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 .
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 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.
Claim Status
Claims 1-7 are pending.
Claims 1-2 and 4-6 are objected to.
Claims 1-7 are rejected.
Priority
The instant Application was filed Aug 9 2023 and does not claim the benefit of an earlier filed application.
Accordingly, each of claims 1-7 are afforded the effective filing date of Aug 9 2023.
Information Disclosure Statement
The information disclosure statement (IDS) filed on Aug 9 2023 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action.
The listing of references in the specification 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.
Drawings
The Drawings submitted Aug 9 2023 are accepted.
Specification
The disclosure is objected to for the following informalities.
Hyperlinks
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. 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. Non-limiting examples include p 38. Applicant will note that this is exemplary and other instances may exist. It is requested that all instances be corrected.
Appropriate correction for all objections to the specification is required.
Claim Objections
The claims are objected to for the following informalities:
Claims 1 and 4-5 contain numerous terms which are underlined, for example “N-glycans I” and “2AB”. These terms should not be underlined because underlining is generally used to denote amendments to the claims, and may cause confusion throughout prosecution.
Recitations of “glycans” through the claims (claim 1: step c); e), lines 1, 3, and 8; table, line 11, p. 51; f), line 2; claim 2: lines 3, 20, and 25; claim 4: lines 6 and 11; claim 5: line 1; claim 6: lines 1 and 24) should be amended to recite “N-glycans” to maintain consistent claim language.
Claim 1 should be amended to recite “A method… comprising:” with “performing” starting on a new line, to improve readability.
Claim 1, line 13, should be amended to recite either “a type[[s]] of glycoside bond” or “types of glycoside bonds”.
Claim 1, line 20, should be amended to recite “the following steps”.
Claim 1, line 23, should be amended to recite “the one or more blood samples”.
Claim 1, step c), should be amended to recite “the IgG”.
Claim 1, step e), line 7, should be amended to add “as part of the quantitative analysis” before the comma to improve readability of the claim.
Claim 1, step e), line 8, should be amended to remove “the” or “said” in “wherein the said glycan peaks”.
Claim 1 is missing an “and” between steps f) and g).
In claim 2, line 13, “determines” should be amended to recite “determined” because the prospective study was previously performed.
Claim Interpretation
Contingent Claiming
In the interest of compact prosecution, the instant claims are examined to consider all claim limitations. However, the claims herein contain recitations of intended use and contingent claim language that affect the scope of the claims, as recited below. The courts have stated that claims must be given their broadest reasonable interpretation (BRI) consistent with the specification. See In re Morris, 127 F.3d 1048, 1054-55, 44 USPQ2d 1023, 1027-28 (Fed. Cir. 1997); In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541,550-551 (CCPA 1969); and In re Zletz, 893 F.2d 319, 321-22, 13 USPQ2d 1320, 1322 (Fed. Cir. 1989) (see MPEP § 2111).
The instant claims include a recitation of contingent claim language.
With respect to contingent claiming, said contingencies as claimed require that the claims are interpreted as provided for in the MPEP at 2111.04 (II), wherein: “the broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met). For example, assume a method claim requires step A, if a first condition happens and step B if a second condition happens. If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim. If the claimed invention requires the first condition to occur, then the broadest reasonable interpretation of the claim requires step A. If the claimed invention requires both the first and second conditions to occur, then the broadest reasonable interpretation of the claim requires both steps A and B”.
In the instant claims, the following is a “contingent” recitation:
Claim 3, step (i): “if the CVDR value is greater than a mean CVDR value of a population, the subject has an increased risk of cardiovascular events in the future compared to the reference population”; and
Claim 7: treating the human subject with a compound selected from the group consisting of acetylsalicylic acid, quercetin, resveratrol, N-acetyl-D-mannosamine, and combinations thereof if the human subject is determined to have an increased risk of cardiovascular events in the future.
With respect to the interpretations above, it is suggested that the claims be amended recite alternative language so as to avoid interpretation of contingent claiming.
Claim Rejections - 35 USC § 112
35 U.S.C. 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 1-7 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.
Claim 1, lines 4-5, recites “performing an analysis process of N-glycans I, bound to immunoglobulin G <IgG>,
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”, and later, in step e), recites “quantitative analysis of thus derivatized glycans by ultra- performance liquid chromatography <UPLC>, wherein numerical values of relative areas under respective glycan peaks GP 9, GP 12, GP 19, and GP 20 within the corresponding UPLC chromatogram are obtained as the numerical values {GP9, GP12,GP 19, GP20}, wherein the said glycan peaks GP 9, GP 12, and GP 19 belong to structures given in the table below:
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”. Those glycans recited in step e) are considered to be related to N-glycan I because step c) recites “release of said glycans”, where the only previously recited glycans are N-glycans I. The claim continues in steps f) and g) to use the relative areas under the glycan peaks GP9, GP12, GP19, and GP20. However, the claim does not recite any uses of N-glycans I as described in the beginning of the claim. It is therefore unclear what purpose N-glycans I serves at the beginning of the claim, if N-glycans I is related to the glycans detected at GP9, GP12, GP19, and GP20, whether the analysis process of N-glycan I and the analysis process outlined in steps a)-g) are related, or even whether N-glycans I is meant to actually claim the structure recited in the claim, which is just recited to provide an exemplary form of a set of N-glycans which are released from IgG. For compact examination, it is assumed that claim 1 requires those glycans set forth in the table which are involved in steps f) and g) and that N-glycans I is meant to provide an exemplary structure of the set of N-glycans released from IgG. The rejection may be overcome by clarifying the role of N-glycan I in the claim. Claims 2-6 are rejected based on their dependency from claim 1.
Claim 1, step e), recites “wherein numerical values of relative areas under respective glycan peaks GP 9, GP 12, GP 19, and GP 20 within the corresponding UPLC chromatogram are obtained as the numerical values {GP9, GP12,GP 19, GP20}”. The interpretation of “{GP9, GP12,GP 19, GP20}” is not clear because it is not clear what the enclosed terms are meant to represent. It is not clear if Applicant intends for the parenthetical terms to be stand-ins for the actual obtained values from the quantitative analysis, if they are intended to somehow refer to the table included in the claim, or if they are just exemplary. For compact examination, it is assumed that they represent the actual obtained values. The rejection may be overcome by clarifying the metes and bounds of the claim. Claims 2-6 are rejected based on their dependency from claim 1.
