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 .
Information Disclosure Statement
The IDS filed 1/22/2026, 12/18/2025, 10/19/2022 have been considered by the Examiner.
Priority
Acknowledgment is made of applicant's claim for foreign priority under 35 U.S.C. 119(a)-(d) to KR10-2022-0001820 filed 01/05/2022.
Status of Claims
Examiner apologizes for the wrong list of claims under consideration and subsequently rejected in the previous Office Action. The claims listed has been corrected and does not change the rejections that were set forth and maintained herein.
Claims 1, 2, 4, 5, 9-10 are under consideration.
Claims 3 and 6 are cancelled.
Claim Objections
The objection to claims 1, 9 and 10 is withdrawn in view of amendments filed 6/09/2026.
Claim Rejections - 35 USC § 101
The instant rejection is maintained for reasons of record in the Office Action filed 3/9/2026 and modified to address amendments filed 6/09/2026.
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, 2, 4, 5, 9-10 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, 2, 4, 5, and 7-8 are drawn to a method, so a process.
Claim 9 is drawn to a system comprising a processor, so a machine.
Claims 10 is drawn to non-transitory computer program recorded on a computer readable medium, so a machine or manufacture.
Step 2A Prong One: Identification of an Abstract Idea
The claim(s) recite(s)
1. a data mapping step of mapping the gene dataset to a network set to generate genetic interaction data.
This step reads on a process that can be performed by the human mind by analyzing gene data with respect to information representing a network to determine genetic interaction data. The step is therefore an abstract idea.
2. a refining step of excluding a synthetic partner for a specific mutant gene from the genetic interaction data based on the genetic interaction network profile or the protein-protein interaction network profile, when the synthetic partner for the specific mutant gene is not located within a predetermined genetic distance from any other synthetic partner for the specific mutant gene in the genetic interaction data.
This step reads on a process that can be performed by the human mind by analyzing genetic distances in a network against gene information data which is the synthetic partner for a mutant gene. The step then requires the mental process of excluding information from a profile of protein interactions and gene interactions wherein the information is a mutant gene. The step is therefore an abstract idea.
3. wherein the mapping step determines a gene a non-expressed gene when an expression score in an expression profile is zero and excludes a depletion score associated with the non-expressed gene from a t-test for characterizing genetic interactions.
This step reads on a mental process of evaluating an expression score and determining that a gene is a non-expressed gene when the expression score is zero. The step is therefore an abstract idea.
4. wherein the t-test statistically characterizes sensitive and resistant genetic interactions by evaluating depletion scores of screened genes between experimental cells and control cells for all possible pairs of iteratively mutated genes and loss-of-function-screened genes.
This step recites a mathematical concept which is a t-test. The step of evaluating depletion scores of screened genes between experimental cells and control cells reads on a mental process of evaluating numerical data and also a mathematical process of calculating scores. The step is therefore an abstract idea.
Claims 2 and 4-5 describe the sources of data used to perform the abstract idea and are therefore also drawn to the abstract idea.
Claims 7-8 recite further abstract idea steps describing the predetermined genetic distance value and deriving a target gene as a therapeutic agent which reads on selecting a gene.
Step 2A Prong Two: Consideration of Practical Application
The claims result in a step of excluding information from profiles wherein that information is a “synthetic partner” for a mutant gene. The claims do not recite any additional elements that integrate the abstract idea 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:
1. a first profile input step of inputting a gene dataset including at least one profile selected from the group consisting of a mutation profile, a loss-of-function profile and an expression profile.
2. a second profile input step of inputting a network set comprising at least one selected from the group consisting of a genetic interaction network profile and a protein-protein interaction network profile.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the steps of inputting information, that is subsequently part of the abstract idea analysis, is extra solution activity as described in MPEP 2106.05(g).
Other elements of the method include the generic process of the system (claim 9) 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 Arguments
Applicant's arguments filed 6/09/2026 have been fully considered but they are not persuasive.
Applicants argue (Remarks, page 7, par. 2) that the claims are directed to a computer implemented technique for processing large-scale biological datasets and molecular network structures which can not be performed by the human mind. Applicants argue that the claims recite a loss-of-function genomic analysis with thousands of genes and hundreds of thousands of lines. Applicants point to the specification par. 0079-0105.
