“0.01 MHz”) and 10 megahertz ([0028]).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have exposed the FFPE sample to ultrasound energy between 20 kilohertz and 2 megahertz, in view of Janzen’s disclosed range of between 10 kilohertz and 10 megahertz. It would have amounted to selecting a range within a range of known frequencies, by known means to yield predictable results. The skilled artisan would have had a reasonable expectation that exposing the sample to ultrasound energy between 20 kilohertz and 2 megahertz would provide a processed FFPE sample comprising chromatin fragments because Janzen teaches that ultrasound sonication in the 10 kilohertz (“0.01 MHz”) to 10 megahertz range converts the precursor droplets to a microbubble that enhances tissue dispersion and DNA fragmentation. The skilled artisan would have been motivated to expose the FFPE sample to ultrasound energy between 20 kilohertz and 2 megahertz, because Janzen teaches a larger range within which the skilled artisan would be motivated to find the optimal conversion energy for enhanced tissue dispersion and DNA fragmentation.
Regarding claims 11-12, the method rendered obvious in paragraph 13 above comprises a solution comprising a nanodroplet cavitation reagent added prior to or during exposure of the sample to ultrasound energy ([0029]-[0039]; [Fig. 1-4]).
Regarding claim 16, the nanodroplets taught by Janzen comprise a liquid perfluorocarbon core that has a boiling point that is below room temperature at atmospheric pressure (“By increasing the pressure on the headspace of the sealed vial using a custom apparatus, the gas core will transition from the gas phase to the liquid phase”, [0033]-[0035]). Janzen teaches the nanodroplets require ultrasound conversion energy to vaporize from their liquid state (“By supplying enough acoustic energy, the droplets may transition back to the gas phase and subsequently cavitate”, [0033], [0035]).
Janzen does not explicitly state that the liquid perfluorocarbon core of the nanodroplets remains liquid for at least one hour at room temperature at one standard atmosphere of pressure. MPEP 2112.01(II) states that “When the structure recited in the reference is substantially identical to that of the claims, claimed properties or functions are presumed to be inherent.” The claim describes a nanodroplet composed of a liquid perfluorocarbon core, wherein the perfluorocarbon has a boiling point that is below room temperature at one standard atmosphere of pressure when it is not part of the nanodroplet. The claim further states that the liquid perfluorocarbon core remains liquid for at least one hour at room temperature at one standard atmosphere of pressure when it is part of the nanodroplet. The specification states that perfluorobutane is a suitable perfluorocarbon core material, which has a boiling point that is below room temperature at one standard atmosphere of pressure (pg. 15, lines 5-10). The specification also states that the nanodroplet encapsulates the liquid core in a stabilizing shell, e.g., a lipid shell comprising DSPC conjugated to PEG (pg. 14, line 29 to pg. 15, line 5).
Janzen teaches nanodroplets comprising each of the aforementioned structural elements (“perfluorobutane”, [0035]; “DSPC… DSPE-PEG2000… decafluorobutane”, [0052]). Janzen’s and the claimed nanodroplets are substantially identical in structure. Thus, the claimed properties and functions are presumed to be inherent features of Janzen’s nanoparticle.
Regarding claims 21-22, Janzen provides working examples of the phase-change nanodroplet based step that produce processed samples comprising DNA peak fragment sizes between 300-500 bp ([0054]; Fig. 7), and 200-500 bp ([0055]; Fig. 8). Janzen’s ranges of DNA fragment sizes lie fully within the claimed ranges.
Regarding claim 23, as shown in Fig. 7, Janzen provides working examples in which the phase-change nano-droplet based step produces DNA fragments between 400-800 bp (see lanes 6-8 and 12-14; Fig. 7).
Regarding claim 24, neither Barrett nor Janzen teach the method uses an antibody. Thus, the method rendered obvious in paragraph 13 above is free of the use of an antibody (see Barrett, pg. 16; pg. 21; Janzen, at least [0022]-[0039]; Figs. 1-4).
Regarding claim 64, the specification provides that “mechanical dissociation step” encompasses the use of a probe sonicator (pg. 18, line 21). Janzen teaches that the phase-change nano-droplet based step includes “a probe for adding sonic energy” ([0046]).
Regarding claim 66, Barrett’s enzymatic solution is free of at least micrococcal nuclease (pg. 16; pg. 21).
Regarding claim 68, Barrett teaches the contacting step of (b) is performed for between 6 and 17 hours (each sample is digested overnight (e.g., 6-17 hours) in 1 mL of a freshly prepared enzymatic cocktail containing… collagenase…,… and hyaluronidase in PBS”, pg. 16). Based on the specification, the term “about” includes ± 20% (pg. 9, lines 29-33). The claimed range of about 4 hours and about 17 hours is interpreted as encompassing ± 20% of the claimed range, i.e., ± 2.6 hours on either end. Barrett’s range of 6-17 hours lies fully within the instantly claimed range of about 4 hours and about 17 hours.
