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 (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Status of the Claims
Claims 1-12 and 17 are pending and examined herein.
Priority
This application, 18/647,791, filed 04/26/2024, is the U.S. national application of PCT/EP2022/080871 filed on 11/04/2022, and claims benefit of provisional application 63/275,581 filed 11/04/2021. This priority is acknowledged and the claims examined herein are treated as having an effective filing date of 11/04/2021.
Information Disclosure Statement
The Information Disclosure Statement filed on 04/26/2024 is acknowledged and has been considered.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-12 and 17 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites “…the severity of the infectious disease in the patient.”. The term “the infectious disease” lacks antecedent basis because it is not recited or defined previously in claim 1, nor does the recited language make evident that “the infectious disease” is specifically a further limitation of “immune system related disease” recited in claim 1.
Claim 1 also recites “…the ratio of levels and affinity of at least two immunogenic proteins….”. The term “the ratio of levels and affinity” lacks antecedent basis because it is not recited or defined previously in claim 1, nor does the recited language make evident that “the ratio of levels and affinity” is specifically a further limitation of “avidity parameters” recited in claim 1. Additionally, the claim is indefinite because there are multiple possible conflicting interpretations based on the claim language and table provided. For example, it is unclear if the claim language “the ratio of levels and affinity” is to be interpreted as the ratio is a comparison of levels to affinity for one immunogenic protein. Or alternatively if interpretation of the claim language would be that the ratios are determined by comparing levels and affinity between two immunogenic proteins. As there are multiple potential conflicting interpretations of the claim language, these claims are indefinite.
Claim 1 also recites “…at high ligand density…” and “…at low but fixed Rmax conditions…”. The recitation of “high” and “low” is relative terminology, and as such the claim is indefinite because it is not readily clear what is encompassed by “…high ligand density…” and “…low but fixed Rmax conditions…”, (i.e., compared to what standard is considered high ligand density and low Rmax).
Additionally, claim 1 recites the term “ligand” which lacks antecedent basis because it is not recited or defined previously in claim 1, nor is it clear whether “ligand” is a further limitation of “immunogenic antigen” recited previously in claim 1. As a result, the scope of the claim is unclear because one having ordinary skill cannot readily determine whether the ligand is the same as the immobilized immunogenic antigen recited previously.
Claim 4 recites “…the flow channel…” which lacks antecedent basis because it is not recited or defined previously in claim 4 or in claim 1 from which it depends.
Claim 5 recites “…the association rate and dissociation rate…”. The terms lack antecedent basis because it is not recited or defined previously in claim 1, nor does the recited language make evident that “the association rate and dissociation rate” is specifically a further limitation of “strength of binding” or “ratio of levels and affinity” recited in claim 1.
Additionally, regarding claim 5, the phrase "such that" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 5 also recites “…where fluidics are designed…”. This recitation renders the claim indefinite because it is unclear how “fluidics are designed” to accomplish the method as claimed.
Claim 9 recites “…where half a flow cell is applied…”. This recitation renders the claim indefinite because it is unclear where and how the flow cell is disposed/designed to accomplish the method as claimed. Additionally, no flow cell is recited in claims 1 or 9 before its use is claimed.
Claims 10 and 11 recite “…the biomolecular interaction on the gradient…”. The terms lack antecedent basis because it is not recited or defined previously in the claims or in claim 1 from which they depend, nor does the recited language make evident that “the biomolecular interaction” is referring to an antigen-antibody interaction which is not specifically recited in claim 1.
Appropriate correction is required.
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 1-3, 6-8, and 10-12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception and a law of nature without significantly more. Claim 1 recites a “Method for predicting Immune system related disease severity by the combination of specific antibody concentration and strength of binding of all antibodies isotypes from a body fluid sample from a patient…wherein the ratio of levels and affinity of at least two immunogenic proteins predicts the severity of the infectious disease in the patient”.
The claims are directed to a judicial exception, mainly they are abstract ideas, specifically, mental processes that can be performed in the human mind, and/or are merely observing naturally occurring correlations (laws of nature/natural correlation). These judicial exceptions are not integrated into a practical application because there is no practical application recited in the claims such as performing a treatment in a way that is particular, and not merely instructions to "apply" the exception in a generic way. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional steps amount to mere data gathering that does not go beyond well-understood, routine, and conventional activity; as detailed below.
