DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. This action is in response to the amendment filed on 16 July 2026. Applicant's arguments and amendments to the claims have been fully considered but do not place the application in condition for allowance. All rejections and objections not reiterated herein are hereby withdrawn.
In particular, the previous objection to claim 1 has been obviated by the amendment to claim 1.
The previous rejection of claim 7 under 35 U.S.C. 112(b) has been obviated by the amendment to claim 7.
The previous rejection of claims 1, 5 and 6 under 35 U.S.C. 102(a)(1) as being anticipated by Legendre et al has been obviated by the amendment to claim 1 to recite “wherein the treating, amplifying and sequencing steps are not performed as part of a whole genome bisulfite sequencing process.”
Claim Status
3. Claims 1-14 are pending and have been examined herein.
Claim Interpretation
4. Regarding the recitation in claim 1 of “CGI selected from Table 1,” the chromosome positions of the CGIs is considered to be with respect to human reference genome hg19, as recited in the title of the column of Table 1 at p. 55.
It is further noted that the specification (para [0039] defines a CpG island” / “CGI” as a region that is “at least 200 bp, with a GC percentage greater than 50%, and an observed-to-expected CpG ratio greater than 60%.” The specification (para [0042] teaches that the PMR is the "proportion of concordantly methylated reads (PMR) (i.e., fully methylated haplotypes)." Also see Figure 15A and para [0031] regarding a comparison of the proportion of fully / concordantly methylated reads (PMR), the proportion of discordant reads (PDR) and the proportion of concordantly un-methylated reads (PUR).
Maintained Claim Rejections - 35 USC § 101
5. 35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 2, 3, 8-12 and 14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to the judicial exception of a law of nature / natural phenomenon, and/or an abstract idea without significantly more. The judicial exception is not integrated into a practical application and the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons that follow.
Applicant' s attention is directed to MPEP 2106 “Patent Subject Matter Eligibility” which discusses the Alice/Mayo two-part test for evaluating subject matter eligibility.
Regarding Step 1 of the subject matter eligibility test set forth at MPEP 2106III, the claims are directed to the statutory category of a process.
Regarding Step 2A, prong one, the claims recite the judicial exception of a law of nature. The claims recite the correlation between the occurrence of circulating
tumor DNA (ctDNA) and the proportion of concordantly methylated CpG islands (claims 3, 8 and 14). As in Mayo Collaborative Services v. Prometheus, the recited relationship is a natural phenomenon that exists apart from any human action. See also Cleveland Clinic Foundation v. True Health Diagnostic, LLC, 2018-1218 (Fed Cir. 2019) which states that “The re-phrasing of the claims does not make them less directed to a natural law.”
The claims also recite the judicial exception of an abstract idea and particularly mental processes.
MPEP 2106.04(a) states that the enumerated groupings of abstract ideas include:
“1) Mathematical concepts – mathematical relationships, mathematical formulas or equations, mathematical calculations (see MPEP § 2106.04(a)(2), subsection I);…
3) Mental processes – concepts performed in the human mind (including an observation, evaluation, judgment, opinion) (see MPEP § 2106.04(a)(2), subsection III).”
The claims require performing the steps of "calculating" the proportion of
concordantly methylated reads (PMR) for the identified CpG island (claims 2, 3, 8-12 and 14); "comparing" the PMR to a control background PMR of normal tissue or epiblast (claims 3, 8-12 and 14); and detecting that ctDNA is present in the sample when the PMR is greater than background (claims 3, 8-12 and 14). Neither the specification nor the claims set forth a limiting definition for "calculating," "comparing" and detecting ctDNA based on the comparison steps and the claims do not set forth how these steps are accomplished. The broadest reasonable interpretation of these steps is that they may be accomplished by mental and critical thinking processes. For example, one may
mentally calculate a PMR and mentally compare that PRM to a control background. And
one may mentally determine that the PMR is greater than the control background PMR.
Accordingly, these steps may be performed mentally and thus are an abstract idea.
To any extent that the calculating step is intended to require the use of pen and
paper, MPEP 2106.04(a)(2) states "The courts consider a mental process (thinking) that
"can be performed in the human mind, or by a human using a pen and paper" to be an
abstract idea." Thus, the calculating step would still be considered to be an abstract
idea even if performed using pen and paper.
To any extent that the calculating step is intended to use a computer or
algorithm, the use of a generic computer or software program to implement an abstract
idea does not itself impart patent eligibility.
