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 .
Election/Restrictions
Applicant’s election without traverse of Invention I (claims 1-51), drawn to a method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components in the reply filed on 03/04/2026 is acknowledged.
Claims 52-58 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Invention II, drawn to A kit for isolating target nucleic acids below a target size from a sample comprising nucleic acid components, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 03/04/2026.
Claims Status
Claims 1-58 are pending.
Claims 52-58 are withdrawn.
Claims 1-51 are currently under examination.
Priority
This application claims priority to, and the benefits of, U.S. Provisional Application having Serial No. 63/381,933 filed on November 2, 2022. The priority date of claim set filed on March 4, 2026, is determined to be November 2, 2022.
Claim Objections
Claims 5-23 and 25-51 are objected to under 37 CFR 1.75(c) as being in improper form because a multiple dependent claim shall not serve as a basis for any other multiple dependent claim. See MPEP § 608.01(n). Accordingly, the claims 5-51 have not been further treated on the merits.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-2 are rejected under 35 U.S.C. 103 as being unpatentable over Johnson-Buck et al. (“Johnson-Buck”; Patent App. Pub. WO 2019118705 A1, Jun. 20, 2019 ).
Claim interpretation: Regarding claim 1, the sample solution of (a) reads on any solution comprising a sample and the fractionation buffer of (c) reads on any buffer.
Johnson-Buck discloses “technology relating to detection of analytes and particularly, but not exclusively, to compositions, methods, and systems for concentrating an analyte at a surface, e.g., for imaging and detection of low-abundance analytes.” (Abstract).
Regarding claim 1, Johnson-Buck teaches a method wherein “In some embodiments, the technology provides for the size selection of analytes, e.g., to provide a defined size range of molecules including the target analytes” (Pg. 87 ln 5-6). Johnson-Buck teaches a method comprising “the method comprises providing an aqueous two-phase system (ATPS) comprising an analyte; concentrating the analyte into a first phase of the ATPS; and contacting said first phase to a substrate.” (Pg. 4 ln 19-21). Johnson-Buck teaches a method comprising “In some embodiments, methods comprise immobilizing an analyte to a solid support. In some embodiments, the solid support is a surface (e.g., a substantially planar surface, a rounded surface), e.g., a surface in contact with a bulk solution, e.g., a bulk solution comprising analyte. In some embodiments, the solid support is a freely diffusible solid support (e.g., a bead” (Pg 59 ln 4-8). Johnson-Buck teaches a method comprising “Dynabead (~1 um) capture and magnetic deposition” (Pg. 98 Table 2) and “magnetic field is used to effect the separation” (Pg. 89 ln 6). Johnson-Buck teaches a method comprising “In some embodiments related to ATPS technologies, the ATPS further comprises… a chaotropic agent” (Pg. 5 ln 29-30). Johnson-Buck teaches a method comprising “adding an analyte containing composition (e.g., a biofluid or sample) to an aqueous two-phase system (ATPS) (e.g., a mixture of materials that forms an aqueous two-phase system upon mixing). In some embodiments, the ATPS is a solid-phase ATPS.” (Pg. 61 ln 30-35). Thus, Johnson-Buck suggests a method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components; comprising the steps of:(a) preparing a sample solution from the sample; (b) contacting a plurality of beads with the sample solution, wherein the nucleic acid components bind to the plurality of beads to form a beads-analyte complex; (c) mixing the beads-analyte complex with a fractionation buffer comprising at least one chaotropic agent to form a bulk fractionation solution, wherein the target nucleic acids below the target size are released from the beads-analyte complex into the bulk fractionation solution; (d) immobilizing the beads-analyte complex; and (e) separating the bulk fractionation solution comprising the isolated target nucleic acids below the target size from the immobilized beads-analyte complex.
Furthermore, Johnson-Buck teaches the limitations of dependent claim 2 which depends on claim 1.
