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 .
Applicant’s arguments and amendments have been thoroughly reviewed and considered. For clarity of the record, the specific claims and remarks being considered are those submitted by Applicant on 3/30/2026. The restriction requirement has been rendered moot, and claims 1, 4-5, 7, 10-11, 14-15, 17, 20-23, 26-27, 29, 31, and 33-47 are pending and are examined on the merits herein.
Response to Applicant’s Amendments
Nucleotide and/or Amino Acid Sequence Disclosures
The specification was objected to for a defective Sequence Incorporation by Reference paragraph. In light of Applicant’s amendments to the specification submitted 3/30/2026, this objection has been withdrawn.
Claim Objections
Claims 1, 11, 23, 26-27, and 33 were objected to for various issues. In light of Applicant’s amendments to the claims submitted 3/30/2026, these objections have been withdrawn. However, see new grounds of objection below.
35 USC 112(b) Rejections
Claims 1-20, 27-28, and 32-33 were rejected under 35 USC 112(b) for various indefiniteness issues. In light of Applicant’s amendments to the claims submitted 3/30/2026, these rejections have been withdrawn for all currently pending claims. Claims 2-3, 6, 8-9, 12-13, 16, 18-19, 28, and 32 have been canceled, and so these rejections have been rendered moot. See also new grounds of rejection below.
35 USC 112(d) Rejections
Claims 1-22 and 32 were rejected for being of improper dependent form.
For those claims preceding claim 23 that also depend on claim 23, Applicant recites MPEP 608.01(n) IV, which states that “the order of claims may change and be in conflict with the requirement that dependent claims refer to a preceding claim.” However, this section does not state that such ordering means that the claims cannot be rejected under 35 USC 112(d). In fact, in section III, the criteria for rejection under 35 USC 112(d) is provided where (i) specifically states that a claim in dependent form shall contain “a reference to a claim previously set forth.” Thus, Applicant’s arguments are not considered persuasive, and the rejections for claims 1, 4-5, 7, 10-11, 14-15, 17, and 20-22 for this reason are maintained. Claims 2-3, 6, 8-9, 12-13, 16, and 18-19 were canceled, and so these rejections are rendered moot. See also new grounds of rejection below.
It is noted that Applicant’s arguments against the rejection of claims 21-22 described in para. 34 of the Non-Final Rejection were persuasive, and that Applicant’s amendments to claims 1 and 32 render the rejections of paras. 32 and 35 of the Non-Final Rejection, respectively, moot.
35 USC 102 Rejections
Claims 21-24, 27-28, 30, and 33 were rejected under 35 U.S.C. 102(a)(1) as being anticipated by Toung et al. (US 2017/0175205 A1).
In light of Applicant’s amendments to the claims submitted 3/30/2026, these rejections have been withdrawn for all currently pending claims. Claims 24, 28, and 30 have been canceled, and so these rejections have been rendered moot.
35 USC 103 Rejections
Claims 1-4, 8-9, 11-14, 18-19, 25, and 31 were rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1) in view of Feber et al. (US 2018/0305765 A1).
Claims 5-6 and 15-16 were rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1), in view of Feber et al. (US 2018/0305765 A1), and further in view of Yu et al. (US 2018/0334720 A1).
Claims 10, 20, and 32 were rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1), in view of Feber et al. (US 2018/0305765 A1), and further in view of Sadikovic et al. (WO 2019/195941 A1).
Claims 7, 17, and 29 were rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1), in view of Feber et al. (US 2018/0305765 A1), in view of Sadikovic et al. (WO 2019/195941 A1), and further in view of Ishioka et al. (US 2017/0356051 A1) and Kusunoki et al. (EP 3,483,282 A1).
In light of Applicant’s amendments to the claims submitted 3/30/2026, these rejections have been withdrawn for all currently pending claims. Claims 2-3, 6, 8-9, 12-13, 16, 18-19, 25, and 32 have been canceled, and so these rejections have been rendered moot. However, see “Response to Applicant’s Arguments” and new grounds of rejection below.
Double Patenting Rejections
Claims 21-23 and 27 are rejected under 35 U.S.C. 101 as claiming the same invention as that of claims 1 and 4 of prior U.S. Patent No. 11,851,711 B2.
Applicant argues that the instant claims comprise biomarkers for particular genomic regions in which the CpG sites lie, whereas the ‘711 patent recites particular CpG sites (Remarks, page 28). This argument is persuasive, and so these rejections have been withdrawn.
