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 .
Claims 23-42 are the current claims hereby under examination.
Claim Objections
Claim 23 is objected to because of the following informalities: Claim 23 at lines 19-20 recites calculating a first value of polygenic risk score, based on “said first custom subset of Single Nucleotide Polymorphisms.” The “said first custom subset” of SNPs lacks antecedent basis, but it appears it is referring back to the “identifying, in the woman’s genetic data, a first personalized subset of.” As such the language should be amended to read -said first personalized subset of- instead of “said first custom subset of.” Additionally, claim 23 recites at line 25 “wherein the determination of said first predetermined set of Single Nucleotide Polymorphisms” is objected to as there is no previous recitation of “determination of said first predetermined set” of SNPs. It appears the language should read -wherein a determination of said first predetermined set of Single Nucleotide Polymorphisms-. Appropriate correction is required.
Claim 25 is objected to for the awkward wording in line 2 where it states “by of”. Appropriate correction is required.
Claim 38 is objected to as the term SCT should include the language (Stacked Clumping + Thresholding) so it is clear as to the category of algorithm being implemented. Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 23-42 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.
A claim fails to satisfy the statutory requirement and is thus invalid for indefiniteness if its language, when read in light of the specification and the prosecution history, “fail[s] to inform, with reasonable certainty, those skilled in the art about the scope of the invention.” Nautilus, Inc. v. Biosig Instruments, Inc., 134 S. Ct. 2120, 2124 (2014). In Nautilus, the Supreme Court expressly rejected that “insolubly ambiguous” or “amenable to construction” standard. Nautilus, 134 S. Ct. at 2124. Rather, the Court “h[e]ld that a patent is invalid for indefiniteness if its claims, read in light of the specification delineating the patent, and the prosecution history, fail to inform, with reasonable certainty, those skilled in the art about the scope of the invention.” Id. The Court explained further: “[i]t cannot be sufficient that a court can ascribe some meaning to a patent’s claim; the definiteness inquiry trains on the understanding of a skilled artisan at the time of the patent application, not that of a court viewing matters post hoc.” Id. at 2130. “A patent must be precise enough to afford clear notice of what is claimed, thereby ‘appris[ing] the public of what is still open to them. Notably a claim is indefinite if its language “might mean several different things and no informed and confident choice is available among the contending definitions.” Id. At 2130 n.8. Although the Court recognized that “[s]ome modicum of uncertainty” may be tolerated, id. at 2128, the patent and prosecution history must disclose a single known approach or establish that, where multiple known approaches exist, a person having ordinary skill in the art would know which approach to select. See Teva, 789 F.3d at 1341, 1344–45 (holding claim indefinite where molecular weight could be measured three different ways and would yield different results and the patent and prosecution history did not provide guidance as to which measure to use).
Claim 23 (and all claims dependent therefrom) recite the steps of
“identifying a first personalized subset of Single Nucleotide Polymorphisms which also belong to a first predetermined set, associated with the phenotype considered, wherein each of the Single Nucleotide Polymorphisms of said first predetermined set comprises an identifier of Single Nucleotide Polymorphisms, and is associated with a respective pre-calculated first relevance parameter;”
“calculating a first value of polygenic risk score, based on said first custom subset of Single Nucleotide Polymorphisms and the respective pre-calculated first relevance parameter;
“determining the predictive prognosis of menopause onset in relation to each of said at least one phenotype, based on the respective first value of polygenic risk score;”
“the determination of said first predetermined set of Single Nucleotide Polymorphisms and the calculation of said first relevance parameters are carried out in a preliminary training step” wherein the step comprises at least one algorithm using machine learning and/or artificial intelligence techniques, on the basis of known data, said training being carried out based on a known dataset containing genetic data of Single Nucleotide Polymorphisms of women whose menopause onset age is known.”
wherein the steps have been deemed as vague and indefinite. The instant claims are process claims and not result claims. Therefore, the steps are required to define how the process steps end in the recited results. For example, the claims are required to define how the results of each of steps 1-5 is obtained and/or what algorithm is used for achieving the results. The steps are clear with regards to the results they produce, but are not clear as to exactly how they are produced. There is no algorithm or prose equivalent recited for performing each of said steps 1-5. Without defining each of the steps it is not possible to have a clear measure of what applicant’s regard as the invention so that it can be determined whether the claimed invention meets all the criteria for patentability. The lacking of properly defined method steps further make the scope of the claim unclear so that a person of ordinary skill in the art would be informed of the boundaries of what constitutes infringement of the patent.