As stated in MPEP 2106.04(a)(2) III "The courts do not distinguish between
mental processes that are performed entirely in the human mind and mental processes
that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation" and that "Nor do the courts distinguish between claims that
recite mental processes performed by humans and claims that recite mental processes
performed on a computer."
Herein, the use of a generic computer or general algorithm to calculate or
compare PMRs would constitute an abstract idea.
Regarding Step 2A, prong two, having determined that the claims recite a judicial exception, it is then determined whether the claims recite additional elements that integrate the judicial exception into a practical application.
Herein, the claims do not recite additional steps or elements that integrate the recited judicial exceptions into a practical application of the exception(s). The
additionally recited non-patent-ineligible steps of obtaining cell-free DNA, treating the
cell-free DNA with bisulfite, amplifying the bisulfite treated DNA and sequencing the
amplified bisulfite treated DNA using next generation sequencing (NGS) are part of the
data gathering process necessary to observe the judicial exception. These steps do not
practically apply the judicial exception.
Regarding claim 14, this claim requires that a second sample from the patient is obtained after the patient has received a treatment for cancer. The treating step is extra-solution activity necessary to observe the judicial exception. This step is not a practical application of the judicial exception.
Applicant’s attention is directed to M.P.E.P. § 2106.04(d)(2)(c), which states:
“The treatment or prophylaxis limitation must impose meaningful limits on the judicial exception, and cannot be extra-solution activity or a field-of-use. For example, consider a claim that recites (a) administering rabies and feline leukemia vaccines to a first group of domestic cats in accordance with different vaccination schedules, and (b) analyzing information about the vaccination schedules and whether the cats later developed chronic immune-mediated disorders to determine a lowest-risk vaccination schedule. Step (b) falls within the mental process grouping of abstract ideas enumerated in MPEP § 2106.04(a). While step (a) administers vaccines to the cats, this administration is performed in order to gather data for the mental analysis step, and is a necessary precursor for all uses of the recited exception. It is thus extra-solution activity, and does not integrate the judicial exception into a practical application.”
Regarding Step 2B, the next question is whether the remaining elements/steps – i.e., the non-patent-ineligible elements/steps - either in isolation or combination, amount to significantly more than the judicial exception.
Herein, the claims as a whole are not considered to recite any additional steps or elements that amount to significantly more than routine and conventional activity and do not add something “significantly more” so as to render the claims patent-eligible. The
additionally recited non-patent-ineligible steps of obtaining cell-free DNA, treating the
cell-free DNA with bisulfite, amplifying the bisulfite treated DNA and sequencing the amplified bisulfite treated DNA using next generation sequencing (NGS) were well-
known, routine and conventional in the prior art. This finding is evidenced by the
teachings in the specification. For instance, the specification states "[0040] The
sample may be screened using whole-genome bisulfite sequencing (WGBS), TCGA
Illumina Infinium HumanMethylation450K BeadChip sequencing (TCGA), and/or
reduced representation bisulfite sequencing (RRBS), or by other suitable methylation
detection assays known in the art." It is further stated that "Since next generation
sequencing is usually applied for DNA methylation, sequencing reads and haplotypes
were utilized interchangeably" (para [0095]).
Further, Lo et al (PGPUB 2015/0011403; cited in the IDS) teaches methods of
obtaining cell-free DNA samples, treating the cell-free DNA with bisulfite, amplifying and
sequencing the DNA containing CGIs using massively parallel (next generation)
sequencing were well-known in the prior art (e.g., para [0092-0094], [0098-0099] and
[0392-0395]). Mueller et al (WO 2017201606; cited in the IDS) teaches methods of obtaining cell-free DNA samples, treating the cell-free DNA with bisulfite, amplifying the bisulfite treated DNA; and performing next-generation sequencing of the bisulfite treated amplified DNA to determine the methylation status of CpGs present in CpG islands (e.g., para [0009],[0098], [0154], [0195] and Figure 6).
See also MPEP 2106.05(d) II which states that:
The courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity.
i. Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
ii. Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
iii. Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
iv. Immunizing a patient against a disease, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
v. Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
vi. Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119 USPQ2d at 1375;
vii. Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014); and
viii. Hybridizing a gene probe, Ambry Genetics, 774 F.3d at 764, 113 USPQ2d at 1247.
To any extent that the claims may intend to require the use of a generic computer
to perform the calculating and/or comparing steps, MPEP 2106.05(a) states:
"Limitations that the courts have found not to be enough to qualify as
‘significantly more’ when recited in a claim with a judicial exception include: i. Adding
the words ‘apply I’" (or an equivalent) with the judicial exception, or mere instructions to
implement an abstract idea on a computer, e.g., a limitation indicating that a particular
function such as creating and maintaining electronic records is performed by a
computer, as discussed in Alice Corp., 134 S. Ct. at 2360, 110 USPQ2d at 1984 (see
MPEP § 2106.05(f)).
