DETAILED ACTION
Applicant’s response, filed 24 June 2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
Claim Status
Claims 1-21 are pending and examined herein.
Claims 1-21 are rejected.
Priority
Claims 1-21 are not granted the claim to the benefit of priority to U.S. Provisional application 63/033272 filed 02 June 2020 because the provisional application does not disclose the newly recited limitation in claim 1 of “wherein the transcriptome correlation method identifies a presence of a disease state prior to the disease state being detectable via a histopathological analysis or a differential expression study of a subject”. Further, the provisional application does not disclose the recited limitations in claim 11 of “showing engagement of T cell activation to indicate a presence of a disease state wherein conventional differential expression showing quantitative differences in gene transcripts fails to show T cell activation in genetically diverse specimens; and wherein the unbiased whole transcriptome analysis identifies the presence of the disease state prior to the disease state being detectable via a histopathological analysis or a differential expression study of a subject”. Thus, the effective filling date of claims 1-21 is 02 April 2021.
Drawings
The drawings received 02 April 2021 are objected to. Figures 1-3 and 6-9 are objected to as noted below:
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2). Figures 1-3 and 6-9 are colored drawings.
Examiner’s Comment
It is noted that no remarks or replacement drawings were provided in the last response. Therefore, the above objection to the drawings stands.
Claim Interpretation
Claim 1 recites “Composite correlation index” which is interpreted to be a correlation coefficient of all correlation coefficients of each gene in each group combination. The instant specification discloses in [081] the Person's correlation R values of each gene with all other genes in the whole transcriptome were calculated in specimens of steatosis vs nonsteatosis, steatosis vs control and nonsteatosis vs control, respectively. The composite correlation (Pc) index was calculated as the Person's R of all R values of each gene in each group combination.
Claim 11 recites “via coordination analysis” which is interpreted to be the steps of calculating a composite correlation index comprising, calculating a correlation coefficient value for each transcript with respect to every other transcript in a transcriptome via at least one pairwise comparison. The instant specification discloses in [081] this process which is disclosed as these two calculations.
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 1-21 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.
Claim 1 recites “wherein the transcriptome correlation method identifies a presence of a disease state prior to the disease state being detectable via a histopathological analysis or a differential expression study of a subject” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if this limitation requires a step of identifying a presence of a disease state or if this phrase is meant to be descriptive. The specification does not provide a clear and precise definition of the limitation, nor would one skilled in the art recognize the metes and bounds of said limitation. Dependent claims 2-10 are further rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, this phrase will be interpreted as being descriptive.
Claim 6 recites “the disease state is steatosis” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if this is meant to further limit “a disease state” which is recited in claim 1 or “a disease state” which is recited in claim 5. For the sake of furthering examination, this will be interpreted as limiting the disease state in claim 5.
Claim 7 recites “a composite correlation index indicative value” which renders the metes and bounds of the claim indefinite. It is unclear what constitutes as a composite correlation index indicative value or if it differs from a composite correlation index. The specification does not provide a clear and precise definition of the limitation, nor would one skilled in the art recognize the metes and bounds of said limitation. For the sake of furthering examination this limitation will be interpreted to be the same as a composite correlation index.
Claim 11 recites “wherein the unbiased whole transcriptome analysis identifies the presence of the disease state prior to the disease state being detectable via a histopathological analysis or a differential expression study of a subject” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if this limitation requires a step of identifying a presence of a disease state or if this phrase is meant to be descriptive. The specification does not provide a clear and precise definition of the limitation, nor would one skilled in the art recognize the metes and bounds of said limitation. Dependent claims 12-21 are further rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, this phrase will be interpreted as being descriptive.
Examiner’s Comment
It is noted that no arguments were provided for the above rejections and the amendments provided do not address the above rejections. Therefore, the above rejections stand.
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 1-21 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.
(Step 1)
Claims 1-21 fall under the statutory category of a process.
