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 .
The Reply, filed by Applicants on 05/27/2026 is hereby acknowledged.
Claims 1, 3, 5-11, 15-17 and 19 are pending and examined herein on the merits.
Claim Rejections - 35 USC § 112
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.
Claims 1, 3, 5-11, 15-17 and 19 remain rejected under 35 U.S.C. 112(a), as failing to comply with the written description requirement. The claims contain 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, had possession of the claimed invention.
The claims are broadly drawn to a soybean plant with any phenotype with any transgene, inserted within its genome on chromosome 4 within specified target sites within SEQ ID NO:4 and 5. It is firstly pointed out that many of the above limitations are not limited by sequence as the claimed platform is flexible such that it can be engineered to recognize any sequence within the genome such that the sites do not constitute any structural difference from a natural soybean plant. According to the Examiner’s BRI of the claims, this encompasses any soybean plant with any transgene on chromosome 4 within the claimed window as well as traits listed wherein it is noted that in addition to the numerous traits listed that many of the categories are broad such that literally thousands of genes some known and some unknown would be encompassed within the claims as currently written. Even with the transgene now required to be within a genomic window of about 1cM, even within the specified sites the claims read on any soybean with any transgene within that window such that any soybean transformation using random insertion with Agrobacterium are encompassed by the claims so long as said insertion site was within the 1cM region at the specified sites, which still reads on literally any trait and any transgene. It is noted that the only requirement appears to be a location which is not novel, but rather present in every soybean plant modified or not. Accordingly, one of skill in the art would not be able to determine whether or not they were in possession of Applicant’s claimed invention.
Response to Arguments
Applicant's arguments filed 03/11/20269 have been fully considered but they are not persuasive.
Applicants urge that contrary to the Examiner’s contention that the recited target sites so not confer a meaningful structural distinction, that the claims are not directed to plants merely having a naturally occurring genomic window, but rather, require integration of donor DNA within a defined set of target sites from a closed list of specific nucleotide sequences and that a double strand break is required such that the resulting plant or cell necessarily comprises a new recombinant genomic structure (see pages 7-8 of response).
This is not persuasive because the claims do not specify, and the specification does not instruct as to what this changed structure is. While Applicant’s specifically point to sites within the genome, whether it is a window, or a closed set of target sites that are more specific, there is no description of what the resultant changed structure and plant is, or what it must have. AS to the contention that it must be recombinant, the claims would read on donor DNA that is identical to the endogenous DNA, furthermore, because the window and sites are specified without any particular set genome sequence for the recipient, the claims currently read on literally any natural or otherwise variation within the cited region and sites.
While it is recognized that Applicants have recognized the location, the location itself, does exist in nature, and as such it is problematic to determine the scope without additional limitations on the structure that would better distinguish the product from prior art. In effect, the claims are drawn to any change or any transgene conferring any function or trait, so long as it is located within the claimed genomic window or at a specific target site.
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 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 1, 3, and 5-11 remain rejected under 35 U.S.C. 103 as being unpatentable over Falco et al (USPGPUB 20130198888) in view of Wu et al (US Patent 9738908), in view of Hyten et al (2010 BMC Genomics 11:38), Kim et al (2012 Theor. Appl. Genet. 125:1353-1369), Mian et al (1996 Theor. Appl. Genet. 93(7) 1011-1016, further in view of Cui et al (USPGPUB20130324408, published December 5, 2013), in view of Finer et al (US Patent 5693512) and further in view of Sastry-Dent US Patent 9909131, filed on 11/04/2013).
The claims are broadly drawn to a soybean plant with any phenotype with any transgene, inserted within its genome on chromosome 4 within the specified target sites listed in the claims. It is firstly pointed out that many of the above limitations are not limited by sequence as the claimed platform is flexible such that it can be engineered to recognize any sequence within the genome such that the sites do not constitute any structural difference from a natural soybean plant. According to the Examiner’s BRI of the claims, this encompasses any soybean plant with any transgene on chromosome 4 within the claimed window at the claimed sites as well as traits listed wherein it is noted that in addition to the numerous traits listed that many of the categories are broad such that literally thousands of genes some known and some unknown would be encompassed within the claims as currently written. Even with the transgene required to be within a genomic window and at the specified sites, the claims read on any soybean with any transgene within that window such that any soybean transformation using random insertion with Agrobacterium are encompassed by the claims so long as said insertion site was within the 1cM region at a specified site, which in the instant case is not defined as to its location. To further underscore the full breadth of the claims, they would additionally read on the replacement of any endogenous genes within the region such that any soybean with variation would read on the product claims as currently claimed.
