DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-7 are pending. Claims 1-5 are amended.
Claims 1-7 are currently under examination.
Response to Amendment
The Amendment filed 8/19/25 has been entered. Claims 1-7 are pending. Applicant’s amendments to claims 1-5 have overcome the objections and 112(b) and 101 rejections previously set forth in the Non-Final Office Action mailed 5/20/25.
Response to Arguments
Applicant’s arguments, see pages 6-15, filed 8/19/25, with respect to the rejections of claims 1-7 under 35 USC 103 and non-statutory double patenting have been fully considered and are found unpersuasive. The rejections documented in the Non-Final mailed on 5/20/25 have been revised to address the claim amendments filed 8/19/25. More detailed responses to Applicant’s arguments are provided at the end of each maintained rejection.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1 and 4-7 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Crawford et al. (2018; WO 2018/035062 A1; FOR citation N in PTO-892 filed on 5/20/25) in view of Thompson (2011; US 2011/0118137 A1; USPat citation B in PTO-892 filed on 5/20/25; publication of US application 12/949,208 which claims the priority of provisional application 60/572,464 filed 5/20/04).
This rejection is necessitated by claim amendments filed on 8/19/25.
(i) Crawford et al. teaches a “Method for Finding Low Abundance Sequences by Hybridization (FLASH)” (Title).
Relevant to claims 1 and 4-5, Crawford et al. Abstract teaches “A method of sample analysis is provided. In some embodiments, the method comprises: (a) digesting a mixed nucleic acid sample with a plurality of reprogrammed nucleic acid-directed endonucleases that target sequences of interest to produce a digested sample, wherein at least some of the fragments in the digested sample comprise: (i) a sequence of interest and (ii) at least one ligatable end that has been generated by endonuclease cleavage; (b) enriching for fragments that contain the sequence of interest; and (c) analyzing the enriched fragments.”
This teaching reads on claims 1 and 4-5 A method of genetic analysis, for detecting low abundance polynucleotides in a sample, comprising the steps of: … (b) digesting at least some of the end-blocked polynucleotides with a nucleic acid-directed endonuclease that cleaves a target polynucleotide comprising a sequence of interest to produce, if the sequence of interest is present in the complex mixture, a polynucleotide that comprises: the sequence of interest and at least one ligatable end generated by endonuclease cleavage.
Further relevant to claims 1 and 4-5, Crawford et al. teaches that “In any embodiment, prior to digestion, the method may comprise end-blocking the mixed nucleic acid sample so that the ends of the nucleic acid fragments are not available for ligation” (page 17, lines 1-2).
This teaching reads on claims 1 and 4-5 (a) providing a complex mixture comprising a plurality of end-blocked polynucleotides.
Further relevant to claims 1 and 4-5, Crawford et al. teaches “In some embodiments, the nucleic acid sample may comprise DNA from at least two organisms…where the DNA from one of the organisms may be at least 10 times, at least 50 times, or at least 100 times, at least 500 times or at least 1,000 times more abundant than the other” (page 18, lines 4-8).
This teaching reads on claims 1 and 4-5 (a)… wherein a ratio of target polynucleotide to non-target polynucleotide present in the complex mixture is 1:1x103 or lower.
Further relevant to claims 1 and 4-5, Crawford et al. teaches “In some embodiments, digestion by the endonuclease may produce fragments that have two ends, both of which are ligatable. In these embodiments, the method comprises ligating adaptors to both ends of the fragments, thereby allowing the ligated fragments to be enriched by PCR using a single pair of primers that hybridize to the adaptors, or complements thereof” (page 15, lines 3-6).
This teaching reads on claims 1 and 4-5 (c) ligating a moiety to a ligatable end of the polynucleotide under conditions in which the moiety cannot be ligated to a polynucleotide that lacks a ligatable end to produce a moiety-target polynucleotide construct.