Regarding claim 70, Janzen teaches the perfluorocarbon comprises decafluorobutane (decafluorobutane”, [0052]).
Regarding claim 71, Janzen teaches the nanodroplets comprise a lipid layer surrounding a liquid layer surrounding a liquid core prior to exposure to ultrasonic energy (“Due to the low boiling point of the perfluorocarbon gas, transition to the liquid phase is achievable…the gas core will transition from the gas phase to the liquid phase, thus creating… lipid-coated perfluorocarbon-based micro- and nano-droplets. By supplying enough acoustic energy, the droplets may transition back to the gas phase and subsequently cavitate”, [0033]; “lipid monolayer-coated microbubbles were created”, [0052]).
Regarding claims 72-73, Janzen teaches the nanodroplets vaporize to form microbubbles upon exposure to ultrasonic energy (“By supplying enough acoustic energy, the droplets may transition back to the gas phase and subsequently cavitate”, [0033]; “The droplets may be converted to microbubbles”, [0034]; “Once vaporized, they grow in diameter… due to the liquid to gas volume change. The resulting bubble…”, [0032]).
Regarding claim 74, Janzen teaches the microbubbles comprise a gaseous core encapsulated in a lipid shell, wherein the gaseous core comprises a perfluorocarbon gas (“Once vaporized, they grow in diameter… due to the liquid to gas volume change. The resulting bubble…”, [0032]; “perfluorobutane”, [0035]; “lipid-monolayer-coated microbubbles were created… DSPC… DSPE-PEG2000… decafluorobutane”, [0052]).
Claim Rejections - 35 USC § 103 – Barrett and Janzen in view of Chiarella
Claims 25-26, and 69 are rejected under 35 U.S.C. 103 as being unpatentable over Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record) as applied to claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74, and in further view of Chiarella (Chiarella et al., 16 April 2018, Biochemistry, 57, p. 2756-2761 and Supplemental Figures; of record). The rejections that follow are maintained from the prior action.
The teachings of Barrett and Janzen are described above and applied as to claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74 above. As described therein, Janzen teaches that there are hurdles to obtaining quality, fragmented DNA from fixed samples, e.g., those used for ChIP ([0004]-[0005]).
Neither Barrett nor Janzen teach or demonstrate that the phase-change nanodroplet based step:
provides a processed sample wherein chromatin fragments derived from precipitation of a protein crosslinked to chromatin are distinguishable from chromatin fragments that do not contain the protein (claim 25), or
provides an amount of/detectable signal from the accessible chromatin that is at least about 1.5 times or more than the amount of/detectable signal from the inaccessible chromatin (claim 26), or
is performed in a cooling bath at between about -10°C and about 10°C (claim 69).
Chiarella teaches a method of extracting chromatin from tissue to perform ChIP (“ChIP is as follows: (1) fixation of cells with formaldehyde, which cross-links chromatin-bound proteins to DNA; (2) isolation of the cross-linked chromatin from the cell nuclei…”, pg. 2756, left col.; Fig. 2A). Like Janzen, Chiarella describes the use of a phase-change nanodroplet-based cavitation reagent, which is mixed with the sample, and upon exposure to ultrasonic energy at 4°C, fragments chromatin in the fixed samples (“Sonication of Fixed Nuclei”, pg. 2757-2758; Fig. 2). Chiarella’s nanodroplet comprises liquid decafluorobutane encapsulated in a lipid shell (Sonication of Fixed Nuclei”, pg. 2758). Chiarella, echoing the teachings of Barrett and Janzen, teaches that “chromatin fragmentation remains an inefficient and inconsistent process… Proper chromatin fragmentation is a bottleneck in current protocols” (pg. 2757, left col.). Chiarella demonstrates that use of the phase-change nanodroplets decreases chromatin fragmentation time, and consistently produced fragments in the 200-500 bp range (pg. 2759, left col.; Fig. 2; Fig. S2).
Regarding claim 25 specifically, Chiarella performed ChIP-qPCR for lysine methyltransferase protein G9a occupancy at a known “G9a negative locus” (BC006361, Fig. 3B) and “G9a positive locus” (PGSF1, Fig. 3A)(Fig. 3A-B; pg. 2759-2760). Chiarella teaches the “presence of nanodroplets resulted in… a 6-fold difference between G9a occupancy at the positive and negative regions” (Fig. 3D, pg. 2760, left col.). Thus, Chiarella teaches the method provides a processed sample wherein chromatin fragments derived from precipitation of a protein crosslinked to chromatin (i.e., “G9a”) are distinguishable from chromatin fragments that do not contain the protein.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have combined the method rendered obvious in paragraph 13 above, with ChIP-qPCR taught by Chiarella, to arrive at the method of instant claim 25. It would have amounted to combining an obvious method of extracting and fragmenting chromatin in FFPE samples, with a known technique to analyze chromatin occupancy (i.e., ChIP-qPCR), by known means to yield predictable results. The skilled artisan would have had a reasonable expectation of success in combining the method rendered obvious over Barrett and Janzen with ChIP-qPCR taught by Chiarella because Chiarella uses a substantially identical phase-change nanodroplet-based DNA extraction and fragmentation step, in fixed tissue, to that of the method of Barrett and Janzen, and Chiarella teaches the step produces “the desired ChIP fragment size distribution of 200-500 bp,” which is substantially identical to the fragment size disclosed by Janzen. The skilled artisan would have been motivated to perform ChIP-qPCR in FFPE tissue because, as evidenced by Barrett and Janzen, genomic profiles obtained from FFPE samples are valuable resources for understanding the molecular basis of cancer, and advancing oncological treatment and diagnosis, and Chiarella provides evidence that the phase-change nanodroplet step overcomes the technical hurdles in obtaining quality, fragmented chromatin from fixed tissue for ChIP.
