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 of Group I without traverse and withdrawal of claims 7-8 in the reply filed June 16, 2026 is acknowledged.
Claims 1-8 are currently pending. Claims 1-6 are examined herein on their merits.
Priority
It is acknowledged that the instant application claims priority to foreign application CN202410285234.9, filed March 13, 2024. It is noted, however, that the foreign priority date is the effective filing date of the claimed invention if:
the foreign application supports the claimed invention under 112(a), and
the applicant has perfected the right of priority by providing
a certified copy of the priority application, and
a translation of the priority application (if not in English)
In the instant case, the applicant has submitted a certified copy of the priority application but it is not in English and the examiner cannot determine if it supports the claimed invention. The effective filing date of the application is considered to be April 11, 2024 which is the actual filing date of the instant application.
Specification
Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps.
Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts.
The abstract of the disclosure is objected to because the abstract is 154 words in length. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Objections
Applicant is advised that should claim 2 be found allowable, claim 4 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claim Interpretation
The instant application does not provide a sequence of the claimed dCAPS marker as although chromosomal positions were given for wheat chromosome 1B, a reference sequence was not provided. In this regard, the primer set recited claim 3 is intended to amplify the claimed marker. Therefore, the Examiner interprets that the molecular marker recited in claim 1 corresponds to the sequence on a wheat reference genome (NC_057795.1) which is flanked by the claimed primers: NC_057795.1:684621092-684621260. The alignment of the primers of claim 3 to NC_057795.1 is shown in the rejection under 35 U.S.C. 103 below.
Claim Rejections - 35 USC § 112
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 1-6 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1-6 are rejected for the recitation of “located at a site of 676077050 to 676084414 base pairs (bp) on a wheat chromosome 1B,” as being indefinite. It is unclear from the claims which genome(s) are being described or are required. ‘Wheat chromosome 1B’ could refer to divergent sequences from a range of species/cultivars which are referred to by the common name ‘wheat’ and which have a chromosome 1B (i.e. common/bread wheat; durum wheat; emmer wheat; etc.). Furthermore, any species’/cultivar’s genome can vary in length and/or composition depending on the reference or build. Thus, a site of 676077050 to 676084414 base pairs (bp) on a wheat chromosome 1B could indicate different sequences in different builds and/or organisms. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claims 1-6 are rejected because it is unclear what is meant by “dCAPS molecular marker.” The marker is described as being “located at a site of 676077050 to 676084414 base pairs (bp) on a wheat chromosome 1B,” which indicates that the marker is inherently present and consists solely of the corresponding nucleotide sequence present at that location in any given wheat chromosome B. However, it is unclear whether or how being a ‘derived cleaved amplified polymorphic sequence (dCAPS) molecular marker’ distinguishes the marker from the sequence inherently present at the given chromosomal location. For example, is the claim meant to be directed toward an artificially-introduced mismatch within an amplicon derived from the given genomic position (following the dCAPS protocol) instead of being directed to the genomic sequence itself? As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claims 2-6 are rejected for the recitation of ‘primer set’ in claims 2-5 as being indefinite. It is unclear whether the term ‘set’ is meant to indicate that the condition of the primers is such that they may not be separated (i.e. that they are mixed together), or if it merely indicates that the primers are meant to be used together for amplification purposes (e.g. a dedicated forward and reverse pairing). As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement. If what is meant is that the primers are present together in a mixture, the claims must be amended to reflect that meaning.
Claim 3 is rejected for the recitation of “is shown as” in lines 2 and 3 because it is unclear what is meant by the limitation. For example, is the claim merely providing sequences which are representative examples of the primers, or is it requiring that the upstream primer be exactly SEQ ID NO: 1 and the downstream primer be exactly SEQ ID NO: 2? As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement. If what is meant is that the nucleotide sequence of the upstream primer is SEQ ID NO: 1 and the nucleotide sequence of the downstream primer is SEQ ID NO: 2, the claim must be amended to reflect that meaning.
