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 .
The amendment filed 28 April 2026 has been received, entered and considered. The following information has been made of record in the instant amendment:
1. Claims 38-42 have been canceled.
2. No new Claims have been added.
3. Claims 35, 43, 46, 52, and 63 have been amended.
4. Remarks drawn to rejections under 35 USC 112, 103 and double patenting.
The following objection(s)/rejection(s) has/have been overcome:
5. The rejection of Claims 52 and 63 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph has been overcome by amendment.
6. The rejection of Claim(s) 38-42 under 35 U.S.C. 103 as being unpatentable over Stoll et al (WO 2017/197399 A1; cited in IDS filed 06/14/2022) in view of Horlitz et al (CN 103930546 A; Machine English Translation, pages 1-42) and further in view of Skog et al (WO 2016/007755 A1; cited in IDS filed 06/14/2022) has been rendered moot by cancelation.
7. The rejection of Claims 38, and 41-42, provisionally rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 35-39, 43-47, 52-70 of copending Application No. 17/785,478 (‘478) in view of Stoll et al (WO 2017/197399 A1; cited in IDS filed 06/14/2022; of record) and further in view of Horlitz et al (CN 103930546 A; Machine English Translation, pages 1-42; of record) and Skog et al (WO 2016/007755 A1; cited in IDS filed 06/14/2022; of record) has been rendered moot by cancelation.
Claims 35-37 and 43-71 are pending in the case. Claims 66-71 have been withdrawn from consideration. Claims 35-37 and 43-65 are under prosecution.
The following rejections are necessitated by Applicant's amendment filed 28 April 2026 wherein the limitations in pending claims 35, 43, 46, 52, and 63 have been amended. Support for the amendment is seen at page 2, line 4, page 9, lines 22-23, page 13, lines 44-45, and page 19, lines 40-41.
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.
Claim(s) 35-37 and 43-65 are rejected under 35 U.S.C. 103 as being unpatentable over Stoll et al (WO 2017/197399 A1; cited in IDS filed 06/14/2022; of record) in view of Horlitz et al (CN 103930546 A; Machine English Translation, pages 1-42; of record) and further in view of Skog et al (WO 2016/007755 A1; cited in IDS filed 06/14/2022; of record).
Stoll teaches a method for enriching extracellular nucleic acids from a sample comprising extracellular vesicles (Abstract; paras 003-005). The method comprises the steps of (a) providing a biological sample (b) contacting the biological sample with a capture surface to retain cell-free DNA and RNA and microvesicles from the sample on or in the capture surface (c) contacting the surface with an elution buffer to release the DNA/RNA to produce a homogenate and extracting the DNA or RNA from the homogenate. The solid capture surface is a bead. The solid surface is functionalized with quaternary amines and tertiary amines. The capture surface can be positively charged and is an anion exchanger. The pH during microvesicle capture is ≤ 7 (paragraphs 7-9, 76, 134 and 134; part of the limitations of claim 35 regarding binding vesicles to anion exchange phase; limitation of claim 36 regarding nucleic acid being RNA; limitation of claim 37; limitation of claim 52-53, claim 57, part (iii) and (v); claim 58, part (v)). In view of this teaching one of ordinary skill in the art can select anion exchange solid phase particles for capturing and prepare the binding mixture in an acidic form as in claim 35, part (aa). The elution buffer contains a detergent like Tween, Triton X-100, etc., which can disrupt the microvesicles and aid the elution of the nucleic acids from the capture surface. The elution buffer also allows for efficient lysis of the microvesicles for release and elution of the nucleic acids (para 69 and 79; step cc in claim 35; step ff in claim 37; limitation of claim 43). This means that the lysis can be done non-chaotropically to release the nucleic acids from the microvesicles as in claim 35 step (cc). This also satisfies conditions (iv) and (vi) in claim 43. According to Stoll its method provides for the isolation of RNA from microvesicles from a sample by capturing the DNA and/or DNA and RNA to a surface, subsequently lysing the microvesicles to release the nucleic acids contained therein and eluting the nucleic acids contained therein from the capture surface (para 0062). Stoll also teaches that the method may also utilize a nucleic acid-binding column to capture the nucleic acids contained within the microvesicles. Once bound the nucleic acids can be eluted using a buffer or a solution suitable to disrupt the interaction between the nucleic acids and the binding column, thereby successfully eluting the nucleic acids (para 00168). These teachings of Stoll tell one of ordinary skill in the art that the microvesicles, when bound to a surface, can be lysed and the released nucleic acids can also be bound to the same surface and then eluted as in claim 35. In view of this one of ordinary skill in the art, wanting to enrich extracellular vesicular nucleic acids from a sample comprising extracellular vesicles, will find it obvious to carry out steps (bb) and (dd) as in claim 35. Separating the anion exchange solid phase as in claim 35, step (bb), and from the lysate as in step (dd) would eliminate the unwanted acidic binding mixture after step (aa), and other unwanted impurities from the lysate after step (cc) when elution of the nucleic acid is performed subsequently for enrichment. Even though steps (bb) and (dd) in claim 35 are not expressly taught, the artisan would perform these steps for the reason stated above.