Regarding claim 26 specifically, the term “accessible” is interpreted as referring to regions of DNA that are actively being transcribed, or part of a regulatory element such as an active enhancer (pg. 2, lines 2-6). The term “inaccessible,” in contrast, is interpreted as referring to regions of DNA that code for inactive genes or regulatory regions (pg. 2, lines 6-10). Chiarella performed ChIP-qPCR using antibodies for H3K4me3, which marks accessible chromatin (“a marker of active gene transcription”) and H3K9me3, which marks inaccessible chromatin (“to mark transcriptional repression”)(pg. 2760, left col.). Using qPCR, Chiarella shows that chromatin fragments derived from accessible chromatin (i.e., precipitated with H3K4me3) are quantifiably distinguishable from chromatin fragments derived from inaccessible chromatin (Fig. 4C). Chiarella does not explicitly teach that the amount of detectable signal derived from the accessible chromatin is about 1.5 times or more than the amount of detectable signal derived from inaccessible chromatin.
However, MPEP 2112.02(I) states that “if a prior art device, in its normal and usual operation, would necessarily perform the method claimed, then the method claimed will be considered to be anticipated by the prior art device. When the prior art device is the same as a device described in the specification for carrying out the claimed method, it can be assumed the device will inherently perform the claimed process.” The method rendered obvious in paragraph 33 above, and the method described in the specification that yields increased levels of DNA fragments from accessible chromatin regions (“nanodroplet assisted sonication”), are the same (pg. 11, line 12 to pg. 12, line 26, Fig. 5). Because the methods are the same, it is assumed that the method rendered obvious in paragraph 33 above performs the claimed element (i.e., increasing the detectable signal of accessible chromatin compared to the detectable signal of inaccessible chromatin) in its normal and usual operation. Thus, claim 26 is obvious over the method rendered obvious in paragraph 33 above.
Regarding claim 69, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have exposed the nanodroplet-FFPE sample mixture in the method rendered obvious in paragraph 13 above to ultrasound energy in a cooling bath at 4°C in view of Chiarella. It would have amounted to performing a known step at a known temperature, by known means to yield predicable results. The skilled artisan would have had a reasonable expectation of success in performing the sonication step in a cooling bath at 4°C because Chiarella’s substantially identical phase-change nanodroplet-based DNA extraction and fragmentation step is performed at 4°C. The skilled artisan would have been motivated to perform the sonication step at 4°C because neither Barrett or Janzen teach a temperature at which the sonication step should be performed, and Chiarella provides a temperature at which the phase-change nanodroplet-based DNA extraction and fragmentation step produces quality, fragmented chromatin from fixed tissue.
Claim Rejections - 35 USC § 103 – Barrett and Janzen in view of Martelotto
Claim 67 is rejected under 35 U.S.C. 103 as being unpatentable over Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record) as applied to claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74, and in further view of Martelotto (Martelotto et al., 6 February 2017, Nature Medicine, Vol. 23, Number 3, p. 376-388; of record). The following rejection is maintained from the prior action.
The teachings of Barrett and Janzen are described above and applied as to claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74 above.
Neither Barrett nor Janzen teach that contacting the sample with an enzymatic solution comprising collagenase and hyaluronidase in step (b) is performed at a temperature of between about 32°C and about 40°C.
Martelotto also teaches a method of extracting DNA from FFPE tissue samples, in which the FFPE tissues are contacted with an enzymatic solution comprising collagenase and hyaluronidase (“The tissues were digested for 16 h at 37 °C in 1 ml of an enzymatic cocktail containing 1 mg/ml of Collagenase or Dispase (Roche) and 100 units/ml of Hyaluronidase (Calbiochem) in PBS with 0.5 mM CaCl2”, Online Methods, “Sample preparation, microdissection and single-nucleus preparation”). Martelotto teaches the samples are digested for 16hr at 37°C (Online Methods, “Sample preparation, microdissection and single-nucleus preparation”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have performed the contacting step of the method rendered obvious in paragraph 13 above at 37°C as taught by Martelotto. It would have amounted to performing a known step at a known temperature, by known means to yield predictable results. The skilled artisan would have been motivated perform the contacting step at 37°C, with a reasonable expectation of success because the contacting steps of Barrett and Martelotto utilize the same enzymes (i.e., collagenase and hyaluronidase), and as evidenced by Martelotto, these enzymes digest FFPE tissue effectively at 37°C.
