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 10/02/2025.
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 Any rejections or objections not reiterated herein have been withdrawn in light of the amendments to the claims or as discussed in this Office Action.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.
Note on The Presentation of Claim Amendments
It is noted that the amendments of 10/02/2025 are not technically compliant with 37 CFR 1.121 (c)(2) which requires:
The text of any added subject matter must be shown by underlining the added text.
In the instant case claims 18 and 19 have added text (i.e.: in each claim there is added a parenthetical phrase and a table of chromosome positions) that is not properly indicated as such with underlining. While it is noted that the parenthetical phrase appears to be a note related to the added table, such text presented in the claim as a not is not proper, and does not address the need for proper mark-up of the additional added text. In the interests of customer service and compact prosecution the claims entered and are examined in this Office Action. Applicants are encouraged to thoroughly review any future submissions to ensure they meet the requirements of 37 CFR 1.121.
Election/Restrictions
In the reply filed on 06/05/2025 Applicants elected, with traverse, the invention of Group 1 (claims directed to predicting age). The requirement was deemed proper and is made FINAL as set forth on page 2 of the Office Action of 07/10/2025.
Additionally, as set forth on pages 2-3 of the Office Action of 07/10/2025, the election as set forth in the reply of 04/24/2025 was extended to the combination of CpG sites provided in Table 1.
Withdrawn Claim Objections
The objection of claim 24, as set forth on page 3 of the Office Action of 07/10/2025, is withdrawn in light of the amendments to the claims.
New Claim Objections
Necessitated by Amendments
Claims 18 and 19 are is objected to because of the following informalities: as noted earlier in this Office Action, each of claims 18 and 19 contain a parenthetical phrase (i.e.: (The following table is newly added and all entries are considered underlined for amendment purposes.)) that appears to be an instruction related to the amendments to the claims, and not an intended claim limitation. Such text in the body of a claim is not appropriate or compliant with the requirements of 37 CFR 1.121 (c)(2).
Claim 38 recites the phrase “are normalized for tissue-specifically”, where the phrase “are normalized [[for]] tissue-specifically” is likely intended.
Appropriate corrections are required.
Withdrawn Claim Rejections - 35 USC § 112 - Indefiniteness
The rejections of claims under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as set forth on pages 3-4 of the Office Action of 07/10/2025, is withdrawn in light of the amendments to the claims.
New Claim Rejections - 35 USC § 112 – Indefiniteness
Necessitated by Amendments
Claims 37-42 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 37-42 are unclear over purpose of the claimed methods as “for measuring age-related methylation”, as recited in the preamble of claim 37, from which claims 38-42 depend. There is no process step in which any aspect of methylation related to the age of “healthy Gallus gallus animals” (as recited in the preamble of claim 37), is calculated or provided. The claims recite a step determining the methylation level of CpG sites in a subject or population to be tested (step (b)), and determining the methylation level the same CpG sites in a reference sample. But these steps themselves are not related to measuring methylation related to age. Step (d) of claim recites a step of analyzing bisulfite reads mapped to a reference genome to calculate methylation ratios at CpG sites, but there is no result in the analysis correlated to age-related methylation. Additionally, step (d) of claim 37 is unclear because there is no antecedent basis for any “bisulfite reads mapped to a reference genome”, and there is no indication that the CpG sites of step (d) are required to be related to the CpG sites referenced in steps (b) and (c). Furthermore, it is not clear what “ratio” is calculated in step (d), where the ratio could be made with the level determined in step (b), or the level determined in step (c), or some comparison of the level determined in step (b) to the level determined in step (c).
Claims 37-42 are unclear because the plural recitation in the preamble of “in healthy Gallus gallus animals” is not consonant with the singular “derived from the Gallus gallus subject” as encompassed by step (a), as recited in claim 37 from which claims 38-42 depend. It is unclear if the claims are intended to encompass methods in which “age-related methylation” is measured in a single animal.
Claim 42 is unclear over recitation of the phrase “wherein the Galliformes subject or population to be tested” because the claim depends from claim 37, and claim 37 is directed to Gallus gallus (i.e.: a particular genus and species of animal), whereas the term Galliformes is a larger order of different animals. Thus, the limitations of claim 42 appear to be broader than the limitations of the claim from which is depends.
Withdrawn Claim Rejections - 35 USC § 112 – Failure to Limit
The rejection of claim 25 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as set forth on pages 4-5 of the Office Action of 07/10/2025, is withdrawn in light of the amendments to the claims.
Claim Rejections - 35 USC § 101
Maintained, and Modified/Newly Applied as Necessitated by Amendments
Claims 16-19 and 24-26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception to patentability encompassing abstract ideas and a natural phenomenon without significantly more.