Note that while the claims recite detecting the methylation status of particular CpGs, the identity of the CpG is part of the judicial exception and not something in addition to the recited judicial exceptions. The claims do not require detecting the methylation status of the CpG using a particular non-conventional reagent, such as a particular, non-conventional probe or primer consisting of or comprising a specific nucleotide sequence so as to add something ‘significantly more’ to the recited judicial exceptions.
In Mayo v. Prometheus, the Supreme Court stated: "[t]o put the matter more succinctly, the claims inform a relevant audience about certain laws of nature; any additional steps consist of well understood, routine, conventional activity already engaged in by the scientific community; and those steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately."
This is similar to the present situation wherein the additional steps and elements are recited at a high degree of generality and are all routine, well understood and conventional in the prior art. The recited steps and elements do not provide the inventive concept necessary to render the claims patent eligible. See also Genetic Technologies Ltd. v. Merial L.L.C. 818 F.3d at 1377, 1379 (Fed. Cir. 2016).
For the reasons set forth above, when the claims are considered as a whole, the claims are not considered to recite something significantly more than a judicial exception and thereby are not directed to patent eligible subject matter.Response to Remarks:
In the reply, Applicant states:
“the Office alleges that the judicial exception is not integrated into a practical application, instead dismissing the already acknowledged patent-eligible subject matter of claim 1 and 13 as mere data gathering steps necessary to observe the judicial exception. While the Office has not provided any citation within the MPEP for support for this argument, it appears to stem from MPEP §2106.05(g)(3) which provides guidance on whether a limitation amounts to necessary data gathering and outputting. Applicants assert that application of MPEP §2106.05(g)(3) in this manner is improper for an analysis under Step 2A, prong two. MPEP §2106.05 provides guidelines for assessing eligibility of the claims at Step 2B, which is only arrived at if the eligibility of the claims was deemed not self-evident and further when the claims were deemed directed to a judicial exception by not integrating the judicial exception into a practical application. Accordingly, Applicants assert that this rejection is improper, as the Office has misapplied the guidelines set forth by the MPEP and has thus improperly discounted the additional limitations of the claims in assessing their eligibility under Step 2A, prong two. For at least this reason, the rejection should be withdrawn.”
Applicant also states:
“the subject matter of claims 1 and 13, including the combination of obtaining, bisulfite treating, amplifying and sequencing at least one CGI of Table 1 was already recognized by the Office as patent eligible, and Applicants assert that adding a calculating step and/or a detection step to this combination of steps should not suddenly convert the claim into a claim that is directed to a judicial exception.”
These arguments have been fully considered but are not persuasive. Claims 1, 4-7 and 13 were found to be patent-eligible because they do not recite a judicial exception. In contrast dependent claims 2, 3, 8-12 and 14 do recite a judicial exception, as discussed in detail in the above rejection. In brief, the dependent claims (and not independent claims 1 and 13) recite the abstract steps of calculating and comparing and recite the judicial exception of a natural phenomenon - i.e., the naturally occurring correlation the between the occurrence of circulating tumor DNA (ctDNA) and the proportion of concordantly methylated CpG islands (claims 3, 8 and 14).
Additionally, regarding Applicant’s argument pertaining to “directed to,” MPEP 2106.04II states:
1. Prong One
Prong One asks does the claim recite an abstract idea, law of nature, or natural phenomenon? In Prong One examiners evaluate whether the claim recites a judicial exception, i.e. whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim. While the terms "set forth" and "described" are thus both equated with "recite", their different language is intended to indicate that there are two ways in which an exception can be recited in a claim….
If the claim recites a judicial exception (i.e., an abstract idea enumerated in MPEP § 2106.04(a), a law of nature, or a natural phenomenon), the claim requires further analysis in Prong Two.” (Emphasis added).
Herein, the claims do recite a judicial exception and thereby the claims were further analyzed in Prong two of Step 2A.
The response argues that “the presently amended claims are not directed to a judicial exception because the amended claims recite additional elements which demonstrate that the claims integrate the exception into a practical application.” It is also stated that “by requiring a cfDNA sample be subjected to bisulfite sequencing to provide methylation reads of specifically identified inventive regions associated with improved properties, Applicants have integrated the judicial exception into a practical application.”
