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 .
CONTINUING DATA
This application has PRO 63/586,737 09/29/2023
This application has PRO 63/517,951 08/07/2023
This application has PRO 63/505,307 05/31/2023
Claims 1-20 are pending.
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 14 and 20 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.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 14 recites the broad recitation “greater than 20%” and the claim also recites “(e.g., 50% or more)” which is the narrower statement of the range/limitation. In the present instance, claim 20 recites the broad recitation “between about 8 and about 11” and the claim also recites “(e.g., between about 8 and about 10)” which is the narrower statement of the range/limitation.
The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-2, 4-5, 7-11, 16-17, and 19 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Donegan (US 2022/0017887 A1, January 20, 2022, cited on IDS).
Donegan teaches the use of Oasis porous DEA particles having a particle size of 20 µm for isolating oligonucleotides from matrix components. See abstract. More broadly, sorbents to be used comprise ionizable surface groups having a pKa of 8-12 [0006] or 8 to 11 [0032]. The elution solution has a pH 10-13 [0018]. The elution solution comprises TEA, water, and methanol [0020]. The sample can comprise blood, plasma, serum, oral fluids, cerebrospinal fluids, fecal samples, nasal samples, urine, liver, kidney, and brain tissue, tissue homogenates, cells, or cell culture supernatants [0021]. The sample is treated with a protease such as proteinase K or guanidine or a mass-spectroscopy-compatible surfactant [0022]. Note that the proteinase K is mentioned separately from the surfactant (suggesting a detergent-free embodiment). Sorbent, denaturant solution, and elution solution are comprised in a kit [0023]. The particle size of the sorbent is 5-100 µm [0060]. The oligonucleotide can be RNA or plasmid (double stranded) [0069] and the oligonucleotides have a size from 25 mer to 200 mer [0016]. The method comprises loading a sample comprising an oligonucleotide and a matrix component onto a porous anion exchange sorbent, whereby the oligonucleotide is retained by the sorbent; flowing at least one washing solution through the sorbent to remove matrix components while leaving the oligonucleotide retained on the sorbent; and flowing an elution solution through the sorbent to release the oligonucleotide [0068]. The washing solution comprises a percentage of methanol [0073]. The elution solvent has a pH of 10-12 [0074] and contains organic solvents [0077]. Before solid phase extraction is performed, the sample is treated with proteinase K or guanidine [0080].
In Example 7 [0088], the sorbent used was the Oasis-based anion exchanger having diethylamino functional groups or BEH 130 and BEH 300 and the samples were 25mer or 50mer [0088]. The BEH 130 and BEH 300 were functionalized with DEAP and were 10 µm in size. See Brief Description of the Drawings.
In one example, the washing solution was 50 mM ammonium acetate followed by 20:80 methanol: ammonium acetate (pH 5.5). The elution solutions were 50:50 MP (formed from 50% methanol, TEA, and HFIP) and TEA. Samples were analyzed by LC/MS [0094].
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.
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) 3 and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Donegan (US 2022/0017887 A1, January 20, 2022, cited on IDS).
Donegan teaches as set forth above, that the protease is proteinase K or guanidine. Donegan does not teach that the protease solution comprises proteinase K and guanidine.
It would have been obvious to one of ordinary skill in the art at the time the application was filed to carry out Donegan’s process wherein the protease solution contained both proteinase K and guanidine because Donegan teaches that each may be used for the same purpose. MPEP 2144.06 states "It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from their having been individually taught in the prior art."
Claim(s) 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Donegan (US 2022/0017887 A1, January 20, 2022, cited on IDS).
Donegan teaches as set forth above, but does not teach diluting the eluate with water.
It would have been obvious to one of ordinary skill in the art at the time the application was filed to dilute the eluate sample with water. The skilled artisan would have diluted the eluate with water as recited in claim 18 in order to facilitate handling and detection methods.
