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 .
Remarks
This action is in response to the amendments filed 04/24/2026.
Claims 1, 6, 7, 9-12, 14, 17, 23, 26, 27, 30-32, and 63-67 are pending.
Response to Arguments
Applicant’s arguments, see page 7, filed 04/24/2026, with respect to the rejection of claims 1, 5-7, 9-12, 14, 17, 23, 26, 27, 30-32, and 61-66 under 35 U.S.C. 112(a) have been fully considered and are persuasive. Independent claim 1 has been amended to specify that the lung condition is lung cancer, and that the assaying comprises a “nucleic acid amplification, array hybridization, nucleic acid sequencing, or any combination thereof”. Claims 5, 61, and 62 have been cancelled. The rejection of the claims under 35 U.S.C. 112(a) has been withdrawn.
Applicant’s arguments, see pages 8-10, filed 04/24/2026, with respect to the rejection of claims 1, 5-7, 9-12, 14, 17, 23, 26, 27, 30-32, and 61-66 under 35 U.S.C. 101 have been fully considered and are persuasive. Independent claim 1 has been amended to specify that the lung condition is lung cancer, and that the assaying comprises a “nucleic acid amplification, array hybridization, nucleic acid sequencing, or any combination thereof”. Claims 5, 61, and 62 have been cancelled. Applicant argues that the claims are not directed to a judicial exception and as a whole recite additional elements beyond any alleged judicial exception. Examiner agrees. The recitation of a specific type of assaying integrates any abstract idea into a practical application and provides significantly more. Therefore, the rejection of the claims under 35 U.S.C. 101 has been withdrawn.
Applicant’s arguments, see pages 10-12, filed 04/24/2026, with respect to the rejection of claims 1, 5-7, 9-12, 14, 17, 23, 26, 27, 30-32, and 61-66 under 35 U.S.C. 103 have been fully considered and are persuasive. Independent claim 1 has been amended to specify that the lung condition is lung cancer, and that the assaying comprises a “nucleic acid amplification, array hybridization, nucleic acid sequencing, or any combination thereof”. Claims 5, 61, and 62 have been cancelled. Applicant argues that the cited references do not teach or suggest, alone or in combination, the amended limitation. Examiner agrees. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground of rejection is made, as explained in the office action below.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 6, 7, 9-12, 14, 17, 23, 26, 27, 30-32, and 63-66 are rejected under 35 U.S.C. 103 as being unpatentable over Harris et al. (US Patent Application Publication 2015/0337385 – of record), hereinafter Harris, further in view of Whitney et al. (International Publication WO 2016/011068 – of record), hereinafter Whitney, further in view of Cohen et al. (International Publication WO 2016/094330 – of record), hereinafter Cohen, further in view of Twine et al. (Twine NA, et al. Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease. PLoS One. 2011 Jan 21;6(1):e16266. doi: 10.1371/journal.pone.0016266. PMID: 21283692; PMCID: PMC3025006. – of record), hereinafter Twine, and further in view of Brody et al. (US Patent Application Publication 2009/0061454 – of record).
Regarding claim 1, Harris teaches a method for screening a subject for a lung cancer (e.g. Abstract), comprising:
(a) computer analyzing health or medical history data of said subject for a presence of one or more risk factors for developing said lung cancer, and based at least on said computer analyzing, identifying said subject as having an increased risk of developing said lung cancer (e.g. Pars. [0010]-[0013]: subject is identified as at risk for developing lung cancer based on the comparison of the classifier with the reference and the levels of biomarkers BRCA1, HIF1A, DLC1, XPO1, and miR-21 with the reference values; Par. [0034]: tissue samples are assayed to determine biomarker levels);
(b) responsive to the first risk being an increased risk of developing said lung cacer, obtaining a tissue sample of said subject at a first point in time (e.g. Par. [0018]: obtaining tissue sample from the lung);
(c) assaying tissue from said tissue sample to identify a presence or absence of one or more biomarkers associated with a risk of developing said lung cancer in said first sample (e.g. Pars. [0010]-[0013]: subject is identified as at risk for developing lung cancer based on the comparison of the classifier with the reference and the levels of biomarkers BRCA1, HIF1A, DLC1, XPO1, and miR-21 with the reference values; Par. [0034]: tissue samples are assayed to determine biomarker levels); and
(d) performing an assay to detect gene expression on other epithelial tissue from a second sample of said subject obtained at a second point in time (e.g. Par. [0027]: if the subject is determined to be at risk of developing lung cancer, further screening/imaging/CT scans are required which occurs at a second time after a first sample is analyzed; Par. [0034]: tissue samples are assayed to determine biomarker levels; Par. [0051]; Par. [0147]: multiple samples can be used).
