DETAILED CORRESPONDENCE
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This action is in response to the papers filed December 29, 2025. Currently, claims 1-15 are pending. Claims 3, 5-15 have been withdrawn as drawn to non-elected subject matter.
Election/Restrictions
Applicant's election with traverse of Group I, salinity tolerance, marker (TAT)8, Claims 1-2, 4 in the paper filed December 29, 2025 is acknowledged.
The response argues “even if the systematic product could be used to make a materially or structurally different process, if will be necessary to search and examine the process of claims 6-15”. This argument has been reviewed but is not persuasive. Restriction practice permits restriction when the product may be used in a materially different method. Here, the restriction requirement set forth this rationale. Further, there would be a burden to search the claimed method and it would require different search and examination criteria.
The requirement is still deemed proper and is therefore made FINAL.
This application contains claims 3, 5-15 drawn to an invention nonelected with traverse in the paper filed July 28, 2025. A complete reply to the final rejection must include cancellation of nonelected claims or other appropriate action (37 CFR 1.144) See MPEP § 821.01.
Priority
This application claims priority to foreign filed Taiwan 111116588, filed May 2, 2022.
It is noted that a translation of the foreign document has not been received.
Drawings
The drawings are acceptable.
Sequence Rules
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 CFR 1.821 through 1.825.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the claims and specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
The markers such as (TAT)8 are sequences that need to be identified by SEQ ID NO:. They are longer than the required minimum length and are directed to sequences. Correction is required.
Improper Markush Rejection
Claims 2, 4 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.
A Markush claim contains an “improper Markush grouping” if:
(1) the species of the Markush group do not share a “single structural similarity,” or (2) the species do not share a common use. 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. Members of a Markush group share a common use when they are disclosed in the specification or known in the art to be functionally equivalent. See MPEP § 2117.
Here each species is considered to be each of the feature sequence markers, including a salinity tolerance marker. Cold hardiness, disease resistance, and salinity tolerance are different markers with different structures and functions. Even within the salinity tolerance markers, claim 4 recites 5 different repeat markers that have different structures and are located in different regions of the genome. Applicant elected (TAT)8 salinity tolerance marker.
The recited alternative species in the groups set forth here do not share a single structural similarity, as each different gene that could be detected is itself located in a separate region of the genome and has its own structure. The genes recited in the instant claims, do not share a single structural similarity since each consists of a different nucleotide sequences with different expression patterns. The only structural similarity present is that all detected positions are part of nucleic acid molecules. The fact that the markers comprise nucleotides per se does not support a conclusion that they have a common single structural similarity because the structure of comprising a nucleotide alone is not essential to the common activity of being correlated with Cold hardiness, disease resistance, or salinity tolerance. Accordingly, while the different markers are asserted to have the property of being expressed in Taiwan tilapia, they do not share a single structural similarity.
MPEP 2117 (II)(A) provides the following guidance as to what constitutes a physical, chemical, or art recognized class:
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”
The recited genes do not belong to a recognized chemical class because there is no expectation from the knowledge in the art that the genes will behave in the same manner and can be substituted for one another with the same intended result achieved. In other words, there is no expectation from the knowledge in the art that each of the recited genes would function in the same way in the claimed method; it is only in the context of this specification that it was disclosed that all members of this group may behave in the same way in the context of the claimed invention. Further there is no evidence of record to establish that it is clear from their very nature that each of the recited genes possess the common property of being associated with salinity tolerance.
MPEP 2117 (II) further states the following:
Where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the compounds do not appear to be members of a recognized physical or chemical class or members of an art-recognized class, the members are considered to share a "single structural similarity" and common use when the alternatively usable compounds share a substantial structural feature that is essential to a common use. Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984).
The recited alternative species do not share a substantial common structure just because they all have a sugar phosphate backbone. The sugar phosphate backbone of a nucleic acid chain is not considered to be a substantial common structural feature to the group of genes being claimed because it is shared by ALL nucleic acids. Further, the fact that the genes all have a sugar phosphate backbone does not support a conclusion that they have a common single structural similarity because the structure of comprising a sugar phosphate backbone alone is not essential to the asserted common use of being associated with salinity tolerance.
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.
Following this analysis, the claims are rejected as containing an improper Markush grouping.
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 1-2, 4 are rejected under 35 U.S.C. 101 because the claimed invention is not directed to patent eligible subject matter. Based upon an analysis with respect to the claim as a whole, the rejected claim(s) do not recite something significantly different than a judicial exception. The rationale for this determination is explained below:
Briefly, Claims 1-2, 4 are rejected because these claims are drawn to a system comprising an environment for breeding tilapia, such as a pond or fish tank with water, nucleic acid molecule markers and primer pairs.