Step 1 – Whether a claim is to a statutory category - YES
The instantly claimed invention is directed to a method for predicting an immune system related disease severity by determining the combination of specific antibody concentration and strength of binding of antibodies isotypes from a body fluid sample from a patient. Therefore, the instantly claimed invention falls into one of the four statutory categories.
Step 2A Prong 1 – Whether the claim is directed to a judicial exception (i.e. Does the claim recite an abstract idea, law of nature, or natural phenomenon?) - YES
Claim 1 recites the following steps which fall under mental processes grouping of abstract ideas and/or laws of nature/natural correlation:
Claim 1 discloses a method for predicting an immune system related disease severity by determining the combination of specific antibody concentration and strength of binding of antibodies isotypes from a body fluid sample from a patient. This is done by exposing a patient’s sample to an immunogenic antigen immobilized on a biosensor, determining the concentration and avidity parameters at certain conditions, and using the ratio of levels and affinity of at least two immunogenic proteins to determine and predict the severity of the infectious disease in the patient.
The broadest reasonable interpretation of this step is measuring a specific antibody concentration and strength of binding of antibodies isotypes in a sample to immunogenic antigens and using the data for the ratio of levels and affinity of two immunogenic proteins to determine or predict the severity of the infectious disease. This limitation recites a law of nature which is a judicial exception, because it is merely observing the correlation between a naturally occurring biomarker (antibody concentration and affinity) and its relationship to a disease/disease state (infectious disease severity).
Regarding the identification of a correlation between the presence of a biomarker in a bodily sample and disease state the courts have held similar claims to be laws of nature and/or natural phenomena, as in Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1361, 123 USPQ2d 1081, 1087 (Fed. Cir. 2017) which involved claims to simply instruct a user to apply a natural law, by correlating naturally occurring enzyme levels with disease risk. In Mayo, the Supreme Court found that a claim was directed to a natural law, where the claim required administering a drug and determining the levels of a metabolite following administration, where the level of metabolite was indicative of a need to increase or decrease the dosage of the drug. See Mayo Collaborative Services V. Prometheus Labs., Inc., 566 U.S. 66, 74 (2012). The instant claims are similar to those in Mayo as they involve a "relation itself [which] exists in principle apart from any human action" (id. at 77), namely the relationship between the naturally occurring levels of a biomarker (antibodies and their binding strength against antigens) that indicates severity or predicted severity of an infectious disease.
The correlation between the recited biomarkers of infectious disease and disease severity is a judicial exception as it exists in principle apart from any human action; the correlation itself therefore cannot form the basis for eligibility.
The steps of “determining”/”predicting” also constitutes an abstract mental process, involving assessing the ratio of levels and affinity of two immunogenic proteins, and then using that information to make an evaluation or judgment as to the disease state of the subject. The “determining” step could be performed in the human mind, or by a human using pen and paper, insofar as it reads on comparing levels and drawing conclusions from this about the health status of a subject.
Thus, claim 1 falls into a judicial exception.
Step 2A: Prong 2 - Does the claim recite additional elements that integrate the judicial exception into a practical application? The Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception.
Claim 1 does not recite any additional element that integrate the exception into a practical application of the exception. The claims also recite the additional steps of using an initial slope of a binding curve under mass transport limited conditions and avidity parameters at low but fixed Rmax conditions on a ligand density gradient, which are insufficient to integrate the exception into a practical application because the purpose is merely to obtain data to observe a naturally occurring correlation.
Regarding dependent claims 2, 3, 6-8, and 10-12, they do not recite any additional elements that integrate the judicial exception into a practical application. The additional steps of having the label-free and real-time biosensor based on Surface Plasmon Resonance (SPR) imaging (2 and 3), where the immune system related disease is an infectious disease (claim 6), where the immobilized immunogenic antigens are at least a Receptor Binding Domain and Nucleocapsid (NCP) of SARS-CoV- 2 and binding constants of the Nucleocapsid antibodies and the binding constants of RBD predict COVID-19 severity of infectious disease in the patient. (claims 7 and 8), the measurement of the biomolecular interaction on the gradient which are simultaneously exposed to concatenated injections of anti- isotype antibodies (claims 10 and 11), and where the strength of binding of isotypes of antibodies using SPR imaging and method to reduce the number of false positives characterized by a print of gradients of ligands exposed to patient samples (claim 12), are insufficient to integrate the exception into a practical application because the purpose is merely to obtain data to observe a naturally occurring correlation and/or perform a mental process.
