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 .
Claims Status
Claims 65-72 filed on 02/11/2026 are pending. Claims 73-84 are withdrawn from consideration as being drawn to a non-elected invention. Claims 65, 66, & 72 are currently under examination directed to the elected species of S100A9, claim 70 is currently under examination to the elected species RNA, and claim 72 is currently under examination to the elected species HOXA9 (see response dated 01/13/2025). All the amendments and arguments have been thoroughly reviewed but are deemed insufficient to place this application in condition for allowance. The following rejections are either newly applied, as necessitated by amendment, or are reiterated. They constitute the complete set being presently applied to the instant application. Response to Applicant’s argument follow. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.
Claim Rejections - 35 USC § 102
Claim(s) 65-70 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Smirnov (Smirnov et al.; Cancer Research, Vol. 66, pages 2918-2922, March 2006).
Regarding claim 65, Smirnov teaches a method for measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9 (expression of marker gene S100A9) and STK4 (reference marker comprises RNA product from expression of STK4) (measuring the amount of at least one gene expression marker and at least one reference marker) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13). In addition, Smirnov teaches expression of candidate genes were measured with quantitative real-time RT-PCR analysis (measuring an amount of at least one gene expression marker comprising using one or more of reverse transcription and polymerase chain reaction) (pg. 2919 column 1 1st full paragraph lines 1-28).
Regarding claim 66, Smirnov teaches measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9, STK4, and FPR1 (one or more products from expression of marker genes selected from FPR1) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13).
Regarding claim 67, Smirnov teaches the sample is blood from cancer patients (pg. 2918 column 2 2nd full paragraph lines 1-5).
Regarding claim 68, Smirnov teaches the gene expression product is RNA (pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13).
Regarding claim 69, Smirnov teaches measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9, STK4, and FPR1 (measuring products from expression of S100A9, STK4, and at least one up to eight additional gene(s) selected from FPR1, PAD14, S100A12, SELL, APOBE3CA, MMP9, TYMP, and STAT1) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13).
Regarding claim 70, Smirnov teaches measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9, STK4, FPR1, and ACTB (at least one reference marker further comprises a gene selected from list including ACTB) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13).
Response to Arguments
The response traverses the rejection. The response asserts that claim 65 requires that product from the expression of the marker gene S100A9 be measure through one or more of reverse transcription, polymerase chain reaction, nucleic acid sequencing, etc. and that the phrase of at least one gene expression marker comprises product from expression of marker gene S100A9 indicates that other marker genes may be measured in addition to S100A9 but not as an alternative to S100A9. Specifically, the response asserts that Smirnov does not disclose or suggest that S100A9 is measured by any of the techniques listed in claim 65 but rather only discloses it measurement by microarray and therefore Smirnov fails to disclose or suggest numerous elements of claim 65 and therefore does not anticipate the claims. This argument has been thoroughly reviewed but was not found persuasive as Smirnov teaches measuring gene expression with the Affymetrix Focus array which comprises oligonucleotides that measure the expression of genes including S100A9 (expression of marker gene S100A9) and the standard protocol for the Affymetrix Focus array requires an RNA pre-amplification step and therefore Smirnov teaches measuring the marker gene S100A9 through one or more of the methods listed in claim 65 comprising polymerase chain reaction as the Affymetrix Focus array comprises oligonucleotides that measure the expression of S100A9. In addition, Smirnov teaches expression of candidate genes were measured with quantitative real-time RT-PCR analysis, therefore comprising measuring an amount of at least one gene expression marker comprising using one or more of reverse transcription and polymerase chain reaction (pg. 2919 column 1 1st full paragraph lines 1-28).
The response also asserts that the candidate genes validated by RT-PCR did not include S100A9 and rather evaluated S100A9 by the initial microarray panel and as such Smirnov discourages the skilled artisan from measuring product from expression of S100A9 by the techniques recited in claim 65 given that is was simply not identified as a candidate for further evaluation following microarray. This argument has been thoroughly reviewed but was not found persuasive for the reasons set forth above.
