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 28-35 & 39-52 filed on 01/20/2026 are pending. Claims 36-38 are withdrawn from consideration as being drawn to a non-elected invention. Claims 28-30, 32, 34, 35, 39, 40, 43, 44, 48, 50, & 51 are currently under examination directed to the elected species of (a) in (A) in claim 28 and corresponding elections in claims 35-39, of cell subpopulation, extracellular nucleic acids, and extracellular vesicles in claim 28, of rare cells, extracellular nucleic acids, and extracellular vesicles in claim 44, of circulating tumor cells in claim 29, of variant A in claim 30, of (i), (ii), and (iii) in claim 32, of circulating body fluid in claim 34, of blood in claims 40, 43, & 48, of R1 is an alkyl residue, R2 and R3 are different and are hydrocarbon residues, and R4 is an oxygen residue in claim 35, (i) in claim 41, of (a) in claim 50, and of (a) in claim 51 (see response dated 06/02/2025). 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Any rejection not reiterated is hereby withdrawn in view of the amendments to the claims.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 § 103
Claim(s) 28-32, 34, 35, 39, 41-47 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wyrich (WO 2014/146781 A1), as cited in the IDS dated 06/25/2022, in view of Geoprge (WO 2019/079743 A1), as cited in the IDS dated 06/25/2022.
Regarding amended claim 28, Wyrich teaches a method for stabilizing cell-containing biological samples, including blood samples, by stabilizing the sample with a primary or secondary carboxylic amide (keeping the stabilized cell-containing bodily fluid sample for a stabilization period, and then isolating (enriching) nucleic acids from the stabilized sample (pg. 5 lines 30-40; pg. 6 lines 1-2, 4-7, & 11-26; pg. 7 lines 5-39). Wyrich also teaches that the nucleic acids isolated (enriched) from the stabilized sample include extracellular nucleic acids, intracellular nucleic acids, and circulating tumor cells (CTCs) (cell subpopulation) contained in a blood sample (enriching three or more biological targets) (pg. 6 lines 11-26; pg. 7 lines 5-39). Wyrich also teaches that extracellular nucleic acids are not usually present “naked” in the sample but are stabilized to a certain extent by being released protected in complexes or by being contained in vesicles (extracellular nucleic acids enriched from extracellular vesicles in the sample) (pg. 4 lines 1-4; pg. 26 lines 37-39). Wyrich also teaches that the stabilization effect of the stabilizing composition is not based on cell lysis (stabilization of the cell-containing body fluid sample does not involve the use of additives wherein the additives would induce or promote lysis of nucleated cells) (pg. 5 lines 37-40; pg. 21 lines 30-32) and that that the stabilizing composition does not have cross-linking properties and therefore does not cause cross-links between nucleic acid molecules or between nucleic acid molecules and proteins (pg. 13 lines 37-40; pg. 14 lines 1-2; pg. 31 lines 4-18). Finally, Wyrich teaches separating the stabilized cell-containing biological sample into a cell-containing fraction and a cell-reduced or cell-depleted fraction (pg. 7 lines 5-39; pg. 12 lines 7-8; pg. 18 lines 1-2; pg. 20 lines 21-24; pg. 21 lines 30-41; pg. 36 lines 19-41; pg. 37 lines 1-29; pg. 38 lines 14-17; pg. 40 lines 18-25) (see claim 45).
Wyrich does not explicitly teach enriching extracellular vesicles from the stabilized cell-containing bodily fluid sample and does not teach that RNA is isolated from the enriched extracellular vesicles and detecting one or more target molecules within the isolated RNA.
Geoprge teaches a method for stabilizing a biological sample, including a blood sample, with a composition comprising one or more amides to stabilize the sample and allow for isolation (enrichment) and analysis of the extracellular vesicles in the stabilized sample in which RNA can be isolated and further analyzed to identify actionable targets (paragraph [0008] line 1; paragraph [0021] lines 1-6; paragraph [0033] lines 1-25; paragraph [0044] lines 8-9). Geoprge also teaches that this method preserves individual components of the sample including extracellular vesicles and nucleic acids and prevents cell lysis so that the sample can be preserved for days without contamination (paragraph [0033] lines 1-25).