Such steps are considered to be insignificant presolution activity, i.e., a mere data gathering step necessary to use the correlation, similar to the fact pattern in In re Grams, 888 F.2d 835 (Fed. Cir. 1989) and Ariosa Diagnostics, Inc. V. Sequenom, Inc. (Fed. Cir. 2015) because their purpose is merely to obtain data to use the correlation.
In particular, of the claims indicated in the rejection heading, none of the additionally recited limitations amount to an additional element or combination of elements that apply, rely on, or use the judicial exceptions in a manner that impose meaningful limit on the judicial exceptions.
Step 2B; Whether the additional elements contribute an “inventive concept”. In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP 2106.05.
Briefly, claims 1-3, 6-8, and 10-12 do not include additional elements that are sufficient to amount to significantly more than the judicial exception because of the following reasons. Simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, has been found to be insufficient to add “significantly more” (MPEP 2106.05(I)(A)).
The additional steps recited above do not add a meaningful limitation to the instant method as they would have been routinely used by those of ordinary skill in the art as supported by Schasfoort et al. (2020). “Presence and strength of binding of IgM, IgG and IgA antibodies against SARS-CoV-2 during CoViD-19 infection”, 06 August 2020, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-52460/v1], (herein referred to as Schasfoort 2020), Schasfoort (2017). “Introduction to surface plasmon resonance”, Chapter 1, Handbook of Surface Plasmon Resonance, 2nd ed., Royal Society of Chemistry, (herein referred to as Schasfoort 2017), Sen et al. (2021). “Predicting COVID-19 severity with a specific nucleocapsid antibody plus disease risk factor score”. Msphere, 6(2), 10-1128, (published 04/28/2021), Carterra, Inc. (2019). Application Note. “Generating High Quality Kinetic Data from Crude Periplasmic Extracts Using High Throughput SPR”, (herein referred to as Carterra), IBIS Technologies B.V., (2015). "Specifications of the MX96”, IBIS White Paper #1.151015, (herein referred to as Ibis), and Abdiche et al. (2011). “Expanding the ProteOn XPR36 biosensor into a 36-ligand array expedites protein interaction analysis”. Analytical biochemistry, 411(1), 139-151.
Schasfoort 2020 teaches the use of surface Plasmon Resonance imaging (SPRi) to determine the presence and strength of binding of IgG, IgM and IgA against the Receptor Binding Domain (RBD) of SARS-CoV-2 in sera of 119 CoViD-19 with critical, severe, moderate and mild symptoms and control sera and, although the patients show a high variation in immune response composition, generally, the strength of binding showed an affinity maturation over time (abstract; page 8, 3rd full paragraph). Schasfoort 2020 also teaches that the sensor is placed in the SPR imager and real-time measurements were performed during three concatenated injections of anti-IgM, anti-IgG and anti-IgA (page 6, 4th paragraph).
Schasfoort 2017 teaches an introduction to surface plasmon resonance (SPR). Schasfoort 2017 teaches SPR concepts such as the steps of an assay, concentration determination, and mass transport-controlled kinetics (“Chapter Contents”). More specifically, Schasfoort 2017 teaches that if the surface concentration of B (ligand) is very high, and the mass transport rate km is small compared with the association rate constant ka, i.e. km≪ka[B], in the extreme boundary condition the interaction is controlled by the mass-transport rate only, and then the complex formation rate is dependent solely on the bulk concentration of analyte A, and the binding signal increases linearly with time (page 15, 1st paragraph).
Sen teaches a method for predicting COVID-19 severity with a specific nucleocapsid antibody plus a disease risk factor score (abstract). Sen teaches the use of enzyme-linked immunosorbent assay (ELISA) and coronavirus antigen microarray (COVAM) analysis to map antibody epitopes (predicted region of the antigenic protein recognized by the antibody’s paratope) in the plasma of COVID-19 patients experiencing a wide range of disease states (abstract).
