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 .
Status of the Application
The Response and the Request for Continued Examination, each filed September 4, 2026, are acknowledged.
Claims 1, 3-4, 9-10, 13-14, 16, 20, 22-23, 32-36, 41-44 and 46-47 are pending and are being examined on the merits.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on September 4, 2026 has been entered.
Response to Arguments
Applicant’s arguments filed September 4, 2026 have been fully considered.
The following rejections are MAINTAINED:
Prior art rejections
Response to arguments regarding prior art rejections
Applicant argues that the prior art rejections should be withdrawn because they disagree with the BRI of “silica spin column” in claim 1 step (c). Specifically, Applicant argues that a “silica spin column” cannot additionally comprise silicon carbide (SiC), as in the Haj Ahmad spin column (Remarks, pp. 5-8).
The Examiner disagrees for several reason. First, Applicant argues that “[t]he term ‘silica spin column’ is used throughout the art, and the specification itself, to refer to a column whose binding substrate is silica, not a hybrid material” (Remarks, p. 5). However, the Examiner notes that the specification only recites “silica spin column” once (para. 11), with one additional reference to “a silica substrate” (para. 27). Neither instance defines or describes in any way what is meant by “silica”, and thus it is not clear how Applicant has arrived at the conclusion that the specification eliminates a silica “hybrid material” as an option for the spin column. Further, as to the “used throughout the art” argument, the Examiner notes that arguments presented by Applicants cannot take the place of evidence in the record, and encourages Applicants to submit such evidence which states that silica spin columns do not comprise any component other than silica. See MPEP 716.01(c)(II). Given Applicant’s statement that the term is used that way “throughout the art”, it seems that it would be straightforward do so. However, Applicant’s position as to the prior art teachings is seemingly incorrect. For example, Gunther1 (US Patent App. Pub. No. 2021/0189377 A1) teaches using spin columns to isolate nucleic acids (para. 175), and further describes silica solid phases, as follows …
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Thus, Gunther describes many “silica” solid phases that are not limited to only silica, such as borosilicate, magnetic particles, and modified silicas.
Second, Applicant argues that Haj-Ahmad makes a three-way distinction between silica columns, SiC columns and hybrid silica/SiC columns (Remarks, pp. 6-8). The Examiner agrees that Haj-Ahmad makes a distinction between silica-based purification methods, and silicon carbide-based detection methods. The Examiner does not agree that Haj-Ahmad refers to the combination of silica/SiC as “a third, distinct category” of detection methods, as Haj-Ahmad is silent as to whether or what category it would be comprised within. Further, the Examiner notes that Haj-Ahmad is referring to silica-based or silicon carbide-based detection methods, but does not refer to spin columns, per se, using the “silica-based” or “silicon carbide-based” language.
Finally, the Examiner notes that if Applicant prefers a narrower BRI so that “silica spin column” is limited literally to silica only, then claim 1 can be amended to recite something like “a consisting of SiO2”. However, if such an amendment is inconsistent with Applicant’s intended BRI, then it is not at all clear how Applicant even intends for “silica spin column” to be construed, other than “a spin column that is not the Haj Ahmad silica/SiC spin column”, which, as noted, the Examiner does not agree with.
Applicant additionally argues that the various additional secondary references cited against the dependent claims do not cure the deficiencies of the rejection as to claim 1 (Remarks, pp. 8-9). As noted, the Examiner disagrees with Applicant’s characterization of the deficiencies of the references cited against claim 1, and thus disagrees with these arguments, as well.
These arguments are not persuasive. The rejections are maintained.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1, 3-4, 9-10, 14, 16, 20, 22-23, 32, 34-36 and 41 are rejected under 35 U.S.C. 103 as being unpatentable over Haj-Ahmad2 (US Patent No. 9,422,596) in view of Kirsch3 (US Patent App. Pub. No. 2013/0041145), as evidenced by 4Norgen Biotek Corporation (Total RNA Purification Kit, Product Insert, 2022; hereinafter, “Norgen”) and 5Norgen Biotek Corporation (Buffer RL, Safety Data Sheet, 2015; hereinafter, “Norgen SDS”).
