DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant's election with traverse of Group I (claims 1-12, 27-29, and 32-35) in the reply filed on 4/30/2026 is acknowledged. The traversal is on the ground(s) that Salter merely teaches the broad concept of chromosome interactions but does not describe the interactions represented by the probes of Tables 1 and 3 (and Table 7 of Group II) but teaches specifically looking at chromosomal interactions at a particular locus. While this argument is found persuasive, the art still lacks unity of invention given that a chromosome interaction shared between Tables 1/3 and Table 7 is known and used in the art for determination of immune health. It is noted here (and in a 112b rejection of claim 1 below) that “determining the immune health of an individual” is being interpreted as any condition or disease that alters the immune system. Salter et al. (eBioMedicine, 2018), teaches using an EpiSwitch array to assess chromosomal conformational changes in healthy vs diseased patient samples to aid in diagnosis of ALS (Abstract-Methods). ALS, an autoimmune condition, is thus an alteration of the immune health of an individual and determination of ALS is a determination of the immune health of the individual. Salter et al. teaches that one of the top 153 markers is a detected chromosomal interaction in IQGAP2 (Table 5). This is a chromosomal interaction that is common between Tables 1/3 (Claim 1) and Table 7 (claim 15), and is used to determine the immune health of an individual, as taught by Salter et al.
The requirement is still deemed proper and is therefore made FINAL.
Applicant’s election of the following species is in the reply filed on 4/30/2026 is also acknowledged:
Claim 1: 13th chromosome interaction (probe SEQ ID NO: 13) from table 1.
Claim 2: 13th chromosome interaction (probe SEQ ID NO: 13), 14th chromosome interaction (probe SEQ ID NO: 14), and 16th chromosome interaction (probe SEQ ID NO: 16) from table 1.
Claim 3: 13th chromosome interaction (probe SEQ ID NO: 13), 14th chromosome interaction (probe SEQ ID NO: 14), and 16th chromosome interaction (probe SEQ ID NO: 16), 20th chromosome interaction (probe SEQ ID NO: 20), 34th chromosome interaction (probe SEQ ID NO: 34), 35th chromosome interaction (probe SEQ ID NO:35), 37th chromosome interaction (probe SEQ ID NO: 37), 40th chromosome interaction (probe SEQ ID NO:40), and 45th chromosome interaction (probe SEQ ID NO: 45) from table 1.
Claim 4: The first three chromosome interactions from table 2a, corresponding to the 13th, 14th, and 16th chromosome interactions from table 1.
Claim 28: 13th chromosome interaction (probe SEQ ID NO: 13) from table 8 (same as the 13th chromosome interaction from table 1).
Claim 29: 1st chromosome interaction from table 11a (probe SEQ ID NO: 1908).
Claim 32: The first 5 chromosome interactions from table 9. These are the same five chromosome interactions as represented in probe SEQ ID NOs: 13, 14, 16, 20, and 34 from table 1.
Claim 33: 1st chromosome interaction from table 12a (probe SEQ ID NO: 736).
Claim 34: The agent abatacept.
Claims 1-12 and 15-36 are pending.
Claims 15-26, 30-31, and 36 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 4/30/2026.
Claims 1-12, 27-29, and 32-35 are being examined on the merits.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement (see, for example, page 14, ln 17-18 and page 24, ln 28-29). 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Title of the Invention
The title of the invention is not descriptive. A new title is required that is clearly indicative of the invention to which the claims are directed.
Specification
The use of the terms “FAM”, “Yakima Yellow” (pg 35), “Texas Red”, “BHQ1”, “BHQ2” (pg 36), which are trade names or marks used in commerce, have been noted in this application. These terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM, or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The examples above are not an exhaustive list of unmarked trade names or marks used in commerce throughout the specification. Please carefully read through and properly notate each instance.
Claim Objections
Claims 5, 9, 29, 34, and 35 are objected to because of the following informalities:
Claim 5 reads “detecting the presence or absence of distal regions” and should read “by detecting the presence or absence of distal regions” to maintain consistent language throughout the claim.
