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 .
Priority
This application, filed June 10, 2022, is a national stage application of PCT/US2020/064508, filed December 11, 2020, which claims the benefit of U.S. provisional application 62/947969, filed December 13, 2019.
Status of the Application
Applicant’s communication, received September 29, 2025, wherein claims 3, 6, 11, 16, 19, 23, 25, 27, 29, and 30 are amended and claims 5, 7, 9, 24, 26, and 28 are canceled, is acknowledged.
Claims 3, 6, 8, 10-23, 25, 27, and 29-33 are pending and examined on the merits herein.
Withdrawn Rejections
Applicant’s amendment, received September 29, 2025, with respect to the rejection of claims 5, 6, 24, and 25 under 35 USC § 112(b) for reciting broad and narrow limitations in the same claim and for lacking units associated with the molecular weight of PVP and Ficoll has been fully considered and found to be persuasive to remove the rejection because claims 5 and 24 are canceled and claims 6 and 25 are amended to remove the narrow limitations and include molecular weight units. Therefore the rejection is withdrawn.
Applicant’s amendment, received September 29, 2025, with respect to the rejection of claim 19 under 35 USC § 112(b) for lacking antecedent basis has been fully considered and found to be persuasive to remove the rejection because claim 19 is amended to depend from claim 16. Therefore the rejection is withdrawn.
Applicant’s amendment, received September 29, 2025, with respect to the rejection of claims 3, 5-12, 14-17, 21, 23-29, and 31-32 under 35 USC § 102 as anticipated by Liu has been fully considered and found to be persuasive to remove the rejection because claims 5, 7, 9, 24, 26, and 28 are canceled and independent claim 3 is amended to require a precipitation mixture comprising Ficoll at a concentration of 20%. Therefore the rejection is withdrawn.
Applicant’s amendment, received September 29, 2025, with respect to the rejection of claims 3, 5-9, 11-12, 14-17, 21, 23-30, and 32-33 under 35 USC § 103 as unpatentable over O’Neil in view of Latham has been fully considered and found to be persuasive to remove the rejection because claims 5, 7, 9, 24, 26, and 28 are canceled, independent claim 3 is amended to require a precipitation mixture comprising Ficoll at a concentration of 20%, which the embodiments of O’Neil and Latham cited in the previous rejection do not teach, independent claim 23 is amended to require the specific size cutoff of 1500-3000 bp, and because independent claim 29 now requires Ficoll, each of which the embodiments of O’Neil and Latham cited in the previous rejection do not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received September 29, 2025, with respect to the rejection of claim 22 under 35 USC § 103 as unpatentable over O’Neil in view of Latham, Huptas, and Earl has been fully considered and found to be persuasive to remove the rejection because independent claim 3 is amended to require a precipitation mixture comprising Ficoll at a concentration of 20%, which the embodiments of O’Neil, Latham, Huptas, and Earl cited in the previous rejection do not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received September 29, 2025, with respect to the rejection of claims 18-20 and 31 under 35 USC § 103 as unpatentable over O’Neil in view of Latham and Wang has been fully considered and found to be persuasive to remove the rejection because independent claim 3 is amended to require a precipitation mixture comprising Ficoll at a concentration of 20% and independent claim 29 now requires Ficoll, each of which the embodiments of O’Neil, Latham, and Wang cited in the previous rejection do not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received September 29, 2025, with respect to the rejection of claims 10 and 13 under 35 USC § 103 as unpatentable over O’Neil in view of Latham and Lis has been fully considered and found to be persuasive to remove the rejection because independent claim 3 is amended to require a precipitation mixture comprising Ficoll at a concentration of 20%, which the embodiments of O’Neil, Latham, and Lis cited in the previous rejection do not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received September 29, 2025, with respect to the nonstatutory double patenting rejection of claims 3, 5-12, 15-16, 18-20, and 23-28 as unpatentable over the claims of U.S. Patent 11,732,254 has been fully considered and found to be persuasive to remove the rejection because claims 5, 7, 9, 24, 26, and 28 are canceled and independent claim 3 is amended to require a precipitation mixture comprising Ficoll at a concentration of 20%, which U.S. Patent 11,732,254 does not claim. Therefore the rejection is withdrawn.
Applicant’s amendment, received September 29, 2025, with respect to the provisional nonstatutory double patenting rejection of claims 3 and 5-12, 15-16, 18-20, and 23-28 as unpatentable over the claims of co-pending U.S. patent application 18/229838 has been fully considered and found to be persuasive to remove the rejection because independent claim 3 is amended to require a precipitation mixture comprising Ficoll at a concentration of 20%, which 18/229838 does not claim. Therefore the rejection is withdrawn.
The following rejection is maintained from the previous Office action mailed March 28, 2025.
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 3, 6, 8, 10-23, 25, 27, and 29-33 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 3, 6, 8, 10-23, 25, 27, and 29-33 contain the trademark/trade name Ficoll. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a highly branched, primarily neutral polysaccharide, and, accordingly, the identification/description is indefinite.
Response to Applicant’s arguments: With respect to the previous rejection under 35 U.S.C. 112(b) for reciting the term “Ficoll,” the Applicant disagrees with the Examiner that the term "Ficoll" renders the claims indefinite, noting, for example, that certain of the claims of Liu (U.S. Patent No. 11,732,254, hereinafter, "Liu '254") recite the same term.
The examiner is understanding of the challenge of describing Ficoll based on the name of the particular product. However, because Ficoll is a registered Trademark and is used to describe a particular material used in the presently claimed method, the claims do not comply with the requirements of 35 U.S.C. 112(b).
MPEP 2173.05(u) states: "If the trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of the 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). … The claim scope is uncertain since the trademark or trade name cannot be used properly to describe any particular material or product. In fact, the value of a trademark would be lost to the extent that it became the generic name of a product, rather than used as an identification of a source or origin of a product. Thus, the use of a trademark or trade name in a claim to describe a material or product would not only render a claim indefinite, but would also constitute an improper use of the trademark or trade name." In this instance, because Ficoll is used to identify a specific material used in the presently claimed method, the claims do not comply with the requirements of 35 U.S.C. 112(b).
Regarding Applicant’s argument that U.S. Patent No. 11,732,254 recites Ficoll, the examiner is unable to comment on prosecution of another U.S. patent application.
The following are new and/or modified grounds of rejection, necessitated by Applicant’s amendment received September 29, 2025. Applicant’s arguments regarding the previous rejections, specifically that the cited references do not teach each and every element of the amended claims, is therefore moot in view of these new and/or modified grounds of rejection.
Claim Objections
Claim 19 is objected to because of the following informalities: Claim 19 recites “during steps a), b), and/or c), d), and/or e).” For the purposes of enhancing clarity in the claims, please amend claim 19 to “during steps a), b), c), d), and/or e).”
Appropriate correction is required.
Claim Interpretation
Claim 29 recites: “A kit for purifying a sample containing nucleic acids to obtain
isolated nucleic acids above a tunable cutoff size between 1500 and 3000 bp, comprising a buffer, a salt, and Ficoll disposed in one or more containers.” Claims 30-33 further limit the contents of the kit recited in claim 29.