Claims 21-26 and 28-33 were rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-9 of U.S. Patent No. 11,851,711 B2. It is noted that although claims 21-23 were erroneously not included in the statement of rejection in the Non-Final Rejection, they are included in the body of the rejection (see para. 87 of the Non-Final Rejection).
Applicant states that these rejections should be withdrawn in view of the instant amendments or be held in abeyance. The former statement does not supply a substantive reply to the rejections, and the request for abeyance is an improper response to a non-statutory double-patenting rejection (see MPEP 804 I (B) 1).
It is noted that claims 24-25, 28, 30, and 32 have been canceled, and so these rejections have been rendered moot. The rejections for claims 21-23, 26, 29, 31, and 33 have been maintained. See also new grounds of rejection below for newly amended and newly added claims.
Claims 21-27 and 29-33 were provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-11 and 14-17 of copending Application No. 18/542,277 (reference application).
In light of the amendments made to the ‘277 application, these claims are no longer patentably indistinct from those of the instant application. Thus, the rejections for the currently pending claims have been withdrawn. Claims 24-25, 30, and 32 have been canceled, and so these rejections have been rendered moot.
Response to Applicant’s Arguments
Regarding the 35 USC 102 Rejections, the Toung reference only recites three of the claimed biomarkers, while newly amended claim 23 requires the use of at least five biomarkers. This is the basis for the withdrawal of these rejections from the currently pending claims.
Regarding the 35 USC 103 Rejections, Applicant argues that the use of the claimed biomarker regions produces unexpectedly good results, pointing to the analysis at para. 67 of the instant specification and Figures 5 and 9. This example used all ten of the claimed biomarkers. Figure 6C shows data for a subset of five biomarkers, and argues that said unexpectedly good results also apply in this case (Remarks, pages 25-26). It is noted that both of these examples are drawn to scenarios involving lung cancer patients. Applicant also argues that the claimed invention can be used in a pan-cancer assay for detecting the eight different cancers presented in Figure 4, which is allegedly unpredictable in view of the prior art.
In evaluating allegations of unexpected results, the criteria described in MPEP 716.02 is used. These criteria require that Applicant establish by what means the described results are unexpected and significant (MPEP 716.02(b)), show results that are commensurate in scope with the claimed invention (MPEP 716.02(d)), and must compare the results with that of the closest prior art (MPEP 716.02(e)).
In the data presented by Applicant, para. 67 of the instant specification and Figures 5A and 9 examines non-small cell lung cancer patients compared to controls, and specifically utilizes data from all ten biomarker regions. This data is therefore not commensurate in scope with independent claims 23 or 38, as neither of these claims require the use of samples from subjects with a particular type of cancer, nor do they require the use of all ten biomarkers, though the use of such biomarkers is encompassed by the claims. As this data is in comparison to a control group, and not to another set of biomarkers, it is also not clear that the claimed biomarkers produce unexpected results, as it would be expected that particular biomarkers can be predictive for particular diseases. Similarly, para. 70 and Figure 6C of the instant specification examines controls and non-small cell lung cancer patients with only five of the claimed biomarkers. The conclusion reached appears to be that the five biomarker subset performs better than the full ten biomarker set, casting doubt on Applicant’s allegedly unexpected results achieved with said ten biomarkers. Again, it is not clear that the results produced are unexpectedly good compared to other biomarkers that may exist in the prior art, and the data concerns a particular cancer and a number of biomarkers that is not wholly commensurate in scope with the claimed invention.
As to Applicant’s discussion of a pan-cancer assay, this also appears to use all ten biomarkers, compares results to non-cancerous controls, and examines multiple cancers individually (para. 21 of the instant specification). The explanation for the data is provided in para. 56 of the instant specification. This data presents similar issues with regard to unexpected results as described above – namely, it is not commensurate in scope with the claimed invention, it is unclear how the results are unexpected, and there is no comparison with the closest prior art.
It is noted that in Applicant’s Remarks, on page 27 they state, “These results could not have been predicted by any one or more of Toung, Feber, Sadikovic, Ishioka, and/or Kusunoki. For at least these reasons, all of the claims are non-obvious over this combination of references.” This is not a comparison with the closest prior art as discussed in MPEP 716.02(e), as no details concerning the prior art references, the data presented by said references, or how they compare to that of the instant data is provided.
