DETAILED ACTION
1. This office action is in response to application 19/342,289 filed on 9/26/2025. Claims 1-19 are pending in this office action.
Notice of Pre-AIA or AIA Status
2. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
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.
3. The term “some steps” in claim 13 is a relative term which renders the claim indefinite. The term “some steps” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention as it is unclear which steps would be implemented from claim 1.
Double Patenting
4. The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 and 13 of U.S. Patent No. 12,451,215 in view of US 2025/0042956 (hereinafter Jacobsen). Although the claims at issue are not identical, they are not patentably distinct from each other because the limitations in bold are the same the differences would have been obvious to an artisan of ordinary skill in the art. For instance with respect to claim 1 the instant application does not calculate a (discounted) cumulative gain for each candidate list (Can1, Can2, Can3 taking into consideration the order of the candidate in the respective list while U.S. Patent No. 12,451,215 does calculate a (discounted) cumulative gain for each candidate list (Can1, Can2, Can3 taking into consideration the order of the candidate in the respective list and it would be obvious to an artisan of ordinary skill in the art that a formula is used to calculate a performance value.
19/342,289 12,451,215
1. A method for identifying at least one candidate (Loc), namely a gene location and/or a sequence variant, indicative for at least one selected (phenotypic) trait of an organism, in particular of a plant, comprising the steps of: a. receiving a plurality of candidate lists (Canl, Can2, Can3) of candidates (Loc), the candidate lists being ordered; b. receiving a reference set (RefDB) with gene locations and/or sequence variants; c. matching at least a subset of candidates (Loc) from the candidate lists (Canl, Can2, Can3) with the reference list (RefDB) to determine an evaluation value (EV) for at least the subset; d. assigning each evaluation value (EV) to the respective candidate (Loc) in the respective candidate lists (Can1, Can2, Can3); e. calculating for each candidate list a performance value based on the evaluation value (EV), in particular by using the evaluation values (EV); and f. selecting at least one candidate (Loc) as (preferred) candidate (Loc) from one of the candidate lists (Can1, Can2, Can3) using the performance values.
1. A method for identifying at least one candidate (Loc), namely a gene location and/or a sequence variant, indicative for at least one selected (phenotypic) trait of an organism, in particular of a plant, comprising the steps of: a. receiving a plurality of candidate lists (Can1, Can2, Can3) of candidates (Loc), the candidate lists being ordered; b. receiving a reference set (RefDB) with gene locations and/or sequence variants; c. matching at least a subset of candidates (Loc) from the candidate lists (Can1, Can2, Can3) with the reference list (RefDB) to determine an evaluation value (EV) for at least the subset; d. assigning each evaluation value (EV) to the respective candidate (Loc) in the respective candidate lists (Can1, Can2, Can3); e. calculating, for each candidate list, a performance value based on the evaluation value (EV), in particular by using the evaluation values (EV), and calculating a (discounted) cumulative gain for each candidate list (Can1, Can2, Can3 taking into consideration the order of the candidate in the respective list and the evaluation value (EV) assigned to the respective candidate in the respective candidate list (Can1, Can2, Can3); and f. selecting at least one candidate (Loc) as (preferred) candidate (Loc) from one of the candidate lists (Can1, Can2, Can3) using the performance values.
2. The method according to claim 1, comprising the step of at least partially creating the reference set (RefDB) by: selecting data sets indicative of a plurality of individuals, wherein the plurality of individuals comprises individuals having the selected phenotypic trait and individuals not having the selected phenotypic trait; analyzing the plurality of individuals using a genomic analysis, a proteomic analysis, a transcriptomic analysis, and/or a cellomic analysis to obtain an analysis result, in particular at least partially sequencing the DNA and/or RNA of the plurality of selected individuals to obtain a DNA and/or RNA sequence; - correlating the analysis result, in particular the DNA and/or RNA sequence, to determine a candidate to be stored in the reference set (RefDB).
2. The method according to claim 1, comprising the step of at least partially creating the reference set (RefDB) by: selecting data sets indicative of a plurality of individuals, wherein the plurality of individuals comprises individuals having the selected phenotypic trait and individuals not having the selected phenotypic trait; analyzing the plurality of individuals using a genomic analysis, a proteomic analysis, a transcriptomic analysis, and/or a cellomic analysis to obtain an analysis result, in particular at least partially sequencing the DNA and/or RNA of the plurality of selected individuals to obtain a DNA and/or RNA sequence; and correlating the analysis result, in particular the DNA and/or RNA sequence, to determine a candidate to be stored in the reference set (RefDB).
3. The method of claim 1, step e) comprising: generating an ordered evaluation list for each candidate list (Can1, Can2, Can3) by giving each evaluation value (EV) an order in the ordered evaluation list that correlates with the order of the candidate that the respective evaluation value (EV) is assigned to.
3. The method of claim 1, step e) comprising: generating an ordered evaluation list for each candidate list (Can1, Can2, Can3) by giving each evaluation value (EV) an order in the ordered evaluation list that correlates with the order of the candidate that the respective evaluation value (EV) is assigned to.
