DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This application is the national stage of PCT/CA2022/050220, filed 16 February 2022. The International Search Report and Written Opinion issued in the PCT application have been received and reviewed.
Priority
PCT/CA2022/050220 claims the benefit of the following US provisional applications: 63/150,249, filed 17 February 2021; 63/275,650, filed 04 November 2021; and 63/284,723, filed 01 December 2021. Claims 1-2, 4-7, 11-13, and 15 find basis in the earliest provisional application filed 17 February 2021. The claimed subject matter of dependent claims 8-10, directed to embodiments related to COVID-19, was first disclosed in provisional application 63/275,650 (filed 04 November 2021), while the subject matter of dependent claim 14, directed to a PBMC sample, was first disclosed in provisional application 63/284,723 (filed 01 December 2021).
Information Disclosure Statement
With regard to the IDS filed 19 April 2024, it is noted that:
Cite no FP1, CA-3129222-A1 was considered based on its English language abstract and the provided English equivalent document, WO 2020/163959 A1 (which was not separately cited, but which has been cited herein by the examiner [see PTO-892]); and
Cite no FP2 was considered based on the provided English language abstract (as a translation was not provided, although one is indicated as having been provided).
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see pages 11, 12, and 18 of the substitute specification filed 19 April 2024). 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.
Drawings
The drawings are objected to because Figure 1 is blurry. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Interpretation
Regarding independent claim 1 and claims dependent therefrom (claims 4-15), it is noted that:
the “wherein” clauses of the claim states what is indicated by a possible (but not required) result of the steps of “collecting”, “measuring”, and “comparing”, rather than setting forth any further concrete limitations on what is claimed (such as a requirement for a particular structure, or that steps be performed, etc.); thus, claim scope is not limited by this claim language (see MPEP 2111.04);
given that the method steps of “collecting”, “measuring”, and ‘comparing” inherently achieve a “monitoring” over time (with the claim language not requiring any changes/differences in level(s) of ABCF1 in different samples), the preamble recitation of “monitoring an inflammatory or immune response, an inflammatory and/or autoimmune disease” is interpreted as an intended use of the claimed method that is inherently met by the practice of the recited method steps; and
regarding the recitation of “c) comparing the level of ABCF1 in each of the samples”, it is noted that given the following “wherein” clause language (reciting optional/possible outcomes of the “comparing” as noted above), it is clear that the type of “comparing” being referenced pertains to comparing the level of ABCF1 in each of the samples collected at different pre-determined intervals with one another (i.e., while the claim does not literally state with respect to what levels are compared, the context of the claim makes this sufficiently clear).
Regarding independent claim 2, the “wherein” clause of the claim stating “wherein a correlation between the ABCF1 level in the patient sample and predefined ABCF1 levels [sic] indicates that the patient has said disease or disorder” indicates (as is the case with the “wherein” language in claim 1) a possible (but not required) result of the steps of “collecting”, “measuring”, and “comparing”, rather than setting forth any further concrete limitations on what is claimed (and accordingly, the preamble recitation of “diagnosing a disease or disorder” is interpreted as an intended use of the method that is not given patentable weight when comparing the claimed invention to the prior art, as the outcome required to achieve such “diagnosing” need not be met based on the language of the body of the claim) (see MPEP 2111.04, as well as MPEP 2111.02).
Regarding claim 12, it is noted that the claim is interpreted as encompassing measurement of any type of circulating biomarker DNA or RNA (as there is no references to any particular type of biomarker in the claim).