Claim 9 reads “the method is carried out on individual that has been preselected” and should read “the method is carried out on an individual that has been preselected”.
Claim 29 reads “A method according to claim 1 comprising determining” and should read “A method according to claim 1 further comprising determining” to make it clear that these chromosomal interactions are determined in addition to the ones determined in claim 1.
Claim 34 reads “administering to any individual identified” and should read “administering to [[any]]the individual identified” to make it clear that this is the same individual from the previous step that was identified as susceptible or not susceptible.
Claim 35 reads “determining the immune health of an individual by the method of claim 1, -administering to the individual an agent which”. The “-administering to the individual an agent which” should either be on its own line or should have the “-“ removed.
Appropriate correction is required.
Improper Markush Group
Claims 1-12, 27-29, and 32-35 are rejected on the basis that it contains 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 grouping of the chromosomal interactions as represented by the probes of Tables 1 or 3 (claims 1-4, 7-8), Tables 8-17 (claim 28), Tables 8-11 and 14-17 (claim 29), Tables 9 and 11 (claim 32), and Tables 12-13 (claim 33) and combinations and subcombinations thereof for each claim, 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 706.03(y) 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 "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 2117(II)).
Herein, the recited alternative species do not share a single structural similarity, as each chromosome interaction occurs at a different location in the genome and involves different nucleotide sequences. Thus, each chromosome interaction has a different chemical structure in that It consists of a different nucleotide sequence. The primers and probes used to detect the chromosome interactions also have a different chemical structure in that they consist of different nucleotide sequences. The only structural similarity present is that all of the chromosome interactions (and probes and primers) comprise nucleotides. The fact that the chromosome interactions 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 immune health. Accordingly, while the different chromosome interactions are asserted to have the property of being correlated with immune, they do not share a substantial structural similarity essential to this activity.
Further, the recited probes and 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 chromosome interactions 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 chromosome interactions possess the common property of being indicative of immune health.
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.
Claim Rejections - 35 USC § 112a - Enablement
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 1-12, 27-29, and 32-35 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.
Nature of the invention and breadth of the claims
The claims broadly encompass determining presence or absence of one or more chromosome interactions represented by probes in Tables 1 or 3 to determine the immune health of an individual. The specification indicates that Table 1 is prognostic for immune overreaction (pg 12) while Table 3 is prognostic for normal immune reaction (pg 12). No specific definition of “immune health” is provided in the specification, but it is mentioned that immune health is determined “typically relevant to diagnosis or prognosis” (page 32, ln 14-15). Given the state of the art and the breadth of the term “immune health”, this term is being interpreted as any health status of the individual (disease or no disease). Moreover, “an individual” can theoretically be any type of organism, given the lack of a limiting definition in the specification as to the type of individual assessed. The nature of the claims broadly encompasses either the presence or absence of a single chromosome interaction (or more) represented by a probe in either table related to different immune responses in any type of organism by any method.
Direction provided by the specification and working example
The specification provides a particular example in which samples from subjects with confirmed COVID-19 diagnosis (either mild or severe) were applied to an EpiSwitch Microarray platform to identify potential markers that can delimit between the two subgroups (pg 43-45). The platform used for this initial assessment is based on the whole human genome, specifically GRCh38 (pg 45). The particular probes used on this array are not disclosed. The markers identified as relevant for distinction between the two subgroups are listed in Tables 1-4, indicating that the “immune health” for claim 1 really only applies to the particular distinction between COVID-19 immune response subgroups of “severe/ICU” and “mild” (pg 46-47). Furthermore, the specification indicates that more than one chromosome interaction is used to assess the subgroup and determine adequate treatments (Table 6). The claims, in light of the specification, thus rely on a strong association between even a single chromosomal interaction and the immune response of an individual to COVID-19 infection specifically in a human.
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 detection chromosomal interaction is high, the unpredictability in associating presence or absence of said chromosomal interactions with any particular immune health is higher. Such unpredictability is demonstrated by the prior art.
