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 .
This Office Action is in reply to Applicants’ correspondence of 09/12/2025.
Applicants’ remarks and amendments have been fully and carefully considered but are not found to be sufficient to put the application in condition for allowance. Any new grounds of rejection presented in this Office Action are necessitated by Applicants’ amendments. Any rejections or objections not reiterated herein have been withdrawn in light of the amendments to the claims or as discussed in this Office Action.
This Action is made FINAL.
Please Note: The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Rejections - 35 USC § 112 – New Matter
Claims 1-5, 7-13, and 15-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The rejected claims include a step of “generating a report indicating the subject's pharmacogenomic profile and risk for developing CKD”, as recited in step (e) of each of claims 1, 9 and 17. But the application as provides not explicit teachings of, or implicit requirement for, any generation of a report. This gap between the amended requirements of the claims and the teachings of the application as originally filed is clear when considering the possible alternatives which may be encompassed by any “report”. The step, as recited in the claims, may be directed to an electronic report that is processed by a database to deduce a treatment regimen, or a written report that is mailed to a healthcare provider, or an oral report that is provided to a patient during an office visit. But there is no support for any such reporting, as encompassed by the claims, in the application as originally filed.
Withdrawn Objection to the Specification
The objection to the disclosure as set forth on page 2 of the Office Action of 05/12/2025 is withdrawn in light of the amendment to the specification provided by applicant in the reply of 09/12/2025, which is entered.
Withdraw Claim Objections
The objection to claim 1, as forth on page 2 of the Office Action of 05/12/2025 is withdrawn in light of the amendments to the claims.
Withdrawn Claim Rejections - 35 USC § 112 - Indefiniteness
Any of the rejections of claims made under 25 USC 112 (b), as set froth in the Office Action of 05/12/2025, which are not reiterated below have been withdrawn in light of the amendments to the claims.
Claim Rejections - 35 USC § 112 – Indefiniteness
Newly Applied as Necessitated by Claim Amendments
Claims 1-5, 7-13, and 15-20 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 1-5, 7-13, and 15-20 are unclear over recitation of the phrase “the genes listed in Table 1 and … the genes listed in Table 2”, as recited in step (b) of each of claims 1, 9 and 17. MPEP 2713.05(s) provides:
Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience." Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993).
In the instant case the claims may be amended to recite gene names or symbols as constant with the application as originally filed.
Claims 1-5, 7-13, and 15-20 are unclear over recitation of the phrase “two or more primers specific for a panel of genes associated with CKD comprising the genes listed in Table 1 and a panel of genes associated with underlying PGX comprising the genes listed in Table 2”, as recited in step (b) of each of claims 1, 9 and 17. The phrase is unclear because the limitation is directed to a Markush style group of alternatively useable elements (i.e.: different combinations and subcombinations of primers directed to genes), but the elements require primers specific for “genes … comprising the genes listed in Table 1 and .. genes listed in Table 2”. In this case the use of the open transitional phrase “comprising” (see MPEP 2111.03) for defining the members of the Markush group makes the metes and bounds of the claim scope unclear. See MPEP 2173.05(h).
Claims 9-13, 15 and 16 are unclear over the stated purpose of the claimed methods as “for diagnosing CKD”, as recited in the preamble of claim 9, in combination with the limitation which sets forth that “one or more DNA sequence alterations in the amplified genetic material indicate that the subject has a risk of developing CKD”. There is a distinction between diagnosing a phenotype (i.e.: diagnosing CKD is determining that the pathology exists in a subject), and an indication of risk in a subject. It is unclear how establishing any risk accomplished the diagnosing as recited in the preamble of the claim.
Claim Rejections - 35 USC § 112 – Written Description
Maintained, Modified as Necessitated by Claim Amendments
Claims 1-5, 7-13, and 15-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
In analyzing the claims for compliance with the written description requirements of 35 U.S.C. 112, first paragraph, a determination is made as to whether the specification contains a written description sufficient to show they had possession of the full scope of their claimed invention at the time the application was filed.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof.
In the present situation, the claims are drawn to methods comprising obtaining a sample of genetic material from a subject, amplifying the genetic material using primers specific for “genes associated with CKD comprising the genes listed in Table 1 and a panel of 40 genes associated with underlying PGX comprising the genes listed in Table 2”, determining the DNA sequences of the amplified genetic material, comparing the DNA sequences of the amplified genetic material to a reference genome, wherein DNA sequence alterations are indicative of aspects of CKD and PGX.