For example, step 1, there are no steps recited or criteria used that describe how the first personalized subset of SNPs is identified. Additionally, there is an existing first predetermined set of SNPs that also lacks any informative framework for how the predetermined set of SNPs is obtained or determined. Step 4 attempts to provide additional information, but only recites that a preliminary training step that comprises at least one algorithm that uses ML and/or AI on known data is used to determine the first predetermined set of SNPs. This also lacks any details of how an algorithm that uses ML and/or AI on known data arrives at the result of the first predetermined set of SNPs. The step is so broad that it covers any and all algorithms along with any and all forms of MLs and/or AI techniques to arrive at the result of determining a first predetermined set of SNPs. Moreover, the same broadness applies to the calculation of the first relevance parameter. It is unclear as to what exactly the relevance parameter represents or how the result of calculating said parameter is achieved. It is also unclear as to what exactly is meant by the term identifier in the step. Additionally, it is unclear as to what is meant by the term “is associated.” It is unclear as to exactly how the identifier of the SNP is linked with a respective pre-calculated first relevance parameter by using the term “is associated.”
With regards to steps 2 and 3, they are similarly unclear as to how the results of the steps are achieved. For instance, in step 2 it is clear what the calculation of the polygenic risk score is based on, but it is unclear as to how to achieve the result as it appears any type of calculation can be used. Similarly in step 3, the result of the step is clear to arrive a predictive prognosis of menopause onset in relation to each of said at least one phenotype and what the value is based upon, but it is unclear as to how the determination step is carried out.
For each of the identified steps 1-4 above, there appears to be multiple or unlimited methods of how to carry out the steps to arrive at the results, wherein the implementation of the different methods may lead to different results. Without guidance as to which method should be used renders the steps/system/claims indefinite. In addition, the specification does not provide any guidance on which method should be used or even whether the possible universe of methods is limiting. Because the variety of methods of implementing each of steps 1-4 would not produce the same results, the method chosen for implementation could affect whether or not a given product infringes the claims (see CAFC Dow v Nova August 2015).
In addition, without defining each of the steps it is not possible to have a clear measure of what applicant’s regard as the invention so that it can be determined whether the claimed invention meets all the criteria for patentability. The lacking of properly defined method steps further make the scope of the claim unclear so that a person of ordinary skill in the art would be informed of the boundaries of what constitutes infringement of the patent. Clarification via clearer claim wording is required.
Claim 23 is further deemed as vague and indefinite as the preamble states it is a “computer-implemented method” wherein there are not explicitly recited hardware elements for performing any of the recited method steps. As such, the claim has been further deemed as vague and indefinite. Clarification via clearer claim wording is required.
Claim 32 is effectively deemed as vague and indefinite as the reasons stated above with regards to claim 23 as claim 32 reiterates similar steps but with regards to identifying a second personalized subset of SNPs etc. Therefore, clarification via clearer claim wording is also required.
Claim 24 comprises the terms “is associated” and “respective allele dosage,” which have been deemed as vague and indefinite. It is unclear as to what exactly is meant by either term. It is unclear as to what value allele dosage represents, such as is it just reflective of the specific copy number present or some other value? Clarification via clearer claim wording is required.
Claim 25 comprises the step of “identifying Single Nucleotide Polymorphisms statistically associated with the phenotype through a genetic association study,” which has been deemed as vague and indefinite. The broad recitation of a statistical association makes the metes and boundaries of the said limitation unclear. It appears to fail to inform with reasonable certainty a person of ordinary skill in the art the metes and boundaries of what exactly is required to satisfy a statistical association between an SNP and a phenotype. Additionally, it is seemingly done through a genetic association study. It is further unclear as to what exactly would constitute or meet the requirement to be considered a “genetic association study.” Again, the terminology appears to fail to inform with reasonable certainty a person of ordinary skill in the art of the metes and bounds of said limitation. Clarification via clearer claim wording is required.