For example, an interaction at the locus of CD40 (listed in Table 1 of the instant application as indicative of an immune overreaction in the context of COVID-19) is also a chromosomal interaction potentially associated with and screened in relation to inadequate response to methotrexate in early rheumatoid arthritis (Table S5, Carini et al., 2018) and with diagnosis of amyotrophic lateral sclerosis (Table 4, Salter et al., 2018). Another example is the gene IQGAP2 (listed in Table 1 of the instant application as indicative of an immune overreaction in the context of COVID-19) and associated with ALS diagnosis in Salter et al., 2018 (Tables 5 and 9).
Quantity of experimentation required
A large and prohibitive amount of experimentation would be required to make and use the claimed invention. Within the scope of the claimed invention, one would have to determine the presence or absence of chromosomal interactions “represented by” probes and associate said presence or absence with any type of disease (given the breadth of “immune health”) in any type of organism (given the lack of the definition of “individual”). Such determinations would require large case:control studies and subsequent validation of any associations. Even if such experimentation were performed, it is unpredictable whether or not any associations beyond those of the instant specification would be identified.
Conclusion
After consideration of the teaching of the specification and the specific working examples, considering the breadth of the claims, and the unpredictability in the art, it is the conclusion that an undue and unreasonable amount of experimentation would be required to make and use the invention that is instantly claimed.
Claim Rejections - 35 USC § 112b - Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-12, 27-29, and 32-35 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.
Claim 1 recites the limitation "the probes" in line 2-3. There is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites “determining the immune health of an individual, comprising determining the presence or absence of one or more chromosome interactions represented by the probes shown in Table 1 or 3, to thereby determine the immune health of the individual”. Several points of this stated methodology are unclear. First, it is unclear what is meant by the “immune health” of an individual. No specific definition of “immune health” is provided in the specification, but it is mentioned that immune health is determined “typically relevant to diagnosis or prognosis” (page 32, ln 14-15). Given the state of the art and the breadth of the term “immune health”, this term is being interpreted as any health status of the individual (disease or no disease). It is additionally unclear how a probe can represent the presence or absence of chromosome interactions. No methodological steps are provided which would indicate how a sequence provided by a probe in either table would be indicative of chromosomal interactions present in an individual.
Claims 3-12, 27-29, and 32-35 depend from claim 1, inherit this deficiency, and are rejected on the same basis.
Claims 1-4, 7-8, 28-29, and 32-34 are rejected over the recitation of Tables from the specification as elements of the claims, for example “one or more chromosome interactions represented by the probes shown in Table 1 or 3” as recited in claim 1. MPEP 2173.05(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) (citations omitted).
In the instant case, claims may be amended to recited elements consistent with the election, for example in claim 1: 60-mer probe SEQ ID NO: 26; AGL.
Claim 5 recites the limitation “said typing” in line 8. There is insufficient antecedent basis for this limitation in the claim. While the claim does say “wherein the chromosome interactions are typed”, there is no methodological step indicating what “said typing” would consist of. Claim 5 also recites the limitation "the chromosome regions" in line 11. There is insufficient antecedent basis for this limitation in the claim.
Claims 7 and 8 depend from claim 5, inherit these deficiencies, and are rejected on the same basis.
Claim 6 recites the limitation "said detecting" in line 1. There is insufficient antecedent basis for this limitation in the claim. No detecting step is recited in claim 1, from which claim 6 depends.
Claim 7 recites the limitation "said ligated DNA" in line 1. There is insufficient antecedent basis for this limitation in the claim. Claim 5, from which claim 7 depends, defines “a ligated nucleic acid” but does not specify that this is DNA (rather than, say, RNA).
Claim 9 recites various intended uses of the method of claim 1 (“the method is carried out to/on….”). However, there are no additional practical steps that are supplied that would indicate practical usage of said method. Therefore, without the additional practical steps, it is unclear how the intended uses are achieved. Additionally, regarding claim 9, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 11: Regarding claim 11, the phrase "for example" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention (see lines 4, 5, 7, and 12). See MPEP § 2173.05(d).
