DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
2. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 28 August 2025 has been entered.
3. Applicant's arguments and amendments to the claims presented in the reply of 28 August 2025 have been fully considered but do not place the application in condition for allowance. All rejections and objections not reiterated herein are hereby withdrawn.
In particular, the previous rejection of the claims under 35 U.S.C. 101 has been obviated by the amendment to the claims. The claims have been amended to recite “c. determining the circadian rhythm using an algorithm comprising a machine learning prediction model trained on RNA expression levels of multiple circadian rhythmically expressed genes measured over time, to predict a periodic output variable corresponding to circadian rhythm from the expression levels quantified in step b from said single sample, and d. treating the subject according to the determined circadian rhythm.” Claims 1 and 44 particularly require “d. treating the subject according to the determined circadian rhythm, wherein the subject has a circadian rhythm sleep-wake disorder, comprising asynchrony between a sleep-wake rhythm of the subject and an external light-dark cycle of the subject, and the subject is administered a chronotherapy, comprising regulated light exposure and/or melatonin.” Thus, the claims require administering a chronotherapy comprising regulated light exposure and/or melatonin to the subject, wherein the subject has a circadian rhythm sleep-wake disorder and the chronotherapy is administered based on the subject’s circadian rhythm - i.e., the administering is personalized to the subject’s internal clock. Claim 43 recites “treating the subject according to the determined circadian rhythm, wherein the subject has cancer or a cardiovascular disease, and the subject is administered a therapeutic cancer or cardiovascular drug, respectively, at a timepoint of the determined circadian rhythm, at which an increased efficacy of said drug is evident, compared to other timepoints of said circadian rhythm.” Accordingly, this claim requires that following the step of determining a subject’s circadian rhythm, the subject, who has a cardiovascular disease or cancer, is administered a therapy for the cardiovascular disease or cancer at a time point that is most effective for the therapy based on the determined circadian rhythm of the subject (see, e.g., para [0008] and [0322]).
It is acknowledged that the response states “Applicant is open to the possibility of an Examiner’s amendment and invites the Examiner to email the undersigned below at Raymond.Smith@knobbe.com or call at (949) 760-0404, as appropriate.”
However, communication via email regarding confidential information requires that Applicant submit a written authorization to communicate via the Internet. See MPEP 713.01 II:
II. SPECIAL REQUIREMENTS FOR USING INTERNET COMMUNICATIONS
Internet email, instant message system, or video conferencing shall NOT be used to conduct an exchange or communications similar to those exchanged during telephone or personal interviews unless authorization from the applicants or an attorney/agent of record has been given to use Internet communications. See MPEP § 502.03.
Form PTO/SB/439 may also be used to provide such authorization (see: https://www.uspto.gov/sites/default/files/documents/sb0439.pdf).
Secondly, the claims were amended so that the majority of the claims are of a broader scope and the amendment raises numerous new issues, as detailed in the rejections below.
Claim Status
4. Claims 1, 3, 4, 7, 10-11, 13-14, and 26-45 are pending.
Claims 28, 29, 31-34, 37, 40, 41, 42, 44 and 45 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim.
Note that in the reply of 29 October 2024, Applicant elected without traverse the species of the combination of the night gene group and day gene group; CIART for the night gene and TGM5 for the day gene and GLI2 as the amplitude prediction gene. Note also that the recitation in, e.g., claim 44 of “at least five circadian phase genes comprising ARNT, CIART…” has been interpreted as requiring that the five genes include at least five of the recited genes; and “at least three amplitude prediction genes comprising…” has been interpreted as requiring that the three genes include at least three of the recited genes.
Claims 1, 3, 4, 7, 10-11, 13-14, 26, 27, 30, 35-36, 38-39 and 43 read on the elected species and have been examined herein. These claims have been examined to the extent that the circadian phase gene is a gene in a day gene group and a gene in the night gene group. Claim 11 has been examined to the extent that it requires the day gene of an early afternoon gene and a nigh gene of a late night gene. Claim 27 has been examined to the extent that it reads on the elected amplitude gene of GLI2. Claim 30 has been examined to the extent that it reads on the early afternoon gene of TGM5. Claim 35 has been examined to the extent that it reads on the elected late night gene of CIART. Claim 38 has been examined to the extent that it requires the CIART and TGM5 genes. The claims encompass the non-elected species of early-day genes and evening genes and other combinations of circadian phase gene groups other than the elected combination of a day gene group and a night gene group and amplitude prediction genes other than GLI2, as well as non-elected early afternoon and night genes and combinations thereof other than TGM5 and CIART. Prior to the allowance of the claims, any non-elected subject matter which has not been rejoined with the elected subject matter will be required to be removed from the claims.