Furthermore claim 25 recites the step of “identifying optimal values of first relevant parameters adapted to optimize the predictive efficacy of the first value of polygenic risk score” which has been deemed as vague and indefinite. The step is carried out from identified SNPs and respective known initial relevance parameters through single or combined use of one or more predictive algorithms. The predictive algorithms are trained on known data sets. Again, the result of the step is clear, but how it is achieved is unclear. The step covers the use of any and all predictive algorithms and does not provide any details, explicit algorithm or prose equivalent, as to how to arrive at the required result of identifying optimal values. As such the step appears to be vague and indefinite. Clarification via clearer claim wording is required.
Claim 29 recites the limitation "the at least one binary phenotype comprises" in lines 1-2 and “the at least one continuous phenotype” in line 6. There is insufficient antecedent basis for these limitation in the claim. It is unclear as to what at least one binary phenotype the limitation is referring. It appears the claim may be intended to depend from claim 28. Clarification via clearer claim wording is required.
Claim 30 recites after the identifying step of claim 23, a step of selecting a first group of SNPs belonging to said first personalized subset of the woman, comprising a first number of SNPs recognized as the most relevant ones based on a predetermined criterion. It is unclear as to what the predetermined criterion comprises or how exactly it is used to be “based on” when selecting a first number of SNPs recognized as the most relevant. How the claim achieves the desired result of the selection appears unclear as there are no details, algorithm, or prose equivalent for carrying out the claim. It appears anything can be used as “predetermined criterion.” As such the claim appears to fail to inform a person of ordinary skill in the art with reasonable certainty of the metes and bounds of the limitations. As such the limitation has been deemed as vague and indefinite. Claim 35 also comprises similar limitations, but with regards to a second personalized subset of SNPs. As such the similar limitations of claim 35 are also deemed as vague and indefinite for similar rationales as explained for claim 30. Clarification via clearer claim wording is required.
Claim 31 comprises the limitation of “the disease,” which appears to lack antecedent basis. It is unclear as to what disease the limitation is referring. Clarification via clearer claim wording is required.
Claim 31 further comprises the step of testing different polygenic risk scores calculated on different SNPs, which has been deemed as vague and indefinite. It is unclear as to exactly what is involved in the testing step or how it is carried out. Additionally, the claim has a step of applying AUC-ROC methodologies. The term is not clear as to exactly what would fall under this scope. As such the limitation fails to inform a person of ordinary skill in the art at the time of the invention as to the metes and bounds of said limitation. Therefore, clarification via clearer claim wording for the identified limitations in claim 31 is required.
Claims 32-33 comprise the limitation of “calculating the menopause onset probability” which lacks antecedent basis. It is unclear as to what calculation step exactly the limitation is referring. Claim 33 further comprises the limitation of “the respective determined first value and/or second value of polygenic risk score.” The limitation also lacks antecedent basis. It is unclear as to what second value of polygenic risk scores the limitation refers. It appears claim 33 may be intended to depend from claim 32. Clarification via clearer claim wording is required.
Claim 37 comprises the limitation in line 2 of “the discrete phenotypes,” which lacks antecedent basis. It is unclear as to what phenotypes exactly are being referred by the limitation “the discrete phenotypes.” Claim 37 further comprises the limitation of “the menopause onset probability,” which also lacks antecedent basis. Clarification via clearer claim wording is required.
Claim 38 comprises a step of determining said first predetermined set of SNPs based on a known set of SNPs identified by GWAS (Genome Wide Association Study). It is unclear what specific study or what is required to be classified as a GWS in order to derive the known set of SNPs used for determining the first predetermined set of SNPs. Claim 38 further comprises the limitation of “taking into account a degree of association (Linkage disequilibrium) between the Single Nucleotide Polymorphisms, and a parameter representative of the fraction of Single Nucleotide Polymorphisms identified as random for the phenotype considered” with regards to calculating said first relevance parameters. It is unclear as to what exactly is meant by the limitation. The limitation appears to fail to inform a person of ordinary skill in the art of the metes and bounds of said limitation. It is further unclear as to how the parameter that represents the fraction of SNPs is determined. Moreover, the entire step of calculating said first relevance parameters is unclear as to how its being carried out as the punctuation and use of terms appears confusing and unclear. Additionally, the step of calculating the first value of polygenic risk score comprises the limitation of “as a weighted sum of the alleles,” wherein the limitation “the alleles” lacks antecedent basis. Clarification via clearer claim wording is required. The limitations deemed vague and indefinite in the step of determining said first predetermined set of SNPs based on a known set of SNPs identified by GWAS similarly apply to the steps under the SCT algorithm.
