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 .
Election/Restrictions
Applicant’s election without traverse of “claims 8-13 (Invention Group II)” and “POU4F1 (as target gene)” and “blood sample (as biological sample)” in the reply filed on December 23, 2024 is acknowledged.
Upon further consideration, the examiner has withdrawn the requirement for restriction with respect to groups I, II, and III as well as the election of species with respect to species of a “biological sample” recited in claim 16.
The election of species requirement with respect to “methylation of the POU4F1 gene or of the HOXD8 gene” is maintained.
In the event that claim(s) directed to methylation of the POU4F1 gene are found to be allowable, any combination comprising methylation of the POU4F1 gene will be considered for rejoinder.
Claim Status/Action Summary
This action is in response to the papers filed on July 22, 2026.
Claims 7 and 11 require determining the level or amount of methylation of the POU4F1 gene and the HOXD8 gene. Applicant elected “POU4F1” as the target gene. Therefore, claims 7 and 11 are withdrawn as directed to a non-elected species (the combination of POU4F1 and HOXD8).
Claim 2 was canceled in the response dated July 22, 2026.
Claims 1, 3-6, 8-10, 12-14, and 16-18 are under examination.
Any objections and rejections not reiterated below are hereby withdrawn.
Priority
This application is a 371 of PCT/EP2020/065099, filed on May 29, 2020 and claims priority to the foreign application EPO 19305695.9, filed on May 29, 2019.
Specification
The listing of references in the specification (pages 28-29) is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code in paragraph 112, line 2. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of the terms “Applied Biosystems”, “EpiMark”, “TaqMan”, “Qiagen”, “Qubit”, “Invitrogen”, “Zymo”, “BioRad”, “KAPA”, “New England Biolabs”, “Raindance Technologies”, “Thermo Fisher”, “Promega”, which are trade names or marks used in commerce, has been noted in this application. Each term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Applicant is reminded that no new matter may be added by amendment.
This objection is reiterated from the previous office action. Applicant has not addressed the objection in the response dated July 22, 2026.
Applicant is reminded that under 37 C.F.R. 111, “reply by the applicant or patent owner must be reduced to a writing which distinctly and specifically points out the supposed errors in the examiner’s action and must reply to every ground of objection and rejection in the prior Office action. The reply must present arguments pointing out the specific distinctions believed to render the claims, including any newly presented claims, patentable over any applied references. If the reply is with respect to an application, a request may be made that objections or requirements as to form not necessary to further consideration of the claims be held in abeyance until allowable subject matter is indicated.”
Claim Rejections - 35 USC § 112 (a) – Scope of Enablement
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claim 14 is/remains rejected under 35 U.S.C. 112(a) because the specification, while being enabling for “a) determining the level or amount of methylation of POU4F1 gene in a biological sample of [a patient/said subject] and comparing said level or amount to a reference value”, does not reasonably provide enablement for “predicting the clinical outcome based on the comparison of step a)” for at least the following reasons.
This rejection has been updated as necessitated by the amendments to the claims.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Wands states at page 1404, “Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”
The nature of the invention and the breadth of claims:
Claim 14 is drawn to “a method for predicting a clinical outcome selected from overall survival, progression-free survival, or both” comprising the steps of: (a) determining the level or amount of methylation of POU4F1 in a biological sample of a subject, comparing said level or amount to a reference value; (b) predicting the clinical outcome based on the comparison of step (a); (c) selecting a treatment based on the predicted clinical outcome; and (d) administering the selected treatment, wherein the treatment is selected from surgery, chemotherapy, radiation therapy, and targeted therapy.
The state of the art:
The invention is in a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
The prior art teaches that a “clinical outcome” is “an outcome that describes or reflects how an individual feels, functions, or survives” and “an outcome is a measurable characteristic (clinical outcome assessment, biomarker) that is influenced or affected by an individual’s baseline state or an intervention as in a clinical trial or other exposure.” (FDA-NIH Biomarker Working Group. BEST (Biomarkers, Endpoints, and other Tools) Resource. Silver Spring (MD): Food and Drug Administration (US); 2016-. Glossary. 2016 Jan 28) The National Cancer Institute teaches that an outcome is “a specific result or effect that can be measured. Examples of outcomes include decreased pain, reduced tumor size, and improvement of disease.” (PDQ Cancer Information Summaries. Bethesda (MD): National Cancer Institute (US); 2002-. Dictionary of Cancer Terms.) Furthermore, Wilson et al., “Outcomes and endpoints in trials of cancer treatment: the past, present, and future” The Lancet Oncology, Volume 16, Issue 1, e32-e42 teaches examples of clinical outcomes in the context of cancer trials include: overall survival, progression-free survival, time to progression, symptom improvement, disease-free survival, objective response rate, complete response, clinical benefit rate, stable disease, and measures of quality of life. (Wilson, Table 1 and Figure 2)
US 2018/0258498 A1 (Ahlquist) teaches diagnosing and predicting the outcome of pancreas cancer in a subject using methylation markers comprising POU4F1. (Ahlquist 0199) Ahlquist teaches POU4F1 is a differentially methylated region in patients with pancreatic cancer compared to non-cancerous controls by reduced representation bisulfite sequencing (RRBS) and methylation states of markers can be correlated with cancer risk, prognosis, determining treatment efficacy, or progression of the cancer. (Ahlquist 0199) However, Ahlquist does not provide evidence that a single marker is associated with, or predictive of, a specific clinical outcome.
