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 .
Status of claims / Response to Amendment
This office action is in response to an amendment filed on July 13, 2026.
Claims 1, 5, 7-9, 16, 21, 24, 30-33, 37, 43, 50, 89-90 and 94-95 were previously pending. Applicant amended claims 1, 5 and 37; added new claims 100-101.
Claims 1, 5, 7-9, 16, 21, 24, 30-33, 37, 43, 50, 89-90, 94-95 and 100-101 are currently pending, with claims 7, 30-32 and 89-90 withdrawn.
Claims 1, 5, 8-9, 16, 21, 24, 33, 37, 43, 50, 94-95 and 100-101 are under examination.
All of the previously presented rejections have been withdrawn as either being addressed o obviated by the amendment of the claims, which introduces new combinations of elements that were not previously considered in the prior rejection (e.g., the amended claims 1 and 5 now both require a step that "chemically converts the first nucleobase or the second nucleobase into a converted nucleobase having altered base pairing specificity" which was not presented in prior claims and not considered in the prior office action).
Thus, the scope of the claims has been changed in a manner that were not considered in the previous rejections.
Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
This office action contains new grounds for rejection necessitated by amendment.
Priority -- Updated in view of Amendment
The priority date of the instant claims 1, 5, 8-9, 16, 21, 24, 33, 37, 43, 50, 94-95 and 100-101 is 11/30/2020, filling date of the US provisional application NO. 63/119,520.
Claim Objections -- New
Claims 1, 5 and 100-101 are objected to because of the following informalities:
In claim 1, part b), it should read "b) after subjecting the sample to [[a]]the procedure that affects [[a]]the first nucleobase in the DNA differently from [[a]]the second nucleobase in the DNA of the sample, " to properly reference the procedure recited in part a).
In claim 5, part b), it should read "b) after subjecting the sample to [[a]]the procedure that affects [[a]]the first nucleobase in the DNA differently from [[a]]the second nucleobase in the DNA of the sample, " to properly reference the procedure recited in part a).
In claim 100, lines 1-2, it should read "wherein the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample comprises bisulfite conversion…"
In claim 101, lines 1-2, it should read "wherein the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample comprises bisulfite conversion…"
Claim 101 is also objected to for not ending the claims with a period.
See MPEP 608.01(m) "Each claim begins with a capital letter and ends with a period."
Claim Interpretation -- Updated in view of Amendment
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, claims 1 and 5 recite "a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample."
The recited "procedure" is interpreted under BRI as encompassing one or more steps of affecting, treating, or processing the nucleobase -containing sample.
This interpretation is consistent with the specification and the claim language.
The specification describes Ox-BS conversion ([000163]) and TAB conversion ([0000164]) as different embodiments of the claimed procedure. Ox-BS comprises two conversion steps, and TAB conversion comprises three conversion steps.
Base claims 1 and 5 recite that the procedure chemically converts a nucleobase; dependent claims 100 and 101 further recite that the procedure comprises enzymatic conversion. Thus, the recited "procedure" is not limited to a single conversion step, but broadly encompasses one or more steps for affecting, treating, or processing the DNA sample, e.g., TAB conversion, which is a procedure that encompasses both a chemical conversion and an enzymatic conversion.
Claims 1 and 5 both recite "b) partitioning the sample into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified nucleobase in the DNA."
The specification defines the term “partitioning” as follows:
"As used herein, “partitioning” of nucleic acids, such as DNA molecules, means separating, fractionating, sorting, or enriching a sample or population of nucleic acids into a plurality of subsamples or subpopulations of nucleic acids based on one or more modifications or features that is in different proportions in each of the plurality of subsamples or subpopulations. Partitioning may include physically partitioning nucleic acid molecules based on the presence or absence of one or more methylated nucleobases. A sample or population may be partitioned into one or more partitioned subsamples or subpopulations based on a characteristic that is indicative of a genetic or epigenetic change or a disease state." ([000139])
Claim 5 recites "c) capturing at least an epigenetic target region set of DNA or a plurality of sets of target regions of DNA from the first and second subsamples."
The specification defines the term “capturing” as follows:
"Capturing” one or more target nucleic acids refers to preferentially isolating or separating the one or more target nucleic acids from non-target nucleic acids." ([00146])
Claims 1 and 5 both recite "the first nucleobase and the second nucleobase have the same base pairing specificity."