Wyrich and Geoprge are considered to be analogous to the claimed invention because they are all in the same field of stabilization of a blood sample with an stabilizing composition comprising an amide. 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 enriching for three or more biological targets in Wyrich to incorporate also enriching and analyzing extracellular vesicles from the stabilized cell-containing bodily fluid sample and detecting RNA target molecules isolated from the enriched extracellular vesicles as taught in Geoprge because Geoprge teaches that doing so would preserve individual components of a sample including extracellular vesicles and nucleic acids for days without contamination from cell lysis.
Regarding amended claim 29, Wyrich teaches that the nucleic acids isolated (enriched) from the stabilized sample include circulating tumor cells (enriched cell subpopulation comprises target rare cells of circulating tumor cells (CTCs)) contained in a blood sample (pg. 6 lines 23-26; pg. 12 lines 7-8).
Regarding amended claim 30, Wyrich teaches separating the stabilized cell-containing biological sample into a cell-containing fraction and a cell-reduced or cell-depleted fraction (aa) and further processing the cell-containing fraction of the sample to isolate (enrich) for intracellular cells and circulating tumor cells (CTCs) (bb) and further processing the cell-depleted fraction of the sample to enrich for extracellular nucleic acids (cc) (pg. 7 lines 5-39; pg. 12 lines 7-8; pg. 18 lines 1-2; pg. 20 lines 21-24; pg. 36 lines 19-41; pg. 37 lines 1-29; pg. 40 lines 18-25).
Regarding amended claims 31 & 32, Wyrich teaches that the cells can be separated from the stabilized sample and intracellular nucleic acids and CTCs can be isolated for analysis (pg. 21 lines 30-41; pg. 22 lines 1-7) and that the extracellular nucleic acid population can be isolated and analyzed (pg. 41 lines 22-27) (see claim 31). Wyrich also teaches that CTCs can be isolated (enriched) and their gene expression profile can be analyzed and/or intracellular nucleic acids can be isolated from the enriched specific CTCs for gene expression profiling and detection of biomarkers (isolating intracellular nucleic acids from the enriched target rare cells and detecting one or more target molecules) (enriching and analyzing target rare cells on a cellular level) (i) (pg. 21 lines 30-41) and that extracellular nucleic acids can be isolated (enriched) from the cell-depleted fraction (ii) (pg. 37 lines 25-29; pg. 38 lines 14-17) (see claim 32).
Wyrich does not teach that extracellular vesicles are processed for analysis (see claim 31) or that RNA is isolated from the enriched extracellular vesicles and detecting one or more target molecules within the isolated RNA (iii) (see claim 32).
Geoprge teaches a method for stabilizing a biological sample, including a blood sample, with a composition comprising one or more amides to stabilize the sample and allow for isolation (enrichment) and analysis of the extracellular vesicles in the stabilized sample in which RNA can be isolated and further analyzed to identify actionable targets (paragraph [0008] line 1; paragraph [0021] lines 1-6; paragraph [0033] lines 1-25; paragraph [0044] lines 8-9). Geoprge also teaches that this method preserves individual components of the sample including extracellular vesicles and nucleic acids and prevents cell lysis so that the sample can be preserved for days without contamination (paragraph [0033] lines 1-25).
Wyrich and Geoprge are considered to be analogous to the claimed invention because they are all in the same field of stabilization of a blood sample with an stabilizing composition comprising an amide. 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 enriching for three or more biological targets in Wyrich to incorporate also enriching and analyzing extracellular vesicles from the stabilized cell-containing bodily fluid sample and detecting RNA target molecules isolated from the enriched extracellular vesicles as taught in Geoprge because Geoprge teaches that doing so would preserve individual components of a sample including extracellular vesicles and nucleic acids for days without contamination from cell lysis.
Regarding claim 34, Wyrich teaches that the cell-containing sample is a blood sample (circulating bodily fluid) (pg. 6 lines 22-26).
Regarding amended claim 35, Wyrich teaches that the stabilizing composition is a primary or secondary carboxylic amide that has the formula 1 wherein R1 is an alkyl residue, R2 and R3 are different and are a hydrocarbon residue, and R4 is an oxygen (pg. 14 lines 4-32).
Regarding claim 39, Wyrich teaches that the stabilizing composition is a primary or secondary carboxylic amide and can additionally comprise further additives including a poly(oxyethylene) polymer as a stabilizing agent and a caspase inhibitor as a stabilizing agent and a chelating agent that enhances the stabilizing effect (pg. 6 lines 28-33 & 39-41; pg. 7 lines 1-2; pg. 16 lines 33-39; pg. 30 lines 21-22).
