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 .
Status of Claims
Claims 1-19 are pending and examined on the merits.
Priority
The instant application filed on 12/15/2022 is a continuation of PCT/JP2021/014592 filed on 4/6/2021 and claims the benefit of foreign priority to Patent Application No. JP2020-106417 filed on 6/19/2020. Thus, the effective filing date of the claims is 6/19/2020.
The applicant is reminded that amendments to the claims and specification must comply with 35 U.S.C. § 120 and 37 C.F.R. § 1.121 to maintain priority to an earlier-filed application. Claim amendments may impact the effective filing date if new subject matter is introduced that lacks support in the originally filed disclosure. If an amendment adds limitations that were not adequately described in the parent application, the claim may no longer be entitled to the priority date of the earlier filing.
Information Disclosure Statement
The information disclosure statements (IDS) filed on 2/15/2023, 1/17/2024, 2/9/2024, 7/15/2025, and 9/12/2025 have been entered and considered. A signed copy of the corresponding 1449 forms have been included with this Office action.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (para.0005). 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.
Appropriate correction is required.
Claim Objections
Claim 2 objected to because of the following informalities: line 4, "related to a biological-sample's characteristic" should read "related to a biological sample's characteristic". Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 11 rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claim 11 recites "increase a weight of an evaluation value of a biomarker having a strength indicator that is within a preset threshold range". The written description of the instant specification does not explicitly disclose a definition for "a strength indicator", but could be interpreted as the limitations of claim 8 regarding assigning a weight to a biomarker evaluation value. To further prosecution, please see the interpretation of this claim under the section regarding 112(b), below.
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 2, 9, 11, and 17 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 2 recites "the processor is configured to select pieces of annotation information related to a biological-sample's characteristic of interest". It is not clear how the processor is determining which "pieces of annotation information" are "related to a biological sample's characteristic of interest". Is there some relational database being queried, or a user making the selection, etc.? To further prosecution, the limitation is interpreted as "the processor is configured to enable a user to select pieces of annotation information related to a biological-sample's characteristic of interest" (support for this can be found in at least para.0055-56 of the instant specification).
Claim 9 recites "determine a piece of annotation information having a relatively high rarity to have a high information value". The metes and bounds of "relatively high rarity" is not clear (i.e. what would be indicative of "high rarity"?). To further prosecution, the limitation is interpreted as "determine a piece of annotation information having a high rarity to have a high information value based on the addition number being below a preset threshold, then increasing the weight of the piece of annotation information" (based on para.0110 "a piece of annotation information whose addition number is relatively small, that is, a piece of annotation information that has a relatively high rarity"). This also necessitates that claim 8 depend from claim 7, as there is now a lack of antecedent basis for the "addition number".
Claim 11 recites "increase a weight of an evaluation value of a biomarker having a strength indicator that is within a preset threshold range". First, there is no weight assigned to the evaluation values of claim 1 for which to perform an increase to. Second, it is not clear what "a strength indicator" is meant to encompass, and a weight may already be interpreted as a kind of strength indicator and therefore renders claim 11 as a duplicate of claim 8 but with a threshold range comparison step. To further prosecution, the limitation is interpreted as "assign a weight to the evaluation value in accordance with a preset threshold range of the pieces of annotation information".
Claim 17 recites "pick, on the basis of the measurement results, pieces of annotation information that influence a characteristic of the biological samples to a relatively large degree from among pieces of annotation information added to the measurement target biomarkers, with a statistical method". The metes and bounds of "a relatively large degree" are not clear. To further prosecution, the limitation is interpreted as "pick, on the basis of the measurement results, pieces of annotation information that statistically significantly influence a characteristic of the biological samples from among pieces of annotation information added to the measurement target biomarkers".
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 1-19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of a mental process, a mathematical concept, organizing human activity, or a law of nature or natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claims 1 and 18-19: “a deriving process for deriving an evaluation value of each of the plurality of biomarkers on the basis of the pieces of annotation information” provides an evaluation (deriving values from annotations involves evaluating data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“a selection process for selecting on the basis of the evaluation value, measurement target biomarkers from among the plurality of biomarkers” provides an evaluation (selecting a measurement target biomarker involves evaluating the "evaluation value") that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 2: “select pieces of annotation information related to a biological-sample's characteristic of interest” (as interpreted above) provides a judgement (selecting annotations of interest involves judgement) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“derive the evaluation value on the basis of only the selected pieces of annotation information” provides an evaluation (deriving values from annotations involves evaluating data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 5: “select a number of biomarkers, the number satisfying the range, from among biomarkers prepared for each category of the plurality of categories, and sort the selected biomarkers into the category as the measurement target biomarkers” provides for organizing information (selecting and sorting biomarkers involves sorting or structuring data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 7: “count an addition number that is the number of pieces of annotation information added to each of the plurality of biomarkers” provides a mathematical calculation (counting the number of pieces of information involves arithmetic) that is considered a mathematical concept, which is an abstract idea.
