DETAILED ACTION
Applicant's response, filed 8/20/2025, 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 .
Priority
The instant application claims benefit of priority to U.S. Patent Application No. 16/022,835 filed on 6/29/2018. The claim to the benefit of priority is acknowledged, however previous application was abandoned. As such, the effective filing date of claims 1-20 is 6/6/2022.
Claim Status
Claims 1, 3-13, and 15-20 are pending.
Claims 1 and 3-10 are under examination.
Claims 1 and 3-10 are rejected.
Claims 2 and 14 are cancelled.
Claims 11-13 and 15-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 8/20/2025.
Drawings
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).
Claim Rejections - 35 USC § 101
Response to Amendment
In view of applicant’s amendments to the claims, previous rejections under 35 U.S.C. 101 have been reviewed, updated, and provided below.
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 and 3-10 are rejected under 35 U.S.C. § 101 because the claimed invention is directed to abstract ideas without significantly more. The independent claim recites a system for generating and analyzing sequencing data to identify clinically relevant genetic variants and display both variant information and potential treatment information.
Framework with which to Analyze Subject Matter Eligibility:
Step 1: Are the claims directed to a category of subject matter (a process, machine, manufacture, or composition of matter)? [see MPEP § 2106.03]
Claims are directed to statutory subject matter, specifically a system (claims 1 and 3-10)
Step 2A Prong One: Do the claims recite a judicially recognized exception, i.e., an abstract idea, law of nature, or natural phenomenon? [see MPEP § 2106.04(a)]
The claims recite abstract ideas.
With respect to the Step 2A Prong One evaluation, the instant claims are found herein to recite abstract ideas that fall into the groupings of mental processes and mathematical concepts.
Independent claim 1: Parsing data to identify one or more gene variants, identifying clinically relevant information, applying filters, selecting display information from data consisting of those specified, and removing data based on a particular condition are processes of curating, selecting, comparing/contrasting, isolating, and presenting information that can be done via pen and paper or within the human mind and are therefore abstract ideas, specifically mental processes.
Claim 3: Filtering based on read depth and allele frequency are merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 5: The recommendation not being one of those specified is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 6: The recommendation being the specified therapy is merely further limiting the data itself which is an abstract idea, specifically a mental process.
Claim 7: Marking the therapy sensitive for the type of cancer with a first indicum is a process of selecting information that can be done with a pen and paper or within the human mind and is therefore an abstract idea, specifically a mental process.
Step 2A Prong Two: If the claims recite a judicial exception under prong one, then is the judicial exception integrated into a practical application? [see MPEP § 2106.04(d)]
Because the claims do recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application.
The following claims recite the following additional elements in the form of non-abstract elements:
Claim 1: A system, sequencing device, and computing device are generic and nonspecific elements of computers that do not improve the function of any computer or technology described herein [See MPEP § 2106.04(d)(1) and MPEP § 2106.05(d)]. Generating variant data, and receiving a user input are insignificant extra solution activities specifically mere data gathering (See Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)]. Visualizing data on a first and second display screen is an insignificant extra solution activity specifically necessary data outputting (See Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 4: A third representation being displayed is an insignificant extra solution activity specifically necessary data outputting (See Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 8: Displaying the first and second representations in a single panel is an insignificant extra solution activity specifically necessary data outputting (See Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 9: The single panel being an individual gene panel representation is an insignificant extra solution activity specifically necessary data outputting (See Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
Claim 10: The second representation is visualized in a first portion and the first representation is visualized in a second portion is an insignificant extra solution activity specifically necessary data outputting (See Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989) and Determining the level of a biomarker in blood, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968. See also PerkinElmer, Inc. v. Intema Ltd., 496 Fed. App'x 65, 73, 105 USPQ2d 1960, 1966 (Fed. Cir. 2012) (assessing or measuring data derived from an ultrasound scan, to be used in a diagnosis)) [See MPEP § 2106.05(g)].
The claims appear to require nothing more than generic computer parts to perform the functions that constitute the judicial exception, and additional steps that are either insignificant extra solution activities, mere data gathering steps or merely selecting a particular data source [see MPEP § 2106.05(d), (f), (g)]. Therefore, these are mere, instructions to apply the judicial; exceptions using computer systems. The additional elements of a system comprising a sequencing device and computing device do not integrate the abstract idea into a practical application. [see MPEP § 2106.04(d)(I) and MPEP § 2106.05(f)]
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? [see MPEP § 2106.05]
Because the additional claim elements do not integrate the abstract idea into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept.