However, Harris does not teach the tissue being epithelial tissue, using a trained machine learning algorithm, wherein said subject has not been identified as having a lung nodule in a lung region by an electronic imaging scan, wherein said subject has not been diagnosed for said lung condition, wherein the trained machine learning algorithm has been trained to identify one or more features associated with said one or more risk factors, specifically identifying said subject as having a low risk of developing said lung condition based on said presence or absence of said one or more biomarkers, wherein the second point in time is at least 24 hours from said first point in time, and specifically identifying the subject as having a first risk of developing said lung condition based on the computer analysis, identifying said subject as having a second risk of developing said lung condition based on the assay, wherein (i) if said second risk is less than said first risk performing an assay, or (ii) if said second risk is greater than or equal to said first risk, providing an output recommending an interventive therapy or imaging analysis, and specifically wherein the assay is a whole-transcriptome ribonucleic (RNA) sequencing assay, wherein the one or more biomarkers comprise one or more genes selected from Tables 4, 6-8, 10, and 13, and wherein said assaying comprises a nucleic acid amplification, array hybridization, nucleic acid sequencing, or any combination thereof.
Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known to use epithelial tissue as the biological sample in order to determine expression levels (e.g. Par. [0025]: biological sample from respiratory epithelium is used; Par. [0026]), using a trained machine learning algorithm, wherein the trained machine learning algorithm has been trained to identify one or more features associated with said one or more risk factors (e.g. Pars. [0089]-[0090]: a trained classifier is used to classify lung cancer using expression levels of biomarkers), and wherein the assaying comprises a nucleic acid amplification, array hybridization, nucleic acid sequencing, or any combination thereof (e.g. Par. [0062]: hybridization assays used).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris to include the tissue being epithelial tissue and a trained machine learning algorithm as taught by Whitney, because doing so would result in determining the expression levels to detect lung cancer.
However, Harris in view of Whitney fail to teach wherein said subject has not been identified as having a lung nodule in a lung region by an electronic imaging scan, wherein said subject has not been diagnosed for said lung condition, specifically identifying said subject as having a low risk of developing said lung condition based on said presence or absence of said one or more biomarkers, wherein the second point in time is at least 24 hours from said first point in time, and specifically identifying the subject as having a first risk of developing said lung condition based on the computer analysis, identifying said subject as having a second risk of developing said lung condition based on the assay, wherein (i) if said second risk is less than said first risk performing an assay, or (ii) if said second risk is greater than or equal to said first risk, providing an output recommending an interventive therapy or imaging analysis, and specifically wherein the assay is a whole-transcriptome ribonucleic (RNA) sequencing assay, and wherein the one or more biomarkers comprise one or more genes selected from Tables 4, 6-8, 10, and 13.
Harris teaches the system being used to diagnose a subject at risk of developing lung cancer (e.g. Pars. [0010]-[0013]), but does not specifically teach the subject has not been identified as having a lung nodule in a lung region by an electronic imaging scan, wherein said subject has not been diagnosed for said lung condition.