Maintained / Modified Improper Markush Grouping Rejection
5. Claims 27, 30, 35 and 38 are rejected on the basis that the claims contain an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush groupings of the amplitude prediction genes of B3GNT2, DUBR, GLI2, LRRC37A3, MOSPD2, PDK1, SLC22A15, TLR5, U2AF1, URB1-AS1, ZNF749 or HERC3 and combinations thereof in claim 27;
the Markush groupings of the early afternoon gene is TGM5, TNS1, RORC, KLRG2, CRY1 or B3GNT2 and combinations and subcombinations thereof in claim 30;
the Markush groupings of the late night gene is NR1D1, CDC25B, ZSCAN31, VWF, TDRKH, DBP, AL391121.1, CNN1, CDCA3, NR1D2, CIART, ZNF296 or U2AF1 and combinations thereof in claim 35; and
the Markush groups of the circadian phase genes of ARNTL, CIART, CRY1, CRY2, DBP, DUBR, GLI2, KRT15, NR1D1, NR1D2, PER1, PER2, PER3, TEF, TGM5, TLR5 or TRIM35 and combinations thereof in claim 38
are improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons:
It is first noted that MPEP 2117 states that “A Markush claim may be rejected under judicially approved "improper Markush grouping" principles when the claim contains an improper grouping of alternatively useable members. A Markush claim contains an "improper Markush grouping" if either: (1) the members of the Markush group do not share a "single structural similarity" or (2) the members do not share a common use. Supplementary Guidelines at 7166 (citing In re Harnisch, 631 F.2d 716, 721-22, 206 USPQ 300, 305 (CCPA 1980)). “ Members of a Markush group share a “single structural similarity” when they belong to the same recognized physical or chemical class or to the same art-recognized class (prong 1) and the members of a Markush group share a common function or use when they are disclosed in the specification or known in the art to be functionally equivalent (prong 2).
The phrase “significant structural element is shared by all of the alternatives” refers to cases where the compounds share a common chemical structure which occupies a large portion of their structures, or in case the compounds have in common only a small portion of their structures, the commonly shared structure constitutes a structurally distinctive portion in view of existing prior art, and the common structure is essential to the common property or activity.
A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein “A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved.” (see MPEP 2117IIA).
Herein, the recited alternative species do not share a single structural similarity, as each gene has a different chemical structure in that it consists of a different nucleotide sequence. The only structural similarity present is that all of the genes comprise nucleotides. The fact that the genes comprise nucleotides per se does not support a conclusion that they have a common single structural similarity because the structure of comprising nucleotides alone is not essential to the asserted common activity of being correlated with an amplitude prediction, early-day expression, late night expression or a circadian phase gene. Accordingly, while the different genes are asserted to have the property of being correlated with a circadian rhythm (phase and/or amplitude), they do not share a substantial structural similarity essential to this activity.
Further, the recited genes do not belong to a chemical or art-recognized class because there is no expectation from the knowledge in the prior art that the genes behave in the same manner and can be substituted for one another with the same intended result achieved. There is no evidence of record to establish that it is clear from their very nature that the recited genes possess the common property of being correlated with a circadian rhythm (phase and/or amplitude).
Following this analysis, the claims are rejected as containing an improper Markush grouping.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use. Response to Remarks:
The response states:
“New claims 27-35 further list specific amplitude prediction genes and specific genes in the various classes of circadian rhythm genes. These amendments obviate the Markush Grouping rejection and the Applicant respectfully requests reconsideration and withdrawal of the rejection..”
These arguments have been fully considered but are not persuasive. New claims 27, 30, 35 and 38 recite improper Markush groupings of genes in the alternative that do not have a common structure essential to the recited use or alternatively do not belong to a chemical or art-recognized class wherein there is an expectation from the knowledge in the prior art that the genes behave in the same manner and can be substituted for one another with the same intended result achieved.
Maintained Claim Rejections - 35 USC § 112(a) – Written Description
6. 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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 of carrying out his invention.
Claims 1, 3, 4, 7, 10- 11, 13-14, 26-27, 30, 35-36, 38-39 and 43 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a Written Description rejection.
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.
For claims drawn to a genus, MPEP § 2163 states:
“The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021) ( "[T]he written description must lead a person of ordinary skill in the art to understand that the inventor possessed the entire scope of the claimed invention. Ariad, 598 F.3d at 1353–54 ('[T]he purpose of the written description requirement is to ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor's contribution to the field of art as described in the patent specification.' (internal quotation marks omitted).").”