The limitation “for purifying a sample containing nucleic acids to obtain isolated nucleic acids above a tunable cutoff size between 1500 and 3000 bp” is interpreted herein as an intended use of the kit recited in claim 29.
MPEP 2111.02 at II states: “During examination, statements in the preamble reciting the
purpose or intended use of the claimed invention must be evaluated to determine whether or not
the recited purpose or intended use results in a structural difference (or, in the case of process
claims, manipulative difference) between the claimed invention and the prior art. If so, the
recitation serves to limit the claim. …To satisfy an intended use limitation which is limiting, a
prior art structure which is capable of performing the intended use as recited in the preamble
meets the claim.” In this instance, claim 29 interpreted as satisfied by a kit that includes the required components recited in claim 29, even if that kit is not used for purifying a sample containing nucleic acids to obtain isolated nucleic acids above a tunable cutoff size between 1500 and 3000 bp.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 8 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 8 depends from claim 3 and requires a concentration of the Ficoll in the precipitation buffer is 0.1%-60% weight/volume (w/v %). However, step a) of claim 3 requires combining a nucleic acid-containing sample with a precipitation buffer in a container to provide a precipitation mixture, wherein the precipitation buffer comprises water, a buffer, a salt, and Ficoll, and wherein the precipitation mixture comprises a Ficoll concentration of 20%.
Because claim 3 requires the precipitating mixture, which is made by mixing a nucleic acid-containing sample and a precipitation buffer, comprises a Ficoll concentration of 20%, it’s unclear how the concentration of the precipitation buffer could comprise less than 20% Ficoll. Therefore, claim 8 fails to include all limitations of the claim upon which it depends.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 3, 8, 10-12, 14-21, 23, 27, and 29-32 are rejected under 35 U.S.C. 103 as being unpatentable over Liu (Publication no. WO 2019006321 A1; cited in IDS received June 10, 2022).
Liu teaches a method for purifying a sample containing nucleic acids to obtain isolated nucleic acids of a desired size range, either above a size cut-off, below a cut-off, or within a defined band of sizes (cover page, Abstract, lines 1-4) (emphasis added). Liu teaches this method includes: a) combining a nucleic acid containing sample with a binding buffer to provide a binding mixture; b) contacting the binding mixture with a silica nanomembrane, wherein the silica nanomembrane adsorbs nucleic acids from the binding mixture within a desired size-range; and c) separating the bound nucleic acid from the remaining sample (cover page, Abstract, lines 4-9).
Liu also teaches a method that involves a precipitation step, wherein 1) a precipitation buffer, containing, but not limited to, water, buffer, salt, and PVP (MW 360,000) is added to the nucleic acid containing sample: 2) the sample-buffer is centrifuged at 8000 g for 30 minutes at room temperature, during this step, the nucleic acid will pellet at the bottom of the tube; 3) the supernatant is removed from the tube; 4) 70 % alcohol is added to the tube and centrifuged at 8000 g for 2 minutes at room temperature; 5) the 70 % alcohol supernatant is removed from the tube and the nucleic acid pellet is re-suspended in elution buffer (p. 29, [0096], lines 1-8) (emphasis added). Liu teaches that elution buffers such as TE-buffer and low EDTA TE buffers may be used (p. 27, [0089], lines 2-4).
Liu further teaches this method may use the molecular crowder Ficoll (p. 28, [0094], lines 1-5, 10), at a concentration between about 0% and about 20% (p. 23, lines 5-6), with higher molecular crowder concentrations reducing the solubility of nucleic acids and decreasing size cutoffs (p. 27, [0087], lines 2-4).
Liu teaches their method may select for nucleic acids greater than or equal to about 200 base pairs (bp) (p. 28, [0093], lines 4-6), and that the sample may range from 200 bp to about 100 kb (p. 28, [0093], lines 1-4).
Liu teaches an example of the method of isolating DNA above a specific size cutoff comprising a precipitation step described above, wherein PVP is used as a molecular crowder and double stranded DNA is recovered above a tunable cutoff size between 1000 and 10000 bp (p. 37, [00125], lines 1-3). Liu teaches this protocol is of utility for third generation long read sequencing (p. 37, [00125], lines 3-4). In this example, the DNA samples are present in solution at concentrations of 100 ng/μL and 200 ng/μL (p. 37, Example 5, [00126]), and NaCl and PVP (present in the stock solution at a concentration at twice the final concentration) were added to the samples and mixed (p. 37, [00127], lines 1-2). Liu teaches the resulting solutions were centrifuged, supernatant removed leaving a DNA pellet, the samples washed with 70% ethanol, centrifuged again, the ethanol supernatant removed, and isolated DNA resuspended in a Tris-EDTA buffer (pp. 37-38, [00127], lines 4-10). Liu teaches that the DNA cutoff changes from 1000 bp to 10000 bp as PVP concentration in the buffer is decreased from 5% to 1.5% (p. 38, [00129], lines 2-4; see results on document p. 57, Figure 7A and 7B). This method satisfies all limitations of present claim 3, except the presence of 20% Ficoll in the precipitation mixture and the tunable cutoff size between 1500 and 3000 bp. Liu also teaches the sizing cutoff may be adjusted by altering other conditions, including molecular crowder concentration, molecular weight, and type, the presence or absence of chaotropic, monovalent, or divalent salts, the salt concentration and type, and the alcohol concentration and type, among others (p. 4, [0010], see items a)-g)). Liu provides that higher chaotropic, monovalent and divalent salt concentrations reduce the solubility of all nucleic acids and can decrease sizing cutoff (p. 22, [0064], lines 6-8), and that higher alcohol concentration reduces the solubility of the nucleic acids and can decrease sizing cutoffs (p. 22, [0065], lines 4-5).
In addition, Liu teaches their method may use a nanomembrane. For example, Liu teaches their disclosure is directed to methods for purifying a sample containing nucleic acids to obtain isolated nucleic acids of a desired size range including the steps of: a) combining a nucleic acid-containing sample with a binding buffer to provide a binding mixture: b) contacting the binding mixture with a nanomembrane (e.g., a silica nanomembrane or the like), wherein the nanomembrane binds nucleic acids in the binding mixture (e.g., within a desired size range); c) selecting the nucleic acids based on size prior to, during, or after binding the nucleic acids with the nanomembrane; and d) separating the bound nucleic acids from the remaining sample (p. 2, [0005], lines 1-8) (emphasis added). Liu teaches that step c) may comprises selectively binding nucleic acids of a specific size range or may comprise performing a size specific precipitation of nucleic acids prior to step a) above (p. 2, [0006], lines 5-6) or after elution (p. 2, [0006], lines 8-9).
Liu teaches that their method is particularly suitable for size selection in the context of a sequencing library (p. 32, [00108], lines 1-2), which is taken as an express teaching that the nucleic acids isolated from this method are intended to be sequenced to produce sequencing reads.
