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 .
Restriction/Election
Applicant’s election without traverse of the following in the replies filed on 9 June 2025, 7 August 2025 and 11 February 2026 is acknowledged:
Reference Sample Type: a reference sample type as in claim 5.
Data Set Compositions: a data set composition as in C as in claims 15-17, 19-20, and 22-23;
Sub-species election (a): Table 17-10, as in 15-17, 19-20, and 22-23;
Sub-species election (b): GVSA as a data analysis type as in claims 20. And 22-23.
10 genes from Table 17-10: SIGLEC1, OTOF, MS4A4A, LAMP3, CD300E, CD300C, CD14, CCL8, SP100, and RSAD2.
Claim Status
Claims 1, 3-5, 7-10, 15-17, 19-20, 22, 24, 28-32 and 34 are currently pending and under exam herein.
Claim 34 is newly added.
Priority
The instant Application is a continuation of International PCT Application No. PCT/US2023/013173, filed February 15, 2023, which claims priority to U.S. Provisional Patent Application No. 63/310,974, filed February 16, 2022; U.S. Provisional Patent Application No. 63/407,591, filed September 16, 2022; U.S. Provisional Patent Application No. 63/424,397, filed November 10, 2022. Priority to the Earliest Effective Filing Date (EFD) of 16 February 2022 is acknowledged.
Information Disclosure Statement
The Information Disclosure Statements filed 7/25/24 (3); 10/0/24; 11/20/24; 6/9/25; 8/7/25; 10/17/25; and 2/11/26 are, in-part, in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action.
It is noted that there are numerous references in the IDS documents as filed that are missing page numbers and have therefore been lined through and not considered, unless appearing on an attached form 892 cited by the Examiner. Applicant will please correct said submissions.
Drawings
The Drawings submitted 24 June 2024 are objected to because numerous instances of blurry Figures are noted herein. See Figures: 2; 3; 4A-B; 5A-C; 6A-C; 7A-B; 8; 9; 10; 12; 13A-C; 14; 22A-B; 23A; 26A-B; 27; 28A-I; 29A-D; 30A-B; 31A; 32A; 33A-B; 34; 38; and 41A; . Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
Note: All references to the Specification herein pertain to the PG publication: US20250022541.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Please see, for example, paragraph [0020]; [0314].
Claim Objections
Claims 1 and 29 is objected to because of the following informalities:
Claim 1 is missing an appropriate semi-colon after “genes expresses a polypeptide:” and should be amended to recite, “genes expresses a polypeptide;”.
Claim 29 is missing the appropriate period at the end of the claim.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)-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.
Claims 24 is rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 24 recites, “wherein (a) comprises providing the data set is provided as an input to a machine-learning model trained to generate an inference of whether the data set is indicative of the patient having lupus”, which is indefinite with respect to input to the machine-learning model trained to generate an inference, as it is unclear if the claim is directed to the active step of “generating an inference” or if the step is merely one of “input” only. As it currently reads, the claim is interpreted as only a step of input of information into an ML model. It is suggested that the claim be amended to recite more positive, active steps herein. Clarification tis requested through clearer claim language.
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, 3-5, 7-10, 15-17, 19-20, 22, 24, 28-32 and 34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1 Analysis: Are claims directed to process, machine, manufacture/composition of matter
With respect to step (1): yes, the claims are directed to a method.
Step 2A, Prong 1 Analysis: Do claims recite abstract idea
With respect to step (2A)(1), the claims recite (a) natural phenomena and (b) abstract ideas and.
With respect to natural phenomena: the MPEP at 2106.04(b) further explains that laws of nature and natural phenomena, as identified by the courts, include naturally occurring principles/relations and nature-based products that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature.
The identified natural phenomena herein are: the natural correlation between gene expression data for a set of genes and classification of a disease (lupus). This natural correlation is one that exists in nature, whether it is measured or not and is absent the hand of man. As such, said claims herein are detected to natural phenomena.