Additionally regarding the recited references, Applicant argues that because each of these references include additional biomarkers other than those recited by the instant claims, this allegedly alters the principle of operation of each reference and further highlights Applicant’s results (Remarks, pages 26-27, joining para.).
In claim 23, the method comprises detecting DNA methylation in CpG sites of the listed biomarker regions. The exclusion of other biomarker regions is therefore not required. In claim 38, the method comprises the listed steps, and in (ii) and (iii) the amplification steps comprise using primers and/or probes for the listed biomarker regions, and therefore may include the analysis of additional biomarker regions. Thus, the fact that the cited references teach additional biomarkers that are not present in the instant claims does not obviate the obviousness rejections. It is not suggested by the Examiner that Toung only examine the biomarkers recited in the instant claims, and the combinations of references that incorporate additional biomarkers do not limit the additional biomarkers to only those claimed. The combination of references also still analyzes methylation of specific biomarkers/CpG sites, and so the principle of operation of the cited references is not considered to be altered.
Thus, Applicant’s arguments are not considered persuasive with regard to the references cited in the Non-Final Rejection. Due to Applicant’s amendments to the claims, new grounds of rejections are provided, but the relevant portions of the references cited in the previous rejections are reiterated below.
Claim Interpretation
Regarding the phrase “substantially cell-free sample,” in the instant specification, such a sample is noted to be blood plasma or blood serum from a subject (para. 35, 41, and 45). Thus, the use of a blood plasma or blood serum in the prior art will be considered a “substantially cell-free sample,” even if the prior art reference does not note it as such.
For simplicity, it is noted that the chromosomal regions written in the claims (e.g. chr11:43602597-43603195) will be referred to throughout this action with their associated CpG IDs as provided by Applicant in Table 1B of the instant specification.
Claim Objections
Claim 1 is objected to because of the following informalities: the preamble should read “The method of claim 23, further comprising…” Additionally, in b)ii), the phrase should end with “the one or more CpG sites; and.” Note the use of “CpG sites” to better match the language of claim 23, from which this claim depends. Additionally, to better correlate the steps described in claim 1 with the method of claim 23, step c) should read “detecting DNA methylation by specifically” rather than “quantifying methylation.” If Applicant wishes to still include the “quantifying methylation” language, it is recommended that a wherein clause be added to this step that includes language such as “wherein the detecting DNA methylation quantifies methylation in the one or more CpG sites,” or similar wording. Finally, at the end of step c) the phrase should end with “the one or more CpG sites in the amplicons.” Appropriate correction is required.
Note that the change to the detecting language would likely impact the language used in claim 5.
Claim 11 is objected to because of the following informalities: in the preamble, there should be a comma after “claim 37.” Additionally, it is recommended to remove the final phrase “with the one or more cancers,” as this specific language does not appear in claim 37, from which this claim depends, and claim 37 already establishes that the subject has “at least one of a plurality of cancers.” Appropriate correction is required.
Claim 23 is objected to because of the following informality: in the list of the biomarker regions, rather than “and” before the final biomarker region, the phrase “and/or” should be used. Appropriate correction is required.
Claim 37 is objected to because of the following informalities: in line 1, “subject” should read “human subject” in order to better match the language of claim 23. Additionally, in line 2, “methylation” should read “DNA methylation” in order to better match the language of claim 23. Appropriate correction is required.
Claim 38 is objected to because of the following informalities at the end of (ii):, “one or more CpGs” should read “one or more CpG sites; and.” Additionally, in line 3 of (iii), “single pair of” should be removed from “using the single pair of forward primer,” and at the end of (iii), “the at least one CpG in the” should read “the at least one CpG site in the.” Finally, in the wherein clause, in the list of the biomarker regions, rather than “and” before the final biomarker region, the phrase “and/or” should be used. Appropriate correction is required.
Claim 39 is objected to because of the following informality: in line 2, “at least two CpGs” should read “at least two CpG sites” to better match the language of claim 38. Appropriate correction is required.
Claim 40 is objected to because of the following informality: the wherein clause should read “wherein the combination of the forward primer, reverse primer, and probe for each biomarker region overlaps to bind to at least seven CpG sites.”
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 14-15 and 43-44 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.