These arguments have been fully considered but are not persuasive. The non-patent-ineligible steps in the claims of bisulfite treating the cfDNA, amplifying the bisulfite treated DNA and sequencing the resulting amplified DNA are not a practical application. These steps are data-gathering steps that generate a dataset of sequencing reads. As set forth in MPEP 2106.05(g), steps of gathering data to be used in a claimed process are pre-solution activity and do not integrate a judicial exception into a practical application.
The response argues that “the process excludes WGBS and requires amplification of at least one CGI from Table 1 (i.e. using primers), which has not been shown by the applied prior art.”
However, the claims do not require any particular primers, such as primers defined by a specific nucleotide sequence. Note that the primers used in RRBS analysis, as encompassed by the claims (and specifically required by claim 4) are universal primers and not primers specific for a particular CGI. The use of primers to amplify bisulfite treated DNA was well-known, routine and conventional in the prior art. Accordingly, the broadly recited amplifying step (using primers) does not add something significantly more to the recited judicial exceptions.
Maintained Claim Rejections - 35 USC § 112(b) - Indefiniteness
6. 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 1-14 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1-14 are indefinite over the recitation of “CGI selected from Table 1.” MPEP 2173.05(s) states:
“Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table “is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.” Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) (citations omitted).”
Herein, the reference to the CGIs of Table 1 renders the claims incomplete. Response to Remarks:
The response traverses the rejection by arguing that the fact pattern herein is different from that in Ex parte Fressola since this decision cited in the MPEP is with respect to an omnibus claim. It is argued that Table 1 is approximately 30 pages and it is more clear and concise to incorporate the Table by reference than to duplicate the table within the claims.
These arguments have been fully considered but are not persuasive. Incorporating Table 1 into the claims by reference to the specification is not in fact clearer. Tables in the specification may be amended and thereby the information therein is not fixed. As stated in MPEP 2173.05(s), and cited above, the claims must be complete in themselves. The exception to this is when there is no practical way to define the invention in words Herein, there is a practical means to define the invention in words, as shown in Table 1 wherein the CGIs are defined in terms of their chromosomal positions. Thus, incorporating Table 1 into claim 1 by reference to the specification is not a “necessity” since Table 1 can be added to claim 1 by copying the contents of Table 1 into claim 1.
Maintained / Modified Double Patenting Rejection
7. 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 1-14 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of copending Application No. 19/018,871 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the present claims and the claims of ‘871 are both inclusive of a method of preparing a dataset of sequencing reads for at least one CpG Island (CGI) for use in detecting circulating tumor DNA (ctDNA) from a patient sample, comprising: treating cell free DNA (cfDNA) obtained from the patient sample with bisulfite; amplifying the at least one CGI from the bisulfite-treated cfDNA; sequencing the amplified DNA using next-generation sequencing (NGS) to generate a dataset comprising a plurality of sequencing reads for the at least one CGI. The claims of ‘871 do not recite that the method of treating with bisulfite, amplifying and sequencing require whole genome bisulfite sequencing. Accordingly, the method claimed in ‘871 is considered to be one in which the treating, amplifying and sequencing are not performed as part of a whole genome bisulfite sequencing process.
Present claim 1 recites that the CGI is selected from the CGIs recited in Table 1, whereas claim 1 of ‘871 recites that the CGI is a CGI hypermethylated in human placenta compared to human embryonic stem cells, or is orthologous to a CGI hypermethylated in mouse extraembryonic ectoderm (ExE) compared to epiblast. When read in light of the specification of ‘871, it is clear that the CGIs that have the property of being hypermethylated in human placenta compared to human embryonic stem cells, or being orthologous to a CGI hypermethylated in mouse ExE compared to epiblast are the CGIs listed in Table 1 therein. Accordingly, claim 1 of ‘871 encompasses methods in which the CGI is a CGI from Table 1.
Dependent claims 2-14 of ‘871 recite the same limitations as present claims 2-14.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.Response to Remarks:
The response requests that the rejection be held in abeyance.
However, rejections are not held in abeyance. The rejection is maintained for the reasons set forth above.
Claim Rejections - 35 USC § 103
Modified Rejections Necessitated by Amendments to the Claims
8. 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) 1, 4, 5, 6 and 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Legendre et al. (Clinical Epigenetics. 2015. 7: 100; p. 1-10), in view of Gu et al (Nature Protocols. 2011. 6(4): 468-481) as evidenced by the specification at para [0117].
