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 .
Applicant's Amendment/Request for Reconsideration-After Non-Final Rejection, filed 14 November 2025, has been entered and fully considered.
Status of Claims
Claim 6 is cancelled.
Claims 1-5 and 7-13 are pending and are examined on the merits.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 62/479,032 filed 3/30/2017 is acknowledged.
Withdrawn Rejections/Objections
The rejections to claims 1-12 under 35 U.S.C. 112(a) in the Office action posted 5/14/2025 are withdrawn in view of claim amendments filed 11/14/2025.
Claim Rejections - 35 USC § 101
This rejection is maintained from a previous Office Action, necessitated by claim amendments.
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 1-5 and 7-13 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
Claims 1-5 and 7-13 are directed to a process, here a "method," for genome editing, with a series functional steps.
Step 2A Prong One: Identification of Abstract Ideas
The claims recite:
Editing a genome sequence with multiple unique combinations of at least three edits simultaneously, without precise knowledge of a phenotypic effect of each individual one of the edits (claim 1);
----This step is interpreted as a simulated genome editing on sequence data under a broadest reasonable interpretation (BRI). Therefore, this step equates to an abstract idea of mental processes.
Subjecting multiple organisms, each having one of the variants of the genome sequence, to a cultivation space.
----This step is interpreted as simulating the growth effects from genome editing on sequence data under a BRI, which can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
For each of the multiple organisms, after cultivation, measuring an aggregate phenotypic effect of the unique combination of edits included in the organism on the phenotypic trait as expressed by the organism.
----Since how to measure an aggregate phenotypic effect is not specified, under a BRI, this step recites an activity than can be achieved in the human mind. Hence this step equates to an abstract idea of mental processes.
Aggregating, by a computing device, the unique combination of edits into multi-dimensional pools.
----This step recites the data manipulation and data re-organization by putting together the unique combination of edits into multi-dimensional pools. Although recited as “by a computing device”, nothing can stop a human from doing so and human mind can easily accomplish such a task. Therefore this step equates to an abstract idea of mental processes.
Determining, by the computing device, based on the aggregate phenotypic effects of contrasting ones of the pool, a combination of edits to the genome sequence having a largest aggregate phenotypic effect on the phenotypic trait.
----This step recites a decision-making activity of “determining”. Although recited as “by the computing device”, nothing can stop a human being from accomplish such as task. Therefore, this step equates to an abstract idea of mental processes.
Identifying, by the computing device, the edits included in the determined combination of edits having the largest aggregate phenotypic effect as the edits most likely to be causing the measured phenotypic effects on the phenotypic trait.
----This step recites a decision-making activity of “identifying …” Although recited as “by the computing device”, nothing can stop a human being from accomplish such as task. Therefore, this step equates to an abstract idea of mental processes.
Editing the genome sequence with multiple further combinations of edits each comprising one of the identified edits.
----This step is interpreted as a simulated genome editing on sequence data under a BRI. Therefore, this step equates to an abstract idea of mental processes.
Subjecting additional multiple organisms, each having one of the further combinations of edits to the genome sequence, to a second cultivation space.
----This step is interpreted as simulating the growth effects from genome editing on sequence data under a BRI, which can be achieved in human mind. Therefore, this step equates to an abstract idea of mental processes.
Confirming, by the computing device, the phenotypic effect of the identified edits on the phenotypic trait by generating a realized aggregate phenotypic effect for each of the further combinations of edits based on expression of the phenotypic trait in the respective organisms having each of the further combinations of edits, to determine the edit(s) responsible for the phenotypic effect without having to confirm the phenotypic effect of each of the more than one hundred different candidate edits individually;
----this step recites a judging activity of “confirming …” Although recited as “by the computing device”, nothing can stop a human being from accomplish such as task. Therefore, this step equates to an abstract idea of mental processes.
The “mental processes” elements are procedures for observing, evaluating, analyzing/ judging and organizing information. they can be achieved by a person with the help of a pen and a paper in their simplest embodiments. Hence, the above identified elements fit the definition for mental processes.