(Step 2A Prong 1)
Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. The instant claims further recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations.
Independent claim 1 recites mathematical concepts of “calculating a composite correlation index…”, “calculating a correlation coefficient value for each transcript…”, “wherein the composite correlation index indicates…”, “wherein the composite correlation showing loss of coordination in the subject…”, “wherein the transcriptome correlation method identifies a presence of a disease state…”, “wherein the transcriptome correlation method comprises an unbiased whole transcriptome analysis of all transcripts of the at least one tissue sample…”.
Independent claim 11 recites mathematical concepts of “determining an extent of expression of all gene transcripts in an organ of a subject via coordination analysis”, “determining via at least one pairwise comparison an extent of transcriptome reorganization”, “wherein conventional differential expression showing quantitative differences in gene transcripts…”, “wherein the unbiased whole transcriptome analysis identifies the presence of the disease state…”,
Independent claim 11 recites a mental process of “showing engagement of T cell activation to indicate a presence of a disease state”.
Dependent claims 8 and 19 further recite a mental process and mathematical concept of “identifying genes exhibiting changes in their transcriptomic profile via calculation of a cumulative composite correlation index”. Dependent claims 10 and 21 further recite a mental process and mathematical concept of “calculating a correlation coefficient value for each transcript with respect to every other transcript in a transcriptome via at least three pairwise comparisons, control versus steatosis, control versus non-steatosis and steatosis versus non-steatosis”.
The claims require a process of calculating a composite correlation index for at least one gene in a subject comprising, calculating a correlation coefficient value for each transcript with respect to every other transcript in a transcriptome via at least one pairwise comparison which are mathematical calculations. It is noted that claim 11 recites using a coordination analysis and pairwise comparison are interpreted as being the process of calculating a composite correlation index for at least one gene in a subject comprising, calculating a correlation coefficient value for each transcript with respect to every other transcript in a transcriptome via at least one pairwise comparison (see [081] in instant specification). Further, claim 11 recites showing T cell engagement which is interpreted as analyzing the data after the calculations have been performed to identify T cell engagement.
Dependent claims 2-7, 9, 12-18, and 20 further limit the mental process/mathematical concept recited in the independent claim but do not change their nature as a mental process/mathematical concept. Thus, claims 1-21 recite abstract ideas.
(Step 2A Prong 2)
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). Integration into a practical application is evaluated by identifying whether there are any additional elements recited in the claim and evaluating those additional elements to determine whether they integrate the exception into a practical application.
The additional element in claims 1 and 11 of “obtaining at least one tissue sample from the subject” does not integrate the judicial exception into a practical application because this is a step of insignificant extra solution activity of data gathering. This additional element is seen as insignificant extra solution activity of data gathering because this additional element and the judicial exceptions only interact in a manner by providing data to be processed by the judicial exceptions.
Thus, the additional elements do not integrate the judicial exceptions into a practical application and claims 1-21 are directed to the abstract idea.
(Step 2B)
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because:
The additional element in claims 1 and 11 of “obtaining at least one tissue sample from the subject” is conventional as shown on page G463 right col. of Suppli et al. (American Journal of Physiology-Gastrointestinal and Liver Physiology 316.4 (2019): G462-G472; newly cited) and on page 12 last paragraph of Haas et al. (Nat Metab 1, 604–614 (2019); previously cited).
Thus, the additional element does not amount to significantly more because the additional element is conventional.
Response to Arguments
Applicant's arguments filed 24 June 2025 have been fully considered but they are not persuasive.
Applicant argues that the amended claims show the technical improvement of wherein the transcriptome correlation method comprises an unbiased whole transcriptome analysis of all transcripts of the at least one tissue sample to reveal via gene coordination in the subject at least one physical change in the subject prior to such physical change being detectable by histopathological or differential expression. Applicant argues detection of physical changes in a subject prior to those physical changes being detectable via current detection means clearly removes the disclosure from the ambit of 101 as without the current invention, no detection would be possible prior to the changes becoming detectable. Applicant further argues this clearly advances how soon a disease may be detected without obvious physical evidence of a disease condition and is a massive technical improvement (Reply p. 6).