Regarding independent claim 1, Haj-Ahmad teaches …
A method for purifying unbiased miRNA from a biological sample consisting of blood, the method comprising: (col. 1, ll. 35-37: “the method of nucleic acid isolation being employed does not favor the isolation of certain sizes of RNA molecules”; col. 3, l. 19: “method can be used to isolate RNA”; col. 4, ll. 21-23: “silicon carbide based purification methods have been shown to exhibit no size-bias when used for RNA purification”; col. 9, ll. 39-41: “isolate nucleic acids from … blood”; col. 15, ll. 23-29: “the purified RNA was used in RT-qPCR reactions for the detection of … microRNA … specific primers for … miR-30b and miR-21”);
(a) obtaining the biological sample, dissolved in a lysis reagent (col. 9, ll. 39-41: “isolate nucleic acids from … blood”);
(b) lysing the biological sample dissolved in the lysis reagent (col. 9, ll. 43-46: “biological samples can be prepared using conventional … lysis methods (as appropriate to the sample type) to provide an aqueous solution containing the nucleic acids to be recovered”; col. 10, ll. 45-46: Lysis Solution from Norgen’s Total RNA Purification Kit (Cat# 17200, Norgen, Thorold Canada);
(c) purifying miRNA from the lysed sample, wherein the purifying does not involve an RNA precipitation step (col. 4, ll. 44-46: “a solid support for the isolation and purification of nucleic acids, the solid support comprising silica and [silicon carbide]”; col. 5, ll. 34-35: “the solid support is provided in a spin column”; col. 9, ll. 53-57 through col. 10, ll. 1-4: “the solid support can comprise a slurry of silica particles and [silicon carbide] particles … slurry mixture can be added to aqueous solution to allow the nucleic acids to bind to the … particles … solid support with the bound nucleic acids can then be separated … the nucleic acids can be eluted … and collected for downstream applications”);
wherein purifying comprises applying the lysed sample to a silica spin column to bind the miRNA to said column (col. 3, ll. 1-3; col. 10, ll. 5-8);
and (d) selectively analyzing the purified miRNA (col. 15, ll. 23-29: “the purified RNA was used in RT-qPCR reactions for the detection of … microRNA … specific primers for … miR-30b and miR-21”);
wherein the purified miRNAs provide a representative unbiased population of the miRNA content of the biological sample (col. 4, ll. 21-30: “silicon carbide based purification methods have been shown to exhibit no size-bias when used for RNA purification … using silica and [silicon carbide] in combination results in an overall higher yield of nucleic acids of all sizes, including small RNAs”; col. 9, ll. 39-41; col. 3, l. 19).
Haj-Ahmad teaches blood as noted above, but does not expressly teach “whole blood”, nor does Haj-Ahmad indicate that the lysis reagent was a “non-precipitating” lysis reagent.
Kirsch teaches that the sample consists of whole blood (abstract). Kirsch also teaches a non-precipitating lysis reagent, and that the lysis reagent comprises a chaotropic salt, specifically guanidium thiocyanate (para. 43: “the aqueous lysis solution is mixed with the sample”; para. 45: “sample can be brought directly in contact with the lysis solution”; para. 47: “lysis substance can … contain a [non-precipitating] chaotropic salt”; see also Example 1, paras. 85-90: describes lysis reagent with GuSCN).
