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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 9/12/2025 has been entered.
Claim Status
Claims 1, 10, 12-15 and 21-28 are pending.
Claims 21-27 are withdrawn as being drawn to unelected inventions.
Claim 1 is newly rejected.
Claims 1, 10, 12-15 and 28 are rejected.
Response to Applicant Arguments - Claim Objections
In response to Applicant’s arguments and amendments made 8/14/2025 the claim objections of record are withdrawn.
Response to Applicant Arguments - 35 USC § 112 Written Description
Applicant’s arguments and amendments made 08/14/2025 have been fully considered but are not found to be persuasive.
Applicant’s arguments are drawn to the following concept:
The independent claim has been amended to recite that the amino acid sequence of the variant polypeptide differs by at most 20 positions, after alignment with a sequence of SEQ ID NOs: 1-7 and further that the independent claim has been limited to recite soybean cells rather than plant cells and therefore the claimed invention has been adequately described.
This argument is not found to be persuasive because while the amendments made to the claims have narrowed the scope, the claims remain broadly drawn to variant sequences.
Importantly, the specification notes in the first paragraph that a soybean Lr67 variant sequence allele conveys fungal pathogen tolerance. However, the applicants provide only a single example of a soybean Lr67 allele the having the G145R and V389L mutations that exhibits that function. Applicant has not described any other specific sequences or features that are linked to that function such that the ordinary artisan would be able to determine if a specific sequence was a soybean Lr67 variant sequence.
In particular applicant claims variants which require a mutation at position G145 but do not require the optional mutation at position V389 and further these variants can comprise an additional 19 mutations.
This introduces two areas of concern.
First, applicant’s claimed variants are required only to have the G145 mutation however applicants only example that is reduced to practice comprises both the G145 and V389 mutations. Given this description in the specification it is not clear whether the G145 or V389 mutations alone are capable of imparting the function of fungal pathogen tolerance which appears to be required for variant sequences or if instead both of these mutations are required.
Second, applicant’s broad genus of claimed variants includes variants which comprise mutations at any position in the reference sequences including those that surround the required mutation at position G145. It is not clear how these other mutations affect the fungal pathogen resistance that appears to be conferred by the G145 and V389 mutations.
Therefore, while applicant has limited the scope to variants that differ from the references at 20 positions or less and provides a large list of possible mutations, this still represents a large list of variants and there is no structure function relationship demonstrated in the specification that would allow the ordinary artisan to determine how these different combinations would affect the function of the claimed variant sequences.
As such applicant’s arguments are not found to be persuasive and the rejections of record are maintained.
Written Description
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.
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.
Due to Applicant’s amendment of the claims, the rejection is modified from the rejection as set forth in the Office action mailed 03/14/2025 as applied to claims 1, 10, 12-15 and 28. Applicant’s arguments filed on 08/14/2025 have been fully considered but they are not persuasive, see response to applicant arguments above.
Claims 1, 10, 12-15 and 28 remain 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.
Independent claim 1 is drawn to a soybean cell comprising a gene encoding a variant polypeptide having an amino acid sequence comprising a mutation at position G145 and where the amino acid sequence of the variant differs by at most 20 positions after alignment, from SEQ ID NOs: 1-7, wherein the additional mutations are selected from a broad list provided in the claim.
Importantly, the specification notes in the first paragraph that a soybean Lr67 variant sequence allele conveys fungal pathogen tolerance.
However, applicant’s description in the examples provided in the specification demonstrates that variants having a mutation at position 145, specifically the G145R mutation and a mutation at position 389, specifically V389L exhibit this fungal pathogen tolerance.
Applicants have not provided a representative number of species sufficient to demonstrate that they were in possession of the claimed genus of variant sequences.
This is because the broadest reasonable interpretation of the independent claim requires the variant to only have a mutation at position 145 and as noted above variant sequences confer fungal pathogen tolerance.