Cohen, in a similar field of endeavor, teaches methods and systems for predicting the likelihood or risk of having cancer. Cohen teaches it is known for the subject to not have been identified as having a lung nodule in a lung region by an electronic imaging scan, wherein said subject has not been diagnosed for said lung condition (e.g. Par. [0024]: imaging of the patient occurs only after risk calculation of occurrence of lung cancer is determined; Par. [0058]: asymptomatic patients are patients that have not previously been diagnosed with cancer risk; Pars. [0101]-[0103]: describing method of determining cancer risk in asymptomatic patients), specifically identifying said subject as having a low risk of developing said lung condition based on said presence or absence of said one or more biomarkers (e.g. Par. [0017]: measuring biomarkers to determine disease likelihood; Par. [0024]), identifying the subject as having a first risk of developing said lung condition based on computer analysis and identifying said subject as having a second risk of developing said lung condition based on the assay (e.g. pars. [0018]-[0019]; par. [0103]; par. [0153]; pars. [0193]-[0195]), wherein if said second risk is greater than or equal to said first risk, providing an output recommending an interventive therapy or imaging analysis (e.g. par. [0181]: if the risk score is higher, the physician can recommend follow up testing such as CT scanning), wherein the second sample is taken at least 24 hours from the first sample (e.g. Par. [0193]: time of biomarker determination can be 3 months, 6 months, and 1 year).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney to include the subject has not been identified as having a lung nodule in a lung region by an electronic imaging scan, wherein said subject has not been diagnosed for said lung condition, specifically identifying said subject as having a low risk of developing said lung condition based on said presence or absence of said one or more biomarkers, and identifying first and second risks of developing the lung condition and providing a recommended output, wherein the second sample is taken at least 24 hours after the first sample as taught by Cohen, because doing so would improve determination of cancer risk in patients in order to provide appropriate preventative action.
However, Harris in view of Whitney and Cohen fail to specifically disclose wherein the assay is a whole-transcriptome ribonucleic (RNA) sequencing assay, and wherein the one or more biomarkers comprise one or more genes selected from Tables 4, 6-8, 10, and 13.
Twine, in a similar field of endeavor, is directed towards whole transcriptome analysis for Alzheimer’s disease. Twin discloses it is known to use a whole-transcriptome ribonucleic (RNA) sequencing assay in order to identify levels of gene expression (e.g. page 10, left column, section titled Discussion: a whole transcriptome sequencing technique was used, “Using a whole transcriptome sequencing technique (RNA-Seq), we were able to identify the levels of differentially expressed genes and establish genes with alternative promoter usage and splicing patterns that changed in association with neurodegeneration.”).
Therefore, it would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney and Cohen to include the whole transcriptome sequencing as taught by Twine as this is a known technique that for identifying levels of gene expression (e.g. Twine, page 10, left column, section titled Discussion).
However, Harris in view of Whitney, Cohen, and Twine fails to disclose wherein the one or more biomarkers comprise one or more genes selected from Tables 4, 6-8, 10, and 13.
Brody, in a similar field of endeavor, is directed towards diagnosis and prognosis of lung cancer using gene expression analysis. Brody discloses using biomarkers UBE1L, P4HB, CCT4, EIF4A1, and DUSP3, which are listed under Table 4 of the instant specification (e.g. Table 1; Par. [0104]: table 1 shows genes that were identified as distinguishing smokers with and without cancer).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, and Twine to include the genes as identified by Brody, because Brody teaches that these genes are known to indicate smokers with and without cancer.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 6, Harris further teaches wherein said lung cancer comprises: a non-small cell lung cancer; an adenocarcinoma; a squamous cell carcinoma; a large cell carcinoma; a small cell lung cancer; or any combination thereof (e.g. Par. [0005]: adenocarcinoma; Par. [0031]: non-small cell lung cancer).
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 7, Harris fails to teach wherein said first sample or said second sample is obtained by a bronchoscopy, bronchial brushing, or nasal brushing. Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known to use bronchial brushing to obtain the sample (e.g. Par. [0025]).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include obtaining the sample by bronchia brushing as taught by Whitney, because doing so would allow the user to obtain the necessary biological sample.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 9, Harris fails to teach wherein said first sample or said second sample comprises a mucous epithelial tissue, a nasal epithelial tissue, a lung epithelial tissue, or any combination thereof. Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known for the biological sample to comprise nasal or lung epithelial tissue (e.g. Par. [0025]: “The respiratory epithelium can be of the mouth, nose, pharynx, trachea, bronchi, bronchioles, or alveoli.”).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include the biological sample comprising nasal or lung epithelial tissue as taught by Whitney, because doing so would result in obtaining the necessary biological sample.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 10, Harris fails to teach wherein said first sample or said second sample comprises epithelial tissue obtained along an airway of said subject. Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known for the biological sample to comprise epithelial tissue obtained along an airway of the subject (e.g. Par. [0025]; Par. [0034]: epithelial cells obtained from airway samples can be used).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include the biological sample comprising epithelial tissue obtained along an airway of the subject as taught by Whitney, because doing so would allow the user to obtain the necessary biological sample.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 11, Harris fails to teach wherein a portion of said first sample or said second sample is subjected to cytological testing that identifies said first sample or said second sample as ambiguous or suspicious. Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known for the sample to be subjected to cytological testing that identifies the sample as suspicious (e.g. Par. [00215]: “Patients were diagnosed as having primary lung cancer based on cytopathology obtained at bronchoscopy”).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include subjecting the sample to cytological testing that identifies the sample as suspicious as taught by Whitney, because it is a known method of diagnosing lung cancer.