With respect to abstract ideas, the MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to abstract ideas, under the (2A)(1) evaluation, the claims are found herein to recite those that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and in conjunction with mathematical concepts (in particular mathematical relationships and formulas).
The claim steps to abstract ideas are as follows:
Claim 1: analyzing the data set using a computer comprising a non-transitory computer-readable storage media encoded with a computer program including instructions to identify a plurality of variably expressed select N genes from the set of genes, wherein the plurality of variably expressed genes comprises at least 100 genes and wherein each of the plurality of variably expressed genes expresses a polypeptide; clustering the expression data for the set of genes based at least in part on co-expression data for the plurality of variably expressed genes to generate a plurality of gene clusters; identifying a plurality of significant gene clusters from the plurality of gene clusters that are capable of classifying a disease in a subject based at least in part on a correlation between the plurality of significant gene clusters and a sample trait of the plurality of subjects, wherein the disease is lupus, wherein under the Broadest Reasonable Interpretation (BRI) of the step of “analysis”, absent any specific detailed step pertaining to the analysis, is one that includes a mere observation and assessment of provided data in the form of N number of sets of data and as such, said operation is a mental activity. The step of “clustering” to generate “gene clusters’ is equally one that is a mental operation that includes no specific details pertaining to the method of clustering and therefore one could mentally place data into groups that constitute “clusters” and is, as such, abstract. Further the step of “identifying” a significant gene cluster, absent any specific details in the claim pertaining to what constitutes a particular identification or classification, is one that is a mental process by which one can assess provided data given known details about what is “significant” as pertains to a lupus gene cluster. As such, each of said operations is abstract.
Dependent claims herein further limit the independent claim steps above and are also directed to judicial exceptions as above. Those include: claim 7 (two gene clusters); claim 8 (two gene clusters); claim 10 (gene clusters as endotypes).
Claim 19: the expression data of the data set is calculated using module eigengenes (1ViEs), wherein the MEs comprise the RNA expression levels of the genes in the modules formed based on the genes selected, wherein said operation is a mathematical process by which “calculations” are performed specifically using eigen values as described for example in the Specification at [0038]-ME correlations (p<0.2); [0065] calculations using eigengenes by Pearson correlations to MEs; {0352]; [0365]and the like. As such, sadi operations are mathematical abstract operations.
Claim 28: analyzing a biological sample from a subject using the plurality of significant gene clusters to determine whether the subject is suffering from lupus, wherein the step of “analysis”, absent any specific detailed step pertaining to the analysis, is one that includes a mere observation and assessment of provided data in the form of N number of sets of data and as such, said operation is a mental activity.
Claim 29: wherein the machine-learning model is trained using linear regression, logistic regression, Ridge regression, Lasso regression, elastic net (EN) regression, support vector machine (SVM), gradient boosted machine (GBM), k nearest neighbors (kNN), generalized linear model (GLM), naive Bayes (NB) classifier, neural network, Random Forest (RF), deep learning algorithm, linear discriminant analysis (LDA), decision tree learning (DTREE), adaptive boosting (ADB), Classification and Regression Tree (CART), hierarchical clustering, or any combination thereof, wherein said operations are mathematical processes and fall into the category of abstract ideas. For example, the steps including logistic regression could be those that are mathematical operations involving linear combinations of input features that are transformed by the sigmoid function to model probabilities between 0 and 1. As such, said operations are abstract.
Claim 30: wherein the machine-learning model comprises a receiver operating characteristic (ROC) curve with an Area-Under-Curve (AUC) of at least 0.8, wherein said operation limits the ROC only and is a mathematical parameter and is abstract.
Claim 34: generating a report comprising a lupus status of the subject, wherein said operation is a mental activity and process of providing data based on analysis and is therefore abstract.
Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas.
In general, the above abstract ideas directed to mental operations are similar to the concepts of collecting information, analyzing it and providing certain results from the collection and analysis (Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations (Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in (Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind with pen and paper, and can include mathematical concepts.