Regarding the teaching in Haj-Ahmad regarding the use of Lysis Solution from Norgen’s Total RNA Purification Kit, it is noted that the Norgen lysis buffer comprises GuSCN (Norgen, p. 1, para. 2: “process involves first lysing the cells … with the provided Bufffer RL”; Norgen SDS, p. 2, section 3: guanidinium thiocyanate). As evidenced by these references, Haj-Ahmad’s method did employ a non-precipitating lysis buffer that contained the same chaotropic salt, guanidium thiocyanate, as Kirsch’s method. Thus, the only difference between the method of claim 1 and Haj-Ahmad’s method is the use of “whole blood”, rather than “blood”.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to practice the method of Haj-Ahmad using whole blood. Firstly, one of ordinary skill in the art would have assumed Haj-Ahmad’s reference to “blood” meant “whole blood”. Secondly, Kirsch demonstrates that it was known and conventional in the art to isolate nucleic acids from “whole blood”.
The ordinary artisan would also have been motivated to incorporate the Kirsch whole blood sample in the Haj-Ahmad method, as Haj-Ahmad specifically teaches that the method can be used on blood, although does not further qualify the type of blood. It would have been obvious to the ordinary artisan to try the whole blood sample in the Haj-Ahmad method, with an expectation of success as Haj-Ahmad teaches a wide variety of biological samples, including blood, and does not limit the specific types of blood samples that may be used.
Regarding dependent claim 3, Kirsch suggests collecting whole blood in a tube comprising the lysis reagent (para. 17: describes a direct lysis prior art method of collecting blood in a tube comprising lysis reagent; para. 25: teaches that direct processing sample is desirable).
Regarding dependent claim 4, Kirsch teaches inactivating nucleases (para. 32: RNases) and suggests inactivating microbes (para. 15: describes prior art method using GuSCN that inactivates pathogens; Example 1, paras. 85-90: describes lysis reagent with GuSCN). As noted above, Haj-Ahmad used a lysis reagent from the Norgen kit containing GuSCN, and so would have inactivated nucleases and pathogens, as noted by Kirsch.
Regarding dependent claim 9, Kirsch additionally teaches wherein the lysis is performed at 20-30°C (para. 95, step 6: 1 min at room temperature), while Haj-Ahmad additionally suggests wherein the purifying is performed at 20-30°C. That is, Haj-Ahmad teaches that the purifying step is performed, in part, using Norgen’s Lysis, Wash and Elution Solutions (Example 2; col. 11, ll. 33-52). Norgen teaches that each of these solutions is intended to be used at room temperature (p. 5: “all solutions are at room temperature prior to use”).
Regarding dependent claim 10, Kirsch additionally teaches wherein the lysis step involves an incubation of at least 1 minute (para. 95, step 6: 1 min at room temperature).
Regarding dependent claims 14 and 16, Kirsch teaches wherein the lysis reagent and sample are mixed at a volume of 0.7-1.5: 0.7-1.5 lysis reagent: sample (para. 43: 1.5:1 to 1:1.5, 1.2:1 to 1:1.2, as recited in claim 14, and wherein the lysis reagent and sample are mixed at 1:1 vol: vol (para. 43), as recited in claim 16.
Regarding dependent claims 22 and 23, as noted above, Haj-Ahmad’s method employed a lysis reagent with a chaotropic salt (GuSCN). In addition, Kirsch teaches that the lysing step further comprises proteinase K digestion (para. 90), as recited in claim 22, and that the lysing step further comprises agitation with one or more beads (para. 56), as recited in claim 23.
Regarding dependent claim 20, Haj-Ahmad’s method did not employ phenol.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to practice the method of Haj-Ahmad using whole blood in view of Kirsch, as discussed above, and further to modify the method according to the teachings of Kirsch by employing the dilution ratios of sample to lysis reagent, the times and temperatures of the incubation steps, and the use of beads and proteinase K digestion as taught by Kirsch, as Kirsch taught these modifications as useful for the extraction of nucleic acids from whole blood.
The ordinary artisan would have been further motivated to collect the blood in a tube with the lysis reagent in order to reduce the number of steps and increase the efficiency of the method.