The specification defines the term “base pairing specificity” as follows:
"As used herein, “base pairing specificity” refers to the standard DNA base (A, C, G, or T) for which a given base most preferentially pairs. For example, unmodified cytosine and 5-methylcytosine have the same base pairing specificity (i.e., specificity for G) whereas uracil and cytosine have different base pairing specificity because uracil has base pairing specificity for A while cytosine has base pairing specificity for G. The ability of uracil to form a wobble pair with G is irrelevant because uracil nonetheless most preferentially pairs with A among the four standard DNA bases." ([000143])
For the purpose of applying prior art, claim 5 recites "epigenetic target region set," which is defined in the specification as follows:
"Epigenetic target region set” refers to a set of target regions that may show sequence-independent changes in neoplastic cells (e.g., tumor cells and cancer cells) relative to normal cells or that may show sequence-independent changes in cfDNA from subjects having cancer relative to cfDNA from healthy subjects. Examples of sequence-independent changes include, but are not limited to, changes in methylation (increases or decreases), nucleosome distribution, cfDNA fragmentation patterns, CCCTC-binding factor (“CTCF”) binding, transcription start sites, and regulatory protein binding regions. Epigenetic target region sets thus include, but are not limited to, hypermethylation variable target region sets, hypomethylation variable target region sets, and fragmentation variable target region sets, such as CTCF binding sites and transcription start sites. For present purposes, loci susceptible to neoplasia-, tumor-, or cancer-associated focal amplifications and/or gene fusions may also be included in an epigenetic target region set because detection of a change in copy number by sequencing or a fused sequence that maps to more than one locus in a reference genome tends to be more similar to detection of exemplary epigenetic changes discussed above than detection of nucleotide substitutions, insertions, or deletions, e.g., in that the focal amplifications and/or gene fusions can be detected at a relatively shallow depth of sequencing because their detection does not depend on the accuracy of base calls at one or a few individual positions. " ([000152])
Thus, because the term “epigenetic target region set” is defined as a set of target regions that "may show" sequence-independent changes in neoplastic cells (e.g., tumor cells and cancer cells) relative to normal cells or that "may show" sequence-independent changes in cfDNA from subjects having cancer relative to cfDNA from healthy subjects, it is understood that the scope of this term does not require these sequence-independent changes.
Under BRI, “epigenetic target region set” is interpreted to encompass any set of target regions within a genome or target DNA, such as methylated CpG islands.
Claim Rejections - 35 USC § 103 -- New Grounds
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.
Claims 1, 5, 8-9, 16, 21, 24, 33, 37, 43, 50 and 100-101 are rejected under 35 U.S.C. 103 as being unpatentable over Arensdorf (Arensdorf et al., US20200024643A1 - Methods for the epigenetic analysis of dna, particularly cell-free dna; Published 2020-01-23), in view of
Xia (Xia, B., Han, D., Lu, X. et al. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nat Methods 12, 1047–1050 (2015). doi.org/10.1038/nmeth.3569), as evidenced by Kennedy (Kennedy et al., WO2018119452A2 - Methods and systems for analyzing nucleic acid molecules; 2018-06-28; cited as Foreign patent document #2 in IDS filed on 01/22/2024).
A) Regarding claims 1 and 5, while they are separate independent method claims, they will be addressed together below as the claims' scopes largely overlap. Claim 5 is narrower in scope than claim 1 and further comprises a capturing step.
Regarding claims 1 and 5, Arensdorf teaches a method comprising:
subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample (Fig. 11, 17-18; [0128] βGT-catalyzed uridine diphosphoglucose 6-azide as described previously, followed by biotinylation of 5hmC),
wherein the first nucleobase is a modified nucleobase (Fig. 11, 17-18, 5hmC), the second nucleobase is an unmodified nucleobase (Fig. 11, unmodified C) different from the first nucleobase, and the first nucleobase and the second nucleobase have the same base pairing specificity; and
partitioning the sample into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified nucleobase in the DNA (Fig. 11; [0128] biotinylated strands and strands containing unmodified (native) 5mC are pulled down simultaneously for further processing), the plurality of subsamples comprising a first subsample (Fig. 11; [0128] subsample comprising 5mC and biotinylated 5hmC after pull down) and a second subsample (Fig. 11; [0128] pull down supernatant depleted of 5mC and biotinylated 5hmC) , wherein the first subsample comprises DNA with a cytosine modification in a greater proportion than the second subsample, and the modified nucleobase recognized by the agent is a modified cytosine (Fig. 11);
capturing at least an epigenetic target region set (Fig. 11; [0128] capture CpG sites in native 5mC-containing strands using methyl-CpG-binding domain (MBD) protein; [0148]; [0150] immunoprecipitation of nucleic acids associate with specific histones or nucleic acid cross-linking (e.g., CTCF) or binding proteins (such as transcription factors ) of DNA,
sequencing the captured DNA in a manner that distinguishes the first nucleobase from the second nucleobase (Fig. 11, 17-18; [0128] lines 24-28 ).