Legendre et al teaches methods comprising: a) treating cell-free DNA (cfDNA) obtained from a sample from a patient with bisulfite; b) amplifying CpG islands (CGIs) from the bisulfite-treated DNA; and sequencing the amplified DNA using next-generation sequencing (NGS) to generate a dataset comprising sequencing reads for the CGIs (e.g., p. 2, col. 2; p. 8 “DNA methylation analysis by whole-genome bisulfite sequencing”; and p. 9 “Data processing and analysis”). Since the method of Legendre is one that amplifies and sequences the whole genome, the method of Legendre is considered to be one that necessarily amplifies and provides sequence reads for at least one of the CGIs listed in Table 1, absence evidence to the contrary.
Legendre teaches that the steps of treating the DNA with bisulfite, amplifying and sequencing are performed as part of a whole genome sequencing assay.
Legendre does not teach that the treating with bisulfite, amplifying and sequencing steps are performed as part of a reduced representation bisulfite sequencing process - i.e., a process that is not a whole genome bisulfite sequencing process.
However, Gu et al teaches methods of reduced representation bisulfite sequencing (RRBS) and discloses that the method enriches for genomic regions that contain CpG dinucleotides and captures most of the CpG islands (e.g., abstract and p. 469). Gu (abstract) states that RRBS is a “bisulfite-based protocol that enriches CG-rich parts of the genome, thereby reducing the amount of sequencing required while capturing the majority of promoters and other relevant genomic regions. the approach provides single-nucleotide resolution, is highly sensitive and provides quantitative DNA methylation measurements. this protocol should enable any standard molecular biology laboratory to generate RRBS libraries of high quality.”
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Legendre so as to have performed RRBS, as taught by Gu, in place of whole genome bisulfite sequencing. One would have been motivated to have done so in order to have provided the benefits set forth by Gu of reducing the amount of sequencing required while capturing the most relevant sequences, including CpG islands (CGIs), while providing a highly sensitive, single-nucleotide resolution method for determining the methylation status of the CGIs and generating high quality sequencing reads.
It is acknowledged that Gu (p. 469, col. 2) states that “RRBS enriches for genomic regions that contain CpG dinucleotides, and as a result it captures the majority (although not all) of CpG islands and promoters.” However, it is expected that modification of the method of Legendre to use the RRBS method of Gu would result in the amplification and generation of sequencing reads for at least one of the CpG island listed in Table 1. This finding is evidenced by the teachings in the specification at para [0117] which indicate that the method of Gu was used to perform RRBS therein and the method detected the methylation status of the CpG islands. Although the present specification teaches that modifications were made to the method of Gu, the noted modifications would not prevent the amplification and sequencing of at least one of the CpG islands set forth in Table 1, absent evidence to the contrary. Note that the present specification is cited only to establish what is a property of the RRBS method of Gu.
Regarding claim 5, Legendre teaches that the sample is a plasma sample (e.g., p. 8 “Sample acquisition and DNA extraction”).
Regarding claim 6, Legendre teaches that the sample is obtained from a subject suffering from cancer (e.g., p. 8 “Sample acquisition and DNA extraction”).
Regarding claim 13, Legendre does not specifically exemplify a method wherein a second sample is obtained from the patient after the patient has received a cancer treatment; the second sample is treated with bisulfite; the bisulfite treated DNA in the second sample is amplified; and the amplified bisulfite-treated DNA from the second sample is sequenced by NGS to generate a second dataset comprising sequencing reads for the at least on CGI.
However, Legendre teaches that the methylation profile of subjects having metastatic breast cancer are different from that of healthy subjects and disease free survivors (DFS) and that the methylome of DFS more closely resembles that of healthy subjects (e.g., p. 2 “GBS demonstrated global hypomethylation and focal hypermethylation in cfDNA of MBC compared with H and DFS, which had a high degree of similarity” and p. 6, col. 1). The reference states “This signature is a potential blood-based biomarker that could be advantageous at the time of surgery and/or after the completion of chemotherapy to indicate patients with micrometastatic disease who are at a high risk of recurrence and who could benefit from additional therapy” (see abstract). The reference concludes “We anticipate that a DNA hypermethylation signature, involving rationally selected CpG hotspots detectable in circulation, can be used to indicate micrometastatic disease in the pre-macrometastatic setting and predict patients at a high-risk of recurrence who could benefit from additional therapy” (p. 8, col. 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Legendre so as to have also obtained a second sample from the patient after the patient is treated and to have assayed for the methylation status of CGIs in the second sample by performing the RRBS assay. One would have been motivated to have done so in order to have generated additional data regarding changes in the methylation status of CGIs in the patient over time and to have compared the changes with those that occur in healthy subjects and DFSs.