“derive the evaluation value on the basis of the addition number” provides an evaluation (deriving values from annotations involves evaluating data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 8: “assign a weight to the evaluation value in accordance with information values of the pieces of annotation information” provides an evaluation (assigning weights based on information values involves evaluating data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 9: “determine a piece of annotation information having a high rarity to have a high information value based on the addition number being below a preset threshold, then increasing the weight of the piece of annotation information” (as interpreted above) provides an evaluation (determining rarity of annotation information involves evaluating the addition number [para.0110]) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 10: “assign the weight to the evaluation value on the basis of orthogonality of the pieces of annotation information” provides an evaluation (determining orthogonality of annotation information involves evaluating the addition number [para.0110]) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 11: “assign a weight to the evaluation value in accordance with a preset threshold range of the pieces of annotation information” (as interpreted above) provides an evaluation (assigning weights based on information values involves evaluating data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 12: “increase weights of evaluation values of the previously known markers” provides a mathematical calculation (increasing weights involves arithmetic) that is considered a mathematical concept, which is an abstract idea.
Claim 13: “select as the measurement target biomarkers, more than 100 and less than or equal to 1000 biomarkers” provides an evaluation (selecting a particular number of biomarkers involves evaluating the number selected to ensure it is within the specified range) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 17: “pick, on the basis of the measurement results, pieces of annotation information that statistically significantly influence a characteristic of the biological samples from among pieces of annotation information added to the measurement target biomarkers” (as interpreted above) provides an evaluation (selecting annotation information involves evaluating statistical significance of the measurement data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
These recitations are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in 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 or are mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Additionally, while claims 1-19 recite performing some aspects of the analysis on “an information processing apparatus, the operation method being performed by a processor” (claim 1), “An information processing apparatus comprising at least one processor” (claim 18), and “A non-transitory computer-readable storage medium storing an operation program for an information processing apparatus for causing a processor to perform” (claim 19), there are no additional limitations that indicate that this requires anything other than carrying out the recited mental processes or mathematical concepts in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then it falls within the “Mental processes” grouping of abstract ideas. As such, claims 1-19 recite an abstract idea (Step 2A, Prong 1: YES).
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). The judicial exceptions listed above are not integrated into a practical application because the claims do not recite an additional element or elements that reflects an improvement to technology. Specifically, the claims recite the following additional elements:
Claim 1: “an information processing apparatus, the operation method being performed by a processor” provides insignificant extra-solution activities (running instructions on generic computer components) that do not serve to integrate the judicial exceptions into a practical application.
“an acquisition process for acquiring pieces of annotation information added to each of a plurality of biomarkers related to biological samples” provides insignificant extra-solution activities (obtaining data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 3: “add the pieces of annotation information to the biomarkers with reference to a database in which the pieces of annotation information for the biomarkers are registered” provides insignificant extra-solution activities (adding data to a database is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 5: “accept a plurality of categories defined in accordance with the types of the biological samples and a range of the number of measurement target biomarkers for each of the plurality of categories, the plurality of categories and the range being specified by a user” provides insignificant extra-solution activities (obtaining data and specifications from a user is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 12: “accept previously known markers specified by a user, the previously known markers being biomarkers already known to influence a characteristic of the biological samples” provides insignificant extra-solution activities (obtaining data from a user is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 17: “acquire measurement results regarding the measurement target biomarkers” provides insignificant extra-solution activities (acquiring measurement data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“present the picked pieces of annotation information to a user” provides insignificant extra-solution activities (presenting results is a post-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 18: “An information processing apparatus comprising at least one processor” provides insignificant extra-solution activities (running instructions on generic computer components) that do not serve to integrate the judicial exceptions into a practical application.
Claim 19: “A non-transitory computer-readable storage medium storing an operation program for an information processing apparatus for causing a processor to perform” provides insignificant extra-solution activities (running instructions on generic computer components) that do not serve to integrate the judicial exceptions into a practical application.