Carterra teaches that the Carterra Continuous Flow Microspotting (CFM) technology enables both uni- and bi-directional (back-and-forth) flow capability, referred to as multi-pass sample delivery (page 2, 2nd paragraph). Carterra teaches that the LSA’s integrated CFM technology uses 96 parallel micro-channels to flow and cycle ligand solutions via a printhead over a defined surface enabling the simultaneous immobilization of 96 individual protein spots in a single step (page 2, 3rd paragraph).
Ibis teaches the specifications of the IBIS MX96 SPR imaging instrument. Ibis teaches that the MX96 uses valve-less injection of samples and patented “back-and-forth” flow-based fluidics requires a sample volume of only 100 microliter to simultaneously measure the interactions on 96 ligand spots, and that the unsurpassed multiplex capacity of this platform provides scope to examine multiple interactions, simultaneously, whilst offering multiple referencing possibilities (up to 48 for 96 spots) (abstract).
Abdiche teaches combine a 36-ligand array with the kinetic titration method to study 36 unique analyte/ligand pairs simultaneously without any regeneration, by injecting the members of an analyte concentration series in succession from low to high concentration through the same flow channel, so that an entire analyte concentration series interrogates each spot (page 140, column 1 3rd paragraph – column 2, 1st paragraph). The kinetic titration method thus enables the use of various multiplexed assay formats. (abstract).
For all of these reasons, the claims fail to include additional elements that are sufficient to amount to significantly more than the judicial exception(s).
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to a law of nature and abstract idea without significantly more. For additional guidance, applicant is directed generally to 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.
Claims 1-3, 6-8, 10-12, and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Schasfoort et al. (2020). “Presence and strength of binding of IgM, IgG and IgA antibodies against SARS-CoV-2 during CoViD-19 infection”, 06 August 2020, PREPRINT (Version 1) available at Research Square [https://doi.org/10.21203/rs.3.rs-52460/v1], (herein referred to as Schasfoort 2020), in view of Schasfoort (2017). “Introduction to surface plasmon resonance”, Chapter 1, Handbook of Surface Plasmon Resonance, 2nd ed., Royal Society of Chemistry, (herein referred to as Schasfoort 2017) and Sen et al. (2021). “Predicting COVID-19 severity with a specific nucleocapsid antibody plus disease risk factor score”. Msphere, 6(2), 10-1128, (published 04/28/2021), (herein referred to as Sen).
Regarding claims 1-3, 6-8, 12, and 17, Schasfoort 2020 teaches the use of surface Plasmon Resonance imaging (SPRi) to determine the presence and strength of binding of IgG, IgM and IgA against the Receptor Binding Domain (RBD) of SARS-CoV-2 in sera of 119 CoViD-19 patients (abstract). More specifically, Schasfoort 2020 teaches the measurement of 119 sera including longitudinal samples obtained from 53 unique positively PCR-tested patients with critical, severe, moderate and mild symptoms and control sera and, although the patients show a high variation in immune response composition, generally, the strength of binding showed an affinity maturation over time (page 8, 3rd full paragraph). Schasfoort 2020 teaches that for SPRi measurements the multiplex SPR imaging instrument and the Carterra LSA platform were used with an installed sensor prism, and that the sensor was exposed for 20 minutes to the Spike RBD his-tag in immobilization buffer (page 5, 3rd full paragraph). Additionally, Schasfoort 2020 teaches that for measurements on the IBIS MX96 a Continuous Flow Microuidic (CFM) system was used to capture 96 sera on a sensor functionalized with RBD-Spike coupled (page 5, 5th paragraph – page 6, 1st paragraph). Schasfoort 2020 also teaches that the molecular weight of RBD with 192 amino acids is smaller than the S domains and immobilization resulted in a higher functional ligand density (Supplementary Data, page 6, 1st paragraph).