Response to Remarks – 35 U.S.C. § 103
Applicant’s remarks regarding the § 103 rejections over Barrett and Janzen, and Barrett and Janzen in view of Chiarella or Martelotto, have been reviewed (see Sections D-F, pgs. 8-9 of the remarks). First, Applicant “reiterates the arguments made in the response filed February 20, 2025, that neither Barrett nor Janzen teaches or suggests methods for extracting intact chromatin.” Examiner has already addressed Applicant’s remarks made in the response filed February 20, 2025. See paragraph 67 of the prior action, which is applied herein. Briefly, as stated therein, there is substantial evidence in the disclosure of Janzen to conclude that Janzen is concerned with the extraction of chromatin from tissue, including from FFPE tissue (“may be applied to extraction and fragmentation of DNA from formalin fixed paraffin embedded (FFPE) tissue slices,” [0057]). The skilled artisan would also know that Barrett is concerned with the extraction of chromatin from FFPE tissue because DNA extracted from FFPE tissue is cross-linked, i.e., it is in the form of chromatin. This is well-known in the art, and supported by the disclosure of Janzen (“Formaldehyde crosslinks protein to DNA… DNA fragmentation for fixed samples such as ChIP or FFPE is even more challenging,” [0005]). Applicant’s remarks regarding this alleged deficiency of Barrett and Janzen remain unpersuasive.
Applicant, referring to Examiner’s use of Ashur and Cejas to respond to Applicant’s previous arguments, states that Ashur “is not available as prior art,” and that “relying on general knowledge in the art without citing relevant references in the statement of rejection is improper.” The rejections maintained above do not rely on Ashur or Cejas. The combination of Barrett and Janzen, in further view of Chiarella or Martelotto, renders obvious each limitation of the instant claims. As such, Ashur’s inability to be applied as prior art in view of the Kati Statement does not affect the rejections above. “Relevant references” have also clearly been cited in the statement of rejection. The use of prior art (i.e., Cejas) to establish what was well known to the ordinary skilled artisan, so as to respond to Applicant’s remarks, is not improper.
Applicant indicates that “the present invention is designed for extraction of accessible regions of chromatin, i.e., DNA not bound by histones.” Applicant asserts that “it would not have been obvious based on the cited art that sonicating FFPE tissues with nanodroplets would be suitable for chromatin accessibility assays, e.g., FAIRE-seq.” Applicant also asserts that the ultrasound parameters also would not have been obvious. Examiner notes that claim 1 is directed to a generic method of extracting chromatin from FFPE tissue. The method does not require the outcomes to which Applicant’s remarks refer, the use of nanodroplets, any downstream steps of, “e.g., FAIRE-seq,” or any specific ultrasound parameters. The outcomes to which Applicant’s remarks refer, the use of nanodroplets, as well as the ultrasound parameters, are found in various dependent claims, which have been rendered obvious over the prior art cited above. Applicant has not presented any convincing evidence that the limitations in the dependent claims would not have been obvious over the prior art cited above.
Applicant states that “the combination of Barrett and Janzen would be suitable for DNA extraction and fragmentation from FFPE tissue.” Applicant alleges that the combined teachings would “result in solubilization of the chromatin for either ChIP assays or total DNA extraction by proteinase K digestion to digest the histones.” Applicant then asserts “that is not the present invention.” Applicant states that “the present invention does not use proteinase K except for a small 10% of the sample which is digested to measure total DNA concentration.” Applicant, again, alleges that the cited prior art uses proteinase K to digest chromatin.
Assuming that the phrase “solubilization of the chromatin” refers to the production of fragments via sonication (see at least pg. 13-14 of the specification), Applicant appears to concede that the combination of Barrett and Janzen does, indeed, result in extracting fragmented chromatin from FFPE tissue, e.g., for use in a ChIP assay. Although Applicant asserts that this is “not the present invention,” the statements do appear to describe “the present invention,” i.e., a method for extracting fragmented chromatin from FFPE tissue (see claim 1). The specification describes use of extracted, fragmented chromatin for ChIP assays (see pg. 10). It is not clear how/if these remarks were intended to support Applicant’s position that the instant claims are unobvious.
Applicant’s remarks regarding the alleged use of proteinase K in the combination above have already been addressed. See paragraph 67, pg. 31-32, of the prior action. Examiner reiterates that the method rendered obvious above does not include any proteinase K within steps (a)-(c). The instant claims require extracting chromatin fragments from a FFPE tissue; the claims do not limit the handling of the chromatin following steps (a)-(c) of the method. There is no apparent deficiency in the method rendered obvious above with respect to the instant claims. Examiner also reiterates, as Applicant asserts in their remarks (“proteinase K digestion to digest the histones”), that the skilled artisan would know that proteinase K is used to reverse cross-links in extracted chromatin so that downstream applications may be performed. Indeed, the specification describes such a use for proteinase K following extraction of chromatin fragments (see Example 1, step 14).