9. Claim(s) 7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Legendre et al. (Clinical Epigenetics. 2015. 7: 100; p. 1-10), in view of Gu et al (Nature Protocols. 2011. 6(4): 468-481) as evidenced by the specification at para [0117], and further in view of Miller et al (Biomolecules. 2016. 6: 45, p. 1-14).
The teachings of Legendre and Gu are presented above.
While Legendre teaches that the sample is obtained from a patient having metastatic breast cancer (MBC), Legendre does not teach that the sample is obtained from a subject having breast invasive carcinoma.
However, Miller teaches that the CpG island methylator phenotype (CIMP) is a pattern of extensive DNA hypermethylation at cytosines located in CpG islands (CGIs; p. 1, final para). Miller teaches analyzing TCGA data on CGI methylation status obtained from studies using, for example Illumina Infinium HumanMethylation27k and HumanMethylation450K arrays to characterize methylation patterns in cancers, including breast invasive carcinoma (e.g., p. 4; p. 5 first para and Figure 2). Miller (p. 5, first para) states:
“we were able to show overall survival curves exhibiting significant differences based on CIMP‐positive and CIMP‐negative subgroups for four cancer types (breast invasive carcinoma, BRCA; kidney renal clear cell carcinoma, KIRC; lung squamous cell carcinoma, LUSC; uterine corpus endometrial carcinoma, UCEC) (Figure 3); overall survival curves for luminal A and luminal B subtypes in BRCA also differed by CIMP.”
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Legendre so as to have specifically applied the method to patients having breast invasive carcinoma. One would have been motivated to have done so because Miller teaches detecting CGI methylation status in patients having breast invasive carcinoma and that data regarding the CGI methylation status of breast invasive carcinoma can be used to predict overall survival of patients and to distinguish between survival of patients having luminal A and luminal B subtypes of breast invasive carcinoma. Thus, such a modification of the method of Legendre would have provided the benefit of determining the methylation profile of CGIs in patients having breast invasive carcinoma and of generating additional data that could be used to further characterize breast invasive carcinoma. Response to Remarks:
The response argues that “the Office has failed to establish that modifying the method of Legendre et al. with the RRBS method of Gu et al. would have necessarily have resulted in amplifying and sequencing at least one CGI from Table 1.” The response also asserts that “the modified method of [0117] does not establish that the unmodified method of Gu et al. would obtain the required claimed result of amplifying and sequencing the at least one CGI of Table 1.”
These arguments have been fully considered but are not persuasive. The claims require only that the method amplifies and provides sequencing reads for one of the CGIs in Table 1. The modifications of the RRBS method would not have been expected to have prevented the amplification and sequencing of at least one of the CGIs in Table 1. There is no evidence of record to support Applicant’s conclusion that the RRBS method of Gu does not amplify and generate sequencing reads for even a single one of the CGIs in Table 1. For instance, the use of a different buffer or eliminating a purification step to reduce DNA loss should not prevent the amplification and sequencing of at least one CGI from Table 1. The present claims also don’t require any particular treating, amplifying or sequencing assay in claim 1 (other than to exclude whole genome bisulfite sequencing) and encompass any RRBS process in claim 4. The claims do not recite any details regarding the treating, amplifying and sequencing steps which distinguish the claimed process over that suggested by the combined teachings of Legendre and Gu. Further, Applicant’s arguments appear to be contrary to the teachings in the specification which discloses that a RRBS assay (or the Illumina Infinium HumanMethylation450K BeadChip) can be used to detect the methylation of the CGIs in Table 1 - see, e.g., para [0041] and [0113].
Regarding claim 13, Applicant argues “the rejection fails to discuss any particular CGI, much less amplification and sequencing of the same at least one CGI from Table 1 from the second patient sample that was amplified and sequenced from the first patient sample, as required by claim 13. Accordingly, the Office has failed to address each and every limitation of claim 13.”
This argument is not persuasive because claim 13 does not require a particular CGI. By repeating the same RRBS analysis, the method would necessarily amplify and sequence the same sequences that include the same CGIs. There is no requirement that the steps performed after the patient has received a cancer treatment amplify and sequence only one or a particular set of CGIs and no other CGIs/sequences comprising CGIs.
Regarding claim 7, Applicant argues “there is no reasonable expectation that CpG island methylator phenotype (CIMP) of breast invasive carcinoma would be applicable to the hypo- and hyper- methylation profile identified by Legendre for metastatic breast cancer.”
