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 .
Applicants Amendment
Applicants’ amendment filed 10/13/2025 has been received and entered. The specification has been amended. Claim 1, 5, 16 have been amended, and claims 9, 13, previously were cancelled.
Claims 1-8, 10-12, 14-16 are pending.
Election/Restriction
Applicant’s election without traverse of Group I in the reply filed on 4/4/2025 was acknowledged. Upon initial search and consideration of the claims it was determined that it would not be an undue burden to examine all three groups together and the restriction requirement was withdrawn.
Claims 1-8, 10-12, 14-16, drawn to a system to store and analyze genetic traits, broadly to a method to analyze genetic traits and to a computer readable medium with instructions are currently under examination.
In view of previous amendments, Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Priority
This application filed 6/24/2021 is national stage filing of PCT/JP2019/051564 filed 12/27/2019 which claims benefit to foreign application JP2018-247959 filed 12/28/2018.
No comments regarding the summary of priority.
Specification
The disclosure objected to because it contains an embedded hyperlink and/or other form of browser-executable code is withdrawn.
The amendment to the specification has addressed the basis of the objection.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
Response to Applicants Comments
Applicants assert that there is sufficient technical detail to demonstrate that the ‘storage unit’, ‘learning unit’ and ‘calculation unit’ as recited are not generic place holders but concrete components configured to carry out specific technical operations.
Examiner acknowledges the literal support but in review of the specification, there is no clear indication that these limitations are ‘concrete components’ as asserted. These are not terms of art and there is no specific guidance for any specific physical type of device that provides for storage, learning or calculation beyond the analysis steps being performed using a computer. To the extent the claim limitations require that they are a unit, this appears to be directed to the ability of a computer to perform these functions such as the use of a memory or processor to practice learning and calculations such as the necessary program code to perform the analysis.
This is not a objection or rejection, the basis of the analysis is provided for completeness and clarity of the record for what the specification provides for the limitations of the claims. Applicants do not point to any specific guidance that demonstrates that these limitations are concrete. The term ‘unit’ is present 141 times in the specification, and the most detailed guidance for the function of these units appears to be related to function, for example on page 21:
“a learning unit configured to learn a relationship between genetic information and trait information from the genetic information on the plurality of individuals and the trait information on the plurality of individuals by forming an image of the genetic information on the plurality of individuals; and a calculation unit for predicting trait information on an individual from genetic information on the individual”
which appears to provide high level indication of what is to be performed without any specific steps for the analysis, and no guidance with respect to any structure to what these limitations comprise.
The basis of the previous analysis is included in the action for completeness of the record.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) are presented in the system claims 1-4, 8, 10-12, 14-15 as it requires three components a ‘storage unit’, a ‘learning unit’ and a ‘calculation unit’ each setting forth an indication of what it is capable of providing when analyzing genetic data and additional information associated with possible traits. In view of the art of record these do not appear to be terms of art and in view of the guidance of the specification there is no unique guidance beyond what they units are to provide to set forth any structure such that these are a physical ‘unit’. But rather these units appear to be consistent with instructions or code which a computer could use to perform the intended outcome set forth in the claims.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
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 1-8, 10-12, 14-16 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.
Claim analysis
Claim 1 has been amended and still is generally directed to system to provide genetic information and traits for individuals, and the ability to correlate the information and to apply the information to predict traits in other individuals. Independent claims 1, 3 and 16 have been amended to provide a new wherein clause that describes that the learning unit is configured to form image data representing the genetic information as pixels by position and color, but providing no detail to how this is represented or how it is tied to the learning unit per se, and it generally appears that genetic data is simply converted into another representation of the same data in the form of an image. In review of the specification, there are not specific rules or guidance on the image is specifically formed, and generally appears to be another way of representing the data. For example on page 9: “[Item B9] The method of any of the preceding items, wherein each of the plurality of genetic factors is associated with a region in the image data, and the step of generating the image data comprises the step of: converting information on a position and a type of a mutation in a sequence of a genetic factor into position and color information within a region associated with the genetic factor.”, or on page 12, the specification teaches “generating image data for storing the sequence data for the genetic factor population and the expression data for the genetic factor population, the image data having a plurality of pixels, each of which comprising position information and color information.” which appears broadly an instruction to represent the genetic information into a pixel of an image, and nowhere does there appear to be a specific means that this is performed, or any necessary guidance on how this used in any calculation in trait prediction. The amendment appears to broadly provide representing one form of data as another, while each still represents the same thing. Dependent claims have not been amended and provide additional instructions for how the genetic and trait information should be assessed. Independent claim 5 provides broadly for forming an image that represents sequence data for a genetic factor and expression data for a population in the form of pixels and color. No specific limitations related to position, color, and the enormous data it could represent, but as exemplified in figures 11-12 can be various forms of data aggregated and presented into a different form.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method and a product.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing sequence and attribute data to provide a possible correlation between genetic data and trait data that might be observed in a population, and as amended, the data is converted into a pixel as part of an image. Generally, the image based on the location of the pixel and the color represent the genetic data. Even wherein the data is put into an image form, the guidance for the step of obtaining and correlating trait data are still found to be instructional steps. Given the breadth of the claims, the limitations appear to be provided by creating any image where the pixel in an image represents the data, and still interpretation is simply a pundit square containing genetic variants and observed phenotypes and/or traits. The judicial exception is a set of instructions for analysis of sequence data and correlating it with observed or defined traits in a population and appear to be directed to the category of Mathematical Concepts, that is mathematical relationships or mathematical calculations such as statistical assessment of the data, and to the category of Mental Processes that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion) as the claims can be practiced by observation of genetic information and associating it with traits. The breadth of the required steps encompasses non-transformative visual assessment of an individual for given phenotype(s), coupled with prior knowledge of the correlation of said phenotype(s) with the presence of particular genotype(s); for example, seed color, flower color, height, silique size, etc., tolerance to stress. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using the natural principle. Although the claims recite presenting the information in the form of pixels and color, the courts have also identified limitations that did not integrate a judicial exception into a practical application; for example, merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f). Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed. Furthermore, the limitation of genotyping breeding individuals at a plurality of markers or alleles does not change the steps to be performed. See MPEP § 2106.05(g) for a discussion on adding insignificant extra-solution (both pre-solution and post-solution) activity to the judicial exception. See also MPEP § 2106.05(h) for a discussion on generally linking the use of a judicial exception to a particular technological environment or field of use. The claims appear to fall into the category of Mathematical Concepts, as it applies the use of statistics and mathematical relationships in analyzing probabilities, and also into the category of mental processes, as concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because there is no apparent complexity to or amount of data that is collected and analyzed as presently claimed.