Regarding amended claim 41, Wyrich teaches that the stabilization effect of the stabilizing composition is not based on cell lysis (stabilization of the cell-containing body fluid sample does not involve the use of additives wherein the additives would induce or promote lysis of nucleated cells) (pg. 5 lines 37-40; pg. 21 lines 30-32) and that the stabilizing composition does not have cross-linking properties and therefore does not cause cross-links between nucleic acid molecules or between nucleic acid molecules and proteins (pg. 13 lines 37-40; pg. 14 lines 1-2; pg. 31 lines 4-18).
Regarding amended claim 42, Wyrich teaches that the stabilizing composition does not have cross-linking properties and therefore does not cause cross-links between nucleic acid molecules or between nucleic acid molecules and proteins (pg. 13 lines 37-40; pg. 14 lines 1-2; pg. 31 lines 4-18).
Regarding amended claim 43, Wyrich teaches that the stabilizing composition is a primary or secondary carboxylic amide according to formula 1 and can additionally comprise further additives including low and high molecular weight poly(oxyethylene) polymer ranging from 200 to 20000 Da (molecular weight at least 3000 and 1000 or less) as a stabilizing agent and a caspase inhibitor as a stabilizing agent and a chelating agent that enhances the stabilizing effect (pg. 6 lines 28-33 & 39-41; pg. 7 lines 1-2; pg. 14 lines 4-32; pg. 30 lines 21-40).
Regarding claim 44, Wyrich teaches that the nucleic acids isolated (enriched) from the stabilized sample include extracellular nucleic acids, intracellular nucleic acids, and circulating tumor cells (CTCs) (rare cells) contained in a blood sample (enriching three or more biological targets) (pg. 4 lines 1-4; pg. 6 lines 11-26; pg. 7 lines 5-39; pg. 26 lines 37-39).
Regarding claims 45 & 46, Wyrich teaches separating the stabilized cell-containing biological sample into a cell-containing fraction and a cell-reduced or cell-depleted fraction (pg. 7 lines 5-39; pg. 12 lines 7-8; pg. 18 lines 1-2; pg. 20 lines 21-24; pg. 21 lines 30-41; pg. 36 lines 19-41; pg. 37 lines 1-29; pg. 38 lines 14-17; pg. 40 lines 18-25) (see claim 45).
Wyrich does not teach that RNA is isolated from the enriched extracellular vesicles and detecting one or more target molecules within the isolated RNA (see claims 45 & 46).
Geoprge teaches a method for stabilizing a biological sample, including a blood sample, with a composition comprising one or more amides to stabilize the sample and allow for isolation (enrichment) and analysis of the extracellular vesicles in the stabilized sample in which RNA can be isolated and further analyzed to identify actionable targets (paragraph [0008] line 1; paragraph [0021] lines 1-6; paragraph [0033] lines 1-25; paragraph [0044] lines 8-9). Geoprge also teaches that this method preserves individual components of the sample including extracellular vesicles and nucleic acids and prevents cell lysis so that the sample can be preserved for days without contamination (paragraph [0033] lines 1-25).
Wyrich and Geoprge are considered to be analogous to the claimed invention because they are all in the same field of stabilization of a blood sample with an stabilizing composition comprising an amide. 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 enriching for three or more biological targets in Wyrich to incorporate also enriching and analyzing extracellular vesicles from the stabilized cell-containing bodily fluid sample and detecting RNA target molecules isolated from the enriched extracellular vesicles as taught in Geoprge because Geoprge teaches that doing so would preserve individual components of a sample including extracellular vesicles and nucleic acids for days without contamination from cell lysis.
Regarding claim 47, Wyrich teaches separating the stabilized cell-containing biological sample into a cell-containing fraction and a cell-reduced or cell-depleted fraction and further processing the cell-containing fraction of the sample to isolate (enrich) for intracellular cells, in which intracellular nucleic acids encompass genomic DNA (isolating genomic DNA from the cell-containing fraction), and circulating tumor cells (CTCs) and further processing the cell-depleted fraction of the sample to enrich for extracellular nucleic acids (pg. 7 lines 5-39; pg. 12 lines 7-8; pg. 18 lines 1-2; pg. 19 lines 16-18; pg. 20 lines 21-24; pg. 36 lines 19-41; pg. 37 lines 1-29; pg. 40 lines 18-25).