The claims do not recite additional elements that are sufficient to amount to significantly more than the judicial exceptions because the claims recite additional elements that are generic, nonspecific, selecting a particular data source, mere data gathering or insignificant extra solution activity.
The additional elements of a system comprising a sequencer (Conventional: Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546) and computing device are all generic and nonspecific elements of a computer that are well-understood, routine and conventional within the art and therefore do not improve the functioning of any computer or technology described therein (Receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), Performing repetitive calculations, Flook, 437 U.S. at 594, 198 USPQ2d at 199 (recomputing or readjusting alarm limit values), and Storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015)) [See MPEP § 2106.05(d)(II)]. Therefore, taken both individually and as a whole, the additional elements do not amount to significantly more than the judicial exception by providing an inventive concept.
The additional elements of generating variant data (Conventional: Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546), displaying the first and second representations in a single panel (Kalocsai et al. 1999 – Teaches the need for visual representations of genetic data and corresponding statistical analyses), the single panel being an individual gene panel representation (Kalocsai et al. 1999 – Teaches the need for visual representations of genetic data and corresponding statistical analyses), and the second representation is visualized in a first portion and the first representation is visualized in a second portion (Kalocsai et al. 1999 – Teaches the need for visual representations of genetic data and corresponding statistical analyses), are all insignificant extra solution activities specifically, mere data gathering (See Receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), TLI Communications LLC v. AV Auto. LLC, 823 F.3d 607, 610, 118 USPQ2d 1744, 1745 (Fed. Cir. 2016) (using a telephone for image transmission), OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), and Storing and retrieving information in memory, Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015)) [See MPEP § 2106.05(g)]. Therefore, taken both individually and as a whole, the additional elements do not amount to significantly more than the judicial exception by providing an inventive concept.
Therefore, claims 1 and 3-10, when the limitations are considered individually and as a whole, are rejected under 35 U.S.C. § 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments filed 8/20/2025 have been fully considered but they are not persuasive.
Applicant asserts on page 8 of the Remarks that the recited additional elements provide for an improved system which integrates the judicial exception into a practical application, specifically citing the visualizations of information. However, applicant is asserting that the improvement lies in the ability of the clinician to more quickly review and understand the presented material, which is not a part of the claimed invention. Additionally, as previous described in the above rejection, all additional elements are in fact state of the art as described within applicant’s own specification (generic and conventional computer elements). Finally, if applicant is claiming that the improvement lies in the ability of the clinician to more quikly review and understand presented material, the invention is directed to the judicial exception, as comprehending information is an abstract idea, specifically a mental process.
Applicant further asserts on page 9 of the Remarks that the specified claim elements, identifying interactions between gene variants and visualizing representations of a recommendation, are unconventional. However, examiner reminds applicant that in the Remarks on page 7, applicant asserts “that each of the pending claims are directed to an improved system, not to an abstract idea”, of which displaying information would qualify under MPEP 2106.05(A) - Simply appending well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, e.g., a claim to an abstract idea requiring no more than a generic computer to perform generic computer functions that are well-understood, routine and conventional activities previously known to the industry, as discussed in Alice Corp., 573 U.S. at 225, 110 USPQ2d at 1984. Additionally, applicant is reminded that under MPEP 2106.05(a) - It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements. For which the process of identifying is a judicial exception as previously described above. Additionally, examiner reminds applicant that the conventionality of methods of the system is not dependent on Sayada et al. only the conventionality of the additional element components of the system itself, and not all of the elements pointed to by applicant are additional elements for which would not be taken into account regarding conventionality. Lastly, a meaningful limit is not placed on the judicial exception except by the claim language itself, visualization is merely the presentation of the data itself, which is in itself a judicial exception, an abstract idea or mental process as described above.
Claim Rejections - 35 USC § 103
Response to Amendment
In view of applicant’s amendments to the claims, previous rejections under 35 U.S.C. 103 have been reviewed, updated, and provided below.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1 and 3-7 are rejected under 35 U.S.C. 103 as being unpatentable over Sayada et al. (US 20140310025 A1) in view of Stern et al. (US 20160333420 A1).
Claim 1 is directed to a system of a sequencing device communicatively coupled to a computing device which generates variant data, parse said variant information for gene variants, input pre-diagnosis of cancer type, identify the clinically relevant information while filtering said information using variant data, visually representing a therapeutic intervention and gene variants and then removing variant data.
