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
Claims 1, 3, 4, 5, 7, and 9-10 are under consideration.
Claims 2, 5, and 8 are cancelled.
Claim Objections
Claims 1, 9 and 10 are objected to because of the following informalities: The first profile input step recites “at least one type of cells,” where it should recite “at least one type of cell.” Appropriate correction is required.
Claim Rejections - 35 USC § 101
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, 3, 4, 5, 7, and 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, 3, 4, 5, and 7 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 a computer program recorded on a computer readable medium which reads on a signal or software per se. A transitory signal such as a carrier wave, or a program, per se, is not a statutory category of invention, as set forth in In re Nuijten. A review of the specification does not show a definition of computer readable media that excludes an embodiment that is information in a signal or software per se. The applicants may overcome the rejection by 1) amendment of the claims to be limited to physical forms of computer readable storage media described in the specification or 2) by amending the claimed subject matter to be limited to “non-transitory”, see the notice regarding Computer Readable Media (1351 OG 212 (23 February 2010)).
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 network profile and the protein-protein interaction network profile in the genetic interaction data 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.
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.
Claim Rejections - 35 USC § 112-2nd paragraph
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 a refining step of excluding a synthetic partner “from the genetic interaction network profile and the protein-protein interaction network profile.” This step renders the claim unclear because the earlier step, “a second profile input step,” requires inputting one of a genetic interaction network profile or a protein-protein interaction network profile.” The connection between the input step and refining steps are unclear because the input step only requires one type of profile to be input but the refining step requires analysis of both the interaction network profile and the protein-protein interaction network profile. It is suggested that the refining step recite “the genetic interaction network profile or the protein-protein interaction network profile.”
Claims 1, 9 and 10 recites a refining step requiring analysis of both the genetic interaction network profile and the protein-protein interaction network profile so as to exclude a synthetic partner. The step then requires that the synthetic partner be excluded from the genetic interaction network profile and the protein-protein interaction network profile in the genetic interaction data. It is unclear if the protein-protein interaction network is to be considered as including genetic interaction data. A protein-protein interaction network is known to those of skill in the art as organizing the cooperative interaction of proteins within a cell. Clarification of the recited step is required. It is suggested that the claim instead recite “the
Claims 1, 9 and 10 recite that the mapping step does not take a depletion score into account in a t-test. The claim then describes the t-test as “wherein the t-test statistically characterizes sensitivity 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.” It is not clear if the claimed method requires a process of performing this t-test that characterizes sensitivity and resistant genetic interactions by evaluating depletion scores of screened genes, as recited. The claims recite that the mapping step does not take into account a depletion score from a t-test. The claims recite that the t-test evaluates depletion scores. It is unclear how this t-test “wherein” clause is intended to limit the method steps of claims 1 and 9-10; the clause describes the processes of the t-test from which the depletion score is not considered anyway. This renders the claimed method unclear; it is unclear if the t-test comprising statistically characterizing genetic interactions for all possible pairs of iteratively musted genes and loss-of-function-screened genes is a process that is intended to be performed as part of the claimed method.
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
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