The claims require a predeterminined environment. The specification teaches a predetermined environment can be selected from a cage culture site, an aquaculture outdoor site, an aquaculture tank, an aquaculture container or the likes (page 12, lines 14-17). The tank comprising water is a naturally occurring element.
The claims are also directed to nucleic acid fragments from the Taiwan tilapia genome, i.e. known naturally occurring nucleic acids. Such isolated nucleic acid molecules, that are identical to fragments of naturally occurring nucleic acid molecules are not patent eligible subject matter, i.e. they are judicial exceptions to patentable subject matter.
MPEP 2106.04(b)(II) discusses products of nature. The MPEP specifically discusses DNA, primers and probes. The isolated DNA of Myriad and the primers of Ambry Genetics were described as products of nature by the courts. Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107, 2116-17, 106 USPQ2d 1972, 1979 (2013); University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 758-59, 113 USPQ2d 1241, 1243 (Fed. Cir. 2014). The MPEP further states the “product of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart. See, e.g., Ambry Genetics, 774 F.3d at 760, 113 USPQ2d at 1244 ("Contrary to Myriad's argument, it makes no difference that the identified gene sequences are synthetically replicated. As the Supreme Court made clear, neither naturally occurring compositions of matter, nor synthetically created compositions that are structurally identical to the naturally occurring compositions, are patent eligible.").” The Federal Circuit in Ambry Genetics reviewed “[t]he Supreme Court held ineligible claims directed to segments as short as 15 nucleotides, the same length as the primer claims at issue here, suggesting that even short strands identical to those found in nature are not patent eligible. Compare ’492 patent col. 170 ll. 32–38, with ’282 patent col. 153 ll. 66–67.”
In the instant case, the claims, embrace probes and primers that are identical to naturally occurring gene fragments and clearly read on nature-based products that themselves do not exhibit markedly different characteristics from the naturally occurring gene. See e.g. Myriad in which one claim at issue was drawn to “[a]n isolated DNA having at least 15 nucleotides [an isolated DNA coding for a BRCA1 polypeptide having the amino acid sequence of SEQ ID NO: 2] (Myriad at 2113). The Court recognized that this claim, if valid, would have given Myriad exclusive right to isolate any strand of 15 or more nucleotides of an individual’s BRCA1 gene (paragraph bridging 2113 and 2114). This is directly analogous to the instant situation wherein Applicant’s claims cover probe and primer molecules that are fragments of a naturally occurring Taiwan tilapia genome sequence. The Court held that “[a] naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated”, and that “Myriad’s claims are not saved by the fact that isolating DNA from the human genome severs the chemical bonds that bind gene molecules together” (page 2118). The Court found that while Myriad had located and sequenced an important gene, Myriad had not created anything, and that “separating that gene from its surrounding genetic material is not an act of invention” (page 2118). Consistent with the findings of the Court in Myriad, the Office finds that the primers and probe molecules embraced by the instant clams are not patent eligible compositions of matter regardless of whether or not they are isolated from the genome. The Guidelines indicate that a change in biological function or activity maybe a characteristic of an isolated product that can provide a marked difference sufficient to distinguish over a naturally occurring product. However, in this case, as in the Ambry case, the function of the nucleic acids is the same function as the relevant portion of the naturally occurring sequence. Just as in nature, primers and probes utilize the innate ability of DNA to bind to itself.
The final element of the claim “an identification result” is deemed to be knowledge, mental thoughts, instructions and/or abstract ideas. These are not tangible elements in the system.
Having established that the claims include a naturally occurring product that is a judicial exception, it must now be determined whether or not the claims recite an element or combination of elements that amount to significantly more than that exception, and whether those additional elements also amount to significantly more for the other claimed exception(s), which ensures that the claim does not have a preemptive effect with respect to any of the recited exceptions. To determine whether a claim that includes a nature-based product limitation recites a “product of nature” exception, an analysis is performed in which it is first determined if a claim includes a nature-based product that has markedly different characteristics from the corresponding naturally occurring product, and if it does not, then it is determined whether or not other elements of the claim are sufficient to ensure that the claim as a whole amounts to significantly more than the exception itself (see the Interim Guidance on Patent Subject Matter Eligibility published 12/16/2014 in the Federal Register at pages 74618-74633). In order to be markedly different the claimed product must possess at least one characteristic that is different from that of the counterpart.