The claim(s) recite(s) a step of measuring relative methylation levels (i.e.: one level as compared to another level, as recited in step (c) of claim 16) in a sample to establish a chronological age (as recited in step (c) of claim 16). The claims also recite aspects of “age-related methylation” (as recited in claim 37) and calculating ratios (as recited in step (d) of claim 37. The claims are thus directed to an abstract idea such as the evaluation of data or information to reach a conclusion (see MPEP 2106.04(a) III). The calculation of a ratio is also an abstract idea (see MPEP 2106.04(a)(2)). Additionally, where the claims are directed to a correlation between methylation status, epigenetic age and chronological age, the claims are directed to the natural association between age and methylation, and thus are directed to a natural phenomenon (see MPEP 2106.04(b) I).
This judicial exception is not integrated into a practical application because there are no required practical steps related to any particular predicted chronological age. The claimed methods end with the establishing of age based on a relative measurement (claim 16) or the calculation of a ratio (claim 37), which are abstract ideas as detailed above.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the data gathering steps of the claims (i.e.: obtaining genomic DNA and determining a methylation level of CpG sites) is activity that was well understood, routine, and conventional in the related art. The specification teaches detection of CpG methylation is performed using commercially available reagents and known techniques (e.g.: pages 14-15). Additionally, the prior art of Zhang et al (2017) (cited on the IDS of 10/26/2022) teaches the analysis of CpG methylation in samples from Gushi hens, including comparisons at different ages, using whole-genome bisulfite sequencing.
Thus the claims are properly rejected as being directed to a judicial exception to patentability without significantly more.
Response to Remarks
Applicants have traversed the rejection of claims under 35 USC 101 as being directed to a judicial exception to patentability without significantly more. Applicants’ arguments (p.15-17 of the Remarks of 10/02/2025) have been fully considered but are not persuasive to withdrawn the rejection as maintained above.
Applicants have initially asserted that the judicial exceptions of the claims are integrated into a practical application. Applicants assert that samples are collected from Galliformes and analyzed with respect to specific genomic sites. The Examiner maintains that the steps of the claims in this regard are the necessary pre-solution activity required to collect the data used in the judicial exceptions, and the steps are recited at a high level of generality (see MPEP 2106.05(g)) and that the steps are encompassed by the well-understood, routine and conventional activity of the prior art (see MPEP 2106.05(d)). Applicants assert that the utilization of specific sites improves accuracy. This argument is not persuasive because any improved accuracy is related to the establishing of an epigenetic or chronological age, and this correlation between methylation and age is itself a judicial exception (an abstract idea that is realized based on a natural phenomenon).
Furthermore it is noted that Applicants argue on page 18 of the Remarks, that “in the present application, the claimed method requires a direct comparison of methylation levels at specific CpG sites to those from an age-correlated reference sample”, thus confirming that the claims are directed to abstract ideas.
Applicants have argued (p.17 of the Remarks) that consideration of any well understood, routine and conventional nature of additional elements of a claim is not appropriate under step 2A, prong 2 of the analysis. The Examiner maintains that the well understood, routine and conventional nature of additional elements is analyzed under step 2B of the analysis, not under step 2A, prong 2; and that the judicial exceptions (establishing age; calculating a ratio) of the claims are not integrated into any practical application of those judicial exceptions.
Applicants have argued that claim 37 recites a step of using a computer to execute an analysis of bisulfite sequencing reads, which “is not an abstract idea or a mental process, because it requires the use of a computer to process large volumes of sequencing data and perform mathematical operations that cannot be carried out in the human mind.” This argument is not persuasive. Initially it is noted that the limitation has been addressed previously in this Office Action under 35 USC 112(b) as indefinite. Here it is noted that such a limitation is not sufficient to overcome the rejection because there is in fact no requirement that the analysis is so complex that it can not be performed in the human mind. Additionally, the recitation of a general use a computer program is not itself sufficient to overcome a rejection made under 35 USC 101 (see MPEP 2106.05(b) and MPEP 2106.04(a)(2)(III)).
Claim Rejections - 35 USC § 112 – Written Description
Maintained, and Modified/Newly Applied as Necessitated by Amendments
Claims 16, 17, 24, 36, 37, 38, 41 and 42 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 instant rejection is relevant to the requirements of the claims for the analysis of methylation in “a set of specific CpG sites in the genomic Galliformes DNA” (as recited in step (b) of claim 16), or Gallus gallus DNA (as recited in step (b) of claim 37). The claims thus encompass a wide genus of nucleic acid positions throughout the genome of any member of the Galliformes order which encompasses 290 species including such diverse animals as turkeys, chickens, quail, partridge, pheasant, peacock, guinea fowl, grouse, chachalacas, guans, and curassows; or any CpG positions in the Gallus gallus genome that are not associated with SNPs of or sex chromosomes (as recited in the negative limitations of claim 37). The breadth of the encompassed structures (i.e.: the sequence context of the genomic loci that include the CpGs) is thus very large. However, the claims, in light of the specification, require a particular functionality for the structures of the claims. The specification provides (at p.6):
The "set of specific CpG sites in the genomic Galliformes/chicken DNA" refers to the CpG locations showing the best correlations with age.