Regarding claim 2, Johnson-Buck teaches a method comprising “the method comprises providing an aqueous two-phase system (ATPS) comprising an analyte; concentrating the analyte into a first phase of the ATPS; and contacting said first phase to a substrate.” (Pg. 4 ln 19-21). Johnson-Buck teaches a method wherein “contact is maintained between the analyte rich phase and the surface by contacting the surface with the ATPS while a force is applied to the ATPS to separate the phases such that the analyte rich phase is produced (e.g., and separated from the analyte poor phase) and contacts the surface. That is, in some embodiments the surface contacts the ATPS (e.g., contacts the analyte rich phase of the ATPS)” (Pg. 62 ln 26-31.). Thus, Johnson-Buck suggests a method wherein the step (a) further comprises (a1) adding the sample to a first aqueous two-phase system (ATPS) to form a mixture that partitions into a first target-rich phase and a first target-poor phase, wherein the nucleic acid components are concentrated in the first target-rich phase; and (a2) isolating the first target-rich phase containing the concentrated nucleic acid components, resulting in the sample solution.
Therefore, the invention as recited in claims 3 and 4 is prima facie obvious over the prior art Gironella et al. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to diagnose human subjects at risk of developing advanced colorectal adenomas (colorectal cancer) according to the limitations of the instant application claims 3 and 4 based on Gironella et al. (Patent App. Pub. No. AU 2015201072 A1).
Claims 3 and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Johnson-Buck et al. (“Johnson-Buck”; Patent App. Pub. WO 2019118705 A1, Jun. 20, 2019) as applied to claims 1 and 2 and further in view of Chiu et al. (“Chiu”; Patent App. Pub. WO 2021037075 A1, Mar. 4, 2021).
To facilitate prosecution, claim 24 is interpreted as dependent from claim 3 in the 103 rejection documented below.
The teachings of Johnson-Buck are documented above in the rejection of claims 1-2 under 35 U.S.C. 103. Claim 3 depends on claim 2, which depends on claim 1. Claim 24 depends on any one of the preceding claims, in this case, claim 3, which depends on claim 2, which depends on claim 1. Johnson-Buck also teaches that “Various modifications and variations of the described compositions, methods, and uses of the technology will be apparent to those skilled in the art without departing from the scope and spirit of the technology as described. Although the technology has been described in connection with specific exemplary embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments.” (Pg. 103 ln 5-10). Johnson-Buck does not explicitly teach the limitations of claim 3 and 24.
Chiu discloses “Provided is a method for isolating and concentrating nucleic acids of selected target sizes (e.g., in increments less than 1000 base pairs) from a biological fluid mixture comprising combining the biological fluid mixture and a first aqueous two-phase system (ATPS) formed from a first phase forming polymer or surfactant component dissolved in a first phase solution, and a second phase solution, such that target nucleic acid fragments below a desired target size partition to said second phase solution and contaminants partition to the first phase solution, extracting and mixing the second phase solution with a second ATPS formed from a second phase forming polymer or surfactant component dissolved in a third phase solution and a fourth phase solution, such that the target nucleic acid fragments partition to and concentrate in the third phase solution, and recovering the concentrated target nucleic acid fragments from the third phase solution. A composition and kit for isolating and concentrating nucleic acids of selected target sizes as described above are also provided.” (Abstract).
Regarding claim 3, Chiu teaches a method wherein “In some embodiments of concentrating step 30, the second phase solution 24 containing target nucleic acid fragments 26 may be extracted from vessel 14 and mixed with concentration components 31 in a second vessel 32, with or without centrifugation, in order to form a second ATPS 34.” (Para. 51; Figure 1 see below). Furthermore, Chiu teaches a method further comprising “the target nucleic acid fragments 26 partition into and concentrate in the third phase solution 36 ( e.g., a polymer-rich upper phase)” (Para. 51) and “the concentrated target nucleic acid fragments 26 may be
recovered from the third phase solution 36. Fig. 1 illustrates one optional method (steps 40a
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through 40c) for recovering the fragments 26” (Para. 61). Thus, Chiu suggests a method wherein the step (a) further comprises the following steps after step (a2):(a3) adding the sample solution in step (a2) to a second ATPS to form a second mixture that partitions into a second target-rich phase and a second target-poor phase, wherein the nucleic acid components are concentrated in the second target-rich phase and (a4) isolating the second target-rich phase containing the concentrated nucleic acid components to form the sample solution in step (a).