The response also asserts that Smirnov discloses that for RT-PCR gene expression levels were normalized using expression levels of RPS27A gene and as such Smirnov also does not disclose using STK4 as a reference marker as presently claimed. This argument has been thoroughly reviewed but was not found persuasive as Smirnov teaches the use of the Affymetrix Focus array that comprises oligonucleotides that measure the expression of genes including S100A9 (expression of marker gene S100A9) and STK4 (reference marker comprises RNA product from expression of STK4) therefore teaching measuring the expression of STK4 as, as the claim is currently amended, the recitation of a reference marker comprising STK4 gene does not structurally alter or define the gene.
For these reasons, and the reasons made of record above to address the claims as currently amended, the rejections are applied to the newly amended claims.
Claim Rejections - 35 USC § 103
Claim(s) 71 & 72 is/are rejected under 35 U.S.C. 103 as being unpatentable over Smirnov (Smirnov et al.; Cancer Research, Vol. 66, pages 2918-2922, March 2006), in view of Shames (Shames et al.; PLoS Medicine, Vol. 3, pages 2244-2263, December 2006).
The teachings of Smirnov with respect to claim 65 is discussed above and incorporated herein.
Regarding claim 71, Smirnov does not to teach measuring an amount of at least one methylation marker DNA and at least one reference marker DNA.
Shames teaches a method to identify cancer-specific methylation markers through first employing a high-throughput global expression profile approach in lung cancer cells and then measuring the methylation of the genes expressed in lung cancer cells (abstract methods and findings paragraph lines 1-8; pg. 2248 column 2 1st full paragraph lines 1-4). In addition, Shames teaches measuring the methylation in genes based on the determined expression pattern and to determine the genes with CpG islands (measuring the amount of at least one methylation marker comprising a differentially methylated target region) compared to genes that did not have CpG islands (measuring the amount of at least one reference marker comprising a reference target region that is not differentially methylated) (pg. 2250 column 1 1st full paragraph lines 1-17; pg. 2250 column 1 2nd full paragraph lines 1-11; pg. 2251 paragraph bridging column 1 & 2 lines 1-19; pg. 2259 column 1 1st full paragraph lines 1-18). Finally, Shames teaches that this method can be used for determining targets for early diagnosis and therapeutic intervention in tumors (pg. 2260 column 2 1st full paragraph lines 1-17).
Smirnov and Shames are considered to be analogous to the claimed invention because they are all in the same field of analysis of nucleic acid biomarkers in lung cancer samples. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of measuring expression levels of one or more gene products including S100A9 and reference marker STK4, as taught by Smirnov, to include measuring DNA methylation markers as taught in Shames because Shames teaches that doing so would aid in determining targets for early diagnosis and therapeutic intervention in tumors.
Regarding claim 72, Smirnov teaches measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9, STK4, and FPR1 (further comprises a product from expression of a marker gene selected from a group including FPR1) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13). In addition, Smirnov teaches that blood from cancer and healthy volunteers were collected in a 10-mL CellSave preservative tube in which 4 mL of this collected blood was used for RNA extraction (DNA and RNA are isolated from blood collected in a single blood collection device) (pg. 2918 column 2 2nd full paragraph lines 1-15).
Claim(s) 65, 67, 68, & 70 is/are rejected under 35 U.S.C. 103 as being unpatentable over Smirnov (Smirnov et al.; Cancer Research, Vol. 66, pages 2918-2922, March 2006), in view of Yan-jun (Yan-jun et al.; Chinese Medical Journal, Vol. 123, pages 2215-2220, April 2010).
Regarding claim 65, Smirnov teaches a method for measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9 (expression of marker gene S100A9) and STK4 (reference marker comprises RNA product from expression of STK4) (measuring the amount of at least one gene expression marker and at least one reference marker) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13). In addition, Smirnov teaches expression of candidate genes were measured with quantitative real-time RT-PCR analysis (measuring an amount of at least one gene expression marker comprising using one or more of reverse transcription and polymerase chain reaction) (pg. 2919 column 1 1st full paragraph lines 1-28).