Arensdorf teaches methods for epigenetic analysis of cell-free DNA, specifically, simultaneously analyzing 5hmC and 5mC in a DNA sample. Arensdorf teaches applying a biotin label to 5hmC, while the unmodified C and 5mC are not labeled. This allows subsequent partitioning of 5hmC (using biotin-binding agent) and 5mC (using 5mC antibody) containing DNA by magnetic pull-down. The separated 5hmC and 5mC fractions can then be further distinguished using a modification-specific schemes so that the epigenetic modifications can be differentiated in downstream sequencing (Fig. 11; [0128]; [0008]).
Although Arensdorf does not explicitly teach chemically converting a nucleobase into a converted nucleobase having altered base pairing specificity, prior to a partitioning step, this feature is obvious in view of Xia.
Xia teaches methods for analyzing genomic 5-formylcytosine (5fC), which is a rare form of epigenetically modified cytosine (p. 1047, left-hand col, para 2, lines 1-3).
Xia teaches there is a need to for genome wide detection of 5fC, as 5fC, similar to 5hmC, may have functional roles in the biological process (p. 1047, left-hand col, para 1-2).
Xia teaches a method using chemical 1,3-indandione to specifically modify 5fC, so that the further modified 5fC is read as thymine (T) instead of cytosine (C) in PCR, due to altered base pairing specificity (Figure 1; p. 1047, right-hand col, lines 17-25).
Xia also teaches enriching for 5fC-containing DNA by converting 5fC to 5fC-AI using an azido derivative of 1,3-indandione (AI), a highly selective reaction for 5fC among all modified cytosines, the 5fC-AI are then labeled with biotin for 5fC-specific magnetic pulldown (Figure 1; p. 1047, right-hand col, para 2).
Accordingly, a person of ordinary skill in the art before the effective filing date of the claimed invention would have found it prima facie obvious to modify the method of Arensdorf to include the improved capability of detecting 5fC as taught by Xia. Specifically, after 5hmC and 5mC are separated from the DNA sample in Arensdorf, the remaining sample containing unmodified C and 5fC would be further treated according to Xia for 5fC enrichment and analysis. This modification includes chemically converting 5fC into 5fC-AI having altered base pairing specificity and further partitioning the sample to obtain an enriched 5fC fraction.
One of ordinary skill in the art would have had a reasonably expectation of success because the two references are in the same field of epigenetic analysis, specifically detection of oxidized derivatives of 5mC (e.g., 5hmC, 5fC) by sequencing. The references provide complementary teachings and use technically similar approaches: each specifically labels a cytosine modification to facilitate downstream enrichment and distinction between different modifications. Therefore, one of ordinary skill in the art, using ordinary creativity, would have readily understood that the remaining sample after 5hmC and 5mC pull-down in Arensdorf still contains 5fC and could be further subjected to 5fC enrichment and sequencing analysis as taught by Xia in order to study its functional roles.
B) Regarding claim 8, Arensdorf teaches the epigenetic target region set comprises a hypermethylation variable target region set by teaching CpG sites (Fig. 11; [0128] capture CpG sites in native 5mC-containing strands using methyl-CpG-binding domain (MBD) protein).
As evidenced by Kennedy, CpG sites captured by methyl-binding domain (MBD) protein comprises hypermethylation variable target region ([000211] “Identifying DNA molecules that are relatively "hypermethylated" in a DNA sample can be achieved by capturing molecules that bind to a methyl-binding domain (MBD) protein, or a fragment or variant thereof.”).
