DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Application
Receipt is acknowledged of Applicants’ amendment and remarks, filed on 11/05/2025, in which claims 1, 4, 6, 8, 11, 13, 17-18, 20-23 and 26 are amended, claims 10 and 25 are canceled, and claim 27 in newly added.
Claims 1-9, 11-24, and 26-27 are pending and are examined on the merits herein.
Priority
The instant application is a 371 of PCT/EP2021/051046 filed on 01/19/2021, which claims foreign priority to UK 2001034.4, filed on 01/24/2020.
Rejections Withdrawn
Applicant’s amendment and remarks, filed 11/05/2025, with respect that claim 25 is rejected under 35 U.S.C. 101 has been fully considered and is persuasive, as claim 25 is canceled. This rejection has been withdrawn.
Applicant’s amendment and remarks, filed 11/05/2025, with respect that claims 1-7, 9-16, 20-21, and 23-25 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention has been fully considered and is persuasive, as the limitation "wherein the majority of the eluted DNA is < 400 bp." in claim 1 is being interpreted broadly to include DNA strands greater than or equal to 400 base pairs of either double or single strands, and claims 10 and 25 are canceled.
This rejection has been withdrawn.
Applicant’s amendment and remarks, filed 11/05/2025, with respect that 1-2, 4-5, and 22 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zainabadi has been fully considered and is persuasive, as claim 1 has been amended to include the limitation of 2-propanol present at a concentration of 15-25% v/v. This rejection has been withdrawn.
Applicant’s amendment and remarks, filed 11/05/2025, with respect that claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Welker has been fully considered and is persuasive, as claim 25 is canceled. This rejection has been withdrawn.
The following are maintained or new grounds of objection and rejection necessitated by Applicant’s amendment, in which claim 1 is amended to recite 2-propanol present at a concentration of 15-25% v/v.
Objection to the Specification
The use of the terms Nonidet and Igepal, Triton, TWEEN, and Tris, which are trade names or marks used in commerce, has been noted in this application. For example, in the instant specification the terms Triton, Nonidet, and Igepal appear at least on page 12 lines 16-17, the term Tween appears at least on page 13 lines 20 and 22, and the term Tris appears at least on page 14 line 4. The terms should be accompanied by the generic terminology.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Response to Arguments
Applicant's arguments filed 11/05/2025 have been fully considered but they are not persuasive. Applicant states that the substitute specification has been amended to modify the appearance of trade names and trademarks. This is not persuasive, as the terms should also be accompanied by the generic terminology.
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 8, 17-19, 22, and 26-27 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 8, 17, 22, and 26-27 contain the trademark/trade name Triton. Claims 18-19 contain the trademark/trade name Tris. 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 surfactant and, accordingly, the identification/description is indefinite.
Response to Arguments
Applicant's arguments filed 11/05/2025 have been fully considered but they are not persuasive.
Applicant states that the term "tris", which appears in "tris-HCl" is not a trade name. This is not persuasive, as Tris is a trade name. Trademarks/trade names may not be included in claims.
Because Applicant’s arguments are not persuasive, the instant claims are rejected for the reasons of record with modifications made to account for the claim amendments filed 11/05/2025.
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.
Claims 1-2, 4-7, 11, 13, 16, 19-24, and 26-27 are rejected under 35 U.S.C. 103 as being unpatentable over Welker et al. (WO 2018/140452; IDS 07/18/2022).
Welker discloses methods for enriching cell-free DNA (cfDNA) fragments from a biological fluid sample (abstract). Welker teaches that the biological fluid sample is a bodily fluid including, among others, blood plasma, serum, or urine [0039]. The sample can be collected by any conventional means [0052]. Analysis of cfDNA is used in genetic testing for genetic disorders and has applications in prenatal screenings and the detection of certain genes that are associated with cancer [003].