Smirnov does not teach measuring the amount of the gene expression marker of S100A9 with one or more of reverse transcription, polymerase chain reaction, nucleic acid sequencing, etc.
Yan-jun teaches a method for determining the expression of S100A9 in lung cancer tissues through semi-quantitative reverse transcriptase-PCR (Sq -Rt-PCR) and immunohistochemical staining (measuring the amount of at least one gene expression marker of S100A9 comprising using one or more of reverse transcription, polymerase chain reaction, and protein immunoprecipitation) (abstract background lines 1-4; abstract methods lines 1-4; abstract results lines 1-4; pg. 2216 paragraph bridging column 1 & 2 lines 1-7; pg. 2216 column 2 1st full paragraph lines 1-18; pg. 2216-2217 paragraph bridging pg. 2216 & pg. 2217 lines 1-21). In addition, Yan-jun teaches that upregulation of S100A9 was found in lung cancer tissue and that the correlation of high expression in inflammatory lung tissues may indicate collaborative effect of inflammation on the progression of cancer and may be an early tumor-genic event (abstract conclusion lines 1-3; pg. 2220 column 1 1st full paragraph lines 1-6).
Smirnov and Yan-jun are considered to be analogous to the claimed invention because they are all in the same field of detection of gene expression markers in lung cancer. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of measuring gene expression in lung cancer samples of candidate biomarkers through quantitative real-time RT-PCR analysis in Smirnov to incorporate measuring the expression of the gene expression marker of S100A9 with RT-PCR and/or with protein immunoprecipitation in lung cancer samples as taught in Yan-jun because Yan-jun teaches that doing so would indicate a collaborative effect in progression of lung cancer and can be used as an indicator of an early tumor-genic event in lung cancer.
Regarding claim 67, Smirnov teaches the sample is blood from cancer patients (pg. 2918 column 2 2nd full paragraph lines 1-5).
Regarding claim 68, Smirnov teaches the gene expression product is RNA (pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13).
Regarding claim 70, Smirnov teaches measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9, STK4, FPR1, and ACTB (at least one reference marker further comprises a gene selected from list including ACTB) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13).
Claim(s) 66 & 69 is/are rejected under 35 U.S.C. 103 as being unpatentable over Smirnov (Smirnov et al.; Cancer Research, Vol. 66, pages 2918-2922, March 2006) and Yan-jun (Yan-jun et al.; Chinese Medical Journal, Vol. 123, pages 2215-2220, April 2010), as applied to claims 65, 67, 68, & 70 above, and further in view of Morris (Morris et al.; Journal of Thoracic Oncology, Vol. 11, pages 1, February 2016).
The teachings of Smirnov and Yan-jun with respect to claim 65 is discussed above.
Regarding claims 66 & 69, Smirnov teaches measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9, STK4, and FPR1 (one or more products from expression of marker genes selected from FPR1) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13). In addition, Smirnov teaches expression of candidate genes were measured with quantitative real-time RT-PCR analysis (measuring an amount of at least one gene expression marker comprising using one or more of reverse transcription and polymerase chain reaction) (pg. 2919 column 1 1st full paragraph lines 1-28).
Yan-jun teaches a method for determining the expression of S100A9 in lung cancer tissues through semi-quantitative reverse transcriptase-PCR (Sq -Rt-PCR) and immunohistochemical staining (measuring the amount of at least one gene expression marker of S100A9 comprising using one or more of reverse transcription, polymerase chain reaction, and protein immunoprecipitation) (abstract background lines 1-4; abstract methods lines 1-4; abstract results lines 1-4; pg. 2216 paragraph bridging column 1 & 2 lines 1-7; pg. 2216 column 2 1st full paragraph lines 1-18; pg. 2216-2217 paragraph bridging pg. 2216 & pg. 2217 lines 1-21).
Smirnov and Yan-jun does not teach measuring the amount of the gene expression marker of S100A9 and further of one or more products from expression of markers selected from FPR1, PAD14, S100A12, SELL, APOBE3CA, MMP9, TYMP, and SAT1 with one or more of reverse transcription, polymerase chain reaction, nucleic acid sequencing, etc.
