DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restriction
Applicant's election without traverse of Species A (iii) Table 3 (as recited in claim 6) is acknowledged. Claim(s) 4, 5, 7 are hereby withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention or species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 06/08/2026.
Applicant's election with traverse of Species B (ii) (as recited in claim 9) is acknowledged. Applicant’s arguments that normalized abundance values and those determined by a feature selection method are not mutually exclusive have been fully considered. In response, applicant’s arguments are not persuasive because the species are still deemed to lack unity of invention because they are not so linked as to form a single general inventive concept under PCT Rule 13.1, as set forth in the Restriction Requirement mailed 03/06/2026. In addition, Applicant has not submitted any evidence to the contrary. Accordingly, the restriction is maintained. The requirement is still deemed proper and is therefore made FINAL. Claim 8 and 10 are hereby withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 06/08/2026.
Applicant's election with traverse of Species C (iii) (as recited in claim 19) is acknowledged. Applicant’s arguments that the restriction is improper because Species C(i) and Species C(ii) have overlapping subject matter are persuasive. Accordingly, this species election is withdrawn. Applicant timely traversed the restriction (election) requirement in the reply filed on 06/08/2026.
Status of Claims
Claims 1-10, 13, 16-21, 24, 26, 27, 28 are pending.
Claim 28 is newly added. Claims 4, 5, 7, 8, 10 are withdrawn.
Claims 1-3, 6, 9, 13, 16-21, 24, 26-28 are under examination.
Priority
This application claims priority to United States Provisional Patent Application No. 62/916,103, filed October 16, 2019.
Information Disclosure Statement
The information disclosure statement (IDS) document(s) submitted is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS document(s) has/have been fully considered by the examiner.
Drawings
The drawings filed 04/15/2022 are acknowledged and acceptable.
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, 9, 13, 16-21, 24, 26-28 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and ‘as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355).
Guidance: Step 1. Under the broadest reasonable interpretation, the claimed invention (claims 1 being representative) is directed to a method for performing a process (evaluating a gynecological disorder) and therefore falls within one of the four statutory categories.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the following steps of claim 1 recite an abstract idea:
c) determining, for each protein in a first set of proteins, a corresponding abundance value for the respective protein in the protein preparation, thereby obtaining a first protein abundance dataset for the subject;
d) determining, using the first protein abundance dataset, values for each of a first set of protein abundance features, thereby obtaining a first feature dataset for the subject; and
e) inputting the first feature set into a classifier trained to distinguish between at least two states of the gynecological disorder based on at least the first set of protein abundance features, thereby obtaining a probability or likelihood from the classifier that the subject has a particular state of a gynecological disorder.
Mental Processes
Under MPEP §2111, during patent examination, claims must be interpreted in their broadest reasonable manner consistent with the specification. This means that examiners consider the claim language in light of the specification as understood by a person of ordinary skill in the art, ensuring that the claims are not unduly narrowed by implicit limitations not explicitly recited in the claim (37 CFR 1.75(d)(1)).
With regards to said determining, a claim “recites” a judicial exception when the judicial exception is “set forth” or “described” in the claim. MPEP 2106.04, subsection II. In this case, under the BRI, the recited acts of determining abundance values sets forth or describes observing data or manipulating data (which scientists can performing using their brains or a pencil and paper). As such, these steps encompass a mental process of observing data and/or manipulating data. MPEP 2106.04(a)(2), section III.
With regards to said inputting, a claim “recites” a judicial exception when the judicial exception is “set forth” or “described” in the claim. MPEP 2106.04, subsection II. In this case, under the BRI, the recited act of inputting data into a “classifier” sets forth or describes observing and/or manipulating data to generate additional data. Moreover, scientists routinely input data into equations (i.e. classifiers) to performing analysis and this can be done in the mind or using a pencil/paper. As such, this step encompasses a mental process of observing data and manipulating data to generate additional data. MPEP 2106.04(a)(2), section III.
It is important to note that “Claims that recite performing information analysis as well as the collection and manipulation of information related to such analysis, have been determined by our reviewing court to be an abstract concept that is not patent eligible. See SAP, 898 F.3d, 1165, 1167, 1168 (Claims reciting "[a] method for providing statistical analysis" (id. at 1165) were determined to be "directed to an abstract idea" (id. at 1168)); see also Content Extraction & Transmission LLC v. Wells Fargo Bank, Nat'l Ass 'n, 776 F.3d 1343, 1345, 1347 (Fed. Cir. 2014) (finding the "claims generally recite ... extracting data ... [and] recognizing specific information from the extracted data" and that the "claims are drawn to the basic concept of data recognition"). "As many cases make clear, even if a process of collecting and analyzing information is limited to particular content or a particular source, that limitation does not make the collection and analysis other than abstract." SAP, 898 F.3d at 1168 (internal quotation marks omitted))." [Step 2A, Prong 1: YES].