Claim 14 recites “the amplifying” in line 1, but nowhere in claims 23, 37, or 11 is an amplifying step described. Therefore, this phrase lacks antecedent basis. It will be interpreted as though the detecting of claim 23 is intended to include such an amplification.
Claim 15 is rejected due to its dependence on rejected claim 14.
Claim 15 is also similarly rejected, as it recites “the quantifying” in line 1 and “the amplifying of step b)ii)” in line 2. Claim 14, from which this claim depends, does describe amplifying, but does not describe a step b)ii), and none of claims 23, 37, 11, or 14 describe a quantifying step. Thus, the phrase “the quantifying” lacks antecedent basis, and the specific amplifying of claim 15 is unclear relative to the amplifying of claim 14. It will be interpreted as though the detecting of claim 23 is intended to include such a quantifying step, and that the amplification step recited by claim 15 is the same as that of claim 14.
Claims 43 and 44 are rejected because they both recite “the DNA extracted in (i).” No extracting, extracted DNA, or (i) is recited in claims 23, 37, or 11, from which these claims depend. These terms therefore lack antecedent basis. It will be interpreted as though the extracted DNA recited in these claims is equivalent to the isolated DNA recited in claim 23.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 1, 4-5, 7, 10-11, 14-15, 17, 20-22, and 31 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 1, 4-5, 7, 10-11, 14-15, 17, and 20-22 are rejected as they all depend directly or indirectly on claim 23, making them of improper dependent form, as they do not make reference to a claim previously set forth, as required by the statue.
Claim 31 is rejected because the claim depends on claim 23, which already recites the use of “at least five” of ten biomarker regions. This means 5-10 of the biomarker regions may be examined. Claim 31 then specifically recites the use of 5-10 biomarker regions. Thus, this claim fails to further limit the subject matter of the claim upon which it depends.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 4, 11, 14, 21-23, 26-27, 31, 33, 37, 41-44, and 46 are rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1) in view of Feber et al. (US 2018/0305765 A1).
Toung teaches measuring methylation levels in cells (Abstract). CpG sites that are useful for monitoring colorectal cancer are set forth in Table II (para. 130). This Table II displays the markers cg00100121, cg01419831, and cg08189989. Example I shows the use of the markers in this table. Plasma samples were isolated from human blood (para. 159; instant claim 46). cfDNA was specifically extracted (para. 159; instant claim 27). The cfDNA was then bisulfite treated and purified, a DNA library was prepared, and targeted capture was performed using probes complementary to the biomarker sites of Table II (paras. 161-163; instant claim 33). The methylation level for each biomarker was then measured and further analyzed (paras. 166-170). This data was also used to confirm the presence of methylation in cancer cells, and para. 170 notes that these methods can be used for improved cancer diagnosis (see also paras. 154-155, 157, 169, 186, and Figure 3; instant claim 37).
Toung notes that the hg19 genome is examined, as a “demethylated” hg19 genome is used for comparison in embodiments of the invention (paras. 165, 180, and 196).
However, Toung only teaches three of the claimed biomarkers, and not at least five, as required in the instant claims.
Additionally, in comparing the method of Toung described above with the limitations of instant claim 1, Toung specifically teaches each step but b)ii) and the detection of methylation in amplicons specifically as recited in c), as amplification with specific primers is not noted by the reference, though specific probes are used (para. 163). It is noted that bisulfite treatment naturally produces the products described in step b)i), and that in Toung, a plurality of markers for different genes are used (see Table II). Additionally, Toung does teach that PCR may be used to measure methylation levels of bisulfite treated CpG sequences (paras. 71-72).