Regarding claim 9, Arensdorf teaches hypermethylation variable target region set comprises regions having a higher degree of methylation in at least one type of tissue than the degree of methylation in cell-free DNA from a healthy subject, by teaching CpG sites (Fig. 11; [0128] capture CpG sites using methyl-CpG-binding domain (MBD) protein).
As evidenced by Kennedy, capturing CpG sites using methyl-CpG-binding domain (MBD) protein captures regions having a higher degree of methylation in at least one type of tissue than the degree of methylation in cell-free DNA from a healthy subject ([000316]; [000317]-[00319]; see also [000237] “hypermethylation of a normally hypomethylated region, such as transcription start site (TSS) of genes involved in normal growth, DNA repair, cell cycle regulation and cell differentiation, may be indicative of cancer. ”; [00218])
For example, in para. [000316], Kennedy describes using methyl-CpG-binding domain (MBD) protein to capture and analyze regions of hypermethylation with higher methylation enrichment in lung cancer samples compared to healthy samples:
"[000316] MBD-partitioned samples were used to discern nucleosomal occupancy in healthy and cancer samples. In this example, blood samples from six lung cancer patients and three non- malignant healthy adults were obtained. Cell-free Nucleic acids from the samples were extracted and partitioned using MBD- affinity purification into hyper-and hypo-methylated partitions. The nucleic acid samples were sequenced using whole genome sequencing. The percentage hypermethylated fragments for each partition and for all the samples were determined. Fig. 16 shows MBD signal in hyper- and hypomethylated partitions from lung cancer patients (rows 1 and 2 from top) and from healthy adults (rows 3 and 4). As shown in Fig. 16, cell-free DNA fragments from lung cancer patients show enrichment of distal intragenic regions in hypermethylated partition (LungSigHyper) when compared with the hypermethylated partition from healthy individuals. In addition, the distribution of characteristics in top 5% highest percentage hypermethylated peaks (LungSigHyper) and hypomethylated peaks (LungSigHypo) shows significant enrichment of hypomethylated peaks in all exons besides of exon 1” (Fig. 16, rows 1 and 2)."
Regarding claim 16, Arensdorf teaches DNA is obtained from a test subject ([0118]).
Regarding claim 21, Arensdorf teaches DNA is amplified before sequencing (Fig. 12; [0140]).
Regarding claim 24, Arensdorf teaches partitioning on the basis of methylation level (Fig. 11).
Regarding claim 33, Arensdorf teaches wherein the plurality of subsamples comprises a third subsample, which comprises DNA with a cytosine modification in a greater proportion than the second subsample but in a lesser proportion than the first subsample (Fig. 16; [0163] Three groups of fragments comprising, 5mC, 5hmC, and unmethylated DNA. With the 5hmC fraction containing lesser proportion of 5mC than the 5mC fraction by MBD protein pull-down, but greater than the unmethylated DNA fraction; see also Fig. 17 and 18, illustrating 5hmC pulldown fraction by streptavidin also comprise 5mC).
Regarding claim 37, the combined teachings of Arensdorf and Xia teaches the first nucleobase is a modified or unmodified cytosine and the second nucleobase is a modified or unmodified cytosine and different from the first nucleobase (see Arensdorf, fig. 11; see also in Xia, Figure 1).
Regarding claim 43, Arensdorf teaches the procedure to which the sample is subjected comprises protection of 5hmC (Fig. 11. 5hmC is protected by biotin functional group from deamination by borane ; [0128] ; see also [0124]).
Regarding claim 50, Arensdorf teaches protection of hmC followed by deamination of mC (Fig. 11; 5hmC is protected by biotin functional group from deamination by borane ; [0128]).
Regarding claims 100-101, Arensdorf teaches enzymatic conversion (Fig. 11, βGT-catalyzed uridine diphosphoglucose 6-azide glycosylation).
Claims 94-95 are rejected under 35 U.S.C. 103 as being unpatentable over Arensdorf, in view of Xia, as applied to claim 1 above and further in view of Quake (WO2017176630A1 - Noninvasive diagnostics by sequencing 5-hydroxymethylated cell-free dna; 2017-10-12).
A) The teachings of Arensdorf and Xia are recited above and applied as for base claim 1.
Arensdorf teaches methods for epigenetic analysis of cell-free DNA, by partitioning nucleic acids into subsets based on incorporation of epigenetic bases such as 5hmC or 5mC, followed by sequencing (e.g., [0148]-[0149]; claim 45; Fig. 11).