Mathematical Concept
With regards to said inputting, a claim “recites” a judicial exception when the judicial exception is “set forth” or “described” in the claim. MPEP 2106.04, subsection II. In this case, under the BRI, the recited act of inputting data into a “classifier” (to obtain a probability or likelihood value) sets forth or describes a mathematical calculation and/or mathematical relationship. This position is further supported by applicant’s own specification, which teaches mathematical algorithms/operations for performing the claimed function (pages 19-20). As such, this step recites a mathematical concept. MPEP 2106.04(a)(2) Section I.
While no specific equation is being claimed, Applicant is reminded that there is no particular word or set of words that indicates a claim recites a mathematical calculation. See MPEP 2106.04(a)(2). Similar to the ineligible claims at issue for In re: Board of Trustees of the Leland Stanford Junior University, 991 F.3d 1245 (Fed. Cir. 2021), the instant claims are written effectively as a method for mathematically manipulating or relating data to ascertain additional data. See MPEP 2106.04 and 2106.05(II). [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception. In this case, the claimed steps that are not part of the abstract idea are as follows:
a) obtaining a first biological fluid sample from the subject;
b) enriching a protein fraction from the first biological fluid, thereby obtaining a first protein preparation;
In this case, the claimed obtaining and enriching steps are both recited at a high level of generality and amount to necessary gathering of data for use by the abstract idea. Therefore, these steps amount to “insignificant extra-solution activity” and do not integrate the judicial exception into a practical application. See MPEP 2106.05(g).
Notably, MPEP 2106.04(d)(1) lists the following considerations for evaluating whether additional elements integrate a judicial exception into a practical application:
An improvement in the functioning of a computer, or an improvement to other technology or technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to affect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
In summary, the claimed invention does not provide any objective evidence of an improvement to the technology, nor does the specification explain the details of an unconventional technical solution expressed in the claim, or identify technical improvements realized by the claim over the prior art. See MPEP 2106.04(d)(1) and MPEP 2106.05(a). Therefore, even when viewed in combination, these additional steps/elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO].
C. Guidance Step 2B:
Under the 2019 PEG, a conclusion that an additional element is insignificant extra-solution activity in Step 2A should be re-evaluated in Step 2B. In this case, the claims do not include additional steps and/or elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons:
As discussed above, the above non-abstract steps (including the full limitations and not just the verbs) amount to nothing more than insignificant extra-solution activity. Moreover, Ly et al. (Proteomics 2011, 11, 513–534) teaches routine and conventional techniques for protein fractionation and enrichment. Therefore, even when viewed as a combination, there is nothing unconventional with regards to the non-abstract steps set forth above. Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. For these reasons, the claim(s) is/are not patent eligible. [Step 2B: NO].
Dependent Claims
Dependent claims 2-3, 6, 9, 13, 16-21, 24, 26-28 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. Regarding claim(s) 13, 16, these are directed to limitations that further limit the specificity of the abstract idea set forth above or the nature of the data being used by the abstract, and therefore are also recite mathematical concepts for reasons discussed above in the Step 2A (prong 1) analysis. Regarding claim(s) 2-3, 6, 9, 17-21, 24, 26-28, these claims further limit the non-abstract functional limitations step forth above and therefore are not patent eligible for all the reasons discussed above in the Step 2A (prong 2) and Step 2B analysis. Therefore, the claims as a whole are not patent eligible. For additional guidance, applicant is directed generally to the October 2019 Revised Patent Subject Matter Eligibility Guidance.
Claim rejections - 35 USC § 112, 1st paragraph
The following is a quotation of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-3, 6, 9, 13, 16-21, 24, 26-28 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. The written description requirement is separate and distinct from the enablement requirement. The specification must: (1) describe the claimed invention in a manner understandable to a person of ordinary skill in the art, and (2) show that the inventor actually invented the claimed subject matter.
Regarding claim(s) 1, the specification fails to provide written description support for the following steps:
d) determining, using the first protein abundance dataset, values for each of a first set of protein abundance features, thereby obtaining a first feature dataset for the subject.
e) inputting the first feature set into a classifier trained to distinguish between at least two states of the gynecological disorder based on at least the first set of protein abundance features, thereby obtaining a probability or likelihood from the classifier that the subject has a particular state of a gynecological disorder.
With regards to step d), this step is not limited to any particular acts or operations and amounts to functional language specifying desired results and/or specific functions. As a result, it is unclear in what way the protein abundance features are being “determined”. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. As such, there is no evidence that applicant has actually disclosed the requisite functionality for achieving the full scope of what is presently embraced by the claims.
