DETAILED ACTION
Applicant’s response, filed 16 Oct. 2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
Status of Claims
Claims 6-7 and 15-16 are cancelled.
Claims 1-5, 8-14, and 17-20 are pending.
Claims 1-5, 8-14, and 17-20 are rejected.
Priority
The instant application does not claim the benefit of priority under 35 U.S.C 119(e) or under 35 U.S.C. 120, 120, or 365(c) to any prior applications. Accordingly, the effective filing date for the instant application is 28 Jan. 2022.
Drawings
The objection to the drawings in the office action mailed 16 July 2025 has been withdrawn in view of the replacement drawing sheet filed 16 Oct. 2025.
The drawings filed 28 Jan. 2022 and 16 Oct. 2025 are accepted.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code at para. [0046] and [0051]. 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.
Response to Arguments
Applicant's arguments filed 16 Oct. 2025 regarding the objection to the specification have been fully considered but they are not persuasive.
Applicant remarks the specification has been amended to overcome the Examiner’s objection and the objection should be withdrawn (Applicant’s remarks at pg. 10, para. 6-7).
This argument is not persuasive because the hyperlinks still contain browser-executable code due to the prefix “www.”. The specification can be amended to remove the prefix and recite “(pgrn.org)” and “(PharmGKB, pharmgkb.org)” to overcome the objection.
Claim Interpretation
Claim 1 recites “…wherein the server is adapted to receive information…and communicate information…”. "[A]pparatus claims cover what a device is, not what a device does." Hewlett-Packard Co. v. Bausch & Lomb Inc., 909 F.2d 1464, 1469, 15 USPQ2d 1525, 1528 (Fed. Cir. 1990) (emphasis in original). A claim containing a "recitation with respect to the manner in which a claimed apparatus is intended to be employed does not differentiate the claimed apparatus from a prior art apparatus" if the prior art apparatus teaches all the structural limitations of the claim. Ex parte Masham, 2 USPQ2d 1647 (Bd. Pat. App. & Inter. 1987). See MPEP 2144 II. In this case, the claim is interpreted to require a server that is capable (i.e. adapted to) receive the recited information.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph 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.
Claims 10-14 and 17-18 are rejected under 35 U.S.C. 112(a) 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, at the time the application was filed, had possession of the claimed invention. This rejection is newly recited and necessitated by claim amendment.
Claim 10, and claims dependent therefrom, recite “…administering the suggested dosing to the patient”. However, Applicant’s specification does not provide support for physically administering a medication to the patient. The only mention of administering in Applicant’s specification is at para. [0027], defining the term “dosing adjustments” or “suggested dosing adjustments” to include not just adjusting the amount or dosing of a medication administered to a patient, but to also include the selection and/or deselection of specific medication(s) to be administered. However, Applicant’s specification only provides support for generating dosing adjustments as part of the pharmacogenomic report (see at least para. [0012]-[0013] and [0029]-[0030]). In view of para. [0027], this provides support for generating dosing adjustment recommendations including not only adjusting the amount or dosing, but also recommending the selection or deselection of medications to be administered. However, nowhere does the specification describe actually administering a recommended dosage adjustment to the patient.
For the reasons discussed above, the specification does not provide a sufficient disclosure of the limitation of “administering the suggested dosing to the patient” recited in claims 10-14 and 17-18 to demonstrate to one of ordinary skill in the art that the inventor possessed the invention at the time the application was filed. THS IS A NEW MATTER REJECTION. For more information regarding the written description requirement, see MPEP §2161.01- §2163.07(b).
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 10-14 and 17-18 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. This rejection is newly recited and necessitated by claim amendment.
Claim 10, and claims dependent therefrom, are indefinite for recitation of “extracting diplotypes from the genomic information”. Claim 10 previously recites “obtaining genomic information from a patient” and also “receiving genomic information related to the patient in hg19 format from a user”. Therefore, it is unclear if “the genomic information” in the extracting step is referring to the obtained genomic information or the received genomic information, or if these are all intended to be the same genomic information. Clarification is requested via claim amendment.
Response to Arguments
Applicant's arguments filed 16 Oct. 2025 regarding 35 U.S.C. 112(b) have been fully considered but they are not persuasive.