Post-filing date, the search for reliable diagnostic and prognostic markers for pancreas cancer appears to be ongoing. Bardol et al., BMC Cancer (2024) 24:709, “Early detection of pancreatic cancer by liquid biopsy “PANLIPSY”: a French nation-wide study project” teaches a clinical trial designed to achieve early detection of Pancreatic ductal adenocarcinoma (PDAC) with high specificity and sensitivity, using a combinatorial approach. Bardol teaches measuring multiple markers in blood samples comprising: circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) (a combination of hypermethylated and control genes including POU4F1), Extracellular Vesicles (EVs), circulating immune cells, circulating cell-free nucleosomes, circulating proteins, and circulating microbiota. (Bardol, fig. 2) Bardol further teaches that assays based on a single analyte (i.e. ctDNA alone) have a low positive predictive value and are not sufficient for screening purposes. (Bardol, page 2, column 2, paragraph 2, lines 17-19) Additionally, Bardol teaches that early cancer detection by liquid biopsy needs to rely on a combination of circulating biomarkers to obtain a precise cancer profile; and liquid biopsy use for the early detection of pancreas cancer faces serious challenges concerning the specificity and sensitivity of the current assays. (Bardol et al., pg 2, column 2, paragraph 2, lines 19-26)
Similarly, Wu et al., BMC Med 20, 458 (2022) “Noninvasive detection of pancreatic ductal adenocarcinoma using the methylation signature of circulating tumour DNA” teaches an assay for diagnosing pancreas cancer comprising measuring a combination of 56 significant methylation markers in circulating blood (Wu et al, page 1, Results) rather than any single marker. Wu teaches that previous studies using individual differentially methylated sites or genes may not capture the complex biology of pancreas cancer. (Wu, page 14, column 2, paragraph 4) Applicant’s own work, Pietrasz et al., British Journal of Cancer 126:440-448 (2021) “Prognostic value of circulating tumour DNA in metastatic pancreatic cancer patients: post-hoc analyses of two clinical trials” teaches overall and progression free survival (i.e. a clinical outcome) is negatively correlated with a ctDNA marker comprising hypermethylation of a combination of genes that includes POU4F1. (Pietrasz, 2021, figure 2 and page 441, column 1, paragraph 8). Pietrasz teaches that the sensitivity of detection of pancreas cancer in tumor tissues was 79% when considering a combination of markers comprising POU4F1. (Pietrasz, page 441, column 2, line 14) However, Pietrasz teaches that the ctDNA marker is not significantly associated with WHO score (a measure of patients’ ability to perform pre-disease daily activities; i.e. a clinical outcome). (Pietrasz, table 1)
Munnings et al., Cancers, 16(19), 3335 (2024) “Evolution of Liquid Biopsies for Detecting Pancreatic Cancer” reviews multiple studies of circulating tumor DNA (ctDNA) hypermethylation, including applicant’s post filing date work (Pietrasz et al 2021). Munnings concludes that the sensitivities of ctDNA hypermethylation tests remain generally low (56.8% for the combination of markers in a large cohort of 372 patients with metastatic pancreas cancer taught by Pietrasz 2021 (Munnings, page 5, paragraph 3, lines 2-4)) and thus have limited clinical utility. (Munnings, page 5, paragraph 3- page 6, paragraph 1) Munnings teaches that studies of ctDNA hypermethylation-based prognostic tests “show potential for ctDNA analysis to guide patient management… but further studies in larger cohorts will be required for clinical validation.” (Munnings, page 6, paragraph 2-3)
It is therefore unpredictable whether POU4F1 hypermethylation alone (i.e. the elected species) is predictive of the full scope of clinical outcomes, as Pietrasz teaches hypermethylation of a combination of genes comprising POUF41 is associated with some clinical outcomes, such as overall survival and progression-free survival, but not a measure of quality of life.
Guidance in the Specification and Working Examples
The specification teaches that POU4F1 is differentially methylated in subjects with pancreas cancer compared to controls, (Figure 1) and the sensitivity and specificity of detection of POU4F1 alone differs from that of a combination of markers comprising POU4F1. (Tables 5 and 6).
The specification does not teach an association between a clinical outcome and POU4F1 hypermethylation alone. Rather, the association between overall and progression-free survival probabilities and ctDNA status are presented for the combination of markers. (Specification, figures 3-4 and page 25, paragraph 3)
The specification defines that a reference value is obtained in a biological sample from a subject that does not have pancreatic cancer, a subject that has been diagnosed with pancreatic cancer, or a non-cancerous biopsy sample from the subject being tested (Specification, page 11, line 18- page 12, line 5)
The specification teaches that POU4F1 hypermethylation has a detection sensitivity of 80% and a specificity of 94% in a small group of 20 pancreatic tumor samples. The specification teaches that “good analytical sensitivity can be achieved only by combining several markers or by complementing pre-existing screening tests, because a single-marker approach is unlikely to have a sufficient sensitivity (>90%)”. (page 4, lines 1-5)
Therefore, it is unpredictable whether detection of hypermethylated POU4F1 alone is sufficiently sensitive to predict a clinical outcome, as the analysis provided in the specification demonstrating an association between “ctDNA status” and measures of survival are restricted to a combination of markers rather than POU4F1 alone and applicant’s post-filing date work teaches lower sensitivity of the combination marker in a larger cohort of patients compared to the analyses conducted prior to the filing date of the instant application.
Quantity of Experimentation
Claim 14 is broadly drawn to a method of predicting overall survival or progression-free survival in a subject with pancreas cancer based on a comparison between the level or amount of methylation of the POU4F1 gene to a reference value.
The specification teaches an association between overall survival or progression-free survival and hypermethylation of a combination of markers comprising POU4F1 relative to a reference value. (figures 3-5) The analysis described in the specification linking a hypermethylated ctDNA marker to clinical outcomes is limited to measurements of the level or amount of methylation of POU4F1 and HOXD8 in combination. The specification does not provide any analysis of elected POU4F1 methylation alone.
The prior art teaches that “clinical outcomes” are a very broad category of measurable characteristics that describes or reflects how an individual feels, functions, or survives that are influenced or affected by an individual’s baseline state or an intervention such as in a clinical trial or other exposure. (FDA-NIH Biomarker Working Group. BEST (Biomarkers, Endpoints, and other Tools) Resource) The art teaches examples of clinical outcomes in the context of cancer trials include: decreased pain, reduced tumor size, improvement of disease, (PDQ Cancer Information Summaries. Bethesda (MD): National Cancer Institute (US); 2002-. Dictionary of Cancer Terms) overall survival, progression-free survival, time to progression, symptom improvement, disease-free survival, objective response rate, complete response, clinical benefit rate, stable disease, and measures of quality of life. (Wilson, Table 1 and Figure 2)
Applicant’s post-filing date work demonstrates that a ctDNA marker comprising multiple hypermethylated biomarkers including POU4F1 is associated with measures of survival, but not with a quality-of-life measure (WHO score) (Pietrasz et al 2021, table 1 and table 2)
Therefore, it is unpredictable that the skilled artisan could predict any clinical outcome such as overall survival, progression-free survival, time to progression, symptom improvement, disease-free survival, objective response rate, complete response, clinical benefit rate, stable disease, and measures of quality of life for a given patient based on hypermethylation of POU4F1 alone as broadly claimed. Applicant’s own work demonstrates it is unpredictable that any particular clinical outcome is associated with methylation status of POU4F1 alone. The skilled artisan would be required to perform additional unpredictable experimentation to determine which, if any clinical outcomes would be associated with POU4F1 alone, as claimed.