With regards to step e), this step not limited to any particular acts or operations and amounts to functional language specifying desired results and/or specific functions. In addition, the claim is not limited to any specific proteins, gynecological disorders, or algorithms and/or mathematical techniques for achieving the claimed function. As a result, it is unclear how the generically recited “classifier” has been identified and trained for obtaining a probability that a subject has a particular state of a gynecological disorder. A review of the specification does not define the claimed classifier or teach the requisite training and model optimization steps necessary to “train” a model capable of predicting a subject’s state of gynecological disorder given the breadth of “classifiers” embraced by the claim. While the claims do recite using a “trained classifier” to achieve the claimed functions, this classifier is generically recited the specification does not provide any sufficient guidance that would serve to clarify the structure of this model, how it was trained, or other specific details with regards to how this model operates, i.e. the invention is essentially using a black box to achieve the claimed functions. The specification generically describes identifying a classifier by “running classification tests and determining optimal classification signature” [0089]. However, this disclosure lacks technical detail and specificity, and thus is not a sufficient disclosure given the breadth of what is being claimed. One of ordinary skill in the art would recognize that methods for deriving, training, and adjusting classifiers (i.e. models) for tasks such as predicting disease classification are not trivial.
Rykunov et al. (Nucleic Acids Research, 2016, Vol. 44, No. 11 e110, pp. 1-11) teaches methods for prediction of cancer pathways using breast, ovarian and colon cancer tumor data. Unlike the claimed invention, Rykunov teaches using a machine learning algorithm for for identifying candidate biomarkers, constructing well-defined classification signature functions based on specific training datasets, and then validating the accuracy of the signatures in test datasets using optimal thresholds. See entire. Rykunov specifically notes that the important practical feature is that the signature function values make it possible to differentiate tumors based on a probability measure on the activation status of a driver pathway [page 9], i.e. the mathematical model is critical.
Cohen et al. (US2018068083; Pub. Date: 03/08/2018) teaches a method for predicting a likelihood of having ovarian cancer in a patient. Unlike the claimed method, Cohen teaches storing a set of data comprising patient record parameters and diagnostic indicators of whether or not the patient has been diagnosed with cancer; selecting a subset of the plurality of parameters for inputs into a machine learning system, wherein the subset includes a panel of at least two different biomarkers and at least one clinical parameter; randomly partitioning the set of data into training data and validation data; generating a classifier using a machine learning system based on the training data and the subset of inputs, wherein each input has an associated weight; and determining whether the classifier meets a predetermined Receiver Operator Characteristic (ROC) statistic, specifying a sensitivity and a specificity, for correct classification of patients. In other words, the training process is much more well-defined in terms of computational operations, weights, parameters, and classifiers. In addition, Cohen teaches that [0007] detecting early stage cancer is also challenging due to factors associated with the modern day practice of medicine.
As such, there is no evidence that applicant has actually disclosed the requisite functionality for achieving the full scope of what is presently embraced by the claims. Furthermore, one of ordinary skill in the art would understand that gynecological diseases such as cancer evolve over time and that different types are correlated with different genetic markers (and hence protein abundance values). In this case, however, a review of the specification does not provide any evidence to suggests that applicant has knowledge of such data and correlations for the full scope of what is being claimed.
Therefore, after careful consideration, the instant specification fails to disclose that applicant had knowledge of the specific classifiers, variables, differential profiles of protein abundance data, and predictive probability values for the full scope of what is being claimed. Therefore, the specification does not establish a reasonable structure-function correlation (with the structure is broadly interpreted as the “trained classifier”). “[A] sufficient description of a genus . . . requires the disclosure of either a representative number* of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can 'visualize or recognize' the members of the genus” (AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69)(emphasis added). Accordingly, one of ordinary skill in the art would not have understood applicant to have invented a method/system of performing the claimed functions with no more than routine experimentation.
For the reasons discussed above, the specification does not satisfy the written description requirement with respect to the full scope of what is being claimed. For more information regarding the written description requirement, see MPEP §2161.01- §2163.07(b).
Claim rejections - 35 USC § 112, 2nd Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-3, 6, 9, 13, 16-21, 24, 26-28 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 pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1 are also rejected due to said dependency.
Claim 1 recites “enriching a protein fraction…”. It is unclear as to the metes and bounds of the term “enriching” such that the artisan would know how to avoid infringement, i.e. what type of enrichment reagents are being used to achieve the claimed function. A review of the specification does not provide any limiting definition that would serve to clarify the scope. Moreover, the artisan would understand processing fluid samples using biomarker enrichment reagents, for example. However, the claimed “enriching” is performed on a ‘protein fraction’ (instead of the fluid sample). This is confusing because no protein fractions have even been obtained from the fluid sample up to this point in the claim (only obtaining a fluid sample). Therefore, it is unclear what positive process is actually being performed (i.e. protein fractionation, sample enrichment, or otherwise). Clarification is requested via amendment.