Finally, Liu teaches and claims kits for purifying a sample containing nucleic acids to obtain isolated nucleic acids of a desired size range comprising a nanomembrane, a binding buffer, and one or more wash buffers (p. 47, claim 23), and further claims the kits contain a molecular crowder selected from PEG and PVP (p. 47, claims 24 and 26). Liu teaches their binding buffer may contain a buffer and salt (e.g., see p. 34, [00112], lines 4-5). As stated above, Liu teaches additional molecular crowding agents as alternatives to PEG and PVP, including Ficoll (p. 27, lines 1-2).
Liu does not teach a method of purifying a sample containing nucleic acids to obtain isolated nucleic acids above a tunable cutoff size between 1500 and 3000 bp, and wherein the precipitation mixture comprises a Ficoll concentration of 20%, as recited in independent claim 3, or a composition wherein a portion of the nucleic acids are present in a nucleic acid pellet that predominantly comprises nucleic acid molecules above a tunable cutoff size between 1500 and 3000 bp selected size cutoff, and wherein a remaining portion of the nucleic acids are present in a supernatant that predominantly comprises nucleic acid molecules below the tunable cutoff size between 1500 and 3000 bp, as recited in claim 23.
In addition, Liu does not teach a specific kit that comprises Ficoll, as required by claim 29. In addition, Liu does not expressly teach a precipitation buffer in a single container that comprises water, the buffer, the salt, and Ficoll, as recited in claim 30.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to substitute Ficoll for PVP in the method above taught by Liu for the purposes of isolating nucleic acids with a tunable size cutoff between 1500 and 3000 g/mol. One of ordinary skill in the art would have been motivated to substitute Ficoll for PVP in the method taught by Liu for the purposes of isolating nucleic acid with a tunable size cutoff between 1500 and 3000 g/mol because Liu discloses a method for isolating nucleic acids above a size cutoff, teaches an example in which the concentration of PVP is manipulated to tune the size cutoff, including within a range of 1500-3000 bp, teaches alternative conditions to tune the size cutoff of nucleic acids isolated by this method, and suggests Ficoll as one molecular crowding agent that may be used in their method. In this instance, because Ficoll is expressly suggested as an alternative molecular crowder to PVP, one of ordinary sill in the art would have reasonably considered substituting Ficoll in place of PVP in the method of Liu.
Regarding the specific size cutoff of 1500-3000 bp in the presence of 20% Ficoll as required by the present claim 3, because Liu discloses a range of Ficoll concentrations that may be used in their method and further teaches that alternative conditions may be used to tune the size cutoff, including embodiments in which the concentration of NaCl and isopropyl alcohol are used to tune the size cutoff, one of ordinary skill in the art would have further considered optimizing these conditions to tune the size cutoff of nucleic acids isolated using this method.
Therefore, one of ordinary skill in the art would have practiced the method of Liu, adjusting a concentration of Ficoll and/or salt in the precipitation mixture to tune their desired nucleic acid size cutoff. In this instance, absent a showing of some superior or unexpected benefit of specifically selecting 20% Ficoll to perform the claimed method for isolating nucleic acids above 1500-3000 bp, one of ordinary skill in the art would have reasonably optimized the method disclosed by Liu with Ficoll as a suggested molecular crowder to isolate nucleic acids above a desired size cutoff.
MPEP 2144.05 II at A states: “Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).”
Regarding the concentration of Ficoll in the precipitation buffer as recited in claims 8 and 27, because Liu teaches the molecular crowder is present in its stock solution at a concentration twice that of the final concentration, one of ordinary skill in the art would have considered a dilution factor of 2x as when considering the concentration of Ficoll in the precipitation buffer.
Regarding the specific step at which the nucleic acids are bound to the nanomembrane, Liu teaches binding to the solid support during precipitation (p. 2, [0006], lines 6-7) and following elution (p. 2, [0006], lines 8-9), which is part of step b of claim 3 and following step e of claim 16, and thus and would satisfy claims 19 and 20. Regarding binding to the nanomembrane before step a) as recited in claim 18, these conditions would be met by, for example, performing the isolation method above that requires binding the nucleic acids to a nanomembrane and subsequently performing a precipitation step taught by Liu following precipitation and following Liu’s guidance regarding isolation of the nucleic acids via precipitation.
Regarding the composition recited in claims 23 and 27, because Liu renders obvious the method of present claim 3, and further renders obvious said method that involves pelleting the precipitated product by centrifugation, a composition that is present at an intermediate step of said method, after the centrifugation step wherein the precipitated nucleic acid is separated from the nucleic acid left in solution, also renders obvious the composition of claims 23 and 27.
Regarding the kits recited in claims 29-32, in view of Liu teaching kits comprising their binding buffers, elution and wash buffers, and nanomembranes, one of ordinary skill in the art would have reasonably considered a kit that packages all components together for the purposes of practicing the method obvious over Liu. Regarding the requirement of claim 30 that a single container comprises a precipitation buffer that comprises water, the buffer, the salt, and Ficoll, because Liu teaches a precipitation buffer that includes buffer, NaCl, water, and PVP (p. 29, [0096], lines 1-8), one of ordinary skill in the art would reasonably consider packaging this buffer comprising in a single container, because each of these components are added at the same time to precipitate the nucleic acid.
Therefore the invention taken as a whole is prima facie obvious.
The publication of Liu shares at least one inventor with the present application. The above rejection relies on prior art eligible under 35 U.S.C. 102(a)(1). This rejection might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(1)(A); or (2) a showing under 37 CFR 1.130(b) of a prior public disclosure by the inventor or a joint inventor or another who obtained the subject matter disclosed directly or indirectly from the inventor or a joint inventor and is thus not prior art in accordance with 35 U.S.C. 102(b)(1)(B).
Claims 6 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Liu as applied to claims 3, 8, 10-12, 14-21, 23, 27, and 29-32 above, and further in view of Latham (U.S. pre-grant publication no. US 20050208510 A1; cited in previous office action).
Liu teaches as described in the above rejection under 35 U.S.C. 103.
Liu does not teach a molecular weight of the Ficoll suggested as a molecular crowding agent, as required by claims 6 and 25.
Latham teaches methods of precipitating nucleic acids using the reagents polyethylene glycol (PEG), polyvinyl pyrrolidinone (PVP), and Ficoll. In one embodiment, Latham teaches that 1 M salt and PEG enhanced the purification of liver RNA compared to the monomer of polyethylene glycol at final concentrations of 26.6, 13.3, and 6.6% polyethylene glycol using dextran beads (p. 24, [0155], lines 5-10). Latham teaches that after binding to the dextran beads, the beads were placed on a magnetic stand, allowed to collect at the bottom of the well, the supernatant was removed, the beads were washed with 80% ethanol, and the sample was eluted with water (p. 25, left column, lines 1-7).