Relevant to claim 6, Crawford et al. teaches “In some embodiments, the method may comprise digesting a mixed nucleic acid sample… with a plurality of reprogrammed nucleic acid-directed endonucleases that target sequences of interest (i.e., a set of Cas9 endonuclease, Agronaut, ortholog or variant of the same that have synthetic guide RNAs or DNAs that target the endonucleases to pre-determined target sites in a target nucleic acid, e.g., a target genome)” (page 12, lines 22-28).
This teaching reads on claim 6 the nucleic acid-directed endonuclease is a CRISPR-associated protein (Cas) and a guide RNA.
Relevant to claim 7, Crawford et al. teaches that “The method may also be used to detect microbial DNA or RNA sequences” (page 21, line 20).
This teaching reads on claim 7 the sequence of interest is a gene sequence of a strain of bacteria.
(ii) Crawford et al. is silent to specifics regarding mass spectrometric detection of targets (claims 1 and 4-5). However, these limitations were known in the prior art and taught by Thompson.
Thompson teaches “Use of Mass Labeled Probes to Detect Target Nucleic Acids Using Mass Spectrometry” (Title).
Relevant to claims 1 and 4-5, Thompson teaches “f) detecting the mass tag by mass spectrometry. The first aspect of the invention set out above relates to a method for detection of a nucleic acid using a circularizable probe in which a mass tag is present in the probe” (paragraphs 0045-0046).
Further relevant to claims 1 and 4-5, Thompson teaches “The use of mass tags to detect circularisation events, as disclosed in this invention, has many advantages, since large arrays of
isotopic tags can be generated. The use of isotopic tags means that accurate quantification is enabled as the relative abundances of isotope tags are an accurate indicator of the levels of the expression products” (paragraph 0062).
These teachings read on claim 1 (d) detecting, using mass spectrometry, the moiety-target polynucleotide construct or a transcription or translation product produced from the moiety-target polynucleotide, wherein detection of the moiety-target polynucleotide indicates the presence of the sequence of interest in the complex mixture; claim 4 (d) detecting, using mass spectrometry, the RNA products, wherein detection of the RNA products indicate the presence of the sequence of interest in the complex mixture; and claim 5 wherein the moiety is an RNA adaptor linked to a mass label to produce RNA adaptored polynucleotides linked to the mass label; and (d) detecting, using mass spectrometry, the RNA adaptored polynucleotides linked to the mass label wherein detection of the adaptored polynucleotides indicate the presence of the sequence of interest in the complex mixture.
Relevant to claim 4, Thompson teaches “In some embodiments of this invention in which linear Rolling Circle Replication is used an RNA polymerase can be used to effect the replication reaction. An RNA polymerase which can carry out transcription in vitro and for which promoter sequences have been identified can be used in the disclosed rolling circle replication method. In this sort of embodiment, the Promoter sequences are used as the Primer Binding Sequences” (paragraph 0179).
This teaching reads on claim 4 the moiety is a nucleotide adaptor comprising an RNA promoter and the moiety-target polynucleotide construct is configured so that transcription initiated at the promoter transcribes at least a portion of the sequences of interest to produce RNA product.
(iii) Although Crawford et al. does not include mass spectrometry, it would have been prima facie obvious to the skilled artisan to include the mass spectrometry of Thompson within the method of genetic analysis. Crawford et al. and Thompson are analogous disclosures to the instant detection methodology.
Thompson teaches “Mass Spectrometry has been used to detect analyte ions or their fragment ions directly, however for many applications such as nucleic acid analysis, the structure of the analyte can be determined from indirect labeling. This is advantageous particularly with respect to the use of mass spectrometry because complex biomolecules such as DNA have complex mass spectra and are detected with relatively poor sensitivity. Indirect detection means that an associated label molecule can be used to identify the original analyte, where the label is designed for sensitive detection and a simple mass spectrum. Simple mass spectra mean that multiple labels can be used to analyse multiple analytes simultaneously. In fact, many more labels than can currently be used simultaneously in fluorescence based assays can be generated” (paragraph 0005).
Thus, the skilled artisan would be motivated to include the Thompson mass spectrometry in order to achieve sensitive, multiplexed detection of nucleic acids. The skilled artisan would have a reasonable expectation of success based on the disclosures of Crawford et al. in view of Thompson.