Falco et al teach plant and methods of producing a complex trait locus in plants including soybean plants (see claims 1, 14, 20) wherein the plant has in its genome a genomic window comprising a first transgenic target site, a second transgenic target site wherein the window is about 10 cM in length (see claim 1) wherein the site is a double-strand-break site (see claim 31) wherein the site is flanked by specific markers (see claim 29), wherein the window comprises a transgene that confers a trait such as herbicide resistance (see claims 8 and 26, for example), wherein the first and second recombination sites comprised by the target are dissimilar to each other (see claim 4) wherein the sites comprise a LOX site, a mutant LOX site an FRT site or a mutant FRT site (see claim 11 or 28, for example), wherein the site comprises an FRT1, FRT5, FRT6, FRT12 or FRT87 site (see claims 11 or 28, for example) and the enzyme is a meganuclease (see under heading Generating a Transgenic Plant Containing the Complex Trait Loci 3A, for example).
Falco et al does not teach the above wherein the enzyme used for the double strand breaks is Cas or wherein the markers flanking the genomic window are SEQ ID NO:4 and SEQ ID NO:19.
Hyten et al teach a polymorphic site within the genomic window instantly claimed. It is additionally noted that several QTLs in the prior art have been mapped within this genomic window and would provide additional motivation for one of skill in the art to make genomic modifications in one or more genes in this region. For example, Kim et al (2012 Theor. Appl. Genet. 125:1353-1369) teach a QTL for seed yield that overlaps this region mapping between 11.51 and 16.61, and Mian et al 1996 Theor. Appl. Genet. 93(7) 1011-1016 teach a QTL associated with seed weight mapping between 17.62 and 19.62 cM, which falls within the window of the instantly claimed markers.
Cui et al teach the genetic modification on soybean chromosome 4, targeting a specific region for gene stacking and state “ The subject, invention discloses herein a specific site 011 chromosome 4 in the soybean genome that is excellent, for insertion of heterologous nucleic acids. Also disclosed is a 5' molecular marker, a 3' molecular marker, a 5' flanking sequence, and a 3' flanking sequence useful in identifying the location of a targeting site on chromosome 4 “ (see claims 1, 7, 17, 19 as well as 6th paragraph preceding the examples as well as Example 10 for gene stacking).
Wu et al teach SEQ ID NOs indicating that genes herein were known in the art, and demonstrate that sequences for generating guide RNAs were already known in the prior art.
Finer et al teach the modification of soybean variety Jack, and all of the soybean varieties claimed were known in the art at the time of filing and are deemed to be design choices for elite and non-elite varieties respectively.
Sastry-Dent et al teach locating optimized positions on chromosome 4 of soybean for genomic modification including the use of CRISPR/Cas (see claims 10, 11 and wherein SEQ ID NO:637 is on chromosome 4).
Given the state of the art at the time of filing, the disclosures by Falco et al , Hyton et al, Kim et al, Mian et al, Cui et al, Wu et al and Sastry-Dent et al it would have been obvious to one of ordinary skill in the art to modify known genes in the region instantly claimed using CRISPR/Cas technology which was known in the art as demonstrated by Sastry-Dent et al, and it would have been further obvious to generate guide RNAs of sequences within the known genes as taught and suggested by Sastry-Dent et al in view of Wu et al. Gene stacking and modification of specific locations within the soybean genome, even of chromosome 4, was known in the prior art as demonstrated by the references cited herein. It is noted that any soybean plant with any CRISPR/Cas genetic modification within a window at the specified locations in chromosome 4 is encompassed within the claims as instantly written. As demonstrated in the prior art, using CRISPR/Cas to alter the genome on soybean chromosome 4 for the purposes of trait stacking was known in the prior art at the time of filing. Furthermore, Hyten et al, Kim et al and Mian et al demonstrate the presence of existing markers, polymorphisms and agronomic traits of interest within the region encompassed by markers SEQ ID NO:4 and SEQ ID NO:50, Accordingly no claims are allowed. It is noted that it is not clear from the claims how any given gene at a specified target site would alter it with respect to a gene inserted elsewhere within the claimed genome and the location would appear to be interchangeable in effect.
It is noted that the method claims do not have any active methods steps requiring specific markers to distinguish from generic methods for selection.
Response to Arguments
Applicant's arguments filed 05/27/2026 have been fully considered but they are not persuasive.
Applicants urge that the claims are amended and that the references do not teach the claims as currently written and do not teach or reasonably suggest the specific target sites listed within the claims.
This is not persuasive because the claims are drawn to products that are not defined as to the structure that is required such that one of skill in the art would be able to distinguish between the cited art references and the instant claims. No structural requirements beyond the location of an insertion are required by the instant claims, it would have been obvious to select any site and any given site is a design choice absent evidence to the contrary.
No claims are allowed.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRENT T PAGE whose telephone number is (571)272-5914. The examiner can normally be reached M-F 7-4 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached at 5712707058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/BRENT T PAGE/Primary Examiner, Art Unit 1663
Prosecution Insights