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 .
Claim Status
Claims 1-20 are pending and examined herein.
Claims 1-20 are rejected.
Claims 5 and 12 are objected to.
Priority
Claims 1-20 are granted the claim to the benefit of priority to U.S. Provisional application 62/986065 filed 06 March 2020. Thus, the effective filling date of claims 1-20 is 06 March 2020.
Information Disclosure Statement
The information disclosure statements (IDS) were received on 02 September 2022 and 29 September 2022. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
Drawings
The drawings received 02 September 2022 are objected to for the reasons set out below.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: “130” in Fig. 1, “302” in Fig. 3, “216A” in Fig. 3, “216B” in Fig. 3, and “312” in Fig. 3. Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
The drawings are objected to because reference numbers 100 and 104 appear to be pointing to the same data entity (i.e., MEDS) while the specification states reference number 100 is the input data set as a whole. To enhance clarity reference number 100 should be pointing to or linked to the “Input Data Set” in Fig. 1 (this may be done in a similar manner to reference number 126 pointing to the “Output”). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on page 8 of the instant disclosure. 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.
Claim Objections
Claims 5 and 12 are objected to because of the following informalities:
Claims 5 and 12 recite “the risk of the patient developing a disease in a given time frame in the future” in lines 2-3 of the claims but should read “a risk of the patient developing a disease…”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
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 2, 3, 6, 7, 8-14, and 16-19 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 2 and 9 recite “calculate the probability P(M) in accordance with Equation (1)” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because these claims use a reference number to refer to an equation. MPEP 2173.05(s) states “where possible, claims are to be complete in themselves”. This rejection may be overcome by amendment of the referenced equation into the claim. For the sake of furthering examination, this limitation will be interpreted as “wherein the probability P(M) is generated in accordance with an equation”.
Claims 3 and 10 recite “a set of ICD-10 codes or the equivalent” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear what “the equivalent” of a set of ICD-10 codes is. The specification does not provide a clear and precise definition of the limitation, nor would one skilled in the art recognize the metes and bounds of said limitation. For the sake of furthering examination, this limitation will be interpreted as “a set of ICD-10 codes or codes representing diagnoses of independent diseases assigned to the patient”.
Claims 6 and 13 recite “the predicted future disease” in in line 2 of claim 6 and in line 2 of claim 13. There is insufficient antecedent basis for this limitation in the claim. The indefiniteness arises because the claim does not make clear what the “the predicted future disease” is. This rejection could be overcome by amendment of these limitations to “a predicted future disease” or “the predicted risk of the patient developing a disease”. For the sake of furthering examination this limitation will be interpreted as “the predicted risk of the patient developing a disease”.
Claims 7 and 14 recite “the likelihood of the patient having an actionable genetic variant based on the prevalence of the genetic variant in the general population” in lines 2-3 in claim 7 and in lines 1-3 of claim 14. There is insufficient antecedent basis for this limitation in the claim. The indefiniteness arises because the claim does not make clear what the “the likelihood of the patient having an actionable genetic variant” or “the general population” are. This rejection could be overcome by amendment of these limitations to “a likelihood of the patient having an actionable genetic variant based on the prevalence of the genetic variant in a general population”. For the sake of furthering examination this limitation will be interpreted as “a likelihood of the patient having an actionable genetic variant”.
Claims 7 and 14 recite “the weight” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if “the weight” is referring to one of the weights of links between the disease status partition and the medications partition (if so which weight of the plurality of weights is the weight referring to), if “the weight” is referring to one of the weights of links between the medications partition and the genetics partition (if so which weight of the plurality of weights is the weight referring to), or if “the weight” is referring to the weight of the likelihood of the patient having an actionable genetic variant based on the prevalence of the genetic variant in the general population. For the sake of furthering examination, this limitation of “the weight” will be interpreted as referring to the weight of the likelihood of the patient having an actionable genetic variant based on the prevalence of the genetic variant in the general population.