The post-filing date art teaches that large-scale clinical trials to evaluate the utility of ctDNA markers (including combinations of hypermethylated POU4F1 with other markers) are ongoing (Bardol, figure 2). Furthermore, Munnings teaches that further studies in larger cohorts (i.e. larger clinical trials) are required to determine the effectiveness of hypermethylated ctDNA as a predictive indicator of pancreatic cancer response to treatment. (Munnings, page 6, paragraph 2-3) Together, the specification, the prior art, and post-filing date art teach that measurements of single markers are not sufficiently accurate for predicting clinical outcomes of pancreas cancer. Rather, ongoing clinical studies in large cohorts incorporate multiple markers (including POU4F1) to increase the sensitivity and specificity of detection and predictions of clinical outcomes of pancreas cancer. Therefore, the skilled artisan would find it unpredictable that one could predict clinical outcome using POU4F1 alone since the data in the specification is limited to analysis of two methylation markers. The skilled artisan would be required to perform additional undue experimentation to determine whether POU4F1 methylation alone would be predictive of any clinical outcome.
The quantity of experimentation in this area is large, since there is no guidance in the specification or art that supports a single biomarker that is adequately predictive of all clinical outcomes in pancreatic cancer. The post filing date art describes ongoing large-cohort (national-scale) clinical studies designed to identify combinations of markers comprising POU4F1 hypermethylated ctDNA that may improve detection and prognosis of pancreas cancer.
Level of Skill in the art
The level of skill in the art is deemed to be high.
Conclusion
In the instant case, given the breadth of the claim to predicting overall survival or progression-free survival based on the level of methylation of the POU4F1 gene in a subject with pancreas cancer, the lack of guidance provided in the specification and prior art as to how to predict the clinical outcome of pancreas cancer using only POU4F1 hypermethylation, the large quantity of ongoing experimentation in the art, lack of demonstrated working examples comprising only POU4F1, and the unpredictability of the art, balanced against only the high level of skill in the art, it is the position of the examiner that it would require undue experimentation for one of skill in the art to perform the method of claim 14 as broadly written.
Response to arguments
The response argues that the narrowing of the scope of “clinical outcome” to “overall survival, progression-free survival, or both” overcomes the 112(a) scope of enablement rejection of record for the following reasons:
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These arguments have been thoroughly considered and are not persuasive. As the response points out, the specification counts a sample positive for ctDNA when: POU4F1 and HOXD8 methylation is detected, OR “samples positive for only one marker gene were further analyzed by [NGS]. Samples that were also positive for the presence of a cancer-related mutation by NGS were further considered as positive for ctDNA” (specification, page 25, paragraph 3). As was described in the response, samples were not called ctDNA positive based on the presence of POU4F1 methylation alone, but rather in combination with detection of known cancer-related mutations by a different assay. While the specification does demonstrate that POU4F1 is hypermethylated in tumor tissue (i.e. not blood) relative to non-tumor tissue from the same subject (figure 1) and teaches a sensitivity and specificity of the presence of POU4F1 hypermethylation in isolation with the presence of a pancreatic cancer (table 5), the specification does not provide any data supporting the claim that POU4F1 hypermethylation is predictive of overall survival or progression-free survival in the absence of additional markers (e.g. HOXD8).
The response further argues that “the Wands factors weigh in favor of enablement… [because] the level of skill in the art is high… the specification provides reference-value definitions, the ddPCR assay, and the specific POU4F1 primers and probes… [and] overall survival and progression-free survival are the demonstrated endpoints” and further states “enablement… requires only that a person of ordinary skill in the art can make and use the claimed method without undue experimentation”.
These arguments have been thoroughly reviewed and are not persuasive for the following reasons. First, the specification does not show that POU4F1 hypermethylation is predictive of an outcome of a pancreas cancer, but only that POU4F1 is hypermethylated in tumor cells relative to non-tumor cells from the same subject and that POU4F1 hypermethylation can be used to detect the presence of (i.e. diagnose) pancreas cancer with a certain sensitivity and specificity. Furthermore, while the level of skill in the art is high, the lack of guidance provided in the specification and prior art as to how to predict the clinical outcome of pancreas cancer using only POU4F1 hypermethylation, the large quantity of ongoing experimentation in the art, lack of demonstrated working examples comprising only POU4F1, and the unpredictability of the art, balanced against only the high level of skill in the art, it is the position of the examiner that it would require undue experimentation for one of skill in the art to perform the method of claim 14 as broadly written.
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.
Claims 1, 3-7, and 16-18 are rejected under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
The following 112(b) rejections are new grounds of rejection necessitated by the amendments to the claims.
Claim 1, as amended, now recites conditional steps of “diagnosing… if the POU4F1 gene… is hypermethylated… as compared with a reference sample; and treating the subject for pancreas cancer…”.
Because the “diagnosing” step is recited as conditional, it is unclear whether the “diagnosing” and “treating” steps are required in all embodiments of the claimed method (e.g. when POU4F1 is not hypermethylated), or are exemplary of a preferred embodiment of the claimed method. Furthermore, it is unclear whether the “treating” step is conditional upon the “diagnosing” step, or whether the claim requires that all subjects are treated for pancreas cancer, regardless of the POU4F1 hypermethylation status. Under the broadest reasonable interpretation of the claim, in embodiments wherein the POU4F1 gene is not hypermethylated, it appears that the claim encompasses a method comprising only the “determining the level or amount of methylation of the POU4F1 gene” step. In this regard, the “treating” step is directed to in vivo, which is not encompassed by the preamble recited in in claim 1 “An in vitro method for ---".
Claims 3-6 and 16-18 are rejected as indefinite because they depend from and necessarily include the indefinite limitation of claim 1.
Claim Rejections - 35 USC § 101
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 1-5, 8-10, 12-14, and 16-18 are/remain rejected under 35 U.S.C 101 because the claimed invention is directed to non-statutory subject matter.
This rejection has been updated as necessitated by the amendments to the claims.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to
one of the four statutory categories, and (2) must not be wholly directed to subject matter
encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial
exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract
intellectual concepts are not patentable, as they are the basic tools of scientific and
technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106,
part II.
Based upon consideration of the claims as a whole, as well as consideration of
elements/steps recited in addition to the judicial exception, the present claims fail to meet
the elements required for patent eligibility.
Question 1
The claimed invention is directed to a process that involves a natural principle and a judicial exception.
Question 2A Prong I
The claims are taken to be directed to a natural phenomenon and abstract ideas.
Claim 1 is directed to “an in vitro method for diagnosing or identifying pancreas cancer in a subject… comprising determining the level or amount of methylation of the POU4F1 gene in a biological sample of said subject; diagnosing the subject… if the POU4F1 gene is hypermethylated… compared with a reference.” Claim 1 requires a comparison to make a diagnosis. Claim 8 is also directed to an in vitro method for monitoring the evolution of pancreas cancer in a subject, additionally comprising determining the level or amount of methylation at two time points and comparing the levels determined to each other or to a reference value. Further, Claim 13 requires adapting/modifying the therapeutic regimen for the subject based on the comparison between the two time points or to a reference value. Finally, Claim 14 requires predicting a clinical outcome in a subject based on comparing the level of POUF41 methylation in a subject to a reference value.