Latham teaches similar studies using Ficoll of molecular weights 40,000 and 70,000 at concentrations of 26.6, 13.3, and 6.6% (p. 25, left column, [0156], lines 1-5), as well as with PVP of molecular weights 10K, 40K, and 360K at various concentrations between ~5% and ~31% (p. 25, [0158], lines 3-5 and Table 27). For Ficoll, RNA yield was increased compared to the dextran monomer (p. 25, [0157], Table 26). PVP was similarly effective in co-precipitating RNA for RNA isolation (p. 25, [0158], Table 27).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to select a Ficoll of molecular weight 40,000 or 70,000 daltons for use in the method of claim 3 and the composition of claim 23 obvious over Liu. One of ordinary skill in the art would have been motivated to select a Ficoll of molecular weight 40,000 or 70,000 daltons for use in the method of claim 3 and the composition of claim 23 obvious over Liu because Liu suggests Ficoll may be used as a molecular crowding agent in their method, which includes the role of precipitating a nucleic acid, and because Latham teaches Ficoll of molecular weight 40,000 or 70,000 daltons may be used for precipitation of RNA. Therefore, in view of Latham, one of ordinary skill in the art would have reasonably considered selecting a Ficoll of molecular weight 40,000 or 70,000 daltons when practicing the method of nucleic acid isolation obvious over Liu, as these molecular weights would be expected to be effective for precipitation of nucleic acid in the method obvious over Liu, as demonstrated by Latham.
Therefore the invention taken as a whole is prima facie obvious.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Liu as applied to claims 3, 8, 10-12, 14-21, 23, 27, and 29-32 above, and further in view of Lis (Lis, J. T.; et al. Nucleic Acids Research 1975, vol. 2, pp. 383-390; cited in previous office action).
Liu teaches as described in the above rejection under 35 U.S.C. 103. In addition, Liu teaches centrifuging the precipitated sample in Example 5 at 8,000 g for 30 minutes at room temperature (pp. 37-38, [00127], lines 4-5).
Liu does not teach wherein step b) comprises centrifuging the precipitation mixture at 10000 g for 30 minutes at room temperature (RT), as required by claim 13.
Lis teaches a method wherein DNA molecules of differing molecular mass are separable by selective precipitation with polyethylene glycol, wherein higher molecular mass DNA precipitates at lower PEG concentrations than lower molecular mass DNA (p. 383, Abstract, lines 1-4). Lis teaches this method works efficiently at DNA concentrations above 10 μg/ml, which is equivalent to 10 ng/μL (p. 383, Introduction section, second paragraph, lines 5-6).
In this method, after adding a precipitation solution comprising PEG and cooling the solution, the sample is centrifuged at 8,000 x g for 10 minutes (p. 384, The standard assay section, lines 1-3
Lis further teaches that after precipitating DNA with 9% PEG, 10 min centrifugations were performed at 480, 1,900, 4,300, l4,600, and 27,000 x g force and the DNA in the pellet of each tube was analyzed by gel electrophoresis. Lis teaches DNA pellets collected by centrifugation between 1,900 to 27,000 x g all had identical amounts of all DNA sizes but reducing the centrifugal force to k30 x g resulted in about a 50% loss of the DNA in all sizes (p. 388, Effect of centrifugal force section, lines 1-8).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to modify the centrifugation step taught by Liu and centrifuge at 10000 g instead of at 8000 g to separate the precipitated nucleic acids. One of ordinary skill in the art would have been motivated to modify the centrifugation step taught by Liu and centrifuge at 10000 g instead of at 8000 g to separate the precipitated nucleic acids because Liu teaches their size-selection method uses a centrifugation step at 8000 g to separate the precipitated nucleic acids, and in view of Lis teaching that DNA pellets collected by centrifugation between 1,900 to 27,000 x g all had identical amounts of all DNA sizes, centrifuging at 10,000 x g would have been one of many suitable centrifugation speeds to select when practicing the method of size-selective isolation of nucleic acid obvious over Liu.
MPEP 2144.05 II at A states: “Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).” In this instance, the specific centrifugation speed would have been optimized using routine experimentation to identify conditions that provide suitable separation of the precipitated nucleic acid from the nucleic acid remaining in solution.
Therefore the invention taken as a whole is prima facie obvious.
Claim 22 is rejected under 35 U.S.C. 103 as being unpatentable over Liu as applied to claims 3, 8, 10-12, 14-21, 23, 27, and 29-32 above, and further in view of Huptas (Huptas, C.; et al. BMC Research Notes 2016, vol. 9, article 269; cited in previous office action) and Earl (Earl, D.; et al. Genome Research 2011, vol. 21, pp. 2224-2241; cited in previous office action).
Liu teaches as described in the above rejection under 35 U.S.C. 103.
Liu does not teach wherein an N50 of the sequencing reads obtained after performing at least steps a)-c) is increased relative to an N50 of sequencing reads obtained in the absence of performing steps a)-c).
Huptas teaches library preparation for bacterial whole genome sequencing and the analyses of factors influencing de novo assembly of the genome (p. 1, Title). Huptas teaches that the estimation of assembly performance with assembly metrics like corrected NG50 and NGA50 showed that libraries with larger insert sizes can result in substantial assembly improvements as long as appropriate assembly tools are chosen (p. 1, Abstract, Results section, lines 6-8).
Earl teaches the NG50 is identical to N50, except that we estimate the length of the genome being assembled as being equal to the average of the length of the two haplotypes, α1 and α2 (p. 2228, right column, N50 and NG50 section, lines 10-13) (emphasis added). This is interpreted as Earl teaching the NG50 and N50 values are correlated.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to apply the method of size selection of nucleic acids obvious over Liu to improve the N50 of sequencing reads of the resulting DNA product. One of ordinary skill in the art would have been motivated to apply the method of size selection of DNA obvious over Liu to improve the N50 value of sequencing reads of the DNA product from this method because the method of Liu selects for nucleic acids above the tunable size cutoff recited in claim 3, Huptas teaches that sequencing libraries with larger insert sizes can result in improved assembly metrics like NG50 and NGA50, and Earl teaches that the N50 and NG50 values are correlated. Thus by applying the size selection method obvious over Liu, one of ordinary skill in the art would have reasonably expected the N50 value of the sequencing reads to increase relative to the equivalent sample that was not subjected to said size selection method.
Therefore the invention taken as a whole is prima facie obvious.
Claim 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Liu as applied to claims 3, 8, 10-12, 14-21, 23, 27, and 29-32 above, and further in view of Wang (U.S. pre-grant publication no. US 20150037802 A1; cited in previous office action).
The examiner believes that claims 18-20 are obvious over Liu, as described in the above rejection under 35 U.S.C. 103. However, for the sake of argument, if, for example, Liu does not provide sufficient disclosure regarding the specific step in their method in which the nanomembrane should be used, then claims 18-20 would have been obvious over Liu in view of Wang.
Liu teaches as described in the above rejection under 35 U.S.C. 103.
