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 .
Remarks
This office action fully acknowledges Applicant’s remarks and amendments filed on 28 May 2026.
Claims 1-9, 13-21, and 43-44 are pending.
Claims 13-21 are withdrawn.
Claims 10-12 and 22-42 are cancelled
Claim 44 is newly added.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-9 and 43 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.
Claims 1 and 43 require several of the method steps to be performed “using” a cartridge wherein it is unclear what method requirements Applicant intends for “using” given that no automation steps or means for automation are provided. Does Applicant intend to positively provide the cartridge through a recitation on the order of “providing a cartridge for performing...”? Similarly, Applicant’s recitation to the method performed “using” appears to require the cartridge through a narrative-type discussion, but as currently recited the performed “using” is drawn to a mere intended use.
Claim 1 recites “nucleic acid fragments” in line 10. There is insufficient antecedent basis for this term in the claims. Applicant may have intended to amend this recitation to “cfDNA” as suggested by the amendments to Claim 1.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 4, 6-9, and 44, as best understood, are rejected under 35 U.S.C. 103 as being unpatentable over Hu et al. (Hu, Fei; et al., “Rapid isolation of cfDNA from large-volume whole blood on a centrifugal microfluidic chip based on immiscible phase filtration”, Analyst, 2019,144, 4162-4174.), hereinafter “Hu”, in view of Rubio et al. (US 2004/0229368 A1), hereinafter “Rubio”, and Williams et al. (US 2018/0344568 A1), hereinafter “Williams”.
Regarding Claim 1, Hu teaches a method for extraction of cell-free DNA (cfDNA) fragments (See the “Functional Principle” section: “extraction and purification of cfDNA” – See also the “Conclusion” section: “The method is able to isolate cfDNA within 15 min, which indicates that 65% cfDNA can be recovered from plasma, and 30% from the whole blood.”) from a blood sample comprising the steps of:
providing a blood sample taken from an individual (See the “Sample preparation and loading” section: “Venous blood was obtained from a healthy volunteer of our laboratory.”);
contacting the plasma sample with a binder material specific to nucleic acids (See the “Sample preparation and loading” section: “lysis/binding buffer (1.25 ml) was introduced into the sample chamber for cfDNA extraction” – See also the “cfDNA extraction by IFAST” section: “lysis/binding buffer to effectively bind the cfDNA” – Further note that Hu produces the plasma sample via gentle centrifugation to remove the whole red blood cells, see Rubio below regarding the fixation and filtering steps.), or alternatively subjecting the plasma sample to electrophoresis in a separating medium, in order to purify cfDNA fragments present in said plasma sample, wherein said separating medium is prepared so that cfDNA fragments are capable of migrating in the separating medium and can be separated in said separating medium by size (See the “Introduction” section: “A variety of microfluidic technologies have been developed for the extraction and purification of cfDNA from blood such as...dielectrophoresis (DEP)”);
collecting the cfDNA fragments (See the “cfDNA extraction by IFAST” section: “After plasma separation, the disk began with the nucleic acid extraction.”); and
wherein the steps are performed using an automated system (See the “The limiting factors of DNA recovery” section: “...automatic and rapid cfDNA extraction from large volume samples.”) comprising a cartridge comprising a first compartment for filtering plasma from the blood sample (See Fig. 1: “plasma separation chamber” – Note that “filtering” is defined as “to remove solids from liquids or gases” as in Cambridge Dictionary.) and a second compartment for contacting the plasma sample with the binder material specific to nucleic acids (See Figs. 4a-c showing the plasma flowing into the nucleic acid extraction structure (Fig. 1) containing binding buffer.),
as in Claim 1.
Further regarding Claim 1, Hu does not specifically teach the method discussed above comprising b) stabilizing blood cells in the sample with a fixative reagent; and c) filtering the blood sample in order to separate plasma from said blood sample and provide a plasma sample using a hollow fiber filter, as in Claim 1.
However, Rubio teaches a respective method for isolating red blood cells from plasma wherein the cells are stabilized using a fixative and filtered out using a hollow fiber filter (See Fig. 2A and paras. [0039, 0044, 0051].) so as to isolate whole cell components from DNA for analysis ([0035]). Similarly, Hu seeks to isolate whole blood components from DNA but does so through gentle centrifugation instead of fixation and filtering, wherein fixation and filtering thereby represent a mere obvious alternative to gentle centrifugation for isolating plasma and DNA from whole cell components, and wherein the fixative provides a stabilization to further prevent blood cell degradation during the separation that may contaminate the plasma (having the cfDNA therein).