Claim Rejections - 35 USC § 112(b)/second paragraph
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-2 and 4-15 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1-2 and 4-15 are indefinite because it is unclear from the language of independent claim 1 whether the claims require monitoring both “an inflammatory or immune response” AND “an inflammatory and/or autoimmune disease”, or whether the claims also embrace methods in which only one or the other of these is monitored. The “wherein” clause of the claim clearly states that a decrease or increase in level of ABCF1 may serve as an indicator of either “inflammatory or immune disease….and/or…. disease”; however, the preamble language “method of monitoring an inflammatory or immune response, an inflammatory and/or autoimmune disease” is unclear with regard to whether monitoring of “an inflammatory or immune response” and “an inflammatory and/or autoimmune disease” are alternative embodiments embraced by the claims, or whether the claim is limited to methods in which both of these are monitored. As there are multiple reasonable interpretations of the claim language that impart different meanings and boundaries on what is claimed, further clarification is required. It is noted that for purposes of comparing the claimed invention to the prior art, the claims have been interpreted as having an intended use of either monitoring “an inflammatory or immune response” OR monitoring “an inflammatory and/or autoimmune disease” (as this is one reasonable interpretation of what is claimed).
Claims 1 and 4-15 are indefinite over the recitation in b) of claim 1 of the limitation “the patient”, because there is insufficient antecedent basis for this limitation in the claim. Claim 1 at a) recites “a subject”, not “a patient”; accordingly, clarification is required.
Claim 2 is indefinite over the recitation in the claim of the limitations ‘the levels of ABCF1” in c) and “the…predefined ABCF1 levels” in the “wherein” clause of the claim. As the claim previously refers to “the level” (singular) of ABCF1 in the patient sample, and a “predefined level” (again singular) employed in the “comparing’ of the claim, there is insufficient antecedent basis for the subsequent references to “the levels of ABCF1” and “the…predefined ABCF1 levels” (and this usage of plural “levels” also creates confusion as to whether something more is required that the previously recited “level”). Further clarification is therefore needed.
Claim 4 is indefinite because the claim recites a further limitation of the intended use of the claimed method (“for monitoring treatment”), as well as a further limitation on what possible outcomes of the method steps would indicate in the context of treatment (“wherein a decrease…indicates…”, etc.), however there are no recited method steps (either in claim 1 or in claim 4) imparting a requirement for performance of any type of treatment (for example, there is no active step of treating the subject/patient, no requirement for a subject undergoing treatment, etc.). Given the manner in which the claim is written, it is not clear what (if anything) is actually required by claim 4 with respect to any type of treatment, and thus the boundaries of what is claimed are not sufficiently clear; further, while some persons of skill in the art might interpret the claim as requiring some type of treatment/treating given the references to treatment in claim 4, the nature of what is/would be required is not clear.
Claim 5 is indefinite because it is unclear how the claim further limits claim 1 (from which it depends), and also unclear with regard to what is encompassed by various alternatives recited in the claim (particularly with regard to what is required/optional, as noted below). First, the claim initially states “wherein the disease is an inflammatory and/or autoimmune disease is selected from….” is confusing given that the type of disease recited in claim 1 is ”an inflammatory and/or autoimmune disease”; given this wording, it is unclear if the claim merely requires the alternative pertaining to “inflammatory and/or autoimmune disease”, or whether a more particular disease is required. Second, the wording of several alternatives set forth in the claims - “arthritis, including but not limited to Rheumatoid Arthritis and other autoimmune arthritis”, “thyroid autoimmune diseases including but not limited to…”, “inflammatory bowel disease including but not limited to…”, “neuroinflammatory diseases and disorders including but not limited to..” – does not make sufficient clear what is required for each of these alternatives. Some persons of ordinary skill in the art would interpret “including but not limited to” as requiring each of the specified conditions while allowing for additional such conditions, whereas other such artisans would reasonably interpret this language as referring to possible examples of conditions, without the claim actually requiring any of those listed examples (i.e., the claim language is so unclear that it could reasonably be interpreted in very different ways by different skilled artisans). Thus, while it is reiterated that claim 1 as written does not clearly require an embodiment related to “disease”, further clarification is required to ensure that the boundaries of the embodiments that do relate to disease are sufficient clear.
Claim 7 is indefinite over the recitation of the limitation “the disorder”, as claim 1 (from which the claim depends) does not recite/refer to any “disorder” (such that antecedent basis for this term is lacking, and the manner in which claim 1 is further limited is not clear).
