Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of the particular partial nucleic acid sequence that is (b), and the particular artificial sequence that is SEQ ID NO: 22, and the additional artificial sequence that is SEQ ID NO: 56 in the reply filed on 04/24/2026 is acknowledged.
In light of Applicants’ reply of 04/24/2026 indicating that elected SEQ ID NOs: 22 and 56 are contained in SEQ ID NO: 60, the election is extended to include SEQ ID NO: 60, and the species election requirement is withdrawn form elected SEQ ID NO: 22 and 56 and SEQ ID NO: 60.
Claim 5 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species (i.e.: requiring non-elected nucleic acid sequences), there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 04/24/2026.
Claim Rejection - Improper Markush Group
Claims 1-4 and 6-9 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(II).
The claims are directed to Markush groupings of different combinations and subcombinations of artificial nucleic acid sequences consisting of a non-naturally occurring nucleic acid sequence recited as (a) (relevant to any of SEQ ID NOs: 8-19), (b) (relevant to any of SEQ ID NOs: 20-31), (c) (relevant to any of SEQ ID NOs: 32-43), (d) (relevant to any of SEQ ID NOs: 44-45 )and (e) (relevant to any of SEQ ID NOs: 56 or 57).
These alternative elements, as recited in the claims, 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(II) 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 (i.e.: the different sequences recited as SEQ ID NO: 8-45, 56 and 57) do not share a single structural similarity, as each artificial sequence has a different chemical structure in that it consists of a different nucleotide, sequence. The only structural similarity present is that all of the sequences comprise nucleotides. The fact that the artificial sequences comprise nucleotides does not per se 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 use of being a non-naturally occurring sequence. Accordingly, while the different sequences are asserted to have the property of being uniquely absent from naturally occurring genomes, and thus suitable for use as a control or standard in an assay, they do not share a substantial structural similarity essential to this activity.
Further, there is no expectation from the knowledge in the prior art that these particular sequences 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 sequences possess the common property of being non-natural and thus suitable for use as a control or standard in an assay.
Following this analysis, the claims are rejected as containing an improper Markush grouping.
Claim Rejections - 35 USC § 112 – Written Description
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.
Claim 3 is 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 breadth of structures encompassed by the claim in light of the functional limitations of the claim. The claim is directed to “additional partial nucleic acid sequence (e) consisting of: …. (e5) an artificial nucleic acid sequence consisting of a non-naturally occurring nucleic acid sequence”. Where the claims does not recite any particular sequence elements or any structural requirements such as length, G:C content, or melting temperature, the claim broadly encompasses any nucleic acid structures. But the claim recites a functional limitation of the claimed artificial nucleic acid sequence as being a “a non-naturally occurring nucleic acid sequence”. The claim thus requires that the sequence of the claims does not occur in any naturally occurring genome. But neither the disclosure of the application as filed, nor the teachings of the related art, allow the skilled artisan to recognize from any particular nucleic acid sequence (i.e.: the structure of a nucleic acid) that such a sequence is “non-naturally occurring”. Such a conclusion can only be made by comparing a sequence to some collection of all known nucleic acid sequences. Even if a conclusion that some sequence was “non-naturally occurring” based on some search of a particular collection of known nucleic acid sequences, the sequence itself may actually be in a some non-indexed genome. An assertion that some particular sequences were found to meet the functional limitations of the claim is not itself a description of the expression levels as required by the claims. This finding is also emphasized in Ex Parte Kubin (No. 2007-0819, Bd. Pat. App. & Int. May 31, 2007), wherein it is stated that:
“Although there is often significant overlap” between the enablement and written description requirements, “they are nonetheless independent of each other.” University of Rochester, 358 F.3d at 921, 69 USPQ2d at 1891. An “invention may be enabled even though it has not been described.” Id. Such is the situation here. While we conclude one skilled in the art would have been able to make and use the full scope of claim 73 through routine experimentation, we find Appellants did not describe the invention of claim 73 sufficiently to show they had possession of the claimed genus of nucleic acids. See, e.g., Noelle v. Lederman, 355 F.3d 1343, 1348, 69 USPQ2d 1508, 1513 (Fed. Cir. 2004) (“invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed”).
