DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group II (claims 46-47, 56-58 and 91-93), drawn to a method of treating cancer in a patient in the reply filed on 05/21/2026 is acknowledged.
Claims 1, 9-11, 73-75, 82-84, and 86-87 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, Groups I and III, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 05/21/2026.
The requirement for specie election mailed on 04/09/2026 of Table 1 as recited in claims 46 and 92-93 int the claim set filed 04/18/2024 has been withdrawn as Table 1 of the prior art comprises the same genes listed in Table 1 of the instant application.
Claims Status
Claims 1, 9-11, 46-47, 56-58, 73-75, 82-84, 86-87 and 91-93 are pending.
Claims 1, 9-11, 73-75, 82-84, and 86-87 are withdrawn.
Claims 46-47, 56-58 and 91-93 are currently under examination
Priority
This application is a U.S. National Stage Application filed under 35 U.S.C. 371, of International Application No. PCT/US2022/022618, filed on March 30, 2022, which claims the benefit of priority to U.S. Provisional Application Serial No. 63/167,745, filed March 30, 2021. Accordingly, the priority date of instant claim set is determined to be March 30, 2021.
Drawings
The drawings are objected to because the figure labels are not legible in Figures 2, 6 and 9-16. 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
The listing of references in the specification is not a proper information disclosure statement. The specification filed on 09/29/2023 includes a list of references on pages 143-145. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 46-47, 56-58 and 91-93 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 46 recites “Table 1", it is unclear what “Table 1”( ln 2-4, and 6-7) is referring to as the claim should be complete and clear by limitations recited in the claims without referring to any tables or drawings disclosed in the specification. Claims 47, 56-58 and 91-93 depend from claim 46. See MPEP § 2173.05(s).
Claim 56 is indefinite over the limitations “TRU (bronchi oid)” (ln 5). It is unclear what “TRU” stands for and if “bronchi oid” is the same as TRU. Claims 57-58 depend on claim 56.
Claim 56 is indefinite over the limitations “PP (magnoid)” (ln 6). It is unclear what “PP” stands for and if “magnoid” is the same as PP. Claims 57-58 depend on claim 56.
Claim 56 is indefinite over the limitations “PI (squamoid)” (ln 8). It is unclear what “PI” stands for and if “squamoid” is the same as PI. Claims 57-58 depend on claim 56.
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 56-58 are rejected under 35 U.S.C. 101 because the claimed invention is directed towards abstract ideas related to mental processes of comparing and mathematical concept of applying a statistical algorithm and routine and conventional steps of measuring expression level of classifier biomarkers predictive of response signature for a cancer sample, without significantly more. The claim(s) recite(s) abstract ideas and routine and conventional methods. This judicial exception is not integrated into a practical application because no additional elements integrate the judicial exceptions into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because no additional elements are considered significantly more than the judicial exceptions.
Claim analysis
The instant claim 56 is directed towards: The method of claim 46, further comprising comparing the detected levels of expression of the plurality of classifier biomarkers of Table 1 to the expression of the plurality of classifier biomarkers of Table 1 in at least one sample training set(s), wherein the at least one sample training set comprises expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma TRU (bronchi oid) sample, expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma PP (magnoid) sample, expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma PI (squamoid) sample, or a combination thereof; and classifying the sample as TRU, PP, or PI based on the results of the comparing step.
The comparing the detected levels of expression of the plurality of classifier biomarkers of Table 1 to the expression of the plurality of classifier biomarkers of Table 1 in at least one sample training set(s) and classifying the sample as TRU, PP, or PI based on the results of the comparing step is considered an abstract idea (mental process) related to organizing or analyzing information in a way that can be performed mentally or is analogous to human mental work and is considered to be active steps requiring the analysis of a sample. The active step is routine and conventional as demonstrated by the 35 USC § 103 rejections stated below.
Dependent claims set forth further limitations about the comparing step and TRU subtype.
The instant claim 57 is directed towards: The method of claim 56, wherein the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the sample and the expression data from the at least one training set(s); and classifying the sample as a TRU, PP, or PI subtype based on the results of the statistical algorithm.
The comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the sample and the expression data from the at least one training set(s); and classifying the sample as a TRU, PP, or PI subtype based on the results of the statistical algorithm is considered an abstract idea (mathematical concept) related to mathematical calculations. Furthermore, applying a statistical algorithm does not integrate the judicial exception into a practical application.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case, the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, abstract ideas.
With regard to claim 56, the claim recites “The method of claim 46, further comprising comparing the detected levels of expression of the plurality of classifier biomarkers of Table 1 to the expression of the plurality of classifier biomarkers of Table 1 in at least one sample training set(s), wherein the at least one sample training set comprises expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma TRU (bronchi oid) sample, expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma PP (magnoid) sample, expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma PI (squamoid) sample, or a combination thereof; and classifying the sample as TRU, PP, or PI based on the results of the comparing step.” The comparing the detected levels of expression of the plurality of classifier biomarkers of Table 1 to the expression of the plurality of classifier biomarkers of Table 1 in at least one sample training set(s) and classifying the sample as TRU, PP, or PI based on the results of the comparing step is considered an abstract idea (mental process) related to organizing or analyzing information in a way that can be performed mentally or is analogous to human mental work.
With regard to claim 57, the claim recites “The method of claim 56, wherein the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the sample and the expression data from the at least one training set(s); and classifying the sample as a TRU, PP, or PI subtype based on the results of the statistical algorithm.” The comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the sample and the expression data from the at least one training set(s); and classifying the sample as a TRU, PP, or PI subtype based on the results of the statistical algorithm is considered an abstract idea (mathematical concept) related to mathematical calculations.
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? No, there are no additional steps that integrate the claims into a practical application.
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No, there are no additional elements that are significantly more than the judicial exceptions.
Regarding claims 56-58, the claim requires the routine and conventional active steps of comparing the detected levels of expression of the plurality of classifier biomarkers and classifying the cancer sample as a TRU, PP, or PI subtype based on comparison similar to that of Faruki et al. (“Faruki”; Patent App. Pub. US 20190338365 A1, Nov. 11, 2019).
Faruki discloses “Methods and compositions are provided for determining a subtype of lung adenocarcinoma (AD) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung adenocarcinoma. Also provided herein are methods and compositions for determining the response of an individual with an adenocarcinoma subtype to a therapy” (Abstract).Thus, the claims do not provide additional steps which are significantly more.
Dependent claims require the comparing step comprising applying a statistical algorithm and TRU subtype indicative of positive response which are all routine and conventional based on Faruki et al. (“Faruki”; Patent App. Pub. US 20190338365 A1, Nov. 11, 2019) as discussed below in the 35 U.S.C. 103 rejection.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 46-47, 56-58 and 91-93 are rejected under 35 U.S.C. 103 as being unpatentable over Faruki et al. (“Faruki”; Patent App. Pub. US 20190338365 A1, Pub. Nov. 11, 2019, filed on May 17, 2017).
Faruki discloses “Methods and compositions are provided for determining a subtype of lung adenocarcinoma (AD) of an individual by detecting the expression level of at least one classifier biomarker selected from a group of gene signatures for lung adenocarcinoma. Also provided herein are methods and compositions for determining the response of an individual with an adenocarcinoma subtype to a therapy” (Abstract).
Regarding claim 46, Faruki teaches a method wherein “method for determining an adenocarcinoma (AD) subtype of a lung tissue sample obtained from a patient comprising detecting an expression level of at least one nucleic acid molecule that encodes a classifier biomarker having a specific expression pattern in lung cancer cells, wherein the classifier biomarker is selected from the group consisting of the classifier genes set forth in Table 1, the method comprising: (a) isolating nucleic acid material from a lung tissue sample from a patient; … (c) detecting expression of the classifier biomarker.” (Para.11). Faruki teaches a method wherein “a method is provided herein for determining a disease outcome or prognosis for a patient suffering from cancer. In some cases, the cancer is lung cancer” (Para. 140). Faruki teaches a method comprising “the at least one nucleic acid molecule that encodes a classifier biomarker comprises a plurality of nucleic acid molecules that encode a plurality of classifier biomarkers” (Para. 11). Thus, Faruki suggests a method comprising: measuring a nucleic acid expression level of a plurality of classifier biomarkers in a sample obtained from a patient suffering from cancer, wherein the plurality of classifier biomarkers are selected from a set of classifier biomarkers listed in Table 1.
