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/Restrictions
Applicant’s election without traverse of Inventive Group I in the reply filed on 06/18/2025 is acknowledged.
Claims 33-38 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 06/18/2025.
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 20, 21, 24, 27, 30, and 32 are rejected under 35 U.S.C. 103 as being unpatentable over Dohmer et al. (US 20050130116 A1) in view of Zhong et al. (CN 104593415 A)
Regarding Claim 20: Dohmer teaches use of a hamster V79 cell line for use in their claimed invention due to their lack of endogenous cytochrome P450 and are therefore ideal for the transfection of cytochrome P450 isoenzymes. (0038) This reads on the claimed method of an in vitro system using target cells that do not express CYP450 and transfection of the target cells with at least one nucleic acid encoding at least one CYP450 variant or orthologue. Dohmer further teaches that the present invention is suitable for identification of metabolically competent cytochrome P450 isoforms for a given substrate (0036) and that the invention is able to detect novel alleles of hCYP2D6, a variant of CYP450, by looking at the differences in formation of specific metabolites. (0050) This reads on the claimed method of culturing g the target cells with at least one substrate and determining the level of CYP450 induced metabolism of the substrate. Dohmer fails to teach use of human cells or transient transfection.
Zhong teaches a hPX-mediated high throughput drug screening model which is able to regulate and control a CYP450 gene product for use of a drug screening method in human kidney HEK293T cells. (Pg 1, Abstract) This reads on use of transient transfection of CYP450 in human cells, and further teaches use in a pharmacogenomic testing model.
Regarding Claim 21: Dohmer teaches that the claimed invention relates to a test system comprising cell lines each expressing a functional human cytochrome P450 2D6 alleles. (0031) This reads on the CYP450 variant being a CYP2D6 variant.
Regarding Claim 24: Dohmer teaches an embodiment of the invention where multiple cell lines are established each with different variants of human CYP2D6, including cell line V79MZh2D6*1-hoR, which had homogenous expression of both CYP2D6*1 and CYPOR, which are both CYP2D6 orthologues. (0228 and Table 2) This reads on the claimed method of a single nucleic acid encoding at least two CYP2D6 variants or orthologues thereof.
Regarding Claim 27: Dohmer teaches use of V79 hamster cells due to their lack of endogenous cytochrome P450. (0038) This reads on the claimed method of use of target cells which do not express a functional CYP450 enzyme variant involved in the metabolism, of the substrate.
Regarding Claim 30: Dohmer teaches that V79 cells are suitable for many different types of substrates which allows for performance of metabolic studies (0039) and details an example of the invention in which two different substrates were used which resulted in different amounts of detected 4-hydroxylation of tamoxifen. (Example 10, 0335, Fig 24)
Regarding Claim 32: Dohmer teaches an example of the invention where metabolites were identified as dihydroxy derivatives by mass spectra, which is another name for mass spectrometry. (0351, Example 10)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Dohmer of establishment of human CYP2D6 in hamster V79 cells with the teachings of Zhong of transient transfection in human HEK293T cells with the goal of use in a drug screening method to create a model of transient CYP2D6 in human cells to be used as a pharmacogenomic testing model. A person of ordinary skill in the art would have had motivation and a reasonable expectation of success based on the teachings of Zhong of use of human HEK293T cells in a transient transfection model to be used in high throughput drug screening.
Claims 22 and 31 are rejected under 35 U.S.C. 103 as being unpatentable over Dohmer et al. (US 20050130116 A1) in view of Zhong et al. (CN 104593415 A), Gu et al. (US 20040158043 A1) and Roussel et al. (Expression and Characterization of Canine Cytochrome P450 2D15, 1998)
The teachings of Dohmer are disclosed above. Dohmer fails to teach use of a luminescence producing enzyme, specifically luciferase.
Regarding Claims 22 and 31: Gu teaches use of fluorescent labels, including luciferase, in the claimed invention in addition to use of canine CYP1A2 polypeptides (0108), which is a subfamily of CYP450 (0003). This reads on the claimed method of both claim 22 (use of a vector encoding an excreted luminescence producing enzyme) and claim 31 (use of luciferase). Both Dohmer and Gu fail to teach use of luciferase with a CYP2D6 analogue. Roussel teaches use of CYP2D15, which is the canine orthologue of human CYP2D6 (pg 27, abstract).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Dohmer of establishment of human CYP2D6 in hamster V79 cells with the teachings of Zhong of transient transfection in human HEK293T cells with the goal of use in a drug screening method with the teachings of Gu of use of luciferase with the teachings of Roussel of use of a canine CYP2D6 equivalent and the teachings of Dohmer to create an in vitro method for determining the functionality of a CYP450 variant that also comprises luciferase. One would have been motivated to do so and had a reasonable expectation of success based on the teachings of Gu, who demonstrates successful luciferase transfection to a canine orthologue of a CYP450 subfamily.