This argument has been fully considered but found to be not persuasive. The determination of an improvement to technology has two steps, the identification of additional elements (the technology) and an evaluation of the interaction between the judicial exceptions with these additional elements to determine if the improvement is realized in the additional elements. In the instant case, the only additional element is obtaining at least one tissue sample from the subject. This additional element interacts with the judicial exception by providing data to be processed by the judicial exceptions and thus falls under insignificant extra solution activity of data gathering. Although the method may provide for better detection, this detection is through abstract ideas of how the data is analyzed which would provide that the improvement is to the abstract idea itself. The MPEP states at 2106.05(a)(II) that “an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology”. Thus, the additional element of the claims does not integrate the recited judicial exceptions into a practical application because the improvement lies in the abstract idea itself and is not realized in the additional element of obtaining at least one tissue sample from the subject.
Claim Rejections - 35 USC § 102
The rejection on the ground of 102 of claims 1-7 in Office action mailed 24 March 2025 is withdrawn in view of the amendment of “obtaining at least one tissue sample from the subject” received 24 June 2025.
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.
Claims 1-7 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (Aging (Albany NY). 2020 Feb 29;12(5):4222-4229; previously cited) in view of Suppli et al. (American Journal of Physiology-Gastrointestinal and Liver Physiology 316.4 (2019): G462-G472; newly cited).
Independent claim 1 is directed to calculating a composite correlation index for at least one gene in a subject comprising
Zhang et al. shows calculating a composite correlation (Pc) for each gene which corresponds to the correlation of the correlation coefficient (R values) this gene has, with the whole transcriptome (Zhang et al. page 4223 right col., page 4226 left col., and page 4266 figure 4).
calculating a correlation coefficient value for each transcript with respect to every other transcript in a transcriptome via at least one pairwise comparison:
Zhang et al. shows calculating the correlation (R, Pearson’s) for genes with the whole transcriptome (Zhang et al. page 4226 left col., and page 4266 figure 4)
wherein the composite correlation index indicates either coordination or abolishment of coordination for the at least one pairwise comparison; wherein the composite correlation showing loss of coordination in the subject for the at least one gene indicates emergence of at least one pathology in the subject; and wherein the transcriptome correlation method identifies a presence of a disease state prior to the disease state being detectable via a histopathological analysis or a differential expression study of a subject
These wherein clauses are interpreted as not limiting to the active steps of the method because it does not further limit any steps of the method. These wherein clauses give description to what the composite correlation index can indicate, but do not limit the active steps in the method (the calculating the composite correlation index) (see MPEP 2111.04(I)).
wherein the transcriptome correlation method comprises an unbiased whole transcriptome analysis of all transcripts of the at least one tissue sample to reveal via gene coordination in the subject at least one physical change in the subject prior to such physical change being detectable by histopathological or differential expression.
Zhang et al. shows performing a coordination analysis of a whole transcriptome (i.e. all transcripts) by arbitrarily selecting genes that displayed at least 70 reads in the NOR group and calculating the correlation for these 178 genes with the whole transcriptome, independently in the NOR and the FRA groups (Zhang et al. page 4226 left col. and page 4226 figure 4). This analysis shows analyzing all transcripts due to the step of correlating highly expressed genes (i.e. the 178 genes) with the whole transcriptome (i.e. all the transcripts from the sample). Further, the limitation of “to reveal via gene coordination in the subject at least one physical change in the subject…” is an intended use of the method and does not recite an active step performed by the method.