Claim 1, step f), recites “wherein numerical results of relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20, that correspond to values {GP9, GP12, GP19, GP20} calculated in step e, are now included in a CVDR model for cardiovascular diseases risk <CVDR>, which is a function of the four glycan arguments: CVDR = CVDR(GP9, GP12, GP19, GP20)”. It is unclear whether the wherein clause is intended to require including the numerical results in the DVDR model within the metes and bounds of the claimed invention, or if it is only further limiting the method such that including the values in the model is not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performance of including the numerical values in the model, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the CVDR model is required to be performed. The rejection may be overcome by clarifying what steps are required to be performed, for example by amending the claim to recite “inputting the numerical values obtained in step c into a CVDR model…” or similar. Claims 2-6 are rejected based on their dependency from claim 1.
Claim 1, step f), recites “wherein numerical results of relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20, that correspond to values {GP9, GP12, GP19, GP20} calculated in step e”. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of numerical results of relative areas calculated in step e or selected glycan peaks. It is noted that step e does, instead recite obtaining “numerical values of relative areas under respective glycan peaks GP 9, GP 12, GP 19, and GP 20”, which is it assumed that step f) intends to refer to. The rejection may be overcome by clarifying the antecedent basis of the limitations. Claims 2-6 are rejected based on their dependency from claim 1.
Claim 1, step f), recites “a function of the four glycan arguments: CVDR = CVDR(GP9, GP12, GP19, GP20)”. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of four glycan arguments. It is not clear if the claim intends to refer to the “four glycan arguments” as part of the recited function that are the numerical results of relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20 or are those that correspond to values {GP9, GP12, GP19, GP20} calculated in step e. For compact examination, it is assumed that the claim intends for the numerical values of relative areas under respective glycan peaks GP 9, GP 12, GP 19, and GP 20 to be input into the CVDR model as four glycan arguments. The rejection may be overcome by clarifying the metes and bounds of the claim. Claims 2-6 are rejected based on their dependency from claim 1.
Claim 1, step g), recites “the risk value” and “the CVDR value”. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of a risk factor. For compact examination, it is assumed that step g) should be amended to recite “[[the]] a risk value” and that the CVDR value refers to the result obtained from the CVDR model.
Claim 2 recites “the variation of quantitative IgG glycans {GP1, …, GP24}”. It is not clear whether the parenthetical limitation is intended to limit the scope or to provide 24 exemplary glycan peaks that could have been examined in the prospective study. As set forth in MPEP 2173.05(d), description of examples or preferences is properly set forth in the specification rather than the claims. For compact examination, it is assumed that the parenthetical terms are exemplary and do not limit the scope of the claim, especially as it is not clear if all 24 of the GPs in the parenthesis are required. The rejection may be overcome by clarifying the metes and bounds of the limitation. Claim 5 is rejected based on its dependency from claim 2.
Claim 2 recites “wherein significantly predictive IgG glycans are determined using regression models that are corrected for multiple confounders, including age, race, sex, statin therapy, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, smoking, and hypertension, and a glycan-based predictive model is constructed based on the determined IgG glycans construct”. It is unclear whether the wherein clause is intended to require determining the significantly predictive IgG glycans and constructing a glycan-based predictive model within the metes and bounds of the claimed invention, or if it is only further limiting the CVDR model such that determining the significantly predictive IgG glycans and constructing a glycan-based predictive model are not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performance of determining the significantly predictive IgG glycans and constructing a glycan-based predictive model, the metes and bounds of the claims are unclear. For compact examination, it is assumed that determining the significantly predictive IgG glycans and constructing a glycan-based predictive model are not required to be performed. The rejection may be overcome by clarifying what steps are required to be performed. Claim 5 is rejected based on its dependency from claim 2.
Claim 2 recites “a glycan-based predictive model is constructed based on the determined IgG glycans construct”. The relationship between the previously recited CVDR model and the glycan-based predictive model is not clear. It is not clear if the models are intended to refer to the same model, if the glycan-based predictive model is a precursor to the CVDR model, or if the glycan-based predictive model is completely unrelated to the CVDR model. For compact examination it is assumed that models are intended to refer to the same model. The rejection may be overcome by clarifying the relationship between the limitations.
Claim 3, limitation (ii), recites “the increase of CVDR value”. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of an increase of CVDR value. For compact examination, it is assumed that the claim should be amended to recite “[[the]] an increase of the CVDR value”. Claim 6 is rejected based on its dependency from claim 3.
Claim 4 recites “where the glycans under the peaks GP9, GP12, GP19, and GP20 are determined by alternative quantitative analytical techniques…”. It is unclear whether the limitation is intended to require performing the alternative quantitative analytical techniques to determine the glycans either in addition to or in place of the previously recited quantitative analysis by UPLC in claim 1 within the metes and bounds of the claimed invention, or if it is only further limiting an intended consequence of the invention such that performing the alternative quantitative analytical techniques are not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses (which is interpreted to be encompassed by “where” as recited in the claims) raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performance of the alternative quantitative analytical techniques, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the alternative quantitative analytical techniques are required to be performed in addition to the previously recited quantitative analysis by UPLC in claim 1. The rejection may be overcome by clarifying what steps are required to be performed. Claims 5-6 are similarly rejected.
Claim 4 recites “where the glycans under the peaks GP9, GP12, GP19, and GP20 are determined by alternative quantitative analytical techniques selected from the group consisting of: MALDI- TOF mass spectrometry, liquid chromatography coupled with mass spectrometry <LC-MS>, or capillary electrophoresis <CE>”. The claim is unclear because it is not clear whether the claim intends for the alternative quantitative analytical techniques to determine the glycans to be performed in addition to or in place of the previously recited quantitative analysis by UPLC in claim 1. Because replacing the previously recited quantitative analysis by UPLC in claim 1 would result in issues under 35 USC 112(d), it is assumed that the claim intends to perform the alternative quantitative analytical techniques in addition to the previously recited quantitative analysis by UPLC in claim 1. Further, it is not clear if the claim intends to require multiple of the alternative quantitative analytical techniques selected from the group, because the claim recites “techniques”, or if only one is required, because the list is separated by an “or”. For compact examination, it is assumed that the claim intends to require the performance of only one of the alternative quantitative analytical techniques. Claims 5-6 are similarly rejected.