The specification provides no examples of a variant sequence comprising only the mutation at position or any examples comprising the mutation at position 389. As such applicants provide no examples which demonstrate that the mutation at position 145 alone is sufficient to produce a variant sequence having the implicit function of enhanced tolerance to fungal pathogens.
Stated differently applicant has not provided adequate description such that the ordinary artisan would be able to determine that the mutation at position 145 is responsible for the fungal pathogen resistance phenotype. Given the examples provided in the claims it could be either the mutation at position 389 or the combination of the two mutations disclosed in applicant’s examples including example 6 which lead to the enhanced fungal pathogen resistance phenotype.
Further, because applicant provides only a single example of a soybean Lr67 allele the having the G145R and V389L mutations that exhibits that function Applicant has not described any other specific sequences or features that are linked to that function such that the ordinary artisan would be able to determine if a specific sequence was a soybean Lr67 variant sequence.
To illustrate, applicant’s claimed variants can comprise 18 additional mutations beyond those at positions 145 and 389 of the reference sequence. The mutations can occur at any position within that sequence including those immediately flanking positions 145 and 389. However, applicant has not provided any representative species having mutations at these flanking residues and it is not clear if these additional mutations would have affected the enhanced fungal pathogen resistance phenotype conferred by the G145R and V389L. As such without further examples of representative species of the claimed variants it is not clear if a sequence comprising the above described additional mutations is one of the claimed variants and as such it does not appear that applicant is in possession of the full scope of the claimed invention.
This is because there is no guidance on how any of the claimed mutations affect pathogen tolerance.
In order to describe a genus, description can be provided which describes a representative number of species of the claimed genus or a structure function relationship between the claimed structure and their claimed or implicit functions.
In the instant case applicant has not provided a structure function relationship between specific mutations in a Lr67 variant sequence and the function of enhanced fungal pathogen tolerance. Similarly applicant has provided a single example of a representative species of the claimed genus which fails to clarify the causal mutation for the enhanced fungal pathogen tolerance phenotype. This single example is therefore not a representative number of species of the claimed invention.
Therefore, given the disparity between what is described in the specification and the recitations in the claim, applicant has not provided any description on the features that must be maintained to identify a variant sequence nor has the applicant provided description of any soybean plant cell having variant sequence with the exception of the single example described above.
While the state of the art is clear on the function and activity of wheat Lr67 as well as Lr67 genes from several other species including grape, Arabidopsis and one legume, it is silent on variant sequences as described in the specification (Dinglasan, Essays in biochemistry 66.5 (2022): 571-580) (Dinglasan, Page 574, First Full Paragraph).
Therefore, as described in the analysis above, it is unclear which combination of mutations at which positions create the claimed variants and what motifs or sequences must be conserved in order to maintain the characteristics of the claimed variant sequences.
Thus, the state of the art at the earliest filing date was such that although the skilled artisan would understand Lr67 resistance genes and understand variant sequences. Would understand the concept of homologous genes and how to identify genes sharing sequence identity. The ordinary artisan would not be able to readily predict which sequences of the broadly claimed genus are variant sequences. Nor would they know which specific motifs, domains, or sequences must be present to retain the desired characteristics of the variant sequences. Further they would not know which sequences, domains or motifs must be present or absent in order for a sequence to be a variant sequence of the instant invention and to have the inherent property of decreased susceptibility to fungal pathogens.
The analysis will now turn to the second element of the court’s decision in Eli Lilly; namely, the description of a representative number of species. As discussed above, the broadly claimed genus of nearly any sequence in nearly any cell is enormous in size--encompassing an extremely large number and nearly any cell.
Given the broad structural variable associated with these embodiments, the claims read on broad and diverse structures encoded by the broad genus of sequences. Thus, in view of the analysis presented above, a skilled artisan would appreciate that the claims are directed to a broad and diverged genus of genes in any soybean cell.