Claim(s) 33, 48-50 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wyrich (WO 2014/146781 A1), as cited in the IDS dated 06/25/2022, and Geoprge (WO 2019/079743 A1), as cited in the IDS dated 06/25/2022, as applied to claims 28-32, 34, 35, 39, 41-47 above, and further in view of Lianidou (US Patent Application Publication US 2019/0085401 A1).
The teachings of Wyrich and Geoprge with respect to claim 28 is discussed above.
Regarding claims 33 & 48-50, Wyrich and Geoprge does not teach enriching target rare cells (CTCs) by affinity capture (see claim 33) or subjecting the stabilized cell-containing bodily fluid sample to dilution followed by a density gradient step (see claims 48-50).
Lianidou teaches a method for isolating CTCs (target rare cells) from a blood sample by diluting the sample with PBS (dilution solution that is an isotonic solution) (see claims 49 & 50) and then isolating the CTCs (encompassed in the cell-containing bodily fluid sample) with a gradient density centrifugation step (see claim 48) and then enriching the sample for CTCs with immunomagnetic coated capture beads (enriching target rare cells (CTCs) by affinity capture) (see claim 33) (paragraph [0129] lines 18-24). In addition, Lianidou teaches that the detection and isolation has a high potential to significantly change therapeutic strategies in cancer patients by providing a reliable and non-invasive method to monitor blood-based biomarkers in real-time (paragraph [0008] lines 1-10).
Wyrich, Geoprge, and Lianidou are considered to be analogous to the claimed invention because they are all in the same field of isolating CTCs from a blood sample. 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 enriching biological targets in Wyrich and Geoprge to incorporate subjecting the cell-containing bodily fluid sample comprising target rare cells (CTCs) to dilution followed by a density gradient step and enriching the target rare cells (CTCs) by affinity capture as taught in Lianidou because Lianidou teaches that doing so would provide a reliable and non-invasive method to monitor blood-based biomarkers in real-time.
Claim(s) 40 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wyrich (WO 2014/146781 A1), as cited in the IDS dated 06/25/2022, and Geoprge (WO 2019/079743 A1), as cited in the IDS dated 06/25/2022, as applied to claims 28-32, 34, 35, 39, 41-47 above, and further in view of Grӧlz (WO 2015/140218 A1), as cited in the IDS dated 06/25/2022.
The teachings of Wyrich and Geoprge with respect to claims 28 & 35 is discussed above.
Regarding amended claim 40, Wyrich teaches that the cell-containing sample is a blood sample and is contacted with a stabilizing composition comprising a primary or secondary carboxylic amide according to formula 1 at a concentration range of 0.25% to 20% (range of 0.3% to 4%) and can additionally comprise further additives including low and high molecular weight poly(oxyethylene) polymers as a stabilizing agent and a pancaspase inhibitor of Q-VD-OPh in the concentration range of 1μM to 30μM (range of 1μM to 10μM) as a stabilizing agent and a chelating agent that enhances the stabilizing effect (pg. 6 lines 28-33 & 39-41; pg. 7 lines 1-2; pg. 14 lines 4-32; pg. 16 lines 33-39; pg. 24 lines 36-39; pg. 25 lines 30-33; pg. 30 lines 21-40).
Wyrich and Geoprge does not teach that the high molecular weight poly(oxyethylene) polymer is in a concentration that lies in a range of 0.2% to 1.5% (w/v) and the low molecular weight poly(oxyethylene) polymer is in a concentration that lies in a range of 1.5% to 10% (w/v).
Grӧlz teaches a method for stabilizing cell-containing biological samples with a stabilizing composition comprising at least one high molecular weight poly(oxyethylene) polymer having a molecular weight of at least 1500 (range of 3000 to 4000) and two or more further additives from at least one low molecular weight poly(oxyethylene) polymer having a molecular weight of 1000 or less, one or more primary, secondary, or tertiary amides, a caspase inhibitor, and an anticoagulant and/or a chelating agent (pg. 5 lines 19-26; pg. 7 lines 20-32). Grӧlz also teaches that the high molecular weight poly(oxyethylene) polymer can be in a concentration range from 0.2% to 2.5% (w/v) (in a range of 0.2% to 1.5% (w/v)) and the low molecular weight poly(oxyethylene) polymer can be in a concentration range from 0.5% to 10% (w/v) (in a range from 1.5% to 10% (w/v)) (pg. 11 lines 14-16; pg. 12 lines 10-14). Finally, Grӧlz teaches that this method of stabilizing cell-containing biological samples with poly(oxyethylene) polymers of different molecular weights and concentrations is capable of stabilizing the sample and reducing the risk that the extracellular nucleic acid population becomes contaminated with genomic DNA (pg. 5 lines 19-26).