The biological sample can be a plasma, serum or urine sample (para 36, 119; page 41, claim 15 of Stoll; as in claim 62). According to Stoll the method can be used to isolate both DNA and RNA from biofluids (paras 107, 115-116). This means that cells from the body fluid can be removed and the cell-depleted body fluid can be provided as a sample as in claim 63, and the biological sample can be subjected to DNA depletion as in claim 64 if the target product is the nucleic acid. According to Stoll the solid surface can be magnetic (para 009; as in claim 51).
Since the teachings of Stoll tell one of ordinary skill in the art that the microvesicles, when bound to a surface, can be lysed and the released nucleic acids can also be bound to the same surface and then eluted as in claim 35, the anion exchange particles should comprise bound extracellular RNA as in claim 46 since the method is for enriching both DNA and RNA. Stoll teaches the pH for binding and acidifying agents that can be used (paras 72-74). In view of this one of ordinary skill in the art can adjust the pH to be lower as in claims 49-50. According to Stoll its method is for isolation of extracellular vesicles and cell free nuclei acids (para 006). Therefore, in view of this one of ordinary skill in the art can carry out the steps in claim 65 to obtain a sample comprising extracellular vesicles.
Even though Stoll teaches that the pH during microvesicle capture is ≤ 7 it does not expressly teach preparing an acidic binding mixture comprising the sample and the anion exchange solid phase as in step aa in claim 35, and does the limitations of claims 44-48, 54-56, 59-61.
Horlitz teaches a method of isolating extracellular nucleic acids from body fluids, which can be blood, plasma, serum or urine, comprising the steps (a) the extracellular nucleic acid is bound to a solid phase in the binding mixture at pH <6 which is acidic (b) separating solid phase with the bound nucleic acid (c) optionally washing the nucleic acid (c) eluting nucleic acid from solid phase and separating nucleic acid from eluent (paras 22-27, 69, 150-156; acidic binding mixture as in claim 35 aa). This combined teaching of Stoll and Horlitz provide the steps that can be used to enrich extracellular nucleic acid as in claim 35.
Horlitz teaches that anion exchange groups can be monoamines, diamines, polyamines and nitrogen containing aromatic or aliphatic heterocyclic groups including X-(CH2)n-Y wherein X=Y=NH2 and n can be 0-20 (paras 125-131). In view of this the artisan would use the anion exchange groups as in claims 54-56 and 59-60 in the method, and would also use anion exchange groups having the number of ionizable groups per anion exchange groups as in claim 58. Horlitz also teaches the use of magnetic particles for the solid phase (para 122). According to Horlitz its method can be performed by using an automated system which can simultaneously process a plurality of samples and avoids operation error (para 67). In view of this teaching the artisan would find it obvious to use magnetic anion exchange particles and perform one or more steps using an automated system as in claim 61.