The steps for obtaining data, adding data to databases, users entering data, acquiring measurement data, and presenting results are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application because they are pre- and post-solution activities involving data gathering, data manipulation, and sample manipulation steps (see MPEP 2106.04(d)(2)). Furthermore, the limitations regarding implementing program instructions do not indicate that they require anything other than mere instructions to implement the abstract idea in a generic way or in a generic computing environment. As such, this limitation equates to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. Therefore, claims 1-19 are directed to an abstract idea (Step 2A, Prong 2: NO).
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 claims recite additional elements that are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application, or equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
As discussed above, there are no additional elements to indicate that the claimed “an information processing apparatus, the operation method being performed by a processor” (claim 1), “An information processing apparatus comprising at least one processor” (claim 18), and “A non-transitory computer-readable storage medium storing an operation program for an information processing apparatus for causing a processor to perform” (claim 19) requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. Additionally, the limitations for obtaining data, adding data to databases, users entering data, acquiring measurement data, and presenting results are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application. Furthermore, no inventive concept is claimed by these limitations as they are well-understood, routine, and conventional.
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-19 are not patent eligible.
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 1-4, 8, 10, 12, 16, and 18-19 rejected under 35 U.S.C. 103 as being unpatentable over Chen et al. (US-20150119289).
Regarding claims 1 and 18-19, Chen teaches acquiring pieces of annotation information added to each of a plurality of biomarkers related to biological samples (Chen teaches acquiring and using gene expression data, which represents annotation information, as each gene may be a biomarker related to a biological sample).
Chen also teaches deriving an evaluation value of each of the plurality of biomarkers on the basis of the pieces of annotation information (Para.0043 "FIG. 17A shows the results of interactive visual querying, in which the name of proteins in the peak or valleys with differential gene expression levels above thresholds in control versus incipient Alzheimer's disease is shown", as the differential gene expression levels are a derived value of the annotated gene expression value, and para.0225 "The score(s) may be calculated as a categorical variable based on the number of target nucleic acids that possess an expression level outside of or different from the reference expression level").
Chen also teaches selecting on the basis of the evaluation value, measurement target biomarkers from among the plurality of biomarkers (Para.0133 "As an example, candidate cancer biomarker proteins were taken from a literature-curated protein-interaction dataset of 1049 cancer candidate biomarkers (M. Polanski, N. Anderson, Biomarker Insights 2, 1 (2006)), which primarily includes differentially expressed proteins or genes in cancer").
It is recognized that the citations and evidence provided above are derived from potentially different embodiments of a single reference. Nevertheless, it 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 to employ combinations and sub-combinations of these complementary embodiments, because Chen et al. explicitly motivates doing so at least in para.0081 "The principle and framework of the disclosed system can be generalized by those of skill in the art for biomarker discovery data explorations far beyond the case study examples disclosed herein", para.0196-197 "Having described the invention with reference to the exemplary embodiments, it Is to be understood that it is not intended that any limitations or elements describing the exemplary embodiment set forth herein are to be incorporated into the meanings of the patent claims unless such limitations or elements are explicitly listed in the claims. Likewise, it is to be understood that it is not necessary to meet any or all of the identified advantages or objects of the Invention disclose herein in order to fall within the scope of any claims, since the invention is defined by the claims and since inherent and/or unforeseen advantages of the present invention may exist even though they may not be explicitly discussed herein. Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims", and otherwise motivating experimentation and optimization. Additionally, doing so merely combines prior art elements according to known methods to yield predictable results.
Regarding claim 2, Chen teaches the methods of Claim 1 on which this claim depends/these claims depend, respectively. Chen also teaches selecting pieces of annotation information related to a biological-sample's characteristic of interest (as interpreted above) (Abstract "Methods of identifying biomarkers affiliated with a condition of interest are provided")
Chen also teaches deriving the evaluation value on the basis of only the selected pieces of annotation information (Para.0062 "It is recognized that a kit of the instant application may provide biomarker detection reagents suitable for use in any method of preferentially evaluating expression of a biomarker of Interest").
Regarding claim 3, Chen teaches the methods of Claim 1 on which this claim depends/these claims depend, respectively. Chen also teaches adding the pieces of annotation information to the biomarkers with reference to a database in which the pieces of annotation information for the biomarkers are registered (Para.0017 "The visualization method includes accessing a protein database containing data regarding genes and protein, and accessing a disease database containing data regarding diseases").
Regarding claim 4, Chen teaches the methods of Claim 1 on which this claim depends/these claims depend, respectively. Chen also teaches the pieces of annotation information are associated with types of the biological samples (Para.0014 "Methods of characterizing a lymphoma related disorder in a subject at risk for a lymphoma related disorder comprising the steps of providing a biological sample obtained from the subject").