Wyrich, Geoprge, and Grӧlz are considered to be analogous to the claimed invention because they are all in the same field of stabilization of a sample with an stabilizing composition comprising an amide. 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 enriching biological targets in Wyrich and Geoprge to incorporate high and low poly(oxyethylene) at specific concentrations in the stabilizing composition as taught in Grӧlz because Grӧlz teaches that doing so would reduce the risk that the extracellular nucleic acid population becomes contaminated with genomic DNA.
Claim(s) 51 & 52 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wyrich (WO 2014/146781 A1), as cited in the IDS dated 06/25/2022, Geoprge (WO 2019/079743 A1), as cited in the IDS dated 06/25/2022, and Lianidou (US Patent Application Publication US 2019/0085401 A1), as applied to claims 33 & 48-50 above, and further in view of Raffo (Raffo, Tito, & Sasso; The International Journal of Transfusion Medicine, Vol. 114, pages 283-289, February 2019).
The teachings of Wyrich, Geoprge, and Lianidou with respect to claim 49 & 50 is discussed above.
Regarding claims 51 & 52, Wyrich, Geoprge, and Lianidou does not teach the dilution solution comprises a reducing sugar (see claim 51) or comprises DMSO (see claim 52).
Raffo teaches diluting blood samples with a mixture of 50/55% DMSO in 40/45% dextrose 5% solution in which dextrose 5% is a glucose solution (dilution solution comprises a reducing sugar optionally glucose in a concentration that lies in a range of 2-10%) (abstract background and objectives paragraph lines 1-2 & 8-9; abstract materials and methods paragraph lines 1-3; pg. 284 column 1 1st full paragraph lines 1-13; pg. 284 paragraph bridging column 1 & 2 lines 1-7). In addition, Raffo teaches that glucose is effective in reducing cell damage during dehydration and provided more viable cells (abstract background and objectives paragraph lines 6-8; abstract conclusion paragraph lines 4-5).
Wyrich, Geoprge, Lianidou, and Raffo are considered to be analogous to the claimed invention because they are all in the same field of treatments of a blood sample. 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 enriching biological targets in Wyrich and Geoprge to incorporate subjecting the cell-containing bodily fluid sample comprising target rare cells (CTCs) to dilution followed by a density gradient step and enriching the target rare cells (CTCs) by affinity capture as taught in Lianidou because Lianidou teaches that doing so would provide a reliable and non-invasive method to monitor blood-based biomarkers in real-time and further to incorporate a dilution solution comprising DMSO and a reducing sugar as taught in Raffo because Raffo teaches that diluting a blood sample with a solution of DMSO and glucose is effective in reducing cell damage and providing more viable cells.
Response to Arguments
The response traverses the rejection. The response asserts that although Geoprge may teach enriching extracellular vesicles, the composition of Geoprge essentially comprises one or more components capable of releasing an aldehyde which can induce protein-nucleic acids or protein-protein crosslinks and that although Geoprge mentions that the extracellular vesicles can be preserved and the cfDNA and cfRNA and other cellular matter located inside the extracellular vesicles may be isolated, Geoprge fails to teach or suggest isolating nucleic acids from the enriched extracellular vesicles. Further, the response asserts that in view of the foregoing, the cited art fails to teach or suggest all the features of claim 28 and since claims 29-35 and 39-52, directly or indirectly, depend on claim 28, the cited art cannot render the subject claims obvious. These arguments have been thoroughly reviewed but were not found persuasive. First, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Second, Geoprge is not relied upon to teach the recitation of “wherein the stabilization of the cell-containing bodily fluid … does not involve the use of additives … would induce or promote lysis of the nucleated cells, wherein the stabilization does not induce protein-nucleic acids or protein-protein cross-links” as recited in claim 28 as currently amended. Further, Geoprge does teach a method for stabilizing a biological sample, including a blood sample, with a composition comprising one or more amides to stabilize the sample and allow for isolation (enrichment) and analysis of the extracellular vesicles in the stabilized sample in which RNA can be isolated and further analyzed to identify actionable targets (isolating nucleic acids from the enriched extracellular vesicles) (paragraph [0008] line 1; paragraph [0021] lines 1-6; paragraph [0033] lines 1-25; paragraph [0044] lines 8-9).