MPEP § 2163 goes on to state:
“An adequate written description of a chemical invention also requires a precise definition, such as by structure, formula, chemical name, or physical properties, and not merely a wish or plan for obtaining the chemical invention claimed. See, e.g., Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927, 69 USPQ2d 1886, 1894-95 (Fed. Cir. 2004).”
In the present situation, the claims are drawn to methods for determining a circadian rhythm of a human subject, including the phase and/or amplitude of the circadian rhythm, wherein the methods (with respect to the elected species) require determining the expression level of at least one gene from “a day gene group” and at least one from “a night gene group” and at least one gene that is from “a group of amplitude prediction genes.”
Claims 1, 3, 4, 7, 10, 11, 13, 14, 26, 27, 30, 35, 36, 39 and 43 do not describe both the day gene or night gene in terms of their complete structure or in terms of any other relevant structural characteristics. Claims 1, 3, 4, 7, 10, 11, 13, 14, 26, 30, 35, 36, 38, 39 and 43 do not describe the amplitude prediction gene in terms of its complete structure or in terms of any other relevant structural characteristics.
The specification states “The most critical step of this study was to identify a set of genes within the more than 20,000 genes in our body that are capable of detecting the exact individual body clock phase as well as the amplitude through a single sample.” Thus, the specification acknowledges the significant breadth of protein-encoding genes in the human genome and the criticality of identifying particular genes within the human genome that have the property of being expressed at peak levels at particular time points in a day.
However, the specification discloses a limited number of day genes, night genes and amplitude prediction genes that can be used to determine the circadian rhythm, including the phase and amplitude of the circadian rhythm of a human subject based on their expression level in a hair root sample. In particular, the specification discloses:
Early day genes that are either an early morning gene selected from TEF, AC016727.1, HLF, PER3, PER2, ZBTB42, PER1, POLR2J4, SLC6A6, BORCS6, SPRR2B and CRY2; or a late morning gene selected from PIF1, LRAT, ALDH3A1 and RPL23AP7;
day genes that are either an early afternoon gene selected from TGM5, TNS1, RORC, KLRG2, CRY1, and B3GNT2, or a late afternoon gene selected from MINOS1, ANO7L1, LRRC37A3, PSMG3-AS1, AC011476.3, SPRR2A, KRT15, CAMKMT, GNB1L, SERPINE2, SAP30, and PLEKHF1;
evening genes that are either an early evening gene selected from PGF, ARNTL, ARSJ, NPAS2, SPRY2 and URB1-AS1, or a late evening gene selected from ZNF510, CLEC11A, NDUFAF4, RBM18, ZNF669, DIO3OS, PIBF1, CDPF1, P4HA1 and PRR34-AS1;
and night genes that are either an early night gene selected from RRAD, POLR3GL, SLC22A15, NR1H3, AC048341.2, STXBP4, CD34, MAP3K14, NME7, SCGB2A2, LAYN, C1orf123, RAI14, FBLN7, PDE6B, GOT1, PDSS1, POLR2I and/or C12orf66, and, or a late night gene selected from NR1D1, CDC25B, ZSCAN31, VWF, TDRKH, DBP, AL391121.1, CNN1, CDCA3, NR1D2, CIART, ZNF296 and U2AF1.
The specification teaches the amplitude prediction genes of B3GNT2, DUBR, GLI2, LRRC37A3, MOSPD2, PDK1, SLC22A15, TLR5, U2AF1, URB1-AS1, ZNF749 and HERC3.
Note that U2AF1 is listed as both an amplitude prediction gene and a late night gene.
The specification does not describe any additional morning, day, evening or night group genes or amplitude prediction genes in terms of their complete structure or any other relevant identifying structural characteristics.
It is acknowledged that the specification teaches the general methodology for analyzing gene expression to identify genes whose expression levels are at particular levels at particular times of the day. Note that the specification states “[t]he present invention uses quantitative analysis of RNA expression level of genes also defined as circadian oscillatory genes, also termed as “circadian phase genes”. For each oscillatory circadian phase gene, the peak of expression corresponds to specific times over the 24-hour day and these genes are grouped into early day gene, day gene, evening gene, and night gene groups.” However, possession 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. See MPEP § 2163.
Thereby, a showing of how to potentially identify other circadian phase genes and amplitude prediction genes is not sufficient to establish that Applicant was in possession of the invention as broadly claimed.
Further, the specification does not disclose a clear structure-function relationship between the genes and the functional property of being a circadian phase gene or amplitude phase gene. No structure has been provided which is shared by, e.g., each of the amplitude phase genes or each of the day genes or night genes.