Regarding claim 46, Faruki teaches a method comprising “predicting the response to a therapy for treating a subtype of lung adenocarcinoma (AD) based on the detected expression level of the classifier biomarker” (Para. 11). Faruki teaches a method comprising “methods of the invention also find use in predicting response to different lines of therapies based on the subtype of lung adenocarcinoma (AD). For example, chemotherapeutic response can be improved by more accurately assigning tumor subtypes.” (Para. 143). Faruki teaches a method wherein “In one embodiment, the Terminal Respiratory Unit (TRU) subtype may have enhanced response to EGFR inhibitors and Pemetrexed” (Para.144). “Pemetrexed” reads on a antifolate. Thus, Faruki suggests a method comprising: wherein the measured expression levels of the plurality of classifier biomarkers provide an antifolate predictive response signature for the sample.
Regarding claim 46, Faruki teaches a method comprising “lung cancer sample” (Para.17). Faruki suggests that “Most lung cancers are classified as non-small cell lung carcinoma (NSCLC) (>85%), which is a diverse group with subtypes occurring throughout the respiratory tract. Adenocarcinoma (AD) and squamous cell carcinomas (SCC or SQ), the two main subtypes of NSCLC, are diagnosed at near equal frequency but are often found at different locations with SCC occurring more centrally” (Para. 6) Faruki teaches a method comprising “determining an adenocarcinoma (AD) subtype” (Para. 11). “Lung cancer sample” and “NSCLC” reads on lung squamous cell carcinoma. Thus, Faruki suggests a method comprising: wherein the cancer is selected from bladder cancer, breast cancer, pancreatic adenocarcinoma, lung squamous cell carcinoma, and head and neck adenocarcinoma.
Regarding claim 46, Faruki teaches a method comprising “upon determining a patient's lung cancer subtype, the patient is administered a suitable therapeutic agent” (Para. 141). Faruki teaches a method wherein “In some cases, the therapy is chemotherapy, angiogenesis inhibitors and/or immunotherapy. In some cases, the subtype of lung AD is TRU and the therapy is chemotherapy or angiogenesis inhibitor. In some cases, the subtype of lung AD is PP and the therapy is chemotherapy” (Para. 11). Faruki also suggests “enhanced Pemetrexed response in the TRU subtype” (Para. 210). “chemotherapy” reads on antifolate agent. “Pemetrexed” reads on antifolate agent. Thus, Faruki suggests a method comprising administering an antifolate agent based on presence of a positive antifolate predictive response signature.
Therefore, the invention as recited in claims 46 is prima facie obvious over the prior art Faruki et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of the claim limitations in view of the teachings of Faruki et al. These claim elements were known in the art and it would have been obvious for one of skill in the art to provide a method of treating cancer in a patient according to the limitations recited in the instant application with no change in the respective functions of the methods, and would have yielded the predictable outcomes based on Faruki et al (Patent App. Pub. No. US 20190338365 A1).
The teachings of Faruki are documented above in the rejection of claim 46 under 35 U.S.C. 105. Claim 47, 56, 91-93 depend on claim 46. Claims 57-58 depend on claim 56, which depends on claim 46.
Regarding claim 47, Faruki teaches a method wherein “subtype may have enhanced response to … Pemetrexed” (Para. 144). Thus, Faruki suggests a method wherein the anti-folate agent is selected from pemetrexed, methotrexate, trimetrexate, lometrexol, raltitrexed and nolatrexed.