Morris teaches a method for measuring FPR1 mRNA expression in whole blood samples from lung cancer patients through RT-PCR (wherein the at least one gene expression marker of S100A9 further comprises one or more products selected from FRP1 using one or more of reverse transcription and polymerase chain reaction) (pg. 1 column 2 1st full paragraph lines 1-15). In addition, Morris teaches that FPR1 mRNA levels in whole blood cancer can identify the presence of lung cancer with high accuracy (pg. 1 2nd column 3rd full paragraph lines 1-2).
Smirnov, Yan-jun, and Morris are considered to be analogous to the claimed invention because they are all in the same field of detection of gene expression markers in lung cancer. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of measuring gene expression in lung cancer samples of candidate biomarkers through quantitative real-time RT-PCR analysis in Smirnov to incorporate measuring the expression of the gene expression marker of S100A9 with RT-PCR and/or with protein immunoprecipitation in lung cancer samples as taught in Yan-jun and to incorporate measuring the expression of the gene expression marker of FRP1 through RT-PCR because Morris teaches that doing so would provide a gene expression marker that can identify the presence of lung cancer with high accuracy.
Claim(s) 71 & 72 is/are rejected under 35 U.S.C. 103 as being unpatentable over Smirnov (Smirnov et al.; Cancer Research, Vol. 66, pages 2918-2922, March 2006) and Yan-jun (Yan-jun et al.; Chinese Medical Journal, Vol. 123, pages 2215-2220, April 2010), as applied to claims 65, 67, 68, & 70 above, and further in view of Shames (Shames et al.; PLoS Medicine, Vol. 3, pages 2244-2263, December 2006).
The teachings of Smirnov and Yan-jun with respect to claim 65 is discussed above.
Regarding claim 71, Smirnov and Yan-jun does not teach measuring an amount of at least one methylation marker DNA and at least one reference marker DNA.
Shames teaches a method to identify cancer-specific methylation markers through first employing a high-throughput global expression profile approach in lung cancer cells and then measuring the methylation of the genes expressed in lung cancer cells (abstract methods and findings paragraph lines 1-8; pg. 2248 column 2 1st full paragraph lines 1-4). In addition, Shames teaches measuring the methylation in genes based on the determined expression pattern and to determine the genes with CpG islands (measuring the amount of at least one methylation marker comprising a differentially methylated target region) compared to genes that did not have CpG islands (measuring the amount of at least one reference marker comprising a reference target region that is not differentially methylated) (pg. 2250 column 1 1st full paragraph lines 1-17; pg. 2250 column 1 2nd full paragraph lines 1-11; pg. 2251 paragraph bridging column 1 & 2 lines 1-19; pg. 2259 column 1 1st full paragraph lines 1-18). Finally, Shames teaches that this method can be used for determining targets for early diagnosis and therapeutic intervention in tumors (pg. 2260 column 2 1st full paragraph lines 1-17).
Smirnov, Yan-jun, and Shames are considered to be analogous to the claimed invention because they are all in the same field of analysis of nucleic acid biomarkers in lung cancer samples. Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of measuring expression levels of one or more gene products including S100A9 and reference marker STK4, as taught by Smirnov, to include measuring DNA methylation markers as taught in Shames because Shames teaches that doing so would aid in determining targets for early diagnosis and therapeutic intervention in tumors.
Regarding claim 72, Smirnov teaches measuring the global gene expression profile obtained from blood samples from cancer patients, including lung, breast, colorectal, prostate, and renal cancer through the Affymetrix Focus array, in which the Affymetrix Focus array comprises oligonucleotides that measure the expression of genes including S100A9, STK4, and FPR1 (further comprises a product from expression of a marker gene selected from a group including FPR1) (abstract lines 1-12; pg. 2918 column 2 2nd full paragraph lines 1-5; pg. 2918-2919 paragraph bridging pg. 2918 & pg. 2919 lines 1-13). In addition, Smirnov teaches that blood from cancer and healthy volunteers were collected in a 10-mL CellSave preservative tube in which 4 mL of this collected blood was used for RNA extraction (DNA and RNA are isolated from blood collected in a single blood collection device) (pg. 2918 column 2 2nd full paragraph lines 1-15).
