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 .
Status of Claims
Claims 1-27 are under examination.
Priority
Applicant’s claim for the benefit of priority under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. This application claims the benefit of U.S. Provisional Patent Application No. 62/983,476 filed February 28, 2020.
Drawings
The drawings filed 08/29/2022 are acceptable.
Information Disclosure Statement(s)
The information disclosure statement (IDS) document(s) submitted is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS document(s) has/have been fully considered by the examiner.
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 1-27 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Guidance Step 1:
The instant invention (claims 1, 14, 27 being representative) is directed to a method and system that performs a series of processes. Thus, the claims are directed to one of the statutory categories of invention. MPEP 2106.03.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the claimed steps that are part of the abstract idea are as follows:
aligning and integrating the spatial and expression data to identify cell linkages between cell type and expression data;
rendering spatial transcriptomics data, wherein the spatial transcriptomics data comprises a transcriptome profile for a cell in the sample in spatial coordinates based on the spatial data and cell linkages;
generating a ligand diffusion map based on spatial data and ligand diffusion information;
predicting cell-cell signaling in the sample based on the concentration of a ligand at a cellular position within the sample.
Mental Processes
Under the broadest reasonable interpretation, the above italicized steps amount to observing data and manipulating/analyzing the data. Notably, the claims do not impose any boundaries on how the italicized functions are actually being achieved. In addition, the instant specification describes using computer algorithms to perform at least some of the claimed functions [0074-0078, 0083]. As such, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks include only data reception and analysis. Accordingly, the above steps clearly fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception or whether the claim is “directed to” the judicial exception. This evaluation is performed by (1) identifying whether there are any additional steps/elements recited in the claim beyond the judicial exception, and (2) evaluating those additional steps/elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. See MPEP 2106.04(d). The additional steps/elements recited in the claim beyond the judicial exception are as follows:
obtaining spatial data and expression data, wherein the spatial data identifies cell type and cell position within a sample based on imaging of the tissue, and wherein the expression data identifies genes being expressed in individual cells;
measuring effective ligand concentration at cellular positions based on the ligand diffusion map;
In this case, the above steps are recited at a high of generality (without any details regarding how it is being performed) and result in nothing more than collecting data for use by the abstract idea. Accordingly, the above steps amount to insignificant extra-solution activity and are not indicative of an integration into a practical application. See MPEP 2106.05(g). Regarding the claimed processor and machine-readable media, (claims 14 and 27), these features are generically recited and merely used as tools to obtain information or perform the abstract idea. Moreover, applicant is reminded that “generic computer components such as a computer and database do not satisfy the inventive concept requirement.” See MPEP 2106.05(f) and 2106.05(h). Even when viewed in combination, these additional steps/elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO].
For a list of considerations when evaluating whether additional elements integrate a judicial exception into a practical application see MPEP 2106.04(d)(1) lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using 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, as discussed in MPEP § 2106.05(e).
C. Guidance Step 2B:
This part of the eligibility analysis evaluates whether the claim as a whole amount to significantly more than the recited exception i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. See MPEP 2106.05. The specification teaches routine and conventional modalities for obtaining spatial and gene expression data [pages 4-6]. In addition, WO 2020/010366 teaches methods for obtaining spatial data and gene expression data [0229, 0230]. Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract steps. See MPEP 2106.05(d)(Part II). Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
D. Dependent Claims
Dependent claims 2-13, 15-26 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. Regarding claim(s) 2, 15, these claims further the type of sample being used to obtain expression data and therefore amounts to insignificant extra-solution activity and are not indicative of an integration into a practical application for reasons discussed above (Step 2A, prong 2 and Step 2B analysis). See MPEP 2106.05(g).Regarding claim(s) 3, the recited treating step does not amount to a particular treatment and therefore does not integrate the abstract idea into a practical application. See MPEP 2106.04(d)(2). Regarding claim(s) 4-13, 16-26, these claims are directed to limitations that further limit the specificity of the abstract idea or the nature of the data being used by the abstract idea. Accordingly, these claims are also directed to an abstract idea for the reasons set forth above (Step 2A, prong 1 analysis). Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more.
Claim Rejections - 35 USC § 112
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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.
This is a written description rejection.
Claims 1-27 are 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The written description requirement is separate and distinct from the enablement requirement. The specification must: (1) describe the claimed invention in a manner understandable to a person of ordinary skill in the art, and (2) show that the inventor actually invented the claimed subject matter.
Regarding claim(s) 1, 14, 27, the specification fails to provide written description support for the following steps:
aligning and integrating the spatial and expression data to identify cell linkages between cell type and expression data;
predicting cell-cell signaling in the sample based on the concentration of a ligand at a cellular position within the sample.
With regards to the aligning and integrating step, these limitations are broadly recited and lack any specificity with regards to the how they are being achieved. As a result, it is unclear how the claimed “aligning” and “integrating” results in identifying “cell linkages” between cell type and expression data. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed functions. The specification does teach a cell linkage dictionary “combined” with the nearest-neighbor linkages to assign a transcriptome profile or a distance-weighted average transcriptome profile of its nearest neighbors to the spatial coordinate of each cell in the spatial data (e.g., CODEX data) [0062]. However, this is not commensurate in scope with what is claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. As such, the instant specification fails to disclose the requisite computational steps and quantitative information that is required in order to realize the claimed functionality for the full scope of what is being claimed.