Claim 1 is directed to a process that involves the judicial exception of a law of nature/natural phenomenon (i.e. the natural correlation between the level or amount of methylation in the POU4F1 gene and diagnosing pancreas cancer) and abstract ideas: “determining the level or amount of methylation” and “diagnosing… if the POU4F1 gene is hypermethylated… as compared with a reference” (i.e. a comparison to a control). As written, the determining step encompasses the mental step of receiving a report because it does not recite an active step for determining the level by a specific active process. The comparison is an abstract idea.
Claim 8 is directed to a process that involves the judicial exception of a law of nature/natural phenomenon (i.e. the natural correlation between the level or amount of methylation in the POU4F1 gene and monitoring the evolution of pancreas cancer), an abstract idea (i.e. comparing the methylation level of POU4F1 determined in a subject with pancreas cancer at one time point to a second time point or to a reference value), and an abstract idea (i.e. determining the level or amount of methylation). As written, the determining step encompasses the mental step of receiving a report because it does not recite an active step for determining the level by a specific active process.
Claim 13 is directed to a process that involves the judicial exception of a law of nature/natural phenomenon (i.e. the natural correlation between the level or amount of methylation in the POU4F1 gene and the presence of pancreas cancer), an abstract idea (i.e. comparing the methylation level of POU4F1 determined in a subject with pancreas cancer at one time point to a second time point or to a reference value), and an abstract idea (i.e. determining the level or amount of methylation). As written, the determining step encompasses the mental step of receiving a report because it does not recite an active step for determining the level by a specific active process. Claim 13 further recites changing the therapeutic regimen for the subject based on the comparison, conditional upon “when the level or amount of methylation… is increased relative to the [first timepoint]”.
Claim 14 is similarly directed to a process that involves the judicial exception of a law of nature/natural phenomenon (i.e. the natural correlation between the level or amount of methylation in the POU4F1 gene and predicting the clinical outcome in a subject with pancreas cancer) and abstract ideas (i.e. comparing the methylation level of POU4F1 determined in a subject with pancreas cancer to a reference value and determining the level or amount of methylation). As written, the determining step encompasses the mental step of receiving a report because it does not recite an active step for determining the level by a specific active process.
A comparison to control is an abstract idea. (See MPEP 2016.04(a)(2)(III)(A); claims to “comparing BRCA sequences and determining the existence of alterations,” where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014)
A correlation that preexists in the human is an unpatentable phenomenon. The association between the level or amount of methylation of the POU4F1 gene and pancreas cancer presence, evolution, or outcome is a law of nature/natural phenomenon. The “diagnosing or identifying”, “monitoring”, and “predicting” steps recited by claims 1, 8, and 14, respectively, amount to no more than an “instruction to apply the natural law.” These diagnosing, monitoring, and predicting steps amount to no more than a mental step. Even if the step requires something more such as to verbalize the discovery of the natural law, this mere verbalization is not an application of the natural law to a new and useful end. Furthermore, the “diagnosing… if…” and “changing… when” steps recited by claims 1 and 13 are recited as conditional upon a result of (a) previous step(s) and are not required by all embodiments of the claims as presently written. Therefore, the “diagnosing”, “monitoring”, “predicting”, and “changing” steps do not require the process user to do anything in light of the correlation. These steps fail to provide the “practical assurance” sought by the Prometheus Court that the “process is more than a drafting effort designed to monopolize the law of nature itself.”
Question 2A Prong II
The exception is not integrated into a practical application of the exception. The claims do not recite any additional elements that integrate the exception into a practical application of the exception. While the claims recite “determining the level or amount of methylation of the POU4F1 gene… in a biological sample of a subject”, this is not an integration of the exception into a practical application. Instead, this element is data gathering required to perform the method. Furthermore, while the claims recite “the sample in step a) is obtained prior to the treatment for pancreas cancer and the sample in step b) is obtained after said subject has been treated for pancreas cancer in step a)”, this is not an integration of the exception into a practical application.
With respect to Claim 10, the treatment of a subject prior to data analysis is not an integration of the judicial exception. Rather, this step constitutes extra-solution activity required to gather data necessary for the method.
With respect to Claim 13, the “changing the therapeutic regimen for the subject based on the comparison… when the level or amount of methylation… is increased relative to the level or amount determined in step (a)” and “treating… with the changed therapeutic regimen… when the level or amount of methylation… is increased…” is not an integration of the judicial exception. Claim 13 does not require the user administer any particular therapy based on the correlation observed by the method. This step is not required by all embodiments of the claims and thus does not require the user to do anything in light of the correlation. Rather, this step is equivalent to mere instructions to apply the judicial exception because it recites only the idea of a solution “changing” with no restriction on how the result is to be accomplished beyond the general instruction to change the preexisting therapeutic regimen. (i.e. no description of a particular therapy based on the natural correlation between POU4F1 hypermethylation and stable or persistent disease). Furthermore, “treating the subject for pancreas cancer by administering a treatment selected from surgery, chemotherapy, radiation therapy, and targeted therapy” steps do not integrate the judicial exceptions into a practical application of the exceptions at least because, when recited a high level of generality, any “surgery”, any “chemotherapy”, any “radiation therapy”, or any “targeted therapy” do not constitute a particular treatment, but rather merely refer the process user to a relevant technological field (oncology) wherein the judicial exceptions may be generically “applied”.
Question 2B
The second step of Alice involves determining whether the remaining elements, either in isolation or combination with the other non-patent eligible elements, are sufficient to “transform the nature of the claims into a patent eligible application” Alice, 134 S. Ct. at
2355 (quoting Mayo, 132 S. Ct. at 1297).
The claims are not sufficiently defined to provide a method which is significantly more than a statement of a natural principle for at least these reasons:
The claims do not apply or use the recited judicial exceptions to effect a particular treatment or prophylaxis, but rather recite “treating the subject for pancreas cancer by administering a treatment selected from surgery, chemotherapy, radiation therapy, and targeted therapy”. When recited at this extremely high level of generality, these “treating” steps recited by the claims do not meaningfully limit the claim by going beyond generally linking the use of the judicial exception to a particular technological environment.