The response also asserts that the claimed invention can provide unexpected results sufficient to establish unobviousness within the meaning of 35 U.S.C. 103 and, as described in the subject specification, despite well-recognized clinical potential of biological targets (including extracellular vesicles, rare cells, extracellular nucleic acids, and intracellular nucleic acids), their utilization at the priority date remained challenging. Further, the response asserts that, as described in the specification, methods based on the analysis of molecular biomarkers comprised in free circulating nucleic acids, EVs, or CTCs for obtaining cancer-related information often had drawbacks with respect to sensitivity and/or robustness, and the subject specification describes that preanalytical conditions can significantly influence results of analytical tests including all liquid biopsy analytes require stabilization if tests are preformed >3-4 hours after blood draw and stabilization of the biological targets of interest must be sufficient and reliable. Further, the response asserts that while some of the tubes for ctDNA analysis compatibility with CTC analysis was claimed, such claims were basically limited to one particular CTC enrichment detection and technology further underlining challenges in analysis of multiple biological targets from liquid biopsy samples. These arguments have been thoroughly reviewed but were not found persuasive. First, it is noted that the findings of unexpected results must be commensurate in scope with the claimed inventions (see MPEP §716.02(d)). The claims recite limitations of contacting the cell-containing bodily fluid with a stabilizing composition, and therefore not commensurate in scope with the results discussed in the response. The response asserts that the preanalytical conditions can significantly influence results of analytical tests, however the claims as currently amended recites steps for contacting a cell-containing bodily fluid with a stabilizing composition and do not recite steps of preanalytical conditions of timing after blood draw and stabilization of target of interest being sufficient and reliable. Accordingly, the scope of the claims does not appear to be commensurate in scope with the unexpected results attributed to the preanalytical conditions discussed in the response and taught in the specification. Further, in response to applicants assertions that utilization of potential biological targets in bodily fluid at the priority date remained challenging and that analysis of molecular biomarkers often had drawbacks with respect to sensitivity and/or robustness, applicants arguments cannot take place of evidence in the record.
The response also asserts that, as described in the subject specification, the use of formaldehyde or formaldehyde-releasing substances has drawbacks as they can compromise the efficacy of extracellular nucleic acid isolation and efficacy of downstream analysis by induction of crosslinks between nucleic acid molecules or proteins and nucleic acids and that Geoprge used a stabilization technology where components capable of releasing aldehyde are used which is disadvantageous for reliable stabilization of multiple biological analytes and can also induce undesirable protein-nucleic acids or protein-protein crosslinks, and thereby can reduce the yield and/or analysability of accordingly stabilized analytes. Further, the response asserts that, as demonstrated in the examples of the present application (including example 4 and 8), the present technology does not induce protein-nucleic acids or protein-protein crosslinks and offers important advantages over known state-of-the-art stabilization technologies such as Geoprge and that these advantages are completely unexpected from the cited art. Further, the response asserts that none of the cited art teaches or suggested enriching extracellular vesicles, and further isolating nucleic acids from the enriched extracellular vesicles while the stabilization does not induce protein-nucleic acids or protein-protein cross links and as Geoprge teaches that if too little of the component capable of releasing an aldehyde is present then no stabilizing effect occurs on the which blood cell, there is no articulated reasoning with some ration underpinning to arrive at the claimed invention. These arguments have been thoroughly reviewed but were not found persuasive. First, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Second, applicants arguments cannot take place of evidence in the record. Third, Geoprge is not relied upon to teach the stabilization composition does not induce protein-nucleic acids or protein-protein cross-links as recited in claim 28 as currently amended. As discussed above and previously, Wyrich teaches a method for stabilizing cell-containing biological samples, including blood samples, by stabilizing the sample with a primary or secondary carboxylic amide in which the stabilization effect of the stabilizing composition is not based on cell lysis (stabilization of the cell-containing body fluid sample does not involve the use of additives wherein the additives would induce or promote lysis of nucleated cells) (pg. 5 lines 37-40; pg. 21 lines 30-32) and