Claim 4 recites “where the corresponding glycans are derivatized with a fluorescent derivatizing agent selected from the group comprising 2-aminobenzamide <2AB>, 8- aminopyrene-1,3,6-trisulfonic acid, trisodium salt <APTS>, procainamide <PR>, or 2,5-dioxopyrrolidine-1-yl-<2N-<2-<N',N'- diethylamino>ethyl>carbamoyl>-quinoline-6-yl-carbamate <RF>”. It is unclear whether the wherein clause is intended to require performing the derivatization within the metes and bounds of the claimed invention, or if it is only further limiting the glycans such that performing the derivatization is not required within the metes and bounds of the invention. As set forth in MPEP 2111.04.I, “wherein” clauses raise the question as to the limiting effect of the language in a claim. As the claims do not recite an active performing the derivatization, the metes and bounds of the claims are unclear. For compact examination, it is assumed that the derivatizing is not required to be performed. The rejection may be overcome by clarifying what steps are required to be performed. Claims 5-6 are similarly rejected.
Claim 4 recites “where the corresponding glycans are derivatized with a fluorescent derivatizing agent selected from the group comprising 2-aminobenzamide <2AB>, 8- aminopyrene-1,3,6-trisulfonic acid, trisodium salt <APTS>, procainamide <PR>, or 2,5-dioxopyrrolidine-1-yl-<2N-<2-<N',N'- diethylamino>ethyl>carbamoyl>-quinoline-6-yl-carbamate <RF>”. However, claim 1 already recites that the method includes “d) fluorescent derivatization with 2-aminobenzamide <2AB> and a reducing agent for reductive amination” after releasing the glycans. Claim 1 is interpreted as already requiring the derivatization of the released glycans with 2AB. It is therefore not clear if claim 4 intends to replace the requirement that 2AB is used for fluorescent derivatization and that other compounds may be used instead, which would result in 35 USC 112(d) issues, or if there is an additional requirement for derivatizing the corresponding glycans again. The rejection may be overcome by clarifying the metes and bounds of the claims. Claims 5-6 are similarly rejected.
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 1-7 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to a method, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
The claims also recite a law of nature or a natural phenomenon. The MPEP at 2106.04(b) further explains that laws of nature and natural phenomena include naturally occurring principles/relations and nature-based products that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature.
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) as well as a law of nature or a natural phenomenon are as follows:
Independent claim 1: performing an analysis process of N-glycans bound to immunoglobulin G <IgG>, where various symbols in I denote monemoric sugar units as recited in the claim, where letters a-d in I determine types of glycoside bond of said N-glycans I as recited in the claim;
where the analysis process comprises following steps:
e) wherein numerical values of relative areas under respective glycan peaks GP 9, GP 12, GP 19, and GP 20 within the corresponding UPLC chromatogram are obtained as the numerical values {GP9, GP12, GP19, GP20};
f) wherein numerical results of relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20, that correspond to values {GP9, GP12, GP19, GP20} calculated in step e, are now included in a CVDR model for cardiovascular diseases risk <CVDR>, which is a function of the four glycan arguments: CVDR = CVDR(GP9, GP12, GP19, GP20);
g) determination of the risk value expressed as the CVDR value.
Dependent claim 2: obtaining the CVDR model via statistical data analysis performed after a prospective study that determines the variation of quantitative IgG glycans {GP1,..., GP24} content in the blood plasma in:- normal subjects, versus, - subjects who experienced the following cardiovascular disease clinical manifestations: myocardial infarction, stroke, coronary revascularization, unstable angina requiring hospitalization, or death, wherein significantly predictive IgG glycans are determined using regression models that are corrected for multiple confounders, including age, race, sex, statin therapy, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, smoking, and hypertension, and a glycan-based predictive model is constructed based on the determined IgG glycans construct.
Dependent claim 3 recites further steps that limit the judicial exceptions in independent claim 1 and, as such, also are directed to those abstract ideas. For example, claim 3 further limits the CVDR model to a specific mathematical formula and describes the conditions for determining the risk value based on the formula.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually determine a risk value for cardiovascular disease based on the IgG N-glycans present in a sample. Without further detail as to the methodology involved in “obtaining”, “including”, “determining”, under the BRI, one may simply, for example, use pen and paper to obtain numerical values of relative areas under glycan peaks in a chromatogram, obtain a CVDR model by statistical data analysis of IgG glycan data obtained in a prospective study, include or input those numerical values into the CVDR model to obtain a CVDR value, and determine a risk of cardiovascular disease based on the CVDR value in comparison to a mean CVDR value of a population. Such actions encompass observations, evaluations, and judgments, which are concepts able to be performed in the human mind. Additionally, each of these steps require mathematical techniques as the only supported embodiments, as they either express mathematical relationships in words (e.g., obtaining numerical values, including values in a model, statistical data analysis, regression models) or directly recite mathematical equations.
The claims also recite the analysis of a naturally occurring IgG associated N-glycan and the natural relationship between the N-glycan and the person’s risk for cardiovascular disease. Therefore, the claims recite a law of nature or a natural phenomenon.
Therefore, claim 1 and those claims dependent therefrom recite an abstract idea and a law of nature/natural phenomenon [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claim 1: performing an analysis process of N-glycans bound to immunoglobulin G <IgG>,
where the analysis process comprises following steps:
a) isolation of plasma from one or more blood samples that have been collected from the human subject under examination,
b) isolation of IgG from blood plasma of the blood samples,
c) release of said glycans from IgG,
d) fluorescent derivatization with 2-aminobenzamide <2AB> and a reducing agent for reductive amination, optionally using a complex of picoline borane <BH3*NC5H4-2-CH3> or sodium cyanoborohydride <NaBH3CN>,
e) quantitative analysis of thus derivatized glycans by ultra-performance liquid chromatography <UPLC>… wherein the said glycan peaks GP 9, GP 12, and GP 19 belong to structures given in the table recited in the claims.
Dependent claims 4-6: where the glycans under the peaks GP9, GP12, GP19, and GP20 are determined by alternative quantitative analytical techniques selected from the group consisting of: MALDI- TOF mass spectrometry, liquid chromatography coupled with mass spectrometry <LC-MS>, or capillary electrophoresis <CE>, where the corresponding glycans are derivatized with a fluorescent derivatizing agent selected from the group comprising 2-aminobenzamide <2AB>, 8- aminopyrene-1,3,6-trisulfonic acid, trisodium salt <APTS>, procainamide <PR>, or 2,5-dioxopyrrolidine-1-yl-<2N-<2-<N',N'- diethylamino>ethyl>carbamoyl>-quinoline-6-yl-carbamate <RF> having respective structures recited in the claims.