Finally, Applicant asserts that neither Chiarella nor Martelotto remedy the alleged deficiencies of Barrett and Janzen. Examiner has addressed the alleged deficiencies of Barrett and Janzen in paragraph 67 of the prior action and immediately above. Chiarella and Martelotto are not relied upon for the same teachings as Barrett and Janzen. There are no apparent deficiencies in the rejections made in further view of Chiarella or Martelotto.
Taken together, Applicant’s remarks are not found persuasive. The rejections over Barrett and Janzen, and Barrett and Janzen in view of Chiarella or Martelotto are maintained, accordingly.
Nonstatutory 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 filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual 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/apply/applying-online/eterminal-disclaimer.
U.S. Patent No. 9,982,290 B2
Claims 1-2, 9, 11-12, 16, 21-24, and 64, 66, 68, and 70-74 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 claims of U.S. Patent No. 9,982,290 B2 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejections are maintained from the prior action.
Patented claim 1 recites “ A method for using nanodroplets to process a biological sample, the method comprising: creating a mixture comprising nanodroplets mixed with a biological sample, wherein the nanodroplets each comprise a liquid core which remains metastable in a liquid form until the application of conversion energy and wherein the biological sample comprises DNA or DNA cross-linked to protein extracted from cells; and
adding the conversion energy to the mixture to cause at least some of the nanodroplets to convert to encapsulated microbubbles, wherein the encapsulated microbubbles comprise of at least one of a lipid, a surfactant, an emulsifier, a polymer, and a protein and adding activation energy to the mixture to cause the encapsulated microbubbles to oscillate or burst, and thereby processing the biological sample sufficiently to shear the DNA or DNA cross-linked to the protein in the biological sample and produce DNA fragments having a size distribution narrower than a size distribution of DNA fragments produced through sonication of the biological sample without using metastable nanodroplets.”
Patented claim 6 recites that “the biological sample comprises at least one of fresh tissue, cryogenically preserved tissue, and fixed and paraffin embedded tissue.”
Patented claims 10 and 19 recite “creating the mixture comprises adding a solution of the nanodroplets to the sample and mixing the solution with the sample” and “creating the mixture comprises adding the nanodroplets to the biological sample prior to or during the addition of the conversion energy,” respectively.
Relative to the instant claims, the patented claims recite a method of processing a biological sample, which may be an FFPE sample, using “metastable” nanodroplets comprising a liquid core, wherein the core may be a perfluorocarbon, that upon addition of “conversion energy,” which may be “sonicat[ion],” processes the biological sample to “sufficiently shear the DNA or DNA cross-linked to the protein” to produce DNA fragments. The instant claims also encompass processing a biological sample to extract DNA cross-linked to protein (i.e., chromatin) from an FFPE tissue using “metastable” nanodroplets comprising a liquid core, wherein the liquid core may be a perfluorocarbon, that upon addition of ultrasound conversion energy produces DNA fragments. However, the patented claims do not recite the processing steps for the biological sample, i.e., initial processing with an organic solvent, enzymatic digestion with collagenase and/or hyaluronidase, or each of the further limitations to the processing steps recited in the instant claims.
The teachings of Barrett and Janzen are recited above in paragraphs 10-27 and applied hereinafter. As described therein, Barrett and Janzen render obvious the methods of instant claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74 wherein FFPE tissue is received, initially processed with an organic solvent, subjected to enzymatic digestion with a solution comprising collagenase and/or hyaluronidase, and then mixed with phase-change nanodroplets comprising a liquid perfluorocarbon core. The sample is then exposed to ultrasound activation energy which causes the liquid perfluorocarbon core in the phase-change nanodroplets to become gaseous, expand, and thereby, disperse the tissue and fragment the chromatin therein.
Regarding instant claims 1-2, 11-12, 21-24, 64, 66, 68, and 70-74, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have used the patented method for extracting chromatin from FFPE tissue as taught by Barrett and Janzen. It would have amounted to using a known method for extracting DNA fragments from a sample, with a known method of processing FFPE tissue for the same, to yield predictable results. A skilled artisan would have had a reasonable expectation of success in using the patented method as taught by Barrett and Janzen because together Barrett and Janzen teach a method which is substantially identical to the patented method, for the same purpose recited in the patented method. A skilled artisan would have been motivated to use the patented method as taught by Barrett and Janzen because together Barrett and Janzen teach a method substantially identical to the patented method, which enhances processing of FFPE tissue, and facilitates extraction of consistently fragmented chromatin for downstream applications, including those which may facilitate development of therapies and diagnostics.
Regarding instant claim 9, patented claims 7-8 recite “wherein adding the activation energy to the mixture comprises sonicating the mixture” and “wherein sonicating the mixture includes applying energy having a frequency in the range from 0.01 MHz to 10.0 MHz.”
