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 .
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements filed 17 April 2024 and 07 October 2024 fail to comply with the provisions of 37 CFR 1.97, 1.98 and MPEP § 609.
Specifically, A4, A8, A9, and A12-15 (from the information disclosure statement filed 17 April 2024) and B2, B4, B6, B8, B13, B18-20, B22, B24, B28, B36, B40, B43, B50, B58, B59, B62-65, B71, B73, B74, B79, B84-87, B91-94, B103, and B110 (from the information disclosure statement filed 07 October 2024) are either improperly cited, cite an alternative version of the literature (i.e. pre-print vs print), or are themselves incomplete (see B18). As a reminder, 37 CFR 1.98(b)(5) requires: Each publication listed in an information disclosure statement must be identified by publisher, author (if any), title, relevant pages of the publication, date, and place of publication. Examiner notes particular issue with missing citations of relevant pages and publication date.
They have been placed in the application file, but the information referred to therein has not been considered as to the merits. Applicant is advised that the date of any re-submission of any item of information contained in this information disclosure statement or the submission of any missing element(s) will be the date of submission for purposes of determining compliance with the requirements based on the time of filing the statement, including all certification requirements for statements under 37 CFR 1.97(e). See MPEP § 609.05(a).
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Claim Objections
Claim 12 is objected to because of the following informalities: the claim should be formatted so that the subsections of (a), (b), (c), and (e) are indented with regards to their heading (see (e)(vi)) for ease of comprehension.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 16 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
As filed, claim 16 depends from claim 1 which has been previously canceled. Therefore, claim 16 can neither further limit the subject matter or include the limitations of claim 1. Based upon the original wording of the claim, for the purposes of prior art, it will be interpreted as depending from claim 8.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 12, 16, and 24 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 16 is rendered indefinite for depending from a canceled claim. As such, the metes and bounds of the claim cannot be determined.
Claim 16 is further indefinite as it attempts to claim a process without setting forth any active, positive steps involved in the process. See Ex parte Erlich, 3 USPQ2d 1011 (BD. Pat. App. & Inter. 1986)(see MPEP § 2173.05(q)).
There is insufficient antecedent basis for the following limitations: "the human" in lines (a), (b), (c), (d), (e), and (f) of claim 12; “the one or more genomic sequences” in lines 3-4 of claim 16; and “the substance” in line 4 of claim 24.
The following is a quotation 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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 of carrying out his invention.
Claims 8, 10, 11, 13-16, and 28 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Specifically, Applicant has failed to demonstrate possession, or put the public in possession of a method for assessing the risk of developing a cardiovascular calcification associated disease by identification of genetic variants in the JAK1, TLR3, IFNB1, IFNA1, XYLT1, or IFNAR1 genes other than the single nucleotide polymorphisms (SNPs) specifically disclosed in the specification and claim 12 (i.e. rs143732508, rs564691204, rs528952911, rs146653955, rs548870644, rs184106700, rs569915578, rs755535058, rs551992948, rs118001479, rs550834189, rs531295111, rs62033189, rs34588333, rs936346, rs554831417)
Claim 8, as well as dependent claims 10, 11, 13-16, and 28, are generic with regard to the genetic variants suitable to serve as predictive markers of cardiovascular calcification associated diseases. MPEP 2163(II)(A)(3)(a)(ii) discusses the situation of claims drawn to a genus. In particular:
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021).
A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014).
Satisfactory disclosure of a "representative number" depends on whether one of skill in the art would recognize that the inventor was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See, e.g., Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are "representative of the full variety or scope of the genus," or by the establishment of "a reasonable structure-function correlation." Such correlations may be established "by the inventor as described in the specification," or they may be "known in the art at the time of the filing date." See AbbVie, 759 F.3d at 1300-01, 111 USPQ2d 1780, 1790-91 (Fed. Cir. 2014).