Applicant remarks claim 10 has been amended to recite “obtaining genomic information from a patient” and thus the rejection of claims 17-18 should be withdrawn (Applicant’s remarks at pg. 11, para. 1-2).
This argument is not persuasive because it does not pertain to the new grounds of rejection set forth above regarding “the genomic information” recited in claim 10, due to the above amendment.
Claim Rejections - 35 USC § 112(d)
The rejection of claims 8 and 17 under 35 U.S.C. 112(d) in the Office action mailed 16 July 2025 has been withdrawn in view of claim amendments received 16 Oct. 2025.
Claim Rejections - 35 USC § 101
The rejection of claims 6-7 and 15-16 under 35 U.S.C. 101 in the Office action mailed 16 Oct. 2025 has been withdrawn in view of the cancellation of these claims received 16 Oct. 2025.
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 1-5, 8-14, and 17-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. This rejection is previously recited; any newly recited portion is necessitated by claim amendment.
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). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1, 10, and 19 are being representative) is directed to a system, method and product for providing dosing recommendations. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claims 1, 10, and 19 recite the following steps which fall under the mental processes and/or certain methods of organizing human activity groupings of abstract ideas:
extracting diplotypes from the genomic information;
assigning allele functionality, phenotype, drug names, and recommended dosage information based upon the extracted diplotypes and a set of stored pharmacogenomic data; and
generating a personalized pharmacogenomics report personalized for the user comprising suggested dosing adjustments to at least one medication.
The identified claim limitations falls into the group of abstract ideas of mental processes, for the following reasons. In this case, extracting diplotypes from genomic information amounts to a mere analysis of the genomic information to read diplotypes of particular positions within the genome. Similarly, assigning allele functionality, phenotype, drug names, and recommended dosage information based upon the extracted diplotypes and pharmacogenomic data can be practically performed int eh mind by comparing the diplotypes with the pharmacogenomic data to gather and/or infer the recited information. Last, the step of generating a personalized pharmacogenomics report can be practically performed in the mind by analyzing the recommended dosage information and comparing the information to current dosages to make appropriate adjustments. Overall the claims are analogous to the mental process recited in a claim to "collecting information, analyzing it, and displaying certain results of the collection and analysis," where the data analysis steps are recited at a high level of generality such that they could practically be performed in the human mind, Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016). That is, other than reciting the steps are carried out by a processor, nothing in the claims precludes the steps from being practically performed in the mind. See MPEP 2106.04(a)(2) III. C.
The limitations further fall into the group of certain methods of organizing human activity for the following reasons. Overall, the steps of analyzing genomic information to characterize phenotypes, drug names, and recommended dosages and then generating a report with suggested dosage adjustments are analogous to a mental process that a doctor and/or pharmacist would follow when determining a dosage for a patient with a given phenotype, analogous to a mental process that a neurologist should follow when testing a patient for nervous system malfunctions, In re Meyer, 688 F.2d 789, 791-93, 215 USPQ 193, 194-96 (CCPA 1982). See MPEP 2106.04(a)(2) II. C.
The claims further recite the law of nature of a natural correlation between diplotype genomic information and responses to particular drugs, analogous to the natural relationship between a patient’s CYP2D6 metabolizer genotype and the risk that the patient will suffer QTc prolongation after administration of a medication called iloperidone, Vanda Pharmaceuticals Inc. v. West-Ward Pharmaceuticals, 887 F.3d 1117, 1135-36, 126 USPQ2d 1266, 1281 (Fed. Cir. 2018). See MPEP 2106.04(b) I.
Dependent claims 2-5, 8-9, 11-14, 17-18, and 20 further recite an abstract idea and/or law of nature and/or are part of the judicial exception discussed above. Dependent claims 2-5, 11-13, and 20 further limit the step of assigning to analyze data relating to a selected set of genes in the pharmacogenomic data. Dependent claims 5 and 14 further limit the mental process of recommending a dosage to be for particular drugs. Dependent claims 8-9 and 17-18 further limit the source of the information being analyzed and the step of generating the report to be for a patient or user, and thus are part of the judicial exception. Therefore, claims 1-5, 8-14, and 17-20 recite an abstract idea and law of nature. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, 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. This judicial exception is not integrated into a practical application for the following reasons.