Dependent claim 7: treating the human subject with a compound selected from the group consisting of acetylsalicylic acid, quercetin, resveratrol, N-acetyl-D-mannosamine, and combinations thereof if the human subject is determined to have an increased risk of cardiovascular events in the future.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “isolating” plasma and IgG, “releasing” glycans, “fluorescent derivatizing” released glycans, and performing UPLC of the glycans, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. The steps in claims 4-6 regarding performing MALDI-TOF, LC-MS, or CE of the glycans or LC-MS of the glycopeptides do not recite any meaningful limits on the claim because they are merely nominally or tangentially related to the invention. The steps merely recite performing another analysis step on the sample (although see the above 35 USC 112(b) rejection above). Data gathering and outputting steps, as well as insignificant, extra-solution activity in general, are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
The step directed to “treating” is conditional based on the determination that the human subject has an increased risk, and is therefore not required to be performed if the human subject does not have an increased risk. As there is no requirement in the claim that the subject be found to have an increased risk, there are embodiments in the claim where no treatment is provided. Therefore, claim 7 does not provide a practical application of the judicial exceptions in all embodiments of the claims.
The specification as published discloses that understanding how differences in the IgG N-glycosylation profile and the effects on IgG function relate to CVD events may lead to novel approaches to CVD prevention that leverages glycobiological mechanisms and pathways at [0012], but does not provide a clear explanation for how the additional elements provide these improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the prior art to Novokmet et al. (Scientific Reports, 2014, 4(1):4347; newly cited; p. 8, col. 1, par. 4 through col. 2, par. 7), Huffman et al. (Molecular & Cellular Proteomics, 2014, 13(6):1598-1610; newly cited; p. 1599, col. 2, par. 3 through p. 1601, col. 2, par. 3), and Yu et al. (Medicine, 2016, 95(28):e4112; newly cited; p. 3, section 2.3) disclose that isolating plasma, isolating IgG, releasing glycans from IgG, fluorescent derivatizing glycan with 2-aminobenzaminde and a reducing agent, and performing ultra-performance UPLC, MALDI-TOF, LC-MS, or CE are data gathering elements that are routine, well-understood and conventional in the art. Further, the prior art reviews to Campbell et al. (JAMA, 2007, 297(18):2018-2024; newly cited; entire document is relevant), Papakyriakopoulou et al. (Pharmaceuticals, 2022, 15(8):1019; newly cited; entire document is relevant), Dyck et al. (International Journal of Molecular Sciences, 20(4), p.904; newly cited; entire document is relevant), and Loaeza-Reyes et al. (Frontiers in Molecular Biosciences, 2021, 8:751637; newly cited; p. 6, col. 1), and the prior art to Peng et al. (Circulation, 2019, 140(24):2005-2018; newly cited; entire document is relevant), disclose that treatment with acetylsalicylic acid (Campbell), quercetin (Papakyriakopoulou), resveratrol (Dyck), and N-acetyl-D-mannosamine (Loaeza-Reyes and Peng), as recited in claim 7, is insignificant, extra-solution activity that is routine, well-understood and conventional in the art. As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
A. Claims 1-3 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over the features of Birukov et al. (Diabetes Care, Nov 2022, 45:2720-2736; cited on the Aug 9 2023 IDS), as evidenced by Birukov et al. (Diabetes Care, Nov 2022, 45, Online Supplement, p. 1-26; newly cited), and in view of Trbojevic-Akmacic et al. (Methods in Enzymology, 2017, 586:37-55; newly cited).
Claim 1 discloses a method for prediction of future cardiovascular disease (CVD) in a human subject which comprises performing an analysis process of N-glycans bound to immunoglobulin G <IgG>,
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where various symbols in I denote monomeric sugar units as below:
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where letters a-d in I determine types of glycoside bond of said N-glycans I as below:
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Birukov discloses an analysis of IgG N-glycans associated with incident type 2 diabetes and cardiovascular disease (CVD) (abstract). Birukov teaches a study population of men and women (i.e., human subjects) (p. 2730, col. 2, par. 2). Birukov teaches analyzing 24 IgG-GPs, or glycan peaks as described in Supplementary Fig. 3 (p. 2730, col. 3, par. 3). Evidentiary Birukov Supplement teaches N-glycan I, its monomeric sugar unit, and glycoside bonds as claimed in Supplemental Figure S3, reproduced below:
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The analysis process of claim 1 comprises following steps:
a) isolation of plasma from one or more blood samples that have been collected from the human subject under examination,
b) isolation of IgG from blood plasma of the blood samples,
Regarding steps a) and b) Birukov teaches isolating IgG from individual plasma samples (p. 2730, col. 3, par. 3) after obtaining blood samples from the men and women (p. 2730, col. 2, par. 2), which is considered to inherently teach isolating plasma from the blood samples as claimed in a).
c) release of said glycans from IgG,
d) fluorescent derivatization with 2-aminobenzamide <2AB> and a reducing agent for reductive amination, optionally using a complex of picoline borane <BH3*NC5H4-2-CH3> or sodium cyanoborohydride <NaBH3CN>:
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Regarding steps c) and d), Birukov teaches that the Supplementary Methods provide a more detailed description of IgG glycoprofiling. Evidentiary Birukov Supplement teaches releasing N-glycans from the isolated IgG and labeling the released N-glycans with a fluorescent dye, 2-aminobenzamide, in a reductive amination reaction (p. 1, par. 2).
e) quantitative analysis of thus derivatized glycans by ultra- performance liquid chromatography <UPLC>, wherein numerical values of relative areas under respective glycan peaks GP 9, GP 12, GP 19, and GP 20 within the corresponding UPLC chromatogram are obtained as the numerical values {GP9, GP12,GP 19, GP20}, wherein the said glycan peaks GP 9, GP 12, and GP 19 belong to structures given in the table below:
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wherein G20 represents a peak at a retention time calibrated to retention times of glucose oligomers labeled with 2-aminobenzamide,
Regarding step e), Birukov teaches performing ultraperformance liquid chromatography on the prepared samples, separating the chromatograms into 24 IgG-GPs, of glycan peaks, and determining the amount of glycans in each peak (i.e., numerical values of relative areas under the respective glycan peaks) to produce the glycans as described in Supplementary Fig. 3 and Supplementary Table 1 (p. 2731, col. 3, par. 3). Evidentiary Birukov Supplement Supplemental Figure S3 and Supplemental Table S1 show that GP9 is
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, GP11 is
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, GP12 is
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, and GP 19 is
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, which reads on the structures of GP9, GP12, and GP19 as instantly claimed. Evidentiary Birukov Supplement teaches using the method of reference 3, or Trbojevic-Akmacic, for sample preparation and UPLC. Trbojevic-Akmacic teaches that the UPLC system is calibrated using an external standard of hydrolyzed and 2-AB-labeled glucose oligomers from which the retention times for the individual glycans are converted to glucose units (p. 48, section 7), which reads on GP20 as instantly claimed.