Regarding claim 56, Faruki teaches a method comprising “the method further comprises comparing the detected levels of expression of the at least one classifier biomarkers of Table 1 to the expression of the at least one classifier biomarkers of Table 1 in at least one sample training set(s), wherein the at least one sample training set comprises expression data of the at least one classifier biomarkers of Table 1 from a reference AD TRU sample, expression data of the at least one classifier biomarkers of Table 1 from a reference AD PP sample, expression data of the at least one classifier biomarkers of Table 1 from a reference AD PI sample or a combination thereof; and classifying the sample as TRU, PP or PI subtype based on the results of the comparing step” (Para.11) Thus, Faruki suggests a method further comprising comparing the detected levels of expression of the plurality of classifier biomarkers of Table 1 to the expression of the plurality of classifier biomarkers of Table 1 in at least one sample training set(s), wherein the at least one sample training set comprises expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma TRU (bronchi oid) sample, expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma PP (magnoid) sample, expression data of the plurality of classifier biomarkers of Table 1 from a reference adenocarcinoma PI (squamoid) sample, or a combination thereof; and classifying the sample as TRU, PP, or PI based on the results of the comparing step.
Regarding claim 57, Faruki teaches a method wherein “the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the sample and the expression data from the at least one training set(s); and classifying the sample as a TRU, PP or PI subtype based on the results of the statistical algorithm” (Para. 11). Thus, Faruki suggests a method wherein the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the expression data obtained from the sample and the expression data from the at least one training set(s); and classifying the sample as a TRU, PP, or PI subtype based on the results of the statistical algorithm.
Regarding claim 58, Faruki suggests “enhanced Pemetrexed response in the TRU subtype” (Para. 210). “Pemetrexed” reads on antifolate agent. Thus, Faruki suggests a method wherein the TRU subtype is indicative of the positive antifolate predictive response signature.
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Regarding claim 91, Faruki teaches Table 1 comprising a essentially the same genes listed in Table 1 of the instant application (Table 1, see below). Faruki also teaches “The biomarkers can be selected from Table 1. In some cases, the plurality of biomarker nucleic acids comprises, consists essentially of or consists of at least … at least 8 biomarker nucleic acids, at least 16 biomarker nucleic acids, at least 24 biomarker nucleic acids, at least 32 biomarker nucleic acids, or all 48 biomarkers nucleic acids of Table 1.” Thus, Faruki suggests a method wherein the plurality of biomarkers selected from Table 1 comprises at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or 100% of the biomarkers from Table 1.
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Regarding claim 92, Faruki teaches a method wherein “The biomarkers can be selected from Table 1. In some cases, the plurality of biomarker nucleic acids comprises, consists essentially of or consists of at least two biomarker nucleic acids, at least 8 biomarker nucleic acids, at least 16 biomarker nucleic acids… of Table 1” (Para. 175). Faruki teaches Table 1 comprising FLGF, CTSH, SCTR, CYP4B1, GPR116, ADHLB, CBX7, HLF, CEP55, TPX2, BUB1B, KIF4A, CCNB2, KIFL4, MELK, KIFL or any combination thereof (Table 1, see above). Thus, Faruki suggests a method wherein the plurality of biomarkers selected from Table 1 comprise FLGF, CTSH, SCTR, CYP4B1, GPR116, ADHLB, CBX7, HLF, CEP55, TPX2, BUB1B, KIF4A, CCNB2, KIFL4, MELK, KIFL or any combination thereof.
Regarding claim 93, Faruki teaches a method wherein “The biomarkers can be selected from Table 1. In some cases, the plurality of biomarker nucleic acids comprises, consists essentially of or consists of at least two biomarker nucleic acids, at least 8 biomarker nucleic acids, at least 16 biomarker nucleic acids, at least 24 biomarker nucleic acids, at least 32 biomarker nucleic acids… of Table 1” (Para. 175). ). Faruki teaches Table 1 comprising “FGL1, PBK, HSPD, TDG, PRC1, DUSP4, GTPBP4, ZWINT, TLR2, CD74, HLA-DPB1, HLA-DPA1, HLA-DRA, ITGB2, FAS, HLA-DRB1, PLAN, GBP1, DSE, CCDC109B, TGFBI, CXCLL0, IGALS1, TUBB6, GJB1, RAP1GAP, CACNA2D2, SELENBP1, TFCP2L1, SORBS2, UNC13B, TACC2” (Table 1, see above). Thus, Faruki suggests a method wherein the plurality of biomarkers of Table 1 comprise FGL1, PBK, HSPD1, TDG, PRC1, DUSP4, GTPBP4, ZWINT, TLR2, CD74, HLA-DPB1, HLA-DPA1, HLA-DRA, ITGB2, FAS, HLA-DRB1, PLAN, GBP1, DSE, CCDC109B, TGFBI, CXCL10, IGALS1, TUBB6, GJB1, RAP1GAP, CACNA2D2, SELENBP1, TFCP2L1, SORBS2, UNC13B, TACC2 or any combination thereof.