In the case of the instant application, considerable variation is expected within the genus of genetic variants suitable to serve as predictive markers of cardiovascular calcification associated diseases such that one could not predict, based upon the disclosed 16 SNPs within the disclosed 6 genes, what other genetic variants within those 6 genes may serve as predictive markers for the same diseases.
See Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004): “[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.”
Therefore, the applicant has not demonstrated possession of the invention as so broadly claimed.
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.
Claim 24 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon (including a product of nature) without significantly more.
The claim recites a kit which comprise either (1) a binding molecule, nucleic acid, probes, primers, or microarray which can detect genetic variants of six genes, or (2) a substance which accumulates in cardiac tissue.
Regarding (1), primers, probes, and microarrays (which are made of primers and probes) are nothing more than strands of nucleic acids whose characteristics are innate to naturally occurring DNA and thus lack markedly different characteristics from nature (see MPEP 2106.04(C).II.C.2; Ambry Genetics, 774 F.3d at 760-61, 113 USPQ2d at 1244). Similarly, “a binding molecule” could include a wide variety of naturally occurring proteins which exist in nature (i.e. polymerases, transcription factors, nucleases), as well as primers or probes, and thus fall within the same judicial exception.
Regarding (2), “a substance” could be broadly interpreted to include any number of naturally occurring substances. Tintut (Tintut Y et al. Biomolecules. 2021 Oct 7;11(10):1482) discloses multiple substates that accumulate in cardiac tissues that are relevant to cardiovascular calcification, including low-density lipoprotein, collagen I, calcium, foam cells, cholesterol crystals, etc.
This judicial exception is not integrated into a practical application because merely placing a product(s) of nature in a kit does nothing more than attempt to generally link it to a technological environment without altering its structure or function. Therefore, this is considered to be insignificant extra-solution activity. The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because there are no additional limitations beyond the judicial exception. Therefore, claim 24 does not contain eligible subject matter.
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.
Claims 20 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Dweck (Dweck MR et al. Circulation. 2012 Jan 3;125(1):76-86) in view of Tepekoylu (Tepekoylu C et al. European Heart Journal. 2018 Aug 1;39(suppl_1):ehy566-P5127, p1069-1070) and Yin (WO 2012099785 A2).
Dweck evaluated the suitability of a combined positron emission tomography (PET) and computed tomography (CT) imaging approach using two common PET tracers which target calcification and inflammation for investigation into the pathogenesis and progression of calcific aortic stenosis (p76-77). Subjects were injected intravenously with either 18F-sodium fluoride (18F-NaF) or 18F-flurodeoxyglucose (18F-FDG). After an uptake period, a CT scan was performed followed by PET imaging and the images from each were fused together for further analysis. (p77). The results showed that calcification and inflammation in the aortic value are quantifiable when using 18F-NaF and 18F-FDG radiotracers, respectively (82). Furthermore, 18F-NaF uptake (aka accumulation) was observed not just in areas displaying existing calcification, but also in areas both adjacent to and remote from said calcification, and increased with increased severity of valve disease (83). As such, this technique is likely capable of detecting disease activity as well as serving as a means of predicting disease progression (p84).
Dweck does not teach the administration of a TLR3 inhibitor to a subject determined to be at risk of developing or suffering from calcific aortic valve disease based upon the results of this technique.
Tepekoylu teaches that TLR3 activation and increased expression due to thoracic radiation leads to increased osteoblastic activity in aortic valves and subsequent initiation of calcific aortic valve disease (CAVD). However, by inhibiting TLR3 activation, the onset of calcification after radiation can be prevented, which indicates that TLR3 could be an effective target for the prevention of CAVD.
Yin discloses multiple compounds that are capable of modulating TLR3 activation, including (R)-2-(3-Chloro-6-fluorobenzo [b] thiophene-2-carboxamido)-3-phenyl-propanoic acid (which Yin labels as “4a”). Through rigorous testing, Yin found that 4a directly and specifically binds to TLR3, showing it to be a potent and effective inhibitor of TLR3 activation (Yin, ¶0053, 0118).