Applicant’s Arguments
Applicant has amended claims 1 and 4-5 to include limitations regarding the ratio of target polynucleotide to non-target polynucleotide and detection of the moiety-target. Applicant argues that “Neither Crawford nor Thompson disclose or suggest a ratio of target polynucleotide to non-target polynucleotide present in the complex mixture, much less the claimed ratio” (Remarks, page 11, paragraph 3, filed 8/19/25). Applicant further argues that “Thompson’s method detects the cleaved tag not the actual polynucleotide construct or its products” (Remarks, page 13, paragraph 1, filed 8/19/25).
Response to Applicant’s Arguments
The rejection of claims 1 and 4-7 under 35 USC 103 has been revised as stated above in this Final Office Action that specifically addresses the amended limitations of claims 1 and 4-5 recited in the Amendments filed 8/19/25.
As discussed above, Crawford et al. teaches “In some embodiments, the nucleic acid sample may comprise DNA from at least two organisms…where the DNA from one of the organisms may be at least 10 times, at least 50 times, or at least 100 times, at least 500 times or at least 1,000 times more abundant than the other” (page 18, lines 4-8). These abundance ratios read on the instant “ratio of target polynucleotide to non-target polynucleotide present in the complex mixture”. Thus, Crawford et al. does disclose the claimed ratio.
Additionally, Thompson teaches “The use of mass tags to detect circularisation events, as disclosed in this invention, has many advantages, since large arrays of isotopic tags can be generated. The use of isotopic tags means that accurate quantification is enabled as the relative abundances of isotope tags are an accurate indicator of the levels of the expression products” (paragraph 0062). Thus, although the Examiner agrees that “Thompson’s method detects the cleaved tag”, Thompson et al. teaches that detection of the cleaved tag enables accurate indication (and detection) of the “actual polynucleotide construct or its products”, as made obvious to the skilled artisan.
Claims 2-3 remain/are rejected under 35 U.S.C. 103 as being unpatentable over Crawford et al. (2018; WO 2018/035062 A1; FOR citation N in PTO-892 filed on 5/20/25) in view of Thompson (2011; US 2011/0118137 A1; USPat citation B in PTO-892 filed on 5/20/25; publication of US application 12/949,208 which claims the priority of provisional application 60/572,464 filed 5/20/04) as applied to claims 1 and 4-7 above, and further in view of Little et al. (2001; US Patent US 6,322,970 B1; USPat citation A in PTO-892 filed on 5/20/25).
The teachings of Crawford et al. in view of Thompson are applied to instantly rejected claims 2-3 as they were previously applied to claims 1 and 4-7 as rendering obvious a method of genetic analysis. The teachings are silent to specifics regarding translation (claim 2 steps (d) – (e) and claim 3), however, these limitations were known in the prior art and taught by Little et al.
Little et al. teaches “Mass Spectrometric Detection of Polypeptides” (Title).
Relevant to claims 2-3, Little et al. teaches “A target polypeptide also can be obtained by in vitro translation of an RNA molecule encoding the target polypeptide; or by in vitro transcription of a nucleic acid encoding the target polypeptide, followed by translation, which can be performed in vitro or in a cell, where the nucleic acid to be transcribed is obtained from a Subject” (column 17, lines 58-63).
This teaching reads on claim 2 (d) translating the RNA products to produce a polypeptide or mixture of polypeptides; (e) detecting, using mass spectrometry, the polypeptide or mixture of polypeptides, wherein detection of the polypeptide or mixture of polypeptides indicates the presence of the sequence of interest in the complex mixture; and claim 3 in vitro transcription and translation are coupled.
Although Crawford et al. in view of Thompson does not disclose the transcription/translation of Little et al., it would have been prima facie obvious to the skilled artisan. Crawford et al., Thompson, and Little et al. are all analogous disclosures to the instant detection methodology.