Regarding claim 24, Chiu teaches a method wherein “The isolation components 17 may include polymer or surfactant components that assist in forming first phase solution 22 and second phase solution 24.” (Para. 47) and “second phase solution 24 may include an isolation component comprising a dissolved salt.” (Para. 48). Thus, Chiu suggests a method wherein the second ATPS comprises second ATPS components capable of forming the second target-rich phase and the second target-poor phase when the second ATPS components are dissolved in an aqueous solution, wherein the second ATPS components are selected from the group consisting of a polymer, salt, surfactant, and combinations thereof.
Johnson-Buck and Chiu are both considered to be analogous to the claimed invention because they are in the same field of process for extracting or separating nucleic acids from biological samples. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components as taught by Johnson-Buck to incorporate the method wherein the step (a) comprises adding the isolated target rich phase from the first ATPS to a second ATPS and further isolating the second target-rich phase as taught by Chiu and provide a method for isolating target nucleic acids from a sample comprising nucleic acid components. These claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions, and the combination would have yielded the predictable outcome according to the limitations of claims 3 and 24. Doing so would allow for increased target nucleic acid yield from the isolation process of a sample.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Johnson-Buck et al. (“Johnson-Buck”; Patent App. Pub. WO 2019118705 A1, Jun. 20, 2019) and further in view of Chiu et al. (“Chiu”; Patent App. Pub. WO 2021037075 A1, Mar. 4, 2021) as applied to claim 3 and further in view of Mather et al. (“Mather”; Patent App. Pub. WO 2009020609 A2, Feb. 12, 2009).
The teachings of Johnson-Buck and Chiu are documented above in the rejection of claim 3 under 35 U.S.C. 103. Claim 4 depends on any one of the preceding claims, in this case, claim 3, which depends on claim 2, which depends on claim 1. Johnson-Buck and Chiu do not explicitly teach the limitations of claim 4.
Mather discloses “Provided are solid supports that contain at least one hydrophilic ligand; and at least one hydrophobic ligand, where amount of the at least one hydrophobic ligand on the solid support relative to the amount of the at least one hydrophilic ligand on the solid support is adjusted for binding target nucleic acid(s) from a sample onto the solid support and/or for eluting the bound target nucleic acid(s) from the solid support, so that the amount of target nucleic acid(s) bound to the solid support and/or recovered after elution from the solid support is about 5% to about 500% greater than the amount of target nucleic acid(s) bound to the solid support and/or recovered from the solid support in the absence of either the at least one hydrophobic ligand or the at least one hydrophilic ligand or both. The solid supports with ligands are used for isolation of nucleic acid molecules from samples.” (Abstract).
Regarding claim 4, Mather teaches a method wherein “A combination for isolating nucleic acids using a solid support can contain a modified solid support as provided herein and further contain one or more reagents including a chaotropic substance, a binding buffer, an elution buffer, or reagents to make the modified solid support and/or the reagents” (Pg. 17 ln 7-11). Mather teaches a method wherein “Prior to the use of the amine-coupled carboxylated paramagnetic beads, or other appropriate solid support, in the isolation of nucleic acids molecules, the beads are typically washed in a buffer” (Pg. 52 ln 8-10). Mather teaches a method wherein “A non-limiting example of a suitable lysis buffer is one that contains 2.5 M guanidinium thiocyanate, 50% isopropyl alcohol, 0.5% lauroylsarcosine, 0.05 M Tris HCl, pH 7.0. Other chaotropic agents can be used, including, but not limited to, guanidinium chloride, and sodium chloride, at varying concentrations” (Pg. 52 ln 24-28). “a buffer” reads on reads on any buffer including that of a sample lysis buffer. Thus, Mather suggests a method wherein the plurality of beads and the sample solution of step (a) are mixed with a binding buffer prior to the step (b), wherein the binding buffer comprises at least one chaotropic agent.