Although Birukov does not teach using the external standard as taught by Trbojevic-Akmacic, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Birukov as evidenced by Birukov Supplement with Trbojevic-Akmacic because each reference discloses methods for N-glycan analysis of IgG. The motivation to include the external calibrant as taught by Trbojevic-Akmacic would have been to calibrate the UPLC system, as taught by Trbojevic-Akmacic (p. 48, section 7).
f) wherein numerical results of relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20, that correspond to values {GP9, GP12, GP19, GP20} calculated in step e, are now included in a CVDR model for cardiovascular diseases risk <CVDR>, which is a function of the four glycan arguments: CVDR = CVDR(GP9, GP12, GP19, GP20),
g) determination of the risk value expressed as the CVDR value.
Regarding steps f) and g), Birukov teaches selecting IgG-GPs significantly associated with end points in models and testing those in Cox proportional hazards models to produce CVD risk scores, where IgG-GP19 is included in the Cox model for men and IgG-GP9 is included in the model for women (p. 2731, col. 1, par. 2; p. 2733, col. 1, par. 2 through col. 2, par. 1). Birukov teaches that IgG-GP9, IgG-GP12, and IgG-GP19 were among the IgG GPs that showed the strongest positive pairwise correlations with cardiometabolic traits (p. 2731, col. 3, par. 2).
Birukov does not teach using GP9, GP12, GP19, and GP20 as four glycan arguments in a CVDR model. However, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify, in the course of routine experimentation and with a reasonable expectation of success, the method of Birukov to examine GP9, GP12, and GP19, as taught by Birukov Supplement, in a Cox proportional hazards models to produce a CVD risk score because Birukov teaches that IgG-GP9, IgG-GP12, and IgG-GP19 were among the IgG GPs that showed the strongest positive pairwise correlations with cardiometabolic traits (p. 2731, col. 3, par. 2). It would have been further obvious to one of ordinary skill in the art to only examine IgG-GP12 as taught by Birukov rather than also including F(6)A2[3]BG1 as instantly claimed because Birukov shows better separation of the compounds such that IgG-GP12 does not include F(6)A2[3]BG1, and only includes A2G2. Alternatively, it would have been obvious to include IgG-GP11 in the model as well because there are a finite number of options of N-glycans measured, only 24, and IgG-GP11 is associated with a risk for type 2 diabetes (abstract), and that the links between low-grade systemic inflammation, type 2 diabetes, and CVD are well established (p. 2730, col. 1, par. 2). Birukov Supplement also teaches that IgG-GP11 were positively associated with CVD in men in the Cox models (Supplemental Figure S9).
Further, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Birukov as evidenced by Birukov Supplement with Trbojevic-Akmacic to include GP20 as part of the Cox proportional hazards models, because Trbojevic-Akmacic teaches using an external standard of hydrolyzed and 2-AB-labeled glucose oligomers from which the retention times for the individual glycans are converted to glucose units, which reads on GP20 as instantly claimed, in order to calibrate the UPLC system (p. 48, section 7). By including GP20 in the model, Birukov would produce an equivalent calibrated risk score.
Regarding claim 2, Birukov as evidenced by Birukov Supplement and in view of Trbojevic-Akmacic teaches claim 1 as described above. Claim 2 further adds obtaining the CVDR model via statistical data analysis performed after a prospective study that determines the variation of quantitative IgG glycans {GP1,..., GP24} content in the blood plasma in:- normal subjects, versus, - subjects who experienced the following cardiovascular disease clinical manifestations: myocardial infarction, stroke, coronary revascularization, unstable angina requiring hospitalization, or death, wherein significantly predictive IgG glycans are determined using regression models that are corrected for multiple confounders, including age, race, sex, statin therapy, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, smoking, and hypertension, and a glycan-based predictive model is constructed based on the determined IgG glycans construct.
Birukov teaches obtaining 24 IgG-GPs, or glycan peaks, from samples collected from over 27,000 individuals (i.e., a prospective study) with follow up to determine whether they developed CVD, including myocardial infarction or stroke (i.e., normal versus subjects who experienced cardiovascular disease) (p. 2730, col. 2, par. 2 through col. 3, par. 4). Birukov teaches statistical analysis of the IgG-GPs using regression analysis (p. 2730, col. 3, par. 5 through p. 2731, col. 1, par. 2). Birukov teaches confounder-adjusted Cox proportional hazards models, where the models are adjusted for age, sex, smoking status, hypertension, intake of aspirin, antihypertensive, or lipid-lowering drugs (i.e., statin therapy), total and HDL cholesterol (i.e., inherently includes low-density lipoprotein cholesterol in addition to high-density lipoprotein cholesterol) (p. 2731, col. 1, par. 2-3).
Although Birukov does not teach including race as a confounder, Birukov Supplemental teaches recording the race of the study participants (Supplemental Table S3). It therefore would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify, in the course of routine experimentation and with a reasonable expectation of success, the method of Birukov to examine race as one of the confounders because that data was already collected by the group.
Regarding claim 3, Birukov as evidenced by Birukov Supplement and in view of Trbojevic-Akmacic teaches claim 1 as described above. Claim 3 further adds where the CVDR model is: CVDR = -3.432-GP9 - 0.509-GP12 + 0.793-GP19 - 0.835-GP20, and where the determination of the risk value expressed as the CVDR value comprises:
(i) if the CVDR value is greater than a mean CVDR value of a population, the subject has an increased risk of cardiovascular events in the future compared to the reference population,
and/or (ii) the increase of CVDR value by 1 unit represents an increased risk of 2.6 fold.
Birukov teaches determining multiple Cox proportional hazard models to determine a CVD risk based on various combinations of IgG-GPs (see p. 2731 throughout).
Although Birukov does not teach the CVDR model as instantly claimed, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify, in the course of routine experimentation and with a reasonable expectation of success, the method of Birukov in view of Trbojevic-Akmacic to include GP9, GP 12, GP 19, and GP20 as described above in claim 1. It is considered that one of ordinary skill in the art would expect such a modification to result in a CVDR model as instantly claimed. One of ordinary skill in the art would have had a reasonable expectation of success in making this modification because both Birukov demonstrates that glycan peak variables derived from quantitative analysis are routinely used as quantitative inputs in Cox proportional hazards models to determine risk for a disease. Regarding steps (i) and (ii), only one is required to be performed, but (i) is conditional. Therefore, neither steps (i) or (ii) are required within the metes and bounds of the claim to be performed, and Birukov in view of Trbojevic-Akmacic is considered to teach the required scope of the claim.