Additionally, Cf. University of Rochester v G.D. Searle & Co., Inc., Monsanto Company, Pharmacia Corporation, and Pfizer Inc., No. 03-1304, 2004 WL 260813 (Fed. Cir., Feb. 13, 2004) held that:
Regardless whether a compound is claimed per se or a method is claimed that entails the use of the compound, the inventor cannot lay claim to that subject matter unless he can provide a description of the compound sufficient to distinguish infringing compounds from non-infringing compounds, or infringing methods from non-infringing methods.
Also, as noted in Vas-Cath Inc. v. Mahurkar (19 USPQ2d 1111, CAFC 1991), the Federal Circuit concluded that:
"...applicant must also convey, with reasonable clarity to those skilled in art, that applicant, as of filing date sought, was in possession of invention, with invention being, for purposes of "written description" inquiry, whatever is presently claimed."
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. 112 is severable from its enablement provision.
With respect to the present invention, there is no record or description which would demonstrate conception of a representative number of amplitude prediction genes or day group genes or night group genes (or with respect to the non-elected species morning group genes or evening group genes) within the broadly claimed genus. Therefore, the claims fail to meet the written description requirement because the claims encompass a potentially significantly large genus of amplitude prediction genes, day group genes, and night group genes (and morning group genes and evening group genes with respect to the non-elected species) which are not described in the specification. Response to Remarks:
The response cites MPEP 2163(II)(3)(ii) as stating:
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus. (emphasis added).
The response argues:
The Applicant submits that these requirements are met due to the disclosure of "relevant, identifying characteristics" in the specification, in particular by showing "physical and/or chemical properties" of the members in each group (synchronized circadian expression), which may be considered as clear "functional characteristics coupled with a correlation between function and structure". In addition to the fact that the various classes of genes can readily be determined by a person having ordinary skill in the art, each gene will have a corresponding regulatory region (a structural feature) that enables synchronous circadian expression within any given time window. Accordingly, the Applicant respectfully requests reconsideration and withdrawal of the rejection.
These arguments have been fully considered but are not persuasive. Applicant states that the genes all have a regulatory region as a structural feature that enables synchronous circadian expression. However, Applicant has not identified any particular regulatory sequence that is shared by all day genes, and particularly all early afternoon genes, or by all night genes, and particularly all late night genes; or by the withdrawn species of early-day genes and evening genes. Applicant also does not point to any evidence to support this assertion. Nor has Applicant established that all amplitude prediction genes share a common regulatory region.
Regarding the argument that the classes of genes can be “readily determined by a person having ordinary skill in the art, teaching how to determine whether a gene has a particular function or does not have that function (i.e., is or is not expressed at a peak level at a particular time of day) is not sufficient to establish that Applicant was in possession of the claimed invention, particularly in unpredictable arts, such as methods of identifying novel genes correlated with a circadian rhythm.
See MPEP § 2163 which states:
“An adequate written description of a chemical invention also requires a precise definition, such as by structure, formula, chemical name, or physical properties, and not merely a wish or plan for obtaining the chemical invention claimed. See, e.g., Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927, 69 USPQ2d 1886, 1894-95 (Fed. Cir. 2004).”
Maintained Claim Rejections - 35 USC § 112(a) - Enablement
7. Claims 1, 3, 4, 7, 10- 11, 13-14, 26-27, 30, 35-36, 38-39 and 43 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The following factors have been considered in formulating this rejection (In re Wands, 858F.2d 731, 8 USPQ2d 1400 (Fed. Cir. 1988): the breadth of the claims, the nature of the invention, the state of the prior art, the relative skill of those in the art, the predictability or unpredictability of the art, the amount of direction or guidance presented, the presence or absence of working examples of the invention and the quantity of experimentation necessary.
The claims are drawn to methods for determining a circadian rhythm of a human subject, comprising: a) obtaining a single sample from a subject that comprises RNA, wherein the sample is a hair root; b) quantifying an RNA expression level of multiple genes in said sample, said multiple genes comprising at least one gene selected from a day gene group and a night gene group (with respect to the elected invention) and at least one gene selected from a group of amplitude prediction genes; and c) determining the circadian rhythm based on the expression levels quantified in step b) from the single sample.
With respect to the elected species, claim 30 defines the day gene as TGM5 and claim 35 defines the night gene as CIART claim 27 defines the amplitude gene as GLI2 and claim 38 is limited to the combination of the TGM5 and CIART genes. The remaining claims do not describe the day gene or night gene or amplitude gene in terms of their complete structure or in terms of any other relevant structural characteristics.