Claims 8-10 are indefinite over the recitation of the limitation “the disease or disorder’ in claim 8 (from which claims 9-10 depend), with claim 9-10 each being further indefinite over the recitation of “the disorder”. Again, claim 1 does not refer to or require a “disorder”, and thus antecedent basis is lacking, and the manner in which these claims further limit claim 1 is unclear and unknown.
Claims 13-14 are indefinite over the recitation in claim 13 to “the sample(s)”, because it is unclear how claim 1 is being further limited. More particularly, claim 1 as written clearly requires multiple “samples”, and it is not clear whether claims 13-14 are further limiting of the type of all such samples, or whether the use of the term “sample(s)” is intended to indicate that only one sample of claim 1 may be of the specified type. As there are multiple reasonable interpretations of claims 13-14 that impart different boundaries on what is claimed, further clarification is required.
Claim 15 is indefinite over the recitation of the limitation “wherein the sample is a blood….and fine-needle aspirates” (i.e., reciting a single “sample” that appears to include numerous types of samples). There is insufficient antecedent basis in claim 1 for the limitation “the sample”, and it is also unclear how such a sample might include all that is required by the literal language of claim 15. As the claim appears to include typographical errors, for purposes of comparing the claimed invention to the prior art, claim 15 has been interpreted as requiring any one of the types of listed samples; however, further clarification is required.
Claim Rejections - 35 USC § 102
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-2 and 4-15 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Lavon et al (WO 2015/140793 A1 [24 Sept 2015]; cited herein).
While it is reiterated that Applicant’s claims as written do not clearly require monitoring or diagnosing disease, or any actual use of a treatment/therapy (as discussed above), it is noted that multiple sclerosis (MS) is among a list of preferred conditions recited in (non-limiting) dependent claim 5; further, the claims as written do clearly require “collecting” a sample/samples from a subject (and with regard to claim 1, multiple samples “at pre-determined intervals”), measuring “the level of ABCF1 in” (a) collected sample/samples, and comparing ABCF1 levels (in claim 1, with levels in other collected sample(s), in claim 2, with “a predefined level”).
Lavon et al teach methods “for diagnosing multiple sclerosis and predicting responsiveness to interferon treatment”, which methods comprise determining and employing gene expression levels/gene expression profiles in both diagnosing multiple sclerosis (MS) and predicting responsiveness of a subject’s MS to interferon (IFN) treatment (as well as “selecting a treatment regimen based on said prediction”); see entire reference, particularly the Abstract). Among the methods taught by Lavon et al are methods of predicting responsiveness of a subject to IFN treatment comprising determining expression levels of genes in a sample from a subject with a control value/reference expression value/expression pattern indicative of responsiveness, wherein the genes employed may be “any subset or combination” of genes selected from a group including ABCF1 (see pages 11-13, in particular page 11, line 29, regarding ABCF1; see also page 13 at lines 3-5 regarding use of a value from a “responder subject” or a “non-responder subject”); it is noted that such a control value/reference expression value inherently constitute a type of “predefined level” employed as a point of comparison, as recited in independent claim 2 (at c). It is also noted that Lavon et al exemplify detecting differential expression of ABCF1 in association with responsiveness of MS patients to IFN treatment; see Example 1 at page 31-32. Lavon et al teach preferred samples including blood, plasma, CSF or serum, and in particular PBMCs (i.e., a preferred sample meeting the requirements of dependent claims 13-14; see page 12 at lines 17-21). Lavon et al clearly teach obtaining a sample from a subject, including via collecting a sample; see again page 12, lines 17-21, and see page 16, line 29-page 17, line 6 regarding specific methods of collecting samples, such that Lavon et al teach “collecting samples” as required by a) of each of the independent claims. With particular regard to claim 1 and claims dependent therefrom, Lavon et al also teach an embodiment of their methods in which samples “are obtained at least once prior to IFN treatment” (with a preferred embodiment of “not more than about two hours before IFN treatment”), as well as “at least once