Johnson-Buck, Chiu and Mather are considered to be analogous to the claimed invention because they are in the same field of process for extracting or separating nucleic acids from biological samples by means of by means of a solid support carrier, e.g. particles, polymers. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components as taught by Johnson-Buck and Chiu to incorporate the method wherein the plurality of beads and the sample solution of step (a) are mixed with a binding buffer prior to the step (b), wherein the binding buffer comprises at least one chaotropic agent as taught by Chiu and provide a method for isolating target nucleic acids from a sample comprising nucleic acid components. These claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions, and the combination would have yielded the predictable outcome according to the limitations of claims 3 and 24. Doing so would allow for increased target nucleic acid yield and stability.
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.
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 15 and 18 of U.S. Patent No. US 12129511 B2 (Pub. Oct. 29, 2024; US App. No. 18/463313). Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over claims 1, 15 and 18 of U.S. Patent No. US 12129511 B2.
Claims 1, 15 and 18 of U.S. Patent No. US 12129511 B2 is drawn to:
“1. A method for concentrating and purifying at least one target analyte from a clinical biological sample, comprising the steps of (a) combining the clinical biological sample with a first aqueous two-phase system (ATPS) composition comprising a polymer, a salt component comprising at least one salt, a surfactant, or any combination thereof dissolved in an aqueous solution to form a target- rich phase solution and a target-poor phase solution, such that the target analyte is concentrated in the target-rich phase;(b) collecting the target-rich phase; (c) optionally adding the target-rich phase to a second ATPS composition comprising a polymer, a salt component comprising at least one salt, a surfactant, or any combination thereof dissolved in an aqueous solution to form a second target-rich phase solution and a second target-poor phase solution, such that the target analyte is concentrated in the second target-rich phase, and collecting the second target-rich phase; (d) optionally mixing the target-rich phase from step (b) or the second target-rich phase from step (c) with a binding buffer to form a mixed solution; (e) contacting the target rich phase from step (b), the second target-rich phase from step (c) or the-mixed solution from step (d) with a solid phase medium configured to selectively bind the target analyte such that the solid phase medium binds to the target analyte; and (f) eluting and collecting the target analyte from the solid phase medium with an eluting solution, resulting in a final solution containing the concentrated and purified target analyte.
15. The method of claim 1, wherein the solid phase medium is a plurality of beads, wherein the beads are selected from the group consisting of magnetic beads, silica-based beads, carboxyl beads, hydroxyl beads, and amine-coated beads; the solid phase extraction complex is a beads-analyte complex; perturbing is spinning; and the flowthrough is the supernatant.
18. The method of claim 15, wherein the target analyte is a nucleic acid less than a target size; the plurality of beads binds to the target analyte and to other nucleic acids; the eluting solution is a fractionation buffer that, when contacted with the beads during the elution step (f), causes the target analyte to be released while not releasing the other nucleic acids, resulting in a final solution containing the concentrated and purified target analyte(s); wherein the fractionation buffer comprises a polymer, a chaotropic agent, or any combination thereof.”
Therefore, the invention as recited in claims 1 is prima facie obvious over the claims 1, 15 and 18 of U.S. Patent No. US 12129511 B2. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to provide a method for isolating target nucleic acids below a target size from a sample according to the limitations of the instant application based on claims 1, 15 and 18 of U.S. Patent No. US 12129511 B2.
Thus, the instant invention is made obvious over the U.S. Patent No. US 12129511 B2.
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4 and 8 of U.S. Patent No. US 12442034 B2 (Pub. Oct. 29, 2024; US App. No. 18/463313). Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over claims 1, 4 and 8 of U.S. Patent No. US 12442034 B2.