In contrast, Applicant has only appeared to describe a single specific sequence having the inherent property of a variant polypeptide (Instant Specification, Page 1, Lines 6-9).
Applicant’s disclosure is not representative of the claimed genus as a whole.
Thus, based on the analysis above, Applicant has not met either of the two elements of the written description requirement as set forth in the court's decision in Eli Lilly. As a result, it is not clear that Applicant was in possession of the claimed genus at the time this application was filed and claims 1, 10, 12-15 and 28 remain rejected as lacking written description.
Response to Applicant Arguments - 35 USC § 112 Scope of Enablement
Applicant’s arguments and amendments made 08/14/2025 have been fully considered but are not found to be persuasive.
Applicant’s arguments are drawn to the following concept:
The independent claim has been amended to recite that the amino acid sequence of the variant polypeptide differs by at most 20 positions, after alignment with a sequence of SEQ ID NOs: 1-7 and further that the independent claim has been limited to recite soybean cells rather than plant cells and therefore the claimed invention has been adequately described.
This argument is not found to be persuasive because while the amendments made to the claims have narrowed the scope, the claims remain broadly drawn to variant sequences.
Importantly, the specification notes in the first paragraph that a soybean Lr67 variant sequence allele conveys fungal pathogen tolerance. However, the applicants provide only a single example of a soybean Lr67 allele the having the G145R and V389L mutations that exhibits that function. Applicant has not described any other specific sequences or features that are linked to that function such that the ordinary artisan would be able to determine if a specific sequence was a soybean Lr67 variant sequence.
In particular applicant claims variants which require a mutation at position G145 but do not require the optional mutation at position V389 and further these variants can comprise an additional 19 mutations.
This introduces two areas of concern.
First, applicant’s claimed variants are required only to have the G145 mutation however applicants only example that is reduced to practice comprises both the G145 and V389 mutations. Given this description in the specification it is not clear whether the G145 or V389 mutations alone are capable of imparting the function of fungal pathogen tolerance which appears to be required for variant sequences or if instead both of these mutations are required.
Second, applicant’s broad genus of claimed variants includes variants which comprise mutations at any position in the reference sequences including those that surround the required mutation at position G145. It is not clear how these other mutations affect the fungal pathogen resistance that appears to be conferred by the G145 and V389 mutations.
Therefore, while applicant has limited the scope to variants that differ from the references at 20 positions or less and provides a large list of possible mutations, this still represents a large list of variants and there is no structure function relationship demonstrated in the specification that would allow the ordinary artisan to determine how these different combinations would affect the function of the claimed variant sequences.
Without further guidance the ordinary artisan would be required to identify any of the large number of claimed variant sequences, screen these putative sequences in order to determine which sequences are variants and define criteria for identifying these genes. Then they would be have to carefully analyze these variants in order to determine which loci were responsible for conferring decreased susceptibility to pathogen infection in soybean, specifically whether either mutations at positions G145 or V389 alone could confer pathogen resistance. Further, the ordinary artisan would then be required to investigate how any combination of 19 other mutations could affect the pathogen resistance phenotype conferred by the other mutations. Then the applicant would have to transform these sequences into any soybean plant cell whatsoever and determine which sequences conferred decreased susceptibility to pathogens to any soybean cell.
This is amount of experimentation is undue and represents an invitation to experiment rather than enabled guidance.
As such applicant’s arguments are not found to be persuasive and the rejections of record are maintained.
Claim Rejections - 35 USC § 112 – Scope of 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.
Due to Applicant’s amendment of the claims, the rejection is modified from the rejection as set forth in the Office action mailed 03/14/2025 as applied to claims 1, 10, 12-15 and 28. Applicant’s arguments filed on 08/14/2025 have been fully considered but they are not persuasive, see response to applicant arguments above.