Claim 39 comprises the limitation of “the step of calculating the menopause onset probability,” which lacks antecedent basis. Clarification via clearer claim wording is required.
Claim 41 comprises the limitation “the algorithms of the aforesaid set of algorithms,” which lacks antecedent basis. Clarification via clearer claim wording is required.
Claim 42 comprises the limitation of carrying out a predictive prognosis of a woman’s menopause onset based on the first value of polygenic risk score and/or the second value” wherein “the second value lacks antecedent basis. Clarification via clearer claim wording is required.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 28 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 28 appears to not further limit the definition of at least one phenotype. Claim 23 from which claim 28 depends defines at least one phenotype comprising at least one age group or an age limit with respect to which the predictive prognosis of menopause onset is to be carried out or an indication of a woman’s age at which the menopause onset is more likely. Claim 28 now indicates that at least one phenotype comprises a plurality of phenotypes comprising at least one binary phenotype, which comprises at least one age group or an age limit with respect or which the prognosis of menopause onset or not is to be determined. Claim 23 requires the predictive prognosis onset to be carried out, but in the dependent claim it may or may not be carried out, which appears to broaden the definition of at least one phenotype instead of further limiting it. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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 23-42 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claimed invention is directed to a predictive prognosis of menopause onset in a woman without significantly more.
Analysis of independent claims 1:
Step 1 of the subject matter eligibility test (see MPEP 2106.03).
Claim 1 is directed to a method, which describes one or more of the four statutory categories of patentable subject matter, i.e., a process. Therefore, further consideration is necessary.
Step 2A of the subject matter eligibility test (see MPEP 2106.04).
Prong One: Claim 1 recites an abstract idea. In particular, the claim recites the following:
a. accessing a woman’s genetic data comprising SNPs;
b. for each phenotype: identifying in genetic data, a first subset of SNPs (that belong to a first predetermined set associated with the phenotype) that comprise an identifier and is associated with a respective pre-calculated first relevance parameter, wherein the predetermined set of SNPs and calculation of the relevance parameter are carried out in a preliminary training step (which comprises training at least one algorithm using ML or AI techniques carried out based on a known dataset containing SNPs of women whose menopause onset age is known) independent of said accessing and said processing step;
c. calculating a first value of polygenic risk score, based on the subset of SNPs and relevance parameter;
d. determine the predictive prognosis of menopause in relation to each of said phenotype based on the polygenic risk score;
e. providing a result of said predictive prognosis.
These elements recited in claim 1 are drawn to an abstract idea since they involve a mental process that can be practically performed in the human mind including observation, evaluation, judgment, and opinion and using pen and paper and/or they involve mathematical concepts in the form of mathematical relationships, mathematical formulas or equations, and/or mathematical calculations.
Step A involves the mental step of obtaining data that can be as simple as looking at paper with sequences. Step B further involves the mental and/or mathematical step of identifying a personalized subset of SNP data, which belongs to a first predetermined set. This subset is derived from a predetermined data set of SNPs that comprise an identifier and associated with a pre-calculated relevance parameter wherein the predetermined data set was determined in a preliminary training step. The claim recites that the predetermined data set was generated based on training at least one algorithm using ML or AI techniques. The claim requires the use of the generated predetermined data set via ML or AI to identify a first personalized subset of SNPs, but does not require performing the ML or AI techniques. The claim only requires that ML or AI techniques were used to derive the predetermined subset of SNPs. The use of a predetermined subset of SNPs to identify a further personalized subset of SNPs can easily be done mentally or by observations and judgement using pen and paper. Similarly, the step B states how the pre-calculation of the relevance parameter was done in a preliminary training step. However, the claim recites the use of the relevance parameter and broadly describes how it was derived, but the pre-calculated value itself appears to have just been obtained via any number of ways, such as receiving the value on a piece of paper, which would read on a mental step. Step c reads on a mathematic step as it is directed explicitly to a calculation of a first value of polygenic risk score. Step d further involves the mental and/or mathematical step of determining the predictive prognosis of menopause onset for each phenotype whereby the step could be calculated using the observed and/or obtained data mentally or using pen and paper. Step e further involves the mental step of simply providing as a result the predictive prognosis, which could simply be any type of communication that could be done mentally or by way of pen and paper.