The patented claims do not recite that the frequency is between about 20 kilohertz (kHz) and about 2 megahertz (MHz). The obviousness of applying ultrasound energy within the instantly recited range is described above in paragraph 15 and applied here.
Regarding instant claim 16, patented claims 16-17 recite that the “nanodroplets comprise a shell surrounding the liquid core, wherein the liquid core converts to a gas upon the addition of the conversion energy” and further “wherein the liquid core comprises a hydrocarbon or a perfluorocarbon.” Thus, instant claim 16 is obvious over patented claims 16-17.
Claim 25-26 and 69 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 claims of U.S. Patent No. 9,982,290 B2 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record), and in further view of Chiarella (Chiarella et al., 16 April 2018, Biochemistry, 57, p. 2756-2761 and Supplemental Figures; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejections are maintained from the prior action.
Regarding instant claims 25-26, and 69, the teachings of Barrett, Janzen, and Chiarella are described above in paragraphs 28-35 and applied hereinafter. As described therein, Barrett and Janzen in view of Chiarella render obvious combining the method of processing FFPE tissue taught by Barrett and Janzen, with ChIP-qPCR taught by Chiarella. The obviousness of combining the method rendered obvious in paragraph 48 above, with ChIP-qPCR taught by Chiarella to arrive at the inventions of instant claims 25-26 is described in paragraphs 33-34 and applied here. The obviousness of performing the sonication step of the method rendered obvious in paragraph 48 above, at 4°C as taught by Chiarella, is described in paragraph 35 and applied here.
Claim 67 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 claims of U.S. Patent No. 9,982,290 B2 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record), and in further view of Martelotto (Martelotto et al., 6 February 2017, Nature Medicine, Vol. 23, Number 3, p. 376-388; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejection is maintained from the prior action.
Regarding instant claim 67, the teachings of Barrett, Janzen, and Martelotto are described above in paragraphs 36-40 and applied hereinafter. The obviousness of performing the contacting step in the method rendered obvious in paragraph 48 above, at 37°C as taught by Martelotto, is described in paragraph 40 above and applied here.
U.S. Patent No. 11,485,994 B2
Claims 1-2, 9, 11-12, 16, 21-24, and 64, 66, 68, and 70-74 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 claims of U.S. Patent No. 11,485,994 B2 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejections are maintained from the prior action.
Patented claim 1 recites “A method for using encapsulated microbubbles to process a biological sample to shear and extract random, unbiased DNA fragments from the sample, the method comprising: creating a mixture comprising encapsulated nanodroplets mixed with a biological sample comprising DNA, wherein creating the mixture comprises adding a solution of encapsulated nanodroplets to the sample and mixing the solution with the sample; adding energy to the mixture to cause at least some of the nanodroplets to form encapsulated microbubbles, which oscillate or burst and thereby process the sample and shear the DNA, and extracting the sheared, random, and unbiased DNA fragments from the sample.”
Patented claims 6-7 recite that “the sample comprises at least one of fresh tissue, cryogenically preserved tissue, and fixed and paraffin embedded tissue” and “wherein the sample comprises fixed and paraffin embedded tissue.”
Patented claim 15 recites that “creating the mixture comprises adding the nanodroplets to the sample prior to or during the addition of the formation energy, wherein, during administration of formation energy, at least some of the nanodroplets vaporize into the bubbles that will oscillate or burst in response to the addition of activation energy.”
Relative to the instant claims, the patented claims recite a method of processing a biological sample, which may be an FFPE sample, using encapsulated nanodroplets comprising a liquid core, wherein the core may be a perfluorocarbon, that upon addition of energy,” which may be “sonicat[ion],” processes the biological sample to “shear the DNA,” and “extracting the sheared, random, and unbiased DNA fragments from the sample,” which in the case of FFPE would be cross-linked, i.e., in chromatin form, owing to its presence in FFPE tissue. The instant claims also encompass processing a biological sample to extract DNA fragments from an FFPE tissue using encapsulated nanodroplets comprising a liquid core, wherein the liquid core may be a perfluorocarbon, that upon addition of ultrasound conversion energy produces DNA fragments. However, the patented claims do not recite the processing steps for the biological sample, i.e., initial processing with an organic solvent, enzymatic digestion with collagenase and/or hyaluronidase, or each of the further limitations to the processing steps recited in the instant claims.
The teachings of Barrett and Janzen are recited above in paragraphs 10-27 and applied hereinafter. As described therein, Barrett and Janzen render obvious the methods of instant claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74 wherein FFPE tissue is received, initially processed with an organic solvent, subjected to enzymatic digestion with a solution comprising collagenase and/or hyaluronidase, and then mixed with phase-change nanodroplets comprising a liquid perfluorocarbon core. The sample is then exposed to ultrasound activation energy which causes the liquid perfluorocarbon core in the phase-change nanodroplets to become gaseous, expand, and thereby, disperse the tissue and fragment the chromatin therein.