Dependent claims 2-5, 8-9, 11-14, 17-18, and 20 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements of claims 1, 10, and 19 include:
a server…, wherein the server is adapted to receive information related to the patient from a suer including a whole genome sequence file and communicate information to the user in the form of a personalized pharmacogenomics report;
a non-transitory memory;
a processor in communication with the server and non-transitory memory;
receiving genomic information in hg19 format from the user (receiving data); and
delivering the personalized pharmacogenomics report to the user (i.e. transmitting data).
The additional elements of claim 10 further include:
obtaining genomic information from a patient (i.e. encompassing receiving data); and
administering the suggested dosing to the patient.
Regarding the independent claims, a processor, server, non-transitory memory, receiving data, and transmitting data, are generic computer components. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
With further regard to the server used to receive and/or transmit the data, this merely serves to limit the technological environment to a network environment, which does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(h). In addition, the steps of receiving and/or obtaining the genomic information and delivering report amount to necessary data gathering and outputting, respectively, which does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g).
Last, the step of “administering the suggested dosing to the patient” does not integrate the recited judicial exception into a practical application of effecting a particular treatment. MPEP 2106.04(d)((2) states the treatment or prophylaxis limitation must be "particular," i.e., specifically identified so that it does not encompass all applications of the judicial exception(s). Consider a claim that recites the same abstract idea and "administering a suitable medication to a patient." This administration step is not particular, and is instead merely instructions to "apply" the exception in a generic way. In the instant case, the claim recites “generating a personalized pharmacogenomics report…comprising suggested dosing adjustments to at least one medication” prior to the administering the suggested dosing. Therefore, the claim encompasses administering any “adjusted” dosage of any medication to the subject, which is analogous to simply “administering a suitable medication to a patient” exemplified in MPEP 2106.04(d)(2). Thus, the additional element amounts to mere instructions to apply the exception, which does not provide integration. See MPEP 2106.05(f).
Therefore, the additionally recited elements amount to insignificant extra-solution activity, mere instructions to apply the exception, and/or merely indicate a technological environment in which to apply the exception, and, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 1-5, 8-14, and 17-20 are directed to an abstract idea and law of nature. [Step 2A, Prong 2: NO]
Step 2B: 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.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception for the following reasons.
Dependent claims 2-5, 8-9, 11-14, 17-18, and 20 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception. The additional elements of claims 1, 10, and 19 are outlined above.
First, regarding the independent claims, a processor, server (i.e. a computer), non-transitory memory, receiving data, and transmitting data, are conventional computer components. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
While the step of “obtaining genomic information from a patient” encompasses simply receiving data on a computer, as discussed above, it is further noted that Applicant’s specification at para. [0006] describes that next-generation sequencing approaches are popular for whole genome sequencing, in addition to commercially available kits for targeted sequencing.
Last, the step of administering the dosage adjustments is well-understood, routine, and conventional. First, Applicant’s specification at para. [0032] discloses a plurality of commercially available medications whose dosages can be adjusted. In addition, the courts have found the following well-understood, routine, and conventional: immunizing a patient against a disease (i.e. administering a medication) in Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011). Last, as explained above, the administering step encompasses administering any suggested dosage of any medication, which amounts to mere instructions to apply an exception as explained above. MPEP 2106.05(f) states the recitation of claim limitations that attempt to cover any solution to an identified problem with no restriction on how the result is accomplished and no description of the mechanism for accomplishing the result, does not integrate a judicial exception into a practical application or provide significantly more because this type of recitation is equivalent to the words "apply it". See Electric Power Group, LLC v. Alstom, S.A., 830 F.3d 1350, 1356, 119 USPQ2d 1739, 1743-44 (Fed. Cir. 2016); Intellectual Ventures I v. Symantec, 838 F.3d 1307, 1327, 120 USPQ2d 1353, 1366 (Fed. Cir. 2016); Internet Patents Corp. v. Active Network, Inc., 790 F.3d 1343, 1348, 115 USPQ2d 1414, 1417 (Fed. Cir. 2015).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea and natural correlation without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Arguments
Applicant's arguments filed 16 Oct. 2025 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks the claims recite “generating a personalized pharmacogenomics report personalized for the patient comprising suggested dosing adjustments to at least one medication”, and additionally claims 10-18 also recite “obtaining genomic information from a patient” and “administering the suggested dosing to the patient” which clearly fall into the statutory class of “process” under 35 U.S.C. 101 and integrates any judicial exception into a practical application and further recite non-abstract features which constitute significantly more than merely mental processes or methods of organizing human activity (Applicant’s remarks at pg. 11, para. 5 to pg. 12, para. 2).