Dependent claim 2 is directed to wherein a negative composite correlation index shows an inversed profile of gene coordination. Dependent claim 3 is directed to wherein a positive composite correlation index shows gene coordination was maintained. Dependent claims 4 is directed to wherein the composite correlation index shows an extent of transcriptional reprogramming for the at least one gene in the subject. Dependent claims 5 is directed to wherein an extent of transcriptional reprogramming indicates a presence of a disease state. Dependent claims 6 is directed to wherein the disease state is steatosis. Dependent claims 7 is directed to wherein a composite correlation index indicates a pro-inflammatory response and transcriptional reprogramming even though no histopathological evidence of inflammation is present.
These wherein clauses are interpreted as being non-limiting because they do not further limit any active steps of the method. These wherein clauses give description to what the composite correlation index can indicate, but do not limit the active steps in the method (the steps for calculating the composite correlation index) (see MPEP 2111.04(I)).
Zhang et al. does not explicitly show obtaining at least one tissue sample from the subject.
Like Zhang et al., Suppli et al. shows analyzing transcriptome data from subjects. Suppli et al. shows obtaining liver biopsy samples (i.e. tissue samples) from subjects which are used for extracting transcription data to be used for in gene expression analysis.
An invention would have been obvious to one or ordinary skill in the art if some motivation in the prior art would have led that person to substitute reference teachings to arrive at the claimed invention. It would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have substituted the peripheral blood mononuclear cell samples used for generating RNA-seq data for transcriptome analysis of Zhang et al. with liver biopsy samples (i.e. tissue samples) of Suppli et al. because both of these samples are used to produce RNA-seq data for gene expression analysis (Suppli et al. page G463 right col.). One would have a reasonable expectation of success because both these samples are used to generate RNA seq data to analyze gene expressions in the sample.
Claims 11-18 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (Aging (Albany NY). 2020 Feb 29;12(5):4222-4229; previously cited) in view of Haas et al. (Nat Metab 1, 604–614 (2019); previously cited).
Independent claim 11 is directed to determining an extent of expression of all gene transcripts in an organ of a subject via coordination analysis; determining via at least one pairwise comparison an extent of transcriptome reorganization;
Zhang et al. shows calculating a composite correlation for each gene which corresponds to the correlation of the R values this gene has, with the whole transcriptome (Zhang et al. page 4223 right col., page 4226 left col., and page 4266 figure 4). Zhang et al. shows calculating the correlation for genes with the whole transcriptome (Zhang et al. page 4226 left col., and page 4266 figure 4). These steps are interpreted as being the process of coordination analysis (see instant specification [081] which provides these steps being done in coordination analysis.
Zhang et al. does not show obtaining at least one tissue sample from the subject, gene transcripts from an organ, showing engagement of T cell activation to indicate a presence of a disease state, wherein conventional differential expression showing quantitative differences in gene transcripts fails to show T cell activation in genetically diverse specimens; and wherein the unbiased whole transcriptome analysis identifies the presence of the disease state prior to the disease state being detectable via a histopathological analysis or a differential expression study of a subject via the unbiased whole transcriptome analysis analyzing all transcripts of the at least one tissue sample to revel via gene coordination in the subject at least one physical change in the subject prior to such physical change being detectable by histopathological or differential expression.
Like Zhang et al., Haas et al. shows the analysis of gene expression data. Haas et al. shows a correlation between expression levels of genes and hepatic CD8 T lymphocyte (Haas et al. pages 24-25 figure 5e). Haas et al. shows that the strongest correlation with hepatic CD8 T lymphocyte was observed for PTPN22, which controls T cell receptor responsiveness and is associated with inflammatory and autoimmune diseases in humans (Haas et al. page 7 last paragraph). Haas et al. shows the transcripts for the analysis where derived from the liver (i.e. a tissue sample) (Haas et al. page 12 last paragraph). These wherein clauses are interpreted as being non-limiting because they do not further limit any active steps of the method (see MPEP 2111.04(I)).
Dependent claim 12 is directed wherein the organ is a liver.