The specification teaches that:
“[t] he present invention uses quantitative analysis of RNA expression level of genes also defined as circadian oscillatory genes, also termed as ‘circadian phase genes’. For each oscillatory circadian phase gene, the peak of expression corresponds to specific times over the 24-hour day and these genes are grouped into early day gene, day gene, evening gene, and night gene groups.”
The specification discloses a limited number of genes characterized therein as day genes, night genes and amplitude prediction genes that can be used to determine the circadian rhythm, including the phase and amplitude of the circadian rhythm of a human subject based on their expression level in a hair root sample. In particular, the specification discloses:
Early day genes that are either an early morning gene selected from TEF, AC016727.1, HLF, PER3, PER2, ZBTB42, PER1, POLR2J4, SLC6A6, BORCS6, SPRR2B and CRY2; or a late morning gene selected from PIF1, LRAT, ALDH3A1 and RPL23AP7;
day genes that are either an early afternoon gene selected from TGM5, TNS1, RORC, KLRG2, CRY1, and B3GNT2, or a late afternoon gene selected from MINOS1, ANO7L1, LRRC37A3, PSMG3-AS1, AC011476.3, SPRR2A, KRT15, CAMKMT, GNB1L, SERPINE2, SAP30, and PLEKHF1;
evening genes that are either an early evening gene selected from PGF, ARNTL, ARSJ, NPAS2, SPRY2 and URB1-AS1, or a late evening gene selected from ZNF510, CLEC11A, NDUFAF4, RBM18, ZNF669, DIO3OS, PIBF1, CDPF1, P4HA1 and PRR34-AS1;
and night genes that are either an early night gene selected from RRAD, POLR3GL, SLC22A15, NR1H3, AC048341.2, STXBP4, CD34, MAP3K14, NME7, SCGB2A2, LAYN, C1orf123, RAI14, FBLN7, PDE6B, GOT1, PDSS1, POLR2I and/or C12orf66, and, or a late night gene selected from NR1D1, CDC25B, ZSCAN31, VWF, TDRKH, DBP, AL391121.1, CNN1, CDCA3, NR1D2, CIART, ZNF296 and U2AF1.
The specification teaches the amplitude prediction genes of B3GNT2, DUBR, GLI2, LRRC37A3, MOSPD2, PDK1, SLC22A15, TLR5, U2AF1, URB1-AS1, ZNF749 and HERC3.
Note that U2AF1 is listed as both an amplitude prediction gene and a late night gene.
The specification does not describe any additional morning, day, evening or night group genes or amplitude prediction genes in terms of their complete structure or any other relevant identifying characteristics.
It is also stated that:
“The inventors have developed a hair test through an extensive study. The plan of the study is shown in FIG. 1 . The most critical step of this study was to identify a set of genes within the more than 20,000 genes in our body that are capable of detecting the exact individual body clock phase as well as the amplitude through a single sample. In the validation studies, we were able to demonstrate that our algorithm, which combines the gene activity values of the identified group of genes, has similar accuracy in predicting an individual's chronotype as the current gold standard method, namely the burdensome dim light melatonin onset (DLMO) test.”
Thus, the specification teaches that extensive experimentation was required to identify the group of genes which are denoted therein as being circadian phase genes and amplitude prediction genes.
This teaching also indicates that the disclosed set of each of the morning genes, day genes, evening genes and night genes in combination (i.e., the set of 90 genes used in Example 1 can be used to determine circadian phase and the set of amplitude prediction genes can be used to determine the amplitude of the circadian rhythm.
For example, the specification states:
“Amplitude of a rhythm was estimated using RNA expression levels of 90 genes from a single sample (instead of measuring a time series) obtained from 13 healthy subjects. The amplitude was defined for example as: (i) number of genes significantly rhythmic with a given p-values; (ii) number of genes with a minimal amplitude; (iii) mean amplitude of the top5 or top10 rhythmic genes. (FIG. 6 ).”
It is further stated that:
“Amplitude prediction genes are, in embodiments, typically not rhythmic, but vary in expression strength. Some amplitude prediction genes may have a low expression level when the amplitude is weak. Some amplitude prediction genes may have a low expression level when the amplitude is strong. Some amplitude prediction genes may have a high expression level when the amplitude is weak. Some amplitude prediction genes may have a high expression level when the amplitude is strong.”
The specification does not establish that the expression level of any day gene and any night gene, together with any amplitude prediction gene can be used to determine the phase and/or amplitude of a human subject’s circadian rhythm.