This argument is not persuasive. It is notable that mere physicality or tangibility of an additional element or elements is not a relevant consideration in Step 2A Prong Two. As the Supreme Court explained in Alice Corp., mere physical or tangible implementation of an exception does not guarantee eligibility. Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208, 224, 110 USPQ2d 1976, 1983-84 (2014) ("The fact that a computer ‘necessarily exist[s] in the physical, rather than purely conceptual, realm,’ is beside the point"). See also Genetic Technologies Ltd. v. Merial LLC, 818 F.3d 1369, 1377, 118 USPQ2d 1541, 1547 (Fed. Cir. 2016) (steps of DNA amplification and analysis are not "sufficient" to render claim 1 patent eligible merely because they are physical steps).
Simply because the claims recite additional elements, including “generating…”, “obtaining…”, and “administering…” does not guarantee eligibility. As explained in the above rejection, limitations that amount to necessary data gathering and outputting (i.e. obtaining genomic information and then outputting the report) are not sufficient to integrate the recited judicial exception into a practical application. See MPEP 2106.05(g). Furthermore, the recited administering step is not particular for the reasons discussed in the above rejection, and instead amounts to mere instructions to apply an exception rather than a particular treatment.
Last, while Applicant alleges the claims recite non-abstract features that constitute “significantly more”, this is not the case, nor has Applicant pointed to any alleged errors in the explanation of the additional elements under step 2B in the previous Office action. As explained above, the courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Applicant’s specification at para. [0006] also describes that next-generation sequencing approaches are popular for whole genome sequencing, in addition to commercially available kits for targeted sequencing. Last, regarding, the courts have found the following well-understood, routine, and conventional: immunizing a patient against a disease (i.e. administering a medication) in Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011).
Claim Rejections - 35 USC § 102
The rejection of claims 6-7 and 15-16 under 35 U.S.C. 102(a)(1) as being anticipated by John in the Office action mailed 16 July 2025 has been withdrawn in view of the cancellation of these claims received 16 Oct. 2025.
The rejection of claims 10-14 and 17-18 under 35 U.S.C. 102(a)(1) as being anticipated by John in the Office action mailed 16 July 2025 has been withdrawn in view of claim amendments received 16 Oct. 2025.
The rejection of claims 1-6, 8-15, and 17-20 under 35 U.S.C. 102(a)(1) as being anticipated by Piriyapongsa (2021) in the Office action mailed 16 July 2025 in view of claim amendments received 16 Oct. 2025
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.
Claims 1-5, 8-9, and 19-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by John (2021). Any newly recited portion is necessitated by claim amendment.
Cited reference: John et al., PharmaKU: A Web-Based Tool Aimed at Improving Outreach and Clinical Utility of Pharmacogenomics, 2021, J. Pers. Med., 11(210), pg. 1-12; cited in IDS filed 07 April 2023; previously cited.
Regarding claims 1 and 19¸ John discloses a system, method and computer memory with instructions for PharmaKu, a method of providing personalized medical recommendations. (Abstract). John discloses a user computer (i.e. processor) that communicates with the PharmaKu software over a web portal (pg. 6, para. 2; Figure 2), which necessarily requires a separate computer (i.e. server) storing the software (i.e. non-transitory memory), and that the separate compute received genomic information from the user and outputs a report (i.e. the server is adapted to receive and communicate information) (Figure 2). John discloses the method, or the instructions for the method, comprises the following steps:
John discloses receiving genomic information as VFC files (Figure 2, e.g. WGS vcf file provided as user input through web interface), wherein the VCF files are in hg19 format (pg. 6, para. 3).
John discloses inferring diplotypes from the genomic information (pg. 6, para. 3 to pg. 7, para. 1).
John discloses gathering (i.e. assigning) allele functionality and phenotype information from gene-diplotypes pairs and diplotype-phenotype tables from PHarmGKB (i.e. stored pharmacogenomic data) based on the diplotypes, in addition to drug names and clinical recommended dosage information (Figure 2, e.g. see report; pg. 7, para. 1, e.g. drugs with FDA label).