Claims 1, 4 and 8 of U.S. Patent No. US 12442034 B2 is drawn to:
“1. A method for concentrating and purifying at least one target analyte from a clinical biological sample, comprising the steps of (a) combining the clinical biological sample with a first aqueous two-phase system (ATPS) composition comprising a polymer and a salt component dissolved in an aqueous solution to form a target-rich phase solution and a target-poor phase solution, such that the target analyte is concentrated in the target-rich phase solution, wherein the polymer comprises 5-60% PEG with a molecular weight of at least 400, and the salt component comprises 0.1-6% K.sub.2HPO.sub.4 and 0.1-18% KH.sub.2PO.sub.4; (b) collecting the target-rich phase solution; (c) adding the target-rich phase solution to a second ATPS composition comprising a second polymer and a second salt component dissolved in an aqueous solution to form a second target-rich phase solution and a second target-poor phase solution, such that the target analyte is concentrated in the second target-rich phase solution, and collecting the second target-rich phase solution, wherein the second polymer comprises 2-25% PEG with a molecular weight of 200 or less, and the second salt component comprises 0.1-50% K.sub.2HPO.sub.4 and 4-40% KH.sub.2PO.sub.4; (d) optionally mixing the second target-rich phase from step (c) with a binding buffer to form a mixed solution; (e) contacting the second target-rich phase from step (c) or the mixed solution from step (d) with a solid phase medium configured to selectively bind the target analyte such that the solid phase medium binds to the target analyte; and (f) eluting and collecting the target analyte from the solid phase medium with an eluting solution, resulting in a final solution containing the concentrated and purified target analyte; (g) subjecting said final solution to a diagnostic assay for detection and quantification of the target analyte; wherein the clinical biological sample is urine; wherein the target analyte is a biomarker indicating the presence or risk of a medical condition or disease in a patient, wherein the medical condition or disease is urogenital cancer.
4. The method of claim 1, wherein the binding buffer comprises a chaotropic agent comprising an anion selected from the group consisting of thiocyanate, isothiocyanate, perchlorate, acetate, trichloroacetate, trifluoroacetate, chloride, and iodide.
8. The method of claim 7, wherein the solid phase medium is a plurality of beads, wherein the beads are selected from the group consisting of magnetic beads, silica-based beads, carboxyl beads, hydroxyl beads, and amine-coated beads; the solid phase extraction complex is a beads-analyte complex; perturbing is spinning; and the flowthrough is the supernatant; and wherein the target analyte is a nucleic acid less than a target size; the plurality of beads binds to the target analyte and to other nucleic acids; the eluting solution is a fractionation buffer that, when contacted with the beads during the elution step (f), causes the target analyte to be released while not releasing the other nucleic acids, resulting in a final solution containing the concentrated and purified target analyte(s); wherein the fractionation buffer comprises a polymer, a chaotropic agent, or any combination thereof.”
Therefore, the invention as recited in claims 1 is prima facie obvious over the claims 1, 4 and 8 of U.S. Patent No. US 12442034 B2. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to provide a method for isolating target nucleic acids below a target size from a sample according to the limitations of the instant application based on claims 1, 4 and 8 of U.S. Patent No. US 12442034 B2
Thus, the instant invention is made obvious over the U.S. Patent No. US 12129511 B2.
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6 and 9 of U.S. Patent No. US 12258616 B2 (Pub. Oct. 29, 2024; US App. No. 18/463313). Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over claims 1, 6 and 9 of U.S. Patent No. US 12258616 B2.
Claims 1, 6 and 9 of U.S. Patent No. US 12258616 B2 is drawn to:
“1. A method for concentrating and purifying at least one target analyte from a clinical biological sample, comprising the steps of (a) combining the clinical biological sample with a first aqueous two-phase system (ATPS) composition comprising a polymer, a salt component comprising at least one salt, a surfactant, or any combination thereof dissolved in an aqueous solution to form a target-rich phase solution and a target-poor phase solution, such that the target analyte is concentrated in the target-rich phase; (b) collecting the target-rich phase; (c) optionally adding the target-rich phase to a second ATPS composition comprising a polymer, a salt component comprising at least one salt, a surfactant, or any combination thereof dissolved in an aqueous solution to form a second target-rich phase solution and a second target-poor phase solution, such that the target analyte is concentrated in the second target-rich phase, and collecting the second target-rich phase; (d) optionally mixing the target-rich phase from step (b) or the second target-rich phase from step (c) with a binding buffer to form a mixed solution; (e) contacting the target rich phase from step (b), the second target-rich phase from step (c) or the mixed solution from step (d) with a solid phase medium configured to selectively bind the target analyte such that the solid phase medium binds to the target analyte; and (f) eluting and collecting the target analyte from the solid phase medium with an eluting solution, resulting in a final solution containing the concentrated and purified target analyte; and (g) subjecting said final solution to a diagnostic assay for detection and quantification of the target analyte; wherein the target analyte is a biomarker indicating the presence or risk of a medical condition or disease in a patient, wherein the medical condition or disease is HPV.