Skog, drawn to a method of enriching extracellular nucleic acids using charged anionic surfaces, teaches the use of anionic detergents like SDS and a buffering agent. The pH is set to 5.5 ≤ (paras 152-153; as in claims 47-48). Proteinase K can be added (para 221; as in claims 44-45).
MPEP 2141 states, "The key to supporting any rejection under 35 U.S.C. 103 is the clear articulation of the reason(s) why the claimed invention would have been obvious. The Supreme Court in KSR noted that the analysis supporting a rejection under 35 U.S.C. 103 should be made explicit. The Court quoting In re Kahn, 441 F.3d 977, 988, 78 USPQ2d 1329, 1336 (Fed. Cir. 2006), stated that "[R]ejections on obviousness cannot be sustained by mere conclusatory statements; instead, there must be some articulated reasoning with some rational underpinning to support the legal conclusion of obviousness.'" KSR, 550 U.S. at, 82 USPQ2d at 1396. Exemplary rationales that may support a conclusion of obviousness include: (A) Combining prior art elements according to known methods to yield predictable results; (B) Simple substitution of one known element for another to obtain predictable results; (C) Use of known technique to improve similar devices (methods, or products) in the same way; (D) Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results; (E) " Obvious to try " choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success; (F) Known work in one field of endeavor may prompt variations of it for use in either the same field or a different one based on design incentives or other market forces if the variations are predictable to one of ordinary skill in the art; (G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention."
According to the rationale discussed in KSR above, the rationale in (G) above is seen to be applicable here since based on the prior art teachings, the method steps including the anion exchange solid phase are known in the art for enriching extracellular nucleic acids from a sample comprising extracellular vehicles. Thus, it is obvious to combine prior art elements and arrive at the claimed method.
Thus, the claimed invention as a whole would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention over the combined teachings of the prior art. The artisan would be motivated to use the claimed method (also taught by the combined teachings of the prior art) since it is preferable to use method steps already known in the art to be used for enriching extracellular nucleic acids. According to the prior art, the method is simple and rapid for separating extracellular nucleic acid. It can be automated and allows for processing large volume samples also (Horlitz-para 0013). The method also provides for improved isolation of extracellular vesicles and co-isolation of cell-free nuclei acids (Stoll-para 0006). These teachings provide additional motivation for the artisan to use the claimed method.
Response to Applicant’s Remarks
Applicant has traversed the rejection of claims 35-37 and 43-65 as it now applies arguing that:
The present method is less laborious than the one disclosed in Stoll. This is achieved by choosing non-chaotropic conditions to lyse the EVs that are bound to the anion matrix. In contrast, Stoll requires lysis of the bound microvesicles with a chaotropic GTC-based elution buffer. This contradicts the conditions set forth in step (cc) of the method in claim 35. As the DNA as well as the nucleic acid released from the microvesicle are eluted from the capture surface under lysing conditions according to the inventions of Stoll, it is explicitly not desired and not realized in Stoll to bind the released vesicular nucleic acid to the same matrix to which the microvesicles were bound before.
Stoll only teaches lysing the microvesicles to release the nucleic acids. Nowhere does it teach or suggest regarding claimed rebinding of the released nucleic acid to the same anion exchange solid phase that was used for binding the extracellular vesicles. While GTC is commonly used to bind nucleic acids to silica matrix, the chaotropic lysis conditions described in Stoll are not suitable to bind the nucleic acids that are released from the vesicles to the anion exchange matrix. This is confirmed by the teachings of Stoll at page 12, para 0078.
Stoll’s method requires the use of a separate solid phase such as silica membrane as disclosed at para 0078, but not the same solid phase that bound the microvesicles before as presently claimed. In Stoll for binding EVs the capture surface has anion exchange properties, while for further purification of the vesicular nucleic acids released from EVs a silica material may be used.
Horlitz describes the binding of extra cellular nucleic acids to a solid phase it is silent regarding the presence and the binding of vesicular nucleic acid to a solid matrix. Horlitz does not explicitly disclose extracellular nucleic acids as encompassing vesicular nucleic acids nor does it even distinguish between vesicular and non-vesicular extracellular nuclei acids t be isolated. Without hindsight, a skilled person would not be motivated to consider the teachings of Horlitz.