after IFN treatment” (with preferred embodiments of “not more than 4, 3 or 2 hours following IFN treatment) (see page 13 lines 10-20); collection of samples at such time points clearly meets the requirement of collecting samples “at pre-determined intervals” as required by independent claim 1. Additionally, while it is reiterated that the claims do not require any particular outcome of the recited collecting, measuring, and comparing of the claims, Lavon et al teach comparing expression levels before and after treatment and drawing conclusions therefrom with regard to therapy responsiveness (e.g., Lavon et al state that a “significant different between the expression level…is indicative of the responsiveness” [page 13, lines 16-20]). With regard to “measuring the level” of disclosed genes, Lavon et al teach a variety of such methods in which RNA levels are detected (see pages 17-24). Thus, Lavon et al clearly teach methods in which all requirements of all of steps a)-c) of independent claims 1-2 are performed. With further regard to claim 1 and claims dependent therefrom, it is reiterated that the “wherein” language of the claim need not be given patentable weight (as discussed above), and the method steps disclosed by Lavon et al meet the requirements of “monitoring” an inflammatory/immune response and/or an autoimmune disease (specifically MS, as taught by Lavon et al), such that claim 1 is anticipated by Lavon et al. With further regard to claim 2, Lavon et al is also anticipatory of this claim, as all required method steps are taught, and as the claim does not require the “correlation” specified in the “wherein” clause, or achieving a “diagnosing” (as discussed further above) (although it is noted that Lavon et al do also teach applying their methods to MS diagnosis; see, e.g., the Abstract).
With further regard to dependent claim 4, Lavon et al clearly teach a monitoring of treatment (with IFN, for the application of treating MS), as outlined above (such that methods meeting the requirements of this indefinite claim is also clearly taught by Lavon et al). Regarding claim 5, while this claim is also indefinite, the claim appears to embrace MS as an alternative, and MS is addressed above (such that claim 5 is also anticipated to the extent that it is presently understood). Regarding claim 6, while Lavon et al do not reference Major Depressive Disorder, this claim is anticipated at least to the extent that it is direct to monitoring inflammatory/immune response to therapy via measurement of ABCF1 expression, as discussed above; it is reiterated that claim 1 as presently written appears to embrace methods related to “disease” only as an alternative embodiment (such that nothing related to “disease” is necessarily/clearly required by the claims). Regarding claims 7-10, these claims are also anticipated given that methods meeting all requirements of claim 1 are disclosed by Lavon et al, and these (indefinite) claims relate to a “disorder” and/or “disease or disorder”, which is not a limitation present in claim 1. Furthermore, it is noted that to the extent that the practice of the methods of the claims may, e.g., achieve diagnosis or allow for monitoring of additional conditions not taught by Lavon et al, Lavon et al anticipate what is claimed by virtue of disclosing methods including all method steps actually required by the claims; the discovery of a previously unappreciated benefit of the performance of such methods does not render that which is old patentable (see MPEP 2112). Regarding claim 11, Lavon et al teach embodiments of their methods in which, e.g., proteins are employed as labels for detection by antisera or monoclonal antibodies (see page 22 at lines 4-8), which meets the requirement of being a type of “immunoassay” (and it is also noted that Lavon et al teach that “level of expression” encompasses levels of both RNA and protein [page 17 at lines 19-23], and that their methods could also be implemented by detection of expressed protein rather than detection of expressed nucleic acids [see page 22 bridging to page 23]). Regarding claim 12, it is reiterated that Lavon et al teach that blood serum and plasma (i.e., samples that inherently contain “circulating biomarker DNA or RNA”) are preferred samples for use in their methods (see again page 12 at lines 17-21); it is also reiterated that blood/PBMCs are taught at page 12, lines 17-21 (meeting the requirements of claims 13-14). Regarding claim 15, Lavon et al teach blood/plasma/serum, as noted above, and also teach other samples types recited in the claim (as well as methods of collection thereof) (see again page 16, line 11-page 17, line 6).
Lavon et al thus anticipate all of claims 1-2 and 4-15.