John discloses generating a personalized pharmacogenomics report for the patient with suggested dosing adjustments (Figure 2; pg. 8, para. 1).
John discloses the personalized report is delivered to the user in pdf format (Figure 2; Abstract).
Regarding claims 2-4 and 20, John discloses the dosing recommendations comprise data relating to nine pharmacogenes (pg. 3, para. 4; Table1), including CYP2B6, CYP2C19, CYPS26, CYP3A5, DPYD, SLCO1B1, TPMT, and UGT1A1 (Table 1).
Regarding claim 5, John discloses the dosing adjustments are for at least Voricanazole (Figure 2; Table 1).
Regarding claim 8, the limitation only serves to define the process in which the received genomic information was previously obtained (i.e. from a patient). However, John discloses receiving genomic information from a person (i.e. user) as discussed above (pg. 6, para. 3; pg. 9, para. 3), which is the same product (i.e. genomic information) as recited in the claims. "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted)
Regarding claim 9, John discloses the user is a physician that receives the report of their patient, wherein a physician is not the same and thus is remote from the patient (9, para. 3).
Thus John anticipates the claimed invention.
Examiner Comment:
It is noted that John et al. qualifiers as prior art under 102(a)(1) because the authors include the presence of additional authors. See MPEP 2153.01(a).
The rejections below are additionally provided in the interest of compact prosecution.
Response to Arguments
Applicant remarks that the Piriyapongsa references fails to anticipate the claims because the present claims fail to recite the genomic information is in hg19 format (Applicant’s remarks at pg. 13, para. 3 to pg. 14, para. 1).
This argument is persuasive. A new grounds of rejection is set forth below under 35 U.S.C. 103.
Applicant's arguments filed 16 Oct. 2025 regarding 35 U.S.C. 102(a)(1) at pg. 12. Para. 6 to pg. 13, para. 2 have been fully considered but they are not persuasive.
Applicant remarks that the authors of the John reference are the same as the inventors of the present application, and in particular the name “Rasheeba Iqbal” listed as coinventor of the application refers to the same person as “Rasheeba Nizam” a co-author in the John reference, and for the avoidance of doubt, Applicant will shortly admit a supplemental ADS and a Request Under Rule 48 to correct the inventors names in this patent application (Applicant’s remarks at pg. 12, para. 6 to pg. 13, para. 2).
This argument is not persuasive because Applicant has not corrected any inventor names. Alternatively, Applicant has not submitted a declaration under 37 CFR 1.130 to explain the presence of the additional authors (i.e. explaining they are the same person). See MPEP 717.01(a)(1). Therefore, the rejection is maintained. However, it is acknowledged that the rejection can overcome by filing the declaration under 37 CFR 1.130 or correcting the inventors names to be consistent with the publication.
Claim Rejections - 35 USC § 103
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 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-5, 8-14, and 17-20 are rejected under 35 U.S.C. 103 as being unpatentable over Piriyapongsa (2021) in view of Pan (2019). This rejection is newly recited and necessitated by claim amendment.
Cited reference:
Piriyapongsa et al., PharmVIP: A Web-Based Tool for Pharmacogenomic Variant Analysis and Interpretation, 2021, J. Pers. Med. 11(1230), pg. 1-17 and Suppl. pg. 18-74) (previously cited); and
Pan et al., Similarities and differences between variants called with human reference genome hg19 or hg38, 2019, PMC Bioinformatics, 20(Suppl 2):101, pg. 18-29 (previously cited).
Regarding claims 1, 10, and 19, Piriyapongsa discloses a method for pharmacogenomic variant analysis and interpretation (Abstract) comprising the following steps:
Piriyapongsa discloses obtaining genomic information from a patient (Figure 1; pg. 1, para. 1, e.g. used for personal drug selection, or a patient)
Piriyapongsa discloses receiving a BAM and/or VCF file for the patient based on alignment to the GrCH38 (i.e. hg38) reference genome from a user (pg. 1, para. 1; pg. 11, para.4- 6; Fig. 1 and 6).
Piriyapongsa discloses identifying diplotypes from provided genotypic data from the VCF file (pg. 5, para. 1; Figure 1).