Claim 12 recites an intended use of the method of claim 1 (“which is carried out to determine prognosis to”). However, there are no additional practical steps that are supplied that would indicate practical usage of said method. Therefore, without the additional practical steps, it is unclear how the intended uses are achieved.
Claim 27 recites the limitations "the typing" in line 1, "the ligated product" in line 2-3, "the ligation site" in line 3, "the chromosome regions" in line 5, and "said ligated product" in line 7. There is insufficient antecedent basis for these limitations in the claim. Additionally, regarding claim 27, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 27 contains the trademarks/trade names “Texas Red”, “HEX”, and “FAM”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a fluorophore and, accordingly, the identification/description is indefinite.
Claim 28 recites the limitation "the probes" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 29: Regarding claim 29, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 33, which depends from claim 1, recites “a method according to claim 1 which is carried out to detect sepsis status of the individual by detecting the presence or absence of any of the chromosome interactions shown in Tables 12 or 13”. It is unclear if immune health is still be determined in addition to also detecting sepsis in this claim and how the two relate. Is the addition of another chromosome interaction (the 13th chromosome interaction from table 1 (probe SEQ ID NO: 13) and the 1st chromosome interaction from table 12a (probe SEQ ID NO: 736) being used together to detect sepsis, or is just SEQ ID NO: 13 used to determine immune health and just SEQ ID NO: 736 used to detect sepsis? Additionally, this claim does not indicate whether the presence or absence of said chromosome interaction indicates sepsis, so it is unclear how this detection is happening.
Claim 34 recites the limitation “identifying whether an individual is susceptible to an immune overreaction or immune side effect by the method of claim 1”. However, claim 1 is merely directed to determining the immune health of an individual by determining the presence or absence of chromosome interactions represented by probes. It is unclear how this method is being used to determine if an individual is susceptible to an immune overreaction or immune side effect. Is it the absence of the elected chromosome interaction in claim 1 or the presence of said chromosome interaction? Which option does the presence or absence of the interaction indicate? Clarification is required. Additionally, claim 34 is directed to “a method…for treatment” and recites the limitation “identifying whether an individual is susceptible”, meaning that it could be that the individual is identified as NOT being susceptible and therefore would not receive treatment. Therefore, the scope of the claim is indefinite in that it is a method for treatment but does not require that treatment be administered.
Claim 35 reads: A method according to claim 1 which:
- controls or modulates the immune system; or
- which prevents or treats an aberrant immune response; or
- prevents or treats an overreaction of an immune response;
comprising determining the immune health of an individual by the method of claim 1, - administering to the individual an agent which
(i) controls or modulates the immune system, or
(ii) which prevents or treats an aberrant immune response, or
(iii) prevents or treats an overreaction of an immune response.
The way this claim is written makes it incredibly difficult to determine what the metes and bounds of said claim are. The scope of the claim encompasses, for example, a method of according to claim 1 which prevents or treats an overreaction of an immune response comprising determining the immune health of an individual by the method of claim 1, - administering to the individual an agent which controls or modulates the immune system. However, this modulation of the immune system could be any sort of modulation, it could decrease or increase the immune response, abolish the immune system, etc. this would not “prevent or treat an overreaction of an immune response”. Additionally, claim 35 encompasses administering an agent to an individual regardless of the determined immune health. It is unclear how this would accomplish any of the claimed objectives other than modulating the immune system. Therefore, the claim is indefinite and further clarification is required.
Claim Rejections - 35 USC § 112d – Failure to Further Limit
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 9 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. As noted in the 112b rejection above, claim 9 recites various intended uses of the method of claim 1 (“the method is carried out to/on….”). However, there are no additional practical steps that are supplied that would indicate practical usage of said method. The presentation of intended uses without practical method steps to employ said method fails to further limit claim 1. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-12, 27-29, and 32-35 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas (e.g.: mental processes) and a natural phenomenon without significantly more.