Sayada et al. teaches in paragraph [0031] “In addition to a UDS analysis, a Sanger-based comparative analysis can be performed, if desired” and in paragraph [0048] “The hardware includes a sequencer capable of performing UDS”, which reads on a system comprising: a sequencing device; and a computing device communicatively coupled to the sequencing device. In combination with paragraph [0048] description of an attached sequencer, Sayada et al. teaches in paragraph [0047] “Once information regarding the patient's variants is obtained, the data can be collected, stored, analyzed, interpreted, and/or validated, and used to generate a personalized healthcare report”, in paragraph [0011] “The selection of appropriate therapeutic regimens can be based, at least in part, on an analysis of the variants, and a correlation of the variants with therapeutic regimens”, in paragraph [0069] “In addition to being used for routine genotyping, the process can also be used for research, for example, to identify types of mutations in a virus following the administration of particular anti-viral or anti-cancer agents. The system can be interfaced with a dedicated Data Exploratory Framework that can be used for research, either on UDS-related molecular data only, or in correlation with clinical data”, and paragraph [0001] “The present invention concerns systems, and/or methods and/or computer program products for guiding the selection of therapeutic treatment regimens for complex disorders, including, but not limited to, cancer…”, and paragraph [0096] “Further, the existence of disorders associated with genetic mutations, in cancer cells, HLAs, and the like, can also be determined, and personalized medicine approaches developed”, reads on the generation of variant data by sequencing a nucleic acid sample collected from a tumor tissue sample of a human patient with the sequencing device. Further in paragraph [0023] Sayada et al. teaches “An essential component of the approach is to identify variants, and mutations present in the variants, associated with the disorder. For example, a biological sample taken from a patient infected with HIV, HCV, or HBV is screened to identify the prevalence of one or more different types or subtypes of the virus, or a patient with cancer can be screened to identify subtypes of the cancer cells, for example, low frequency somatic mutations in cancer samples. Each type or subtype can be screened for the presence of mutations that render particular therapeutic regimens more or less effective”, reading on automatically parsing the generated variant data to identify one or more gene variants. Paragraph [0020] of Sayada et al. teaches “Patient information is ideally inputted into a system, which can then use the information to determine an appropriate treatment regimen”, which reads on receiving a first user input of a pre-diagnosed type of cancer for the human patient. In paragraph [0020] Sayada et al. teaches “Because the present invention provides information on which mutations are present in which variants, appropriate therapeutic modalities can be prescribed”, in paragraph [0021] “In one embodiment, after entering the patient's genetic information, a user-defined therapeutic treatment regimen for the disease can be entered. Advisory information for the user-defined combination therapeutic treatment regimen can then be generated, and/or an evaluation of the end-user treatment and/or monitoring decision(s) can be evaluated by the Method/System, leading the end-user to revise its initial decision(s)”, and in paragraph [0024] “By using an integrated genotyping solution incorporating a UDS platform, such as UDS-454.RTM., and a powerful software system capable of processing the sequencing information, one can generate assess the quality of the UDS generated data, generate also clinically meaningful genotyping reports”, which reads on automatically identifying clinically relevant information from a curated database pertaining to the identified one or more gene variants based on the received first user input of the pre-diagnosed type of cancer. Paragraph [0023] of Sayada et al. teaches “For example, a biological sample taken from a patient infected with HIV, HCV, or HBV is screened to identify the prevalence of one or more different types or subtypes of the virus, or a patient with cancer can be screened to identify subtypes of the cancer cells, for example, low frequency somatic mutations in cancer samples” and in paragraph [0039] “The expert system can consider factors such as viral load, drug therapies already being used by the particular patient, and the like, and used to filter available information to provide relevant clinical and molecular data for appropriate clinical decision and treatment adaptation” which reads on automatically applying one or more filters to the identified clinically relevant information pertaining to the generated variant data to provide a reduced data set. Sayada et al. further teaches in paragraph [0031] “In addition to a UDS analysis, a Sanger-based comparative analysis can be performed, if desired. If a Sanger-based comparative analysis is performed, one has the ability to display on each individual report a report of each sequence, and comments related to the determined mutations” and in paragraph [00354] “Specific visualization, editing, filtering interfaces can be applied…” and Figure 13 which depicts a Patients, Labs, Treatments, ARV, Status and Conditions, etc. pages for visualization, reads on both sections of claim 1 (vi) and (vii). Finally, in paragraph [0037] Sayada et al. teaches “…guidelines can be stored in a knowledge base, and updated automatically and/or on a regular basis” reading on automatically removing variant data from the generated variant data if a variant for the pre- diagnosed type of cancer is not present in the curated database.
Sayada et al. does not teach the specific visualizations of claim 1(vi) and claim 1(vii) and the removal of data based on some based on its presence in a database.