However, Miller teaches detecting CGI methylation status in patients having breast invasive carcinoma and that data regarding the CGI methylation status can be used to further characterize breast invasive carcinoma. Present claim 7 requires only that the cancer is a breast invasive carcinoma. It is maintained that modification of the method of Legendre in view of Gu to apply the method to breast invasive carcinoma, as taught by Miller, can be effectively used to amplify and sequence cfDNA comprising at least one of the CGIs of Table 1 in samples from patients with breast invasive carcinoma with a reasonable expectation of success. New grounds of rejection necessitated by Applicant’s amendments to the claims. Note also that the newly applied Bibikova reference was newly cited in the IDS filed on 16 July 2026, with the timing fee set froth in 37 CFR 1.17(p).
10. Claim(s) 1, 5, 6 and 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Legendre et al. (Clinical Epigenetics. 2015. 7: 100; p. 1-10), in view of Bibikova et al (Genomics. 2011. 98: 288-295; cited in the IDS of 07/16/2026).
Legendre et al teaches methods comprising: a) treating cell-free DNA (cfDNA) obtained from a sample from a patient with bisulfite; b) amplifying CpG islands (CGIs) from the bisulfite-treated DNA; and sequencing the amplified DNA using next-generation sequencing (NGS) to generate a dataset comprising sequencing reads for the CGIs (e.g., p. 2, col. 2; p. 8 “DNA methylation analysis by whole-genome bisulfite sequencing”; and p. 9 “Data processing and analysis”). Since the method of Legendre is one that amplifies and sequences the whole genome, the method of Legendre is considered to be one that necessarily amplifies and provides sequence reads for at least one of the CGIs listed in Table 1, absence evidence to the contrary.
Legendre teaches that the steps of treating the DNA with bisulfite, amplifying and sequencing are performed as part of a whole genome sequencing assay.
Legendre does not teach that the treating with bisulfite, amplifying and sequencing steps are performed as part of a process that is not a whole genome bisulfite sequencing process, and particularly as part of a process using a high density DNA methylation array process.
However, Bibikova et al teaches methods of using the HumanMethylation450 array to perform DNA methylation profiling (e.g., abstract and p. 288). It is stated that the array was developed to specifically capture methylation of CpG islands (CGIs) and covers 96% of CGIs In particular, Bibikova (p. 288, col 2) states:
“Here we describe the development of a microarray that combines the benefits of Infinium chemistry with substantially expanded genome coverage to provide high quality, genome-wide content with target selection guided by researchers' needs rather than technical limitations…. An emphasis was placed on gene and CpG island regions, for which 99% and 96% coverage, respectively, were achieved. In addition, 12-sample per array format provides a throughput capacity for cost and time efficient analysis of large sample cohorts. The array data show strong reproducibility between replicates and high correlation with whole genome bisulfite sequencing data generated on the same samples. By providing a unique combination of high quality content, throughput and affordability, the Infinium HumanMethylation450 provides the research community with a powerful tool for assessing epigenetic changes across a wide range of study designs.”
Bibikova teaches that the Infinium methylation assay using the HumanMethylation450 array comprises the steps of bisulfite treating DNA, amplifying the bisulfite treated DNA (by whole genome amplification) and sequencing the amplified, bisulfite treated DNA using the Infinium HumanMethylation450 array (p. 293, sections 4.3, 4.4 and 4.5). Bibikova teaches applying the assay to samples of human tumor lung tissue and normal lung tissue (e.g., abstract and p. 293, section 4.2).
Bibikova compared the results obtained with whole genome bisulfite sequencing with the HumanMethylation450 array and reports that the “results indicate that the beta values generated by the Infinium HumanMethylation450 array and whole genome bisulfite sequencing are consistent in reporting DNA methylation state across queried CpG loci (Fig. 5B)” (p. 292, col. 1, first para). Bibikova teaches that the Infinium methylation assay using the HumanMethylation450 array provides the benefits of an affordable, rapid and high-throughput assay for detecting methylation of CGIs, while providing high quality genome-wide sequence content (e.g., p. 288 “Introduction” and p. 292, “Discussion”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Legendre so as to have performed the methylation analysis using the Infinium HumanMethylation450 array assay disclosed by Bibikova in place of whole genome bisulfite sequencing. One would have been motivated to have done so in order to have provided the benefits set forth by Bibikova of providing a more affordable, rapid and high-throughput assay for assaying for the methylation status of the CGIs and generating high quality sequencing reads.
