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 .
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.
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Claims 3, 14, 25, 29, 32-43, 48-60, 63-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 11,306,355. Although the claims at issue are not identical, they are not patentably distinct from each other because they both claim:
A method comprising the steps of:
Providing a nucleic acid sample comprising one or more 5caC or 5fC residues and contacting the sample with a borane reducing agent under conditions that reduce 5caC and/or 5fC to DHU, further comprising a sequencing step where the sequencing step distinguishes modified and unmodified cytosine in the nucleic acid sample. They claim that the nucleic acid sample is oxidized by a TET enzyme, to produce 5caC and/or 5fC residues.
They both claim wherein the borane reducing agent is 2-picoline borane.
Claims 3, 14, 25, 29, 32-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No.12,071,660; over claims 1-18 of U.S. Patent No.11,987,843; over claims 1-17 of U.S. Patent No.11,959,136. Although the claims at issue are not identical, they are not patentably distinct from each other because they both claim:
A method comprising the steps of:
Providing a nucleic acid sample comprising one or more 5caC or 5fC residues and contacting the sample with a borane reducing agent under conditions that reduce 5caC and/or 5fC to DHU, further comprising a sequencing step where the sequencing step distinguishes modified and unmodified cytosine in the nucleic acid sample. They claim that the nucleic acid sample is oxidized by a chemical oxidizing agent or TET enzyme, to produce 5caC and/or 5fC residues.
They both claim wherein the borane reducing agent is 2-picoline borane.
They both claim the method further comprises a step of blocking one or more modified cytosines and comprise a 5hmC.
Claims 3, 14, 25, 32-64 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-8 of U.S. Patent No.12,601,006. Although the claims at issue are not identical, they are not patentably distinct from each other because they both claim:
A method comprising the steps of:
Providing a nucleic acid sample and contacting the sample with a borane reducing agent under conditions that reduce 5caC and/or 5fC to DHU. They claim that the nucleic acid sample is oxidized by a TET enzyme, to produce 5caC and/or 5fC residues.
They both claim wherein the borane reducing agent is 2-picoline borane.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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 32-47 is/are rejected under 35 U.S.C. 103 as being unpatentable over He US 20140322707 in view of Schuler et al. "Sequencing the Sixth Base (5-ydroxymethylcytosine): Selective DNA Oxidation Enables Base-Pair Resolution," Angewandte Chemie International Edition, 22 October 2012 (22.10.2012), Vol. 51, No. 43, Pgs. 10704-1070 (hereinafter Schuler) in view of New England Biolabs, Inc. US 20140127678 (hereinafter New England Biolabs).
He discloses a method for identifying 5mC or 5hmC in a target nucleic acid (Para. [0002], methods and compositions for modifying 5-methylcytosine (5mC) and/or 5-hydroxymethylcytosine (5hmC) and subsequently detecting, evaluating, sequencing, and/or mapping 5-methylmodified as well as 5-hydroxymethyl-modified cytosine bases within a nucleic acid molecule), comprising the steps of: a. modifying a target DNA comprising the steps of: i. contacting the target DNA with an oxidizing agent to convert 5mC and/or 5hmC in the target DNA to 5-carboxylcytosine (5caC) and/or 5fC (Para. [0128], Oxidizing 5mC to 5caC. Oxidation of 5mC to 5caC can be accomplished by contacting the modified nucleic acid of step 1 with a methylcytosine dioxygenases (e.g., TET1, TET2 and TET3); [0133], It is known that 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins. Recently, it has been discovered that in addition to 5hmC, the Tet proteins can convert 5mC to 5-formylcytosine (5fC) and 5-carboxylcytosine 5caC) in an enzymatic activity-dependent manner); and ii. converting the 5caC and/or 5fC to 5-carboxyuracil (5caU) to provide a modified nucleic acid sample comprising a modified target nucleic acid (Para. [0380], After blocking 5hmC, all 5mC is converted to 5caC by oxidation with excess of recombinant Tetl protein. Bisulfite treatment