Skog only teaches lysing the microvesicles to release the nucleic acids, particularly RNA contained therein. Skog does not teach or suggest regarding claimed rebinding of the released nucleic acids to the same anion exchange solid phase. Skog also teaches that the agent used for on-membrane lysis may be a guanidinium-based reagent, which is a chaotropic salt that may interfere with the binding of the released vesicular RNA to the anion exchange particles.
For the above reasons the instant claims are not rendered obvious (Remarks-pages 13-17).
Applicant’s arguments have been considered but are not found to be persuasive.
As set forth in the rejection Stoll teaches a method for enriching extracellular nucleic acids from a sample comprising extracellular vesicles. The method comprises the steps of (a) providing a biological sample (b) contacting the biological sample with a capture surface to retain cell-free DNA and RNA and microvesicles from the sample on or in the capture surface (c) contacting the surface with an elution buffer to release the DNA/RNA to produce a homogenate and extracting the DNA or RNA from the homogenate. The solid capture surface is a bead. The solid surface is functionalized with quaternary amines and tertiary amines. The capture surface can be positively charged and is an anion exchanger.
Stoll teaches that the elution buffer contains a detergent like Tween, Triton X-100, etc., which can disrupt the microvesicles and aid the elution of the nucleic acids from the capture surface. The elution buffer also allows for efficient lysis of the microvesicles for release and elution of the nucleic acids (para 69 and 79). This means that the lysis can be done non-chaotropically to release the nucleic acids from the microvesicles as in claim 35 step (cc). After the nucleic acids are released, they should immediately bind to the same anion exchange solid phase to which the vesicles were bound, and the nucleic acid can then be eluted. Since Stoll suggests using lysing agents that are not chaotropic there should be not problem for the released nucleic acids to bind to the same solid surface. In Stoll it is just an embodiment for binding EVs the capture surface has anion exchange properties, while for further purification of the vesicular nucleic acids released from EVs a silica material may be used. But, as explained above, from the teachings of Stoll there is a suggestion that the lysis can be done using agents that are not chaotropic, which should not cause any problems binding the released nucleic acids to the same anion exchange solid phase unlike GTC. GTC is also one of the lysis agents that can be used in Stoll’s method but it is not the only agent that can be used.
Horlitz is drawn to isolating extracellular nucleic acids from body fluids, which can be blood, plasma, serum or urine, comprising the steps (a) the extracellular nucleic acid is bound to a solid phase in the binding mixture at pH <6 which is acidic (b) separating solid phase with the bound nucleic acid (c) optionally washing the nucleic acid (d) eluting nucleic acid from solid phase and separating nucleic acid from eluent. This combined teaching of Stoll and Horlitz provide the steps that can be used to enrich extracellular nucleic acid as in claim 35.
Horlitz may be silent regarding the presence and the binding of vesicular nucleic acid to a solid matrix. But it teaches using the same solid phase for isolating extra cellular nucleic acids. Since Stoll teaches the presence and the binding of vesicular nucleic acid to a solid matrix, it need not necessarily teach the same. One of ordinary skill in the art will recognize that the teachings of Horlitz can be extended to the method of Stoll.
Skog also need not teach or suggest regarding claimed rebinding of the released nucleic acids to the same anion exchange solid phase. Skog teaches that the agent used for on-membrane lysis may be a guanidinium-based reagent, which is a chaotropic salt that may interfere with the binding of the released vesicular RNA to the anion exchange particles. However, Stoll, as explained above, suggests the use of non-chaotropic lysing agents which can lyse the bound vesicles to release the nucleic acids, which should bind to the same anion exchange solid phase without any interference from the lysing agent. The released nucleic acids which are bound to the same solid phase can then be eluted. Skog, which is drawn to a method of enriching extracellular nucleic acids using charged anionic surfaces, is cited for teaching the use of anionic detergents like SDS and a buffering agent, pH being is set to 5.5 ≤, and the use of Proteinase K. This teaching is relevant to the method of Stoll and can be used in the method of Stoll by the artisan with a reasonable expectation of success.