Schasfoort 2020 also teaches that the sensor is placed in the SPR imager and real-time measurements were performed during three concatenated injections of anti-IgM, anti-IgG and anti-IgA (page 6, 4th paragraph). Schasfoort 2020 teaches the Rmax value was determined using a special biphasic fit algorithm (page 6, 1st full paragraph). Schasfoort 2020 also teaches that the ratio of bound immunoglobulins can be calculated by determining the Rmax values from the anti-isotype antibodies binding signals (page 6, 2nd full paragraph). Schasfoort 2020 also teaches that the off-rate is also dependent on the ligand density, and therefore, they decided to spot the anti-RBD antibodies from the same patient in 4 densities (Fig. S6 caption). Additionally, Schasfoort 2020 teaches that the value of the off-rate was determined at R=1000 RU by interpolating the values obtained in the ligand density gradient (Fig. S6 caption). Shasfoort 2020 also teaches that the quality of the immune response is not only determined by the quantity of antibodies but also by the overall strength of binding of the pool of potential neutralizing antibodies that binds to the relevant immunogenic proteins of the Corona virus (page 3, 2nd paragraph). Finally, Schasfoort 2020 teaches that any protein targeted by an immune response can be immobilized to the sensor surface allowing for a very high-throughput, quantitative, and reproducible means of characterizing immunity, and that the real-time monitoring of signals in SPRi makes it well suited too for rapid deployment and optimization (page 8, 2nd full paragraph).
However, Schasfoot 2020 does not teach specifically using its method to predict disease severity, determining a concentration using an initial slope of a binding curve under mass transport limited conditions, or measuring a ratio of levels and affinity of at least two immunogenic proteins and having the second protein being Nucleocapsid (NCP) of SARS-CoV- 2.
Schasfoort 2017 teaches an introduction to surface plasmon resonance (SPR). Schasfoort 2017 teaches SPR concepts such as the steps of an assay, concentration determination, and mass transport-controlled kinetics (“Chapter Contents”). More specifically, Schasfoort 2017 teaches that if the surface concentration of B (ligand) is very high, and the mass transport rate km is small compared with the association rate constant ka, i.e. km≪ka[B], in the extreme boundary condition the interaction is controlled by the mass-transport rate only, and then the complex formation rate is dependent solely on the bulk concentration of analyte A, and the binding signal increases linearly with time (page 15, 1st paragraph). Schasfoort 2017 teaches that an equation can therefore be used for the determination of the concentration of analyte A, since the slope of the initial stage of the binding curve is proportional to the analyte concentration (page 15, 1st paragraph). Shasfoort 2017 also teaches that using calibration-free concentration analysis (CFCA) allows the functional concentration of an analyte to be determined by SPR without the need for a calibration curve, leading to a flow cell constant, FCMW, which can be used to calculate an unknown analyte concentration with the same molecular weight by measuring the initial slope of the association phase under two different mass transport-limited conditions set by the flow rate (page 17, 2nd full paragraph).
Sen teaches a method for predicting COVID-19 severity with a specific nucleocapsid antibody plus a disease risk factor score (abstract). Sen teaches the use of enzyme-linked immunosorbent assay (ELISA) and coronavirus antigen microarray (COVAM) analysis to map antibody epitopes (predicted region of the antigenic protein recognized by the antibody’s paratope) in the plasma of COVID-19 patients experiencing a wide range of disease states (abstract). Sen also teaches that the 21 candidate SARS-CoV-2 epitopes spanned the S, N, M, or E proteins and were on average 34 amino acids in length (page 2, 4th full paragraph). Sen teaches that the experiments identified antibodies to a 21-residue epitope from nucleocapsid (termed Ep9) associated with severe disease, including admission to the intensive care unit (ICU), requirement for ventilators, or death (abstract). Lastly, Sen teaches that the presence of antibodies specifically binding to this epitope plus a score cutoff can predict severe COVID-19 outcomes with 96.7% specificity (abstract). Sen also teaches that among patients with αEp9 Abs (n = 23), a DRFS of ≥3 determined disease severity with 92.3% sensitivity (1/13 false negatives) and 80% specificity (2/10 false positives) (page 6, 1st full paragraph).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of using SPR to determine the concentration and strength of binding of antibodies against RBD of SARS-CoV-2 in sera of CoViD-19 patients as taught by Schasfoort 2020, to determine antibody concentration using an initial slope of a binding curve under mass transport limited conditions, as taught by Schasfoort 2017, as it would be “obvious to try”. There are a limited number of methods of determining antibody concentration using surface plasmon resonance imaging, and as Schasfoort 2017 acts as a standard reference for implementing such determination techniques and uses the same IBIS MX96 SPR imaging platform and underlying flow mechanics. As such, one would be motivated to consult Schasfoort 2017 and implement their method of determining concentration at high ligand density. A person of ordinary skill would have had a reasonable expectation of success in modifying the method of Schasfoort 2020 because both references teach measuring antibody concentration using SPR, even using the same imaging system, and ligand sensor layout.