The claims thus require that the CpGs of the claims are correlated with age, and in fact require that the correlation is superior to any other CpGs. But neither the specification nor the related are provide that skilled artisan with the ability to pick from the broadly encompassed genus (as addressed above) those particular species that satisfy the functionality of the claims. And while the specification teaches several particular set of CpG loci from Gallus gallus, this teachings does not provide any specific characteristics (e.g: locus sequence; chromosomal positions) that will provide the identification of any other different CpG loci, from any other organism of other CpGs in Gallus gallus, that will provide the required functionality. The disclosure of some particular CpGs does not inform the skilled artisan about the nature of any other different loci, nor does the disclosure of some particular CpGs provide evidence that the inventors were in possession of any other loci that satisfy the functional requirements of the claims. In the instant case. a showing of how to potentially identify some CpG loci is not sufficient to establish that Applicants were in possession of the invention as broadly claimed. Where the claims are directed to a large genus of possible structures, the inventors have not provided a sufficient description of a representative number of species by actual reduction to practice or by disclosure of relevant, identifying characteristics, (i.e.: structure or other physical and/or chemical properties), or by functional characteristics coupled with a known or disclosed correlation between function and structure (see MPEP 2163).
Response to Remarks
Applicants have traversed the rejection of claims under 35 USC 112 as encompassing subject matter not adequately described by the application as originally filed. Applicants’ arguments (p.12-13 of the Remarks of 10/02/2025) have been fully considered but are not persuasive to withdrawn the rejection as maintained above.
Applicants have asserted that “it is scientifically reasonable to extrapolate age determination methods based on genomic methylation patterns from one species to others within the Galliformes order”. The argument is not persuasive. The Examiner maintains that while the biological association between methylation and age may be largely applicable to different organism, it is generally accepted that epigenetic clocks are species-specific (e.g.: Horvath et al (2021) and Stubbs et al (2017)). That is to say that while there may be an epigenetic clock that can be established in any different organism, the particular CpG sites, and there age-correlated methylation, is generally accepted to be unique for any particular organism, and the particular CpG sites of any clock must be determined empirically.
Thus, while the Applicants argue that “the present application provides all of the information needed to construct a methylation clock in the detailed description of the invention and especially the Examples”, the examiner maintains that the particular exemplification in the specification of a CpG set from Gallus gallus (e.g.: the 45 CpG sites from Table 1 as recited in claims 18, 19, 39 and 40) that is asserted to meet the limitations of the claims does not demonstrate possession of any other different CpG sets (e.g.: from different species; or comprised of different CpG sites from Gallus gallus that fulfill the limitations of the claims. A showing of how to potentially identify CpGs that may be related to age in an organism is not sufficient to establish that Applicants were in possession of the invention as broadly claimed.
Claim Rejections - 35 USC § 112 – Scope of Enablement
Maintained, and Modified/Newly Applied as Necessitated by Amendments
Claims 16-19, 24, 26, 26, and 37-42 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for (consonant with the election):
methods for predicting the chronological age of a Gallus gallus subject comprising comparing, using a statistical prediction method, the levels of methylation of the CpG sites in Table 1 from a tissue sample of the subject to the levels of the CpG sites in Table 1 from the same tissue type from a plurality of age-correlated populations of different ages
does not reasonably provide enablement for the methods as claimed which encompass the analysis of any CpG loci from any Galliformes species and any comparisons of methylation among any different tissue types. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Here it is noted that the subject matter of claims 37-42 has been addressed previously in this Office Action under 35 USC 112(b) as indefinite; the claim are included here as they recite “measuring age-related methylation” and include steps related to calculating ratios of CpG site methylation, and in light of Applicants arguments in the Remarks that “the claimed method requires a direct comparison of methylation levels at CpG sites to those from an age-correlated reference sample … to establish both the epigenetic and chronological age of the subject or population”.
Nature of the invention and the breadth of the claims
The rejected claims are directed to methods of predicting the chronological age of a Galliformes subject and encompass the detection of methylation of a wide variety of CpG loci in any tissue sample form any Galliformes animal. The claims further encompass any comparison of methylation with any age-correlated reference sample. The claims thus require knowledge of a reliable relationship between any methylation status of CpGs form different sample types and chronological age in different subject organisms.
Direction provided by the specification and working example
The instant specification provides an example (p.14) of the analysis of chronological age and methylation status in chickens (Gallus gallus). The specification teaches that methylation from particular tissues was compared among three age-correlated reference populations, and that a set of 45 particular CpGs (relevant to the election) was identified by as indicative of chronological age using statistical analysis of the methylation.