Thus, one of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to modify the method of Hu further comprising b) stabilizing blood cells in the sample with a fixative reagent; and c) filtering the blood sample in order to separate plasma from said blood sample by using a hollow fiber filter, such as suggested by Rubio, as a mere obvious alternative for achieving the identical result of removal of whole red blood cell components in Hu, and would have a reasonable expectation of success therein.
Further regarding Claim 1, Hu does not specifically teach the method discussed above comprising f) mixing the cfDNA fragments with a preservative or a stabilizing agent, as in Claim 1.
However, Williams teaches a patient sample collection system 100 for nucleic acid samples having a sample collection chamber loaded 110 with a sample preservation reagent 108 (Fig. 1 and para. [0037]: “the reagent or buffering solution stabilizes at least one element or compound within the sample (e.g., nucleic acids, such as DNA and RNA, protein, and combinations thereof) during transfer, transportation, and/or storage at a laboratory, clinic, or other destination.”), wherein this arrangement reduces sample degradation while samples are stored for future analysis, thereby reducing errors related to degraded samples.
Thus, one of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to modify the method of Hu further comprising f) mixing the nucleic acid fragments with a preservative or a stabilizing agent, such as suggested by Williams, so as to reduce sample degradation while samples are stored for future analysis, thereby reducing errors related to degraded samples.
Regarding Claim 4, the prior art meets the limitations of Claim 1 as discussed above. Further, Hu teaches the method discussed above wherein the length of said cfDNA fragments is less than 400 bp (See the “Sample preparation and loading” section: “100–200 bp cfDNA”), as in Claim 4.
Further note limitations based on the intended use of a structure do not confer patentability if the prior art is capable of performing the same function – see MPEP 2111.02(II).
Regarding Claim 6, the prior art meets the limitations of Claim 1 as discussed above with respect to Hu in view of Rubio (and Williams). Further, as discussed above regarding Claim 1, Hu is modified with a hollow fiber filter supplied by Rubio via obvious modification as an obvious alternative to the gentle centrifugation in Hu. Furthermore thereto, Rubio discloses the hollow fiber filter as a hollow fiber membrane ([0039] – See also [0005].), as in Claim 6.
Thus, one of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious that, when modifying the device of Hu with the hollow fiber filter of Rubio, as in Claim 1, to provide said hollow fiber filter as a hollow fiber membrane so as to achieve the intended filtering effects sought by Rubio.
Regarding Claim 7, the prior art meets the limitations of Claim 1 as discussed above. Further, Hu teaches the method discussed above wherein the plasma sample is contacted with a binder material specific to nucleic acids (See the “Sample preparation and loading” section: “The lysis/binding buffer, elution buffer, and magnetic bead suspension used in this study were obtained from the MagMAX Cell-Free Total Nucleic Acid Kit (A36716, ThermoFisher, USA).” – See also the “cfDNA extraction by IFAST” section.), as in Claim 7.
Regarding Claim 8, the prior art meets the limitations of Claim 7 as discussed above. Further, Hu teaches the method discussed above wherein said binder material comprises magnetic beads (See the “cfDNA extraction by IFAST” section: “mix magnetic beads with plasma and lysis/binding buffer to effectively bind the cfDNA onto the surface of magnetic beads”), as in Claim 8.
Regarding Claim 9, the prior art meets the limitations of Claim 1 as discussed above. Further, Hu teaches the method discussed above further comprising contacting the cfDNA fragments bound to said binder material with a nucleic acid binding dye and measuring the amount of collected cfDNA fragments (See the “Real-time fluorescence quantitative PCR” section: “probes”.), as in Claim 9.
Regarding Claim 44, the prior art meets the limitations of Claim 1 as discussed above. Further, Hu does not specifically teach the method discussed above further comprising, after step (c), washing the hollow fiber filter with a wash solution, collecting washout from the washing, and contacting the washout with the binder material or alternatively subjecting the washout to electrophoresis in the separating medium, in order to purify cfDNA present both in said plasma sample and said washout, as in Claim 44.