Welker, in Example 3, discloses a method for enrichment of small cfDNA of 20-60 bp in which 4 volumes of binding solution was added to 1 volume of pretreated sample. The binding solution comprises 2.5 M guanidine thiocyanate, 10% Triton, 40% isopropanol, and magnetic silica beads. The sample is incubated for 10 minutes to allow larger DNA species to bind to the beads. The sample is then placed on a magnetic rack to and the supernatant containing smaller DNA species is transferred to a new tube, leaving behind the magnetic silica beads bound to larger DNA species. In the new tube, additional magnetic silica beads are added and 3 volumes of 100% isopropanol is added. The mixture was incubated at room temperature for 10 minutes, and the supernatant was removed. The DNA was eluted from the silica beads using a 10 mM Tris-HCl + 0.1 mM EDTA buffer. The resulting DNA is a size-selected cfDNA that is 20-60 bp [00127-00128]. Welker teaches that the magnetic silica beads may be Dynabeads MyOne Silane beads [0042]. Welker additionally teaches that the beads can be washed to remove contaminants after removing the beads by subjecting the beads to a magnetic field. The beads can be washed using an alcoholic solution [0067]. Alcoholic solutions in Welker include solutions comprising ethanol [0037]. Welker teaches that DNA can be eluted with an elution buffer adjusted to a pH of between 7.0 to 9.0, such as pH 8.0 [0068]. The methods of Welker may produce an eluate which is enriched with cfDNA fragments of about, among others, 300 base pairs in length (claim 4). Welker teaches that compositions for enriching cfDNA fragments from a biological fluid sample may be provided as kits [00102].
The teachings of Welker differ from that of the instantly claimed invention in that Welker does not expressly teach a washing step after forming a binding mixture (instant claims 1 and 13).
One of ordinary skill in the art would have been motivated to wash the magnetic microbeads in the method of Welker with a wash buffer comprising ethanol because Welker teaches that washing the beads using an alcoholic solution, which includes solutions comprising ethanol, removes contaminants from the beads. One of ordinary skill in the art would have a reasonable expectation of success because Welker teaches that a washing step may be included in embodiments of the disclosed method.
Welker does not expressly teach that the isopropanol is at around 15-25% v/v in the binding mixture. However, Welker does teach that the addition of alcohol favors the binding of the cfDNA to silica particles, with larger cfDNA fragments binding first followed by binding of smaller cfDNA fragments [0023]. Thus Welker teaches that the alcohol concentration is a result effective variable such that one of ordinary skill in the art would have been motivated to optimize the concentration of alcohol in the binding mixture in order to optimize the size of the bound DNA and thereby optimize the size of cfDNA that is enriched.
Regarding instant claims 7, 16, and 23 Welker does not expressly disclose a concentration of a blood plasma sample at around 25-40% v/v in the binding mixture (instant claims 7 and 16) or where 0.5-4 mL of blood plasma is used (instant claim 23). However, Welker teaches that with the lower volume of sample, lower volumes of reagents can be used during the enrichment of cfDNA methods described herein, thus making the downstream isolation procedures more manageable and reducing the amount of required reagents and hence expense [0021]. Welker further teaches that large sample volumes, such as a large volume of blood, are often impractical and put the patient at risk [006]. Thus, one of ordinary skill in the art would have been motivated to optimize the amount of blood plasma used in the method of Welker because Welker teaches that reducing the volume of sample used makes isolation procedures more manageable and less expensive, and safer to patients.
Regarding instant claim 19, Welker teaches that the elution buffer is 10 mM Tris-HCl + 0.1 mM EDTA buffer [00128] and that the pH of the elution buffer can be adjusted to a pH 8.0 [0068 and 0092]. The instant specification does not provide a definition for “around” for the limitation of EDTA at around 0.5 mM found in claim 19. The 0.1 mM EDTA buffer of Welker is interpreted as comprising EDTA at around 0.5 mM and thus meets the limitation of the instant claim.
Regarding instant claim 21, Welker discloses a method in which a detergent, a chaotropic agent, microbeads and isopropanol are added together and then a sample is added. Instant claim 21 is directed to a method in which a detergent, a chaotropic agent, microbeads and a sample are added together and then 2-propanol is added. MPEP 2144.04(IV)(C) states that selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results. Furthermore, selection of any order of mixing ingredients is prima facie obvious. Thus the method of Welker renders obvious instant claim 21.
Regarding instant claim 24, Welker discloses methods and compositions for enriching cfDNA of different size ranges from a biological fluid sample [002]. Welker teaches a method for enriching cfDNA fragments of about 300 base pairs in length (claim 4), and that the methods can also be used to obtain cfDNA fragments having a length of less than about 100 base pairs, such as about 10 base pairs and 80 base pairs [008 and 0027]. As discussed above, Welker additionally teaches one of ordinary skill in the art how to optimize the length of the cfDNA particles that are enriched by optimizing the alcohol concentration (see for example [0023]).