Claim 8 recites “An improved computer configured to…” which renders the metes and bounds of the claim indefinite. The indefinites arises because it unclear what constitutes as “an improved computer” and what characteristics does the “improved computer” have that differentiate from a computer. The specification does not provide a clear and precise definition of the limitation, nor would one skilled in the art recognize the metes and bounds of said limitation. Dependent claims 9-14 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, this limitation will be interpreted as “a computer configured to…”.
Claim 8 recites “the processing unit” in line 23 of the claim. There is insufficient antecedent basis for this limitation in the claim. The indefiniteness arises because the claim does not make clear what the “the processing unit” is and it is unclear if the processing unit and the processing system are meant to be the same. This rejection could be overcome by amendment of these limitations to “the processing system”. Dependent claims 9-14 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination this limitation will be interpreted as “the processing system”.
Claims 9-12 recite “The apparatus of claim 8” in line 1 of the claims. There is insufficient antecedent basis for this limitation in the claim. The indefiniteness arises because the claim does not make clear what the “The apparatus of claim 8” is. This rejection could be overcome by amendment of these limitations to “The computer of claim 8”. Dependent claims 13-14 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination this limitation will be interpreted as “The computer of claim 8”.
Claim 11 recites “wherein the instructions further include a threshold for recommending a pharmacogenetics test…” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is not clear if the executable instructions require recommending the pharmacogenomics test using the threshold or if the instructions are only required to contain a threshold with the intended use of recommending. For the sake of furthering examination, this limitation will be interpreted as requiring executable instructions that recommend the pharmacogenomics test using the threshold.
Regarding claim 17, the phrase "such as" 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). For the sake of furthering examination, claim 17 will be interpreted as “wherein the input data of step a) comprises one of (a) patient medical record number or (b) patient identifying information”.
Claims 16, 18, and 19 recites the limitation “the healthcare provider” in line 2 of claim 16, line 1 of claim 18, and line 1 of claim 19. There is insufficient antecedent basis for this limitation in the claim. The indefiniteness arises because the claim does not make clear what the “healthcare provider” is. This rejection could be overcome by amendment of these limitations to “a healthcare provider”. For the sake of furthering examination this limitation will be interpreted as “a healthcare provider”.
Claim 19 recites “wherein the healthcare provider is the United States Veterans Administration or a subdivision thereof” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear due to “the United States Veterans Administration or a subdivision thereof” being used to define a source of the provider without the structure of the source being claimed (i.e., hospital or clinic). For the sake of furthering examination this limitation will be interpreted as “wherein the healthcare provider is a hospital”.
112/d
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 20 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 20 is an improper dependent claim for failing to include all the base limitations of claim 8 which claim 20 depends from. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements. This rejection may be overcome by amending the apparatus of claim 20 to include the computer of claim 8 (rather than having an apparatus with an applications programing interface for inputting data into the computer of claim 8 where claim 8 is outside the scope of the apparatus itself such that the programming of the computer of claim 8 is not required within the apparatus of claim 20).
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 1-19 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.
(Step 1)
Claims 1-7 and 15-19 fall under the statutory category of a process and claims 8-14 fall under the statutory category of a machine.
(Step 2A Prong 1)
Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. The instant claims further recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations.
Claims 1 and 8 recite mathematical concepts and mental processes of “implementing a Bayesian network representable as a tripartite graph having links between three partitions: a disease status partition… a medications partition… a genetics partition… wherein weights of links between the disease status partition and the medications partition are based on an analysis of a corpus of patient data… wherein weights of links between the medications partition and the genetics partition have binary values that depend on whether a pharmacogenomics relationship…” and “generating from the Bayesian network a probability of the patient being prescribed a particular medication having a pharmacogenomics relationship with one of the genetic variations…”.