However, as discussed above regarding Claim 1, Hu is modified in view of rubio to provide a hollow fiber filter for removing cell components from a sample so as to provide the plasma. Therein, Rubio further teaches washing of the filter commensurately as claimed (See paras [0047-0068] discussing the wash solution as being PBS buffer.). As such washing would merely further improve the yield of the filtrate, one of ordinary skill in the art would have recognized the benefit thereto when implementing the hollow fiber filter in Hu.
Thus, one of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to modify the method of Hu further comprising, after step (c), washing the hollow fiber filter with a wash solution, collecting washout from the washing, such as suggested by Rubio, and contacting the washout with the binder material, as provided by Hu, in order to purify cfDNA present both in said plasma sample and said washout, so as to further improve the yield of recovered cfDNA washed from the removed cells.
Claims 2-3, as best understood, are rejected under 35 U.S.C. 103 as being unpatentable over Hu in view of Rubio and Williams, as applied to Claims 1, 4, 6-9, and 44 above, and in further view of Kloke et al. (Kloke, A.; et al., “The LabTube – a novel microfluidic platform for assay automation in laboratory centrifuges”, Lab Chip, 2014,14, 1527-1537.), hereinafter “Kloke”.
Regarding Claim 2, the prior art meets the limitations of Claim 1 as discussed above. Further, Hu/Rubio/Williams does not specifically teach the method discussed above wherein in step f) the obtained mix of the cfDNA fragments and said preservative or a stabilizing agent is stored into a removable container, as in Claim 2.
However, Kloke teaches a respective method for DNA extraction from whole blood (Abstract) comprising a three-stage revolving system wherein the first stage is for sample input, the third stage is for DNA extraction, and the third stage is for collection of the extracted DNA sample in a removable tube (See Fig. 2 and the “Cartridge design and integrated unit operations” section.), thereby allowing the isolated DNA sample to be automatically stored in a standard container for future analysis. Thus, one of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to modify the method of Hu/Rubio/Williams wherein the obtained mix of the cfDNA fragments and said preservative or a stabilizing agent is stored into a removable container, such as suggested by Kloke, so as to allow the isolated DNA sample to be automatically stored in a standard container for future analysis.
Regarding Claim 3, the prior art meets the limitations of Claim 2 as discussed above. Further, given that Hu/Rubio/Williams teaches binding of the nucleic acid fragments without specifying a reversal step (of the DNA becoming unbound), the mix recited in Claim 2 as flowing into a removable container (provided by Kloke) thereby comprises the cfDNA fragments bound to said binder material, as in Claim 2.
Claim 5, as best understood, is rejected under 35 U.S.C. 103 as being unpatentable over Hu in view of Rubio and Williams, as applied to Claims 1, 4, 6-9, and 44 above, and in further view of Augello et al. (US PAT 6,821,789 B2), hereinafter “Augello”.
Regarding Claim 5, the prior art meets the limitations of Claim 1 as discussed above. Further, Hu/Rubio/Williams does not specifically teach the method discussed above wherein the blood sample is mixed with an anticoagulant before subjecting the sample to the filtering step, as in Claim 5.
However, Augello teaches a respective method for nucleic acids isolation from a whole blood sample wherein the blood sample is collected directly into a tube pre-loaded with citrate anticoagulant and stabilization buffer (See Example 4.). Thereafter, the sample is subject to a filtration step through a membrane (See Example 4.). Therein, this arrangement prevents the blood sample from coagulating and clogging the filter, which would be similarly appreciated for its anti-clogging effects in the narrow channels of the microfluidic device of Hu.
Thus, one of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to modify the method of Hu/Rubio/Williams wherein the blood sample is mixed with an anticoagulant before subjecting the sample to the filtering step, such as suggested by Augello, so as to prevent the blood sample from coagulating and clogging the filter, which would be similarly appreciated for its anti-clogging effects in the narrow channels of the microfluidic device of Hu.
Claim 43, as best understood, is rejected under 35 U.S.C. 103 as being unpatentable over Hu in view of Rubio. Hu and Rubio have been discussed above.