Regarding dependent claim 32, Haj-Ahmad additionally teaches that the lysed sample is diluted in an alcohol, specifically ethanol, prior to applying said lysed sample to the column (col. 10, ll. 47-48). Kirsch also teaches diluting the mixture in alcohol prior to applying the mixture to the column, and teaches that either ethanol or isopropanol are suitable for that purpose (para. 59). Kirsch does not specifically teach that proportion should be an equal volume of lysate to isopropanol, but does give some guidance on appropriate alcohol content of the final mixture. The ordinary artisan would have been able to optimize both the particular alcohol and the appropriate dilution volume through routine optimization to arrive at the claimed limitation.
Regarding dependent claim 34, Haj-Ahmad additionally teaches that the purifying further comprises removal of the guanidium thiocyanate (col. 10, ll. 18-22: “spin column can be washed … to remove materials not bound to the solid support”).
Regarding dependent claim 35, Haj-Ahmad teaches washing the column with a buffer comprising ethanol (col. 10, ll. 52-55: “Wash Solution from Norgen’s Total RNA Purification Kit … was added to each column … wash step was repeated two more times). In addition, Norgen teaches that the Wash Solution is supplied as a concentrated solution to which ethanol is to be added by the end user (p. 5). Thus, the Norgen Wash Solution used on the column comprises ethanol.
Regarding dependent claim 36, Haj-Ahmad’s method does not employ phase separation (i.e. an organic extraction such as the Trizol/BCP method).
Regarding dependent claim 41, Haj-Ahmad additionally teaches selectively analyzing the purified miRNA by performing qRT-PCR (col. 15, ll. 23-29).
Claims 13 and 33 are rejected under 35 U.S.C. 103 as being unpatentable over Haj-Ahmad (US Patent No. 9,422,596) in view of Kirsch (US Patent App. Pub. No. 2013/0041145) as evidenced by Norgen Biotek Corporation (Total RNA Purification Kit, Product Insert, 2022; hereinafter, “Norgen”) and Norgen Biotek Corporation (Buffer RL, Safety Data Sheet, 2015; hereinafter, “Norgen SDS”), as applied to claims 1 and 10 above, and further in view of Schuster (WO 2017/137573 A1; citations below are to English version of application, US Patent App. Pub. No. 2019/01277296).
Regarding dependent claim 13, Schuster additionally teaches wherein the incubation
comprises storing the sample at less than 10°C for at least one day (para. 40: “at least 0°C … up to 22.5°C”).
Regarding dependent claim 33, Kirsch additionally teaches wherein the purifying further comprises performing DNase digestion (paras. 60-61), while Schuster specifically teaches DNase I (para. 61).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to practice the method suggested by the combined teachings of Haj-Ahmad and Kirsch, discussed above, and to store the sample in the lysis reagent prior to further processing. The ordinary artisan would have been motivated to do so with the expected advantage that it would improve the collection and transport of the blood sample to the testing facility. The ordinary artisan would have been further motivated to perform DNase digestion, as taught by Kirsch, to increase the purity of the final product, and to select DNAse I, in particular, as taught by Schuster, as it is obvious to select a known material based on its suitability for its intended use. The ordinary artisan would have had an expectation of success as optimizing nucleic acid isolation methods is well-known in the art.
Claims 42-44 are rejected under 35 U.S.C. 103 as being unpatentable over Haj-Ahmad (US Patent No. 9,422,596) in view of Kirsch (US Patent App. Pub. No. 2013/0041145), as evidenced by Norgen Biotek Corporation (Total RNA Purification Kit, Product Insert, 2022; hereinafter, “Norgen”) and Norgen Biotek Corporation (Buffer RL, Safety Data Sheet, 2015; hereinafter, “Norgen SDS”), as applied to claim 1 above, and further in view of Knutsen7 (Performance Comparison of Digital microRNA Profiling Technologies Applied on Human Breast Cancer Cell Lines, PLOS ONE, 8(10, e75813, 2013), as evidenced by Illumina8 (TruSeq Small RNA Sample Preparation Guide, 2010).