Haas et al. shows the transcripts for the analysis where derived from the liver (Haas et al. page 12 last paragraph)
Dependent claim 13 is directed to wherein the disease state is steatosis.
Haas et al. shows hepatic CD8 T cells are linked to an increased expression of genes from the signature of active non-alcoholic steatohepatitis (NASH) (which is a form of steatosis) (Haas et al. page 7 last paragraph).
Dependent claim 14 is directed to wherein a negative composite correlation index shows an inversed profile of gene coordination. Dependent claim 15 is directed to wherein a positive composite correlation index shows gene coordination was maintained. Dependent claims 16 is directed to wherein the composite correlation index shows an extent of transcriptional reprogramming for the at least one gene in the subject. Dependent claims 17 is directed to wherein an extent of transcriptional reprogramming indicates a presence of a disease state. Dependent claims 18 is directed to wherein a composite correlation index indicates a pro-inflammatory response and transcriptional reprogramming even though no histopathological evidence of inflammation is present.
These wherein clauses are interpreted as being non-limiting because they do not further limit any active steps of the method. These wherein clauses give description to what the composite correlation index can indicate, but do not limit the active steps in the method (the steps for calculating the composite correlation index which is done in the coordination analysis) (see MPEP 2111.04(I)).
An invention would have been obvious to one or ordinary skill in the art if some motivation in the prior art would have led that person to combined reference teachings to arrive at the claimed invention. It would have been obvious to one of ordinary skill in the art before the effective filling date to have combined the use of coordination analysis of gene expression data to distinguish coordination between a disease and non-disease group of Zhang et al. with showing T cell activation in a liver using gene expression data which indicates a disease (NASH) of Haas et al. because this allows for a method that can identify potential targets to control a disease state as shown by Haas et al. “hepatic gene expression and immune signatures of NASH activity reveals CD8 T cells as a potential target to control hepatic inflammation, cytotoxic responses in the liver” (Haas et al. page 7 last paragraph). One would have a reasonable expectation of success because both Zhang et al. and Haas et al. analyze gene expression data.
Response to Arguments
Applicant's arguments filed 24 June 2025 have been fully considered but they are not persuasive.
Applicant argues that Zhang presents a small-scales analysis limited to only 178 genes, whereas the present disclosure applies an unbiased, whole transcriptome approach. Applicant further argues that Zhang focuses on preselected, defined sets of genes and it is not related to applicants whole-transcriptome approach that can be applied for discovery (Reply p. 7).
This argument has been fully considered but found to be not persuasive. Zhang shows calculating the correlation for these 178 highly expressed genes with the whole transcriptome (Zhang et al. page 4226 left col. and page 4226 figure 4) which shows that the analysis utilizes all transcripts in the sample. Although the analysis starts by selecting 178 high expressed genes, the analysis is not limited to only analyzing these genes because a correlation for each of these genes is calculated with the entire transcriptome in the sample.
Applicant argues with respect to combining Haas with Zhang, Haas is based on selected genes with thresholds, in contrast to Applicant’s unbiased methodology. Applicant further argues Haas focuses on within group gene expression correlations, while Applicant’s compute a composite correlation coefficient that integrates the correlations between different groups, which offers a fundamentally different perspective and application (Reply p. 7).
This argument has been fully considered but found to be not persuasive. Haas was relied upon for the limitation of showing engagement of T cell activation and the correlation between gene expression and T cell activation. Haas was not relied upon to show the computation of a composite correlation coefficient (Zhang shows this limitation). The combination of these references shows a method that computes a composite correlation coefficient along with showing engagement of T-cell activation. Thus, the method is obvious over Zhang in view of Haas as described in the above rejection.
Conclusion
No claims are allowed.
As discussed in the previous Office Action claims 8-10 and 19-21 are free from the prior art of record.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JONATHAN EDWARD HAYES whose telephone number is (571)272-6165. The examiner can normally be reached M-F 9am-5pm.
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/J.E.H./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685