The skilled artisan would be motivated to include the Little et al. limitations within the detection methodology rendered obvious by Crawford et al. in view of Thompson because Little et al. teaches “Another advantage [of the invention] is that relatively short polypeptides can be synthesized from a target nucleic acid, thus providing an accurate measurement of molecular weight by mass spectrometry, as compared to analysis of the nucleic acid itself” (column 4, lines 9-14).
Thus, the skilled artisan would be motivated to combine the teachings to reach a more accurate detection of target nucleic acids. The skilled artisan would have a reasonable expectation of success based on the disclosures of Crawford et al. in view of Thompson, and further in view of Little et al.
Applicant’s Arguments
Applicant has amended claim 2 to include limitations regarding the ratio of target polynucleotide to non-target polynucleotide and detection of the moiety-target. Applicant argues that the references do not teach the instant ratio of target polynucleotide to non-target polynucleotide present in the complex mixture (Remarks, page 14, paragraph 2, filed 8/19/25). Applicant further argues that “Little does not teach digesting/cleaving target polynucleotides” (Remarks, page 14, paragraph 2, filed 8/19/25).
Response to Applicant’s Arguments
The rejection of claims 2-3 under 35 USC 103 has been revised as stated above in this Final Office Action that specifically addresses the amended limitations of claims 2-3 recited in the Amendments filed 8/19/25.
As discussed within the rejections of claims 1 and 4-7, Crawford teaches the claimed ratio (see Crawford et al. page 18, lines 4-8). Additionally, the Examiner has not asserted that Little et al. teaches digesting/cleaving target polynucleotides. The Non-Final Office Action mailed 5/20/25 noted that “The teachings of Crawford et al. in view of Thompson are applied to instantly rejected claims 2-3 as they were previously applied to claims 1 and 4-7 as rendering obvious a method of genetic analysis. The teachings are silent to specifics regarding translation (claim 2 steps (d) – (f) and claim 3), however, these limitations were known in the prior art and taught by Little et al.” (emphasis added, Non-Final page 11, paragraph 2).
The above Non-Final excerpt attributes the digesting and cleaving of target polynucleotides to Crawford et al., not Little et al. as interpreted by the Applicant. The above excerpt should be interpreted as: the teachings of Crawford et al. in view of Thompson et al. are applied to instantly rejected claims 2-3. Crawford et al. in view of Thompson et al. teaches all of the recited claims 2-3 limitations, however, is silent only to translation relevant to claim 2 steps (d) – (f) and claim 3. Little et al. teaches these silent translation limitations.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claim 1 is/remains rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of U.S. Patent No. 11,046,995 B2 (hereafter patent ‘995; USPat citation C in PTO-892 filed on 5/20/25) in view of Crawford et al. (2018; WO 2018/035062 A1; FOR citation N in PTO-892 filed on 5/20/25) and Thompson (2011; US 2011/0118137 A1; USPat citation B in PTO-892 filed on 5/20/25; publication of US application 12/949,208 which claims the priority of provisional application 60/572,464 filed 5/20/04).
(i) Instant claim 1 steps (a) – (c) are read on by patent ‘995 claims 1-2 (excerpted below).
Relevant to claim 1 steps (a) – (b), the instant method of genetic analysis, comprising: (a) providing a complex mixture comprising a plurality of end-blocked polynucleotides; (b) digesting at least some of the end-blocked polynucleotides… is equivalent to patent ‘995 claim 1 “A method of sample analysis, comprising: (a) digesting a phosphatase-treated mixed nucleic acid sample…”. Patent ‘995 “phosphatase-treated” nucleic acids are equivalent to the instant end-blocked polynucleotides.
Relevant to claim 1 step (c), the instant (c) ligating a moiety to a ligatable end… is equivalent to patent ‘995 claim 2 “ligating an adaptor to the ligatable ends…”.
(ii) Patent ‘995 is silent to specifics regarding ratios of target:non-target polynucleotides (claim 1 step (a)). However, these limitations were known in the prior art and taught by Crawford et al. It is noted that Crawford et al. is the WIPO publication of patent ‘995.