Claim 11 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 12, Harris further teaches upon identifying said first sample or said second sample as ambiguous or suspicious, performing (d) on a second portion of said first sample or second sample, which second portion comprises said epithelial tissue (e.g. Par. [0027]: if the subject is determined to be at risk of developing lung cancer, further screening/imaging is required; Par. [0051]; Par. [0147]: multiple samples can be used).
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 14, Harris fails to teach wherein said second sample is a different sample type from said first sample. Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known for the second sample to be a different sample type from the first sample (e.g. Par. [0025]: multiple sample types can be taken).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include the second sample to be a different sample type from the first sample as taught by Whitney, because doing so would result in obtaining the biological sample.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 17, Harris further teaches wherein (c) comprises comparing said presence or absence of said one or more biomarkers to a reference set of one or more biomarkers (e.g. Pars. [0010]-[0013]: subject is identified as at risk for developing lung cancer based on the comparison of the classifier with the reference and the levels of biomarkers BRCA1, HIF1A, DLC1, XPO1, and miR-21 with the reference values).
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 23, Harris further teaches wherein said one or more risk factors comprise: smoking; exposure to environmental smoke; exposure to radon; exposure to air pollution; exposure to radiation; exposure to an industrial substance; inherited or environmentally-acquired gene mutations; a subject's age; a subject having a secondary health condition; or any combination thereof (e.g. Page 27, Par. [0180], lines 21-23: “…clinically relevant risk factors such as age, smoking and stage.”).
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 26, Harris further teaches wherein said one or more biomarkers comprise one or more of: a gene or fragment thereof; a sequence variant; a fusion; a mitochondrial transcript; an epigenetic modification; a copy number variation; a loss of heterozygosity (LOH); or any combination thereof (e.g. Abstract: four genes are used).
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 27, Harris further teaches wherein said presence or absence of said one or more biomarkers comprises a level of expression (e.g. Par. [0129]: levels of certain biomarkers are detected).
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 30, Harris fails to teach wherein said trained machine learning algorithm is trained by a training set comprising epithelial cells obtained from an airway of an individual. Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known to train the machine learning algorithm with a training set comprising epithelial cells obtained from an airway of an individual (e.g. Par. [0034]: epithelial cells obtained from airway samples can be used; Par. [0090]: classifier is trained on a dataset comprising information about biological samples).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include training the machine learning algorithm with a training set comprising epithelial cells obtained from an airway of an individual as taught by Whitney, because doing so would aid in the detection of lung cancer.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 31, Harris fails to teach wherein said trained machine learning algorithm is trained by a training set comprising samples benign for said lung cancer and samples malignant for said lung cancer. Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known for the training set to comprise samples both benign and malignant for lung cancer in order to increase the confidence of classification (e.g. Par. [0090]: the training set includes data for both subjects having lung cancer and not having lung cancer).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include the training set to comprise samples both benign and malignant for lung cancer as taught by Whitney, because doing so would result in increased confidence of classification.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 32, Harris fails to teach wherein said trained machine learning algorithm is trained by a training set comprising samples obtained from subjects having one or more risk factors. Whitney, in a similar field of endeavor, teaches methods for evaluating lung cancer status. Whitney teaches it is known for the training set to comprise samples obtained from subjects having a risk factor of smoking (e.g. Par. [0090]: the population can include subjects who are smokers or former smokers) in order to accurately classify lung cancer.