The fact that these natural products are organized into a system with an intended use adds nothing to the judicial exceptions that would distinguish them from the naturally occurring material. The system must be considered in the context of whether or not the combination can provide some way of ensuring it does not limit the public’s access to the naturally occurring material. That does not occur in this case because the naturally occurring material exists as a distinct entity within the system, and is not integrated in terms of form or function with any other element of the kit. A claim to a system in which one of the kit elements is naturally-occurring product that is separate and distinct from the other kit elements would forestall the use of that naturally occurring product.
Therefore, the claims are properly rejected under 35 USC 101 as being drawn to patent-ineligible subject matter.
Claim Rejections - 35 USC § 112-Description
The following is a quotation 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.
Claims 1-2 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.
The claims are broadly drawn to feature sequence markers from Taiwan Tilapias which comprise any structurally undefined variant or polymorphism in the gene which possess the functionality of being associated with a feature including Cold hardiness, disease resistance, and salinity tolerance. The specification teaches 5 repeats asserted to be associated with salinity tolerance markers across the Taiwan tilapia genome.
Relevant to the lack of particular structural limitations in the rejected claims drawn to nucleic acids, MPEP 2163 states:
The claimed invention as a whole may not be adequately described if the claims require an essential or critical feature which is not adequately described in the specification and which is not conventional in the art or known to one of ordinary skill in the art.
In the case of the instant claims, the functionality of markers including repeat regions, polymorphisms or variants diagnostic of cold hardiness, disease resistance, and salinity tolerance is a critical feature of the claimed methods. The specification teaches identifying 5 repeat variants in the Taiwan tilapia genome.
It is clear from the art of Yang (Aquaculture, Vol. 596, No. 741762, 2025), salt tolerance genes exist on chromosome 11 and 18. Yang teaches QTL on LG11 suggests the presence of previously unrecognized genetic factors contributing to salt tolerance (abstract). Yang teaches acot5 and slc6a6 are genes with markers for salt tolerance. The instant specification does not describe these markers associated with salt tolerance.
Given the guidance in the specification and what was taught in the art prior to the invention, the skilled artisan would be unable to predictably correlate structural changes in the gene encoding TREX1 with LE, simply based on their existence.
In analyzing whether the written description requirement is met for a genus claim, it is first determined whether a representative number of species have been described by their complete structure. The 5 species of repeat markers for salinity tolerance markers across the Taiwan Tilapia genome does not represent the genus of feature sequence markers. There is substantial variability among the species of DNAs encompassed within the scope of the claims. Applicants have not adequately disclosed the relevant identifying characteristics of a representative number of species within the claimed genus. Each of the species is a different repeat length, different repeat and not located in the same region of the genome. The genus includes an enormous number of variants, polymorphisms and mutations for which no written description is provided in the specification. This large genus is represented in the specification by a few repeat markers; however, this disclosure does not provide for a predictable association with any polymorphism or variant in the Taiwan tilapia as is broadly claimed. Here, no common element or attributes of the sequences are disclosed which would permit selection of sequences as polymorphisms. No structural limitations or requirements which provide guidance on the identification of sequences which meet the functional limitations of being salinity tolerance markers. The specification provides no correlation between the structure of the recited repeats and the claimed function of such polymorphisms. Therefore, the mere presence of repeats or polymorphisms are not representative of the genus of any polymorphism associated with Cold hardiness, disease resistance, and salinity tolerance because it is not clear which polymorphisms or mutations would have the same affect. Therefore, the specification fails to teach how to distinguish members of the claimed genus of polymorphisms and variants which possess the claimed functionality from non members.
The general knowledge and level of skill in the art do not supplement the omitted description because specific, not general guidance is what is needed. Since the disclosure fails to describe the common attributes or characteristics that identify members of the genus, and because the genus is highly variant, feature sequence markers alone is insufficient to describe the genus. There is no description of the mutational sites that exist in nature. The general knowledge in the art concerning variants does not provide any indication of how the structure of one allele is representative of unknown alleles. The nature of alleles is such that they are variant structures, and in the present state of the art the structure of one does not provide guidance to the structure of others. The common attributes are not described. The specification provides no correlation between structure of polymorphisms and the function of such polymorphisms. The polymorphisms shown are not representative of the genus of any polymorphism associated with salinity tolerance markers because it is not clear which polymorphisms would have the same effect. One of skill in the art would conclude that applicant was not in possession of the claimed genus because a description of only one member of this genus is not representative of the variants of the genus and is insufficient to support the claim.
Even with respect to Claim 4, the art does not describe the location or context for these repeat markers. The description of a single TAT repeat is not representative of all TAT repeat markers.