Claims 1, 10, 12-15 and 28 remain rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for soybean or agrobacterium cells comprising one specific soybean allele; Glyma.01g238800.1G145R_V389L, does not reasonably provide enablement for the broadly claimed genus of any soybean cell whatsoever having a variant sequence as claimed. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
Independent claim 1 is drawn to a soybean cell comprising a gene encoding a variant polypeptide having an amino acid sequence comprising a mutation at position G145 and where the amino acid sequence of the variant differs by at most 20 positions after alignment, from SEQ ID NOs: 1-7, wherein the additional mutations are selected from a broad list provided in the claim.
Importantly, the specification notes in the first paragraph that a soybean Lr67 variant sequence allele conveys fungal pathogen tolerance.
An “analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.” MPEP 2164.01. “A conclusion of lack of enablement means that. . . the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention [i.e. commensurate scope] without undue experimentation.” In re Wright, 999 F.2d 1557,1562, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993); MPEP 2164.01.
In In re Wands, 858 F.2d 731,8 USPQ2d 1400 (Fed. Cir. 1988), several factors implicated in determination of whether a disclosure satisfies the enablement requirement and whether any necessary experimentation is “undue” are identified. These factors include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). No single factor is independently determinative of enablement; rather “[i]t is improper to conclude that a disclosure is not enabling based on an analysis of only one of the above factors while ignoring one or more of the others.” MPEP 2164.01. Likewise, all factors may not be relevant to the enablement analysis of any individual claim.
Here the claims recite the broad genus as described above. This is broad for several reasons, first, as there are 522 different positions, each with at least two possible mutations listed and given that the variant sequence can include any number up to 20 of these mutations which can occur at any one position or combination of positions the number of variant sequences is large.
As noted above, the specification notes in the first paragraph that a soybean Lr67 variant sequence allele conveys fungal pathogen tolerance. However, applicant’s description in the examples provided in the specification demonstrates that variants having a mutation at position 145, specifically the G145R mutation and a mutation at position 389, specifically V389L exhibit this fungal pathogen tolerance.
Applicants have not provided sufficient guidance such that a representative number of species sufficient to demonstrate that they were in possession of the claimed genus of variant sequences.
This is because the broadest reasonable interpretation of the independent claim requires the variant to only have a mutation at position 145 and as noted above variant sequences confer fungal pathogen tolerance.
The specification provides no guidance of a variant sequence comprising only the mutation at position or any examples comprising the mutation at position 389. As such applicants provide no guidance which demonstrates that the mutation at position 145 alone is sufficient to produce a variant sequence having the implicit function of enhanced tolerance to fungal pathogens.
Stated differently applicant has not provided guidance such that the ordinary artisan would be able to determine that the mutation at position 145 is responsible for the fungal pathogen resistance phenotype. Given the guidance provided in the claims it could be either the mutation at position 389 or the combination of the two mutations disclosed in applicant’s examples including example 6 which lead to the enhanced fungal pathogen resistance phenotype.
Further, because applicant provides only a single example of a soybean Lr67 allele the having the G145R and V389L mutations that exhibits that function Applicant has not described any other specific sequences or features that are linked to that function such that the ordinary artisan would be able to determine if a specific sequence was a soybean Lr67 variant sequence.
To illustrate, applicant’s claimed variants can comprise 18 additional mutations beyond those at positions 145 and 389 of the reference sequence. The mutations can occur at any position within that sequence including those immediately flanking positions 145 and 389. However, applicant has not provided any guidance on variants having mutations at these flanking residues and it is not clear if these additional mutations would have affected the enhanced fungal pathogen resistance phenotype conferred by the G145R and V389L. As such without further guidance on the claimed variants it is not clear if a sequence comprising the above described additional mutations is one of the claimed variants and as such it does not appear that applicant is in possession of the full scope of the claimed invention.
This is because there is no guidance on how any of the claimed mutations affect pathogen tolerance.