Additionally, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of using SPR to determine the concentration and strength of binding of antibodies against Receptor Binding RBD of SARS-CoV-2 in sera of CoViD-19 patients as taught by Schasfoort 2020, to measure at least two immunogenic proteins to predict the severity of an infectious disease in a patient and the second protein being the SARS-CoV-2 nucleocapsid protein, as taught by Sen, as a matter of combining prior art elements according to known methods to yield predictable results. Sen teaches that anti-Ep9 antibodies can accurately predicts severe COVID-19 outcomes, and Schasfoort teaches that that the most potent, highest affinity neutralizing antibodies were directed to the receptor-binding domain (RBD) of SARS-CoV-2, and that during the course of the disease, the IgG levels and strength of binding against RBD increased. Therefore, it would have been obvious to measure antibodies against both RBD and the nucleocapsid protein of SARS-CoV-2, with the motivation of creating a method/model that most accurately predicts the severity of COVID-19 in the patient, and reduces false positives, as taught by Ren. A person of ordinary skill would have had a reasonable expectation of success in modifying the method of Schasfoort 2020 because both references are in the same field of measuring the concentration and affinity of antibodies in the context of examining immune responses during COVID-19 infection.
Regarding claims 10 and 11, Schasfoort 2020 teaches that in one iteration, the sensor is placed in the SPR imager and real-time measurements were performed during three concatenated injections of anti-IgM, anti-IgG and anti-IgA (page 6, 4th paragraph). Schasfoort 2020 also teaches the use of a patient overlay for calculating the Rmax values of anti-IgM, anti-IgG and anti-IgA which is proportional to the bound IgM, IgG and IgA anti-RBD (page 7 1st paragraph). Schasfoort 2020 also teaches that after converting the data by local referencing, zeroing the baseline and aligning the injection points of the three injections, the Rmax value was determined using a special biphasic fit algorithm (page 6, 1st full paragraph). Schasfoort 2020 teaches that this enables the application of a biphasic binding model for calculation of Rmax for the three isotypes (page 7 1st paragraph). Schasfoort 2020 also teaches that sensorgrams were measured for all samples simultaneously and shown as an overlay plot in Figure 2 (page 7 1st paragraph). Additionally, Schasfoort 2020 teaches that the value of the off-rate was determined at R=1000 RU by interpolating the values obtained in the ligand density gradient (Fig. S6 caption). Schasfoort 2020 also teaches the calculation of global dissociation- or global off-rate constant from the same sample within one assay run (page 6, 2nd full paragraph), as well as the measurement of the association rate (on-rate) (Fig. S1 caption).
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Schasfoort (2020), in view of Schasfoort (2017) and Sen as applied to claim 1 above, and further in view of Carterra, Inc. (2019). Application Note. “Generating High Quality Kinetic Data from Crude Periplasmic Extracts Using High Throughput SPR”, (herein referred to as Carterra).
The teachings of Schasfoort 2020, in view of Schasfoort 2017 and Sen are incorporated herein.
Regarding claim 4, Schasfoort 2020 in view of Schasfoort 2017 and Sen recites all of the limitations of claim 1, and Schasfoort 2020 additionally teaches that for measurements on the IBIS MX96 a Continuous Flow Microuidic (CFM) system (Carterra Salt Lake City Page 5/15 UT, US) was used to capture 96 sera on a sensor functionalized with RBD-Spike coupled (page 5, 5th paragraph – page 6, 1st paragraph). Schasfoort 2020 also teaches controlled injection of ligand to create a ligand density gradient (Fig. S6 caption).
However, Schasfoort 2020 in view of Schasfoort 2017 and Sen does not specifically teach that the gradient is created by differences in contact time using at least a single back and forth flow of the sample in the flow channel in contact with a sensor surface.