Because the steps do recite abstract ideas, the claims must therefore be examined further to determine whether the claims integrate the above-identified abstract ideas into a practical application (MPEP 2106.04(d)).
Step 2A Prong Two: Consideration of Practical Application
The claims result in a process of confirming, by the computing device, the phenotypic effect of the identified edits on the phenotypic trait, which reads on a mental activity. The claims do not recite any additional elements that integrate the abstract idea/judicial exception into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
Subjecting multiple organisms, each having one of the variants of the genome sequence, to a cultivation space (claim 1);
Subjecting additional multiple organisms, each having one of the further combinations of edits to the genome sequence, to a second cultivation space (claim 1); and
A computing device (claims 1-3).
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the four additional elements outlined above are necessary for data gathering hence they are drawn to insignificant extra-solution activities to collect data to validate the gene edited organisms (MPEP §2106.05(g)).
The claims do not include additional elements that are sufficient to amount of significantly more than the judicial exception because it is routine and conventional to perform the acts of editing genes and culture the organism in the desired environment to observe editing effects. The first two additional elements encompassing data collection of gene editing and organism transformation, are conventional elements. It has been a long tradition in the industry of plant gene engineering to modify existing genes or genomes to acquire desired plants with economical gain. For example Belhaj taught in 2013 “We foresee the CRISPR technology to become a routine method in plants for making targeted single and multiple gene knock-outs, introducing SNPs into a gene of interest, expressing proteins tagged with affinity or fluorescent tags at their native loci in the genome and much more.” (Belhaj: "Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system." Plant methods 9.1 (2013): 1-10 (pg. 8, col 1, last para) as cited on the 4/21/2023 IDS). Naqvi taught “Clearly, these early successes with 5–10 transgenes will lead to more ambitious projects and the simultaneous introduction of tens of transgenes into plants now seems a distinct possibility. This is achieved routinely in microbes through the use of large, low copy number vectors such as BACs and PACs in bacteria and YACs in yeast. As discussed, this trend is emerging in plants, with large capacity T-DNA-based vectors and artificial chromosomes.” (Naqvi: "When more is better: multigene engineering in plants." Trends in plant science 15.1 (2010): 48-56 (pg. 55, col 1, 3rd para) as cited on the 4/21/2023 IDS). In fact, Faux had a software (AlphaSim) ready (hence a computing device is implied) for simulating the aggregated gene editing effects, as Faux taught “it (AlphaSim) integrates biotechnologies such as doubled-haploids (DHs) and gene editing and allows the user to simulate multiple traits and multiple environments, specify recombination hot spots and cold spots, specify gene jungles and deserts, perform genomic predictions, and apply optimal contribution selection” (Faux: “AlphaSim: Software for Breeding Program Simulation,” The Plant Genome, Vol 9 Issue 3, 01 November 2016 (pg. 1, Section “Abstract”. Emphasis and an annotation added) as cited on the 10/26/2022 IDS). Consequently, these additional elements considered alone and as a whole, failed to provide something in a un-conventional way to integrate the JEs into a practical application.
Other elements of the method include “a computing device” which is a recitation of generic computer structure that serves to perform generic computer functions that are well-understood, routine, and conventional activities previously known to the pertinent industry. Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Applicant’s Argument
In the Remarks filed 14 November 2025, Applicant argued (page 7, 2nd para through page 8, 2nd para) that instant invention identified edits required for the phenotype in a more efficient way. This argument refers to the Step 2A/Prong two in the 101 analysis, relating to whether the claims are integrated into a practical application through a technical improvement. The argument is not persuasive. Pooled editing test (here the multiple genome editing), leading to quick and efficient identification of traits responsible for the phenotype is expected when the traits responsible for the phenotype are rare in the pool of testing traits. It seems that if one of the individual edits do carry the phenotype, the additional element of the last step in claim 1 will capture that. However, the additional element does not guarantee to capture the technical improvement 100% of the time.