Regarding dependent claims 42-44, Knutsen teaches constructing a library for miRNA
sequencing and performing next generation miRNA sequencing on said library (p. 2, right col., paras. 3-4), as recited in claim 42. In addition, Knutsen as evidenced by Illumina teaches ligating adaptors to each end of the microRNAs, as recited in claim 43, and wherein the adaptors comprise barcodes, as recited in claim 44. Specifically, Knutsen teaches Illumina HiSeq next generation sequencing (p. 2, right col., paras. 3-4), while Illumina teaches ligating adaptors to each end of the microRNAs (Fig. 1), and where the adapters comprise an index sequence (i.e., a barcode) which is incorporated into the adapter during PCR (Fig. 1).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to practice the method suggested by the combined teachings of Haj-Ahmad and Kirsch, discussed above, and to construct a library for and performing next generation sequencing, as taught by Knutsen, as doing so merely represents combining prior art elements according to known methods to yield predictable results (MPEP 2143(I)). The ordinary artisan would have had an expectation of success as preparing libraries and performing nucleic acid sequencing is well-known in the art.
Claims 46-47 are rejected under 35 U.S.C. 103 as being unpatentable over Haj-Ahmad (US Patent No. 9,422,596) in view of Kirsch (US Patent App. Pub. No. 2013/0041145), as evidenced by Norgen Biotek Corporation (Total RNA Purification Kit, Product Insert, 2022; hereinafter, “Norgen”) and Norgen Biotek Corporation (Buffer RL, Safety Data Sheet, 2015; hereinafter, “Norgen SDS”) in view of Knutsen (Performance Comparison of Digital microRNA Profiling Technologies Applied on Human Breast Cancer Cell Lines, PLOS ONE, 8(10, e75813, 2013), as evidenced by Illumina (TruSeq Small RNA Sample Preparation Guide, 2010) as applied to claim 42 above, and further in view of Hsiao9 (Gene Sets Enrichment Analysis of miRNA Expression Profile, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 12460463, 2011).
Regarding dependent claims 46-47, Hsiao teaches performing unbiased miRNA
functional enrichment analysis (e.g., abstract), as recited in claim 46, and where said analysis comprises using a target prediction program, gene annotation data and applying statistical analysis (p. 450, Analysis Framework), as recited in claim 47.
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to practice the method suggested by the combined teachings of Haj-Ahmad, Kirsch and Knutsen, discussed above, and to perform the particular data analysis of Hsiao, as doing so merely represents combining prior art elements according to known methods to yield predictable results (MPEP 2143(I)). The ordinary artisan would have had an expectation of success as performing data analysis is well-known in the art.
Conclusion
Claims 1, 3-4, 9-10, 13-14, 16, 20, 22-23, 32-36, 41-44 and 46-47 are being examined, and are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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/CAROLYN L GREENE/Primary Examiner, Art Unit 1681
1 Gunther was cited in the PTO-892 Notice of References Cited mailed April 18, 2023.
2 Haj-Ahmad was cited in the PTO-892 Notice of References Cited mailed June 24, 2022.
3 Kirsch was cited in the PTO-892 Notice of References Cited mailed November 10, 2021.
4 Norgen was cited in the PTO-892 Notice of References Cited mailed June 24, 2022.
5 Norgen SDS was cited in the PTO-892 Notice of References Cited mailed June 24, 2022.
6 Schuster ‘729 application was cited in the PTO-892 Notice of References Cited mailed November 10, 2021.
7 Knutsen was cited in the PTO-892 Notice of References Cited mailed November 10, 2021.
8 Illumina was cited in the PTO-892 Notice of References Cited mailed June 24, 2022.
9 Hsiao was cited in the PTO-892 Notice of References Cited mailed November 10, 2022.