Claim 1 recites “determining…a corresponding abundance value for the respective protein in the protein preparation, thereby obtaining a first protein abundance dataset for the subject”. Firstly, the usage of the term “thereby” renders it unclear what positive functional limitation is actually being performed, e.g. determining a plurality of abundance values, obtaining a first protein abundance dataset, both, or otherwise. Applicant is reminded that claim scope is not limited by claim language that “suggests” but does not limit a claim to a particular function. See MPEP 2111.04. Secondly, it is unclear in what way the abundance values are being “determined”. Such generic functional claim language amounts to descriptions of problems to be solved and covers all means or methods of performing the claimed function. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. Clarification is requested via amendment.
Claim 1 recites “determining, using the first protein abundance dataset, values for each of a first set of protein abundance features, thereby obtaining a first feature dataset for the subject.” Firstly, it is unclear as to the metes and bounds of the term “protein abundance features”. A review of the specification does not provide any limiting definition that would serve to clarify the scope. Secondly, the usage of the term “thereby” renders it unclear what positive functional limitation is actually being performed, e.g. determining values, obtaining a first feature dataset, both, or otherwise. Applicant is reminded that claim scope is not limited by claim language that “suggests” but does not limit a claim to a particular function. See MPEP 2111.04. Lastly, it is unclear in what way the values are being “determined”. Such generic functional claim language amounts to descriptions of problems to be solved and covers all means or methods of performing the claimed function. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed function. Applicant is also reminded that a claim is indefinite where it merely recites a use without any active, positive steps delimiting how this use is actually practiced. See MPEP § 2173.05(q). As a result, it is unclear what computational techniques are included or excluded by the claim language such that one of ordinary skill in the art would know how to avoid infringement. Clarification is requested via amendment.
Claim 1 recites “inputting the first feature set into a classifier trained to distinguish between at least two states of the gynecological disorder based on at least the first set of protein abundance features, thereby obtaining a probability or likelihood from the classifier that the subject has a particular state of a gynecological disorder.” Firstly, the usage of the term “thereby” renders it unclear what positive functional limitation is actually being performed, e.g. inputting data into a classifier/model, calculating a probability or likelihood value (using the classifier), both, or otherwise. Applicant is reminded that claim scope is not limited by claim language that “suggests” but does not limit a claim to a particular function. See MPEP 2111.04. It is noted with particularity that merely “inputting” data into a model does not necessarily result in a calculation. Secondly, it is unclear as to the metes and bounds of the claimed “classifier” such that the artisan would know what structural limitation is intended, i.e. specific parameters, equations, etc. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that would serve to clarify the scope. Lastly, as a result, it is also unclear what limiting effect is intended by the past tense phrase “trained to distinguish between….”such that the artisan would recognize what steps are minimally encompassed and what internal structure of the claimed model is intended. For example, the artisan would recognize that “training” a model generally requires feature selection, adjusting model parameters, optimizing loss functions, etc. However, the instant claims do not define the model in terms of parameters nor do they set forth any steps involved in the method/process of training. As a result, it is unclear what method/process applicant is intending to encompass to achieve the claimed function. Clarification is requested via amendment.
Claim 1 recites “…a particular state of a gynecological disorder.” It is unclear as to the metes and bounds of “a particular state of a gynecological disorder” such that the artisan would recognize what limiting effect is intended. A review of the specification does not provide any limiting definition that would serve to clarify the scope of this term. Clarification is requested via amendment.
Claim 6 recites the term “Table 3” and is indefinite because it refers to tables and/or figures in the specification. In this case, the proteins associated with the recited table can be readily incorporated into the claim, therefore reference to the specification is improper. See MPEP 2173.05(s), which states: “Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience." Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993).” Accordingly, correction is requested via amendment.
Cited Prior Art
The following prior art made of record and not presently relied upon is considered pertinent to applicant' s disclosure.
Alaiya et al. (Electrophoresis 2000, 21, 1210-1217), which teaches methods of cancer proteomics From identification of novel markers to creation of artificial learning models for tumor classification.
Lopez et al. (Clinical Chemistry, 2007, 53:6, pp.1067–1074), which teaches a high-throughput method for identification of protein-bound biokmarker candidates in ovarian cancer samples.
Ly et al. (Proteomics 2011, 11, 513–534) teaches routine and conventional techniques for protein fractionation and enrichment.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619