Feber teaches methods for determining the methylation status of particular locations in DNA related to bladder cancer in patients (Abstract). This reference teaches that methylation loci can be amplified via PCR, where a PCR-based approach can involve methylation-specific primers that hybridize to DNA with the methylated sequence of interest (para. 112). Particularly, Feber notes that methylation-specific primers that work with bisulfite-converted DNA can be designed with generally available and well-known software (para. 146). The reference also notes exemplary primers specific to methylated sequences (para. 206 and Table 2). In paras. 23-26, Feber notes that using methylation-specific primers can indicate if a particular region of interest is methylated or not based on the presence or absence of an amplified product, indicating that amplification will only occur if methylation occurs. Feber also notes methylation sites associated with bladder cancer in Table 1 (see paras. 246 and 250). This table includes cg00339556, cg14732324, and cg01419831 (note that this latter biomarker is shared with Toung). Feber notes that these markers are useful for diagnostic purposes (para. 103).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the PCR primer design and technique taught by Feber with the methods of Toung. Toung notes that PCR generally may be used to measure methylation levels, and the ordinary artisan would be motivated to incorporate PCR in the methylation measuring methods of Toung so that additional amplification product (i.e. the sequences of interest) would be present in the reaction mixture and could be analyzed, increasing overall method accuracy. Feber then notes that it is possible to use primers specific to only the methylated sequences of interest, so that the only amplification product present would be from methylated sequences – this would make analysis of methylation levels in downstream analyses more efficient, as there would be no need to filter out non-methylated amplification products. This would motivate the ordinary artisan. There would be a reasonable expectation of success as both Toung and Feber teach use of PCR primers, and Feber teaches that designing PCR primers for specific methylated regions can be accomplished by the ordinary artisan.
Additionally, prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to add the methylation markers described by Feber to the methods of Toung. Though the two references focus on different cancers, it would be motivating to the ordinary artisan to examine methylation biomarkers associated with different types of cancer together, particularly in cases where the type of cancer a patient may have is unknown and requires further testing, or in cases where cancer is in very early stages and may not be showing distinct symptoms. There would be a reasonable expectation of success as both Feber and Toung demonstrate the use of their biomarkers in association with cancer, and successfully measure the methylation levels of each target region.
Thus, claims 1, 4, 21-23, 26-27, 31, 33, 37, 41, and 46 are prima facie obvious over Toung in view of Ferber.
Regarding claim 11, Toung notes that their methods can be used before and after treatments to evaluate cancer progression. The reference specifically states that treatment options may be surgery, chemotherapy, or radiation therapy (paras. 109 and 111-112).
Regarding claim 14, as noted above, Toung teaches that PCR may be used to measure methylation levels of bisulfite treated CpG sequences (paras. 71-72).
Regarding claims 42 and 44, Toung also teaches that circulating serum DNA can be used as the sample in methylation analyses (para. 27).
Regarding claim 43, Toung teaches the use of plasma samples that were isolated from human blood, where cfDNA was specifically extracted (para. 159).
Claims 5 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1), in view of Feber et al. (US 2018/0305765 A1), and further in view of Yu et al. (US 2018/0334720 A1).
Regarding claims 5 and 15, Toung in view of Feber teaches the methods of claims 1, 4, 11, 14, and 23, as described above. However, neither of these references teach the use of qPCR during quantification and analysis of methylation.
Yu teaches measuring methylation levels of a specific gene associated with gastric cancer (Abstract). In their methods, they teach determining methylation status via the use of qPCR (para. 24), and Figures 9-14 detail quantification and analysis via qPCR (paras. 37-42). Para. 204 notes that qPCR can be used with bisulfite treatment, and paras. 212-219 detail an example associated with quantification and analysis using qPCR. Yu notes that these methods can aid in prognostic predication and non-invasive diagnosis of cancer (para. 219), and shows that these methods allow for comparison of methylation levels with those of normal samples (e.g. Figure 14B).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the qPCR described by Yu in the method of Toung in view of Feber. While Toung in view of Feber teaches PCR for amplifying methylated regions of interest, Yu shows that PCR can provide additional uses by using qPCR specifically – namely by aiding in quantifying and scoring methylation levels in samples. By utilizing amplification methods for not only amplification, but also for downstream processes, this limits the number of protocols and resources needed to perform the method of Toung in view of Feber, which would be motivating to the ordinary artisan. As Yu teaches that these qPCR methods are compatible with bisulfite treatments and the measurement of methylation levels, there would be a reasonable expectation of success.
Thus, the methods of claims 5 and 15 are prima facie obvious over Toung, in view of Feber, and further in view of Yu.
Claims 10, 20, 34-35, 45, and 47 are rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1), in view of Feber et al. (US 2018/0305765 A1), and further in view of Sadikovic et al. (WO 2019/195941 A1).
Regarding claims 10, 20, 34-35, 45, and 47, Toung teaches the methods of claim 23, and Toung in view of Feber teaches the methods of claims 1, 11, 23, and 37, as described above.
However, combined, these references only teach five of the ten claimed biomarkers (it is noted that both references teach cg01419831), and neither of these references teach any of the additional claimed biomarkers.