The claims do not add a specific limitation other than what is well-understood, routine, and conventional in the field. Steps directed to determining the level or amount of methylation of the POU4F1 gene (before and after, or irrespective of “a subject has been treated for pancreas cancer”) are mere data gathering steps that amount to extra solution activity to the judicial exception. Claims 4-5 recite “determining the level or amount of methylation of the POU4F1 gene”: “by Next Generation Sequencing (NGS) or by quantitative PCR (qPCR)” or “in the nucleotide region of SEQ ID NO:1”. The determining step tells users to measure DNA methylation by NGS or qPCR. Determining the amount or level of methylation in DNA was well known in the art at the time the invention was made. The prior art, for example, Ahlquist, teaches measuring methylation of genes including POU4F1 in a subject’s blood for pancreas cancer diagnosis (Ahlquist, page 54 (table 10), and 0369) using Next Generation Sequencing (Ahlquist, 0041) or by quantitative methylation specific PCR (Ahlquist, 0297-0298). Furthermore, Zhang teaches determining the level or amount of DNA methylation in the nucleotide region of SEQ ID NO:1 in the POU4F1 gene. (Zhang, 0067 and Table 4) The claims do not require the use of any particular non-conventional reagents. Additionally, the specification teaches that NGS technologies such as whole-genome bisulfite sequencing and quantitative methylation specific PCR (qMS-PCR) are well known in the art. (Specification, page 13, lines 5-17) Even more, the specification teaches that digital PCR (dPCR) is used interchangeably with droplet digital PCR (ddPCR), and is routinely used in the art for clonal amplification of samples for Next Generation Sequencing. (Specification, page 14, lines 3-10)
Furthermore, 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 or as insignificant extra-solution activity:
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);
Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. Ltd. 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);
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)
Hybridizing a gene probe, Ambry Genetics, 774 F.3d at 764, 113 USPQ2d at 1247.
For these reasons, the claims are rejected under section 101 as being directed to non-statutory subject matter.
Response to arguments
The response asserts that the claims as amended integrate the recited judicial exceptions into a practical application and the ordered combination of steps recited by the claims amounts to significantly more than a statement of the judicial exceptions.
These arguments have been thoroughly reviewed and are not persuasive.
As described in the updated 101 rejection above, “changing the therapeutic regimen for the subject based on the comparison… when the level or amount of methylation… is increased relative to the level or amount determined in step (a)” and “treating… with the changed therapeutic regimen… when the level or amount of methylation… is increased…” is not an integration of the judicial exception. Claim 13 does not require the user administer any particular therapy based on the correlation observed by the method. This step is not required by all embodiments of the claims and thus does not require the user to do anything in light of the correlation. Rather, this step is equivalent to mere instructions to apply the judicial exception because it recites only the idea of a solution “changing” with no restriction on how the result is to be accomplished beyond the general instruction to change the preexisting therapeutic regimen. (i.e. no description of a particular therapy based on the natural correlation between POU4F1 hypermethylation and stable or persistent disease). Furthermore, “treating the subject for pancreas cancer by administering a treatment selected from surgery, chemotherapy, radiation therapy, and targeted therapy” steps do not integrate the judicial exceptions into a practical application of the exceptions at least because, when recited a high level of generality, any “surgery”, any “chemotherapy”, any “radiation therapy”, or any “targeted therapy” do not constitute a particular treatment, but rather merely refer the process user to a relevant technological field (oncology) wherein the judicial exceptions may be generically “applied”.
Furthermore, the claims do not apply or use the recited judicial exceptions to effect a particular treatment or prophylaxis, but rather recite “treating the subject for pancreas cancer by administering a treatment selected from surgery, chemotherapy, radiation therapy, and targeted therapy”. When recited at this extremely high level of generality, these “treating” steps recited by the claims do not meaningfully limit the claim by going beyond generally linking the use of the judicial exception to a particular technological environment.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1 and 5 are/remain rejected under rejected under 35 U.S.C. 102(a)(1) as being anticipated by Raphael et al., Cancer Cell 32, 185–203 August 14, 2017 “Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma”.
This rejection has been updated as necessitated by the amendments to the claims. This rejection is over claim 1 wherein the conditional “diagnosing said subject as suffering from pancreas cancer if the POU4F1 gene… is hypermethylated… as compared with a reference sample” is not satisfied (i.e. embodiments encompassed by the claims requiring only “determining a level or amount of methylation”.
Regarding claim 1, Raphael teaches determining the level or amount of methylation in tumor samples of pancreas cancer subjects (Raphael, page 185, Significance box) using the Illumina Infinium DNA methylation platform HumanMethylation450 (HM450) (Raphael, e9, paragraph 10) compared to unmethylated negative control DNA (Raphael, e10, paragraph 1) and to samples that were classified as non-cancerous by expert pathology review (Raphael, e10, paragraph 6). The Illumina array used by Raphael comprises probes specific to cg19497031, cg14123923, cg11806672, and cg02532577 in the POU4F1 gene. (See UCSC genome browser figure below) Therefore, Raphael teaches all of the limitations of claim 1.
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The limitation “diagnosing said subject as suffering from pancreas cancer if the POU4F1 gene… is hypermethylated… as compared with a reference sample “ encompasses the alternative negative case, wherein no method step is taken. It is noted that the steps recited in claim 1 are not required to be performed in any particular order as presently written. Therefore, the limitation “treating the subject for pancreas cancer by administering a treatment selected from surgery, chemotherapy, radiation therapy, and targeted therapy” is satisfied by the teachings of Raphael at least at page 187, column 1, paragraph 2 describing collection of samples by surgical resection of primary infiltrating adenocarcinomas of the pancreas.
Therefore, Raphael teaches all of the limitations of claim 1.
Regarding claim 5, Raphael teaches determining a level or amount of methylation of cg19497031, cg14123923, cg11806672, and cg02532577, which are all within the nucleotide region of SEQ ID NO: 1 of the claimed invention.
Response to arguments
The response asserts that Raphael’s measurement of differential methylation using the Illumina HM450 array which cover SEQ ID NO: 1 within the POU4F1 gene, does not “identify, measure, or report POU4F1 methylation…[and] the mere capability of a commercial platform to interrogate a locus is not an express or inherent disclosure of actually determining the methylation of that locus and using the result to diagnose pancreas cancer”.
This argument has been reviewed and is not persuasive for the following reasons: a) the argument is not commensurate in scope with the claim, which does not require a diagnosis step in all embodiments of the claim; b) Raphael teaches “DNA methylation status of up to 482,421 CpG and 3,091 non-CpG (CpH) sites throughout the genome. It covers 99% of RefSeq genes with multiple probes per gene, as well as 96% of CpG islands from the UCSC database and their flanking regions.”, therefore Raphael teaches “determining the level or amount of DNA methylation” at all loci represented on the cited array, which includes more than 9 probes within the transcribed region of POU4F1, of which 4 probes are within the recited SEQ ID NO: 1, and further, 1 probe is within the amplicon produced by the primers of SEQ ID NO: 5 and SEQ ID NO: 6.