of the resulting DNA then converts all C and 5caC (derived from 5mC) to uracil or 5caU, respectively, while the original 5hmC bases remain protected as 5gmC); and c. detecting the sequence of the modified DNA; wherein a cytosine (C) to thymine (T) transition in the sequence of the modified target DNA compared to the target DNA provides the location of either a 5mC or 5hmC in the target DNA (Para. [0039], Methods and compositions involve detecting, characterizing, and/or distinguishing between methylcytosine after modifying the 5mC. Methods may involve identifying 5mC in the nucleic acids by comparing modified nucleic acids with unmodified nucleic acids or to nucleic acids whose modification state is already known; [0083], In some embodiments, methods include performing traditional bisulfate sequencing, without protecting 5hmC so as to distinguish cytosine from methylcytosine. The results from traditional bisulfate sequencing (performed without the hmC labeling or protection prior to exposure to a methyldioxygenase) may be compared to the results of methods discussed herein that distinguish 5hmC from 5mC; [0242], which in a subsequent sequencing reaction base calling are identified as "T" instead of "C", when compared with a non bisulfite treated reference. Subsequent to bisulfite treatment, the sample is subjected to a conventional sequencing protocol).
He fails to explicitly disclose converting the 5caC and/or 5fC to dihydrouracil (DHU).
Schuler teaches 5caC or 5caU can be treated with reducing agents such as bisulfite to yield uracil or borane to yield dihydrouracil (Pg. 10706, Col. 1, Para. 5, it is extremely likely that bisulfite treatment of 5caC-containing DNA results in decarboxylation and deamination to give U, a reaction demonstrated by Isono on 5-carboxycytosine base as early as 1972, In 1984, Pal showed that treatment of 5-carboxyuracil (5) with borane provides 5,6-dihydrouracil (6) (Scheme 4a) Recently, Carell showed that similar chemistry occurs with 5-carboxycytosine derivatives).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify He with the teaching of Schuler for the purpose of converting a modified cytosine to a uracil as taught by Schuler (Pg. 10706, Col. 1, Para. 5, While not directly addressed in the He manuscript, it is extremely likely that bisulfite treatment of 5caC-containing DNA results in decarboxylation and deamination to give U).
New England Biolabs teaches conversion of 5caC and/or 5fC with reducing agents (Para. [0008], The method can optionally differentiate pre-existing 5-hmC in a nucleic acid from newly formed as a result of the reduction of 5-fC or 5-caC), such as borane pyridine complex, or 2-picoline borane complex (Para. [0050], Other reducing strategies include the use of borane pyridine complex, 2-picoline borane complex), which are preferred reducing agents as specified in the instant application (Para. [0207], (of the instant application), The reaction on a single 5caC nucleoside was repeated and confirmed that pyridine borane and pic-borane convert 5caC to dihydrouracil (DHU) (Figs. 3, 4B). Interestingly, pyridine borane and pic-borane was found to also convert 5fC to DHU through an apparent reductive decarboxylation/ deamination mechanism (Figs. 4C and 6). The detailed mechanism of both reactions remains to be defined. Quantitative analysis of the borane reaction on the DNA oligo by HPLC-MS/MS confirms that pic-borane converts 5caC and 5fC to DHU with around 98% efficiency and has no activity against unmethylated cytosine, 5mC or 5hmC). New England Biolabs teaches preparations useful for converting methylcytosine or an oxidized nucleotide, such as 5-fC or 5-caC, or to a glucosylated nucleotide. The preparations include a reducing agent, such as NaBH4, or an oxidizing agent, such as mYOX1, a TET enzyme, or an inorganic oxidizing agent such as KRuO4; a glycosyltransferase, …; a UDP-GlcN or a UDP derivative, such as UDP-Glc or UDP-azido-glucose (Summary of the invention).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify He with the teaching of New England Biolabs for the purpose of using a reducing agent for identifying methylated cytosine residues as taught by New England Biolabs (Para. [0008], The method can optionally differentiate pre-existing 5-hmC in a nucleic acid from newly formed as a result of the reduction of 5-fC or 5-caC).