Regarding claim 94, while Arensdorf does not explicitly teach determining the likelihood of a subject having cancer, it states that its methods have utility in diagnostics ([0002]), and incorporates Quake by reference ([0055]).
Quake, in turn, teaches non-invasive cancer diagnostic methods through sequencing of 5hmC in cfDNA, comprising determining a likelihood that the subject has cancer (Figs. 4A-4C, Cancer type and stage prediction with cell-free 5hmC; page 40-41).
Accordingly, a skilled artisan would readily appreciate and find it obvious that the sequencing methods in Arensdorf for analyzing epigenetics of cfDNA could be applied to determine the likelihood of a subject having cancer. This combination would have been obvious as it represents the KSR principle of predictable use of prior art elements (i.e., hydroxymethylation sequencing in cfDNA) according to a known method (i.e., using hydroxymethylation sequencing in cfDNA for cancer diagnosis) to yield predictable results. (See MPEP §2143).
B) Regarding claim 95, Quake teaches the sequencing generates a plurality of sequencing reads (page 35, lines 31-32) ; and the method further comprises mapping the plurality of sequence reads to one or more reference sequences to generate mapped sequence reads (page 35, lines 33-34 to page 36, lines ), and processing the mapped sequence reads corresponding to the sequence-variable target region set and to the epigenetic target region set to determine the likelihood that the subject has cancer (page 36, lines 7-34 to page 37, lines 1-9; 29-34; page 41, lines 1-2).
Double Patenting- Obvious Type -- New Grounds of Rejections
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, 5, 8, 24, 33, 37, 43 and 100-101 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6, 8-9, 12, 18-19 of U.S. Patent No. 11891653B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are obvious over claims of the '653 patent.
Instant claim 1 recites:
A method of analyzing DNA in a sample, the method comprising:
a) subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample (‘653 Patent, claim 1),
wherein the first nucleobase is a modified or unmodified nucleobase, the second nucleobase is a modified or unmodified nucleobase different from the first nucleobase, and
the first nucleobase and the second nucleobase have the same base pairing specificity(‘653 Patent, claim 1) ;
and wherein the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample chemically converts the first nucleobase or the second nucleobase into a converted nucleobase having altered base pairing specificity (‘653 Patent, claim 19, Tet-assisted bisulfite conversion);
b) after subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample, partitioning the sample into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified nucleobase in the DNA (‘653 Patent, claim 1, 9) ,
the plurality of subsamples comprising a first subsample and a second subsample,
wherein the first subsample comprises DNA with a cytosine modification in a greater proportion than the second subsample(‘653 Patent, claim 1), and
the modified nucleobase recognized by the agent is a modified cytosine (‘653 Patent, claim 1, 9) or a product of the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample ; and
c) sequencing DNA in at least one of the first and second subsamples in a manner that distinguishes the first nucleobase from the second nucleobase(‘653 Patent, claim 1).
Therefore, instant claims 1,5, 37, 100-101 are anticipated by claims 1, 9 and 19 of the '653 patent. Instant claims 8; 24; 33; 43 are anticipated by claims 6; 8; 12; 18 of the '653 patent, respectively.
Claims 1,5, 8, 24, 33, 37, 43, 50 and 100-101 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6, 8, 12, 28, 20 of U.S. Patent No. 12655469. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are obvious over claims of the '469 patent.
Instant claim 1 recites:
A method of analyzing DNA in a sample, the method comprising:
a) subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample (‘469 Patent, claim 1),
wherein
the first nucleobase is a modified or unmodified nucleobase,
the second nucleobase is a modified or unmodified nucleobase different from the first nucleobase, and
the first nucleobase and the second nucleobase have the same base pairing specificity, and
wherein the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample chemically converts the first nucleobase or the second nucleobase into a converted nucleobase having altered base pairing specificity (‘469 Patent, claim 20/19, APOBEC deaminase, which takes unmodified cytosines converting them to uracils);
b) after subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample, partitioning the sample into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified nucleobase in the DNA(‘469 Patent, claim 1), the plurality of subsamples comprising a first subsample and a second subsample, wherein the first subsample comprises DNA with a cytosine modification in a greater proportion than the second subsample, and the modified nucleobase recognized by the agent is a modified cytosine or a product of the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample; and
c) sequencing DNA in at least one of the first and second subsamples in a manner that distinguishes the first nucleobase from the second nucleobase (‘469 Patent, claim 1).