Thus, considering the breadth of the polynucleotides required by the claimed methods, their specific required functionalities, and the teachings of the instant specification, it is the conclusion that the specification does not provide an adequate written description of the broadly claimed subject matter.
Claim Rejections - 35 USC § 112- Second Paragraph
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.
Claims 1-2, 4 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 pre-AIA the applicant regards as the invention.
Claim 1 recites “obtained from seeking at least one nucleotide mark in the baited Taiwan Tilapias. Claim 1 is indefinite because it claims both product and methods steps for using the products. As the limitations of the claim are drawn to how a user obtained the marker, and not to the product itself, there is confusion as to when direct infringement occurs. See MPEP 2173.05(p). Claim 1 further provides “an identification result” which shows a correct source or incorrect source of original baited Taiwan tilapias. The limitations of results being correct or incorrect is also method steps for using the product. Correction is required.
Claim 1 further recites a primer pair “corresponding to the feature sequence marker” however it is unclear what correspondence is required. It is unclear whether the claims are primers for amplifying the sequence marker or whether the primers correspond in length, melting temperatures, for example. Applicant is required to clarify how primer pairs correspond to feature sequence markers.
Claim 4 is directed to repeat markers with no context. It is unclear where these (TAT)8 sequence markers are located as they have no relationship to a gene, chromosome or provide any particular flanking sequences. It is unclear which (TAT)8 sequence markers are salinity tolerance markers. Clarification is required.
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.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claim(s) 1-2 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Streelman et al. (US 2003/0047143, March 13, 2003).
Streelman teaches a system comprising a tank (i.e. a predetermined environment), a microsatellite marker close to the start of prl1 transcription and primers for amplifying the microsatellite (para 23). Streelman teaches forward and reverse primers for Prl 1 (para 25). The markers were the amplicons of either the LL or SS or SL genotype (see para 41). Streelman teaches the microsatellite was a salinity tolerance marker (para 28).
The “identification result obtained from identifying an unknown DNA sample” is deemed knowledge or instructions. With regard to the limitation that the system contains instructions, the inclusion of instructions is not considered to provide a patentable limitation on the claims because the instructions merely represent a statement of intended use in the form of instructions in a kit. See In re Ngai, 367 F.3d 1336, 70 U.S.P.Q.2d 1862 (Fed. Cir. 2004)(holding that an inventor could not patent known kits by simply attaching new set of instructions to that product).
Claim(s) 1-2 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chen et al. (Genes, Vol. 13, No. 99, December 31, 2021).
Chen teaches a system comprising a tank (i.e. a predetermined environment), a microsatellite marker of disease-resistance associated DNA markers and primers. Chen teaches tilapia from Taiwan were collected from fish farms in south Taiwan and cultured in a tank (Section 2.1). Primers were used in the system for qPCR and amplicons were generated (namely sequence markers and primer pairs). Table 1 sets forth disease-resistance associated microsatellites as well as the associated gene (see page 12).
The “identification result obtained from identifying an unknown DNA sample” is deemed knowledge or instructions. With regard to the limitation that the system contains instructions, the inclusion of instructions is not considered to provide a patentable limitation on the claims because the instructions merely represent a statement of intended use in the form of instructions in a kit. See In re Ngai, 367 F.3d 1336, 70 U.S.P.Q.2d 1862 (Fed. Cir. 2004)(holding that an inventor could not patent known kits by simply attaching new set of instructions to that product).
Claim(s) 1-2 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Chu et al. (Animals, Vol. 11, No. 3538, December 13, 2021).
Chu teaches a system comprising a tank (i.e. a predetermined environment), a microsatellite marker of cold tolerance associated DNA markers and primers. Chu teaches 38,377 simple sequence repeats (SSRs) and 65,527 SNPS were identified. The 38 cold tolerance related genes that were identified using differential expression with 13 microsatellites and 37 SNPs (abstract). Chu teaches Taiwan tilapia strains were collected and kept in separate fish tanks. The DNA was genotyped with primers and PCR products were separated on gels. Table 3 and 4 list the SSR and SNP markers in Taiwan tilapia (page 13).
The “identification result obtained from identifying an unknown DNA sample” is deemed knowledge or instructions. With regard to the limitation that the system contains instructions, the inclusion of instructions is not considered to provide a patentable limitation on the claims because the instructions merely represent a statement of intended use in the form of instructions in a kit. See In re Ngai, 367 F.3d 1336, 70 U.S.P.Q.2d 1862 (Fed. Cir. 2004)(holding that an inventor could not patent known kits by simply attaching new set of instructions to that product).
Conclusion
No claims allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
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/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682
February 13, 2026