Claim(s) 6 is/are rejected under 35 U.S.C. 103 as being unpatentable over Donegan (US 2022/0017887 A1, January 20, 2022, cited on IDS) in view of Weng (Analytical and Bioanalytical Chemistry (2019) 411:4167-4173).
Donegan teaches as set forth above, but does not teach that the eluate is injected into an ion pairing reversed phase separation.
Weng teaches that oligonucleotides are usually analyzed by ion-pair reversed-phase liquid chromatography. See abstract. The sample was injected after elution with no mention of an evaporation step. Page 4169, first paragraph.
It would have been obvious to one of ordinary skill in the art at the time the application was filed to carry out Donegan’s process wherein the method further comprises IR-RPLC MS analysis because oligonucleotides are usually analyzed by ion-pair reversed-phase liquid chromatography.
Claim(s) 12-15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Donegan (US 2022/0017887 A1, January 20, 2022, cited on IDS) in view of Rundlett (Anal. Chem. 1996, 68, 3493-3497) and KR 100386325 B1 (2003, machine translation).
Donegan teaches that the sample can be homogenized tissue as set forth above, but does not teach that the homogenization step is surfactant free. Donegan also teaches that the sample is treated with a protease.
Rundlett teaches that surfactants interfere with electrospray ionization mass spectrometric detection of analytes, and can completely quench signals. See abstract. Rundlett also suggests adding solvents such as short-chain alcohols. Page 3497, second column.
KR 100386325 B1 teaches that brain tissue can be homogenized in the absence of surfactant. See claim 1.
It would have been obvious to one of ordinary skill in the art at the time the application was filed to prepare Donegan’s homogenized tissue sample in the absence of surfactant because surfactant can interfere with detection. Donegan also recognizes that certain surfactants are MS-compatible, suggesting that others are not compatible. The skilled artisan would have either used a MS-compatible surfactant as suggested by Donegan, or simply omitted the surfactant as taught by KR 100386325 B1 and implied by Donegan as discussed above, in order to avoid the problems caused by surfactant. It would have been obvious to carry out the homogenization at the same time as protease treatment or sequentially because reversing the order or prior art process steps is an example of supporting rationale for an obviousness rejection. See MPEP 2144.04. Selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results. The skilled artisan would have utilized solvent in the homogenization step in order to facilitate the homogenization and improve the excess surface concentration of charged molecules as taught by Rundlett. The skilled artisan would have optimized the amount of solvent using routine experimentation. The skilled artisan would have diluted the tissue homogenate with water before proteinase K treatment because enzymatic treatments are typically done in the presence of water.
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 1-3, 7-11, 17-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-7, 10-17, 19-23, 26, 28-29 of copending Application No. 17/375,325 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because reference claim 1 recites a method comprising extracting oligosaccharides by loading a sample comprising oligosaccharides and matrix components onto a porous anion exchange sorbent comprising a diethylaminopropyl surface group (pKa about 10), wherein the target oligonucleotides and matrix components are retained by the sorbent; flowing washing solutions through the sorbent to remove matrix components and leaving oligonucleotides retained on the sorbent; and flowing elution solutions through the sorbents to release oligonucleotides. Reference claim 1 does not include proteolytically digesting the sample as required by current claim 1, but reference claim 23 recites that the sample is treated with a denaturing agent such as proteinase K or guanidine, so it would have been obvious to one of ordinary skill in the art at the time the application was filed to include the denaturing step. Reference claim 16 recites that the washing solution comprises an organic solvent. Reference claim 17 recites that the elution solution has a pH 10-13. The elution solution comprises organic amine, etc. or TEA and methanol. Claims 19-20. The samples are whole blood or tissue homogenates, or liver tissues, etc. Claim 21.
It would have been obvious to one of ordinary skill in the art at the time the application was filed to carry out the reference process wherein the protease solution contained both proteinase K and guanidine because the reference application claims each for the same purpose. MPEP 2144.06 states "It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from their having been individually taught in the prior art."