Sadikovic teaches methods for diagnosing prostate cancer involving measuring the methylation levels of particular CpG loci in a subject (Abstract). These target loci are presented in Table 1, and include cg08189989, cg01419831, cg01893212, cg07302069, cg03306374. These biomarkers can be used to diagnose prostate cancer, distinguish malignant from benign lesions, and aid in detecting metastasis (pages 5-6). Sadikovic specifically teaches that the methylation status and level of these markers can be measured (page 7, para. 1 and page 14, para. 4), and states that these markers are differentially regulated in prostate cancer specimens compared to normal tissue (page 8, para. 3). These markers can be targeted with specific probes (page 13, para. 3).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to add the methylation markers described by Sadikovic to the methods of Toung in view of Feber. Though this reference focuses on a different cancer than those presented in Toung (colorectal cancer) and Feber (bladder cancer), it would be motivating to the ordinary artisan to examine methylation biomarkers associated with different types of cancer together, particularly in cases where the type of cancer a patient may have is unknown and requires further testing, or in cases where cancer is in very early stages and may not be showing distinct symptoms. Additionally, Sadikovic teaches that prostate cancer is the most common malignancy in men, making its early detection and diagnosis of paramount importance in oncology settings (page 17, para. 3). There would be a reasonable expectation of success as Sadikovic demonstrates the use of their biomarkers in association with cancer, and successfully measured the methylation levels of each target region.
Thus, claims 10, 20, 34-35, 45, and 47 are prima facie obvious over Toung, in view of Feber, and further in view of Sadikovic.
Claim 36 is rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1), in view of Feber et al. (US 2018/0305765 A1), in view of Sadikovic et al. (WO 2019/195941 A1), and further in view of Ishioka et al. (US 2017/0356051 A1).
Regarding claim 36, Toung in view of Feber teaches the methods of claim 23, as described above.
Toung, in view of Feber, and further in view of Sadikovic teaches eight of the ten claimed biomarkers, and does not teach the detection of cg25875213 or cg14416371.
Ishioka teaches analyzing DNA methylation levels associated with colorectal cancer (Abstract). Table 7 lists the claimed biomarkers cg03306374, cg14732324, and cg25875213, and the methylation level of these markers was able to be measured to evaluate treatment effects (para. 117). Multiple markers at once can be used for this purpose (para. 19), and probes can be developed for the specific detection of these markers (paras. 20 and 73). Any of the genes in Table 7 may be evaluated (paras. 54 and 61).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to add the biomarkers described by Ishioka to the method of Toung, in view of Feber, and further in view of Sadikovic. Ishioka teaches additional biomarkers whose methylation levels can be useful for detecting and diagnosing colorectal cancer, which is already discussed in Toung. By adding additional markers for this cancer, this can provide more accurate testing results and clinical information, which may affect patient prognosis and treatment plans, thus motivating the ordinary artisan. There would be a reasonable expectation of success as Ishioka teaches the successful measuring of methylation levels of these biomarkers, and provides evidence that the sequences for these regions are known and can be hybridized to.
Thus, claim 36 is prima facie obvious over Toung, in view of Feber, in view of Sadikovic, and further in view of Ishioka.
Claims 7, 17, and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1), in view of Feber et al. (US 2018/0305765 A1), in view of Sadikovic et al. (WO 2019/195941 A1), and further in view of Ishioka et al. (US 2017/0356051 A1) and Kusunoki et al. (EP 3,483,282 A1).
Regarding claims 7, 17, and 29, Toung in view of Feber teaches the methods of claims 1, 11, 23, and 37, as described above.
Toung, in view of Feber, and further in view of Sadikovic teaches eight of the ten claimed biomarkers, and does not teach the detection of cg25875213 or cg14416371.
Ishioka teaches analyzing DNA methylation levels associated with colorectal cancer (Abstract). Table 7 lists the claimed biomarkers cg03306374, cg14732324, and cg25875213, and the methylation level of these markers was able to be measured to evaluate treatment effects (para. 117). Multiple markers at once can be used for this purpose (para. 19), and probes can be developed for the specific detection of these markers (paras. 20 and 73). Any of the genes in Table 7 may be evaluated (paras. 54 and 61).