Regarding claim 8, Chen teaches the methods of Claim 1 on which this claim depends/these claims depend, respectively. Chen also teaches assigning a weight to the evaluation value in accordance with information values of the pieces of annotation information (Para.0100 "An adapted node-weighted-and-edge-weighted spring embedder graph drawing algorithm can be used to generate the graph node layouts in the base network. This spring embedder graph drawing algorithm can work as follows: if an edge connects a pair of nodes then the resting distance of the spring connecting the pair of nodes is inversely proportional [to] the edge score; otherwise, the resting distance of the spring connecting the pair of nodes Is proportional to the summation of the node weights, which defines an area of influence for each node").
Regarding claim 10, Chen teaches the methods of Claim 8 on which this claim depends/these claims depend, respectively. Chen also teaches assigning the weight to the evaluation value on the basis of orthogonality of the pieces of annotation information (Para.0087 "FIG. 1c illustrates that a phenotype-molecule correlation score is derived for every pair of a phenotype and a molecule forming the nodes in the molecular network terrain and the phenotypic network terrain. These correlation scores can be derived from literature mining").
Regarding claim 12, Chen teaches the methods of Claim 1 on which this claim depends/these claims depend, respectively. Chen also teaches accepting previously known markers specified by a user, the previously known markers being biomarkers already known to influence a characteristic of the biological samples (Para.0188 "Specificity of the four member lymphoma related biomarker panel, TNFRSF8, FSCN1, BCL6 and PIM1, and the other 152 candidate lymphoma biomarkers were analyzed for the percentage of all lymphoma samples in the lymphoma dominated class when comparing leukemia samples against lymphoma samples. In the case of disease specificity, the higher the y value of the detected panel indicates the better the panel distinguishes lymphoma conditions from leukemia conditions [Y value presents the portion of the benchmark population whose error rates are equal to or less than x]").
Regarding claim 16, Chen teaches the methods of Claim 1 on which this claim depends/these claims depend, respectively. Chen also teaches each of the pieces of annotation information includes a term defined by Gene Ontology (Para.0081 "In fact, other biological ontology networks, including disease networks, pathway networks, and their dynamics can also be visualized and explored using the disclosed framework and system, given the appropriate goals of investigation and the definitions of vertices and their relationships in the networks" suggests GO terms could be used).
Claims 5-7, 11, 13-15, and 17 rejected under 35 U.S.C. 103 as being unpatentable over Chen et al. (US-20150119289) as applied to claims 1-4, 8, 10, 12, 16, and 18-19 above, and further in view of Steelman et al. (US-20200181710).
Chen et al. is applied to claims 1-4, 8, 10, 12, 16, and 18-19.
Regarding claim 5, Chen teaches the method of Claim 1 on which this claim depends/these claims depend.
Chen teaches selecting a number of biomarkers, the number satisfying the range, from among biomarkers prepared for each category of the plurality of categories, and sort the selected biomarkers into the category as the measurement target biomarkers (Para.0154 "User Interaction can be provided for visual exploration. The labels can be toggled on to support an overview of the distribution of protein nodes. The label of an individual protein can be toggled on by querying the name of the protein. To enable multi-scale visualization, a threshold T (T>0) can be set and only proteins whose height values are larger than T will be displayed").
Chen does not explicitly teach accepting a plurality of categories defined in accordance with the types of the biological samples and a range of the number of measurement target biomarkers for each of the plurality of categories, the plurality of categories and the range being specified by a user.
However, Steelman teaches a user interaction for obtaining an analysis, and the analysis returning categories for the user (Para.0012 "The device may require three or fewer interactions by a user in order to obtain an interpretation of the target nucleic acid expression level" and para.0141 "The multivariate analysis may be used to detect or diagnose a complex disease, which is only characterized by multiple analytes in the composition and is specifically not characterized by any one of the component analytes; assign a subtype or subcategory to the cellular specimen (e.g. breast cancer subtype); and stratify risk (e.g. probability of malignancy, probability of a future event)").
Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Chen as taught by Steelman in order to assign categories to different types of biological compounds that might be assays by Chen (Chen, para.0067 "By "assaying" is intended measuring, quantifying, scoring, or detecting the amount, concentration, or relative abundance of a substance. Methods of evaluating biological compounds are known in the art. It is recognized that a method of assaying one type of biological compound, such as a protein, may not be suitable for assaying another type of biological compound, such as a nucleic acid. It is recognized that methods of assaying a biological compound include direct measurements and indirect measurements. One skilled in the art would be able to select an appropriate method of assaying a particular biological compound"). One skilled in the art would have a reasonable expectation of success because both methods provide for analysis of biological data for identification of biomarkers.