The claims do not describe the primers for genes “comprising” the genes listed in Table 1 and 2 (note that this aspect of the claims has been addressed previously in this Office Action under 35 USC 112(b) as unclear) in terms of their complete structure or in terms of any other relevant structural characteristics. The size of the claimed genus is significantly large given the breadth of the claims as encompassing any gene that could cause or otherwise be associated with CKD or PGX.
The size of the genus is further expanded by the fact that the claims encompass detecting the gene alterations in any subject, including any non-human subjects. It is well accepted that genes and gene alterations that cause or are associated with diseases may vary between organisms. Thereby, “genes underlying” CKD and/or PGX in a human subject may be distinct from those present in any other subject organism.
The instant rejection is further relevant to the claims as they generically encompass any gene alterations, in the generically encompassed genes or in particular genes recited in Tables 1 and 2. Here it is noted that the “alterations” that are generically encompassed by the claims are sufficiently broad to encompass any single or multiple nucleotide insertions, deletions or substitutions, as well as any larger gains, losses, rearrangements or translocations. Thus, the structures of the encompassed genus of alterations is extremely large. But the generically encompassed alteration structures of the claims are accompanied by a functional requirement of association with CKD diagnosis or risk, and/or PGX related profiles or haplotypes. However, neither the application as filed nor the related art provide the skill artisan with the ability to pick from the broad genus those particular species with the require functionality. This is especially true where genotype:phenotype associations may be difficult to establish. See for example the teachings of Hirschhorn et al (2002), which teaches that most reported associations between genetic variants and diseases are not robust. Similarly, Cohen et al (2020) teaches that recent studies suggest “that a large portion of SNP studies are not reproducible”(e.g.: Cohen et al - Abstract). Even the specification of the instant application teaches the difficulty in providing a genotype:phenotype association, where para [0042] provides:
A common polymorphism, c.12627T>G, p.Pro4210Pro, was detected in the PKD1 gene from Patient 2. This polymorphism is present in about 20% of the general population. The polymorphism was detected in 48% of the total reads, indicating this donor is heterozygous for this variant. This polymorphism does not correlate with CKD.
Furthermore, the specification recites a plurality of genes without any associated “Disease Name”. See for example “APOE” on pages. Thus, the teachings in the specification make clear that a comparison of the DNA sequence of a subject’s genes “underlying CKD” with that of a control sample, and finding an alteration in the DNA sequence of the subject that is not present in a normal control sample does not necessarily result in the identification of a genetic alteration indicative of CKD.
While the specification teaches the general methodology for screening for mutations in genes, possession of the claimed invention may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features. A showing of how to potentially identify some genes that may be associated with CKD or PGX, or mutation that may be associated with CKD or PGX, is not sufficient to establish that Applicants were in possession of the invention as broadly claimed. The naming of a gene in terms of its functional attributes is not sufficient to describe that gene. More than a statement of biological function is required to satisfy the 35 USC 112(a), written description requirement for a genus of DNA molecules or mutations therein. The specification does not disclose a clear structure-function relationship between the claimed genus of genes, and the generic breadth of alterations therein, and the functional property of being indicative of CKD phenotypes and/or PGX profiles.
Response to Remarks
Applicants have traversed the rejection of claims under 35 USC 112(a) for lack of an adequate written description in the application as filed. Applicants’ arguments (p.8-9 of the Remarks of 09/12/2025) have been considered but are not persuasive to withdraw the rejection. Applicants have initially argued that the specification provides support for the claimed genes of Tables 1 and 2. This argument is not persuasive because, as set forth in the instant rejection (and as detailed in the rejection of claims under 35 USC 112(b) as indefinite), the claims are not clearly directed/limited to the gene symbols recited in the Tables of the specification. Additionally, the argument does not address the generic breadth of the alterations encompassed by the claims (i.e.: any alterations in the genes, as well as genes from any subject organism), as detailed in the rejection, in combination with the functional requirements recited in the claims (indicative of a PGX profile and risk of CDK). Applicants have next argued that the claims are enabled by the specification because the skilled artisan could practice the steps of the claims using routine laboratory steps without the need for any inventive development. This argument is not persuasive. Initially it is noted that the claims are rejected for lack of an adequate written description, and not for lack of enablement, and although there is often significant overlap between the enablement and written description requirements, they are nonetheless independent of each other. The Examiner maintains that the claims are not just to methods of sequence analysis of known genes, but also include the detection of any sequence variants that are indicative of a PGX profile and a risk of CDK. Neither the particular teachings of the specification nor teachings of the related art provide the skilled artisan with the ability to select from the broadly encompassed genus those particular elements which meet the functional requirements of the claims.