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody with the training set comprising samples obtained from subjects having one or more risk factors as taught by Whitney, because doing so would result in accurate classification of lung cancer.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 63, Harris fails to teach wherein said second point in time is at least 1 month from said first point in time. Cohen, in a similar field of endeavor, teaches methods and systems for predicting the likelihood or risk of having cancer. Cohen discloses that the second point in time for sample collection is at least 1 month from said first point in time (e.g. Par. [0193]: time of biomarker determination can be 3 months, 6 months, and 1 year).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include the second point in time for sample collection being at least 1 month from said first point in time as taught by Cohen, because doing so would allow monitoring the progression of the disease in a patient.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 64, Harris fails to teach wherein said second point in time is at least 1 year from said first point in time. Cohen, in a similar field of endeavor, teaches methods and systems for predicting the likelihood or risk of having cancer. Cohen discloses that the second point in time for sample collection is at least 1 year from said first point in time (e.g. Par. [0193]: time of biomarker determination can be 3 months, 6 months, and 1 year).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include the second point in time for sample collection being at least 1 year from said first point in time as taught by Cohen, because doing so would allow monitoring the progression of the disease in a patient.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 65, Harris fails to teach wherein said second risk is less than said first risk. Cohen, in a similar field of endeavor, teaches methods and systems for predicting the likelihood or risk of having cancer. Cohen discloses wherein said second risk is less than said first risk (e.g. Par. [0193]: classifying patient as low risk if biomarker velocity decreases).
Therefore, it would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include identifying and comparing a first and second risk of developing a condition as taught by Cohen to result in earlier identification and treatment of cancer.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 66, Harris fails to teach wherein said second risk is greater than or equal to said first risk. Cohen, in a similar field of endeavor, teaches methods and systems for predicting the likelihood or risk of having cancer. Cohen discloses wherein said second risk is greater than or equal to said first risk (e.g. Par. [0193]: classifying patient as high risk if biomarker velocity increases).
Therefore, it would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include identifying and comparing a first and second risk of developing a condition as taught by Cohen in order to result in earlier identification and treatment of cancer.
Claim 67 is rejected under 35 U.S.C. 103 as being unpatentable over Harris et al. (US Patent Application Publication 2015/0337385 – of record), hereinafter Harris, further in view of Whitney et al. (International Publication WO 2016/011068 – of record), hereinafter Whitney, further in view of Cohen et al. (International Publication WO 2016/094330 – of record), hereinafter Cohen, further in view of Twine et al. (Twine NA, et al. Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease. PLoS One. 2011 Jan 21;6(1):e16266. doi: 10.1371/journal.pone.0016266. PMID: 21283692; PMCID: PMC3025006. – of record), hereinafter Twine, and further in view of Brody et al. (US Patent Application Publication 2009/0061454 – of record), hereinafter Brody, as applied to claim 1 above, and further in view of Halvardson et al. (Halvardson J, et al. Exome RNA sequencing reveals rare and novel alternative transcripts. Nucleic Acids Res. 2013 Jan 7;41(1):e6. doi: 10.1093/nar/gks816. Epub 2012 Aug 31. PMID: 22941640; PMCID: PMC3592422. – of record), hereinafter Halvardson.
Claim 1 is obvious over Harris, Whitney, Cohen, Twine, and Brody, as indicated above. Regarding claim 67, Harris fails to disclose wherein said whole-transcriptome RNA sequencing assay comprises exome-enriched RNA sequencing. Halvardson is directed towards whole exome enrichment of RNA. Halvardson discloses using exome enriched RNA sequencing in order to identify transcripts present at low levels (e.g. Abstract: exome enrichment was used prior to RNA sequencing in order to identify transcripts present at low levels).
It would have been obvious to a person having ordinary skill in the art before the effective filing date of the claimed invention to modify the invention of Harris in view of Whitney, Cohen, Twine, and Brody to include using exome enriched RNA sequencing as taught by Halvardson as this is a known technique that provides the results of identifying transcripts present at low levels (e.g. Halvardson, abstract).
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/SHREYA ANJARIA/Examiner, Art Unit 3796
/ALLEN PORTER/Primary Examiner, Art Unit 3796
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