Regarding claim 6, Chen and Steelman teach the method of Claim 5 on which this claim depends/these claims depend. Steelman also teaches the categories include categories of iPS cell, ectoderm, mesoderm, and endoderm (Para.0323 "Exemplary solid samples include, by way of example only, feces, tissue biopsy (such as tumor biopsy, resected tumor, or other tissue biopsy that includes endoderm, mesoderm, ectoderm, or some combination thereof)").
Regarding claim 7, Chen and Steelman teach the method of Claim 1 on which this claim depends/these claims depend. Steelman also teaches counting an addition number that is the number of pieces of annotation information added to each of the plurality of biomarkers, and deriving the evaluation value on the basis of the addition number (Para.0478 "Concordance study 1. Collecting the 200 RNA-Seq gene entries differentially expressed in this 2. Collecting the 200 RNA-Seq gene entries over expressed in tissue vs. healthy 3. Agilent Reporter_ID mapped to Gene_Symbol 4. Agilent level3 data analyses 5. RNA-Seq top 200 overexpressed vs. Agilent array top 200 over- expressed. 6. Distribution of the 130 genes overexpressed in tumor vs. normal").
Regarding claim 11, Chen and Steelman teach the method of Claim 1 on which this claim depends/these claims depend. Steelman also teaches assigning a weight to the evaluation value in accordance with a preset threshold range of the pieces of annotation information (as interpreted above) (Para.0225 "The score(s) may be calculated as a categorical variable based on the number of target nucleic acids that possess an expression level outside of or different from the reference expression level").
Regarding claims 13 and 14, Chen and Steelman teach the method of Claim 1 on which this claim depends/these claims depend. Steelman also teaches selecting as the measurement target biomarkers, more than 100 and less than or equal to 1000 biomarkers; and the biomarkers include genes (Para.0478 "Collecting the 200 RNA-Seq gene entries over expressed in tissue vs. healthy").
Regarding claim 15, Chen and Steelman teach the method of Claim 1 on which this claim depends/these claims depend. Steelman also teaches the genes include differentially expressed genes having significantly different expression levels (Para.0038 "Step 1 attribute filtering (by differential expression and p-value").
Regarding claim 17, Chen and Steelman teach the method of Claim 1 on which this claim depends/these claims depend. Steelman also teaches acquiring measurement results regarding the measurement target biomarkers (Para.0353 "Measurement data are acquired and processed using on-board custom software").
Steelman also teaches picking, on the basis of the measurement results, pieces of annotation information that statistically significantly influence a characteristic of the biological samples from among pieces of annotation information added to the measurement target biomarkers (as interpreted above) (Para.0038 "Step 1 attribute filtering (by differential expression and p-value, Step 2 attribute selection (using feature selection methods)" suggests filtering/identifying/selecting statistically significant genes using differential expression analysis).
Steelman also teaches presenting the picked pieces of annotation information to a user (Para.0214 "An integrated touch screen (see, e.g., FIG. 3 component 345) may display instrument status, identities of the selected test, subject information, and/or user information; testing parameters; testing progress; and final results").
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-19 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of US-20240242777. Although the claims at issue are not identical, they are not patentably distinct from each other because both involve acquiring pieces of annotation information about a biomarker of a sample, deriving an evaluation value (a feature) of each biomarker based on the pieces of annotation information, and selecting measurement target biomarkers (a specific biomarker or a measurable amount/value for that biomarker) from among the biomarkers.
Claims 1-19 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 of US-20230066188. Although the claims at issue are not identical, they are not patentably distinct from each other because both involve acquiring pieces of annotation information about a biomarker of a sample, deriving an evaluation value (a feature) of each biomarker based on the pieces of annotation information, and selecting measurement target biomarkers (a specific biomarker or a measurable amount/value for that biomarker) from among the biomarkers.
Conclusion
No claims are allowed.
Claim 9 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims. The closest prior art is considered to be Steelman and Chen, as discussed above relating to the rejection of claims 7 and 8 under 35 U.S.C. 103, respectively. As discussed above, Steelman teaches the limitations of claim 7, counting reads per gene (i.e. counting addition numbers per biomarker) and determining an evaluation value based on these counts. Chen teaches the limitations of claim 8weighting evaluation values based on the annotated information. Examiner notes that in regards to claim 9, high rarity is an inherent property for a low frequency item below a particular threshold, however, increasing some weight value for that item based on the idea that it would also have the property of a "high information value" was not found to be taught or suggested by the prior art.
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/R.A.P./Examiner, Art Unit 1686
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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