Welker additionally teaches that the size of cfDNA fragments correlates to the origin of the cfDNA fragment. For example, large cfDNA fragments originate from the urinary tract while small cfDNA fragments in the urinary tract arise from both the blood and urinary tract system [00116]; cfDNA fragments of 150 bp are typical in size of DNA that is protected by a single octameric nucleosome core [0075]. Thus it would have been prima facie obvious to optimize the cfDNA fragment size distribution obtained in the methods of Welker because it is prima facie obvious to apply a known technique to a known method ready for improvement to yield predictable results, and Welker teaches methods for obtaining cfDNA fragments of different size ranges and teaches that the size of cfDNA fragments to be obtained depends on the desired DNA fragments to be enriched.
Claims 3 and 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Welker et al. (WO 2018/140452; IDS 07/18/2022) as applied to claims 1-2 and 13 above, in view of Toro et al. (Clinical Biochemistry, 2015; PTO-892).
Welker teaches as above.
The teachings of Welker differ from that of the instantly claimed invention in that Welker does not teach that the blood plasma is obtained from whole blood collected in cell-free DNA stabilizing tube (instant claims 3 and 14-15).
Toro teaches that circulating plasma DNA is being increasingly used for biomedical and clinical research as a substrate for genetic testing. However, cell lysis can occur hours after venipuncture when using standard tubes for blood collection, leading to an increase in contaminating cellular DNA that may hinder analysis of circulating plasma DNA (abstract). Toro compares the efficacy of two cell stabilizing reagents, the cell-free DNA BCT tube and the PAXgene tube, in their ability to prevent lysis and cellular release of genomic DNA of blood samples from cancer patients (abstract). Toro teaches that cell-free DNA BCT tubes have been extensively tested and shown to stabilize cell membranes in whole blood and minimize cell lysis and subsequent release of cellular DNA into plasma and have previously been tested for use in analyzing circulating fetal DNA in maternal blood (paragraph bridging pages 993-994). Toro concludes that cell-free DNA BCT tubes are valuable for plasma DNA analysis of DNA (page 998, paragraph 2).
One of ordinary skill in the art would have been motivated to collect the blood sample for analysis by the method of Welker using the cell-free DNA BCT tubes of Toro because Toro teaches that the tubes minimize cell lysis and subsequent release of cellular DNA into plasma that would otherwise hinder analysis of circulating plasma DNA. One of ordinary skill in the art would have a reasonable expectation of success in using the cell-free DNA BCT tubes of Toro to collect samples for use in the method of Welker because Welker teaches that the sample may be blood plasma, and that the sample can be collected by any conventional means.
Regarding instant claim 15, the claim recites the method of claim 14 with an additional optional step. The claim encompasses methods the do not expressly include the optional step, and so is met by art meeting the limitations of claim 14.
Claim 8-9 and 17-18 are rejected under 35 U.S.C. 103 as being unpatentable over Welker et al. (WO 2018/140452; IDS 07/18/2022) as applied to claims 1, 4, and 13 above, in view of Stray et al. (US 2018/0237841 A1; IDS 07/18/2022).
Welker teaches as above. Welker further discloses a method for enriching cell-free DNA comprising the step eluting cfDNA fragments from a plurality of DNA-binding particles (claim 1) which are silica magnetic bead particles (claim 2). Welker teaches that the term "elution" or "eluting" refers generally to the process of extracting one material from another by washing with a solvent [0044]. Welker teaches that the elution obtained from the method may be additionally enriched with cfDNA fragments having various lengths, including a length of about 300 base pairs [0073]. Welker also teaches that any number of elution procedures can be used to elute the bound DNA [0068]. Welker teaches an elution buffer that is a 10 mM Tris-HCl + 1 mM EDTA buffer and that the pH of the elution buffer can be adjusted to a pH 8.0 [0068 and 0092].
The teachings of Welker differ from that of the instantly claimed invention in that Welker does not teach a single embodiment in which Triton X-100 is included at around 20-30% (instant claim 8) and guanidinium thiocyanate is included at around 1.5-2.5 M (instant claim 9). Welker also does not expressly disclose washing the beads with a buffer that comprises guanidinium thiocyanate at around 2.0 M and Triton X-100 at about 22% w/v (instant claim 17) or a polysorbate-type non-ionic surfactant (instant claim 18).