Claim 1 further recites a mental process of “predicting whether the patient will likely benefit from a pharmacogenomics test based on the generated probability P(M)”
Dependent claim 4 recites a mental process of “comparing the probability P(M) to a threshold that is less than or equal to 0.01”. Dependent claims 5 and 12 recite a mental process and mathematical concept of “generating a prediction of the risk of the patient developing a disease in a given time frame in the future”. Dependent claims 6 and 13 recite mental processes and mathematical concepts of “predicting medications for the predicted future disease” and “generating with the Bayesian network a prediction of the probability that the patient will be prescribed a medication with a pharmacogenomics relationship in the future”. Dependent claims 7 and 14 recite mental processes and mathematical concepts of “assigning a weight to the likelihood of the patient having an actionable genetic variant based on the prevalence of the genetic variant in the general population” and “using the weight in the Bayesian network to generate the prediction of the probability that the patient will be prescribed a medication with a pharmacogenomics relationship in the future”. Dependent claim 15 recite mental processes of “conducting the method of claim 1 for each of the multitude of patients based on the input data”, “using the predictions P(M) for each of the patients to select a subset of the multitude of patients to subject to pharmacogenomics testing”. Dependent claim 16 recites mental processes of repeating the identified mental processes of claim 15 daily.
The claims recite mental processes of analyzing/evaluating data of implementing a mathematical model (i.e., the Bayesian Network), generating probability predictions utilizing this Bayesian network (using a series of probability calculations using an equation see instant disclosure page 8), and predicting whether the patient will likely benefit from a pharmacogenomics test based the calculated probability predictions. The claims recite mathematical concepts of generating mathematical relationships as a mathematical model of the Bayesian Network and mathematical calculations of generating probability predictions utilizing this Bayesian network (using a series of probability calculations using an equation see instant disclosure page 8). Dependent claims 2, 3, 9-11 and 17-19 further limit the mental process/mathematical concept recited in the independent claim but do not change their nature as a mental process/mathematical concept.
(Step 2A Prong 2)
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). Integration into a practical application is evaluated by identifying whether there are any additional elements recited in the claim and evaluating those additional elements to determine whether they integrate the exception into a practical application.
The additional element in claim 1 of obtaining an input data set comprising at least one of data indicative of a disease status of the patient or data indicative of currently prescribed medications for the patient, the additional elements in claim 15 and 16 of obtaining input data for each of the multitude of patients do not integrate the judicial exceptions into a practical application because these are steps that are insignificant extra solution activity of data gathering. These additional elements constitute as data gathering (the additional elements in claims 1, 15, and 16 of obtaining/inputting data) because they only interact with the judicial exceptions in a manner by providing data to the judicial exceptions to process.
The additional element in claims 1 of using a generic computer to perform judicial exceptions and the additional element in claim 8 of a generic computer (i.e., a computer comprising a memory and a processing system) that performs judicial exceptions does not integrate the judicial exceptions into a practical application because this is simply applying the judicial exceptions to a generic computer without and improvement to computer functionality. The additional element of the computer only interacts with the judicial exceptions in manner that the computer is utilized as a tool to perform the judicial exceptions.
The additional element in claim 15 of conducting pharmacogenomics testing does not integrate the judicial exceptions into a practical application because this is generally linking the use of the judicial exceptions to the technological environment of pharmacogenomics testing. This additional element constitutes as generally linking the use of the judicial exceptions to pharmacogenomics testing because the claim generally recites selecting a subset of patients to subject to pharmacogenomics using the predictions then conducting the pharmacogenomics test on the subset. The subset selection is general and does not limit the subset of patients in a manner that only includes a subset of patients that are likely to benefit from the pharmacogenomics test (i.e., the selection process encompasses selecting patients that are not likely to benefit from the test).
Thus, the additional elements do not integrate the judicial exceptions into a practical application and claims 1-19 are directed to the abstract idea.
(Step 2B)
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because:
The additional element in claims 1 of using a generic computer to perform judicial exceptions and the additional element in claim 8 of a generic computer (i.e., a computer comprising a memory and a processing system) that performs judicial exceptions are conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II).
The additional element in claim 1 of obtaining an input data set comprising at least one of data indicative of a disease status of the patient or data indicative of currently prescribed medications for the patient and the additional elements in claim 15 and 16 of obtaining input data for each of the multitude of patients are conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II).