With regards to the predicting step, this is broadly recited and lacks any specificity with regards to the how this step is being achieved. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed functions. The specification teaches generally discloses an example for “predicting inter-cellular signaling in skeletal muscle regeneration” [Example 1, 0072-0085], but lacks any sufficient description of a predictive model for achieving the claimed function. The specification teaches that “linkages were created across these datasets by finding the nearest neighbor, or the "sister cell", of each cell in the combination of scRNA-Seq and CODEX datasets in high dimensional space [0075, Figure 5]. However, this is not commensurate in scope with what is claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. Moreover, one of ordinary skill in the art would recognize that models for predicting cells signal and/or spatial modeling of cell signaling networks are not trivial. For example, Eungdamrong et al. (Biol Cell. 2004 June ; 96(5): 355–362) teaches that modeling cell signaling networks requires knowledge of specific pathways, reactions, well-defined mathematical equations, and model testing [pages 2-5, Sections 2 and 3]; as well as accurate estimation of both the concentration of signaling components inside the cells, and the kinetic parameters for each biochemical reaction [Section 4]. As such, the instant specification fails to disclose the requisite computational steps and quantitative information that is required in order to realize the claimed functionality for the full scope of what is being claimed.
Regarding claim(s) 3, this claim further comprises identifying a treatment to block the cell-cell signaling and treating an individual with the treatment. This limitation is broadly recited and lacks any specificity with regards to the how this step is being achieved. The claim is also not limited to any particular treatments or any particular type of cancer. A review of the specification also does not provide a sufficient examples or guidance of such steps, and the artisan would recognize that the knowledge required for identifying “treatments to block cell signaling within a tumor” is not trivial. As such, the instant specification fails to disclose the requisite computational steps and quantitative information that is required in order to realize the claimed functionality for the full scope of what is being claimed.
For the reasons discussed above, the specification does not provide a sufficient disclosure of the critical aspects of the claim necessary to demonstrate to one of ordinary skill in the art that the inventor possessed the requisite functionality for achieving the full scope of what is presently embraced by the claims. For more information regarding the written description requirement, see MPEP §2161.01- §2163.07(b).
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 1-27 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 that depend directly or indirectly from claim(s) 1, 14, 27 are also rejected due to said dependency.
Claims 1, 14, 27 recite “aligning and integrating the spatial and expression data to identify cell linkages between cell type and expression data.” Such generic functional claim language amounts to descriptions of problems to be solved and covers all means or methods of performing the claimed functions. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed functions. As a result, it is unclear what computational techniques are included or excluded by said “aligning” and “integrating” such that one of ordinary skill in the art would know what computational limitations are intended, i.e. in what way is the spatial data being aligned and integrated. The specification teaches a cell linkage dictionary combined with the nearest-neighbor linkages to assign a transcriptome profile or a distance-weighted average transcriptome profile of its nearest neighbors to the spatial coordinate of each cell in the spatial data (e.g., CODEX data) [0062]. However, this is not commensurate in scope with what is claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. Clarification is requested via amendment. In addition, it is also unclear as to the metes and bounds of “cell linkages”. A review of the specification does not provide any limiting definition that would serve to clarify the scope. The specification does disclose a ‘cell linkage dictionary’ [0062], as discussed above. However, this is not a limiting definition and it is improper to import narrowing limitations into the claims. MPEP 2111.01. Clarification is requested via amendment.
Claims 1, 14, 27 recite “predicting cell-cell signaling in the sample based on the concentration of a ligand at a cellular position within the sample.” Such generic functional claim language amounts to descriptions of problems to be solved and covers all means or methods of performing the claimed functions. A review of the specification does not describe, to any appreciable extent, any algorithms, equations, or prose equivalent that correspond to the claimed “predicting”. The specification teaches that “linkages were created across these datasets by finding the nearest neighbor, or the "sister cell", of each cell in the combination of scRNA-Seq and CODEX datasets in high dimensional space [0075, Figure 5]. However, this is not commensurate in scope with what is claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. As a result, it is unclear what computational techniques are included or excluded such that one of ordinary skill in the art would know what computational limitations are intended. Clarification is requested via amendment.
Cited Prior Art
In light of the confusing aspects of the claimed invention, as discussed in the rejections under 35 USC 112(b), above, the Examiner was not able to properly interpret the claims for purposes of applying prior art. Accordingly, the following prior art made of record and not relied upon is considered pertinent to applicant' s disclosure.
Regev et al. (US2019/0218276), which teaches methods for determining spatial and temporal gene expression dynamics in single cells.
Gartner et al. (WO 2020/010366; Pub. Date: 01/09/2020), which teaches a method for quantifying RNA. Gartner teaches obtaining spatial data (acquiring cell type data; [0229], [0230]); expression data [0229], [0230]); and cell position within a sample (identifying a spatial position of cells within a sample; claim 85) based on imaging of the tissue (tissue imaging; para [0275]).
Cowan et al. (Methods in Cell Biology, 2012, Volume 110, Pages 195-221), which teaches methods for spatial modeling of cell signaling networks.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/PABLO S WHALEY/Primary Examiner, Art Unit 3619