Modification of the method of Legendre so as to have used the method of Bibikova for bisulfite treating the cfDNA, amplifying the bisulfite treated DNA and sequencing the amplified bisulfite treated DNA would have resulted in a method that necessarily amplifies and provides sequence reads for at least one of the CGIs listed in Table 1, given the extensive CGI coverage of the method of Bibikova..
Regarding claim 5, Legendre teaches that the sample is a plasma sample (e.g., p. 8 “Sample acquisition and DNA extraction”).
Regarding claim 6, Legendre teaches that the sample is obtained from a subject suffering from cancer (e.g., p. 8 “Sample acquisition and DNA extraction”).
Regarding claim 13, Legendre does not specifically exemplify a method wherein a second sample is obtained from the patient after the patient has received a cancer treatment; the second sample is treated with bisulfite; the bisulfite treated DNA in the second sample is amplified; and the amplified bisulfite-treated DNA from the second sample is sequenced by NGS to generate a second dataset comprising sequencing reads for the at least on CGI.
However, Legendre teaches that the methylation profile of subjects having metastatic breast cancer are different from that of healthy subjects and disease free survivors (DFS) and that the methylome of DFS more closely resembles that of healthy subjects (e.g., p. 2 “GBS demonstrated global hypomethylation and focal hypermethylation in cfDNA of MBC compared with H and DFS, which had a high degree of similarity” and p. 6, col. 1). The reference states “This signature is a potential blood-based biomarker that could be advantageous at the time of surgery and/or after the completion of chemotherapy to indicate patients with micrometastatic disease who are at a high risk of recurrence and who could benefit from additional therapy” (see abstract). The reference concludes “We anticipate that a DNA hypermethylation signature, involving rationally selected CpG hotspots detectable in circulation, can be used to indicate micrometastatic disease in the pre-macrometastatic setting and predict patients at a high-risk of recurrence who could benefit from additional therapy” (p. 8, col. 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Legendre so as to have also obtained a second sample from the patient after the patient is treated and to have assayed for the methylation status of CGIs in the second sample by amplifying bisulfite treated DNA from the second sample and performing sequencing with the HumanMethylation450 array of the amplified, bisulfite treated DNA. One would have been motivated to have done so in order to have generated additional data regarding changes in the methylation status of CGIs in the patient over time and to have compared the changes with those that occur in healthy subjects and DFSs.
11. Claim(s) 7 is/are rejected under 35 U.S.C. 103 as being unpatentable over Legendre et al. (Clinical Epigenetics. 2015. 7: 100; p. 1-10), in view of Bibikova et al (Genomics. 2011. 98: 288-295; cited in the IDS of 07/16/2026), and further in view of Miller et al (Biomolecules. 2016. 6: 45, p. 1-14).
The teachings of Legendre and Bibikova are presented above.
While Legendre teaches that the sample is obtained from a patient having metastatic breast cancer (MBC), Legendre does not teach that the sample is obtained from a subject having breast invasive carcinoma.
However, Miller teaches that the CpG island methylator phenotype (CIMP) is a pattern of extensive DNA hypermethylation at cytosines located in CpG islands (CGIs; p. 1, final para). Miller teaches analyzing TCGA data on CGI methylation status obtained from studies using, for example Illumina Infinium HumanMethylation27k and HumanMethylation450K arrays to characterize methylation patterns in cancers, including breast invasive carcinoma (e.g., p. 4; p. 5 first para and Figure 2). Miller (p. 5, first para) states:
“we were able to show overall survival curves exhibiting significant differences based on CIMP‐positive and CIMP‐negative subgroups for four cancer types (breast invasive carcinoma, BRCA; kidney renal clear cell carcinoma, KIRC; lung squamous cell carcinoma, LUSC; uterine corpus endometrial carcinoma, UCEC) (Figure 3); overall survival curves for luminal A and luminal B subtypes in BRCA also differed by CIMP.”
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Legendre so as to have specifically applied the method to patients having breast invasive carcinoma. One would have been motivated to have done so because Miller teaches detecting CGI methylation status in patients having breast invasive carcinoma and that data regarding the CGI methylation status of breast invasive carcinoma can be used to predict overall survival of patients and to distinguish between survival of patients having luminal A and luminal B subtypes of breast invasive carcinoma. Thus, such a modification of the method of Legendre would have provided the benefit of determining the methylation profile of CGIs in patients having breast invasive carcinoma and of generating additional data that could be used to further characterize breast invasive carcinoma.
Conclusion
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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/CARLA J MYERS/Primary Examiner, Art Unit 1682
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