Claim 25 and 39 are rejected under 35 U.S.C. 103 as being unpatentable over Dohmer et al. (US 20050130116 A1) in view of Zhong et al. (CN 104593415 A), Roussel et al. (Expression and Characterization of Canine Cytochrome P450 2D15, 1998), and Mössner et al. (Inhibition of cytochrome P450 enzymes involved in ketamine metabolism by use of liver microsomes and specific cytochrome P450 enzymes from horses, dogs, and humans, 2011)
The teachings of Dohmer and Zhong are described above. Both fail to teach use of a canine, equine, or feline orthologue to CYP2D6.
Regarding Claim 25: Roussel teaches that CYP2D15 is the canine orthologue of human CYP2D6 (pg 27, abstract) and methods of transfection of the sequence into insect cells for experimental use. (Pg 29, Expression of the CYP2D15 Clones in Insect Cells) This reads on the claimed method of use of a horse, dog, or cat orthologue of CYP2D6.
Regarding claim 39: Roussel teaches use of CYPD15, the canine orthologue of human CYP2D6. Roussel fails to teach use of specifically an equine orthologue of CYP2D6. However, Mössner teaches use of human CYP3A4 and CYP2C9 enzymes and their canine orthologues and how they function of the metabolism of racemic ketamine in human, canine, and equine liver microsomes. (Pg 1505, Objective and Sample) A person of ordinary skill in the art would have been motivated to try using the equine orthologue of CYP2D6, as the teachings of Mössner examine the function of both canine and human orthologues within the microsome of the equine, in addition to both human and dog. Based on MPEP 2143.1.E “Obvious to Try”, a person of ordinary skill in the art would have understood that the exploration of the behavior of both canine and human orthologues would have naturally led one skilled in the art to examine the equine CYP2D6 orthologue as it functioned in the human, canine, and equine microsomes.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teaching of Roussel of use of a CYP2D6 orthologue with the teachings of Dohmer of establishment of human CYP2D6 in hamster V79 cells with the teachings of Zhong of transient transfection in human HEK293T cells with the goal of use in a drug screening method to create an in vitro method for determining the functionality of a canine orthologue of CYP2D6 (CYP2D15). One would have been motivated to do so and had a reasonable expectation of success based on the teachings of Roussel, who details isolation and transfection of a canine orthologue of CYP2D6 into insect cells. One would have been further motivated to incorporate an equine CYP2D6 orthologue based on the teachings of Mössner, who study the microsome of canine, human, and equine samples and how canine and human orthologues of CYP2D6 behave metabolically, yet do not incorporate an equine orthologue.
Claims 23 and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Dohmer et al. (US 20050130116 A1) in view of Dawson et al. (US 20040072235 A1)
The teachings of Dohmer and Zhong are described above. Both fail to disclose a sequence matching SEQ ID NO. 1 or SEQ ID NO. 2 and use of two or more nucleic acids being used to transfect a cell, both encoding at least one CYP2D6 variant or orthologue thereof.
Regarding Claim 23: Dawson teaches a method of screening a polynucleotide sample to detect and identify the presence of one or more CYP2D6 variants, which includes providing a polynucleotide sample comprising one or more sequences of variant CYP2D6 polynucleotides. (Claim 11) This reads on the claimed method of the cells being transfected with two or more nucleic acids each encoding at least one CYP2D6 variant or orthologue thereof.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the claimed method taught by Dawson of use of one or more polynucleotides to transfect CYP2D6 variants with the in vitro method for determining the functionality of a CYP450 variant taught by Dohmer and use of human cells and transient transfection as taught by Zhong to create a cell transfected with two or more nucleic acids each encoding at least one CYP2D6 variant or orthologue thereof to be used in vitro. One would have been motivated to do so based on the teachings of Dawson (use of multiple CYP2D6 variants in a primer to transfect cells) and Dohmer who details a method of transfection for the human cell line V79 with CYP450 variants.
Regarding Claim 26: Dawson teaches a primer set used to screen and identify variants in the CYP2D6 gene with the goal of predicting the potential for altered metabolism for a substance. (57, Abstract) Specifically, Dawson teaches an embodiment of the invention that identifies novel purified and isolated variants of CYP2D6 (0040, Table 2) including SEQ ID NO. 2 which matches the claimed SEQ ID NO. 2 by 99.4%, as shown below:
PNG
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822
744
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Greyscale
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820
726
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Greyscale
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456
726
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Greyscale
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the CYP2D6 variant matching 99.4% to SEQ ID NO. 2 as taught by Dawson with the in vitro method for determining the functionality of a CYP450 variant to create an in vitro method for determining the functionality of a CYP450 variant matching SEQ ID NO. 2 by at least 75%. One would have been motivated to do so based on the teachings of Dohmer, who details a method of transfection for the human cell line V79 with CYP450 variants, Zhong who teaches transient transfection in human cells, and Dawson, who teaches an orthologue matching at least 75% of SEQ ID NO. 2.