Claims 4 and 6 are rejected for the recitation of “a detection reagent” in claim 4, as being indefinite. It is not clear how the recited language is meant to limit the primer set of claim 2. For example, is the language intended to provide some structural limitation with regard to the primers, or does it merely recite an intended use of the primers? Primers which amplify molecular markers already fall within the plain meaning encompassed by “detection reagents.” If the limitation is intended to provide a structural requirement for the primers, it is not clear what the structural requirement would be. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claims 5 and 6 are rejected for the recitation of “a detection kit,” as being indefinite. It is not clear how the recited language is meant to limit the primer set of claim 2 and/or the detection reagent of claim 4. For example, is the language ‘detection kit’ intended to provide some structural limitation with regard to the primers/reagent, or does it merely recite an intended use of the primers/reagent? The term ‘kit’ already broadly encompasses a collection of reagents. If the limitation is intended to provide a structural requirement for the primers/reagent, it is not clear what the structural requirement would be. As a result, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
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 1-6 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims have been evaluated using the 2019 Revised Patent Subject Matter Eligibility Guidance (see Federal Register Vol. 84, No. 4, Monday, January 7, 2019).
Step 1: The claims are directed to the statutory category of a product.
Step 2A, prong one: Evaluate Whether the Claim Recites a Judicial Exception
Claim 1 is drawn to a derived cleaved amplified polymorphic sequence (dCAPS) molecular marker for identifying resistance of wheat to Fusarium crown rot caused by Fusarium pseudograminearum. Claims 2-6 are directed to a primer set configured to amplify the dCAPS molecular marker and a reagent or kits comprising the primers. The dCAPS marker and the primers are nature-based products. The markedly different characteristics analysis has been used to determine if the nature-based products are an exception. The nature-based products have been compared to their natural counterparts.
There is no indication that the dCAPS marker has any characteristics that are different from the naturally occurring nucleic acid sequence. Although the sequence of the dCAPS marker is not given (or a reference sequence to which the chromosomal positions refer), the primer set of claim 3 is intended to amplify the marker. Therefore, the Examiner interprets that the molecular marker according to claim 1 corresponds to the sequence on a wheat reference genome (NC_057795.1) which is flanked by the claimed primers: NC_057795.1:684621092-684621260. This region was aligned against a sequence from a wild wheat species (NC_041381.1):
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In this case, the wild, naturally-occurring sequence and the molecular marker of claim 1 are the same sequence. There is no difference in function, structure, or other properties. It is noted that claim 1 recites the use of the molecular marker as a dCAPS molecular marker for identifying resistance in wheat. However, the intended use of the molecular marker does not in any way change the natural structure, function, or other properties of the marker. Because the claimed nucleic acids do not have markedly different characteristics, they are a product of nature exception.
There is no indication that the primers of claims 2 and 4-6 are different from naturally occurring nucleic acid sequences. The claimed primers, which are configured to amplify the dCAPS molecular marker, encompass nucleic acids which are identical to naturally-occurring nucleic acids. Although primers are synthetically created, the court found in Ambry Genetics that primers are not markedly different than their corresponding strands of DNA in nature because they have the same genetic structure and nucleotide sequence (see MPEP 2106.04(c)(II)(C)(2)).
It is noted that claim 3 recites specific primer sequences. These primers were examined to determine their differences to natural counterparts. For example, the primers were aligned to the reference genome of wild emmer wheat (NC_041381.1), which represents a sequence found in nature:
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The downstream primer represented by SEQ ID NO 2 (in the alignment above, this is referred to as the ‘reverse primer’) is indistinguishable from the sequence found in nature. There is no difference in function, structure, or other properties. The upstream primer represented by SEQ ID NO 1 (in the alignment above, this is referred to as the ‘forward primer’) has a single nucleotide difference with respect to sequences found in nature and appears to represent a non-naturally-occurring mismatch sequence.
It is noted that claims 1-6 recite the use of the marker and primers to identify resistance of wheat to Fusarium crown rot and the use of the primers to amplify the molecular marker. However, the intended use of the primers does not in any way change the natural structure, function, or other properties of the nucleic acids. It is noted that the nucleic acid primers are recited as being comprised in a detection reagent (claim 4) or kit (claims 5 and 6). There are no other recited elements of the reagent and kit compositions, therefore the nucleic acids do not interact with other elements of those compositions. There is no indication that the nucleic acids being present in the compositions changes the function, structure, or other properties of the nucleic acids. Because the claimed nucleic acids do not have markedly different characteristics, they are a product of nature exception.