In the Remarks, Applicant argued (page 8, 3rd para through page 9, 2nd para) that in the instant invention, the transform of organisms is realized and confirmed by a particular effect to a phenotypic trait. This argument refers to the Step 2A/Prong two in the 101 analysis, relating to whether claims are integrated into a practical application or not due to physical transformation of things. Applicant’s argument is not persuasive. Transformation requires a physical transformation of matter. However, claim 1 is interpreted as an in silico design and simulation method ([0002], Fig. 1, Fig. 3).
In the Remarks, Applicant argued (page 9, 3rd para through page 11, 1st para) that claim 1 recites a multi-step, “ordered combination of operations required for identifying which edits to the genome sequence, from the more than one hundred available candidate edits, actually cause the particular phenotypic effect on the desired phenotypic trait, without requiring analysis of each one of the more than one hundred candidate edits individually.” To response, this argument refers to the Step 2A/Prong two in the 101 analysis, relating to whether claims are integrated into a practical application or not due to a technical improvement or physical transformation of things. Applicant’s argument is not persuasive. Transformation requires a physical transformation of matters. However, claim 1 is interpreted as an in silico design and simulation method ([0002], Fig. 1, Fig. 3).
Applicants cite McRO, however McRO s not analogous to the instant claims. In McRO the specific types of rules are captured and reflected in the more realistic lip synchronization and facial expression which was deemed an improvement to technology and also a practical application
In the Remarks, Applicant argued (page 11, 2nd ~4th paras) that “the additional elements also amount to an inventive concept (and something significantly more than the alleged abstract idea).” This argument refers to the Step 2B one in the 101 analysis, relating to whether the claims recite inventive concepts. The argument is not persuasive. As discussed above in the 101 rejection, gene editing and organism transformation are conventional elements. The ordered multi-step gene editing-cultivation-gene editing-cultivation, are actually two rounds of transformations. It has been a long tradition in the industry of plant gene engineering to modify existing genes or genomes to acquire desired plants with economical gain. For example Belhaj taught in 2013 “We foresee the CRISPR technology to become a routine method in plants for making targeted single and multiple gene knock-outs, introducing SNPs into a gene of interest, expressing proteins tagged with affinity or fluorescent tags at their native loci in the genome and much more.” (Belhaj: "Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system." Plant methods 9.1 (2013): 1-10 (pg. 8, col 1, last para) as cited on the 4/21/2023 IDS). Naqvi taught “Clearly, these early successes with 5–10 transgenes will lead to more ambitious projects and the simultaneous introduction of tens of transgenes into plants now seems a distinct possibility. This is achieved routinely in microbes through the use of large, low copy number vectors such as BACs and PACs in bacteria and YACs in yeast. As discussed, this trend is emerging in plants, with large capacity T-DNA-based vectors and artificial chromosomes.” (Naqvi: "When more is better: multigene engineering in plants." Trends in plant science 15.1 (2010): 48-56 (pg. 55, col 1, 3rd para) as cited on the 4/21/2023 IDS). In fact, Faux had a software (AlphaSim) ready for simulating the aggregated gene editing effects (hence a computing device is implied), as Faux taught “it (AlphaSim) integrates biotechnologies such as doubled-haploids (DHs) and gene editing and allows the user to simulate multiple traits and multiple environments, specify recombination hot spots and cold spots, specify gene jungles and deserts, perform genomic predictions, and apply optimal contribution selection” (Faux: “AlphaSim: Software for Breeding Program Simulation,” The Plant Genome, Vol 9 Issue 3, 01 November 2016 (pg. 1, Section “Abstract”. Emphasis and an annotation added) as cited on the 10/26/2022 IDS). Consequently, these additional elements considered alone and as a whole, failed to provide something in a non-conventional way to integrate the JEs into a practical application.
For the above reasons, the 101 rejection is maintained.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635