The claim(s) recite(s) methods of determining the presence or absence of chromosome interactions and determining the immune health of an individual (claim 1) with practical steps of in vitro crosslinking of epigenetic chromosomal interactions, cleaving the cross-linked DNA, ligating the cross-linked cleaved DNA ends to form ligated DNA (claim 6), and detection of the ligated DNA via probe or PCR (claim 8) or via qPCR (claim 27). The claims are thus directed to the assessment of collected data, which is an abstract idea that is a mental process (e.g.: MPEP 2106.04(a (2)(III)(A)); it is the observation and evaluation of information to reach a judgment or conclusion, as set forth in claim 1. Where the evaluation of data to reach a conclusion is based in the asserted correlation between chromosome interaction and the immune health of an individual, such an association is an accepted part of how a biological organism functions (i.e.: genotpype:phenotype relationships), and as such this element of the claims is a natural phenomenon (e.g.: MPEP 2106.04(b)(I)). This judicial exception is not integrated into a practical application because there are no practical steps related to the determination of immune health in an individual. There are no additional steps of the claims that are directed to applying or using the judicial exception(s) noted above (e.g.: MPEP 2106.04(d)(I)). The claims end with an asserted association between the presence or absence of a chromosome interaction and the presence of a pathology, which is an abstract idea (as noted above). It is noted that claims 34 and 35 contains limitations regarding administering a treatment to an individual. Claim 34 comprises “administering to any individual identified as being susceptible to an immune overreaction or immune side effect an agent”, however the scope of the claim encompasses NOT identifying that the individual is susceptible to either immune overreaction or side effect (“identifying whether an individual is susceptible”). Claim 35 comprises “administering to the individual an agent”. However, there are no required particular practical steps recited with specificity related to determining the immune health of the individual, such as applying a particular agent that performs a particular function to the individual (no specific “immune health” is practically recited in the claim and therefore the treatment itself cannot be particular).
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims only broadly recite steps of detecting the presence or absence of chromosomal interactions (claims 6, 8, and 27). However, such steps were well understood, routine and conventional in the prior art (e.g.: MPEP 2106.05(d)). For example: Yan (Yan et al., Surgery 2019) teaches using EpiSwitch chromatin conformation capture assays to identify chromosomal interactions involving fixing chromatin with formaldehyde (crosslinking), cleaving the crosslinked DNA, ligating the cleaved DNA ends, and identifying the presence via PCR (Methods – Identification of candidate biomarkers). Additionally, as reviewed in Sati and Cavalli (Chromosoma, 2017), chromosome conformation capture technologies have existed since the invention of 3C in 2002 (Introduction). This technology involves crosslinking of DNA, restriction digestion, and proximity ligation (Introduction and Figure 2). These ligated junctions can then be assessed via PCR (The birth and the maturation of 3C). The chromosomal interactions can also be assessed through qPCR, as taught by Hagège (Hagège et al., Nature Protocols 2007).
For these reasons the claims are rejected under 35 USC 101 as directed to subject matter that is not significantly more than a judicial exception.
Double Patenting
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 1-2, 4-11, 27-29, and 32-35 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 4-10, 23-25, and 28-31 of copending Application No. 18/259,908 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because while claim 1 of ‘908 refers to “detecting prognosis for coronavirus infection in an individual”, given the lack of a definition of immune health in the instant claims, detecting prognosis for coronavirus infection reads on “determining the immune health of an individual”. Moreover, Table 1 as listed in claim 1 of ‘908 includes the elected chromosome interaction as represented by probe Hg38_1_99631771_99639876_99708395_99714403_FF (same as interaction number 13 in the instant application). Moreover, Tables 1-17 appear to be the same between the instant application and ‘908, meaning all elected species in the instant application are anticipated by the claims of ‘908 which reference said shared tables/elected species.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
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/KAILEY ELIZABETH CASH/ Examiner, Art Unit 1683
/STEPHEN T KAPUSHOC/ Primary Examiner, Art Unit 1683
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