Liu does not teach a specific embodiment that involves, prior to step a) combining the nucleic acid-containing sample with a binding buffer to provide a binding mixture; contacting the binding mixture with a nanomembrane, wherein the nanomembrane binds nucleic acids in the binding mixture to produce bound nucleic acids; and separating the bound nucleic acids from remaining components of the binding mixture, as recited in claim 18, contacting the nucleic acids with a nanomembrane in the precipitation mixture, wherein the nanomembrane binds nucleic acids in the precipitation mixture to produce bound nucleic acids during steps a), b), and/or c), as recited in claim 19, or further comprising during or after step e) contacting the resuspended nucleic acids with a nanomembrane, wherein the nanomembrane binds nucleic acids in the resuspension buffer to produce bound nucleic acids; and separating the bound nucleic acids from remaining components of the resuspension buffer as recited in claim 20.
Wang teaches silica nanomembranes that can be used for solid phase extraction of nucleic acids (cover page, Abstract, lines 5-6). Wang teaches that a fundamental problem in nucleic acid analysis is sample preparation, and that a sample to be investigated usually comprises cells or tissue with partially insoluble constituents which can interfere with the subsequent isolation and analysis (p. 1, [0003], lines 1-5). Wang teaches one benefit of their silica nanomembranes is their extremely high nucleic acid capacity due to its significantly
enlarged specific surface area of silica (cover page, Abstract, lines 10-12).
Wang further teaches a method for extracting nucleic acids from a sample comprising: a) obtaining a sample comprising nucleic acids; b) contacting the sample with a sufficient amount of silica nanomembranes; c) allowing the nucleic acids in the sample to adsorb onto the silica nanomembranes; d) washing the silica nanomembranes to remove any non-nucleic acid components; and e) desorbing the nucleic acids from the silica nanomembranes to obtain the
isolated and purified nucleic acids from the sample (pp. 1-2, [0012], lines 1-10).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to modify the method obvious over Liu and include the solid support with the nanomembrane taught by Wang. One of ordinary skill in the art would have been motivated to modify the method obvious over Liu and include the solid support with the nanomembrane taught by Wang because Wang teaches their silica nanomembranes have extremely high nucleic acid capacity due to its significantly enlarged specific surface area, and thus the nanomembranes of Wang may improve the yield of nucleic acids isolated using the method obvious over Liu.
Regarding the specific step at which the nucleic acids are bound to the nanomembrane, Liu teaches binding to the solid support during precipitation (p. 2, [0006], lines 6-7) and following elution (p. 2, [0006], lines 8-9), which is part of step b of claim 3 and following step e of claim 16, and thus and would satisfy claims 19 and 20.
Regarding binding to the nanomembrane before step a) as recited in claim 18, one of ordinary skill in the art would have recognized that the nanomembrane may be used to remove impurities from cells or tissues prior to the size selection method obvious over Liu, and thus would have considered binding the nucleic acids to nanomembranes before size selection to remove the impurities from cells or tissues taught by Wang, that may interfere with the size-selection process.
In addition, regarding binding to the nanomembrane after step e) as recited in claim 20, one of ordinary skill in the art would have contemplated binding the sample to the nanomembrane following step e) of claim 16 because this step is suggested by Liu and, as taught by Wang, the process of binding and eluting from the nanomembrane may be used to remove remaining impurities from the sample. Therefore, one of ordinary skill in the art would have contemplated this step in order to remove reagents that may interfere with downstream sample steps. As one example, the binding to the nanomembrane may be used to remove a component present in the TE buffer taught by Liu that may interfere with subsequent analysis of the sample, as taught by Wang.
Therefore the invention taken as a whole is prima facie obvious.
Claim 33 is rejected under 35 U.S.C. 103 as being unpatentable over Liu (Publication no. WO 2019006321 A1; cited in IDS received June 10, 2022) as applied to claims 3, 8, 10-12, 14-21, 23, 27, and 29-32 above, and further in view of O’Neil (U.S. pre-grant publication no. US 20180291365 A1; cited in previous office action).
Liu teaches as described in the above rejections under 35 U.S.C. 103.
Liu does not teach the kit of claim 29, further comprising one or more sequencing reagents, as recited in claim 33.
O’Neil teaches a poly(alkylene oxide) polymer-based size-selective DNA isolation method for isolating DNA molecules having a size above a certain cut-off value from a DNA containing sample (cover page, Abstract, lines 1-4).
O’Neil teaches kits that may be used for the size selective isolation of target DNA molecules having a size above a desired cut-off value from a DNA in their described method containing sample comprising: a binding buffer comprising at least one poly(alkylene oxide) polymer, at least one divalent cation and at least one buffering agent wherein the binding buffer has a pH value that lies in the range of 8 to 10, a solid surface, a washing solution, and an elution solution (p. 16, [0174]-[0178]).
In addition, O’Neil teaches that multiplexing strategies for sequencing can be used in conjunction with the teaching of their invention to reduce the sequencing cost of each sample (p. 15, [0165], lines 1-6). O’Neil teaches that indexing approaches are known in the prior art and index adapters are also commercially available and are, for example, provided in the TruSeq® DNA sample prep kits suitable for use in the Illumina platform (p. 15, [0165], lines 27-30). These indexing kits are interpreted as included within the scope of sequencing reagents recited in claim 33.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to prepare a kit that comprises the components of claim 29 with additional sequencing reagents. One of ordinary skill in the art would have been motivated to prepare a kit that comprises the components of claim 29 with additional sequencing reagents because Liu teaches a method and kits for size-selecting nucleic acids by selectively precipitating the nucleic acids with a molecular crowding agent such as Ficoll that may be used to prepare samples for DNA sequencing, and because O’Neil teaches that multiplex sequencing strategies can be used with their invention to reduce the cost of sequencing, such as indexing methods known in the prior art. Therefore, one of ordinary skill in the art would have reasonably considered a kit as taught by Liu with additional sequencing reagents, because the method of Liu may benefit from multiplex sequencing strategies to reduce sequencing cost, and thus including reagents to enable multiplexing in a kit of Liu would facilitate performing said method.
Therefore the invention taken as a whole is prima facie obvious.
Claims 29-30 and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Latham (U.S. pre-grant publication no. US 20050208510 A1; cited in previous office action).
Latham teaches as described in the above rejection under 35 U.S.C. 103. In addition, Latham teaches that kits may comprise one or more of a binding buffer and at least one polymer-modified surface. Latham teaches the binding buffer comprises a suitable salt and organic solvent at concentrations suitable for binding polynucleotides to the surface (p. 4, [0034], lines 1-7). This buffer is interpreted as an aqueous buffer, absent evidence to the contrary. Latham further teaches their kit may further comprise an elution buffer or one or more components thereof and a wash buffer or one or more components thereof (p. 4, [0034], lines 12-20). Latham teaches that purification of nucleic acid in the absence of organic reagents can also be desirable, and as a result, kits may also include salt and a non-organic component, such as Ficoll, PVP, and/or other nucleic acid co-precipitants (p. 4, [0034], lines 22-24).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to prepare a kit for purifying a sample containing nucleic acids to obtain isolated nucleic acids comprising a buffer, a salt, and Ficoll disposed in one or more containers because Latham teaches a method of isolating polynucleotides by precipitation with Ficoll, and further kits that include a binding buffer comprising salt and Ficoll also comprising elution and wash buffers.