Therefore, instant claims 1,5, 37, 50 and 100-101 are anticipated by claims 1,20 of the '469 patent. Instant claims 8; 24; 33; 43 are anticipated by claims 6; 8; 12; 18 of the '469 patent, respectively.
Claims 1, 5, 16, 21, 24, 37, 43, 50, 94 and 100-101 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6, 16, 25, 27 of copending Application No. 19/279,313 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are anticipated by the claims (filed on 10/13/2025) of the '313 application.
Instant claim 1 recites:
A method of analyzing DNA in a sample, the method comprising:
a) subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample (‘313 Application, claim 1),
wherein the first nucleobase is a modified or unmodified nucleobase, the second nucleobase is a modified or unmodified nucleobase different from the first nucleobase, and
the first nucleobase and the second nucleobase have the same base pairing specificity;
and
wherein the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample chemically converts the first nucleobase or the second nucleobase into a converted nucleobase having altered base pairing specificity (‘313 Application, claim 1, conversion procedure that selectively converts the base pairing specificity of 5-methylcytosines (5mC) or unmethylated cytosines (C) in the nucleic acids; claim 16 "Tet-assisted conversion of nucleic acids with a substituted borane reducing agent")
b) after subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample, partitioning the sample into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified nucleobase in the DNA (‘313 Application, claim 1, 6),
the plurality of subsamples comprising a first subsample and a second subsample,
wherein the first subsample comprises DNA with a cytosine modification in a greater proportion than the second subsample, and
the modified nucleobase recognized by the agent is a modified cytosine or a product of the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample; and
c) sequencing DNA in at least one of the first and second subsamples in a manner that distinguishes the first nucleobase from the second nucleobase (‘313 Application, claim 1).
Therefore, instant claims 1, 21, 24, 37, 50, 100-101 are anticipated by claims 1, 6, 16 of the '313 application. Instant claims 5; 16, 94; 43 are anticipated by claims 25; 27 of the '313 application, respectively.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1, 5, 8-9, 16, 21, 24, 33, 37, 94 and 100-101 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 9, 11-12, 15, 19, 21, 24 of U.S. Patent No. 12234518B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are obvious over claims of the '518 patent.
Instant claim 1 recites:
A method of analyzing DNA in a sample, the method comprising:
a) subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample (‘518 Patent, claim 1) ,
wherein the first nucleobase is a modified or unmodified nucleobase, the second nucleobase is a modified or unmodified nucleobase different from the first nucleobase, and
the first nucleobase and the second nucleobase have the same base pairing specificity,
and wherein the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample chemically converts the first nucleobase or the second nucleobase into a converted nucleobase having altered base pairing specificity (‘518 Patent, claim 24, "Tet-assisted conversion with a substituted borane reducing agent")
b) after subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample, partitioning the sample into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified nucleobase in the DNA(‘518 Patent, claim 1, " capturing a target region set comprising epigenetic target regions from the treated subsample," 11),
the plurality of subsamples comprising a first subsample and a second subsample,
wherein the first subsample comprises DNA with a cytosine modification in a greater proportion than the second subsample, and
the modified nucleobase recognized by the agent is a modified cytosine or a product of the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample; and
c) sequencing DNA in at least one of the first and second subsamples in a manner that distinguishes the first nucleobase from the second nucleobase(‘518 Patent, claim 1).
Therefore, instant claims 1, 5, 24, 37 and 100-101 are anticipated by claims 1, 11, 24 of the '518 patent. Instant claims 8-9; 16; 21; 33; 94 are anticipated by claims 11-12; 9; 15; 19; 21 of the '518 patent, respectively.
Claims 1, 5, 8, 16, 21, 24, 94-95 and 100-101 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 12, 83, 86, 97, 100, 122 of copending Application No. 18/447,749 (reference application, amended claims filed on 03/28/2024), in view of Hayatsu (Hayatsu et al., DNA methylation analysis: speedup of bisulfite-mediated deamination of cytosine in the genomic sequencing procedure. Proc Jpn Acad Ser B Phys Biol Sci. 2004 Mar;80(4):189–94. Epub 2004 Apr 1. PMCID: PMC8153359.)