Regarding instant claims 1-2, 11-12, 21-24, 64, 66, 68, and 70-74, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have used the patented method for extracting chromatin from FFPE tissue as taught by Barrett and Janzen. It would have amounted to using a known method for extracting DNA fragments from a sample, with a known method of processing FFPE tissue for the same, to yield predictable results. A skilled artisan would have had a reasonable expectation of success in using the patented method as taught by Barrett and Janzen because together Barrett and Janzen teach a method which is substantially identical to the patented method, for the same purpose recited in the patented method. A skilled artisan would have been motivated to use the patented method as taught by Barrett and Janzen because together Barrett and Janzen teach a method substantially identical to the patented method, which enhances processing of FFPE tissue, and facilitates extraction of consistently fragmented chromatin for downstream applications, including those which may facilitate development of therapies and diagnostics.
Regarding instant claim 9, patented claims 8-9 recite that “adding the energy to the mixture comprises sonicating the mixture” and wherein “sonicating the mixture includes applying energy having a frequency in the range from 0.01 MHz to 10.0 MHz.”
Patented claims 8-9 do not recite that the frequency is between about 20 kilohertz (kHz) and about 2 megahertz (MHz). The obviousness of applying ultrasound energy within the instantly recited range is described above in paragraph 15 and applied here.
Regarding instant claim 16, patented claims 11-12 recite that “the nanodroplets comprise a shell surrounding a liquid core which converts to a gas upon the addition of the energy, wherein the energy comprises at least one of acoustic, thermal, and optical energy” and wherein “the liquid core comprises a hydrocarbon or a perfluorocarbon.” Thus, instant claim 16 is obvious over patented claims 11-12.
Claims 25-26, and 69 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 claims of U.S. Patent No. 11,485,994 B2 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record), and in further view of Chiarella (Chiarella et al., 16 April 2018, Biochemistry, 57, p. 2756-2761 and Supplemental Figures; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejections are maintained from the prior action.
Regarding instant claims 25-26, and 69, the teachings of Barrett, Janzen, and Chiarella are described above in paragraphs 28-35 and applied hereinafter. As described therein, Barrett and Janzen in view of Chiarella render obvious combining the method of processing FFPE tissue taught by Barrett and Janzen, with ChIP-qPCR taught by Chiarella. The obviousness of combining the method rendered obvious in paragraph 61 above, with ChIP-qPCR taught by Chiarella to arrive at the inventions of instant claims 25-26 is described in paragraphs 33-34 and applied here. The obviousness of performing the sonication step of the method rendered obvious in paragraph 61 above, at 4°C as taught by Chiarella, is described in paragraph 35 and applied here.
Claim 67 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 claims of U.S. Patent No. 11,485,994 B2 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record), and in further view of Martelotto (Martelotto et al., 6 February 2017, Nature Medicine, Vol. 23, Number 3, p. 376-388; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejection is maintained from the prior action.
Regarding instant claim 67, the teachings of Barrett, Janzen, and Martelotto are described above in paragraphs 36-40 and applied hereinafter. The obviousness of performing the contacting step in the method rendered obvious in paragraph 61 above, at 37°C as taught by Martelotto, is described in paragraph 40 above and applied here.
Co-pending Application No. 17/961,538
Claims 1-2, 9, 11-12, 16, 21-24, and 64, 66, 68, and 70-74 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3, 5-6, and 8-9 of co-pending Application No. 17/961,538 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejections are maintained from the prior action with modification necessitated by amendments to the co-pending claims.
Co-pending claim 3 recites “The system of claim 1, wherein the activation energy is ultrasound having a frequency in the range from 0.01 MHz to 10 MHz.”
Co-pending claim 1 recites a “system for delivering microbubbles to a biological sample, the system comprising: a container for holding a solution of microbubbles or a solution that will formulate encapsulated microbubbles when processed; an energy source for providing thermal, sonic, or light activation energy to the microbubbles that causes the microbubbles to oscillate or burst and thereby process the biological sample; and at least one outlet for delivering the solution of microbubbles to the biological sample.
Co-pending claim 5 recites “The system of claim 1, wherein the biological sample comprises DNA or DNA that has been cross-linked to protein and wherein processing the sample comprises shearing the DNA.”
Co-pending claim 6 recites “The system of claim 1, wherein the biological sample comprises cells and wherein processing the sample comprises effecting cell lysis, optionally wherein the cells comprise bacteria or yeast cells.”
Co-pending claim 8 recites “The system of claim 1, wherein the sample comprises tissue and wherein processing the sample comprises performing tissue dispersion.”
Co-pending claim 9 recites “The system of claim 1 wherein the sample comprises at least one of fresh tissue, cryogenically preserved tissue, and fixed and paraffin embedded tissue.”