Step 2A, prong two: Evaluate Whether the Judicial Exception Is Integrated Into a Practical Application
Claims 1-6 recite the use of the marker and primers to identify resistance of wheat to Fusarium crown rot and the use of the primers to amplify the molecular marker. Claims 4 and 6 include an additional element of the use of the primers for amplification of the molecular marker as a “detection reagent.” Claims 5 and 6 include an additional element of the use of the primers for amplification of the molecular marker within a “detection kit.” A kit broadly encompasses a collection of reagents, and the primers themselves fall within the definition of ‘detection reagent.’ These elements fail to meaningfully limit the claims and are the equivalent of adding the words “apply it” to the judicial exceptions. Accordingly, there are no additional elements that integrate the recited judicial exception into a practical application.
Claim 3 requires a primer pair containing one sequence (SEQ ID NO: 1) which contains a non-naturally occurring mismatch which may be used to create a restriction enzyme motif in the amplified product. Although SEQ ID NO: 1 itself has a difference from naturally-occurring sequences that is integrated into a practical application, SEQ ID NO: 2 (which is identical to a naturally-occurring sequence) is not meaningfully integrated. The naturally-occurring sequence SEQ ID NO: 2 being present in a set of primers does not meaningfully limit it and is the equivalent of adding the words “apply it” to the judicial exception. Accordingly, there are no additional elements that integrate the recited judicial exception into a practical application.
Step 2B: Evaluate Whether the Claim Provides and Inventive Concept
Claims 1-6 recite the use of the marker and primers to identify resistance of wheat to Fusarium crown rot and the use of the primers to amplify the molecular marker. At the time the invention was made, the use of molecular markers and primers to identify disease resistance, and the use of primers to amplify a molecular marker, were well-established, routine, and conventional. Claims 4 and 6 include an additional element of the use of the primers for amplification of the molecular marker as a “detection reagent.” Claims 5 and 6 include an additional element of the use of the primers for amplification of the molecular marker within a “detection kit.” A kit broadly encompasses a collection of reagents, and the primers themselves fall within the definition of ‘detection reagent.’ At the time the invention was made, use of primers in kits and as detection reagents was well-established, routine, and conventional. Thus, the claims as a whole do not amount to significantly more than each product of nature by itself, and the claims do not qualify as eligible subject matter.
Claim 3 requires a primer pair containing one sequence (SEQ ID NO: 1) which contains a non-naturally occurring mismatch and one naturally-occurring sequence (SEQ ID NO: 2) which may be used to create a restriction enzyme motif in the amplified product. At the time the invention was made, the use of this type of primers to create a restriction enzyme motif in an amplified product was well-established, routine, and conventional (known as the dCAPS method). Thus, the claims as a whole do not amount to significantly more than each product of nature by itself, and the claims do not qualify as eligible subject matter.
Claim Rejections - 35 USC § 102
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 (i.e., changing from AIA to pre-AIA ) 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.
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 1 is rejected under 35 U.S.C. 102(a)(1) as anticipated by Zhu et al. (published May 16, 2021; Zhu et al. Plant J. 2021 Jul;107(1):303-314), as evidenced by GenBank 1 (published online prior to print of Zhu et al. in 2021; GenBank: NC_057795.1).
Zhu discloses the dCAPS molecular marker of claim 1 within the project PRJNA669381 (pg. 313: Data availability). Project PRJNA669381 contains the genome assembly of IWGSC CS RefSeq v2.1 (GCA_018294505.1), from sequencing of Triticum aestivum (commonly known as bread wheat). The whole genome shotgun sequence of said assembly is found under NCBI Reference Sequence: NC_057795.1. This sequence includes a section (NC_057795.1:684621092-684621260) which corresponds to the dCAPS molecular marker of claim 1, as explained in the Claim Interpretation section above. This sequence can also be accessed as LOC123149162 in NCBI’s Gene Database.
Zhu does not disclose that the marker is used “for identifying resistance of wheat to Fusarium crown rot caused by Fusarium pseudograminearum.” However, as noted in MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Accordingly, the claim language of “for identifying resistance of wheat to Fusarium crown rot caused by Fusarium pseudograminearum” merely sets forth the intended use of the claimed composition, but does not limit the scope of the claims.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 2-6 are rejected under 35 U.S.C. 103 as unpatentable over Zhu et al. (published May 16, 2021; Zhu et al. Plant J. 2021 Jul;107(1):303-314; sequence available as LOC123149162 in NCBI’s Gene Database) in view of Neff et al. (published May 1998; Neff et al. Plant J. 1998 May;14(3):387-92) and Oyiga et al. (published Nov 3, 2018; Oyiga et al. Theor Appl Genet. 2019 Feb;132(2):323-346), and as evidenced by GenBank 2 (GenBank 2: LOC123149162) and UniProt 1 (UniProt: TraesCS1B03G1244600).