Further, see MPEP § 2106.04(a)(2), subsection III. The courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (see, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674: noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016): holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper"). Nor do the courts distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer. As the Federal Circuit has explained, "[c]ourts have examined claims that required the use of a computer and still found that the underlying, patent-ineligible invention could be performed via pen and paper or in a person’s mind" (see Versata Dev. Group v. SAP Am., Inc., 793 F.3d 1306, 1335, 115 USPQ2d 1681, 1702 (Fed. Cir. 2015); Mortgage Grader, Inc. v. First Choice Loan Servs. Inc., 811 F.3d 1314, 1324, 117 USPQ2d 1693, 1699 (Fed. Cir. 2016): holding that computer-implemented method for "anonymous loan shopping" was an abstract idea because it could be "performed by humans without a computer").
In general, claim steps pertaining to mathematical operations are similar to a mathematical formula for calculating an alarm limit, Parker v. Flook, 437 U.S. 584, 588-89, 198 USPQ2d 193, 195 (1978); the Arrhenius equation, Diamond v. Diehr, 450 U.S. 175, 191, 209 USPQ 1, 15 (1981); and a mathematical formula for hedging, Bilski v. Kappos, 561 U.S. 593, 611, 95 USPQ 2d 1001, 1004 (2010); and performing a resampled statistical analysis to generate a resampled distribution, SAP America, Inc. v. InvestPic, LLC, 898 F.3d 1161, 1163-65, 127 USPQ2d 1597, 1598-1600 (Fed. Cir. 2018), modifying SAP America, Inc. v. InvestPic, LLC, 890 F.3d 1016, 126 USPQ2d 1638 (Fed. Cir. 2018).
Step 2A, Prong 2 Analysis: Integration to a Practical Application
Because the claims do recite judicial exceptions, direction under (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements:
Claim 1: providing a data set comprising expression data for a set of genes from a plurality of subjects, wherein the set of genes comprises at least 500 genes; …using a computer comprising a non-transitory computer-readable storage media encoded with a computer program including instructions, wherein providing data is a step that is “extra-solution activity” for getting data to be used in the process of which is “analysis” and “clustering” and “identifying” as in the abstract ideas above. As explained by the Supreme Court, the addition of insignificant extra-solution activity does not amount to an inventive concept, particularly when the activity is well-understood or conventional. Parker v. Flook, 437 U.S. 584, 588-89, 198 USPQ 193, 196 (1978). In Flook, the Court reasoned that "[t]he notion that post-solution activity, no matter how conventional or obvious in itself, can transform an unpatentable principle into a patentable process exalts form over substance.
With respect to the recitation of “computer” and “non-transitory computer-readable media encoded with a computer program including instructions”, said recitation nis directed to a general purpose computer that merely acts to apply the judicial exceptions by use of conventional computer functions and therefore does not qualify as a particular machine herein See Ultramercial, Inc. v. Hulu, LLC, 772 F.3d 709, 716-17, 112 USPQ2d 1750, 1755-56 (Fed. Cir. 2014). See also TLI Communications LLC v. AV Automotive LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (mere recitation of concrete or tangible components is not an inventive concept); Eon Corp. IP Holdings LLC v. AT&T Mobility LLC, 785 F.3d 616, 623, 114 USPQ2d 1711, 1715 (Fed. Cir. 2015) (noting that Alappat’s rationale that an otherwise ineligible algorithm or software could be made patent-eligible by merely adding a generic computer to the claim was superseded by the Supreme Court’s Bilski and Alice Corp. decisions).
The dependent claims herein serve to limit the types of data present in the data gathering steps such as: claims 3-5 (data set types); claims 7-8 (cluster types); claim 9 (subject types); claim 15 (derivation of data sets); claim 16 (number in the sets of data); claim 17 (data set genes); claim 20 (derivation of data); claim 22 (derivation of data); claim 24 (data for input); claim 31 (type of sample from which data is derived); claim 32 (type of sample from which data is derived).