The identified abstract steps, recited at the high level of generality, do not suggest an undue level of complexity for a person with ordinary skill in the art to be practically performed in the human mind with the aid of pen and paper.
Prong Two: Claim 1 does not recite additional elements that integrate the exception into a practical application. Therefore, the claims are “directed to” the abstract idea. There is no practical application because the abstract idea is not applied, relied on, or used in a meaningful way. The processing performed remains in the abstract realm, i.e., the result is not used for a treatment. No improvement to the technology is evident.
However, with regards to the preamble indicating that this is a ‘computer-implemented method” wherein the preamble is given weight, patenting abstract ideas cannot be circumvented by attempting to limit the use [the idea] to a particular technological environment. In the instant claims, the computer-implemented method amounts to mere instruction to implement an abstract idea. The use of a computer does not offer a meaningful limitation beyond generally linking “the use of the method to a particular technological environment,' that is, implementation via computers.” see Alice Corp v. CLS Bank Int' l 573 U.S. (2014).
Step 2B of the subject matter eligibility test (see MPEP 2106.05).
Claim 1 does not include additional elements outside of the identified JE. Therefore, there are no additional elements that integrate the exception into a practical application or amount to significantly more than the above-judicial exception (the abstract idea). Looking at the limitations as an ordered combination (that is, as a whole) adds nothing that is not already present when looking at the elements individually. There is no indication that the combination of elements improves the functioning of a computer, for example, or improves any other technology. There is no indication that the combination of elements permits automation of specific tasks that previously could not be automated. There is no indication that the combination of elements includes a particular solution to a computer-based problem or a particular way to achieve a desired computer-based outcome.
Analysis of the dependent claims:
Claims 24 and 27- 37, and 41-42, depend from independent claim 23. The dependent claims merely further define the abstract idea and are, therefore, directed to an abstract idea for similar reasons: they merely describe additional details of the SNP data, phenotypes, calculations, identifying additional subsets of SNPs and additional calculations of polygenic risk scores, or further describe the acquired type of data.
Dependent claims 25-26 and 38-40 further describe details of the preliminary training step, which are further limitations of the identified abstract idea. The details are recited at such a broad and high level that they can be read on steps that can be carried out mentally or through observation judgement and pen and paper. Therefore, the limitations are not considered to integrate the JE into a practice application nor add significantly to the JE itself.
Examiner’s Comment
In light of the claim rejections for indefiniteness under 35 U.S.C. 112 2nd paragraph, as set forth above, the Examiner was not able to perform a meaningful search of the prior art. Applicant is reminded that prior art rejections under 35 U.S.C. 102 and/or 35 U.S.C. 103 may be applied in the next Office action in light of applicant's amendments, and that the next Office action can properly be made "Final" if these rejections are necessitated by amendment. See MPEP 706.07.
Conclusion
No claim is allowed
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jason Sims, whose telephone number is (571)-272-7540.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s supervisor, Jonathan Moffat can be reached via telephone (571)-272-4390.
Papers related to this application may be submitted to Technical Center 1600 by facsimile transmission. Papers should be faxed to Technical Center 1600 via the Central PTO Fax Center. The faxing of such papers must conform with the notices published in the Official Gazette, 1096 OG 30 (November 15, 1988), 1156 OG 61 (November 16, 1993), and 1157 OG 94 (December 28, 1993) (See 37 CFR § 1.6(d)). The Central PTO Fax Center number is (571)-273-8300.
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/JASON M SIMS/Supervisory Patent Examiner, Art Unit 3791