Thereby, a showing of how to potentially identify sequence that might be used in the claimed methods is not sufficient to establish that Applicants were in possession of the invention as broadly encompassed by the rejected claim.
Claim Rejections - 35 USC § 112 - 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.
Claim 9 is 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 9 is unclear over the structural requirements of the claimed probe. The required and encompassed structure of the claimed probe is unclear because the probe which is claimed is set forth in terms of its identity to another nucleic acid sequence (i.e.: at least 90% identical to a nucleic acid sequence comprising at least 15 continuous nucleotides in an artificial nucleic acid sequence selected from the group consisting of SEQ ID NOs: 8 to 57 (the election encompass SEQ ID NO: 22 and 56)). But the term “comprising” in the recitation “at least 90% identical to a nucleic acid sequence comprising” makes the required identity, and thus the claimed probe, unclear. The term “comprising” is an open term (see MPEP 2111.03; inclusive or open-ended and does not exclude additional, unrecited elements or method steps) making the sequence to which the probe has identity inclusive of any other additional sequence. So in that regard it is unclear what probes are intended to be encompassed by the claim.
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.
Claim 9 is rejected under 35 U.S.C. 101 because the claimed invention is directed to nucleic acids that encompass portions of naturally occurring nucleic acids without significantly more.
The rejected is directed to a probe comprising a sequence that is “90% identical to a nucleic acid sequence comprising at least 15 continuous nucleotides” of SEQ ID NO: 22 or 57, as consonant with the election. The claimed probe is defined in terms of a sequence to which the probe has identity. The claim is directed to nucleic acids sequences that encompass portions of naturally occurring genomes.
Because claims recite a nature-based product limitation (the probe of the claim), the “markedly different characteristics analysis” is used to determine if the nature-based product limitation is a product of nature exception. MPEP 2106.04(c)(I). The claim does not recite or require any additional elements beyond the claimed probe; the markedly different characteristics analysis is applied only to the nature-based product limitation (i.e.: the claimed probe). MPEP 2106.04(c)(I)(A). The markedly different characteristics analysis is performed by comparing the nature-based product limitation (in this case the claimed probe) to its naturally occurring counterpart to determine if it has markedly different characteristics from the counterpart. MPEP 2106.04(c)(II). Here, a closest natural counterpart is a Alteromonas mediterranea genome t (e.g.: GenBank locus CP018024) that is found in cells. When the claimed nucleic acid is compared to this counterpart, the comparison indicates that there are no differences in structure, hybridization ability, or other characteristics. Therefore, the nucleic acid of the claims is a product of nature exception. For example, positions 1,716,990 – 1,717,008 of CP018024 are 5’-gtcgcttagc cggttcaag-3’, which is a sequence that is identical to positions 155-173 of SEQ ID NO: 22 of the instant application.
This judicial exception is not integrated into a practical application because the claims do not recite any additional physical elements that clearly integrate the nucleic acids into a practical application.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because, as noted above, the claim does not recite or require and elements beyond the claimed probe.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 9 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by GenBank CP018024 (2016).
The structural limitations of the probe of the rejected claim have been addressed previously in this Office Action. GenBank CP018024 provides a nucleic acid that comprises a sequence that is at least 90% identical to 15 continuous nucleotides of SEQ ID NO: 22. Positions 1,716,990 – 1,717,008 of CP018024 are 5’-gtcgcttagc cggttcaag-3’, which is a sequence that is identical to positions 155-173 of SEQ ID NO: 22 of the instant application.
Conclusion
No claim is allowed.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Tourlousse et al (2016) (cited on the IDS of 12/07/2023) is the closest prior art with regard to providing artificial nucleic acid sequences consisting of anon-naturally occurring nucleic acid sequence. The reference teaches providing control sequences that represent full-length 16S rRNA genes containing artificial variable regions with negligible identity to known nucleotide sequences, permitting unambiguous identification of spike-in sequences in 16S-seq read data from any microbiome sample. The Supplementary Data for the reference provides (Supplementary Table S1) the sequences of these control sequences, which are different than the sequence requirements of the instant claims as consonant with the election.
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Stephen Kapushoc
Primary Examiner
Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683
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