Response to Arguments
The response traverses the rejection. The response asserts that as described above, Smirnov does not disclose or suggest the method of claim 65 as, as described above, Smirnov does not disclose a suggest measuring product from expression of S100A9 by the recited techniques and does not disclose or suggest STK4 as a reference marker. Further, the response asserts that, Shames is not relevant to claim 65 but is recited for the identification of cancer-specific methylation markers and as such, Smirnov and Shames, whether considered alone or in combination, fail to disclose or suggest the method of claim 65. Further, the response asserts that claim 71 & 72 depend from claim 65 and are therefore also patentable for at least the same reasons. These arguments have been thoroughly reviewed but were not found persuasive as the claim as, as discussed above, Smirnov teaches measuring gene expression with the Affymetrix Focus array which comprises oligonucleotides that measure the expression of genes including S100A9 (expression of marker gene S100A9) and the standard protocol for the Affymetrix Focus array requires an RNA pre-amplification step and therefore Smirnov teaches measuring the marker gene S100A9 through one or more of the methods listed in claim 65 comprising polymerase chain reaction as the Affymetrix Focus array comprises oligonucleotides that measure the expression of S100A9. In addition, Smirnov teaches expression of candidate genes were measured with quantitative real-time RT-PCR analysis, therefore comprising measuring an amount of at least one gene expression marker comprising using one or more of reverse transcription and polymerase chain reaction (pg. 2919 column 1 1st full paragraph lines 1-28). Further, Smirnov teaches the use of the Affymetrix Focus array that comprises oligonucleotides that measure the expression of genes including S100A9 (expression of marker gene S100A9) and STK4 (reference marker comprises RNA product from expression of STK4) therefore teaching measuring the expression of STK4 as, as the claim is currently amended, the recitation of a reference marker comprising STK4 gene does not structurally alter or define the gene.
The response also asserts that Smirnov does not disclose or suggest measuring product from expression of S100A9 by the recited techniques and does not disclose STK4 as a reference marker. Further, the response asserts that Yan-jun does not compensate for theses deficiencies of Smirnov as Yan-jun also does not disclose or suggest STK4 as a reference marker and rather Yan-jun discloses normalization against β-actin. Specifically, the response asserts that claim 65 is patentable over Smirnov in view of Yan-jun at least in that neither reference discloses or suggests STK4 as a reference marker much less the combination with measuring product from expression of marker gene S100A9 using one or more of the listed techniques. These arguments have been thoroughly reviewed but were not found persuasive for the reasons set forth above and as Yan-jun is not relied upon for teaching a reference marker of STK4.
The response also asserts that claims 66 & 69 depend from claim 65, which as described above is patentable over Smirnov and Yan-jun and further that Morris is not cited as relevant to claim 65 but rather is cited as allegedly relevant to addition markers recited in claims 66 & 69. Specifically, the response asserts that Morris does not cure the deficiencies of Smirnov and Yan-jun with respect to claim 65 at least in the Morris also does not disclose the reference maker STK4. These arguments have been thoroughly reviewed but were not found persuasive for the reasons set forth above and as Morris is not relied upon for teaching a reference marker of STK4.
The response also asserts that that claims 71 & 72 depend from claim 65, which as described above is patentable over Smirnov and Yan-jun and further that Shames is only cited as relevant to cancer-specific methylation markers. Specifically, the response asserts that claim 65 is patentable over Smirnov, Yan-jun, and Shames and therefore claims 71 & 72 are patentable at least for the same reasons. These arguments have been thoroughly reviewed but were not found persuasive for the reasons set forth above.
For these reasons, and the reasons modified to address the claims as currently amended, the rejections are applied to the newly amended claims.
Conclusion
Claims 65-72 are rejected.
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY C BUCHANAN whose telephone number is (703)756-1315. The examiner can normally be reached Monday-Friday 8:00am-5:00pm ET.
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/BAILEY BUCHANAN/Examiner, Art Unit 1682
/JEHANNE S SITTON/Primary Examiner, Art Unit 1682
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