4. The method of claim 1, step e) comprising: calculating a (discounted) cumulative gain for each candidate list (Can1, Can2, Can3) based on the ordered evaluation list.
4. The method of claim 1, step e) comprising: calculating a (discounted) cumulative gain for each candidate list (Can1, Can2, Can3) based on the ordered evaluation list.
5. The method of claim 1, step c) comprising: calculating a (discounted) cumulative gain for each candidate list (Can1, Can2, Can3) taking into consideration the order of the candidate in the respective list and the evaluation value (EV) assigned to the respective candidate in the respective candidate list (Canl, Can2, Can3).
4. The method of claim 1, step e) comprising: calculating a (discounted) cumulative gain for each candidate list (Can1, Can2, Can3) based on the ordered evaluation list.
6. The method of claim 1, step f) comprising: calculating a normalized performance (120) value for each candidate list, in particular by using a softmax algorithm.
5. The method of claim 1, step f) comprising: calculating a normalized performance (120) value for each candidate list, in particular by using a softmax algorithm.
7. The method of claim 1, wherein the reference list (RefDB) assigns at least one category to each candidate in the reference list, the method comprising the steps of: determining a numerical value for each category; using the numerical value to determine the evaluation values.
6. The method of claim 1, wherein the reference list (RefDB) assigns at least one category to each candidate in the reference list, the method comprising the steps of: determining a numerical value for each category; and using the numerical value to determine the evaluation values.
8. The method of claim 1, comprising the step of assigning a null value or a negative value as evaluation value to candidates which are not contained in the reference list (RefDB).
7. The method of claim 1, comprising the step of assigning a null value or a negative value as evaluation value to candidates which are not contained in the reference list (RefDB).
9. The method of claim 1, comprising measuring aggregated effects in an organism; updating or adding entries in the reference list based on the measured aggregated effect, the entries comprising an indication of a gene location and/or sequence variant as well as an evaluation value (EV).
8. The method of claim 1, comprising measuring aggregated effects in an organism; and updating or adding entries in the reference list based on the measured aggregated effect, the entries comprising an indication of a gene location and/or sequence variant as well as an evaluation value (EV).
10. A method for identifying an individual comprising the steps of: a. identifying a candidate indicative for at least one phenotypic trait of an organism in accordance with the method of claim 1; b. determining based on the selected candidate a target sequence variant and/or gene location which is likely to be associated with the (phenotypic) trait; c. identifying an individual comprising said sequence variant.
9. A method for identifying an individual comprising the steps of: a. identifying a candidate indicative for at least one phenotypic trait of an organism in accordance with the method of claim 1; b. determining based on the selected candidate a target sequence variant and/or gene location which is likely to be associated with the (phenotypic) trait; and c. identifying an individual comprising said sequence variant.
11. The method of claim 10, wherein the identification of the individual comprises a genomic analysis, a proteomic analysis, a transcriptomic analysis, and/or a cellomic analysis of a plurality of individuals of the organism.
10. The method of claim 9, wherein the identification of the individual comprises a genomic analysis, a proteomic analysis, a transcriptomic analysis, and/or a cellomic analysis of a plurality of individuals of the organism.
12. The method of claim 11, wherein the identification of the individual comprises sequencing the DNA and/or RNA of a plurality of individuals of the organism and comparing the target sequence variant with the sequence variant of the individuals; and/or wherein determining the target sequence variant comprises: obtaining a plurality of individuals showing the selected (phenotypic) trait; sequencing the DNA and/or RNA of the plurality of individuals to obtain genetic information; -using the genetic information of the plurality of individuals to determine the target sequence variant.
11. The method of claim 10, wherein the identification of the individual comprises sequencing the DNA and/or RNA of a plurality of individuals of the organism and comparing the target sequence variant with the sequence variant of the individuals; and/or wherein determining the target sequence variant comprises: obtaining a plurality of individuals showing the selected (phenotypic) trait; sequencing the DNA and/or RNA of the plurality of individuals to obtain genetic information; and using the genetic information of the plurality of individuals to determine the target sequence variant.
13. A computer readable medium comprising instructions, the instructions implementing the method of claim 1 when being executed or at least some steps of the method of claim 1.
(See the rejection of claim 1).
14. A method for modifying at least one phenotypic trait of an organism, in particular of a plant, comprising the steps of: a. selecting a first and a second individual in accordance with the method of claim 10; b. crossing the first and the second individual to create the organism with the phenotypic trait.
13. A method for modifying at least one phenotypic trait of an organism, in particular of a plant, comprising the steps of: a. selecting a first and a second individual in accordance with the method of claim 9; and b. crossing the first and the second individual to create the organism with the phenotypic trait.