As described in the above claim interpretation section, the limitation “for purifying a sample containing nucleic acids to obtain isolated nucleic acids above a tunable cutoff size between 1500 and 3000 bp” is interpreted herein as an intended use of the kit recited in claim 29. See MPEP 2111.02 at II. Therefore, claim 29 interpreted as satisfied by a kit that includes the required components recited in claim 29, even if that kit is not used for purifying a sample containing nucleic acids to obtain isolated nucleic acids above a tunable cutoff size between 1500 and 3000 bp.
Regarding the requirement of claim 30 that a single container comprises a precipitation buffer that comprises water, the buffer, the salt, and Ficoll, because Latham teaches an embodiment that requires adding salt and an aqueous solution of Ficoll, another molecular crowder, to a nucleic acid solution at the same time for the purposes of precipitating said nucleic acid solution, and because Latham teaches kits comprising buffers for facilitating binding to a surface, one of ordinary skill in the art would reasonably consider packaging this buffer in a single container, because the binding buffer components, comprising salt and Ficoll, are all added at the same time to precipitate the nucleic acid to a surface, and thus one would have considered packaging them together in the kit obvious over Latham.
Therefore the invention taken as a whole is prima facie obvious.
Claim 31 is rejected under 35 U.S.C. 103 as being unpatentable over Latham as applied to claims 29-30 and 32 above, and further in view of Wang (U.S. pre-grant publication no. US 20150037802 A1; cited in previous office action).
Latham teaches as described in the above rejections under 35 U.S.C. 103.
Latham does not teach the kit of claim 29, further comprising further comprising a nanomembrane, as recited in claim 31.
Wang teaches as described in the above rejection under 35 U.S.C. 103.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to include a nanomembrane in the kit obvious over Latham. One of ordinary skill in the art would have been motivated to include a nanomembrane in the kit obvious over Latham because Latham teaches a method of precipitating a polynucleotide to a solid surface, because the nanomembrane taught by Wang because each of the solid support and nanomembrane of Wang bind to nucleic acids, and because Wang teaches their silica nanomembranes have extremely high nucleic acid capacity due to its significantly enlarged specific surface area, which may improve the yield of nucleic acids isolated using the method of Latham. Accordingly in view of the benefits of the nanomembranes taught by Wang, one of ordinary skill in the art would have considered the kits obvious over Latham further comprising the nanomembrane of Wang.
Therefore the invention taken as a whole is prima facie obvious.
Claims 29 and 33 are rejected under 35 U.S.C. 103 as being unpatentable over O’Neil (U.S. pre-grant publication no. US 20180291365 A1; cited in previous office action) in view of Latham (U.S. pre-grant publication no. US 20050208510 A1; cited in previous office action).
O’Neil teaches as described in the above rejections under 35 U.S.C. 103.
O’Neil does not teach the kit of claim 29, or the kit of claim 29, further comprising one or more sequencing reagents, as recited in claim 33.
Latham teaches as described in the above rejections under 35 U.S.C. 103.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to prepare a kit that comprises the components of claim 29 with additional sequencing reagents. One of ordinary skill in the art would have been motivated to prepare a kit that comprises the components of claim 29 because O’Neil teaches a method and kits for size-selecting nucleic acids by selectively precipitating the nucleic acids with PEG, and because Latham teaches Ficoll may be used to precipitate nucleic acids. Accordingly, Therefore, one of ordinary skill in the art would have reasonably considered a kit comprising the components as described by O’Neil, with Ficoll in place of PEG, because Latham teaches Ficoll may also be used as an agent for precipitating nucleic acids and thus would be reasonably substituted in the method of O’Neil. Moreover, because O’Neil teaches their method may be used to prepare samples for sequencing, one of ordinary skill in the art would have considered including sequencing reagents in the kit obvious over O’Neil in view of Latham, to facilitate performing the method of sample preparation for multiplexed sequencing.
Therefore the invention taken as a whole is prima facie obvious.
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.
Claims 3, 8, 10, 11, 12, 14-21, 23, and 27 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16-26, 28, and 30 of U.S. Patent No. 11,732,254 (reference patent, herein referred to as ‘254) in view of Liu (Publication no. WO 2019006321 A1; cited in IDS received June 10, 2022).
The present application and ‘254 are each assigned to Pacific Biosciences Of California, Inc.
Claim 16 of ‘254 claims a method of size selecting nucleic acids, the method comprising:
a. adding a precipitation solution comprising water, salt, and polyvinylpyrrolidone (PVP) and/or Ficoll to a nucleic acid-containing sample in a tube to produce a sample-solution; b. centrifuging the sample-solution to produce a nucleic acid pellet in the tube, wherein the nucleic acid pellet comprises nucleic acids of one or more selected sizes that precipitate driven by the PVP and/or the Ficoll and wherein a supernatant comprises nucleic acids remaining in solution; c. removing the supernatant from the tube; and, d. re-suspending the nucleic acid pellet in an aqueous solution, wherein the method lacks a separate magnetic bead purification step, claim 18 claims wherein the precipitated nucleic acids comprise all sizes above a cutoff value, and claim 23 claims the precipitation solution comprises a buffer.
Claims 16, 18, and 23 do not claim the above a tunable cutoff size between 1500 and 3000 bp, and wherein the precipitation mixture comprises a Ficoll concentration of 20%, as required by claim 3.
Liu teaches as described in the above rejections under 35 U.S.C. 103.
It would therefore have been prima facie obvious to optimize the method of claim 16 of ‘254 to achieve a tunable size cutoff of 1500-3000 bp in the presence of 20% Ficoll, because the claims of ‘254 claim a method of size selecting nucleic acids with because Liu discloses a range of Ficoll concentrations that may be used in their method, and because Liu further teaches that alternative conditions may be used to tune the size cutoff, including embodiments in which the concentration of NaCl and isopropyl alcohol are used to tune the size cutoff, one would have further considered optimizing these conditions to affect the size cutoff of nucleic acids isolated using the method obvious over the claims of ‘254 in view of Liu.
Therefore, one of ordinary skill in the art, in view of the claims of ‘254 and Liu, would have adjusted a concentration of Ficoll and/or salt in the precipitation mixture to tune their desired size cutoff. In this instance, absent a showing of some superior or unexpected benefit of specifically selecting 20% Ficoll to perform the claimed method and select nucleic acids above 1500-3000 bp, one of ordinary skill in the art would have reasonably optimized the method disclosed by Liu with Ficoll as a suggested molecular crowder to isolate nucleic acids above a desired tunable size cutoff, such as 1500-3000 bp. See MPEP 2144.05 II at A.
In addition, the method obvious over the claims of ‘254 in view of Liu renders obvious the composition comprising nucleic acids and a precipitation buffer, wherein the precipitation buffer comprises water, a buffer, a salt, and polyvinyl pyrrolidinone (PVP) and/or Ficoll, wherein a portion of the nucleic acids are present in a nucleic acid pellet that predominantly comprises nucleic acid molecules above a selected size cutoff value and wherein a remaining portion of the nucleic acids are present in a supernatant that predominantly comprises nucleic acid molecules below the selected size cutoff value, because such a composition must be formed when practicing this method. Similarly, the concentration of Ficoll in the precipitation buffer required by claim 27 is also obvious over the claims of ‘254 in view of Liu.