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 1-2 and 4-15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Regarding claims 1 and 4-15, independent claim 1 recites “monitoring an inflammatory or immune response, an inflammatory and/or autoimmune disease” and “comparing” levels of ABCF1 in different samples, with the levels having been previously measured in collected samples; such a “monitoring” and “comparing” can be conducted entirely in the human mind (such as by reading/thinking about test results and the implications thereof), and the claims therefore recite an abstract idea (i.e., a type of judicial exception [JE]). Independent claim 2 similarly recites “comparing” a level of ABCF1 previously measured in a collected sample with a “predefined level”, which method may result in “diagnosing a disease or disorder”; such a “comparing” and “diagnosing” may also be conducted entirely in the human mind (i.e., claim 2 also recites an abstract idea). These judicial exceptions are not integrated into a practical application because the active steps of “collecting” a sample or samples and “measuring the level of” ABCF1 are data gathering steps that do not add a meaningful limitation to the method as they are insignificant extrasolution activity; nothing amounting to an application/implementation of a JE is provided by such activities. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the activities of collecting samples and measuring expression levels (including of ABCF1 in particular), whether considered individually or in combination, constitute well-understood, routine, and conventional activity as of Applicant’s effective filing date; see, e.g., Lavon et al (WO 2015/140793 A1 [24 Sept 2015]; cited and discussed above), as well as other prior disclosures of the measurement of ABCF1 expression levels in collected samples (e.g., Powell et al [J. Psychopharmacology 27(7):609 [2013]; cited in IDS]; WO 2020/163959 A1 [20 Aug 2020]; cited herein). Thus, neither independent claim 1 nor independent claim 2 is directed to patent eligible subject matter. With regard to the “wherein” language of independent claim 1, it is also noted that this language (while not given patentable weight, as it merely states what is “indicated” by a possible result) recites a natural phenomenon – i.e., a characteristic of patient samples resulting from naturally occurring inflammatory or disease processes – rather than anything “more” than a JE (and an inventive concept cannot be furnished by a judicial exception [i.e., a law of nature/natural phenomenon/abstract idea] itself [see MPEP 2106.05(I)]). Similarly, regarding independent claim 2, a “correlation” in patient sample levels with other such levels that results from natural phenomena (such as a disease/disorder) does not constitute something “more” than a JE.
With further regard to dependent claim 4, it is again noted that this claim does not clearly require anything beyond what is required by claim 1 other than a different intended use (given the lack of any clear requirements related to treating/treatment, a treated subject, etc., in the claim); thus, there is nothing clearly constituting an application/implementation set forth in the claim, nor is anything more than a JE added. Regarding claim 5-10, all of these claims either relate to or appear to be intended to relate to what is indicated by a result of one embodiment of the method of claim 1 (which embodiment is not required by the claim); nothing set forth in these claims requires anything “more” than a JE, or any type of application/implementation of a JE.
Claim 11 sets forth a requirement for a general category of testing, which relates to the manner in which data gathering is conducted (i.e., further limits an element of the claim that constitutes insignificant extrasolution activity, rather than an application of a JE); further, the recited general techniques for gathering expression data are clearly well-known, routine, and conventional, and thus fail to add anything “significantly more” than a JE. Claims 12-15 each recite well-known types of samples for the gathering of expression data; nothing amounting to an application of a JE is recited, and these types of samples were also clearly well-known as of Applicant’s effective filing date (see again, e.g., Lavon et al). Accordingly, none of claims 1-2 and 4-15 is directed to patent eligible subject matter.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Arora (UBC Thesis, August 2018; cited herein) discloses that ABCF1 is involved in immune regulation including viral immune response, as well as in the pathophysiology of rheumatoid arthritis and autoimmune pancreatis (see entire reference). Powell et al (Journal of Psychopharmacology 27(7):609 [2013]; cited in IDS) teach that ABCF1 is a possible therapeutic target of escitalopram (which is used in treatment of major depressive disorder) (see entire reference).
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/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682