Regarding claim 7, Birukov as evidenced by Birukov Supplement and in view of Trbojevic-Akmacic teaches claim 1 as described above. Claim 7 further adds treating the human subject with a compound selected from the group consisting of acetylsalicylic acid, quercetin, resveratrol, N-acetyl-D-mannosamine, and combinations thereof if the human subject is determined to have an increased risk of cardiovascular events in the future.
The limitation recited in claim 7 is contingent upon the human subject being determined to have an increased risk of cardiovascular events in the future and is therefore not required to be performed. Therefore, as Birukov as evidenced by Birukov Supplement and in view of Trbojevic-Akmacic teaches claim 1 as described above, it is also considered that Birukov as evidenced by Birukov Supplement and in view of Trbojevic-Akmacic teaches claim 7 as required.
B. Claims 4-6 are rejected under 35 U.S.C. 103 as being unpatentable over the features of Birukov as evidenced by Birukov Supplement and in view of Trbojevic-Akmacic, as applied to claims 1-3 above, and in further view of Pucic et al. (Mol Cell Proteomics 2011;10:M111 010090; newly cited).
Regarding claims 4-6, Birukov as evidenced by Birukov Supplement and in view of Trbojevic-Akmacic teaches claims 1-3 as described above. Claims 4-6 further add that the glycans under the peaks GP9, GP12, GP19, and GP20 are determined by alternative quantitative analytical techniques selected from the group consisting of: MALDI- TOF mass spectrometry, liquid chromatography coupled with mass spectrometry <LC-MS>, or capillary electrophoresis <CE>, where the corresponding glycans are derivatized with a fluorescent derivatizing agent selected from the group comprising 2-aminobenzamide <2AB>, 8- aminopyrene-1,3,6-trisulfonic acid, trisodium salt <APTS>, procainamide <PR>, or 2,5-dioxopyrrolidine-1-yl-<2N-<2-<N',N'- diethylamino>ethyl>carbamoyl>-quinoline-6-yl-carbamate <RF> having respective structures as below:
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Neither Birukov or Trbojevic-Akmacic teach these limitations. However, Birukov Supplement teaches that glycan structures in each peak were previously confirmed using mass spectrometry, referencing Pucic.
Pucic discloses a novel 96-well protein G monolithic plate and used it to rapidly isolate IgG from plasma of 2298 individuals from three isolated human populations, where N-glycans were released by PNGase F, labeled with 2-aminobenzamide and analyzed by hydrophilic interaction chromatography with fluorescence detection (abstract). Pucic teaches that the 2-AB labeled IgG N-glycan pool was fractionated by HILIC to provide the same separation as UPLC, and the 2-AB labeled glycan fractions were then analyzed by liquid chromatography mass spectrometry and MALDI-TOF MS (p. 3, col. 2, par. 6 through p. 4, col. 1, par. 4).
Regarding claims 4-6, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Birukov as evidenced by Birukov Supplement and in view of Trbojevic-Akmacic with Pucic because each reference discloses methods for the analysis of IgG glycans. Birukov Supplement motivates performing an additional analysis of the glycans under the UPLC peaks in order to confirm their structure (p. 1, par. 2).
C. Claims 1-7 are rejected under 35 U.S.C. 103 as being unpatentable over the features of Lauc et al. (US 2016/0103137; newly cited) in view of Trbojevic-Akmacic et al. (Methods in Enzymology, 2017, 586:37-55; newly cited) and Menni et al. (Circulation Research, 2018, 122(11):1555-1564 and Supplementary Material, p. 11-28; newly cited).
The prior art to Lauc discloses a method for the analysis of N-glycans attached to immunoglobulin G (IgG) or IgG N-glycopeptides from human blood plasma in which relative abundance of two or more glycans is determined (abstract). Lauc, indicated by the open circles, teaches the instant features, indicated by the closed circles, as follows. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims.
Claim 1 discloses a method for prediction of future cardiovascular disease (CVD) in a human subject which comprises performing an analysis process of N-glycans bound to immunoglobulin G <IgG>,
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where various symbols in I denote monomeric sugar units as below:
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where letters a-d in I determine types of glycoside bond of said N-glycans I as below:
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Lauc teaches a typical chromatogram obtained by the quantitative analysis of IgG N-glycans by ultra performance liquid chromatography (UPLC) in FIG. 1 [0042; 0114], reproduced below, which teaches the above limitations:
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The analysis process of claim 1 comprises following steps:
a) isolation of plasma from one or more blood samples that have been collected from the human subject under examination,
b) isolation of IgG from blood plasma of the blood samples,
c) release of said glycans from IgG,
d) fluorescent derivatization with 2-aminobenzamide <2AB> and a reducing agent for reductive amination, optionally using a complex of picoline borane <BH3*NC5H4-2-CH3> or sodium cyanoborohydride <NaBH3CN>:
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e) quantitative analysis of thus derivatized glycans by ultra- performance liquid chromatography <UPLC>, wherein numerical values of relative areas under respective glycan peaks GP 9, GP 12, GP 19, and GP 20 within the corresponding UPLC chromatogram are obtained as the numerical values {GP9, GP12,GP 19, GP20}, wherein the said glycan peaks GP 9, GP 12, and GP 19 belong to structures given in the table below:
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wherein G20 represents a peak at a retention time calibrated to retention times of glucose oligomers labeled with 2-aminobenzamide,
Regarding steps a), b), c), d), and e), Lauc teaches the following steps for the study of N-glycans attached to immunoglobulin (IgG) in human blood plasma from isolated populations and the procedure for IgG glycans analysis: isolation of blood plasma from blood (i.e., a)); purification of immunoglobulin G (IgG) with attached N-glycans by affinity chromatography with help of protein G attached to monolithic chromatography columns (i.e., b)); releasing glycans from the attachment to immunoglobulin G (IgG) (i.e., c)); treating the obtained sample with a mixture of favourable amine with ultraviolet absorbing group (so-called “fluorescent colour”) and favourable reducing agent to fluorescently label released glycans by reductive amination (i.e., d)); quantitative analysis of such a prepared sample, which contains fluorescently-derivatized IgG glycans by means of a favourable analytical method (i.e., e)) [0097-0104].