Nor does the specification establish that expression of the night gene of CIART, the day gene of TGM5 and the amplitude prediction gene of GLI2 can be used alone to determine a human subject’s circadian rhythm.
The specification teaches that a special algorithm is used to calculate the circadian phase and amplitude. For instance, the specification (para [0314] states:
“The algorithm then calculates the circadian phase and amplitude for determining the circadian rhythm/body clock (chronotype) of the subject. To identify circadian phase genes and amplitude prediction genes (Example 1) we applied the LASSO method of Hughey et al. (2016). Central to the ZeitZeiger method is a supervised sparse PCA that reduces the variation associated with the periodic variable in the training set (in our case: internal time) to a low-dimensional subspace (two sparse principal components: SPC1, SPC2) of the hair root transcriptome. The LASSO and PLS algorithm were also applied. RNA expression levels of the subject for the circadian phase genes and amplitude prediction genes identified, were applied to the biomathematical model ZeitZeiger and/or LASSO and/or PLS being trained with reference data set as obtained in Example 1.”
The specification does not provide sufficient guidance as to how to use the expression levels of the day group gene, night group gene and amplitude prediction gene in any manner – e.g., by adding the expression levels – to determine the phase and amplitude of a subject’s circadian rhythm.
It is noted that the claims as amended recite “determining the circadian rhythm using an algorithm comprising a machine learning prediction model trained on RNA expression levels of multiple circadian rhythmically expressed genes measured over time, to predict a periodic output variable corresponding to circadian rhythm from the expression levels quantified in step b from said single sample.” However, the claims do not specify the identity of the multiple circadian rhythmically expressed genes or the source of the RNA expression levels. The teachings in the specification (Table 1) establish that there is a high level of variability between the expression levels of the circadian phase genes between subjects. Further, Wu et al (Genome Medicine. 2020. 12:73; cited in the IDS) teaches that there is substantial variability in the level of peak expression of circadian genes in different subjects (see Figure 1).
The teachings in the specification indicate that not all methods or models can be used to effectively analyze the gene expression data as indicative of a subject’s circadian rhythm. For instance, the specification states:
“The seven samples with low prediction accuracy in ZeitZeiger were predicted much better with the LASSO models (MAE: 2.4 hours).
Thus, LASSO models seem are better suited to predict such kind of samples. We suspected that they were derived from subjects with low circadian amplitudes.”
Additionally, Example 5 (para [0323]) of the specification states:
“A practical application of the hair root test was used to predict the phase of the internal circadian rhythm, exemplified by the ability to quantify jet lag after traveling across multiple time zones. A traveler (Berlin to Florida on day 1 (May 14, 2022) and return five days later (May 19, 2022)) collected a hair root sample at approximately the same (absolute) time each day (i.e., 12 noon in Berlin and 6 a.m. in Florida), which were stored in a stabilizing solution until return and then processed as described so that a DLMO value could be predicted for each day. Note that for this individual, the internal phase (expressed as predicted DLMO) changes abruptly (May 16, 2022) when traveling west, changes more slowly and gradually when traveling east, and returns approximately to the initial measured phase before the trip, after about 8 days after returning to Berlin. Results are presented in FIG. 13.”
However, in Example 5, multiple samples from the subject were obtained – i.e., on different days from 11-05-2022 to 01-06-2022. Example 5 does not establish that the circadian rhythm of the subject can be determined using a single sample obtained from the subject, as required by the present claims, and comparing the expression level in this sample with the RNA expression level of unspecified multiple circadian rhythmically expressed genes measured over time obtained from any unspecified source.
There is a high level of unpredictability in the art in determining if a gene is expressed at a peak level at a particular time point as indicative that the gene is a day group gene or a night group gene or an amplitude prediction gene. There is no common structure disclosed in the specification between genes that have the property of being a “day group gene” or a “night group gene” or an “amplitude prediction gene” so that one could reliably predict which genes in the human genome would meet the criteria of a being a “day group gene” or a “night group gene” or an “amplitude prediction gene.” Thereby, it is highly unpredictable as to what would be the identity of additional day group genes, night group genes and amplitude prediction genes. It is also highly unpredictable as to whether the expression level of a single day group gene in combination with a single night group gene and a single amplitude prediction gene can be used to determine the phase and/or amplitude of a circadian rhythm since the specification exemplifies only methods wherein the combination of the 90 disclosed genes are used together with the amplitude prediction genes in the disclosed “LASSO models” to predict the phase and amplitude of a human subject’s circadian rhythm.