Therefore, one of ordinary skill in the art prior to the effective filling date of the claimed invention would have been motivated to administer a TLR3 inhibitor, such as Yin’s compound 4a, to a subject determined to be at increased risk of developing, or suffering from, CAVD as Tepekoylu teaches that TLR3 is an effective CAVD prevention target.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Dweck, Tepekoylu, and Yin, as applied to claim 20 above, and further in view of Shi (Shi D et al. Journal of Cellular and Molecular Medicine. 2019 Dec;23(12):8305-13) and Zhao (Zhao J et al. American Journal of Transplantation. 2021 Oct 1;21(10):3268-79).
Neither Dweck, Tepekoylu, or Yin teach the use of a radioactively-labeled, TLR3-specific ligand, an antibody, or a nucleic acid probe.
According to Shi, while 18F-FDG PET/CT imaging is widely used in clinical settings, 18F-FDG is non-specific and thus can lead to false positive results (Shi, p8306). To address this concern, Shi developed a method for non-invasively imaging triple-negative breast cancer (TNBC) tumors using a radioactively-labeled TLR5 antibody (125I-antiTLR5 mAb) (Shi, abstract). While TLRs in general are targets of great interest in molecular imaging, TLR5 was specifically chosen by Shi as it is highly expressed in, and tightly correlated to progression of, TNBC and non-TNBC cancers (Shi, p8306). Shi’s findings included that TLR5 is suitable for use as a non-invasive, in vivo biomarker for TNBC; and that 125I-antiTLR5 mAb exhibited tumor cell-specificity and favorable non-target clearance, making it a promising radiotracer for TNBC imaging in vivo (Shi, p8312). Therefore, Shi shows that TLRs can be targeted with radioactive antibodies for in vivo imaging purposes.
Zhao investigated the use of TLR3 has a potential therapeutic target in preventing cardiac transplant rejection (Zhao, abstract). By staining endothelial cells developed from mouse heart with anti-TLR3 antibodies, Zhao demonstrated that the cells exhibit a high level of surface TLR3 expression (Zhao, p3271, Fig. 1a). While Zhao analyzed the stained cells via flow cytometry, rather than through a radioimaging technique, Zhao nonetheless shows that TLR3 specific antibodies were known in the art prior to the effective filling date of the claimed invention (Zhao, Fig. 1a).
Therefore, one of ordinary skill in the art, looking to develop an in vivo imaging technique for determining the calcification state of aortic valves for diagnostic purposes, would have been motivated to modify the imaging technique of Dweck to target TLR3, shown by Tepekoylu to be overly expressed in CAVD. Furthermore, as Shi demonstrated that radioactively-labeled antibodies are suitable for use as radiotracers and Zhao demonstrated that TLR3-specific antibodies are known in the art, the skilled artisan would have been motivated to radioactively label TLR3-specfic antibodies for use in this modified method thereby arriving at the claimed invention.
The Supreme Court decided that a claim can be proved obvious merely by showing that the combination of known elements was obvious to try. In this regard, the Supreme Court explained that, “[w]hen there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill in the art has a good reason to pursue the known options within his or her technical grasp.” An obviousness determination is not the result of a rigid formula disassociated from the consideration of the facts of the case. Indeed, the common sense of those skilled in the art demonstrates why some combinations would have been obvious where others would not. Therefore, choosing from a finite number of identified, predictable solutions, with a reasonable expectation for success, is likely to be obvious to a person if ordinary skill in the art. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 – 97 (2007) (see MPEP § 2143, E.).
Claim 24 is rejected under 35 U.S.C. 103 as being unpatentable over Dweck in view of Polansky (US 2004/0023207).
Dweck showed 18F-NaF exhibited increased accumulation in the valves of diseased patients and is useful for identifying pathological calcification (Dweck, p84). However, Dweck does not disclose providing 18F-NaF as part of a kit.