Co-pending claims 3, 5-6, and 8-9 recite systems for delivering microbubbles to a biological sample, which may be a FFPE tissue or a sample in which DNA is cross-linked to protein, wherein an energy source in the system provides activation energy to the microbubbles, causing them to oscillate or burst, and thereby process the biological sample, wherein processing the sample comprises, for example, shearing the DNA in the sample. The co-pending claims, while reciting that the intended use of the system is to “process the biological sample” (claim 1), e.g., wherein processing is “shearing the DNA” (claims 5-6) or “performing tissue dispersion” (claim 8), do not recite a method of using the system that comprises steps (a)-(c) of instant claim 1.
The teachings of Barrett and Janzen are recited above in paragraphs 10-27 and applied hereinafter. As described therein, Barrett and Janzen render obvious the methods of instant claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74 wherein FFPE tissue received, initially processed with an organic solvent, subjected to enzymatic digestion with a solution comprising collagenase and/or hyaluronidase, and then mixed with phase-change nanodroplets comprising a liquid perfluorocarbon core. The sample is then exposed to ultrasound activation energy which causes the liquid perfluorocarbon core in the phase-change nanodroplets to become gaseous, expand, and thereby, disperse the tissue and fragment the chromatin therein.
Regarding instant claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74, it would have been obvious to one skilled in the art before the effective filing date of the claimed invention to have used the co-pending systems for their recited intended use as taught by Barrett and Janzen. It would have amounted to combining a known system for processing biological tissue, with a known method of processing FFPE tissue to extract chromatin, by known means to yield predictable results. A skilled artisan would have had a reasonable expectation of success in using the co-pending systems as taught by Barrett and Janzen because together Barrett and Janzen teach a method of using a system which is substantially identical to the co-pending system, for the same purpose as recited in the co-pending claims. A skilled artisan would have been motivated to use the co-pending system as taught by Barrett and Janzen because together Barrett and Janzen teach a method of using a system substantially identical to the co-pending system, which enhances processing of FFPE tissue, and facilitates extraction of consistently fragmented chromatin for downstream applications, including those which may facilitate development of therapies and diagnostics.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 25-26, and 69 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3, 5-6, and 8-9 of co-pending Application No. 17/961,538 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record), and in further view of Chiarella (Chiarella et al., 16 April 2018, Biochemistry, 57, p. 2756-2761 and Supplemental Figures; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejections are maintained from the prior action with modification necessitated by amendments to the co-pending claims.
Regarding instant claims 25-26, and 69, the teachings of Barrett, Janzen, and Chiarella are described above in paragraphs 28-35 and applied hereinafter. As described therein, Barrett and Janzen in view of Chiarella render obvious combining the method of processing FFPE tissue taught by Barrett and Janzen, with ChIP-qPCR taught by Chiarella. The obviousness of combining the method rendered obvious in paragraph 76 above, with ChIP-qPCR taught by Chiarella to arrive at the inventions of instant claims 25-26 is described in paragraphs 33-34 and applied here. The obviousness of performing the sonication step of the method rendered obvious in paragraph 76 above, at 4°C as taught by Chiarella, is described in paragraph 35 and applied here.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 67 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3, 5-6, and 8-9 of co-pending Application No. 17/961,538 in view of Barrett (Barrett et al., WO 2013/123463 A1, published 22 August 2013; of record) and Janzen (Janzen et al., US 2015/0252355 A1, published 10 September 2015; of record), and in further view of Martelotto (Martelotto et al., 6 February 2017, Nature Medicine, Vol. 23, Number 3, p. 376-388; of record). Although the claims at issue are not identical, they are not patentably distinct from each other for the reasons that follow. The following rejection is maintained from the prior action with modification necessitated by amendments to the co-pending claims.
Regarding instant claim 67, the teachings of Barrett, Janzen, and Martelotto are described above in paragraphs 36-40 and applied hereinafter. The obviousness of performing the contacting step in the method rendered obvious in paragraph 76 above, at 37°C as taught by Martelotto, is described in paragraph 40 above and applied here.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Remarks – Nonstatutory Double Patenting
Applicant’s remarks regarding the nonstatutory double patenting rejections raised in the prior action have been reviewed. Applicant submits that the patented and co-pending claims fail to teach the instant method of extracting chromatin from FFPE tissue, and that the prior art fails to remedy the deficiencies of the patented and co-pending claims for the reasons described as for the obviousness rejections.
The alleged deficiencies of the prior art are addressed above and applied hereinafter. Barrett and Janzen render obvious each limitation of instant claims 1-2, 9, 11-12, 16, 21-24, 64, 66, 68, and 70-74. Similarly, the patented and co-pending methods encompass processing a biological sample with microbubbles, wherein the biological sample may be a “fixed and paraffin embedded tissue” sample, and wherein the method shears and/or extracts DNA or “DNA cross-linked to protein.” As described above, together, the patented or co-pending claims with Barrett, Janzen, Chiarella, and Martelotto, render obvious each of the instant claims. There are no apparent deficiencies in the combinations above with respect to the instantly claimed limitations. The nonstatutory double patenting rejections are therefore maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/JENNA L PERSONS/Examiner, Art Unit 1637
/Soren Harward/Primary Examiner, TC 1600