Extensive experimentation would be required to practice the broadly claimed invention given the high level of unpredictability in the art and the significant breadth of the claims which cover methods that determine the amplitude and/or phase a circadian rhythm by detecting any two genes from an unspecified group of day genes and an unspecified group of night genes, as well as an unspecified group of amplitude prediction genes, as well as methods that determine the amplitude and/or phase a circadian rhythm by detecting only the CIART, TGM5 and GLI2 genes in a single hair follicle sample from a subject, as well as determining that a subject has a circadian rhythm disorder selected from an advanced or delayed sleep-wake phase disorder, a non-24-hour sleep-wake rhythm disorder, a shift work disorder, and/or a jet lag disorder.
Case law has established that “(t)o be enabling, the specification of a patent must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation.” In re Wright 990 F.2d 1557, 1561. In re Fisher, 427 F.2d 833, 839, 166 USPQ 18, 24 (CCPA 1970) it was determined that “(t)he scope of the claims must bear a reasonable correlation to the scope of enablement provided by the specification to persons of ordinary skill in the art.” The amount of guidance needed to enable the invention is related to the amount of knowledge in the art as well as the predictability in the art. Further, the Court in Genetech Inc. v Novo Nordisk 42 USPQ2d 1001 held that “(I)t is the specification, not the knowledge of one skilled in the art that must supply the novel aspects of the invention in order to constitute adequate enablement."
Additionally, as set forth in Rasmusson v. SmithKline Beecham Co., 75 USPQ2d 1297, 1302 (CAFC 2005), enablement cannot be established unless one skilled in the art "would accept without question" an Applicant's statements regarding an invention, particularly in the absence of evidence regarding the effect of a claimed invention.
Specifically:
"As we have explained, we have required a greater measure of proof, and for good reason. If mere plausibility were the test for enablement under section 112, applicants could obtain patent rights to "inventions consisting of little more than respectable guesses as to the likelihood of their success. When one of the guesses later proved true, the "inventor" would be rewarded the spoils instead of the party who demonstrated that the method actually worked. That scenario is not consistent with the statutory requirement that the inventor enable an invention rather than merely proposing an unproved hypothesis."
Herein, although the level of skill in the art is high, given the lack of disclosure in the specification and in the prior art and the unpredictability of the art, it would require undue experimentation for one of skill in the art to make and use the invention as broadly claimed.
Response to remarks:
The response states:
“Applicant submits that each of the gene groups recited in claim 1 has been described with a sufficient number of genes in the specification, so that a skilled person can reliably determine the gene expression levels and use these gene expression levels to determine the circadian rhythm of the subject. Reference is made to pages 20-24. The specification not only describes the identification of such genes, but it also discloses up to 19 species (e.g., the early night genes) in each group.
This argument has been fully considered but is not persuasive. Applicant has not established that the 6 early afternoon genes disclosed at para [0140] of the specification is representative of the genus of any gene with peak expression between 12pm and 3pm population of human subjects; or that the 13 late night genes disclosed at para [0138] is representative of the genus of any gene with a peak expression between 12 am and 3 am in the population of human subjects; or that the 12 amplitude prediction genes disclosed at para [0152] of the specification is representative of the genus of any gene whose expression level correlates with the amplitude of the circadian rhythm of the population of human subjects.
The response argues that it does not require undue effort to identify additional circadian rhythm genes and amplitude genes because methods of obtaining samples, isolating RNA from the samples and quantifying RNA levels were well known to a skilled person.
These arguments have been fully considered but are not persuasive. Teaching methods for identifying gene expression is not sufficient to establish that Applicant has enabled the invention as broadly claimed. First, it is again noted that extensive experimentation is required to identify a representative number of additional genes which meet the requirements of peak gene expression times in each of the recited circadian gene groups and amplitude prediction genes required by the claims. Secondly, it has not been established that methods that determine the expression level of only one day gene, including one early afternoon gene, and one night gene, including one late night gene, can be used together with any single amplitude prediction gene to determine a subject’s circadian rhythm.
Further, the teachings in the specification at Example 1 highlight the high level of experimentation and unpredictability in the art in that the specification states:
“The most critical step of this study was to identify a set of genes within the more than 20,000 genes in our body that are capable of detecting the exact individual body clock phase as well as the amplitude through a single sample. In the validation studies, we were able to demonstrate that our algorithm, which combines the gene activity values of the identified group of genes, has similar accuracy in predicting an individual's chronotype as the current gold standard method, namely the burdensome dim light melatonin onset (DLMO) test.”
Thus, the specification does not teach that it is routine to identify genes whose expression is correlated with circadian phases and that any algorithm can be used to predict a human subject’s circadian rhythm based on such gene expression levels.