Claims 1, 3-4, 8-10, 12-14, and 16-18 are/remain rejected under 35 U.S.C. 102(a)(1) as being anticipated by US 2018/0258498 A1 (Ahlquist).
This rejection has been updated as necessitated by the amendments to the claims.
Regarding claim 1, Ahlquist teaches a method of detecting pancreatic cancer comprising determining the level of methylation of the POU4F1 gene (Ahlquist, page 54, table 10) in a biological sample of a subject. (Ahlquist, 0369)
Additionally, Ahlquist further teaches that the change in the methylation state of a marker listed in Table 10 (i.e. POU4F1) is used for diagnosis of pancreas cancer. (Ahlquist 0013 and 0037) Ahlquist further teaches hypermethylation of the markers in table 10 (i.e. POU4F1) is associated with a cancer. (Ahlquist 0191)
Ahlquist further teaches methods for diagnosis of pancreatic cancer comprising measuring the level or amount of DNA methylation at differentially methylated region(s) including POU4F1 (Ahlquist, paragraph 0130-0135 and table 10).
Finally, Ahlquist teaches administering treatments to patients comprising performing surgery (Ahlquist, paragraph 0194).
Regarding claims 3, 16, and 17, Ahlquist teaches that the biological sample comprises blood (i.e. a body effluent). (Ahlquist, 0040 and 0192)
Regarding claim 4, Ahlquist teaches methylation may be determined by Next Generation Sequencing (Ahlquist, 0041) or by quantitative methylation specific PCR (Ahlquist, 0297-0298)
Regarding claim 8, Ahlquist teaches that monitoring the methylation state of the biomarker(s) (i.e. POU4F1) monitors the progression (i.e. evolution) of pancreatic cancer over time (i.e. determining and comparing the methylation level for at least two time points) during the course of therapy. (Ahlquist, 0197)
Regarding claims 9-10, Ahlquist teaches a first time point can be selected prior to initiation of a treatment and a second time point can be selected at some time after initiation of the treatment. Methylation states can be measured in each of the samples taken from different time points and qualitative and/or quantitative differences noted. (Ahlquist, 0199)
Regarding claim 12, Ahlquist teaches comparing measured methylation states to a normal control sample obtained from a patient who does not have cancer. (Ahlquist, 203)
Regarding claim 13, Ahlquist teaches determining the level of biomarkers comprising POU4F1 methylation before or during treatment, after treatment, comparing the two levels, and monitoring the efficacy of and selecting appropriate treatment (i.e. modifying the therapeutic regimen based on the comparison) (Ahlquist 0197).
Regarding claim 14, Ahlquist teaches changes in the methylation states of biomarkers comprising POU4F1 (i.e. determining the level of POU4F1 methylation compared to a reference value) over the time period can be used to predict clinical outcome. (Ahlquist 0199)
Regarding claim 18, Ahlquist teaches that determination of methylation can be accomplished by digital PCR (i.e. dPCR). (Ahlquist, 0072, page 9, column 1, line 12)
Response to arguments
The response asserts that Ahlquist does not teach that a diagnosis could be made based on POU4F1 methylation status because “Ahlquist’s mere listing of POU4F1 among hundreds of candidate markers does not disclose determining POU4F1 methylation and using that determination to diagnose the subject and treat the subject for pancreas cancer”.
These arguments have been thoroughly reviewed and are not persuasive. As described above, Ahlquist expressly teaches that the change in the methylation state of a marker listed in Table 10 (i.e. POU4F1) is used for diagnosis of pancreas cancer (Ahlquist 0013 and 0037). Ahlquist further teaches that the markers of table 10 may be used in combination to diagnose pancreatic cancers (Ahlquist paragraph 0137). It is noted that the claim as presently written does not require determining a level or amount of POU4F1 methylation alone in all embodiments of the claim, but rather uses open “comprising” language that encompasses methods of measuring POU4F1 methylation in combination with other markers.
Regarding the arguments referencing claim 5, these arguments are not relevant to the 102 rejection over Ahlquist, as this claim was not rejected under 35 U.S.C. 102 over Ahlquist in the first action on the merits dated February 27, 2025.
The response further asserts that Ahlquist teaches it does not reliably determine POU4F1 methylation in blood with reference to paragraph 0012, 0020, and 0211.
This assertion has been thoroughly reviewed is not persuasive. The references at 0020 and 0211 appear to be introductory statements setting forth the need for the invention described in Ahlquist, while the reference at 0012 is specific to three non-claimed markers in a “stool-based comparison” (e.g. not blood). Furthermore, Ahlquist explicitly teaches “the methods of the present invention are suitable for the analysis of biological samples of a heterogenous nature, e.g. a low concentration of tumor cells, or biological materials therefrom, within a background of a remote sample (e.g., blood, organ effluent, or stool).” (Ahlquist paragraph 0134).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application is 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, 3-5, 8-10, 12-14, and 16-18 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2015/116837 A1 (Zhang) in view of Ahlquist et al., US 2018/0258498 A1.
This is a new grounds of rejection adapted from the 102(a)(1) rejection of record over Zhang in the office action dated February 27, 2025 under the interpretation of the claims requiring treating the subject after the “determining” and “diagnosing” steps.
Regarding claims 1,3, 5 and 16-17, Zhang teaches a method of detecting methylation markers in plasma samples (i.e. a blood sample) from patients with pancreatic cancer and in normal individuals with no detectable cancer as negative controls, including POU4F1 methylation (Zhang, 0066-0067).
Zhang et al. further teach that methods of detecting methylation markers can be implemented as non-invasive monitoring of tumor loads in cancer patients after treatments or early-stage cancer detection (Zhang et al., paragraph 0034).
Zhang et al. do not appear to explicitly teach treating a subject for pancreas cancer after “determining” and “diagnosing” steps.
However, Ahlquist teaches that the change in the methylation state of a marker listed in Table 10 (i.e. POU4F1) is used for diagnosis of pancreas cancer. (Ahlquist 0013 and 0037) Ahlquist further teaches hypermethylation of the markers in table 10 (i.e. POU4F1) is associated with a cancer. (Ahlquist 0191)
Ahlquist further teaches methods for diagnosis of pancreatic cancer comprising measuring the level or amount of DNA methylation at differentially methylated region(s) including POU4F1 (Ahlquist, paragraph 0130-0135 and table 10).
Finally, Ahlquist teaches administering treatments to patients comprising performing surgery (Ahlquist, paragraph 0194).