Carterra teaches that the Carterra Continuous Flow Microspotting (CFM) technology enables both uni- and bi-directional (back-and-forth) flow capability, referred to as multi-pass sample delivery (page 2, 2nd paragraph). Carterra teaches that the LSA’s integrated CFM technology uses 96 parallel micro-channels to flow and cycle ligand solutions via a printhead over a defined surface enabling the simultaneous immobilization of 96 individual protein spots in a single step (page 2, 3rd paragraph). Carterrra also teaches that each of the 96 micro-channels creates an independent fixed loop for every sample so that by utilizing multi-pass flow, each sample can move back-and-forth across the surface for a user defined time period, thereby in-line enriching the concentration of low expressing clones during immobilization (using affinity-capture or coupling chemistry), hereby termed flow printing (page 2, 3rd paragraph). Carterra teaches that proteins are maintained in a stable liquid environment throughout the immobilization step, producing highly defined active spots with coverage that can approach saturation, which overcomes the immobilization sensitivity issue, enabling very low expressing PPEs to be kinetically screened with confidence without the need for prior enrichment (page 2, 3rd paragraph).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of using SPR to determine the concentration and strength of binding of antibodies against two immunogenic proteins as taught by Schasfoort 2020 in view of Schasfoort 2017 and Sen, to create the ligand gradient by differences in contact time using at least a single back and forth flow of the sample in the flow channel in contact with a sensor surface, as taught by Carterra, as it would be “obvious to try”. Schasfoort 2020 uses the same system (Carterra LSA using CFM technology) as taught by Carterra, and it would be obvious of one of ordinary skill in the art to look to Carterra, a technical document for the same system, in order to determine how a ligand gradient can be generated, and by what techniques the system can produce them.
Additionally, a skilled artisan would have been motivated to make these modifications to the method taught by Schasfoort 2020 because Carterra teaches that using such a technique produces highly defined active spots with coverage that can approach saturation, which overcomes the immobilization sensitivity issue, and enables very low expressing PPEs to be kinetically screened with confidence without the need for prior enrichment. A person of ordinary skill would have had a reasonable expectation of success in modifying the method of Schasfoort 2020 because both references teach the use of the Carterra LSA system to create a ligand gradient.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Schasfoort (2020), in view of Schasfoort (2017) and Sen as applied to claim 1 above, and further in view of IBIS Technologies B.V., (2015). "Specifications of the MX96”, IBIS White Paper #1.151015, (herein referred to as Ibis).
The teachings of Schasfoort 2020, in view of Schasfoort 2017 and Sen are incorporated herein.
Regarding claim 5, Schasfoort 2020 in view of Schasfoort 2017 and Sen recites all of the limitations of claim 1 of the application, and Schasfoort 2020 also teaches the calculation of global dissociation- or global off-rate constant from the same sample within one assay run (page 6, 2nd full paragraph), as well as the measurement of the association rate (on-rate) (Fig. S1 caption), and the use of the same SPR imaging instrument (IBIS MX96) as taught by Ibis (page 5, 3rd full paragraph). Schasfoort 2020 also teaches that the value of the off-rate was determined at R=1000 RU by interpolating the values obtained in the ligand density gradient (Fig. S6 caption)
However, Schasfoort 2020 in view of Schasfoort 2017 and Sen does not explicitly teach the fluidics that allows measurements to be made simultaneously across at least two channels or more.
Ibis teaches the specifications of the IBIS MX96 SPR imaging instrument. Ibis teaches that the MX96 uses valve-less injection of samples and patented “back-and-forth” flow-based fluidics requires a sample volume of only 100 microliter to simultaneously measure the interactions on 96 ligand spots, and that the unsurpassed multiplex capacity of this platform provides scope to examine multiple interactions, simultaneously, whilst offering multiple referencing possibilities (up to 48 for 96 spots) (abstract).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of using SPR to determine the concentration and strength of binding of antibodies against two immunogenic proteins as taught by Schasfoort 2020 in view of Schasfoort 2017 and Sen, to employ fluidics that allows measurements to be made simultaneously across at least two channels or more, as taught by Ibis, as it would be “obvious to try”. Ibis teaches that the fluidics design are an inherent capability of the IBIS MX96, the same instrument used for measurements by Schasfoort 2020. Therefore, modifying the method of Schasfoort 2020 is merely using a fundamental feature of the device already used for measurements. A person of ordinary skill in the art would have reasonably consulted Ibis, which is a technical document for the device used by Schasfoort 2020. A person of ordinary skill would have had a reasonable expectation of success in modifying the method of Schasfoort 2020 in view of Schasfoort 2017 and Sen because the IBIS MX96 SPR imaging instrument used in both Schasfoort 2020 and Ibis, the system is commercially available, and Schasfoort 2020 demonstrated that the device can be used for simultaneous duplex measurements.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Schasfoort (2020), in view of Schasfoort (2017), Sen, and Carterra as applied to claim 4 above, and further in view of Abdiche et al. (2011). “Expanding the ProteOn XPR36 biosensor into a 36-ligand array expedites protein interaction analysis”. Analytical biochemistry, 411(1), 139-151.