Claim 17 of ‘254 depends from claim 16 and requires tuning at least one condition of the precipitation solution to determine a selected size cutoff value, wherein the condition is selected from the group that includes PVP and/or Ficoll concentration. Thus claim 17, together with claims 16, 18, and 23, render obvious present claim 11.
Claims 19-21 of ‘254 depend from claim 16 and require performing steps a-d prior to, after, or concurrently with a nanomembrane purification method. These claims, together with claims 16, 18, and 23, render obvious present claims 18-20.
Claim 22 of ‘254 claims adding alcohol to the tube, centrifuging the tube, and removing alcohol supernatant from the tube after performing step c). Claim 24 of ‘254 claims the aqueous solution comprises an elution buffer. Thus claims 22 and 24 of ‘254, together with claims 16, 18, and 23, render obvious present claim 16. In this instance, elution buffer is interpreted as equivalent to the presently claimed resuspension buffer of claim 16.
Claim 28 of ‘254 depends from claim 16 and requires size selecting the nucleic acids at a nucleic acid concentration greater than 50 ng/μL in the sample-solution. Thus claim 28, together with claims 16, 18, and 23, render obvious present claim 10. In this instance, because 50 ng/μL is recited as the low concentration, one of ordinary skill in the art would have contemplated concentrations of 50 ng/ μL and above, which significantly overlap with the range of 1-2,000 ng/μL recited in claim 10.
Claims 6 and 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16-26, 28, and 30 of ‘254 in view of Liu as applied to claims 3, 8, 10, 11, 12, 14-21, 23, and 27 above, and further in view of Latham (U.S. pre-grant publication no. US 20050208510 A1; cited in previous office action).
The claims of ‘254 claim as described in the above nonstatutory double patenting rejection.
Liu teaches as described in the above rejections under 35 U.S.C. 103 and in the above nonstatutory double patenting rejection.
Neither the claims of ‘254 or Liu teach a molecular weight of the Ficoll suggested as a molecular crowding agent, as required by claims 6 and 25.
Latham teaches as described in the above rejections under 35 U.S.C. 103.
It therefore would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to select a Ficoll of molecular weight 40,000 or 70,000 daltons for use in the method of claim 3 and the composition of claim 23 obvious over the claims of 254 and Liu because ‘254 claims a method of size selecting nucleic acids by precipitation with Ficoll, Liu teaches Ficoll may be used as a molecular crowding agent in their method and provides guidance on the Ficoll concentration and selection of variables that enable tuning the size cutoff, and because Latham teaches Ficoll of molecular weight 40,000 or 70,000 daltons may be used for precipitation of polynucleotides. Therefore, in view of Latham, one of ordinary skill in the art would have reasonably considered selecting a Ficoll of molecular weight 40,000 or 70,000 daltons when practicing the method of nucleic acid isolation obvious over the claims of ‘254 and Liu, as these Ficoll polymers would be expected to be effective for precipitation of nucleic acid in the method obvious over the claims of ‘254 and Liu, as taught by Latham.
Claims 29-33 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16 and 18-24 of ‘254 in view of O’Neil (U.S. pre-grant publication no. US 20180291365 A1; cited in previous office action).
The claims of ‘254 claim as described in the above non-statutory double patenting rejection.
The claims of ‘254 do not claim a kit comprising the components required to perform the method claimed by ‘254 as recited in claims 29-33.
O’Neil teaches as described in the above rejection under 35 U.S.C. 103.
It would therefore have been prima facie obvious to one of ordinary skill in the art to package the components necessary to perform the method claimed by ‘254, including buffer, salt, water, and Ficoll, in view of O’Neil also teaching methods of size-selecting nucleic acids and teaching a kit comprising the components required to perform their method, because such a kit would reduce the likelihood of error in preparation of buffers and reagents necessary for performing said method, and thus would maximize the likelihood of the users success for said method. Moreover, because O’Neil teaches the benefits of their size-selection method for preparing sequencing libraries, one of ordinary skill in the art would have considered including sequencing reagents, such as reagents to add indices for multiplexed sequencing, as taught by O’Neil, to the kit comprising the reagents for library size selection.
Regarding the requirement of claim 30 that the precipitation buffer that comprises water, the buffer, the salt, and the Ficoll in a single container, absent a showing of unexpected results regarding the stability of the precipitation buffer, because these components are added to the nucleic acids in the method claimed by ‘254 at the same time, one of ordinary skill in the art would have reasonably packaged them together, absent evidence to the contrary.
Claims 3, 8, 10, 11, 12, 14-21, 23, and 27 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 33-41, 43, 45, and 50 of co-pending U.S. patent application 18/229838 (reference application, hereafter ‘838) in view of Liu (Publication no. WO 2019006321 A1; cited in IDS received June 10, 2022).
The present application and ‘838 are each assigned to Pacific Biosciences of California, Inc.
The amended claims received April 11, 2024 are cited in this provisional non-statutory double patenting rejection.
Claim 33 of ‘838 recites a method of size selecting nucleic acids, the method comprising: a. adding a precipitation solution comprising water, salt, and polyethylene glycol (PEG) to a nucleic acid-containing sample in a tube to produce a sample-solution; b. centrifuging the sample-solution to produce a nucleic acid pellet in the tube, wherein the nucleic acid pellet comprises nucleic acids of one or more selected sizes that precipitate driven by the PEG and wherein a supernatant comprises nucleic acids remaining in solution; c. removing the supernatant from the tube; and, d. re-suspending the nucleic acid pellet in an aqueous solution, wherein the method lacks a separate magnetic bead purification step.
Claim 34 of ‘838 depends from claim 33 and requires comprising tuning at least one condition of the precipitation solution to determine a selected size cutoff value, wherein the condition is selected from the group that includes PEG concentration and salt concentration, claim 35 requires the nucleic acids that were precipitated comprise all sizes above a cutoff value, claims 36-38 require performing steps a)-d) prior to, after, or concurrently with performing a nanomembrane purification method, claim 39 requires adding alcohol to the tube, centrifuging the tube, and removing alcohol supernatant from the tube after performing step c), claim 40 requires the precipitation solution further comprises a buffer, claim 41 requires the aqueous solution further comprises an elution buffer, claim 43 requires the concentration of the PEG in the sample solution is such that the one or more selected sizes of the nucleic acids is from 1000 base pairs to 10 kilobases, and claim 45 requires size-selecting the nucleic acids at a nucleic acid concentration greater than 50 ng/μL in the sample-solution.