that that the stabilizing composition does not have cross-linking properties and therefore does not cause cross-links between nucleic acid molecules or between nucleic acid molecules and proteins (pg. 13 lines 37-40; pg. 14 lines 1-2; pg. 31 lines 4-18). Further, Geoprge does teach a method for stabilizing a biological sample, including a blood sample, with a composition comprising one or more amides to stabilize the sample and allow for isolation (enrichment) and analysis of the extracellular vesicles in the stabilized sample in which RNA can be isolated and further analyzed to identify actionable targets (isolating nucleic acids from the enriched extracellular vesicles) (paragraph [0008] line 1; paragraph [0021] lines 1-6; paragraph [0033] lines 1-25; paragraph [0044] lines 8-9). Further, Wyrich and Geoprge are considered to be analogous to the claimed invention because they are all in the same field of stabilization of a blood sample with an stabilizing composition comprising an amide. 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 enriching for three or more biological targets in Wyrich to incorporate also enriching and analyzing extracellular vesicles from the stabilized cell-containing bodily fluid sample and detecting RNA target molecules isolated from the enriched extracellular vesicles as taught in Geoprge because Geoprge teaches that doing so would preserve individual components of a sample including extracellular vesicles and nucleic acids for days without contamination from cell lysis.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Double Patenting
Claims 28, 31, 34, 35, 41, & 42 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4, 5, 7, & 9-11 of U.S. Patent No. 10,724,074. Although the claims at issue are not identical, they are not patentably distinct from each other because each patent application provides a method for stabilizing a cell-containing biological sample with an amide according to formula 1.
Regarding claims 28 & 35, U.S. Patent No. 10,724,074 claims a method for stabilizing a cell-containing biological sample comprising contacting the sample with at least one compound according to formula 1, in which formula 1 comprising an R1 that is an alkyl residue, R2 and R3 that are different hydrocarbon residues, and R4 that is an oxygen (see claim 1). U.S. Patent No. 10,724,074 also claims the method comprises isolating (enriching) nucleic acids, intracellular nucleic acids, and extracellular nucleic acids (three or more biological targets) (see claims 7 & 9-11).
Regarding claim 31, U.S. Patent No. 10,724,074 claims the method has one or more of the following characteristics including the stabilized cell-containing sample is subjected to nucleic acid analysis and/or detection method and intra- and/or extracellular nucleic acids are isolated (enriched) from the stabilized sample and the isolated (enriched) nucleic acids are analyzed and/or detected (see claim 7).
Regarding claim 34, U.S. Patent No. 10,724,074 claims the cell-containing biological sample is a blood sample (see claim 4).
Regarding claims 41 & 42, U.S. Patent No. 10,724,074 claims the method has one or more of the following characteristics including the stabilization does not promote lysis of nucleated cells contained in the cell-containing sample and the stabilization does not involve the use of a cross-linking agent that induce nucleic-nucleic acid, protein-nucleic acid, and/or protein-protein cross-links (see claim 5).
Response to Arguments
The response traverses the rejection. The response asserts that it is noted that the instant claim 28 recites “processing that stabilized cell-containing bodily fluid sample in order to enrich three or more biological targets” and in contrast claim 9 of U.S. Pat No. 10,724,074 recites “isolating nucleic acids” and claim 10 further limits claim 9 to “intracellular nucleic acids” and claim 11 further limits claim 9 to “extracellular nucleic acids”, and that is, claims of U.S. Pat. No. 10,724,074 B2 recite isolating only one biological target in the list of alternatives and even in claim 10 and 11 were combined, this combination only suggests two biological targets are isolated at most and therefore claims 28, 31, 34, 35, 41, and 41 of the subject application and claims 1, 4, 5, 7, and 9-11 of U.S. Pat. No. 10,724,074 B2 are patentably distinct from each other. This argument has been thoroughly reviewed but was not found persuasive as claim 7 of U.S. Pat. No. 10,724,074 B2, which depends from claim 1 of U.S. Pat. No. 10,724,074 B2, claims wherein the method has one or more of the following characteristics including analyzing the stabilized cell-containing sample (a cell subpopulation) and/or analyzing intra- and/or extracellular nucleic acids (isolating (enriching) three or more biological targets) therefore encompassing enriching three biological targets.
For these reasons, and the reasons already made of record and modified to address the claims as currently amended, the rejections are maintained and applied to the newly amended claims.
Conclusion
Claims 28-35 & 39-52 are rejected.
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.
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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