Instant claim 1 recites:
A method of analyzing DNA in a sample, the method comprising:
a) subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample (‘749 Application, claim 97),
wherein the first nucleobase is a modified or unmodified nucleobase, the second nucleobase is a modified or unmodified nucleobase different from the first nucleobase, and
the first nucleobase and the second nucleobase have the same base pairing specificity,
and wherein the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample chemically converts the first nucleobase or the second nucleobase into a converted nucleobase having altered base pairing specificity;
b) after subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample, partitioning the sample into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified nucleobase in the DNA (‘749 Application, claim 97),
the plurality of subsamples comprising a first subsample and a second subsample,
wherein the first subsample comprises DNA with a cytosine modification in a greater proportion than the second subsample, and
the modified nucleobase recognized by the agent is a modified cytosine or a product of the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample; and
c) sequencing DNA in at least one of the first and second subsamples in a manner that distinguishes the first nucleobase from the second nucleobase (‘749 Application, claim 1).
The claims of the '749 Application largely overlap with the instant claim 1. While the '749 Application claims a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample, it does not specifically claim its procedure chemically converts a nucleobase into a converted nucleobase having altered base pairing specificity. However, this feature is obvious in view of the knowledge in the prior art.
As taught by Hayatsu, "a standard method for analyzing the methylation at position 5 of cytosines in genomic DNA involves chemical modification of the DNA with bisulfite, followed by PCR amplification and sequencing." (Abstract).
Bisulfite-treated cytosine is converted to uracil (Hayatsu, introduction), with altered base pairing specificity; while the methylated cytosine remains unaffected.
Given these teachings, it would have been obvious for one of ordinary skill in the art to apply bisulfite conversion as taught by Hayatsu in the claimed methylation analysis process in '749 Application. The use of bisulfite conversion in the claimed procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample, represents a predictable use of prior art elements according to known methods to yield predictable results (see MPEP §2143).
Therefore, instant claim 1 and 100-101 are obvious over claims 1, 97 of the ‘749 Application , in view of Hayatsu. Instant claims 5, 21; 8; 16; 21; 24; 94; 95 are obvious over claims 3; 86; 12; 100; 83; 122 of the ‘749 Application, in view of Hayatsu.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1, 5, 8, 16, 21, 24, 37, 43, 50, 94 and 100-101 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 12-13, 16, 18, 21, 25, 30 of copending Application No. 18/365,744 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are obvious over the claims (filed on 04/13/2026) of the '744 application.
Instant claim 1 recites:
A method of analyzing DNA in a sample, the method comprising:
a) subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample (‘ 744 Application, claim 2),
wherein the first nucleobase is a modified or unmodified nucleobase, the second nucleobase is a modified or unmodified nucleobase different from the first nucleobase, and
the first nucleobase and the second nucleobase have the same base pairing specificity,
and wherein the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample chemically converts the first nucleobase or the second nucleobase into a converted nucleobase having altered base pairing specificity (‘ 744 Application, claim 2, 3, bisulfite conversion);
b) after subjecting the sample to a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the sample, partitioning the sample into a plurality of subsamples by contacting the DNA with an agent that recognizes a modified nucleobase in the DNA (‘ 744 Application, claim 21),
the plurality of subsamples comprising a first subsample and a second subsample,
wherein the first subsample comprises DNA with a cytosine modification in a greater proportion than the second subsample, and
the modified nucleobase recognized by the agent is a modified cytosine or a product of the procedure that affects the first nucleobase in the DNA differently from the second nucleobase in the DNA of the sample; and
c) sequencing DNA in at least one of the first and second subsamples in a manner that distinguishes the first nucleobase from the second nucleobase (‘744 Application, claim 1).
Therefore, instant claims 1, 24 and 100 are obvious over claims 1-3, 21 of the '744 application. Instant claims 5, 101; 8; 16; 21; 37; 43, 50; 94 are obvious over claims 16; 18; 12; 30; 4; 25; 13 of the '744 application, respectively.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Claims 1, 5 and 100-101 are objected to; claims 1, 5, 8-9, 16, 21, 24, 33, 37, 43, 50, 94-95 and 100-101 are rejected. No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
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