Claim 50 of ‘838 claims a method of size selecting nucleic acids, the method comprising:
a. adding a precipitation solution comprising water, salt, and polyvinylpyrrolidone (PVP) and/or Ficoll to a nucleic acid-containing sample to produce a sample-solution; b. centrifuging the sample-solution at about room temperature to produce a nucleic acid pellet, wherein the nucleic acid pellet comprises nucleic acids of one or more selected sizes that precipitate driven by the PVP and/or the Ficoll and wherein a supernatant comprises nucleic acids remaining in solution;
c. removing the supernatant from the tube; and, d. re-suspending the nucleic acid pellet in an aqueous solution, wherein the method lacks a separate magnetic bead purification step.
The claims of ‘838 do not claim a method of precipitating nucleic acids above a selected size cutoff using PVP and/or Ficoll, as required by present claim 3.
Liu teaches as described in the above rejections under 35 U.S.C. 103.
It would therefore have been prima facie obvious to substitute PVP or Ficoll, as recited in claim 50 of ‘838, in place of PEG in the method recited in claim 17 of ‘838, because the claims of ‘838 claim the use of PEG, PVP, and Ficoll as components in the precipitation solution for precipitating nucleic acids, and thus one of ordinary skill in the art would have reasonably expected that PVP and Ficoll may also precipitate additional nucleic acids above a selected size range, as claimed by ‘838 using PEG in the precipitation reaction.
Regarding the tunable size cutoff of 1500-3000 bp in the presence of 20% Ficoll as required by the present claim 3, because Liu discloses a range of Ficoll concentrations that may be used in their method, and because Liu further teaches that alternative conditions may be used to tune the size cutoff, including embodiments in which the concentration of NaCl and isopropyl alcohol are used to tune the size cutoff, one of ordinary skill in the art would have further considered optimizing these conditions to affect the size cutoff of nucleic acids isolated using the method obvious over the claims of ‘838 in view of Liu.
Therefore, one of ordinary skill in the art, in view of the claims of ‘838 and Liu, would have adjusted a concentration of Ficoll and/or salt in the precipitation mixture to tune their desired size cutoff. In this instance, absent a showing of some superior or unexpected benefit of specifically selecting 20% Ficoll to perform the claimed method and select nucleic acids above 1500-3000 bp, one of ordinary skill in the art would have reasonably optimized the method disclosed by Liu with Ficoll as a suggested molecular crowder to isolate nucleic acids above a desired size cutoff.
In addition, the method obvious over the claims of ‘838 in view of Liu renders obvious the composition comprising nucleic acids and a precipitation buffer, wherein the precipitation buffer comprises water, a buffer, a salt, and polyvinyl pyrrolidinone (PVP) and/or Ficoll, wherein a portion of the nucleic acids are present in a nucleic acid pellet that predominantly comprises nucleic acid molecules above a selected size cutoff value and wherein a remaining portion of the nucleic acids are present in a supernatant that predominantly comprises nucleic acid molecules below the selected size cutoff value, because such a composition must be formed when practicing the method obvious over the claims of ‘838 in view of Liu.
This is a provisional non-statutory double patenting rejection because the patentably indistinct claims have not been patented.
Claims 6 and 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 16-26, 28, and 30 of ‘838 in view of Liu as applied to claims 3, 8, 10-21, 23, and 27 above, and further in view of Latham (U.S. pre-grant publication no. US 20050208510 A1; cited in previous office action).
The claims of ‘838 claim as described in the above nonstatutory double patenting rejection.
Liu teaches as described in the above rejections under 35 U.S.C. 103 and in the above nonstatutory double patenting rejections.
Neither the claims of ‘838 nor Liu teach a molecular weight of the Ficoll suggested as a molecular crowding agent, as required by claims 6 and 25.
Latham teaches as described in the above rejections under 35 U.S.C. 103.
It therefore would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to select a Ficoll of molecular weight 40,000 or 70,000 daltons for use in the method of claim 3 and the composition of claim 23 obvious over the claims of 254 and Liu because ‘838 claims a method of size selecting nucleic acids by precipitation with Ficoll, Liu teaches Ficoll may be used as a molecular crowding agent in their method and provides guidance on the Ficoll concentration and selection of variables that enable tuning the size cutoff, and because Latham teaches Ficoll of molecular weight 40,000 or 70,000 daltons may be used for precipitation of polynucleotides. Therefore, in view of Latham, one of ordinary skill in the art would have reasonably considered selecting a Ficoll of molecular weight 40,000 or 70,000 daltons when practicing the method of nucleic acid isolation obvious over the claims of ‘838 and Liu, as these Ficoll polymers would be expected to be effective for precipitation of nucleic acid in the method obvious over the claims of ‘838 and Liu, as taught by Latham.
This is a provisional non-statutory double patenting rejection because the patentably indistinct claims have not been patented.
Claims 29-33 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 50 of co-pending U.S. patent application 18/229838 (reference application, hereafter ‘838) in view of O’Neil (U.S. pre-grant publication no. US 20180291365 A1; cited in previous office action).
Claims 29 claims a kit for purifying a sample containing nucleic acids to obtain isolated nucleic acids of a desired size range, comprising a buffer, a salt, and Ficoll disposed in one or more containers. Claims 30-33 require additional kit components.
Claim 50 of ‘838 claims a method of size selecting nucleic acids, the method comprising:
a. adding a precipitation solution comprising water, salt, and polyvinylpyrrolidone (PVP) and/or Ficoll to a nucleic acid-containing sample to produce a sample-solution; b. centrifuging the sample-solution at about room temperature to produce a nucleic acid pellet, wherein the nucleic acid pellet comprises nucleic acids of one or more selected sizes that precipitate driven by the PVP and/or the Ficoll and wherein a supernatant comprises nucleic acids remaining in solution;
c. removing the supernatant from the tube; and, d. re-suspending the nucleic acid pellet in an aqueous solution, wherein the method lacks a separate magnetic bead purification step.
The claims of ‘838 do not claim a method of precipitating nucleic acids above a selected size cutoff using PVP and/or Ficoll, as required by the current claims.
The claims of ‘838 do not claim a kit comprising the components required to perform the method of claim 50.
O’Neil teaches as described in the above rejection under 35 U.S.C. 103.
It would therefore have been prima facie obvious to one of ordinary skill in the art to package the components necessary to perform the method obvious over the claims of ‘838, in view of O’Neil also teaching methods of size-selecting nucleic acids and teaching a kit comprising the components required to perform their method, because such a kit would reduce the likelihood of error in preparation of buffers and reagents necessary for performing said method and thus maximize the likelihood of the users success for said method. Moreover, because O’Neil teaches the benefits of their size-selection method for preparing sequencing libraries, one of ordinary skill in the art would have considered including sequencing reagents, such as reagents to add indices for multiplexed sequencing, as taught by O’Neil, to the kit comprising the reagents for library size selection.
Regarding the requirement of claim 30 that the precipitation buffer that comprises water, the buffer, the salt, and the Ficoll in a single container, absent a showing of unexpected results regarding the stability of the precipitation buffer, because
This is a provisional non-statutory double patenting rejection because the patentably indistinct claims have not been patented.
Conclusion
No claims are allowed.
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.M.B./Examiner, Art Unit 1693
/ANDREA OLSON/Primary Examiner, Art Unit 1693