Therefore, the combined teachings of the cited prior art do render the instant claims obvious. The rejection is maintained.
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 obviousness-type 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); and 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 a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
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Claims 35-37, 43-45, 47-62 and 64-65 are provisionally rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 35-39, 43-47, 52-70 of copending Application No. 17/785,478 (‘478) in view of Stoll et al (WO 2017/197399 A1; cited in IDS filed 06/14/2022; of record) and further in view of Horlitz et al (CN 103930546 A; Machine English Translation, pages 1-42; of record) and Skog et al (WO 2016/007755 A1; cited in IDS filed 06/14/2022; of record). Although the claims at issue are not identical, they are not patentably distinct from each other because:
Instant claim 35 is drawn to a method of enriching extracellular nucleic acids from a sample comprising extracellular vesicles comprising preparing an acidic binding mixture comprising the sample and anion exchange solid phase, separating the solid phase comprising the bound extracellular vesicles, lysing the vesicles in the presence of at least one detergent to release nucleic acids, and separating anion exchange solid phase with the bound nucleic acids. Dependent claims 36-37, 43-45, 47-62 and 64-65 recite limitations drawn to nucleic acid being extracellular RNA, further steps of washing and eluting nucleic acids, use of detergent and buffering agent, pH of acidic lysis reagent, characteristics of lysis reagent, use of protease, proteinase K, characteristics of the acidic reagent, magnetic anion exchange particles, pH difference of binding mixture and ionized anion exchange group, characteristics of anion exchange particles and exchange groups, types of amino groups, number of ionizable groups, polymeric and polyallylamine groups, characteristics of the sample, , removal of cells from body fluid sample.
Copending claim 35 of ‘478 is drawn to a method of enriching extracellular DNA from a biological sample comprising the said DNA and extracellular vesicles by preparing a binding mixture comprising the biological sample, a solid phase comprising anion exchange groups and an acidic binding buffer and binding the extracellular DNA to the solid phase and separating the solid phase from the binding mixture wherein the remaining binding mixture comprises extracellular vesicles. The dependent claims recite limitations that overlap with those of the instant claims.
The copending claims of ‘478 differ from the instant claims in that the instant claims are drawn to method which includes extracellular nucleic acids which includes all types of nuclei acids whereas ‘478 is drawn to enriching extracellular DNA.
The teachings of the secondary references are set forth above.
It would have been obvious to one of ordinary skill in the art at the time of filing of the instant invention to arrive at the claimed method in view of the combined teachings of the cited prior art, since the secondary references teach that DNA, RNA and extracellular vesicles can be enriched using the claimed steps and also provide motivation for using the same.
This is a provisional obviousness-type double patenting rejection because the conflicting claims have not in fact been patented.
Response to Applicant’s Remarks
Applicant has traversed the double patenting rejection arguing that the amendments to claim 35 herein should be deemed sufficient to render the provisional nonstatutory double patenting rejection moot.
Applicant’s arguments are not found to be persuasive. Stoll teaches that its method is for co-isolation of extra cellular DNA, which is also cell free DNA and extracellular vesicles from a biological sample using the steps claimed, which are also seen in ‘478. From Stoll it is also seen that the lysis can be done in a non-chaotropic manner. Therefore, one of ordinary skill in the art will find it obvious to arrive at the claimed method in view of ‘478 and the secondary references with a reasonable expectation of success. The amendment to claim 35 is not seen to be sufficient to render the rejection moot. The rejection is maintained.
Conclusion
1. Elected claims 35-37 and 43-65 (Group I) are rejected.
2. Group II, claims 66-71 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a non-elected invention, there being no allowable generic or linking claim.
3. Claims 38-42 have been canceled.
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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/GANAPATHY KRISHNAN/Primary Examiner, Art Unit 1693
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