Relevant to claim 1 step (a), Crawford et al. teaches “In some embodiments, the nucleic acid sample may comprise DNA from at least two organisms…where the DNA from one of the organisms may be at least 10 times, at least 50 times, or at least 100 times, at least 500 times or at least 1,000 times more abundant than the other” (page 18, lines 4-8).
This Crawford et al. teaching (also discussed within the above 103 rejections) establishes that the patent ‘995 “mixed nucleic acid sample” can include the instantly claimed ratio of polynucleotides.
(iii) Patent ‘995 is silent to specifics regarding mass spectrometric detection (claim 1 step (d)). However, these limitations were known in the prior art and taught by Thompson.
Relevant to claim 1 step (d), Thompson teaches “f) detecting the mass tag by mass spectrometry. The first aspect of the invention set out above relates to a method for detection of a nucleic acid using a circularizable probe in which a mass tag is present in the probe” (paragraphs 0045-0046).
Further relevant to claim 1 step (d), Thompson teaches “The use of mass tags to detect circularisation events, as disclosed in this invention, has many advantages, since large arrays of
isotopic tags can be generated. The use of isotopic tags means that accurate quantification is enabled as the relative abundances of isotope tags are an accurate indicator of the levels of the expression products” (paragraph 0062).
These teachings read on claim 1 step (d).
(iv) Although patent ‘995 is silent to the Crawford et al. polynucleotide ratios and Thompson mass spectrometers, the skilled artisan would find these limitations prima facie obvious. Patent ‘995, Crawford et al., and Thompson are analogous disclosures to the instant detection methodology.
The skilled artisan would be motivated to include the Crawford et al. polynucleotide ratios within the patent ‘995 methodology because the Crawford et al. disclosure is the WIPO publication linked to patent ‘995. The skilled artisan would find it obvious, and be motivated, to include the Crawford et al. teachings as they provide contextualization for the patent ‘995 methodologies.
The skilled artisan would be motivated to include the Thompson mass spectrometry within the patent ‘995 methodology because Thompson teaches “Mass Spectrometry has been used to detect analyte ions or their fragment ions directly, however for many applications such as nucleic acid analysis, the structure of the analyte can be determined from indirect labeling. This is advantageous particularly with respect to the use of mass spectrometry because complex biomolecules such as DNA have complex mass spectra and are detected with relatively poor sensitivity. Indirect detection means that an associated label molecule can be used to identify the original analyte, where the label is designed for sensitive detection and a simple mass spectrum. Simple mass spectra mean that multiple labels can be used to analyse multiple analytes simultaneously. In fact, many more labels than can currently be used simultaneously in fluorescence-based assays can be generated” (paragraph 0005).
Thus, the skilled artisan would be motivated to include the Thompson mass spectrometry in order to achieve sensitive, multiplexed detection of nucleic acids. The skilled artisan would have a reasonable expectation of success based on the disclosures of patent ‘995 in view of Crawford et al. and Thompson.
Applicant’s Arguments
Applicant has amended claim 1 to include limitations regarding the ratio of target polynucleotide to non-target polynucleotide and detection of the moiety-target polynucleotide. Applicant argues that “independent claim 1 recites the ratio of target polynucleotide to non-target polynucleotide present in the complex mixture is 1:1x103 or lower. The ‘995 patent claims, alone or in combination with Thompson do not disclose or suggest this limitation” (Remarks, page 15, paragraph 4, filed 8/19/25).
Response to Applicant’s Arguments
The rejection of claim 1 under nonstatutory double patenting has been revised as stated above in this Final Office Action that specifically addresses the amended limitations of claim 1 cited in the Amendments filed 8/19/25.
As discussed in the rejection of claim 1 under 35 USC 103, Crawford et al. does teach the claimed ratio (see Crawford et al. page 18, lines 4-8) and Thompson does teach that detection of the cleaved tag enables accurate indication (and detection) of the “actual polynucleotide construct or its products” (Thompson paragraph 0062), as made obvious to the skilled artisan.
Claims 1 and 2 of U.S. Patent No. 11,046,995 B2
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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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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682