Claim(s) 14, 25, 29, 48-64 is/are rejected under 35 U.S.C. 103 as being unpatentable over New England Biolabs, Inc. US 20140127678 (hereinafter New England Biolabs) in view of Schuler et al. "Sequencing the Sixth Base (5-ydroxymethylcytosine): Selective DNA Oxidation Enables Base-Pair Resolution," Angewandte Chemie International Edition, 22 October 2012 (22.10.2012), Vol. 51, No. 43, Pgs. 10704-1070 (hereinafter Schuler).
New England Biolabs discloses a method for identifying 5caC or 5fC in a target nucleic acid (Para. [0003], The present invention provides a variety of reagents, kits and methods for selectively altering and identifying modified nucleotides in a nucleic acid such as DNA. The modified nucleotides that can be identified include, for example, 5-mC, 5-hmC, 5-fC and 5-caC), comprising the steps of: a. contacting a target DNA with a reducing to convert 5caC and 5fC to 5hmC to provide a modified target DNA (Para. [0008], the methods include the subsequent step of reacting the nucleic acid with a reducing agent. The reducing agent promotes the reduction of a nucleotide in a higher oxidation state, such as 5-fC or 5-caC, to a hydroxymethylated nucleotide); b. amplifying the copy number of the modified target DNA (Para. [0010], An adapter molecule can then be ligated to the cleaved end of the endonuclease reaction product, facilitating the subsequent purification, amplification or sequencing of the nucleic acid); and c. detecting the sequence of the modified target DNA (Para. [0030], It is expected that the use of endonucleases with preferential specificity for a specific modified nucleotide over other modified and unmodified nucleotides can be detected using the method described herein for 5-mC, 5-hmC, 5-fC, and 5-caC. In combination with the cofactor UDP-Gk, this system enables sequencing different epigenetic states of 5-mC and greatly enhances the ability to determine the epigenetic modification at a single base resolution level).
New England Biolabs further discloses reducing agents capable of converting the 5caC and 5fC to dihydrouracil (DHU) (Para. [0008], The method can optionally differentiate pre-existing 5-hmC in a nucleic acid from newly formed as a result of the reduction of 5-fC or 5-caC; [0050], Other reducing strategies include the use of borane borane pyridine complex, 2-picoline borane complex), according to the specification of the instant application (Para. [0207], (of the instant application), The reaction on a single 5caC nucleoside was repeated and confirmed that pyridine borane and pic-borane convert 5caC to dihydrouracil (DHU) (Figs. 3, 4B). Interestingly, pyridine borane and pic-borane was found to also convert 5fC to DHU through an apparent reductive decarboxylation/ deamination mechanism (Figs. 4C and 6)).
With regards to claim 25, New England Biolabs discloses performing a PCR or primer extension (Para. [0010], An adapter molecule can then be ligated to the cleaved end of the endonuclease reaction product, facilitating the subsequent purification, amplification or sequencing of the nucleic acid).
With regards to claim 29, New England Biolabs discloses detecting the sequence of the modified target DNA comprises sequencing (Para. [0030], It is expected that the use of endonucleases with preferential specificity for a specific modified nucleotide over other modified and unmodified nucleotides can be detected using the method described herein for 5-mC, 5-hmC, 5-fC, and 5-caC. In combination with the cofactor UDP-Gk, this system enables sequencing different epigenetic states of 5-mC and greatly enhances the ability to determine the epigenetic modification at a single base resolution level).