Claims 28 and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Dohmer et al. (US 20050130116 A1) in view of Zhong et al. (CN 104593415 A), Gu et al. (US 20040158043 A1) and Del Tredici et al. (Frequency of CYP2D6 Alleles Including Structural Variants in the United States, 2018)
The teachings of Dohmer and Zhong are described above. Both fail to teach a complete loss of function CYP2D6 variant.
Regarding Claims 28 and 29: Gu teaches use of human embryonic kidney (HEK) cells to be transfected with the canine CYP1A2 protein (0094), which is a subfamily of the canine CYP450 protein. (0003) This reads on the claimed method of use of HEK cells, but fails to read on the claimed method of use of a non-functional variant of CYP2D6.
Del Tredici teaches an analysis of CYP2D6 alleles and structural variants within poor metabolizers of CYP2D6. (Pg 1, abstract) Specifically, Del Tredici found that the variant CYP2D6*4 accounted for 25% of allelic variants that had no function. (Pg 6, Discussion)
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Gu (HEK cells) with the teachings of Del Tredici (CYP2D6*4 allele), Dohmer, and Zhong to create an in vitro method for determining the functionality of a complete loss-of-function CYP2D6 variant in HEK cells. One would have been motivated to do so and had a reasonable expectation of success based on the teachings of Gu (successful transfection of a CYP450 subfamily member in HEK cells) and Del Tredici, who states that CYP2D6*4 is the most common CYP2D6 allele that has no function.
Claims 40-44 are rejected under 35 U.S.C. 103 as being unpatentable over Dohmer et al. (US 20050130116 A1) in view of Zhong et al. (CN 104593415 A) and Goh et al. (Analysis of Genetic Variation in CYP450 Genes for Clinical Implementation, 2017)
The teachings of Dohmer and Zhong are described above. Both fail to teach a method resulting in determining the functional activity of the CYP450 variant within 24h after transfection.
Regarding claims 40-44: Goh teaches a method of PGx testing for clinical laboratory use which recognizes CYP2D6 alleles which is determined by Sequenome mass array and droplet digital PCR. (Pg 1, Methods) This method is specifically intended to be used to identify patients who may be prone to drug toxicity with standard doses of drug therapy, and represents a simple, robust assay for use in the clinic. (Pg 1, Conclusion) Specifically, real-time PCR was used to genotype samples that were collected from multiple ethnic groups and the following analysis was used (Pg 3-4, CYP2D6 copy number variation analysis):
Initiation at 95C for 10 minutes
40 cycles of 95C for 15 seconds and 60C for one minutes
Taken together, the total time for the PCR based assay was 40 minutes at 60c, 10 minutes at 90c, and 10 minutes at 95c, resulting in a total assay time of one hour, which reads on the following claims:
Claim 40: providing a patient-specific functional assessment of CYP2D6 variants for drug therapy optimization
Claim 41: functional activity is determined within a few days
Claim 42: functional activity is determined within 48h
Claim 43: functional activity is determined within 24h
Claim 44: functional activity is determined within a “period of several hours”
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Dohmer of establishment of human CYP2D6 in hamster V79 cells with the teachings of Zhong of transient transfection in human HEK293T cells and Goh of a method of analysis for variant functionality within a period of several hours after transfection to create a human transfected CYP2D6 cell line capable of being analyzed for CYP450 variants within a period of several hours after transfection. A person of ordinary skill in the art would have been motivated to do so and had a reasonable expectation of success based on the teachings of Goh who detail a method of analysis which determines CYP2D6 variations in a gene within a matter of hours in human cells.
Response to Arguments
Applicant's arguments filed 11/04/2025 have been fully considered but they are not persuasive. Applicant’s primary argument is that Dohmer describes a method of analytical/screening testing with biomechanical or microsomal assays, whereas Applicant teaches specific pharmacogenomic testing for functional characterization. This is unpersuasive; Dohmer teaches an embodiment of the invention in which genomic DNA of cell lines that had had integration of hCYP2D6 genes inserted. (0239, 0246-0253) This reads on pharmacogenetic testing by way of analyzing the DNA of said test cells for variations within the genome as a response to the hCYP2D6 applied.
Applicant further argues that Dohmer fails to teach transient transfection and fails to teach use of human cells, instead using a hamster cell line. Examiner finds this persuasive, and the 102(a)(1) over Dohmer has been rescinded. However, as Applicant correctly noted use of hamster cells in Dohmer, Examiner has supplied a secondary first action on the merits to correct the deficiencies of Dohmer. These changes are reflected in the above rejections.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to HANNA M THUESON whose telephone number is (571) 272-3680. The examiner can normally be reached M-F 7:30-5 EST. 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.
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/HANNA MARIE THUESON/ Examiner, Art Unit 1638
/Tracy Vivlemore/ Supervisory Primary Examiner, Art Unit 1638