Piriyapongsa discloses predicting HLA allele functionality, a phenotype/metabolizer status (i.e. phenotype), and CPIC guideline recommendations including dosing recommendations for relevant gene-drug pairs (i.e. drug names and recommended dosages) (Figure 1; pg. 3, para. 4; pg. 5, para. 1 to pg. 6, para. 1), wherein the predictions are made by mapping diplotypes (i.e. the extracted diplotypes) to relevant drug dosing guidelines, analyzing HLA and adverse drug reaction databases, and databases such as PharmGKB (i.e. stored pharmacogenomic data) (pg. 5, para. 1 to pg. 6, para. 1).
Piriyapongsa discloses generating a personalized pharmacogenomics report with suggested dosing recommendations of drugs (pg. 3, para. 4; pg. 5, para. 1; see summary reports on pg. 19-20).
Piriyapongsa discloses delivering the report to the user via a results button (Figure 2; pg. 3, para. 5).
Further regarding claims 1 and 19, Piriyapongsa discloses the method is embodied in software in a web-based tool that is used by a user, which inherently requires a computer storing instructions for the method (i.e. a processor in communication with non-transitory memory storing instructions), and that the method is implemented in a PharmVIP web server that receives the input and outputs the result (pg. 3, para. 2; Figure 1). Furthermore given the software is a web-based tool.
Further regarding claims 1, 10, and 19, Piriyapongsa does not disclose the genomic information is received in hg19 format.
However, Pan overviews the human reference genome hg19 and hg38, and discloses the analysis of next generation sequencing data involves the selection of a reference genome, and current practice employes one of the two most recent reference genome versions: hg19 or hg38 (Abstract; pg. 18, col. 1, para. 2). Pan discloses historically, the newest reference genome release is recommended for its accuracy, but to build on previous research results or make current studies comparable to results obtained using previous human reference genome versions, genetic variants observed from one reference genome must sometimes be converted to another version (pg. 18, col. 1, para. 2). Pan discloses several tools have been developed for converting between different human genome versions, including between the hg19 and hg38 genome (pg. 18, col. 1, para. 3 to col. 2, para. 1).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the method of Piriyapongsa, to have received genomic information in an older hg19 format, as disclosed by Pan (Abstract; pg. 18, col. 1, para. 2 to col. 2, para. 1). One of ordinary skill in the art would have been motivated to combine the methods of Piriyapongsa and Pan by using genomic information in an older format in order to build on previous research results, as shown by Pan (pg. 18, col. 1, para. 2), given Piriyapongsa also discloses the tool is used for research (pg. 15, para. 1). This modification would have had a reasonable expectation of success given Piriyapongsa discloses various tools are available to convert results from an hg19 reference genome to an hg38 reference genome (pg. 18, col. 1, para. 3 to col. 2, para. 1), such that the resulting data could be applied to the method of Piriyapongsa, which utilizes VCF files based on an hg38 (i.e. GrCh38) reference genome (pg. 11, para. 4).
Further regarding claim 10¸ Piriyapongsa does not explicitly disclose administering the suggested dosing to the patient.
However, As discussed above, Piriyapongsa discloses generating a personalized pharmacogenomics report with suggested dosing recommendations of drugs (pg. 3, para. 4; pg. 5, para. 1; see summary reports on pg. 19-20), and then delivering the report to the user via a results button (Figure 2; pg. 3, para. 5). Piriyapongsa further discloses Piriyapongsa discloses personalized pharmacogenomics prevents adverse effects and optimizes therapeutic efficacy (pg. 1, para. 1) and that the tool for personal pharmacogenomics is intended to facilitate clinical application and practice (pg. 2, para. 2-3; pg. 10, para. 2), suggesting the suggested doses are intended to be administered to the patient (i.e. to optimize therapeutic efficacy in clinical application).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Piriyapongsa to have further administered the suggested dosage to the patient, as suggested by Piriyapongsa, discussed above. One of ordinary skill in the art would have been motivated to administer the suggested dosing in order to optimize an individual’s therapeutic outcome, as shown by Piriyapongsa (pg. 1, para. 1). This modification would have had a reasonable expectation of success given Piriyapongsa states the purpose of the tool is clinical application (i.e. drug dosing) as discussed above.