In response, MPEP 2111, states that “During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification,” but also that “Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment." As such, the instant claims do not recite the large volumes of date that Applicants are arguing. The claim limitations are examined as written, using Broadest Reasonable Interpretation wherein the claims do not limit the process to the embodiment pointed to in the specification by Applicants. Furthermore, while there is no actual step of processing thousands of genes, for the record, it is important to explain that analyzing a lot of data does not augment the steps being performed to analyze the data, which are abstract ideas. Computations on a lot of data performed mentally, or with paper and pencil, would take considerable time and effort, but that is, of course, the singular purpose of computers and computer networks, to perform large numbers of calculations, via algorithms, rapidly, and without error (assuming no error in user input). Although a general purpose computer can perform calculations at a rate and accuracy that can far outstrip the mental performance of a skilled artisan, the nature of the activity is essentially the same, and constitutes an abstract idea. See Bancorp Serves., L.L. C. v. Sun Life Assur. Co. of Canada (U.S.), 687 F.3d 1266,1278 (Fed. Cir. 2012) (holding that “the fact that the required calculations could be performed more efficiently via a computer does not materially alter the patent eligibility of the claimed subject matter”); see also See SiRF Tech., Inc. v. Int’l Trade Comm ’n, 601 F.3d 1319,1333 (Fed. Cir. 2010) (holding that: In order for the addition of a machine to impose a meaningful limit on the scope of a claim, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly, i.e., through the utilization of a computer for performing calculations).
Applicants argue (Remarks, page 7, par. 3 to page 8, par. 1) that the claims do not merely recite generic analysis but instead recite specific computational operations. Applicants argue that even if individual elements involve mathematical operations, the recited combination constitutes a specific computational workflow applied to structured biological datasets.
In response, specificity of recited judicial exceptions is not a criteria of consideration under the Two Step analysis, set forth in MPEP 2106.04 and 2106.05. Specific data analyzed by specific mathematical steps or mental steps is not sufficient to render the claims patent eligible. “Without additional limitations, a process that employs mathematical algorithms to manipulate existing information to generate additional information is not patent eligible. “If a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is nonstatutory.” Parker v. Flook, 437 U.S. 584, 595 (1978) (internal quotations omitted).” (Precedential CAFC decision: Digitech Image Technologies, LLC. v. Electronics for Imaging, Inc., decided July 11,2014). It is noted that Data which is abstract, even if it is meaningful or specific information, applied to an abstract idea does not equate to a practical application.
Applicants argue (Remarks, page 8, par. 2-3) that the claimed method reduces false positives through expression based exclusion and network constrained refinement. Applicants argue that the specification identifies a technical problem in the field of computational genomics and gene screening such as CRISPER and RNAi.
In response, Applicants appear to be arguing a field of use (MPEP 2106.05(h) rather than additional elements that integrate the abstract idea into a practical application (Step 2A Prong Two). In order to constitute an improvement to a computer or computer technology the improvement should be reflected in the claims with additional elements. Currently, the claims do not recite any additional elements that integrate the claims into a practical application or reflect an improvement to technology.
Applicants argue that the claims improve the functioning of a computational genetic interaction analysis system by transforming noisy experimental data into a refined and biologically meaningful output.
In response, the “computational genetic interaction analysis system” does not necessitate any computer product that would constitute more than a series of mental analysis steps or math. Improvement to an abstract idea is not sufficient to render claims patent eligible. Furthermore, transforming noisy experimental data into a refined and biologically meaningful output does not require any additional elements. Transforming noisy experimental data into a refined and biologically meaningful output encompasses for example filtering data which is an abstract idea. To that, the court in BASCOM put forth that “[t]he claims do not merely recite the abstract idea of filtering content along with the requirement to perform it on the Internet, or to perform it on a set of generic computer components.” Here, it is indicated that filtering data is an abstract idea as it merely involves selecting which data to keep and which to remove, which can be performed by decisions made by the human mind or with mathematics.
Applicants argue (Remarks, page 9, par. 1) that the recited steps impose specific biological and structural constraints that materially alter the data processing pipeline and improve its technical performance. Applicants argue that the claims integrate the abstract idea into a practical application by improving the field of computational genomics.
In response, the claims should recite additional elements that reflect an improvement to technology. Here, it is not clear what the technology is because each step of the claims, as recited, reads on an abstract idea, i.e. mental process or math. The claims do not recite any “structural constraints” by way of additional elements that could be considered as a practical application under Step 2A Prong Two.