Zhu discloses the marker of claim 1, as discussed in the rejection under 35 U.S.C. 102(a)(1) above.
Regarding claim 3, Zhu teaches a genomic sequence which corresponds to downstream primer SEQ ID NO: 2 (‘Forward primer’ in the figure below). Although this sequence is the reverse complement of SEQ ID NO: 2, the sequence of Zhu was present as a DNA duplex, and therefore the reverse complementary sequence is also taught by Zhu. Likewise, Zhu teaches a sequence which corresponds to a single nucleotide variant of claimed SEQ ID NO: 1.
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Regarding claims 2-6, Zhu does not explicitly teach primers for amplification, nor detection reagents and/or kits. Regarding claim 3, Zhu does not explicitly teach a sequence which is 100% identical to SEQ ID NO: 1.
Neff teaches a method described as ‘dCAPS’ or ‘derived cleaved amplified polymorphic sequence’ analysis, which assesses the presence of target mutations in a sample by introduction of a restriction enzyme recognition site to PCR product from the sample (Abstract).
Regarding claims 2-6, Neff teaches the use of primers configured to amplify polymorphic markers in plant genomes (Abstract). Although Neff does not teach that these primers are explicitly “for identifying resistance of wheat to Fusarium crown rot caused by Fusarium pseudograminearum,” MPEP 2111.02 states: “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Accordingly, the claim language of “for identifying resistance of wheat to Fusarium crown rot caused by Fusarium pseudograminearum” merely sets forth the intended use of the claimed composition, but does not limit the scope of the claims.
Regarding claim 3, Neff teaches primers which contain one or more residues which are mismatched relative to template DNA (pg. 387, col. 2, last par.).
Regarding claims 4-6, Neff does not explicitly teach a ‘detection reagent’ or a ‘detection kit,’ but Neff does teach primers used in combination with other reagents to detect polymorphisms. Given that the term ‘kit’ broadly encompasses a collection of reagents, and that primers themselves fall within the definition of ‘detection reagent,’ Neff is considered to have met the limitations of claims 4-6.
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Zhu and Neff to develop primers which amplify a dCAPS molecular marker at the claimed position on wheat chromosome 1B. One would have had reasonable expectation of success because Neff demonstrates the dCAPS method in plants (pg. 388, col. 1, 1st full par.).
Further, given that there are a finite number of solutions (i.e. a finite number of sites in the sequence of interest which both contain the genetic marker and which may be modified with a dCAPS mismatch primer set to introduce a restriction enzyme cutting motif), and there is no evidence of unexpected results, it would have been obvious to a person with ordinary skill in the art to try introducing the mismatch at positions including the claimed position in SEQ ID NO: 1. One would have had reasonable expectation of success because Neff demonstrates that programs are available which are able to assist in the design of dCAPS primers for a given polymorphism (pg. 389, col. 1, last par.)
One would have been motivated to design dCAPS primers for claimed marker as well as to analyze different mutation positions, because Oyiga recites wheat lysine-specific demethylase ‘JMJ703’ (an H3K4 lysine-specific demethylase) as a potential stress response indicator in wheat (Fig. 3) which is potentially useful for facilitating genomic research and breeding programs to improve wheat stress tolerance and productivity (Oyiga: pg. 324, col. 2, 1st full par.).
It is noted that the claimed marker represented by NC_057795.1:684621092-684621260 corresponds to TraesCS1B03G1244600, which was available as early as July 2022 (see GenBank 2: Location; Genomic Regions). As early as January 24, 2024, TraesCS1B03G1244600 was annotated as an H3K4 lysine-specific demethylase on wheat chromosome 1B (see UniProt 1). Therefore, Oyiga’s teaching regarding wheat lysine-specific demethylase would have provided motive to an ordinary artisan before the effective filing date of the instant invention.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Christine M Jones whose telephone number is (571)272-2585. The examiner can normally be reached Monday - Friday, 8AM - 4PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Shen can be reached at (571)272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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