Regarding Claim 43, Hu teaches a method for extracting cell-free DNA (cfDNA) fragments (See the “Functional Principle” section: “extraction and purification of cfDNA” – See also the “Conclusion” section: “The method is able to isolate cfDNA within 15 min, which indicates that 65% cfDNA can be recovered from plasma, and 30% from the whole blood.”) from a blood sample, comprising:
providing a blood sample obtained from an individual (See the “Sample preparation and loading” section: “Venous blood was obtained from a healthy volunteer of our laboratory.”);
separating plasma from the blood sample (See Fig. 4 and the “Plasma separation” section.);
isolating cfDNA fragments from the plasma by contacting the plasma with a binder material specific to nucleic acids (See the “Sample preparation and loading” section: “lysis/binding buffer (1.25 ml) was introduced into the sample chamber for cfDNA extraction” – See also the “cfDNA extraction by IFAST” section: “lysis/binding buffer to effectively bind the cfDNA” – Further note that Hu produces the plasma sample via gentle centrifugation to remove the whole red blood cells, see Rubio below regarding the fixation and filtering steps.) or by subjecting the plasma to electrophoresis in a separating medium (See the “Introduction” section: “A variety of microfluidic technologies have been developed for the extraction and purification of cfDNA from blood such as...dielectrophoresis (DEP)”),
wherein at least steps (b) and (c) are performed using a cartridge comprising a first compartment (Fig. 1: “plasma separation chamber) where step (b) of separating plasma is carried out (See Fig. 4 and the “plasma separation” section.) and a second compartment (Fig. 1: “nucleic acid extraction structure”) where step (c) of isolating cfDNA fragments is carried out (See Fig. 4 and the “cfDNA extraction by IFAST” section.),
as in Claim 43.
Further regarding Claim 43, Hu does not specifically teach the method discussed above wherein the plasma separation step is performed using a hollow fiber filter, as in Claim 43.
However, Rubio teaches a respective method for isolating red blood cells from plasma wherein the cells are stabilized using a fixative and filtered out using a hollow fiber filter (See Fig. 2A and paras. [0039, 0044, 0051].) so as to isolate whole cell components from DNA for analysis ([0035]). Similarly, Hu seeks to isolate whole blood components from DNA but does so through gentle centrifugation instead of fixation and filtering, wherein fixation and filtering thereby represent a mere obvious alternative to gentle centrifugation for isolating plasma and DNA from whole cell components.
Thus, one of ordinary skill in the art before the effective filing date of the claimed invention would have found it obvious to modify the method of Hu wherein the plasma separation step is performed using a hollow fiber filter, such as suggested by Rubio, as a mere obvious alternative for achieving the identical result of removal of whole red blood cell components in Hu, and would have a reasonable expectation of success therein.
Response to Arguments
35 USC 112(b) Applicant’s amendments sufficiently overcome the rejection of Claims 2-3 as being indefinite under 35 USC 112(b). As such, those rejections of Claims 2-3 under 35 USC 112(b) are withdrawn.
Applicant’s amendments to the methods reciting “using” the cartridge are not sufficient for providing the intended method steps constituting “using” as in Claims 1 and 43. As such, Examiner maintains the rejection of Claims 1 and 43 under 35 USC 112(b) for failing to particularly claim and point out the recited “using”.
35 USC 103 (Claim 1)
Applicant’s arguments are on the alleged grounds that merely using filtration as in Rubio in stead of centrifugation as in Hu for producing a plasma sample, as set forth by the prior office action over Claim 1, fundamentally changes the operating principle of Hu.
Applicant’s arguments are not persuasive because merely implementing a hollow-fiber filter in the centrifugal chip of Hu would not change its mode of operation using centrifugal forces for actuating fluid through the device. Instead, one of ordinary skill in the art would merely substitute the centrifugal depositional method of Hu with a hollow-fiber filter in one of the channels-chambers so as to commensurately afford the identical result of providing a plasma sample for further analysis. Merely because Hu relies on centrifugal deposition of the plasma sample would not preclude one of ordinary skill in the art from recognizing a hollow-fiber filter as a suitable substitute achieving the same result.
Applicant further argues that if a hollow fiber filter were substituted into the system, that a “dead end” filter would be produced.