In the instant case applicant has not provided a structure function relationship between specific mutations in a Lr67 variant sequence and the function of enhanced fungal pathogen tolerance. Similarly applicant has provided guidance on a single example of a member of the claimed genus of variants which fails to clarify the causal mutation for the enhanced fungal pathogen tolerance phenotype. This single guidance is therefore not sufficient for the ordinary artisan to make and use the invention without undue experimentation.
Therefore, given the disparity between what is described in the specification and the recitations in the claim, applicant has not provided any enabled guidance on the features that must be maintained to identify a variant sequence nor has the applicant provided description of any soybean plant cell having variant sequence with the exception of the single example described above.
Thus, the state of the art at the earliest filing date was such that although the skilled artisan would understand Lr67 resistance genes and understand variant sequences. Would understand the concept of homologous genes and how to identify genes sharing sequence identity. The ordinary artisan would not be able to readily predict which sequences of the broadly claimed genus are variant sequences having the implicit function of enhanced tolerance to fungal pathogens. Nor would they know which specific motifs, domains, or sequences must be present to retain the desired characteristics of the variant sequences. Further they would not know which sequences, domains or motifs must be present or absent in order for a sequence to be a variant sequence of the instant invention and to have the inherent property of decreased susceptibility to fungal pathogens.
Without some guidance on how to determine if a sequence from the large genus is the claimed variant, the ordinary artisan at the time of filing would not have be able to identify a variant sequence, identify or generate a variant sequence and then introduce that sequence into any soybean cell whatsoever without undue experimentation.
This experimentation would have been undue because Applicant has not provided enabling guidance for any member of a large genus of sequences in any soybean cell whatsoever, to be able to reduce or abolish the susceptibility of a soybean plant to infection.
Instead there is a single enabled example which is narrowly drawn to a very specific DNA sequence in single soybean cell type.
Without further guidance the ordinary artisan would be required to identify any of the large number of claimed variant sequences, screen these putative sequences in order to determine which sequences are variants and define criteria for identifying these genes (Emphasis added). Then they would be have to carefully analyze these genes in order to determine which loci were responsible for conferring decreased susceptibility to pathogen infection in soybean. Then the applicant would have to transform these sequences into any soybean plant cell whatsoever and determine which sequences conferred decreased susceptibility to pathogens to any soybean cell.
This is amount of experimentation is undue and represents an invitation to experiment rather than enabled guidance.
As demonstrated above, in the absence of guidance from either the instant disclosure or the art, it would require trial and error experimentation for a skilled artisan to identify a variant sequence as claimed, generate the claimed modifications and then determine if it functioned as described to reduce susceptibility to pathogenesis.
Thus, in view of the unpredictability associated with pathogen resistance, the lack of enabling guidance from either the instant disclosure or the art, and breath and diversity of the embodiments encompassed by the claimed genus, the lack of sufficient working examples, and the level of the art at the time of the invention, one of ordinary skill in the art must rely on undue trial and error experimentation to make and test the numerous variant sequences in any plant cell in order to make and/or use the invention within the full scope of these Claims.
For at least this reason, the Specification does not teach a person with skill in the art how to make and/or use the subject matter within the full scope of these Claims. Therefore, claims 1, 10, 12-15 and 28 remain rejected as lacking enablement.
Art Rejections
As noted above in the written description and scope of enablement rejections the scope of the terms Lr67 genes and alleles appear to be extremely broad while the description and guidance provided in the specification are limited to a single example.
Art rejections would have been applied, however, independent claim 1 recites the limitation “the one or more mutations comprise, in the numbering according to SEQ ID NO. 1, a substitution at position G145”. This specific residue appears to be highly conserved in sequences having sequence identity to the sequences of instant SEQ ID NOs: 1-7 and therefore art rejections were not applied at this time.
Conclusion
All examined claims are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN JAMES SULLIVAN whose telephone number is (571)272-0561. The examiner can normally be reached 7:30 to 5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached on (571)270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BRIAN JAMES SULLIVAN/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663