Claim Rejections - 35 USC § 101
Maintained, Modified as Necessitated by Claim Amendments
Claims 1-5, 7-13, and 15-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
The claim(s) recite(s) abstract ideas. For example, step (d) of each of claims 1, 9 and 17 is directed to a comparison of data to a reference to detect an alteration. As stated in MPEP 2106.04(a)(2) Ill “the ‘mental processes’ abstract idea grouping is defined as concepts performed in the human mind, and examples of mental processes include observations, evaluations, judgments, and opinions.” As such the comparison of information to reach a conclusion is properly considered to be an abstract idea. Additionally, where the claims are directed to genotype:phenotype associations (e.g.: the presence of an alteration is indicative of a risk for developing CKD), the recited relationship is a natural phenomenon that exists apart from any human action. The particular phrasing of the claims does not make them less directed to a natural law.
This judicial exception(s) is not integrated into a practical application because the claims end with the recites “comparing” and the “wherein” clause that establishes the asserted natural law. The claims to not require any additional practical steps that are predicated on the determination of any particular PGX or CKD diagnosis. Here it is noted that while the claims include “generating a report”, it is well established that merely presenting the results of a process otherwise unpatentable under section 101 is properly considered to be insufficient to establish eligibility under the 35 USC 101. See FairWarning IP, LLC v. Iatric Sys., Inc., (Fed. Cir. Oct. 11, 2016).
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because there are no particular practical steps that are required by the claimed methods other than the amplification of genetic material, which is well understood, routine and conventional in the related art. Here it is noted that the specification teaches that the data collection of the claims (i.e.: the gene sequences from a subject) are obtained by known methods (e.g.: pages 6, 20 and 21). Additionally, Samorodnitsky et al (2015) teaches that amplification of genes in whole-exome sequencing was conventional in the related art. Here it is noted that while the specification asserts that “unique primer pool aliquots are used to amplify” the regions of interest from the genentic material (e.g.: para [0031], none of the claims include any aspects of unique pools of any particular primers.
For the reasons set forth above, when the claims are considered as a whole, the claims are not considered to recite something significantly more than a judicial exception(s) and thereby are not directed to patent eligible subject matter.
Response to Remarks
Applicants have traversed the rejection of claims under 35 USC 101 as being directed to a judicial exception without significantly more. Applicants’ arguments (p.9-10 of the Remarks of 09/12/2025) have been considered but are not persuasive to withdraw the rejection. Applicants have initially argued that the claims are directed to a test that provides both diagnostic (CKD) and therapeutic (PGX) guidance. This argument is not persuasive because the argument only indicates that two abstract ideas (i.e.: associating gene variants with CKD; and associating gene variants with PGX) are required for the claimed methods. In this regard, MPEP 2106.05 provides that “while abstract ideas, natural phenomena, and laws of nature are not eligible for patenting by themselves, claims that integrate these exceptions into an inventive concept are thereby transformed into patent-eligible inventions.” But the MPEP also makes clear that “An inventive concept cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself.” Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016).” MPEP section 2106.05, second paragraph. Basically, integration of the judicial exception in an unconventional way so as to improve a conventional technology or process may yield an eligible claim. However, if the judicial exception itself is the purported improvement, such as the recognition of the association between sets of markers and phenotypes, then this is a claim directed to the judicial exception, not an eligible improvement to a technology or technical field through integration of the judicial exception into a system or process. Determining the CKD risk status of a subject using a first marker panel is an abstract idea. Identifying a PGX characteristic of the subject based on a second marker panel is a natural correlation.
Applicants have next argued that the claims recite a practical application of genetic knowledge because the methods allow clinicians to immediately initiate personalized therapy following genetic diagnosis. This argument is not persuasive because it is not commensurate in scope with the claims. The claims do not require the application of any particular therapeutic regimen to any subject identified as having some specific genetic markers.