With regards to claims 52 and 55-64, New England Biolabs teaches preparations useful for converting methylcytosine or an oxidized nucleotide, such as 5-fC or 5-caC, or to a glucosylated nucleotide. The preparations include a reducing agent, such as NaBH4, or an oxidizing agent, such as mYOX1, a TET enzyme, or an inorganic oxidizing agent such as KRuO4; a glycosyltransferase, …; a UDP-GlcN or a UDP derivative, such as UDP-Glc or UDP-azido-glucose (Summary of the invention). New England Biolabs discloses “The 5-mC may be chemically or enzymatically converted to 5-hmC by reacting the 5-mC with mYOX1, TET enzymes or chemical oxidizing agents. Similarly, oxidation of 5-mC to 5-hmC to 5-fc to 5-CaC can be achieved by chemical or enzymatic oxidation using mYOX1 or TET. Specific chemical oxidation of 5-hmC to 5-fC in synthetic nucleotide oligomer single strand (ssDNA) containing 5-hmC can be achieved with potassium perruthenate, KRuO4. KRuO4 can oxidize 5-hmC in double-stranded DNA (dsDNA), with an initial denaturing step before the addition of the oxidant, resulting in quantitative conversion of 5-hmC to 5-fC. Other oxidants known in art, such as Osmium (VIII)-based oxidants, Cerium (IV)-based oxidants, and Chromium (VI)-based oxidants may be used for the oxidation of 5-hmC to 5-fC. ([0033])
New England Biolabs fails to explicitly disclose converting the 5caC and 5fC to dihydrouracil (DHU); wherein a cytosine (C) to thymine (T) transition in the sequence of the modified target DNA compared to the target DNA provides the location of either a 5caC or 5fC in the target nucleic acid.
Schuler teaches 5caC or 5caU can be treated with reducing agents such as bisulfite to yield uracil or borane to yield dihydrouracil (Pg. 10706, Col. 1, Para. 5, it is extremely likely that bisulfite treatment of 5caC-containing DNA results in decarboxylation and deamination to give U, a reaction demonstrated by Isono on 5-carboxycytosine base as early as 1972 In 1984, Pal showed that treatment of 5-carboxyuracil (5) with borane provides 5,6-dihydrouracil (6) (Scheme 4a) Recently, Carell showed that similar chemistry occurs with 5-carboxycytosine derivatives). Schuler further teaches wherein a cytosine (C) to thymine (T) transition in the sequence of the modified target DNA compared to the target DNA provides the location of either a 5caC or 5fC in the target nucleic acid (Pg. 10704, Col. 1, The bisulfite-mediated deamination of cytosines to uridines has played a crucial role in understanding DNA methylation It was subsequently discovered that deamination of 5mC to thymidine (T), via 3 and 4, is nearly two orders of magnitude slower than for C. This rate difference is taken advantage of in what is known as bisulfite sequencing (BS-Seq) Comparison of normal and bisulfite sequencing data reveals the location of 5mC in DNA; Pg. 10705, Col. 1, Para. 2, the DNA is treated with excess Tet1 to oxidize 5mC loci to 5caC. Subsequent bisulfite treatment converts all C and presumably all 5caC bases (vide infra) to U while the 5gmC bases remain unaffected. After amplification (5gmC amplifies to C) and sequencing, the positions that are read as C indicate where a 5hmC resides. Comparison of this data to the results of a standard BS-Seq run then reveals the positions of 5mC residues; Pg. 10706, Col. 1, Para. 5, it is extremely likely that bisulfite treatment of 5caC-containing DNA results in decarboxylation and deamination to give U).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify New England Biolabs with the teaching of Schuler for the purpose of converting a modified cytosine to a uracil as taught by Schuler (Pg. 10706, Col. 1, Para. 5, While not directly addressed in the He manuscript, it is extremely likely that bisulfite treatment of 5caC-containing DNA results in decarboxylation and deamination to give U).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEZIA RILEY whose telephone number is (571)272-0786. The examiner can normally be reached 7:30-6:00pm.
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/JEZIA RILEY/ Primary Examiner, Art Unit 1681 19 September 2026
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