The additional element in claim 15 of conducting pharmacogenomics testing on patients is conventional as shown by Gross et al. (Mental Health Clinician 8.5 (2018): 235-241) which reviews conducting pharmacogenomic testing in clinical practice.
Thus, the additional elements are not sufficient to amount to significantly more than the judicial exception because they are conventional.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless – (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim 20 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bagaev et al. (US 20180358132 A1).
Claim 20 is directed to an apparatus with a user interface comprising a display, a processing system configured to implement an application programming interface that provides information entered in the user interface to a computer wherein the information entered in the user interface is converted by the applications programming interface to the input data set for the computer, wherein the user interface is also configured to report a prediction generated by the computer.
The BRI of this claim requires an apparatus with a user interface comprising a display, a computer system configured to implement an application programing interface to provide information to a different computer system (such as a server or remote device), and a user interface configured to report a prediction generated by the different computer system (such as a server or remote device). It is noted that the preamble which provides what the apparatus is used for (i.e., determining whether to perform pharmacogenomics testing on a patient) and how the user interface is intended to be used (operable by a patient) is an intended use of the claimed apparatus. Further, the recitation of “the computer of claim 8” only requires that the that the application programing interface on a computing system provides data to a different computer system (such as a sever or remote device) because claim 20 fails to include all the base limitations of claim 8 (see 112/d above). The computer of claim 8 is not part of the apparatus of claim 20 and only serves to recite where the information provided by the applications programming interface is intended to be received outside the metes and bounds of the claimed apparatus.
Bagaev et al. shows a computer environment with a graphical user interface, servers with devices remote from the user, a network which links multiple computing devices to transfer data, a computing device utilizing an application program interface for presenting information on a graphical user interface, databases containing information which are accessible to servers, and a graphical user interface configured to display predictions generated by a remote computing device (Bagaey et al. [0153]-[0169], Fig. 1A, 1C, and 9-15).
Conclusion
No claims are allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure is Samwald et al. (PLOS ONE 11(10): e0164972 (2016)) which shows estimating the number of high-risk drug-phenotype co-occurrences utilizing the probability a patient is prescribed a PGx drug, Schildcrout et al. (J Clin Epidemiol. 2016 Apr;72:107-15) which shows a Cox proportional hazard regression to estimate exposure risk to PGx drugs, Chanfreau-Coffinier et al. (JAMA network open 2.6 (2019): e195345) which shows an analysis of the prevalence of PGx drugs and actionable variants in among US Veterans Health Administration pharmacy users, and Mills et al. (Current Genetic Medicine Reports 6.2 (2018): 43-51) which shows situations in which patients benefit from pharmacogenomics testing.
Claims 1-19 are free of the prior art of record. Samwald et al. (PLOS ONE 11(10): e0164972 (2016)) and Schildcrout et al. (J Clin Epidemiol. 2016 Apr;72:107-15) are the closest prior art of record. Samwald et al. shows estimating the number of high-risk drug-phenotype co-occurrences by calculating the probability that a PGx drug is prescribed to a patient who has a drug metabolizing phenotype that puts the patient at risk for developing an adverse drug reaction by using the probability that a patient is prescribed a PGx drug in the observed time frame. Schildcrout et al. shows a predictive model based on clinical variables to estimate the medication exposure risk of statin, clopidogrel, or warfarin using Cox proportional hazards regression. However, Samwald et al., Schildcrout et al., and the other references made of record do not show or render obvious implementing or utilizing the particular Bayesian Network with a disease partition, a medication partition, and a genetic partition for generating the probability of a patient being prescribed a medication having a pharmacogenomics relationship with one of the genetic variations in the genetic partition. Thus, claims 1-19 are free of the prior art of record.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JONATHAN EDWARD HAYES whose telephone number is (571)272-6165. The examiner can normally be reached M-F 9am-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at 571-272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/J.E.H./Examiner, Art Unit 1685
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685