Further with respect to the additional elements in the instant claims, those steps directed to data gathering perform functions of collecting the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or on how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application. (MPEP 2106.05(g).
Step 2B Analysis: Do Claims Provide an Inventive Concept
The claims are lastly evaluated using the (2B) analysis, wherein it is determined that because the claims recite abstract ideas, and do not integrate that abstract ideas into a practical application, the claims also lack a specific inventive concept. Applicant is reminded that the judicial exception alone cannot provide the inventive concept or the practical application and that the identification of whether the additional elements amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the steps directed to providing data sets of gene expression data are those directed to data gathering and are further steps that do not provide for an inventive concept herein, as steps directed to providing data that includes gene expression data are those that are conventionally practiced steps in the art of gene expression analysis for correlations with disease, as is instantly claimed. The instant Specification provide evidence to this fact in that it outlines a laundry list of well-known and conventional techniques that may be used for said data gathering procedures, such as those that are found at, for example, [0270]; [0297] and the like. With respect to the specific gene sets, the prior art discloses the Affymetrix Human Transcriptome Array 2.0 (HTA-2.0) chipset as in the Specification at [0339] of which includes each of said genes listed in Table 17-10 (see Hunter et al. in J. Biomol. Tech. (2014) May; 25 Suppl:S20-S21).
Further, 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 (see MPEP 2106.05(d)II.): 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)); 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)).
The dependent claims have been analyzed with respect to step 2B and none of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception.
For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
1. Claims 1, 3-5, 7-10, 15-17, 19-20, 22, 24, 28-32 and 34 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by WO 2020/102043 to Lipsky et al. (IDS reference) and evidenced by Hoffman et al. [GSE88884 as disclosed as by Hoffman et al. in NCBI [citation: Hoffman RW et al. in Arthritis Rheumatol 2017 Mar;69(3):643-654].
With respect to 102(a)(2) the applied reference has a common inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Claim 1 is anticipated by the prior art to Lipsky et al. as follows:
A method comprising:
(a) providing a data set comprising expression data for a set of genes from a plurality of subjects, wherein the set of genes comprises at least 500 genes- Lipsky et al. disclose providing datasets that comprise gene expression data for sets of genes and wherein the genes comprise data from at least 500 genes as disclosed in at least [0463]; [0590]; [0653] disclosing multiple genes sets from multiple subjects;
(b) analyzing the data set using a computer comprising a non-transitory computer- readable storage media encoded with a computer program including instructions to identify a plurality of variably expressed genes from the set of genes, wherein the plurality of variably expressed genes comprises at least 100 genes and wherein each of the plurality of variably expressed genes expresses a polypeptide- Lipsky et al. disclose computer-readable media implementation [0107]; [0108]; Lipsky et al. disclose identification of variably expressed genes from sets of genes that comprise at least 100 genes at least at [0592];
(c) clustering the expression data for the set of genes based at least in part on co-expression data for the plurality of variably expressed genes to generate a plurality of gene clusters; and- Lipsky et al. disclose BIG-C analysis for gene clustering, for example and is in multiple embodiments of the disclosed invention for various lupus forms. See Lipsky at least at [0687];
(d) identifying a plurality of significant gene clusters from the plurality of gene clusters that are capable of classifying a disease in a subject based at least in part on a correlation between the plurality of significant gene clusters and a sample trait of the plurality of subjects, wherein the disease is lupus- Lipsky et al. disclose trait classification with gene expression as pertains to lupus at least at [0501]; [0502].
With respect to claims 3 and 4, Lipsky et al. disclose genes that comprise more than 100 genes and thus encompass the parameters as claimed. See Lipsky at least at [0691] disclosing gene sets from GSVA on GSE88884 (GSE88884 is disclosed to be cited as [citation: Hoffman RW, et al. in Arthritis Rheumatol 2017 Mar;69(3):643-654; Li Y et al. in PLoS One 2019;14(12):e0225651] See included NCBI accession display from Gene Expression Omnibus.
With respect to claim 5, Lipsky et al. disclose expression sets from a plurality of reference samples at least at [0488].