Stern et al. teaches in paragraph [0073] “Alternatively, one skilled in the art can remove any one or a few of the 28 identified prostate cancer signature genes so long as those remaining provide a sufficient statistical correlation for use in methods of the disclosure”, reading on wherein the computing device is further configured to automatically remove variant data from the generated variant data if a variant for the pre- diagnosed type of cancer is not present in the curated database.
It would be obvious to a person skilled in the art to take the teachings of Sayada et al. and apply additional visualizations to the reporting of the system. This is obvious given the generic and nonspecific visualizations given within the claim and Sayada et al. already describing such visualizations. Additionally, MPEP 2144.04 states “In re Seid, 161 F.2d 229, 73 USPQ 431 (CCPA 1947) - Claims were directed to an advertising display device comprising a bottle and a hollow member in the shape of a human figure from the waist up which was adapted to fit over and cover the neck of the bottle, wherein the hollow member and the bottle together give the impression of a human body. Appellant argued that certain limitations in the upper part of the body, including the arrangement of the arms, were not taught by the prior art. The court found that matters relating to ornamentation only which have no mechanical function cannot be relied upon to patentably distinguish the claimed invention from the prior art.”. Furthermore, it would have been obvious at the time of first filing to modify the teachings of Sayada et al. for the majority of the system described in claim 1, with the teachings of Stern et al. for the removal of data as both described and are directed to the prognosis and treatment of cancer in individuals, and as described in paragraphs [0071]-[0072] of Stern et al., the removal of data and features (filtering) will affect the sensitivity/specificity of model predictions. One would have had a reasonable expectation of success given the generic nature of the visualizations and Sayada et al. already describing such visualizations, and Stern et al. providing a similar application in which data removal (filtering) is already used. Therefore, it would be obvious to one with ordinary skill in the art to incorporate the teachings of each and to be successful.
Claim 3 is directed to the system of claim 1 but further specifies that the one or more filters comprise read depth and variant allele frequency filters.
Sayada et al. teaches in paragraph [0354] “Sequence quality assessment can be performed at the reads level. Specific visualization, editing, filtering interfaces can be applied, to work on the reads. One or more types of filters can be used, for example, a homopolymer check at positions of interest” and in paragraph [0395] “Data can be filtered by protein, type of sequence (UDS/Sanger), threshold, mutations of interest, and other parameters”. This reads on claim 3, wherein the one or more filters comprise read depth filters and variant allele frequency filters, as while Sayada et al. does not teach the exact filtering as claim 3 of the application, it does teach sequence filtering which renders the specific type obvious.
Claim 4 is directed to the system of claim 1 but further specifies a representation be displayed that comprises the clinically relevant information pertaining to a second of the at least two gene variants.
Sayada et al. teaches in paragraph [0031] “a specific report can be created…and optionally embedded in the patient report…”, in paragraph [0047] “Once information regarding the patient's variants is obtained, the data can be collected, stored, analyzed, interpreted, and/or validated, and used to generate a personalized healthcare report”, in paragraph [0056] “The reports can be prepared to offer guidelines for effective treatment modalities”, in paragraph [0057] “The report can optionally include a listing of silent mutations, all mutations, or just mutations of interest based on a specific category”, and in paragraph [0354] “Specific visualization, editing, filtering interfaces can be applied…”. These read on claim 4, wherein a third representation is displayed comprising clinically relevant information pertaining to a second of the at least two gene variants for which an interaction was identified.
Claim 5 is directed to the system of claim 1 but further specifies that the therapeutic recommendation is to not administer a drug, biotherapeutic or treatment for the pre-diagnosed type of cancer.
Sayada et al. teaches in paragraph [0065] “Additional types of information that can be included in the report include, but are not limited to, risk factors, clinical data, labs samples, labs results, embedded FibroMeter determination, HIV infection, HBV viral load, HCV viral load, HCV genotype, treatment outcome, exams, treatments and adverse effects, and recommended follow-up”, which makes obvious claim 5 as a report with treatments might include no treatment in the case of known treatments having adverse effects in the presence of known variants.
Claim 6 is directed to the system of claim 1 but further specifies that the recommendation be a therapy sensitive for the pre-diagnosed type of cancer.
Sayada et al. teaches in paragraph [0065] “Additional types of information that can be included in the report include, but are not limited to, risk factors, clinical data, labs samples, labs results, embedded FibroMeter determination, HIV infection, HBV viral load, HCV viral load, HCV genotype, treatment outcome, exams, treatments and adverse effects, and recommended follow-up” and in paragraph [0023] “For example, a biological sample taken from a patient infected with HIV, HCV, or HBV is screened to identify the prevalence of one or more different types or subtypes of the virus, or a patient with cancer can be screened to identify subtypes of the cancer cells”. These read on claim 6, wherein the therapeutic recommendation is a therapy sensitive for the pre-diagnosed type of cancer.