6. The method of claim 1, wherein the binding buffer comprises a chaotropic agent comprising an anion selected from the group consisting of thiocyanate, isothiocyanate, perchlorate, acetate, trichloroacetate, trifluoroacetate, chloride, and iodide.
9. The method of claim 8, wherein the solid phase medium is a plurality of beads, wherein the beads are selected from the group consisting of magnetic beads, silica-based beads, carboxyl beads, hydroxyl beads, and amine-coated beads; the solid phase extraction complex is a beads-analyte complex; perturbing is spinning; and the flowthrough is the supernatant; wherein the target analyte is a nucleic acid less than a target size; the plurality of beads binds to the target analyte and to other nucleic acids; the eluting solution is a fractionation buffer that, when contacted with the beads during the elution step (f), causes the target analyte to be released while not releasing the other nucleic acids, resulting in a final solution containing the concentrated and purified target analyte(s); wherein the fractionation buffer comprises a polymer, a chaotropic agent, or any combination thereof.”
Therefore, the invention as recited in claims 1 is prima facie obvious over the claims 1, 6 and 9 of U.S. Patent No. US 12258616 B2. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to provide a method for isolating target nucleic acids below a target size from a sample according to the limitations of the instant application based on claims 1, 6 and 9 of U.S. Patent No. US 12258616 B2.
Thus, the instant invention is made obvious over the U.S. Patent No. US 12258616 B2.
Claim 1 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133). Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133.
Claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133 is drawn to:
“1. A method for concentrating and purifying at least one target analyte from a clinical biological sample, comprising the steps of (a) combining the clinical biological sample with a first aqueous two-phase system (ATPS) composition comprising a polymer, a salt component comprising at least one salt, a surfactant, or any combination thereof dissolved in an aqueous solution to form a target-rich phase solution and a target-poor phase solution, such that the target analyte is concentrated in the target-rich phase solution;(b) collecting the target-rich phase solution;(c) optionally adding the target-rich phase solution to a second ATPS composition comprising a polymer, a salt component comprising at least one salt, a surfactant, or any combination thereof dissolved in an aqueous solution to form a second target-rich phase solution and a second target-poor phase solution, such that the target analyte is concentrated in the second target-rich phase solution, and collecting the second target-rich phase solution;(d) optionally mixing the target-rich phase solution from step (b) or the second target- rich phase solution from step (c) with a binding buffer to form a mixed solution;(e) contacting the target-rich phase solution from step (b), the second target-rich phase solution from step (c) or the mixed solution from step (d) with a solid phase medium configured to selectively bind the target analyte such that the solid phase medium binds to the target analyte; and(f) eluting and collecting the target analyte from the solid phase medium with an eluting solution, resulting in a final solution containing the concentrated and purified target analyte; wherein the clinical biological sample is urine; and wherein the target analyte is cell-free DNA (cfDNA) or circulating fetal DNA.
4. The method of claim 1, wherein the binding buffer comprises a chaotropic agent comprising an anion selected from the group consisting of thiocyanate, isothiocyanate, perchlorate, acetate, trichloroacetate, trifluoroacetate, chloride, and iodide.+
7. The method of claim 6, wherein the solid phase medium is a plurality of beads, wherein the beads are selected from the group consisting of magnetic beads, silica- based beads, carboxyl beads, hydroxyl beads, and amine-coated beads; the solid phase extraction complex is a beads-analyte complex; perturbing is spinning; and the flowthrough is the supernatant.
Therefore, the invention as recited in claims 1 is prima facie obvious over the claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to provide a method for isolating target nucleic acids below a target size from a sample according to the limitations of the instant application based on claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133.
Thus, the instant invention is made obvious over the copending U.S. Patent App. No. 19/262133.
Conclusion
No claims are in condition for allowance.
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Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached at (571)272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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