Further regarding step d), Lauc teaches that fluorescent labelling (derivatization) of glycans by reductive amination is executed with favourable amines which, in their structure, contain aromatic or other ultraviolet absorbing group, where the aromatic amine that is used for fluorescent derivatization of glycans according to the invention has been chosen from a group that consists of: 2-aminobenzamide (2AB), 9-aminopyrene-1 3 6-trisulfonic acid (APTS), ethyl 4-aminobenzoate, 2-aminopyridine, anthranillic acid [0108].
Further regarding step e), Lauc teaches obtaining 24 glycan peaks using UPLC, where the glycan peaks include CP9, GP11, GP12, GP19, and GP20 (FIG. 1; Table 1). GP9 corresponds to FA2G1[3] with the structure
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; GP11/12 corresponds to FA2BG1[e] with the structure
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; GP12 corresponds to A2G2 with the structure
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; and GP19 corresponds to FA2BG2S1 with the structure
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(Table 1). Lauc therefore teaches GP9, GP12, and GP19 as instantly claimed. Lauc teaches determining the relative abundance of individual glycans based on the area underneath the signal/chromatographic peak (i.e., numerical values of relative areas under respective glycan peaks) [0116]. Lauc teaches normalization of the area underneath the signal (chromatographic peak) of a certain fluorescently derivatized glycan with total area underneath all signals (peaks) of fluorescently derivatized glycans [0116], but does not teach GP20 which represents a peak at a retention time calibrated to retention times of glucose oligomers labeled with 2-aminobenzamide as instantly claimed. See below for teachings by Trbojevic-Akmacic regarding this limitation.
f) wherein numerical results of relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20, that correspond to values {GP9, GP12, GP19, GP20} calculated in step e, are now included in a CVDR model for cardiovascular diseases risk <CVDR>, which is a function of the four glycan arguments: CVDR = CVDR(GP9, GP12, GP19, GP20),
g) determination of the risk value expressed as the CVDR value.
Regarding steps f) and g), Lauc teaches a linear model to calculate a glycan age index (i.e., risk) based on the quantitative analysis of two or more glycans characteristic for age [0131-0132]. Lauc teaches using the method to monitor progression of diseases as a result of the aging process, including atherosclerosis (i.e., cardiovascular disease) [0001; 0003; 0022; 0089-0095]. Lauc does not teach including the relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20 in a CVDR model for cardiovascular diseases risk.
Lauc does not teach GP20 which represents a peak at a retention time calibrated to retention times of glucose oligomers labeled with 2-aminobenzamide in step e) or including the relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20 in a CVDR model for cardiovascular diseases risk in steps f) and g).
However, Trbojevic-Akmacic discloses a simple, robust, and affordable protocol for immunoglobulin G N-glycan analysis by hydrophilic interaction liquid chromatography–ultra-performance liquid chromatography (HILIC-UPLC) (abstract). Trbojevic-Akmacic teaches that the UPLC system is calibrated using an external standard of hydrolyzed and 2-AB-labeled glucose oligomers from which the retention times for the individual glycans are converted to glucose units (p. 48, section 7), which reads on GP20 as instantly claimed.
Although Lauc does not teach using the external standard as taught by Trbojevic-Akmacic, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Lauc with Trbojevic-Akmacic because each reference discloses methods for N-glycan analysis of IgG. The motivation to include the external calibrant as taught by Trbojevic-Akmacic would have been to calibrate the UPLC system, as taught by Trbojevic-Akmacic (p. 48, section 7).
Lauc does not including the relative areas under the selected glycan peaks GP9, GP12, GP19, and GP20 in a CVDR model for cardiovascular diseases risk in steps f) and g).
However, the prior art to Menni discloses an assessment of the role of a comprehensive panel of IgG glycosylation traits on traditional risk factors for cardiovascular disease and on presence of subclinical atherosclerosis (abstract). Menni teaches measuring IgG glycosylation trains in ~3000 women and correlating the traits to an atherosclerotic cardiovascular disease risk score (abstract). Menni teaches creating a glycan risk score to assess the combined effects of all the glycan traits (i.e., a CVDR model with three glycan arguments of GP9, GP12, and GP19) (p. 1557, col. 2, par. 9). Menni teaches that GP9, or FA2[3]G1, GP11, or FA2[3]BG1, GP12, or A2G2, and GP19, or FA2BG2S1, each had a significant association with the atherosclerotic cardiovascular disease risk score (Online Table I, p. 12-13).
Neither Lauc, Trbojevic-Akmacic, nor Menni teach using GP9, GP12, GP19, and GP20 as four glycan arguments in a CVDR model. However, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify, in the course of routine experimentation and with a reasonable expectation of success, the method of Lauc in view of Trbojevic-Akmacic and Menni to examine GP9, GP12, and GP19, as taught by Lauc and Menni Supplement, in a model to produce a CVD risk score because Menni teaches that IgG-GP9, IgG-GP12, and IgG-GP19 , each had a significant association with the atherosclerotic cardiovascular disease risk score (Online Table I, p. 12-13).
Further, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, of Lauc, Trbojevic-Akmacic, and Menni to include GP20 as part of the model, because Trbojevic-Akmacic teaches using an external standard of hydrolyzed and 2-AB-labeled glucose oligomers from which the retention times for the individual glycans are converted to glucose units, which reads on GP20 as instantly claimed, in order to calibrate the UPLC system (p. 48, section 7). By including GP20 in the model, Lauc would produce an equivalent calibrated risk score.
Regarding claim 2, Lauc in view of Trbojevic-Akmacic and Menni teaches claim 1 as described above. Claim 2 further adds obtaining the CVDR model via statistical data analysis performed after a prospective study that determines the variation of quantitative IgG glycans {GP1,..., GP24} content in the blood plasma in:- normal subjects, versus, - subjects who experienced the following cardiovascular disease clinical manifestations: myocardial infarction, stroke, coronary revascularization, unstable angina requiring hospitalization, or death, wherein significantly predictive IgG glycans are determined using regression models that are corrected for multiple confounders, including age, race, sex, statin therapy, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, smoking, and hypertension, and a glycan-based predictive model is constructed based on the determined IgG glycans construct.
Lauc teaches obtaining 24 glycan peaks (FIG. 1, Table 1). Lauc teaches performing the IgG N-glycan analysis on data from different populations of people (i.e., a prospective study) [0096]. Lauc teaches correcting chronological age in their model [0135].