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to have combined the methods comprising determining POU4F1 methylation in subjects in subjects that may have pancreas cancer, taught by Zhang, with the methods of treating subjects diagnosed for pancreas cancer based upon differential methylation at loci comprising POU4F1 with surgery, taught by Ahlquist et al. because both Zhang and Ahlquist teach diagnosis of pancreas cancer comprising determining the level of POU4F1 methylation and surgical resection is a well-known treatment for pancreas cancer, as taught by Ahlquist. The ordinary artisan would have been motivated to further treat subjects diagnosed by the methods of Zhang with the “performing surgery” step taught by Ahlquist because of the teaching of Ahlquist that pancreas cancer is routinely treated with potentially curative surgery (Ahlquist et al., paragraph 0003).
Regarding claim 4, Ahlquist teaches methylation may be determined by Next Generation Sequencing (Ahlquist, 0041) or by quantitative methylation specific PCR (Ahlquist, 0297-0298)
Regarding claim 5, Zhang teaches determining the level or amount of methylation is determined in the nucleotide region of SEQ ID NO: 1 in the POU4F1 gene, specifically “chr13:79176431-79176566” in pancreatic cancer patients relative to controls. (Zhang 0067, table 4, and UCSC browser figure below showing the location of the claimed sequences as well as the Zhang and Ahlquist POU4F1 targets on the human genome)
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Regarding claim 8, Ahlquist teaches that monitoring the methylation state of the biomarker(s) (i.e. POU4F1) monitors the progression (i.e. evolution) of pancreatic cancer over time (i.e. determining and comparing the methylation level for at least two time points) during the course of therapy. (Ahlquist, 0197)
Regarding claims 9-10, Ahlquist teaches a first time point can be selected prior to initiation of a treatment and a second time point can be selected at some time after initiation of the treatment. Methylation states can be measured in each of the samples taken from different time points and qualitative and/or quantitative differences noted. (Ahlquist, 0199)
Regarding claim 12, Ahlquist teaches comparing measured methylation states to a normal control sample obtained from a patient who does not have cancer. (Ahlquist, 203)
Regarding claim 13, Ahlquist teaches determining the level of biomarkers comprising POU4F1 methylation before or during treatment, after treatment, comparing the two levels, and monitoring the efficacy of and selecting appropriate treatment (i.e. modifying the therapeutic regimen based on the comparison) (Ahlquist 0197).
Regarding claim 14, Ahlquist teaches changes in the methylation states of biomarkers comprising POU4F1 (i.e. determining the level of POU4F1 methylation compared to a reference value) over the time period can be used to predict clinical outcome. (Ahlquist 0199)
Regarding claim 18, Ahlquist teaches that determination of methylation can be accomplished by digital PCR (i.e. dPCR). (Ahlquist, 0072, page 9, column 1, line 12).
Claim 6 is/remains rejected under 35 U.S.C. 103 as being unpatentable over US 2018/0258498 A1 (Ahlquist) in view of WO 2015/116837 A1 (Zhang), Rychlik (Nucleic Acids Research, Vol. 17, No. 21, Pg 8543-8551, 1989), and Buck (Biotechniques, Vol. 27, Pg. 528-536, 1999).
Regarding claim 6, Ahlquist teaches a method of detecting pancreatic cancer comprising determining the level of methylation of the POU4F1 gene (Ahlquist, page 54, table 10) in a biological sample of a subject. (Ahlquist, 0369) Ahlquist further teaches that the methylation markers are determined by quantitative allele-specific real-time target and signal amplification (QuARTS) assay (Ahlquist, 0163) Ahlquist teaches that the QuARTS assay comprises amplifying a target sequence with specific primers and binding a specific detection probe to the amplicon. Ahlquist additionally teaches that target sequences can be amplified by digital PCR (i.e. dPCR). (Ahlquist, 0072, page 9, column 1, line 12)
Ahlquist does not teach that the level of methylation of the POU4F1 gene is determined in the nucleotide region of SEQ ID NO: 1 in the POU4F1 gene. Rather, Ahlquist teaches a target amplicon ~800 bp upstream of the claimed target nucleotide region of SEQ ID NO: 1.
However, Zhang teaches a method of detecting methylation markers in plasma samples from patients with pancreatic cancer and in normal individuals with no detectable cancer as negative controls. (Zhang, 0066) Zhang further teaches multiple loci within the POU4F1 gene are differently methylated in pancreatic cancer patients relative to controls. (Zhang, 0067 and Table 4) Zhang teaches determining “methylation haplotypes” (the combinatorial or linked methylation status of multiple methylation sites in a single DNA molecule i.e. multiple loci within a single gene). Zhang teaches multi-locus haplotypes are robust to the presence of random technical errors on individual loci, and hence provide a much greater power in distinguishing true signatures at a low abundance from technical errors. (Zhang, 0032) Finally, Zhang teaches determining the level or amount of methylation is determined in the nucleotide region of SEQ ID NO: 1 in the POU4F1 gene, specifically “chr13:79176431-79176566”. (Zhang table 4 and UCSC browser figure below showing the location of the claimed sequences as well as the Zhang and Ahlquist POU4F1 targets on the human genome)
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Neither Ahlquist nor Zhang teach determining the amount of methylation using the primers of SEQ ID NO: 5 and SEQ ID NO: 6 and using the probe of SEQ ID NO: 9.
However, the probe of SEQ ID NO: 9 is identical to a portion of the padlock probe (SEQ ID NO: 2304 taught by Zhang. Additionally, the primers of SEQ ID NO: 5 and 6 and probe of SEQ ID NO: 9 differ from the naturally occurring sequence of POU4F1 only in that the non-CpG cytosines have been replaced with thymine (mimicking the known bisulfite-converted sequence) in order to specifically amplify and hybridize to the known bisulfite-converted sequence of SEQ ID NO: 1. Claimed primer SEQ ID NO: 5 and probe SEQ ID NO: 9 are within the padlock probe SEQ ID NO: 2304 taught by Zhang. Claimed primer SEQ ID NO: 6 is located 9 bases upstream from the padlock probe taught by Zhang. (See “zoomed in” UCSC browser figure below showing the location of the claimed sequences relative to the Zhang POU4F1 targets on the human genome and highlighted 9 base difference between the claimed primer SEQ ID NO:6 and the probe taught by Zhang)
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Rychlik teaches it is routine and predictable to make primers for DNA amplification wherein primers are designed to a known oligonucleotide sequence. Rychlik teaches criteria to design suitable primers for DNA amplification (see whole document and Abstract).