The reference application does not teach diluting the eluate with water. It would have been obvious to one of ordinary skill in the art at the time the application was filed to dilute the eluate sample with water. The skilled artisan would have diluted the eluate with water as recited in claim 18 in order to facilitate handling and detection methods.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 4-5 and 16 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-7, 10-17, 19-23, 26, 28-29 of copending Application No. 17/375,325 (reference application) in view of Donegan.
The reference application claims as set forth above, but does not claim the particle size of the sorbent material and does not claim subjecting the eluate to an analysis as recited in current claim 4. The reference application does not claim the identity of the oligonucleotide.
Donegan teaches as set forth above.
It would have been obvious to one of ordinary skill in the art at the time the application was filed to carry out the reference application method using a sorbent having a particle size 5-100 µm because Donegan teaches a sorbent used for the same purpose which has a particle size in that range. It would have been obvious to one of ordinary skill in the art at the time the application was filed to carry out the reference application method further comprising subjecting the eluate to an analysis such as MS because Donegan teaches that analyzing the oligonucleotide eluent by MS can be done in order to detect the presence of the oligonucleotide in the eluent. It would have been obvious to carry out the reference application wherein the nucleotide is DNA or RNA because an analogous process taught by Donegan is one which is suitable for obtaining DNA or RNA.
This is a provisional nonstatutory double patenting rejection.
Claim 6 is are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-7, 10-17, 19-23, 26, 28-29 of copending Application No. 17/375,325 (reference application) in view of Weng (Analytical and Bioanalytical Chemistry (2019) 411:4167-4173).
The reference patent claims as set forth above, but does not claim that the eluate is injected into an ion pairing reversed phase separation.
Weng teaches that oligonucleotides are usually analyzed by ion-pair reversed-phase liquid chromatography. See abstract. The sample was injected after elution with no mention of an evaporation step. Page 4169, first paragraph.
It would have been obvious to one of ordinary skill in the art at the time the application was filed to carry out the reference application process wherein the method further comprises IR-RPLC MS analysis because oligonucleotides are usually analyzed by ion-pair reversed-phase liquid chromatography.
This is a provisional nonstatutory double patenting rejection.
Claims 12-15 is are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-7, 10-17, 19-23, 26, 28-29 of copending Application No. 17/375,325 (reference application) in view of Rundlett (Anal. Chem. 1996, 68, 3493-3497) and KR 100386325 B1 (2003, machine translation).
The reference application claims that the sample can be homogenized tissue as set forth above, but does not teach that the homogenization step is surfactant free. The reference application also claims that the sample is treated with a protease or a mass spectroscopy compatible surfactant (claim 23).
Rundlett teaches that surfactants interfere with electrospray ionization mass spectrometric detection of analytes, and can completely quench signals. See abstract. Rundlett also suggests adding solvents such as short-chain alcohols. Page 3497, second column.
KR 100386325 B1 teaches that brain tissue can be homogenized in the absence of surfactant. See claim 1.
It would have been obvious to one of ordinary skill in the art at the time the application was filed to prepare the reference application’s homogenized tissue sample in the absence of surfactant because surfactant can interfere with detection. The reference application also claims the use of surfactants which are MS-compatible, suggesting that others are not compatible. The skilled artisan would have either used a MS-compatible surfactant as suggested by claim 23 of the reference application, or simply omitted the surfactant as taught by KR 100386325 B1 and implied by the reference application because surfactant is listed separately from proteinase K, in order to avoid the problems caused by surfactant. It would have been obvious to carry out the homogenization at the same time as protease treatment or sequentially because reversing the order or prior art process steps is an example of supporting rationale for an obviousness rejection. See MPEP 2144.04. Selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results. The skilled artisan would have utilized solvent in the homogenization step in order to facilitate the homogenization and improve the excess surface concentration of a charged molecule as taught by Rundlett. The skilled artisan would have optimized the amount of solvent using routine experimentation. The skilled artisan would have diluted the tissue homogenate with water before protease treatment because enzymatic treatments are typically done in the presence of water.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
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/LAYLA D BERRY/ Primary Examiner, Art Unit 1693
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