Regarding claims 2 and 11, Piriyapongsa discloses further the stored pharmacogenomic data includes data on selected pharmacogenes (pg. 3, para. 4; pg. 5, para. 1).
Regarding claims 3-4, 12-13, and 20, Piriyapongsa further discloses the stored pharmacogenomic data includes data on CYP2B6, CYP2C19, CYP2C9, CYP2D6, CYP3A5, DYPD, SLCO1B1, TPMT, and UGT1A1 (pg. 18-25).
Regarding claims 5 and 14, Piriyapongsa further discloses the suggesting dosing adjustments include adjustments for at least amitriptyline, clomipramine, doxepin, imipramine, trimipramine, atomoxetine, codeine, desipramine, fluvoxamine, notriptyline, ondansetron, paroxetine, tamoxifen, tropisetron, tacrolimus, capecitabine, fluorouracil, and simvastatin (pg. 39-48, e.g. see Guideline module full report).
Regarding claims 8 and 17, Piriyapongsa further discloses the user can be of the pharmacogenomics community for research and informational purposes (Abstract; pg. 15, para. 1), which could include a patient (Table 1, e.g. analyzing patient samples; pg. 9, para. 2). Claims 8 and 17 generally serve to further limit the genomic information being obtained to have been generated from the user (i.e. the same as the patient), but the genomic information (i.e. the product) of user is the same as of a patient, given the user may be a patient. "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted).
Regarding claims 9 and 18, Piriyapongsa further discloses the user can be of the pharmacogenomics community for research and informational purposes (Abstract; pg. 15, para. 1), such that the user is different than the patient data being analyzed (Table 1, e.g. analyzing patient samples; pg. 9, para. 2).
Therefore, the invention is prima facie obvious.
Response to Arguments
Applicant's arguments filed 16 Oct. 2025 regarding 35 U.S.C 103 have been fully considered but they are not persuasive.
Applicant remarks the Piriyapongsa reference fails to disclose “receiving genomic information related to the patient in hg19 format”, but the Pan reference does not supplement this deficiency because Pan does not describe a pharmacogenomics tool for providing personalized medication dosing recommendations for a patient, and instead discuses the differences and similarities in variants called with human reference genome hg19 or grch38 (Applicant’s remarks at pg. 15, para. 4 to pg. 16, para. 1). Applicant further remarks that the Pan reference discloses that a considerable number of variants could not be converted between the reference genomes and recommends caution when converting an hg38 genome to hg19, and further remarks the Pan reference is different from the claimed subject matter because the claims do not perform conversion of variants and thus the rejection should be withdrawn (Applicant’s remarks at pg. 15, para. 1-2).
This argument is not persuasive. First, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Pan was not used to rely on teaching any pharmacogenomics tool, which is instead taught by Piriyapongsa.
Furthermore, while the claimed subject matter does not recite converting variants from an hg38 genome to hg19, the claims use the transitional phrase “comprising”. The transitional term "comprising", which is synonymous with "including," "containing," or "characterized by," is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. See, e.g., Mars Inc. v. H.J. Heinz Co., 377 F.3d 1369, 1376, 71 USPQ2d 1837, 1843 (Fed. Cir. 2004). The claims only require “receiving genomic information in hg19 format”, but do not preclude the hg19 format was derived from converting genomic information in Grch38 format to hg19 format.
Last, while Pan does disclose that a considerable number of variants could not be converted between the reference genomes and recommends caution when converting an hg38 genome to hg19, Pan discloses that to build on previous research results or make current studies comparable to results obtained using previous human reference genome versions, genetic variants observed from one reference genome must sometimes be converted to another version (pg. 18, col. 1, para. 2). Therefore, while Pan may disclose some disadvantages of using converted hg19 genomic data relative to normal hg 19 genomic information, Pan does not teach away from using this data and instead teaches using converted genomic data is necessary to build on previous research results or make current studies comparable. A prior art reference that "teaches away" from the claimed invention is a significant factor to be considered in determining obviousness. However, "the nature of the teaching is highly relevant and must be weighed in substance. A known or obvious composition does not become patentable simply because it has been described as somewhat inferior to some other product for the same use." In re Gurley, 27 F.3d 551, 553, 31 USPQ2d 1130, 1132 (Fed. Cir. 1994). See MPEP 2145.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685