Buck expressly provides evidence of the equivalence of primers. Specifically, Buck invited primer submissions from a number of labs (39) (Pg. 532, Column 3), with 69 different primers being submitted (Pg 530, Column 1). Buck also tested 95 primers spaced at 3 nucleotide intervals along the entire sequence at issue, thereby testing more than 1/3 of all possible 18-mer primers on the 300 base pair sequence (Pg. 530, Column 1). When Buck tested each of the primers selected by the methods of the different labs, Buck found that every single primer worked (Pg 533, Column 1). Further, every single control primer functioned as well (Pg 533, Column 1). Buck expressly states, “The results of the empirical sequencing analysis were surprising in that nearly all of the primers yielded data of extremely high quality” (Pg. 535, Column 2). Therefore, Buck provides direct evidence that all primers would be expected to function, and in particular, all primers designed according to the ordinary criteria. This clearly shows that every primer would have a reasonable expectation of success.
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention for one of ordinary skill in the art to modify the method of diagnosing pancreatic cancer in a subject comprising determining the level of methylation of the POU4F1 gene using a single target amplicon, taught by Ahlquist, to further comprise multiple target amplicons within the POU4F1 gene (including in the region of SEQID NO: 1 and the Ahlquist target locus) as taught by Zhang. The ordinary artisan would have been motivated to modify the method of diagnosing pancreatic cancer by determining the level of methylation in POU4F1 using target-specific primers and probes, taught by Ahlquist, to additionally comprise determine the level of methylation in the region of SEQ ID NO: 1 as taught by Zhang by the teaching of Zhang that determining “methylation haplotypes” (the combinatorial or linked methylation status of multiple methylation sites in a single DNA molecule). Multi-locus haplotypes are robust with the presence of random technical errors on individual loci, and hence provide a much greater power in distinguishing true signatures at a low abundance from technical errors (Zhang, 0032) and the teaching of Zhang of the pancreatic cancer marker comprising a differentially methylated region between patients and healthy controls at chr13:79176431-79176566 (which is within the claimed SEQ ID NO: 1). (Zhang, table 4) The ordinary artisan would have been reasonably confident that measuring additional methylation markers in the POU4F1 gene, including at chr13:79176431-79176566, as taught by Zhang, would have successfully improved the method taught by Ahlquist because Zhang teaches that measuring multiple loci within a single gene provides much greater power in distinguishing true, low abundance signals from technical errors (noise). (Zhang, 0032)
With respect to Claim 6 and primers of SEQ ID NO: 5 and 6, and probe of SEQ ID NO: 9, Zhang teaches analyzing the region of SEQ ID NO: 1 directed to POU4F1. The probe target taught by Zhang overlaps instant SEQ ID NO: 5 and 9. The primer of SEQ ID NO: 6 anneals to the POU4F1 sequence 9 bases upstream of the target taught by Zhang. The ordinary artisan would have been motivated to design oligonucleotide primers and probes from the known POU4F1 sequence for the detection of methylation in a biological sample based on the teachings of Zhang and Ahlquist. The complete nucleotide sequence of POU4F1, which is disclosed in Zhang or (GenBank Accession Number Gene ID: 5457), presented the ordinary artisan with a finite number of possible primers for amplification of the methylated region. Then, since Buck taught that a large number of primers designed to detect the same target functioned reasonably well, an ordinary artisan would have expected predictable results, and thus would have had a reasonable expectation of success, when testing the finite number of possible amplification primers and probes suggested by Genbank Gene ID: 5457 and Zhang. The ordinary artisan would have been reasonably confident that any primer combination designed to amplify the known sequence of bisulfite-converted SEQ ID NO: 1, such as SEQ ID NO: 5 and 6 would have successfully amplified a target amplicon within said sequence because of the teachings of Rychlik and Buck that design of primers to known sequences is routine and predictable.
Response to arguments
The response asserts that: a) because Ahlquist and Zhang do not teach the sequence of SEQ ID NO: 6, but rather differs from the claimed invention in that the primer of SEQ ID NO: 6 anneals to the POU4F1 sequence 9 bases upstream of the target taught by Zhang, that “SEQ ID NO: 6 falls outside the region that Zhang actually teaches, and arriving at this specific primer is not merely a matter of designing a primer to a sequence disclosed by Zhang; b) that the proposed combination amounts to impermissible hindsight, and c) Ahlquist teaches that tissue-level methylation differences are obscured in distant samples and requires a “selection filter”, undercutting any reasonable expectation of success.
These arguments have been thoroughly reviewed and are not persuasive. As described in the 103 rejection of record:
The complete nucleotide sequence of POU4F1, which is disclosed in Zhang or (GenBank Accession Number Gene ID: 5457), presented the ordinary artisan with a finite number of possible primers for amplification of the methylated region.
Zhang teaches that measuring multiple loci within a single gene provides much greater power in distinguishing true, low abundance signals from technical errors (noise). (Zhang, 0032)
Rychlik and Buck teach that design of primers to known sequences is routine and predictable.
As previously described, these three teachings would have motivated the ordinary artisan to select any number of primer pairs from the sequence of POU4F1 for methylation analysis.
In support of this argument, it is noted that all of the probes and primers for POU4F1 taught by Alquist and Zhang (and claimed SEQ ID NO: 1) fall within a single CpG island, predicted by the methods developed by G. Micklem and L. Hiller Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol. 1987 Jul 20;196(2):261-82. PMID: 3656447.
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In the absence of any particular unexpected result from the use of the primer SEQ ID NO: 6, it is the position of the examiner that, based upon the teachings discussed at length above, the ordinary artisan would have been motivated to select any number of primer pairs within the differentially methylated regions taught by Zhang and Ahlquist spanning the known CpG island in POU4F1, designed by routine methods, with a reasonable expectation that the primers would successfully amplify their target sequences, as taught by Rychlik and Buck.
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
Regarding the assertion that the “selection filter” and “obscured by background methylation” disclosures of Ahlquist undercut expectation of success, it is noted that the differentially methylated regions of tables 10 and 11 are “filtered” regions (Ahlquist, paragraph 0369) and Table 11 further teaches the area under the ROC curve (AUC) for each marker, including POU4F1, which was taught to have an AUC of 0.79 (Ahlquist, table 11). It is noted that this AUC appears to be commensurate with the single biomarker sensitivity and specificities taught in the present disclosure. Furthermore, as noted above, Ahlquist explicitly teaches “the methods of the present invention are suitable for the analysis of biological samples of a heterogenous nature, e.g. a low concentration of tumor cells, or biological materials therefrom, within a background of a remote sample (e.g., blood, organ effluent, or stool).” (Ahlquist paragraph 0134).
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ZACHARY MARK TURPIN whose telephone number is (703)756-5917. The examiner can normally be reached Monday-Friday 8:00 am - 5:00 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/Z.M.T./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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