Kusunoki teaches determining the likelihood of colorectal cancer by measuring methylation levels at particular CpG sites in a sample (Abstract). The CpG sites used can be those shown in Table 12 (para. 19). Table 12 shows cg14416371, and it is noted that patients have a high likelihood of developing colorectal cancer when this site has higher levels of methylation compared to controls (para. 23).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to add the biomarkers described by Ishioka and Kusunoki to the method of Toung, in view of Feber, and further in view of Sadikovic. Ishioka and Kusunoki teach additional biomarkers whose methylation levels can be useful for detecting and diagnosing colorectal cancer, which is already discussed in Toung. By adding additional markers for this cancer, this can provide more accurate testing results and clinical information, which may affect patient prognosis and treatment plans, thus motivating the ordinary artisan. There would be a reasonable expectation of success as Ishioka and Kusunoki teach the successful measuring of methylation levels of these biomarkers, and provide evidence that the sequences for these regions are known and can be hybridized to.
Thus, claims 7, 17, and 29 are prima facie obvious over Toung, in view of Feber, in view of Sadikovic, and further in view of Ishioka and Kusunoki.
Claims 38-40 are rejected under 35 U.S.C. 103 as being unpatentable over Toung et al. (US 2017/0175205 A1), in view of Feber et al. (US 2018/0305765 A1), in view of Yu et al. (US 2018/0334720 A1), and further in view of Shames et al. (WO 2013/170191 A1).
It is noted that claim 38 describes the use of “separate” qPCRs in (iii), but the term “separate” is not specifically defined in the instant specification. Thus, a “separate” qPCR reaction can be considered each individual use of a primer pair and probe as described in (iii), and does not necessarily require the use of a separate physical container.
Toung in view of Feber teaches the treatment of DNA with sodium bisulfite and the detection of CpG sites in at least five of the claimed biomarkers as described above in the rejection of claims 1 and 23. Yu also renders obvious the use of qPCR with the method of Toung in view of Feber, as described above in the rejection of claims 5 and 15. However, these references do not teach performing two amplification reactions as described in (ii) and (iii) of the instant claim. It is noted that Toung does teach the use of methylation-specific PCR (para. 72), and specifically notes that such PCR involves the use of multiple primers together in an amplification reaction.
Shames teaches measuring the methylation status of CpG islands for a specific DNA region (para. 32). This measuring can be done in association with cancer (paras. 6-7), including colorectal cancer (para. 34). Para. 42 describes a method including isolating DNA, treating it with sodium bisulfite, amplifying the CpG site with quantitative methylation specific PCR (QMSP), and determining the methylation level. Para. 43 notes that step c) (the amplifying step) can involve pre-amplification of the desired CpG site prior to quantitative methylation specific PCR. Para. 386 describes a specific example where the pre-amplification and QMSP PCR can involve the same primers and probes. These are shown in Tables 3 and 4. Para. 388 notes that these primers and probes were used together in a single reaction mix.
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the guidance provided by Shames to add a pre-amplification step as described by Shames before the qPCR described by Toung, in view of Feber, and in view of Yu. This pre-amplification was used in Shames on small amounts of DNA (picogram amounts of a sample, see para. 388), and the ordinary artisan would recognize that this would increase the chances that a target sequence could be readily analyzed in a sample with qPCR and other downstream methods, as the amount of said target would increase. Para. 84 of Toung teaches that the amount of DNA used in their method can be altered by changing the amount of blood drawn from a patient, but a pre-amplification procedure would eliminate the need for large blood draws, which would improve patient comfort. Para. 8 of Toung also notes that circulating tumor DNA is typically present in low quantities compared to non-tumor DNA, which would further motivate the ordinary artisan to turn to the pre-amplification methods of Shames. As Shames teaches that this pre-amplification can involve the same primers and probes as subsequent amplification reactions, there would be no need to design additional primers for the pre-amplification, simplifying the process for the ordinary artisan and providing a reasonable expectation of success that such pre-amplification could be done.
As noted above, Toung, in view of Feber, and in view of Yu render obvious the use of qPCR. However, Shames specifically teaches the use of QMSP PCR, which would provide the benefits of qPCR while also utilizing primers specific for methylation regions. Such specific targeting would motivate the ordinary artisan to use QMSP PCR specifically as the qPCR of Toung, in view of Feber, and in view of Yu, as this method is focused on the analysis of methylation sites. As Toung, Yu, Shames, and Feber (para. 112) teach methylation specific PCR, showing that this is a well-known amplification method, and providing a reasonable expectation of success.