Applicants have also argued that the claims recite practical methods related to obtaining a sample, amplifying genetic material, and sequencing the amplified material. This argument is not persuasive to withdraw the rejection because while these steps represent practical methodology, such steps, as broadly recited in the claims, are well understood, routine and conventional in the related art. Furthermore, where the steps are the necessary data gathering steps required perform the judicial exception to which the claims are direc4ed, and the steps are recited at a high level of generality, such elements of the claims are properly considered insignificant extra solution activity (see MPEP 2106.05(g)).
Applicants’ final argument is the instantly claimed methods are distinguished from the ineligible method of Mayo and Myriad because the claims require a novel combination of hundreds of CKD and PGX genes, the performance of specific technical steps such as amplification, sequencing, and comparison, and the generation of an actionable output that allows physicians to diagnose CKD and select or adjust therapy in real time. This argument is not persuasive. Initially it is noted that the aspect of the required genes has been addressed previously in this Office Action under 35 USC 112(b) where it is unclear what particular genes are analyzed by the claimed methods; in this regard it is noted that the claims recite “two or mor primers”, thus making it unclear if the steps of the claims in fact require analysis of the “combination of hundreds of CKD and PGX genes” as recited in the arguments. Additionally, as noted above, the steps are recited at a high level of generality such that they are considered to be well understood, routine and conventional data gathering steps.
Withdrawn Claim Rejections - 35 USC § 103
The rejection of claims under 35 U.S.C. 103 as being unpatentable over Ero et al in view of Padullés et al, as set forth on pages 11-12 of the Office Action of 05/12/2025, is withdrawn in light of the amendments to the claims.
New Claim Rejections - 35 USC § 103
Necessitated by Claim Amendments
In comparing the claims to the prior art, it is noted that the claims were previously rejected in this Office Action for lack of adequate written description. The claims are rejected here in so far as the prior art renders obvious at least some embodiment encompassed by the claims. But the application as filed does not specifically describe the methods suggested by the prior art where the application does not principally contemplate or describe those elements as provided in the prior art. Additionally, it is noted that the particular embodiments of the prior art are not suitable to establish a description of the generic breadth of the methods as claimed.
Claim(s) 1-5, 7-13 and 15-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ero et al (US PG Pub 2015/0337377) in view of Padullés et al (2014) and Sturm et al (2012).
Relevant to the steps of the instantly rejected claims as recited in claims1, 9 and 17, Ero et al teaches methods related to analysis of genotype:phenotype associations (exemplifying identifying risk of pathology by identifying variations in genes of interest). Ero et al includes obtaining genetic material, amplification of genes of interest using specific primers, sequencing the amplified material, comparing the sequence to a reference, and identifying alterations that are indicative of risk of pathology (see for example Ero et al claim 1 on page 185).
Ero et al additionally teaches that alterations may be variants, mutations or polymorphisms (e.g.: claims 1, 2 and 3 on page 185), relevant to the rejection of claims 2-4, 10-12 and 18-20.
Ero et al teaches that the analysis may be performed 48 hours, or 5 days, after receipt of a sample (e.g.: claims 8 and 9 on page 185), relevant to the rejection of claims 7, 8, 15 and 16.
Ero et al does not teach analysis of genetic alterations related to chronic kidney disease (CKD) or pharmacogenomics (PGX), or the generation of a report related to detected genetic content; but the analysis of gene alterations related to CKD and PGX was known in the prior art and is taught by Padullés et al; and the providing of reports related to phenotypes associated with detected genotypes was known in the prior art and is taught by Sturm et al.