The specification teaches (p.16) that for the analysis of a new sample the methylation ratios of the 45 particular CpGs must be provided.
The specification does not teach any analysis of any subject other than Gallus gallus.
The specification does not disclose any particular formula or specific relationship between methylation and chronological age.
State of the art, level of skill in the art, and level of unpredictability
While the state of the art and level of skill in the art with regard to the analysis of methylation levels of CpGs in any sample is high, the unpredictability in associating any methylation levels with a particular chronological age is higher. Such unpredictability is demonstrated by the related art and the instant specification.
Because the claims generically encompass a wide variety of CpGs from any tissue samples in any Galliformes subject organism, it is relevant to point out the unpredictable associated with epigenetic modification of such broadly encompassed genomic loci.
Initially it is noted that the specification teaches (p.4) that different tissues have “different aging trajectories”, and that different tissues have different “correction factors” (Table 1) when considering age-associated methylation. Similarly, Stubbs et al (2017) teaches that age-related methylation is different among different tissues. And Bell et al (2019) teaches several aspects related to the unpredictability of using CpG methylation to establish a chronological age of a subject.
Because the claims generically encompass any Galliformes subjects, it is relevant to point out that epigenetic clocks themselves are generally species-specific and not directly transferable between different organisms (Stubbs et al (2017)). This means that a clock CpG loci used in a calculation for Gallus gallus won’t accurately predict the age of any different species (Field et al (2018)).
Quantity of experimentation required
A large and prohibitive amount of experimentation would be required to make and use the claimed invention. Such experimentation would require case:control analysis of samples from any subjects of interest to try to establish the broadly required associations of the claims. Even if such experimentation were to be performed, given the unpredictability of the subject matter of the claims, there is no assurance that the required associations would beyond those specifically disclosed in the application would be detected.
Conclusion
Taking into consideration the factors outlined above, including the nature of the invention and breadth of the claims, the state of the art, the level of skill in the art and its high level of unpredictability, the lack of guidance by the applicant and the particular examples, it is the conclusion that an undue amount of experimentation would be required to make and use the invention in the full scope as claimed.
Response to Remarks
Applicants have traversed the rejection of claims under 35 USC 112 as encompassing subject matter not enabled by the application as originally filed. Applicants’ arguments (p.13-15 of the Remarks of 10/02/2025) have been fully considered but are not persuasive to withdrawn the rejection as maintained above.
The Examiners provides the argument that the particular teachings of the specification are not predicably extrapolated to other organisms, and the Applicants have agreed that the identity of CpGs may vary between species. But while Applicants assert that the specification conveys possession of the broader concept of constructing methylation clocks across Galliformes by teaching the methodology for Gallus gallus, the Examiner maintains that the claims are not directed to methods of deducing or identifying associations between CpG methylation and age; the claim are directed to the determination of age of a subject using a direct comparison of methylation levels at CpG sites to those from an age-correlated reference sample, and it is unpredictable as to what thot require CpG sites are beyond the particular CpGs disclosed in the application as suitable for the claimed methods.
Similarly, the fact that clocks can be developed in mammals as distantly related as whales and mice, as argued by Applicants (p.14 of the Remarks), fails to remedy the gap between the particular teachings of the specification, and the breadth of the claim, in light of the unpredictability by of the required associations. The claims are not directed to developing a clock, which broadly speaking may be obvious in view of the prior art, but are directed to the use of some specific set of CpG sites to establish the age of a subject animal.
Withdrawn Claim Rejections - Double Patenting
The rejection of claims for double patenting made over the conflicting claims of co-pending application 18/836,232, as set forth on page 13 of the Office Action of 07/10/2025, is withdrawn in light of Applicants’ Remarks (p. 19 of the Remarks of 10/02/2025).
Double Patenting
Maintained, and Modified/Newly Applied as Necessitated by Amendments
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 16-19, 24, 26 and 36-42 are are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 15-25 of copending Application No. 17/759,194 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the conflicting claims are directed to establishing a relationship between the chronological age of a sample using methylation of the same broadly claimed CpG loci as the instantly rejected claims. The conflicting claims include (i.e.: conflicting claim 25) the same specific CpG sites recited in instantly rejected claims 18, 19, 39 and 40.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Remarks
Applicants have traversed the rejection of claims for issue related to double patenting in view of conflicting application 17/759,194. Applicants’ arguments (p.17-19 of the Remarks of 10/02/2025) have been fully considered but are not persuasive to withdrawn the rejection as maintained above.
Applicants have argued that the claims of the reference application use a penalized regression model to process data, and as such the claims of the instant application are distinct because they require an empirical comparison to a reference sample. The argument is not persuasive because the conflicting claims include the analysis of multiple samples and correlating methylation ratio and read coverage to a chronological age.
Conclusion
No claim is 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.
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