Additionally, in Example I of Toung, the probes used to analyze each CpG site are used together for all of the markers described in Table 2 (paras. 163 and 165). Para. 72 also notes that when performing methylation specific PCR, pooling of primers for multiple sites is done (“PCR primers specific to each of the methylated and non-methylated states of the DNA are used in PCR amplification. Products of the amplification reaction are then detected…,” emphasis added). Thus, it would be prima facie obvious to perform the pre-amplification and QMSP together for the biomarkers of Toung, in view of Feber, in view of Yu, and further in view of Shames.
Thus, claim 38 is prima facie obvious over Toung, in view of Feber, in view of Yu, and further in view of Shames.
Regarding claim 39, Toung teaches in Example 1 that their probes are capable of targeting up to four CpG sites each (para. 158), and these probe sequences were chosen based on an existing array (the Illumina Infinium HM450 array) and based on particular design principles (Figure 1). Thus, in the method of Toung, in view of Feber, in view of Yu, and further in view of Shames described above, it would be prima facie obvious to use the same probe design for all biomarkers examined, as these biomarkers are all known (as evidenced by their Illumina nomenclature designation), and so probes could be designed in such a fashion, and this would ensure that each probe acts similarly to one another in terms of hybridization ability, providing clear comparable results between each biomarker.
Thus, claim 39 is prima facie obvious over Toung, in view of Feber, in view of Yu, and further in view of Shames.
Regarding claim 40, as noted above in the rejection of claim 39, each probe in Toung, in view of Feber, in view of Yu, and further in view of Shames can target four CpG sites. Though the specific number of CpG sites bound to a particular primer and probe set may depend on the specific gene/site being examined, it would be prima facie obvious that a similar design (i.e. being capable of hybridizing to 1-4 CpG sites) could be employed for the forward and reverse primers used in Toung, in view of Feber, in view of Yu, and further in view of Shames. Using the same design principles for the primers and probes would decrease the time and resources necessary for assay design overall, and as the design of the probes of Toung have been shown to successfully bind to and detect particular CpG sites, there would be a reasonable expectation of success. Additionally, as QMSP specifically uses primers that target methylation specific locations, it would be prima facie obvious to the ordinary artisan to design each primer of a primer pair to target at least one CpG site.
Thus, claim 40 is prima facie obvious over Toung, in view of Feber, in view of Yu, and further in view of Shames.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 21-23, 26-27, 29, 31, 33-36, 45, and 47 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-9 of U.S. Patent No. 11,851,711 B2. Although the claims at issue are not identical, they are not patentably distinct from each other.
Claim 1 of the ‘711 patent requires the use of ten CpG sites that correspond to those that encompass the listed biomarker regions in Table 1B of the instant specification, and so read on the claimed biomarker regions of instant claim 23. Both claims also require the use of primers or probes, and require a DNA sample isolated from a human subject. These CpG sites of claim 1 of the ‘711 patent are also encompassed by the regions described in instant claims 21 and 22 as listed in Table 1B of the instant specification. Instant claims 29, 31, 34-36, 45, and 47 require the detection of different numbers of these biomarkers (e.g. 5-10), but these claims all comprise the measurement of these biomarkers, and so can include additional biomarkers. Thus, measuring the ten biomarkers described in claim 1 of the ‘711 patent would also read on these claims.
Claim 2 of the ‘711 patent notes that PCR may be used to detect DNA methylation, and so reads on instant claim 26.
Claim 3 of the ‘711 patent requires bisulfite treatment and purification of DNA prior to methylation detection, and so reads on instant claim 33.
Claim 4 of the ‘711 patent requires processing the DNA to be cell-free, and so reads on instant claim 27.
Claim 5 of the ‘711 patent uses bisulfite treatment on cell-fee DNA taken from a liquid biopsy (e.g. blood serum or plasma) and amplifies it, using the ten methylation markers described in claim 1 of this patent. This claim thus reads on instant claims 21-23, which can involve the use of primers (which are used in amplification), as well as claims 27, 29, 31, 33-36, 45, and 47, for similar reasons as described above.
Claims 6-9 of the ‘711 patent describe various PCR parameters, and so read on instant claim 26, which requires any type of PCR protocol. Claim 8 specifically requires qPCR, and so also reads on claim 26, which notes the use of qPCR.
Conclusion
No claims are currently allowable.
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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/F.F.G./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681
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