The response requests reconsideration of the claims in view of the amendments to the claims and in view of the teachings of Maier et al (bioRxiv 2025 reference). It is stated that “Three different algorithms/models were trained on the data from the HairTime study, showing that different machine learning algorithms are capable of generating effective models to determine circadian rhythm. Because multiple algorithms are proven to be effective, it appears that further limitation of the algorithm as recited in claim 1, due to an alleged lack of enablement, would be undue.” Applicant states that the Maier reference teaches that the measurement of 90 genes was not necessary to determine a subject’s circadian rhythm. It is further stated that “The specific genes recited in dependent claims 27-35, 37, 38, 40, 41, 42, 44 and 45 closely reflect the data presented in Maier (Fig. 1C, 2E, Results, page 6, 8, and Discussion, page 12), and represent non-limiting, clearly enabled embodiments of the invention.”
These arguments have been fully considered but are not persuasive. It is first noted that the Maier et al reference (bioRxiv. 13 March 2025, 21 pages, available via URL: < biorxiv.org/content/10.1101/2025.03.07.641864v1.full.pdf>) is co-authored by the present inventor. As such, the information therein is not objective in nature. No affidavit or declaration has been provided which includes the information disclosed in the Maier et al reference. The reason for requiring evidence in declaration or affidavit form is to obtain the assurances that any statements or representations made are correct, as provided by 35 U.S.C. 25 and 18 U.S.C. 1001.
Secondly, Maier teaches using a combination of 17 circadian phase genes to determine a human subject’s circadian rhythm - i.e., the combination of each of the ARNTL, CIART, CRY1, CRY2, DPB, DUBR, GLI2, KRT15, NR1D1, NR1D2, PER1, PER2, PER3, IEF, TGM5, TLR5 and TRIM35 genes (see Figure 1C). For instance, Maier (p. 6) states:
“To identify the most effective genes for predicting internal time (DLMO) from a single sample, we applied three machine learning methods—ZeitZeiger, LASSO, and partial least squares (PLS) -combined with a leave-one-out cross-validation approach (see Methods for details). For each method, we selected two models that achieved optimal prediction accuracy while minimizing the number of required genes. To ensure a balanced estimate and mitigate potential biases, chronotype predictions were averaged across the selected ZeitZeiger, LASSO, and partial least squares models. In total, 17 genes were identified for chronotype prediction (Figure 1C, Supplementary Table 4).
While the prediction accuracy was remarkably high (median absolute deviation [MdAE] from saliva DLMO of approximately one hour, Figure 1D), nearly 20% of samples in the training dataset exhibited a prediction deviation of more than two hours. Interestingly, in these samples, the three prediction models frequently did not agree.”
The teachings of Maier (p. 6) also highlight the unpredictability in the art in that Maier states:
“the prediction models exhibited considerable inconsistencies when using samples collected between approximately four hours before and eight hours after DLMO (i.e., during the evening and nighttime), and were particularly inaccurate when preformed on nighttime samples (Figure 1F). Moreover, we observed substantial interindividual differences in mean prediction accuracy, which correlated significantly with the mean standard deviation of the prediction models across all samples from a given individual (Figure 1G). This provides further support for the hypothesis that discrepancies between prediction models may serve as an indicator of accuracy.”
Regarding the amplitude prediction genes, Maier (p. 8) states:
“A model using six genes (DUBR, GLI2, MOSPD2, PDK1, ZNF296, and ZNF749) was identified for amplitude prediction. The predicted amplitudes based on these genes showed a significant correlation with measured amplitude values, providing confidence in their applicability for predicting amplitudes in the 35 HairVali sample (Figure 2F).”
It is further stated (p. 13):
“To predict this amplitude score from a single timepoint, we identified six genes with minimal variation in expression throughout the day and trained a model to estimate amplitude based on their absolute expression levels in the morning. As expected, in the validation study, the predicted amplitude score correlated with the accuracy of chronotype prediction.”
At p. 14, Maier states:
“The assay relies on fewer than 20 transcript biomarkers and combines three models to predict chronotype, with the agreement between models serving as an indicator of accuracy. However, it is important to note that the models were trained on
a relatively small cohort, which may limit their generalizability. Additionally, the association between lower amplitudes and higher prediction error suggests that future studies should evaluate HairTime’s accuracy in individuals with mistimed sleep in controlled settings (e.g., manipulated rest-activity rhythms). Further testing in men and women with diverse genetic backgrounds, as well as in relevant patient groups, is warranted.”
Thus, the “HairTi