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 .
Election/Restrictions
Applicant’s election without traverse of Group I, a method for classifying a subject, in the reply filed on 3/2/26 is acknowledged.
Claims 1-35 are pending. Claims 21-35 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 3/2/26.
Applicant’s election without traverse of species election of a pre-defined set of genes as comprising ITGA2B, MKI67, and AZU1 in the reply filed on 3/2/26 is acknowledged.
Claims 36-37 are cancelled.
Claims 1-20 are currently under examination.
Priority
The instant application 18/264,077 filed on 8/3/23 is a 371 US national phase of
PCT/US2022/015195 filed on 2/4/22, and claims domestic priority to provisional application
63/146,212 filed on 2/5/21. The priority date is determined to be 2/5/21.
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.
Claims 6-8, 15-16, and 20 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 6-7 recite tables. MPEP 2173.05(s) states:
Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience." Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) (citations omitted).
Appropriate correction is required.
Claims 7-8, 15, and 20 contain the “e.g.” abbreviation of exempli gratia, which translates to the phrase "for example", and renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d). For purposes of compact prosecution, the limitations following the phrases are not part of the claimed invention.
Regarding claim 16, the phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d). For purposes of compact prosecution, the limitations following the phrases are not part of the claimed invention.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims have been evaluated using the 2019 Revised Patent Subject Matter Eligibility Guidance (see Federal Register Vol. 84, No. 4 Monday, January 7, 2019).
Step 1: The claims are directed to the statutory categories of a process.
Step 2A, prong one: The claim recites a judicial exception.
Claim 1 recites a correlation of gene expression levels and infection. This phenotype-genotype correlation is a law of nature and natural phenomena (see MPEP 2106.04(b)).
Claims 1 additionally recites “classifying” a subject based upon the gene expression levels, which is an abstract mental process (see MPEP 2106.04(a)(2), subsection III). Although a “classifier” is used to classify the subject, this limitation is still performed in the human mind (see MPEP 2106.04(a), subsection (III)(C)).
Step 2A, prong two: The judicial exception is not integrated into a practical application.
Claims 1-20 recite extra-solution and data-gathering limitations for the judicial exceptions of law of nature/natural phenomena and mental process. These limitations generate the input data of the judicial exceptions, with no specification of a particular treatment or prophylaxis (see MPEP 2106.04(d)(2)).
Step 2B: The claim does not provide an inventive concept.
MPEP 2106.05(d)):
The courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity:
i. Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
ii. Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
iii. Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
iv. Immunizing a patient against a disease, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
v. Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377, 118 USPQ2d at 1546;
vi. Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119 USPQ2d at 1375;
vii. Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014); and
viii. Hybridizing a gene probe, Ambry Genetics, 774 F.3d at 764, 113 USPQ2d at 1247.
The claims are directed to well-understood, routine, and conventional activities in the life science arts recited at a high-level of generality. Additionally, gene expression level indicia of infections are not inventive (see Brown et al. US 2016/0041153 A1).
For the reasons set forth above, claims 1-20 are not directed to patent eligible subject matter.
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.
Claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Brown et al. (2016; US 2016/0041153 A1).
Relevant to claim 1 preamble and (a), Brown et al. paragraph 0097 teaches “Disclosed herein are methods and systems for characterizing a phenotype of a biological sample, e.g., a sample from a cell culture, an organism, or a subject. The phenotype can be characterized by assessing one or more biomarkers.”
Relevant to claim 1 (b), Brown et al. paragraph 0113 teaches that “The phenotype may also comprise an infectious disease, such as a bacterial, viral or yeast infection.”
Further relevant to claim 1 (b), Brown et al. paragraph 0101 teaches “A phenotype can result from a subject's gene expression”. Brown et al paragraph 0511 teaches “Methods for establishing gene expression profiles”.
Further relevant to claim 1 (b), Brown et al. paragraphs 0423 (Table 22: AZU1), 0428 (CD41 is equivalent to instant ITGA2B; see below GeneCards excerpt), and 0444 (Table 11: MKI67) teach that the phenotypic biomarkers include instantly elected ITGA2B, MKI67, AZU1.
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Relevant to claim 1 (c), Brown et al. paragraph 0293 teaches limitations relevant to classifiers, including relevant excerpt: “One or more biomarkers, e.g., a panel of biomarkers that forms a biosignature, can be discovered that can be used to build a classifier that differentiates between the two or more groups.”
Relevant to claim 1 (d), Brown et al. paragraph 0293 teaches “Biosignature according to the invention can be used to classify a sample.” Taken with the above teachings relevant to claim 1, Brown et al. teaches a method for classifying a subject.
Relevant to claim 2, Brown et al. paragraphs 0530 and 0520 teach normalized gene expression values and calculating the probability of infection.
Relevant to claim 3, Brown et al. paragraphs 0674 and 0950 teach generation of a report for the biosignatures and phenotype characterizations.
Relevant to claim 4, Brown et al. Abstract teaches “Biomarkers can be assessed for diagnostic, therapy-related or prognostic methods to identify phenotypes, such as a condition or disease, or the stage or progression of a disease, select candidate treatment regimens for diseases, conditions, disease stages, and stages of a condition, and to determine treatment efficacy.”
Relevant to claims 5-7, Brown et al. paragraphs 0423 (Table 22: AZU1), 0428 (CD41 is equivalent to instant ITGA2B; see below GeneCards excerpt), and 0444 (Table 11: MKI67) teach that the phenotypic biomarkers include instantly elected ITGA2B, MKI67, AZU1.
Relevant to claims 8-9, Brown et al. paragraph 0352 teaches limitations of subjects with symptoms of infection and sepsis.
Relevant to claims 10-12, Brown et al. claim 55 teaches the sample can include peripheral blood and bronchoalveolar lavage.
Relevant to claim 13, Brown et al. paragraph 0098 teaches isolating RNA from the sample.
Relevant to claims 14-15, Brown et al. paragraph 0119 teaches methods for measuring the gene expression that include nucleic acid sequencing, PCR amplification, and array platform.
Relevant to claim 16, Brown et al. paragraph 0113 teaches that “The phenotype may also comprise an infectious disease, such as a bacterial, viral or yeast infection.”
Relevant to claims 17-20, Brown et al. paragraphs 0293-0322 teach classifier limitations.
Brown et al. does not teach a specific embodiment having all the claimed elements. That being said, however, it must be remembered that "[w]hen a patent simply arranges old elements with each performing the same function it had been known to perform and yields no more than one would expect from such an arrangement, the combination is obvious." KSR v. Teleflex, 127 S.Ct. 1727, 1740 (2007) (quoting Sakraida v. AG. Pro, 425 U.S. 273, 282 (1976)). "[W]hen the question is whether a patent claiming the combination of elements of prior art is obvious," the relevant question is "whether the improvement is more than the predictable use of prior art elements according to their established functions." (Id.). Addressing the issue of obviousness, the Supreme Court noted that the analysis under 35 USC 103 "need not seek out precise teachings directed to the specific subject matter of the challenged claim, for a court can take account of the inferences and creative steps that a person of ordinary skill in the art would employ." KSR at 1741. The Court emphasized that "[a] person of ordinary skill is... a person of ordinary creativity, not an automaton." Id. At 1742.
Consistent with this reasoning, it would have been prima facie obvious to have selected various combinations of various disclosed elements — including biological samples, signatures, pre-defined set of genes, and classifiers — for a method, to arrive at compositions "yielding no more than one would expect from such an arrangement."
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Sarah J Kennedy whose telephone number is (571)272-1816. The examiner can normally be reached Monday - Friday 8a - 5p.
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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682