Stray discloses methods for isolating nucleic acids from a biological sample comprising binding the DNA to a matrix (abstract). The DNA in particular is cfDNA and the matrix may be silica [0030]. Stray teaches that increasing the amount of the detergent Triton (Triton X100) in solution preferentially increased the recovery of small DNA fragments ([0011-0012] and Figures 5-6). Stray teaches that detergents include Triton X100 and TWEEN-20, among others [0042]. Stray further teaches that recovery of short dsDNA increased as the concentration of the chaotropic agent guanidine chloride was increased ([0009-0010] and Figures 3-4). Stray teaches that chaotropic agents include guanidine chloride and guanidine isothiocyanate, among others [0039].
One of ordinary skill in the art would have been motivated include a chaotropic agent such as guanidine isothiocyanate or a detergent such as Triton X100 or TWEEN-20 and to optimize the amounts of these compounds in the elution buffer in the method of Welker because Stray teaches that these compounds can be used to control the size of DNA fragments recovered from a silica matrix in a method for isolating cfDNA. One of ordinary skill in the art would have been similarly motivated to optimize the amount of Triton and chaotropic agent in the binding mixture of Welker in order to control the size of DNA fragments recovered from a silica matrix in a method for isolating cfDNA. One of ordinary skill in the art would have had a reasonable expectation of success because Welker teaches that any number of elution procedures can be used to elute the bound DNA, and that the elution obtained from the method may be additionally enriched with cfDNA fragments having various lengths.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Welker et al. (WO 2018/140452; IDS 07/18/2022) as applied to claims 1 and 11 above, in view of Life Technologies (Dynabeads MyOne Silane Catalog nos. 37002D, 37005D, 2012; PTO-892).
Welker teaches as above.
The teachings of Welker differ from that of the instantly claimed invention in that Welker does not teach that the magnetic microbeads are formulated in an aqueous suspension at 20-200 mg/mL.
Life Technologies teaches that Dynabeads MyOne Silane provide an excellent tool for highly predictable and consistent isolation of nucleic acids from biological samples (page 1, paragraph 5). The beads are supplied at a concentration of 40 mg/mL in water containing 0.02% sodium azide as a preservative (page 1, paragraph 12). Alternative particles from other suppliers often have a random size range distribution, surface area, and binding capacity. This could compromise the reproducibility of results (page 1, paragraph 4).
One of ordinary skill in the art would have been motivated to select Dynabeads MyOne Silane formulated in a 40 mg/mL aqueous suspension as the magnetic microbeads in the method of Welker because Life Technologies teaches that Dynabeads MyOne Silane provide highly predictable and consistent isolation of nucleic acids from biological samples and that alternative particles from other suppliers often have a random size range distribution, surface area, and binding capacity that could compromise the reproducibility of results. One of ordinary skill in the art would have had a reasonable expectation of success because Welker teaches that the magnetic silica beads may be Dynabeads MyOne Silane beads.
Response to Arguments
Applicant's arguments filed 11/05/2025 have been fully considered but they are not persuasive.
Applicant argues that the amended claims require 2-propanol present in the binding reaction at a concentration of 15-25% v/v, which results in enrichment and recovery of small fragment cfDNA, while at the same time minimizing the recovery of high molecular weight, larger genomic DNA fragments (Remarks, page 8, paragraph 8). This is not persuasive.
As discussed in the above grounds of rejection, Welker discloses a method for enrichment of small cfDNA of 20-60 bp, and thus this result is taught in the art and is not unexpected. Furthermore, Applicant does not demonstrate the criticality of the claimed range of 2-propanol. MPEP 2144.05(II)(A) states that, 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. The instant specification does not provide evidence that this claimed range is critical. For example, Example 5 beginning on page 17 of the instant specification provides examples in which the 2-propanol is at 4.7, 9.4, 14.2, 18.9, and 25.2%. However, there is no demonstration that the examples in the claimed range of 15-25% have any significant difference from the examples outside of the claimed range. In addition, the instant specification states that not only 2-propanol concentration, but also Triton X-100 and GuSCN concentrations are manipulated to obtain the desired DNA fragment recovery profile from plasma samples. Thus it is not apparent that any unexpected results would be commensurate in scope with the claimed invention, which encompasses the scope of any detergent and any chaotropic agent at any concentration.
Because Applicant’s arguments are not persuasive, the instant claims are rejected for the reasons of record with modifications made to account for the claim amendments filed 11/05/2025.
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 extension fee 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 date of this final action.
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/S.G.H./Examiner, Art Unit 1693
/SCARLETT Y GOON/Supervisory Patent Examiner, Art Unit 1693