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 46, 56-57 and 93 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 5 and 10 of U.S. Patent No. US 10934595 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over the claims of U.S. Patent No. US 10934595 B2.
The claims of U.S. Patent No. US 10934595 B2 are drawn to:
“5. A method of treating lung cancer in a subject, the method comprising: (a) determining the subtype of a lung sample obtained from the subject, wherein the lung sample is an adenocarcinoma lung cancer sample, wherein the determining the subtype comprises: (i) measuring a nucleic acid expression level of each biomarker of a plurality of biomarkers consisting of only FIGF, CTSH, SCTR, CYP4B1, GPR116, ADH1B, CBX7, HLF, CEP55, TPX2, BUB1B, KIF4A, CCNB2, KIF14, MELK, KIF11, FGL1, PBK, HSPD1, TDG, PRC1, DUSP4, GTPBP4, ZWINT, TLR2, CD74, HLA-DPB1, HLA-DPA1, HLA-DRA, ITGB2, FAS, HLA-DRB1, PLAU, GBP1, DSE, CCDC109B, TGFBI, CXCL10, LGALS1, TUBB6, GJB1, RAP1GAP, CACNA2D2, SELENBP1, TFCP2L1, SORBS2, UNC13B and TACC2 in the lung sample obtained from the subject; (ii) comparing the measured nucleic acid expression levels of each biomarker of the plurality of the biomarkers of (α)(i) in at least one sample training set(s), wherein the at least one sample training set is a reference lung adenocarcinoma bronchioid (terminal respiratory unit) sample, a reference lung adenocarcinoma magnoid (proximal proliferative) sample, a reference lung adenocarcinoma squamoid (proximal inflammatory) sample or a combination thereof; and (iii) classifying the subtype of lung adenocarcinoma as bronchioid (terminal respiratory unit), magnoid (proximal proliferative) or squamoid (proximal inflammatory) based on the results of the comparing step; and (b) administering a therapeutic agent based on the subtype of the lung adenocarcinoma, wherein a squamoid (proximal inflammatory) subtype is administered a checkpoint inhibitor, a magnoid (proximal proliferative) subtype is administered a chemotherapeutic agent and a bronchioid (terminal respiratory unit) subtype is administered a therapeutic agent selected from a chemotherapeutic agent and an angiogenesis inhibitor.
10. The method of claim 5, wherein the comparing step comprises applying a statistical algorithm which comprises determining a correlation between the nucleic acid expression levels of each biomarker from the plurality of biomarkers obtained from the lung sample and the nucleic acid expression levels of each biomarker from the plurality of biomarkers from the at least one training set(s); and classifying the subtype of the lung adenocarcinoma sample as a bronchioid (terminal respiratory unit), magnoid (proximal proliferative) or squamoid (proximal inflammatory) subtype based on the results of the statistical algorithm.
11. The method of claim 5, wherein the chemotherapeutic agent administered to the bronchioid (terminal respiratory unit) subtype is selected from EGFR inhibitors and Pemetrexed”
Therefore, the invention as recited in claims 46, 56-57, and 93 is prima facie obvious over claims 5 and 10-11 of U.S. Patent No. US 10934595 B2. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of the claims over claims 5 and 10-11 of U.S. Patent No. US 10934595 B2. These claim elements were known in the art and it would have been obvious for one of skill in the art to provide a method of treating cancer in a patient according to the limitations recited in claims 46, 56-57, and 93 of the instant application based on claims 5 and 10-11 of U.S. Patent No. US 10934595 B2 with no change in the respective functions of the methods, and would have yielded the predictable outcomes according to the limitations of claims 46, 56-57, and 93.
Conclusion
No claims are in condition for allowance.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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