15. A modified plant, produced by a method comprising the steps of: selecting a first individual and a second individual by a. identifying a candidate indicative for at least one phenotypic trait of an organism in accordance with the method of claim 1; b. determining, based on the selected candidate, a target sequence variant and/or gene location which is likely to be associated with the phenotypic trait; and c. identifying an individual comprising said sequence variant; and crossing the first and the second individual to create the modified plant, wherein the modified plant has the phenotypic trait.
9. A method for identifying an individual comprising the steps of: a. identifying a candidate indicative for at least one phenotypic trait of an organism in accordance with the method of claim 1; b. determining based on the selected candidate a target sequence variant and/or gene location which is likely to be associated with the (phenotypic) trait; and c. identifying an individual comprising said sequence variant.
With respect to claim 16 Jacobsen discloses: wherein the modified plant comprises a vegetable plant (See paragraph 0258 note suitable plants include vegetables). It would have been obvious to an artisan of ordinary skill in the pertinent at the time the instantly claimed invention was filed to have incorporated the teaching of Jacobsen into the system of US 12,451,215. The modification would have been obvious because the two references are concerned with the solution to problem of plant modification (See Jacobsen and US 12,451,215 abstracts), therefore there is an implicit motivation to combine these references (i.e. motivation from the references themselves). In other words, the ordinary skilled artisan, during his/her quest for a solution to the cited problem, would look to the cited references at the time the invention was made. Consequently, the ordinary skilled artisan would have been motivated to combine the cited references since Jacobsen’s teaching would enable users of the US 12,451,215 system to have more efficient processing of plant information.
With respect to claim 17 Jacobsen discloses: wherein the modified plant comprises a sugar beet, maize, cereal, rapeseed, sorghum, sunflower, potato, pea, pepper, tomato, spinach, cucumber, bean, or cabbage plant (See paragraph 0258 note cucumber, tomato, lima beans etc.). It would have been obvious to an artisan of ordinary skill in the pertinent at the time the instantly claimed invention was filed to have incorporated the teaching of Jacobsen into the system of US 12,451,215. The modification would have been obvious because the two references are concerned with the solution to problem of plant modification (See Jacobsen and US 12,451,215 abstracts), therefore there is an implicit motivation to combine these references (i.e. motivation from the references themselves). In other words, the ordinary skilled artisan, during his/her quest for a solution to the cited problem, would look to the cited references at the time the invention was made. Consequently, the ordinary skilled artisan would have been motivated to combine the cited references since Jacobsen’s teaching would enable users of the US 12,451,215 system to have more efficient processing of plant information.
With respect to claim 18 Jacobsen discloses: wherein the modified plant comprises a member of a genus selected from the group consisting of Hordeum, Sorghum, Saccharum, Zea, Setaria, Oryza, Triticum, Secale, Triticale, Malus, Brachypodium, Aegilops, Daucus, Beta, Eucalyptus, Nicotiana, Solanum, Coffea, Vitis, Erythrante, Genlisea, Cucumis, Marus, Arabidopsis, Crucihimalaya, Cardamine, Lepidium, Capsella, Olmarabidopsis, Arabis, Brassica, Eruca, Raphanus, Citrus, Jatropha, Populus, Medicago, Cicer, Cajanus, Phaseolus, Glycine, Gossypium, Astragalus, Lotus, Torenia, Allium, and Helianthus (See paragraph 0256 note hordeum, citrus etc.) It would have been obvious to an artisan of ordinary skill in the pertinent at the time the instantly claimed invention was filed to have incorporated the teaching of Jacobsen into the system of US 12,451,215. The modification would have been obvious because the two references are concerned with the solution to problem of plant modification (See Jacobsen and US 12,451,215 abstracts), therefore there is an implicit motivation to combine these references (i.e. motivation from the references themselves). In other words, the ordinary skilled artisan, during his/her quest for a solution to the cited problem, would look to the cited references at the time the invention was made. Consequently, the ordinary skilled artisan would have been motivated to combine the cited references since Jacobsen’s teaching would enable users of the US 12,451,215 system to have more efficient processing of plant information.
With respect to claim 19 Jacobsen discloses: wherein the modified plant comprises a subspecies of Beta vulgaris (See paragraph 0257 note beta vulgaris). It would have been obvious to an artisan of ordinary skill in the pertinent at the time the instantly claimed invention was filed to have incorporated the teaching of Jacobsen into the system of US 12,451,215. The modification would have been obvious because the two references are concerned with the solution to problem of plant modification (See Jacobsen and US 12,451,215 abstracts), therefore there is an implicit motivation to combine these references (i.e. motivation from the references themselves). In other words, the ordinary skilled artisan, during his/her quest for a solution to the cited problem, would look to the cited references at the time the invention was made. Consequently, the ordinary skilled artisan would have been motivated to combine the cited references since Jacobsen’s teaching would enable users of the US 12,451,215 system to have more efficient processing of plant information.
Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIYAH STONE HARPER whose telephone number is (571)272-0759. The examiner can normally be reached on Monday-Friday 10:00 am - 6:00 pm.
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/Eliyah S. Harper/Primary Examiner, Art Unit 2166 July 9, 2026
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