Polansky teaches that the inclusion of individual components in a commercial kit impart well known advantages such as convenience and reproducibility due to manufacturing standardization, quality control, and validation procedures (Polanksy, 0919). Therefore, one of ordinary skill in the art prior to the effective filling date of the claimed invention would have been motivated to include 18F-NaF in a kit to facilitate standardized preparation and use in clinical settings, achieving the well-known benefits described by Polansky.
Potentially Allowable Subject Matter
Claims 8, 10-16, and 28 would be allowable if rewritten or amended to overcome the rejection(s) set forth in this Office action.
The following is a statement of reasons for the indication of allowable subject matter:
Liu (Liu M et al. Lipids in health and disease. 2018 Jul 18;17(1):154) investigated the role of differential gene expression in the presence and extent of coronary artery disease (CAD).
In particular, TLR2, TLR4, and IFNAR1 (among others) were found to be differentially expressed in CAD patients. Altogether, they found that 12 genes related to the toll-like receptor signaling pathway are significant in predicting coronary artery disease. However, Liu was investigating the levels of transcription products present in peripheral blood, which can be altered for a variety of reasons, rather than examining genetic variation as claimed by the Applicant. Additionally, Liu explicitly states that the molecular mechanism of the TLR pathway as it relates to CAD progression is unknown further analysis into both the mechanism and in identifying key genes and transcriptional regulators is required (Liu, abstract, p6-8).
Nelson (Nelson CP et al. Arteriosclerosis, Thrombosis, and Vascular Biology. 2015 Jun;35(6):1456-62) tested whether genetic predisposition to increased type-I IFN production affects risk of CAD in systemic lupus erythematosus patients by analyzing 11 single nucleotide polymorphisms (SNPs) identified as being potentially enriched for variants by genome wide association studies. However, none of the examined SNPs were found to correlate to risk of CAD in 22,233 cases and 64,762 controls (Nelson, abstract). Therefore, while Nelson indicates genetic variation may be able to play a role in estimating the risk of developing CAD, they were unable to identify SNPs capable of doing so.
Finally, van Setten (van Setten et al. Atherosclerosis. 2013 Jun 1;228(2):400-5) performed a genome wide association study on coronary artery calcification (CAC), as well as further investigating 24 published and validated CAD/myocardial infarction risk SNPs, to identify SNPs associated with CAC. In total, over 2.5 million SNPs were investigated. As a result, three SNPs were identified: one at 9p21 (rs4977574), one in the ADAMTS7 gene (rs3825807), and one in the PHACTR1 gene (rs12526453). However, van Setten states that their study was limited in sample size, impacting their ability to detect novel SNPs, and larger studies must be performed, especially as it relates to difference parts of the vasculature and determining causative variants. Therefore, while van Setten identifies SNPs which could play a role in identifying CAC risk and provide general motivation for further studies, no motivation is provided to investigate the specific genes, or the specific SNPs, claimed by the Applicant. While Tepekoylu (cited previously in this office action) suggests the use of TLR3 as a therapeutic target for CAVD, the skilled artisan would not necessarily be motivated to modify van Setten to target SNPs in the TLR3 gene. Tepekoylu studied differential expression of the transcribed protein and its impact on downstream protein expression. This can arise from non-genetic mechanisms, such as promoter activation, epigenetic modification, alternative splicing, translation efficiency, etc., none of which imply or require any genetic variation in the TLR3 gene itself.
As such, any of the listed references could be considered the closest prior art, but the claims of the instant application are not obvious over them either independently or in combination.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Kara N Kovach whose telephone number is (571)272-8134. The examiner can normally be reached Monday - Friday, 9am - 3pm.
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/K.N.K./Examiner, Art Unit 1681
/SAMUEL C WOOLWINE/Primary Examiner, Art Unit 1681
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