Lauc does not teach determining the variation of quantitative IgG glycans {GP1,..., GP24} content in the blood plasma in:- normal subjects, versus, - subjects who experienced the following cardiovascular disease clinical manifestations: myocardial infarction, stroke, coronary revascularization, unstable angina requiring hospitalization, or death, or using regression models that are corrected for multiple confounders, including race, sex, statin therapy, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, smoking, and hypertension.
However, Menni teaches using a linear mixed model (i.e., regression model) that adjusts for the risk factor covariates smoking, total and HDL cholesterol (i.e., inherently includes low-density lipoprotein cholesterol in addition to high-density lipoprotein cholesterol), and systolic blood pressure (i.e., hypertension) (p. 1557, col. 2, par. 7; p. 1558 col. 1, par. 4). As Menni teaches that the atherosclerotic cardiovascular disease score is a sex- and race-specific score that is also based on age, sex, ethnicity, total cholesterol and high-density lipoprotein (HDL) cholesterol, systolic blood pressure, smoking status, use of blood pressure–lowering medications, and the presence of type 2 diabetes mellitus (T2D) (p. 1556, col. 1, par. 1), it is considered that the linear models of Menni also correct for sex, race, and statin therapy by correlating to the atherosclerotic cardiovascular disease score. Menni also teaches a logistic regression model which accounts for the atherosclerotic cardiovascular disease score (p. 1559, col. 2, par. 2), which reads on the confounders as claimed for the same reasons as described regarding the linear mixed model. Although Menni does not explicitly teach “a prospective study… in:- normal subjects, versus, - subjects who experienced the following cardiovascular disease clinical manifestations: myocardial infarction, stroke, coronary revascularization, unstable angina requiring hospitalization, or death”, such a limitation is interpreted as a product-by-process limitation (see MPEP 2113). Product-by-process limitations are not limited to the manipulation of the recited steps, only the structure implied by the steps. The implied “structure” in the claims is glycan data that reflects a difference between normal subjects versus those with specific cardiovascular disease clinical manifestations. The data of Menni reflects structurally similar glycan data because they correlate the glycan data with the atherosclerotic cardiovascular disease score, which provides additional information about the risk of myocardial infarction, stroke, and CVD mortality (p. 1556, col. 1, par. 1), which reads on the implied structure of the glycan data as claimed.
Regarding claim 3, Lauc in view of Trbojevic-Akmacic and Menni teaches claim 1 as described above. Claim 3 further adds where the CVDR model is: CVDR = -3.432-GP9 - 0.509-GP12 + 0.793-GP19 - 0.835-GP20, and where the determination of the risk value expressed as the CVDR value comprises:
(i) if the CVDR value is greater than a mean CVDR value of a population, the subject has an increased risk of cardiovascular events in the future compared to the reference population,
and/or (ii) the increase of CVDR value by 1 unit represents an increased risk of 2.6 fold.
Lauc in view of Trbojevic-Akmacic and Menni teach a CVDR model as described above regarding claim 1.
Although Neither Lauc, Trbojevic-Akmacic nor Menni teach the CVDR model as instantly claimed in claim 3, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify, in the course of routine experimentation and with a reasonable expectation of success, the method of Lauc in view of Trbojevic-Akmacic and Menni to include GP9, GP 12, GP 19, and GP20 as described above in claim 1. It is further considered that it would have been obvious to include only those glycan peaks in the model of Lauc because there are a finite number of options of N-glycans measured, only 24, and Menni demonstrates that each of GP9, GP 12, and GP 19 are significantly correlated with cardiovascular disease risk (Online Table I). It is considered that one of ordinary skill in the art would expect such a modification to result in a CVDR model as instantly claimed. One of ordinary skill in the art would have had a reasonable expectation of success in making this modification because Lauc and Menni both demonstrate that glycan peak variables derived from quantitative analysis are routinely used as quantitative inputs in Cox proportional hazards models to determine risk for a disease. Regarding steps (i) and (ii), only one is required to be performed, but (i) is conditional. Therefore, neither steps (i) or (ii) are required within the metes and bounds of the claim to be performed, and Lauc in view of Trbojevic-Akmacic and Menni are considered to teach the required scope of the claim.
Regarding claims 4-6, Lauc in view of Trbojevic-Akmacic and Menni teaches claims 1-3 as described above. Claims 4-6 further add that the glycans under the peaks GP9, GP12, GP19, and GP20 are determined by alternative quantitative analytical techniques selected from the group consisting of: MALDI- TOF mass spectrometry, liquid chromatography coupled with mass spectrometry <LC-MS>, or capillary electrophoresis <CE>, where the corresponding glycans are derivatized with a fluorescent derivatizing agent selected from the group comprising 2-aminobenzamide <2AB>, 8- aminopyrene-1,3,6-trisulfonic acid, trisodium salt <APTS>, procainamide <PR>, or 2,5-dioxopyrrolidine-1-yl-<2N-<2-<N',N'- diethylamino>ethyl>carbamoyl>-quinoline-6-yl-carbamate <RF> having respective structures as below:
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360
690
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Lauc teaches that fluorescent labelling (derivatization) of glycans by reductive amination is executed with favourable amines which, in their structure, contain aromatic or other ultraviolet absorbing group, and the aromatic amine that is used for fluorescent derivatization of glycans according to the invention has been chosen from a group that consists of: 2-aminobenzamide (2AB), 9-aminopyrene-1 3 6-trisulfonic acid (APTS), ethyl 4-aminobenzoate, 2-aminopyridine, anthranillic acid [0108]. Lauc teaches that quantitative analysis of derivatized glycans or glycopeptides can be executed by one of analytical techniques, chosen from a group that consists of: ultra performance liquid chromatography (UPLC), MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry, liquid chromatography-mass spectrometry (LC-MS), capillary electrophoresis (CE) [0112], providing examples of each [0113; 0115; 0153-0163].
Regarding claim 7, Lauc in view of Trbojevic-Akmacic and Menni teaches claim 1 as described above. Claim 7 further adds treating the human subject with a compound selected from the group consisting of acetylsalicylic acid, quercetin, resveratrol, N-acetyl-D-mannosamine, and combinations thereof if the human subject is determined to have an increased risk of cardiovascular events in the future.
The limitation recited in claim 7 is contingent upon the human subject being determined to have an increased risk of cardiovascular events in the future and is therefore not required to be performed. Therefore, Lauc in view of Trbojevic-Akmacic and Menni teaches claim 1 as described above, it is also considered that Lauc in view of Trbojevic-Akmacic and Menni teaches claim 7 as required.
Conclusion
No claims are allowed.
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/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685
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