The teachings of Schasfoort 2020, in view of Schasfoort 2017, Sen, and Carterra are incorporated herein.
Regarding claim 9, Schasfoort 2020 in view of Schasfoort 2017, Sen, and Carterra recites all of the limitations of claim 1, and Schasfoort 2020 also teaches controlled injection of ligand to create a ligand density gradient (Fig. S6 caption).
However, Schasfoort 2020 in view of Schasfoort 2017, Sen, and Carterra does not teach rotating the sensor 180 degrees to allow a next immobilization with the second protein in a timely exposure from inlet to outlet of the flow cell at the top section while the first gradient is still on the down section.
Abdiche teaches combine a 36-ligand array with the kinetic titration method to study 36 unique analyte/ligand pairs simultaneously without any regeneration, by injecting the members of an analyte concentration series in succession from low to high concentration through the same flow channel, so that an entire analyte concentration series interrogates each spot (page 140, column 1 3rd paragraph – column 2, 1st paragraph). The kinetic titration method thus enables the use of various multiplexed assay formats. (abstract). Abdiche teaches that BioRad’s ProteOn XPR36 platform addresses interactions on 36 reaction spots simultaneously by combining the use of six parallel flow channels with a microfluidic pathway that can rotate between vertical and horizontal directions (page 139, column 2, 1st full paragraph). Abdiche teaches that this creates a two-dimensional interaction array within which the intersecting and nonintersecting flow paths define the reaction and reference spots, respectively (page 139, column 2, 1st full paragraph).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of using SPR to determine the concentration and strength of binding of antibodies against two immunogenic proteins using a ligand gradient on the sensor surface created by differences in contact time of flow, as taught by Schasfoort 2020 in view of Schasfoort 2017, Sen, and Carterra, to rotate the sensor to allow for the binding of an additional protein/ligand, as taught by Abdiche, as a matter of applying a known technique to a known method ready for improvement to yield predictable results. While Abdiche teaches a 90° rotation (between vertical and horizontal positions) and not a 180° rotation as recited in claim 9, making such a modification would be routine and predictable to one of ordinary skill in the art. Abdiche merely teaches a 90° rotation to achieve the desired layout of their flow cells/channels, and the rotation technique is not inherently limited to 90° only. In combination with the 6 flow channels, the 90° rotation of the sensors allows for a stacked crisscross (horizontal and vertical) configuration which creates an array with 36 spots. If a person of ordinary skill in the art was seeking to implement Abdiche’s rotation-based ligand-immobilization/sensor conformation technique to a method with only two ligands, as taught in the instant application, it would have been obvious to instead have rotated the sensor 180° as a simple solution to position the second ligand gradient in the opposite direction of the first.
Additionally, a skilled artisan would have been motivated to make these modifications to the method taught Schasfoort 2020 in view of Schasfoort 2017, Sen, and Carterra in order to immobilize a second ligand in addition to the first on the same array in a way that does not disturb the immobilization of the first ligand, in order to have a multiplex assay using SPR. A person of ordinary skill would have had a reasonable expectation of success in modifying the method of Schasfoort 2020 in view of Schasfoort 2017, Sen, and Carterra, because Abdiche is in the same field of endeavor as Schasfoort 2020 (as well as Schasfoort 2017 and Carterra) which is the use of SPR systems to analyze antibody/ligand interactions in a multiplex format. Additionally, the SPR systems used by these references are commercially available, and the prior art demonstrates that it is possible to 1) put ligand gradients on the sensor, and 2) have ligand gradients on the sensor.
Conclusion
For all the reasons discussed above, claims 1-12 and 17 are rejected and therefore no claims are allowed.
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/ALEXANDER J. HOFFMAN/ Examiner, Art Unit 1677
/BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 July 30, 2026
