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 .
Election/Restrictions
Applicant's election with traverse of the invention of Group 1 (methods of predicting pathology), and the particular genes (relevant to the species election requirement) that are ATXN1, B4GALT5, CFLAR and LDLR (the species election is made without traverse), in the reply filed on 12/03/2025 is acknowledged. The traversal is on the ground(s) that the different groups have a special technical feature because they are directed to a closed listed of 80 markers. This is not found persuasive because the method as recited in claim 1 is directed to a method comprising determining the levels of markers selected from a group marker, and thus while the method must include the analysis of expression of the markers (i.e.: ATXN1, B4GALT5, CFLAR and LDLR, as consonant with the election), the claim does not preclude the analysis of any other additional markers.
The requirement is still deemed proper and is therefore made FINAL.
Claims 12 and 13 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected inventions (i.e.: non elected product claims), there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 12/03/2025.
Claims 15-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected combination of genes (i.e.: the claims require markers that are not limited to the elected ATXN1, B4GALT5, CFLAR and LDLR), there being no allowable generic or linking claim. Election (i.e.: the species election directed to a particular combination of genes) was made without traverse in the reply filed on 12/05/2025.
Claim Rejections - 35 USC § 112 - Indefiniteness
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.
Claim 18 is 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 18 is unclear over recitation of the limitation “an appropriate mathematical model” because it is unclear what is intended to be required by the term “appropriate”. It is unclear if the claim is intended to encompass any sort of model that may provide any indication of a prediction of development of the recited pathologies, or if the phrase is intended to require some level of sensitivity, specificity, or accuracy in a prediction rendered using the model.
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, 14 and 18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more.
The claim(s) are directed to methods for predicting pathology (infection and/or organ dysfunction and/or sepsis) and recite an abstract idea that encompass a mental process (see MPEP 21106.04(a)(2)). Where claim 1 recites using determined levels of nucleic acid markers to “to predict the development of infection and/or organ dysfunction and/or sepsis”, such a concepts may be performed in the human mind (e.g.: observations, evaluations, judgments, and opinions; see MPEP 21106.04(a)(2) III). Additionally, claims 18 recites a limitation related to analyzing data using a computer implemented mathematical model, where this step of data manipulation is directed to mathematical calculations that also are interpreted as being abstract ideas (e.g.: see MPEP 21106.04(a)(2) I). Furthermore, it is noted that where the subject matter of the claims is directed to the use of gene expression values associated with infection and/or organ dysfunction and/or sepsis, such an association is a natural aspect of the biological response to infection (i.e.: a gene expression:phenotype relationship) , and as such the claims are directed to a judicial exception that is a law of nature and/or a natural phenomenon (e.g.: MPEP 2106.04(b). With regard to claim 18, it is noted that claims can be directed to a mental process even if they are claimed as being performed on a computer (e.g.: MPEP 2106.04(a)(2)(III)(C)).
This judicial exception(s), as identified above, are not integrated into a practical application because the claims do not require any active process step that is performed based on a particular result of the abstract ideas of the claims. The claims are directed to the analysis of nucleic acid levels, but the methods end with the abstract idea of using the levels “predict the development” of a pathology.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the data collection of the claims uses well understood, routine and conventional methods that are properly considered insignificant extra-solution activity (e.g.: see MPEP 2106.05(g)). The data gathering steps themselves (e.g.: determining levels of ATXN1, B4GALT5, CFLAR and LDLR, as consonant with the election, in a biological sample) were known in the art. The instant application teaches that the data collection of the instantly claimed methods may be performed using well known technologies (e.g.: p.15-16). And the prior art demonstrates that collection of the required data was routinely practiced in the art; Zhai et al (2020) provides examples (Table 1) of the analysis of gene expression levels in blood samples using a U133 array from Affymetrix, which includes probes for detecting levels of the required nucleic acids.
Claim Rejections - 35 USC § 103
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.
Claim(s) 1, 14 and 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Lukaszewski et al (WO 2020/096984 A1) in view of Hossain et al (US PG Pub 2009/0203534).
Relevant to the methods of the rejected claims Lukaszewski et al teaches methods of predicting the presence of sepsis in a subject using a gene signature of a plurality of genes (p.110-125) and teaches determining levels of the relevant nucleic acids (e.g.: p.21). The reference teaches analysis of nucleic acids from genes including: B4GALT5 (e.g.: p. 58, p.66, p.102); CFLAR (e.g.: p.59, p.66, p.95. p.107) and LDLR (e.g.: p.62, p.67).
Relevant to claim 18, Lukaszewski et al teaches analyzing gene expression values using Support Vector Machine combined with Recursive Feature Elimination (SVM-RFE), which a mathematical analysis of the data.
Lukaszewski et al does not teach analysis of nucleic acids from the gene ATXN1, as required by the claims, in the analysis of sepsis in a subject.
However, an association between ATXN1 nucleic acid level and a prediction of sepsis was known in the prior art and is taught by Hossain et al.
Hossain et al teaches that gene expression may be used to predict early symptoms of a sepsis as well as to prognose the severity of disease which is to be expected (e.g.: Abstract; para 0028 para 0071), and teaches that ATXN1 has expression levels that provide an indication of the sepsis phenotype (e.g.: p.10; p.137). It is additionally noted that Hossain et al also teaches sepsis related expression of B4GALT5 (e.g.: p.138) and LDLR (e.g.: p.149)
Further relevant to claim 18, Hossain et al teaches the analysis of gene expression using computer software (e.g.: para 0103).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have included the expression level of ATXN1, as taught by Hossain et al, in the methods of sepsis prediction provided by Lukaszewski et al. The skilled artisan would have been motivated to include additional biomarkers of sepsis prediction based on the expressed teachings of Hossain et al that the markers are related to sepsis; the skilled artisan would recognize that including additional markers may add to the sensitivity or specificity of the prediction based on gene expression.
Claim(s) 1, 14 and 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hossain et al (US PG Pub 2009/0203534) in view of Russwurm et al (US PG Pub 2008/0070235).
Relevant to the methods of the rejected clams, Hossain et al teaches that gene expression may be used to predict early symptoms of a sepsis as well as to prognose the severity of disease which is to be expected (e.g.: Abstract; para 0028 para 0071). The reference teaches that ATXN1 (e.g.: p.10; p.137), B4GALT5 (e.g.: p.138) and LDLR (e.g.: p.149) have expression levels that provide an indication of the sepsis phenotype.
Further relevant to claim 18, Hossain et al teaches the analysis of gene expression using computer software (e.g.: para 0103).
Hossain et al does not teach analysis of nucleic acids from the gene CFLAR, as required by the claims, in the analysis of sepsis in a subject.
However, an association between CFLAR nucleic acid level and sepsis was known in the prior art and is taught by Russwurm et al.
Russwurm et al teaches that gene expression may be used to diagnose sepsis at an early stage (e.g.: para. 0026; para. 0053), and teaches that CFLAR has expression levels that provide an indication of the sepsis phenotype (e.g.: Table 2, p.8; Table 13, p.17).
Further relevant to claim 18, Russwurm et al teaches the analysis of gene expression using computer software (e.g.: para 0154).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have included the expression level of CFLAR, as taught by Russwurm et al, in the methods of sepsis prediction provided by Hossain et al. The skilled artisan would have been motivated to include additional biomarkers of sepsis prediction based on the expressed teachings of Russwurm et al that the markers are related to sepsis; the skilled artisan would recognize that including additional markers may add to the sensitivity or specificity of the prediction based on gene expression.
Conclusion
No claim is allowed.
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Stephen Kapushoc
Primary Examiner
Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683