With respect to claims 7 and 8, Lipsky et al. disclose at least two clusters at least at [0498].
With respect to claim 9, Lipsky et al. disclose that subjects comprise at least two as disclosed at least at [0600].
With respect to claim 10, Lipsky et al. disclose a plurality of significant gene clusters that comprise endotypes at least at [0243]; [1073].
With respect to claim 15, Lipsky et al. disclose data sets from RNA measurements of at least two genes, such as SPATLS2l and RSAD2 which are disclosed in Table 17-10, at least at [0423].
With respect to claim 16, Lipsky et al. disclose data sets from RNA measurements of at least 10 genes, such as SPATLS2l, RSAD2, EDFAK2, USP18, IFIH1, PL5CR1, IFI27; HERC5, MX1; STAT1, which are disclosed in Table 17-10, at least at [0423]; [1604]; and [0220].
With respect to claim 17, Lipsky et al. disclose genes as listed (SIGLECI, OTOF, MS4A4A, LAMP3, CD300E, CD300C, CD14, CCL8, SP100, and RSAD2) at Table 43 [1277]; Table 71B [1634]; Table 71C [1635]; [1258]; Table 71C [1635]; Table 71B [1643]; [0220]; Table 71B [1634]; Table 20 [0472]; and [0423], respectively.
With respect to claim 19, Lipsky et al. disclose expression data calculated using module eigengenes as disclosed at least at [0489].
With respect to claim 20, Lipsky et al. disclose expression data as derived from RNA expression measurements at least at [0559]; [0691]; [0752].
With respect to claim 22, Lipsky et al. disclose expression data as derived from RNA expression measurements that include one or more scores at least at [0654].
With respect to claim 24, Lipsky et al. disclose data sets input into a machine learning model to indicate lupus at least at [0040]; [0089].
With respect to claim 28, Lipsky et al. disclose determination of a subject suffering from lupus at least at [0089].
With respect to claim 29, Lipsky et al. disclose machine learning as trained using, for example, support vector machines, at least at [0089].
With respect to claim 30, Lipsky et al. disclose wherein the machine-learning model comprises an ROC curve with an AUC of at least 0.85 at least at [0038].
With respect to claim 31, Lipsky et al. disclose that the biological sample is selected at least rom whole blood (WB) samples at least at [0043].
With respect to claim 32, Lipsky et al. disclose that the biological sample is purified to obtain a purified cell sample at least at [0428].
With respect to claim 34, Lipsky et al. disclose that a report may be generated to indicate the lupus status of a subject at least at [0048]; [0075]; [0101].
As such, the prior art to Lipsky et a;. as cited above anticipates each of the pending claims.
Conclusion
No claims are allowed.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting following form via EFS-Web or Central Fax (571-273-8300): PTO/SB/439. Applicant is encouraged to do so as early in prosecution as possible, so as to facilitate communication during examination.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowronek can be reached on (571) 272-9047.
Any inquiry of a general nature or relating to the status of this application or proceeding should be directed to (571) 272-0547.
Patent applicants with problems or questions regarding electronic images that can be viewed in the Patent Application Information Retrieval system (PAIR) can now contact the USPTO’s Patent Electronic Business Center (Patent EBC) for assistance. Representatives are available to answer your questions daily from 6 am to midnight (EST). The toll free number is (866) 217-9197. When calling please have your application serial or patent number, the type of document you are having an image problem with, the number of pages and the specific nature of the problem. The Patent Electronic Business Center will notify applicants of the resolution of the problem within 5-7 business days. Applicants can also check PAIR to confirm that the problem has been corrected. The USPTO’s Patent Electronic Business Center is a complete service center supporting all patent business on the Internet. The USPTO’s PAIR system provides Internet-based access to patent application status and history information. It also enables applicants to view the scanned images of their own application file folder(s) as well as general patent information available to the public.
/Lori A. Clow/ Primary Examiner, Art Unit 1687
Prosecution Insights