However, Applicant’s arguments are not persuasive because one of ordinary skill in the art would not merely take the hollow fiber filter of Rubio and directly attach such filter to the chamber walls resulting in a “dead end”. One of ordinary skill in the art would find it obvious that, when modifying Hu with the filter of Rubio, to optimize the contact surfaces and angles so as to permit fluid flow through the filter and on to the rest of the device, via mere routine experimentation so as to achieve the plasma separation desired by Rubio. See KSR International Co. v. Teleflex Inc.: "A person of ordinary skill is also a person of ordinary creativity, not an automaton." Applicant further argues that the pores of the filter would be blocked by red blood cells, however, even if the pores were to be blocked, an amount of plasma would have passed through the filter and on for further processing. Further, one of ordinary skill in the art would find it obvious to optimize the filter to avoid blockages from forming, such as by a pre-filtering step, as such filter blockage/clogging is a well-known and recognized problem of filtration.
Applicant further argues that Rubio discusses “permeabilizing the cells of interest” wherein the claimed method is directed to avoiding collection of intracellular material. However, Rubio specifically discloses that such permeabilization does not result in leakage of cell components: [0008]: “In addition to the need to permeabilize the cell membrane, the sample-preparation process for intracellular assays also requires that cell membranes and contents of the cell be “fixed” prior to the permeabilization step in order to maintain the integrity of the membrane during permeabilization and to prevent the intracellular material from diffusing out of the cells after permeabilization.”.
Applicant argues that the prior office action oversimplifies the plasma separation via filtration of Rubio as a mere alternative to the centrifugal method of Hu. However, Applicant has not sufficiently shown that one of ordinary skill in the art would not have recognized that the hollow fiber filtration method of Rubio achieves the identical result of the centrifugal method of Hu for producing a plasma sample from whole blood by trapping and filtering cells ([0039]) from a whole blood sample. Applicant further contends that use of the filter would reduce yield; however, Applicant relies on their own specification for this teaching and not of Hu or Rubio. Thus, one of skill in the art still would have not been precluded from exploring the hollow-fiber filter optionof Rubio in the cartridge of Hu.
Applicant further contends that the prior office action does not establish a reasonable expectation of success of the hollow-fiber filter in Hu as cfDNA isolation is a sensitive procedure. However, Rubio’s mere statement that the hollow-fiber filter removes fixed cellular components represents an expectation of success of producing plasma in Hu, wherein such a process is merely removing cells from the extracellular fluid matrix. Therein, it is further noted that one of ordinary skill in the art need not necessarily eliminate the centrifugal-separation method of Hu, but rather provide the hollow-fiber filter as an additional filtration step so as to satisfy the language of the claim, and so as to provide an even further purified plasma sample in Hu. Rubio further discusses both centrifugation and filtration through the hollow fiber as steps for isolating the sample ([0005, 0044]). As such, one of ordinary skill in the art would still find it obvious to provide the hollow fiber of Rubio to the centrifugal device of Hu while maintaining the centrifugal separation step in Hu, so as to further improve the purity of the separated product.
Applicant further contends that Williams does not remedy the above discussed alleged deficiencies in Hu/Rubio. However, as discussed above, no such deficiencies are admitted in Hu/Rubio herein. Thus, Applicant’s argument that Williams fails to cure those alleged deficiencies is moot. Williams is merely relied on for storage and preservation of the isolated sample.
35 USC 103 (Claim 43)
Applicant argues on similar grounds as discussed above that using filtration as in Rubio instead of centrifugation as in Hu for producing a plasma sample fundamentally changes the operating principle of Hu, and that the permeabilization step in Rubio is contrary to the purpose of the method of Claim 43.
However, as discussed above, the operating principle of Hu using centrifugal forces to actuate a sample through a cartridge would not be fundamentally changed by the mere addition of a hollow fiber filter. Further, as discussed above, the permeabilization step in Rubio does not result in leakage of extracellular components. Rubio is merely relied on for showing a hollow fiber filter capable of removing cells and cellular components from whole blood ([0039]).
New Claim 44
Claim 44 is rejected under 35 USC 103 as being unpatentable over Hu in view of Rubio, as discussed above in the body of the action.
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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/B.J.K./Examiner, Art Unit 1798
/NEIL N TURK/Primary Examiner, Art Unit 1798
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