Claim 7 is directed to the system of claim 1 but further specifies that the therapy that is sensitive to the pre-diagnosed type of cancer be marked with a first indicium.
Sayada et al teaches in paragraph [0324] “When a user opens a patient record for editing, the medical history user interface 50 appears with patient data in the various fields. Preferably color is used to highlight critical or required information in a patient record”, which makes obvious claim 7, wherein the therapy sensitive for the pre- diagnosed type of cancer is marked with a first indiciaum.
Claims 8-10 are rejected under 35 U.S.C. 103 as being unpatentable over Sayada et al. (US 20140310025 A1) and Stern et al. (US 20160333420 A1) as applied to claims 1 above, and further in view of Stelzer et al. (Current Protocols in Bioinformatics (2016) 1-35).
Claim 8 is directed to the system of claim 1 but further specifies that the first and second representations are displayed in a single panel.
Sayada et al. and Stern et al. teach the system of claim 1 as previously described.
Stelzer et al. teaches on page 1, the gene card representation where genes are represented in a single panel, including multiple of their representations, reading on wherein the first and second representations are displayed within a single panel.
It would have been obvious at the time of first filing to modify the teachings of Sayada et al. and Stern et al. for the system of claim 1, with the teachings of Stelzer et al., for the UI or display of gene information as the latter is widely known and popular a database whose sole purpose is the display of such information. One would have had a reasonable expectation of success given that it is merely the display/presentation of information and does not alter the system or method. Therefore, it would have been obvious at the time of first filing to have modified the teachings of each and to be successful.
Claim 9 is directed to the system of claim 8 and thus claim 1, but further specifies that the single panel is an individual gene panel representation.
Sayada et al. and Stern et al. teach the system of claim 1 as previously described.
Stelzer et al. teaches on page 1 that an individual gene panel representation is used for a single gene panel including its interations on page 3, reading on wherein the single panel is an individual gene panel representation.
Claim 10 is directed to the system of claim 9 and thus claim 1, but further specifies that the second representation is visualized in a first portion and the first representation is visualized in the second portion of the gene panel.
Sayada et al. and Stern et al. teach the system of claim 1 as previously described.
Stelzer et al. teaches on pages 6 and 7 that there is a first and second representation that is visualized in the gene panel, reading on wherein the second representation is visualized in a first portion of the individual gene panel representation and wherein the first representation is visualized in a second portion of the individual gene panel representation.
Response to Arguments
Applicant's arguments filed 8/20/2025 have been fully considered but they are not persuasive. Applicant asserts on page 11 of the Remarks that Sayada et al. does not account for the correlation or interactions between identified variants. Examiner directs applicant to paragraph [0011] of Sayada et al. “The selection of appropriate therapeutic regimens can be based, at least in part, on an analysis of the variants, and a correlation of the variants with therapeutic regimens”, and a correlation of multiple variants with a therapeutic regimen would inherently imply a correlation between the variants. Finally, applicant asserts on page 11 of the Remarks that the office action does not disclose any passage that discloses an identification of clinically relevant interactions between at least two gene variants. However, paragraph [0006] of Sayada et al. teaches “Currently, there are no methods for reliably and automatically determining a patient's unique profile of major and minor variants…”, and in paragraph [0008] “It would be advantageous to have methods of screening patients to identify both majority and minority variants associated with their viral, bacterial, or other disorders, and to identify appropriate therapeutic treatments for both the majority and minority variants”. Additionally, Sayada et al. teaches in paragraph [0011] “The selection of appropriate therapeutic regimens can be based, at least in part, on an analysis of the variants, and a correlation of the variants with therapeutic regimens”, in paragraph [0069] “In addition to being used for routine genotyping, the process can also be used for research, for example, to identify types of mutations in a virus following the administration of particular anti-viral or anti-cancer agents. The system can be interfaced with a dedicated Data Exploratory Framework that can be used for research, either on UDS-related molecular data only, or in correlation with clinical data”. Correlations between genes, therapies, and clinical data would constitute a clinically relevant interaction.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEENAN NEIL ANDERSON-FEARS whose telephone number is (571)272-0108. The examiner can normally be reached M-Th, alternate F, 8-5.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowroneck can be reached on 571-272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/K.N.A./Examiner, Art Unit 1687
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685