Relevant to the instantly rejected claims, Padullés et al teaches that various particular genetic markers can be predictive or related to CKD progression physiopathology as well related to a different pattern of response to treatment (e.g.: p.251 – Abstract). Relevant to the rejected claims, Padullés et al teaches alterations that are polymorphisms (which are themselves variants) and mutations associated with PGX (e.g.: p.253 - Phase I enzymes (CYP1A2 and CYP3A5) which are recited in Table 2 of the instant specification; p.254 - ABCB1 also recited in Table 2))and CKD (e.g.: p.256 - Polymorphisms in CKD pathogenesis, Table I of the prior art which includes genes such as MYH9 which is recited in Table 1 of the instant application).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have applied the methodological steps of Ero et al to the analysis of gene variations associated with CKD and PGX. The skilled artisan would have been motivated to apply the methodological steps of Ero et al to CKD and PGX based on the expressed teachings of Ero et al that such methods provide an improved method for rapid detection of gene alterations that have been previously reported as associated with a pathological phenotype (e.g.: para [0012]), and the expressed teachings of Padullés et al that genotype-based pharmacotherapy, risk prediction, drug target recognition, and personalized treatments, would allow prediction of risks relative to drug exposure that could guide physicians in evaluating cost-effectiveness of new strategies in CKD patients. The skilled artisan would have had a reasonable expectation of success based on the expressed teachings of Padullés et al that particular alleles of specific genes are associated with pharmacogenomic profiles and increased likelihood and CKD. With regard to the rejection of claims 5 and 13, where Padullés et al teaches that genome-wide studies are performed to find genetic risk alleles (e.g.: p.251 – Abstract; p.260 – right col), the skilled artisan would have recognized that the analysis of any of the known risk alleles in the genome, in any number of genes, would allow for a comprehensive analysis of pathology risk.
It would have been prima facie obvious to someone with ordinary skill In the relevant art before the effective filing date of the rejected claims to provide a generated report of the results of analysis of mutations, as taught by Ero et al, in CKD and PGX genes, as taught by Padullés et al. The skilled artisan would have been motivated to provide a generated report based on the expressed teachings of Sturm et al that such a report can be used in genetic counseling of a subject (e.g.: p.404 – Case preparation). The skilled artisan would have had a reasonable expectation of success based on the expressed teachings of Strum et al that printed copies of reports and electronic reports (e.g.: web portal) containing information can be provided.
Response to Remarks
Applicants have traversed the rejection of claims under 35 USC 103 as being obvious in view of the cited prior art. Initially it is noted that in light of the amendments to the claims, a new rejection has been set forth above. Applicants’ arguments (p.10-11 of the Remarks of 09/12/2025) have been considered but are not persuasive to withdraw the rejection; to that extent as the arguments are germane to the new rejection, the arguments are address below.
Applicants have initially argued that the claims are directed to a novel and non-obvious genetic panel that includes markers related to both CKD and PGX, and that the combination provides unexpected utility not taught or suggested by the prior art. This argument is not persuasive. Initially it is noted that the genes required for analysis in the claimed methods has been addressed earlier in this Office Action (e.g.: it is unclear what genes are required, and the claims don’t clearly require an analysis of all of the genes in Tables 1 and 2). And as set forth in the rejection, Padullés et al specifically addresses at least one gene, and specific alleles of that gene, associated with CDK risk, and at least one gene, and specific alleles of that gene, associated with PGX.
Applicants next address the teaching of Padullés et al as “aspirational” with regard to the detection of both PGX and CKD markers, and Applicants assert that the skilled artisan would have no motivation, nor would the skilled artisan find success, in merging the analysis of markers directed to PGX and CKD. This argument is not persuasive. Applicants’ argument ignores the plain teachings of Padullés et al, as detailed in the rejection, which include that genotyping has applications that have benefits for CKD risk prediction, guided treatment, and guided individualized strategies (e.g.: p.261 - Developments in pharmacogenomics – clinical implications and personalized therapies). Applicants’ assertion that the application of a “dual-use” panel provides unexpected clinical utility by providing immediate pharmacogenomic guidance at the point of diagnosis is not persuasive when properly considering the teachings of Padullés et al which provides for a connection between both PGX markers and CKD markers in the identification of CKD risk and the deciding what treatments of CKD in a patient may be more successful.
Conclusion
No claim is allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. The Renasight Genetic Test Video (Oct. 2, 2020) from https://www.natera.com/ provides a teaching related to a test of over 380 genes associated with kidney disease using next generation sequencing to detect disease causing variants, and includes genes from Table 1 (e.g.: ACE) (https://www.natera.com/organ-health/renasight-genetic-testing/gene-conditions-list/).
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHEN THOMAS KAPUSHOC whose telephone number is (571)272-3312. The examiner can normally be reached M-F, 8am-5pm.
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Stephen Kapushoc
Primary Examiner
Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683