Applicants argue (Remarks, page 9, par. 2) that the claims recite a specific ordered combination of steps that is not routine or conventional including: receiving multi-modal data sets, excluding non-expressed genes, statistically characterizing genetic interactions and applying network-based distance constraints.
In response, the step of receiving multi-modal data sets is an extra solution activity of data gathering as described in MPEP 2106.05(g). The other pointed to limitations of excluding non-expressed genes, statistically characterizing genetic interactions and applying network-based distance constraints are abstract ideas. Under Step 2B it is noted that it is the combination of additional elements that are evaluated with respect to whether they are routine, conventional and well understood or not. In buySAFE, Inc. v. Google, Inc., the court put forth that:
Such a claim falls outside section 101 if (a) it is “directed to” matter in one of the three excluded categories and (b) “the additional elements” do not supply an “inventive concept” in the physical realm of things and acts—a “new and useful application” of the ineligible matter in the physical realm—that ensures that the patent is on something “significantly more than” the ineligible matter itself.
Therefore the courts have made clear that additional elements are limitations recited in additional to the abstract idea (mental process steps or math). The additional elements are not steps that can be performed by the human mind or math.
Applicants also argue (Remarks, page 9, lines 1-4 from bottom) that the specification provides empirical evidence that the recited method removes false positives and improves precision relative to known datasets.
In response, as set forth above, limitations from the specification are not read into the claims and the claims are examined using the standard of Broadest Reasonable Interpretation. The removal of false positives and improvement of precision relative to known datasets, if accomplished as a result of steps that can be performed by the human mind or with math would amount to data analysis result accomplished by way of an abstract idea. Without additional elements to integrate the abstract idea into a practical application or reflect an improvement to technology, the claim as a whole is directed to a judicial exception.
Applicants argue (Remarks, page 10, par. 1) that the Office Action does not include any rejection under 35 USC 102 or 103.
In response, MPEP 2106.05 states:
As made clear by the courts, the "‘novelty’ of any element or steps in a process, or even of the process itself, is of no relevance in determining whether the subject matter of a claim falls within the § 101 categories of possibly patentable subject matter."
Therefore the consideration of novelty under prior art is a separate consideration to that of subject matter eligibility. For the reasons set forth above, the instant rejection is maintained.
Claim Rejections - 35 USC § 112-2nd paragraph
The instant rejection is maintained and modified in view of Applicant’s amendments filed 6/09/2026. Applicant’s amendments have clarified the 112(b) issues in the “refining step.” The step of mapping and wherein clause describing the t-test remain unclear for the following reasons.
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, 3, 4, 5, 7, and 9-10 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 pre-AIA the applicant regards as the invention.
Claims 1, 9 and 10 recite that the mapping step “excludes a depletion score associated with the non-expressed gene from a t-test for characterizing genetic interactions,” and that “wherein the t-test statistically characterizes sensitive and resistant genetic interactions by evaluating depletion scores of screened genes between experimental cells and control cells.” It is unclear how these limitations limit the claimed process because the claim does not recite a step of performing a t-test. It is unclear at which point in the process of inputting, mapping and refining, taking a t-test is performed. It is unclear as to whether the t-test and excluding a depletion score associated with a t-test is a conditional limitation or a necessary step in the process of claim 1.
Response to Arguments
Applicant's arguments filed 6/09/2026 have been fully considered but they are not persuasive.
Applicant’s amendments have in part cured the issues set forth under 35 USC 112(b). However, as set forth above in the maintained 35 USC 112(b), the limitation drawn to that mapping step that “excludes a depletion score associated with the non-expressed gene from a t-test for characterizing genetic interactions,” and that “wherein the t-test statistically characterizes…” remain unclear. Suggestions for amendment: It is suggested that the claim be amended to recite clear conditions under which the t-test is take that the results would include a depletion score. Alternatively, it is suggested that the t-test and results therefrom be recited as an active step along with the input, mapping and refining steps.
E-mail communication Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anna Skibinsky whose telephone number is (571) 272-4373. The examiner can normally be reached on 12 pm - 8:30 pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Ram Shukla can be reached on (571) 272-7035. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Anna Skibinsky/
Primary Examiner, AU 1635
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