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element and only provide for analysis and presentation of the information. This judicial exception requires steps recited at high level of generality and are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, each of the independent claims recites additional elements and are found to be the steps of obtaining sequence and trait data. As such, the claims do not provide for any additional element to consider under step 2B. It is noted that in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to analysis of sequence and trait data. While the instruction are stored on a medium (claim 16) and could be implemented on a computer, together the steps do not appear to result in significantly more than a means to compare sequences and traits that might be associated with them in a population. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer. Dependent claims set forth additional steps which are more specifically define the considerations and steps of calculating, and comparing, and do not add additional elements which result in significantly more to the claimed method for the analysis. No additional steps are recited in the instantly claimed invention that would amount to significantly more than the judicial exception. Without additional limitations, a process that employs mathematical algorithms (correlating sequences and traits) to manipulate existing information and to generate additional information (presented as pixels and color) is not patent eligible. Furthermore, 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 non-statutory. In other words, patenting abstract idea cannot be circumvented by attempting to limit the use to a particular technological environment or purpose and desired result.
Response to arguments
Applicants notes the claims have been amended and that the claims are not directed an abstract idea but rather computerized technologies in the medical field for ‘prediction of a tendency of development of a disease in advance’ and ‘determination of suitable treatment or the like’ noting specification [0201].
In response, the claims have been amended to set forth genetic information is represented in an image form, and broadly do not require that any correlation that might exist provides anything related to disease or treatment. The claims broadly provide generic steps to provide a correlation between genetic information and trait information. While it can be performed using a computer, it appears broadly to comprise correlating mutations with possible conditions/disease, such as mutations in the BRCA1/2 genes to possibility of cancer. Representing the data as an image does not appear to change that the invention is directed to making the correlation which the learning and calculations are to provide. There is no specific guidance on how any learning is to be performed, nor calculations are to be done, nor how converting genetic data into an image is to be performed which suggests that the correlation between genetic information and traits is patent eligible.
Applicants argue that the conversion of the data requires structural image data, and that it is tied to concrete computer processing and not mere abstract idea or statistical correlation.
In response, the claim requirements and generic teaching of the specification do not appear to provide any evidence that there is an improvement in the art or that converting the genetic data into an image provided better processing or imaging. The claims as a whole are consistent with the pre-amble where genetic data is provided and analyzed to provide any possible correlation that might be made. The specification does not provide any new or special rules for making the correlation, nor with regard to the amendments any particular means of converting the genetic information into an image which material affects the data or any possible correlation that could be made.
Therefore, for the reasons above and of record, the rejection is maintained.
As noted previously, one way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-8, 10-12, 14-16 rejected under 35 U.S.C. 103 as being unpatentable over Boyle et al. (2017, of record) and Goddard et al. (2016) is withdrawn.
Claim 1 has been amended to require the genetic data is converted into an image, which is not taught in either of the cited references. While the analysis and correlation of genetic markers with specific traits seen in people and in populations is well known, there does not appear a reason to convert the data into an image for analysis as set forth in the claims.
Conclusion
No claim is 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.
The art of record demonstrates that the analysis and correlation of genetic markers with specific traits seen in people and in populations is an active area of research. It is well known that there are a huge number of genes contribute to the heritability of traits and for complex diseases. Boyle et al teach that there are challenges to fully understanding the impact of very small effects in organismal systems and that it is important to develop highly precise, high throughput techniques for mapping networks in diverse cell types and provide a system that provides for a system that stores, analyzes and predicts correlations between genetic data and phenotypic traits. Boyle et al. provide evidence for the basis of analyzing a wide variety of genotypes and demonstrate the ability to associate simple and complex genotypes with a variety of observable traits. Boyle et al do not specifically state the exact tools or analysis done, but provide a well reference review of the many approaches. Similarly, Goddard et al. provides evidence that observable traits are not only phenotypic but also correlate with changes at the cellular level, and provide an array of specific examples for analyzing complex multi-allelic phenotypes and an expanded view of complex traits showing an importance of polygenic analysis. It is demonstrated that genetics of complex traits can be performed and that prediction of phenotype, identification of causal polymorphisms and genetic architecture can be established.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached at 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Joseph Woitach/Primary Examiner, Art Unit 1687