DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 112
3. The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
4. Claims 191 and 192 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 191 and 192 each recite the phrase “…the TSR…,” this phrase does not have sufficient antecedent basis in claim 190’s recitation of “a TSR…” because claim 190 states that the first bridge probe and the second probe comprise a TSR, but claims 191 and 192 state that the TSR is located on the 3'/5' portion of the first bridge probe and the second bridge probe. Claims 191 and 192 are written in a way that implies that the TSR is a single TSR that is the same on the first and second bridge probes. It is unclear if this is intended to be the case, or if the TSR on the first and second bridge probes are different as indicated in applicant’s specification and drawings. Therefore, these claims are indefinite.
Claim Rejections - 35 USC § 103
5. 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.
6. This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
7. Claims 170,172-178 and 190-192 are rejected under 35 U.S.C. 103 as being unpatentable over Gross et al (United States Patent Application No. US20210238694, with valid priority to 27 September 2018) in view of Karadeema et al (The owl sensor: a ‘fragile’ DNA nanostructure for the analysis of single nucleotide variations, Nanoscale, 21, published 26 April 2018).
Regarding claim 170, Gross teaches a method of enriching cfDNA corresponding to selective genomic regions using capture probes (i.e., an anchor probe) that are coupled to a solid support after hybridization ([0008] and [0258]).
Regarding claims 172-174, Gross teaches that the capture probe (i.e., the anchor probe) comprises a biotin moiety to facilitate the isolation of target nucleic acids using a streptavidin-coated bead ([0258]).
Regarding claim 175, Gross teaches that an adapter is ligated to the template nucleic acid molecule ([0256]). It is noted that Gross teaches this adapter ligation prior to forming the hybridization complex with the capture probe, however, the courts have held that any order of performing process steps is prima facie obvious in the absence of new or unexpected results (In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930); Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959)). See MPEP §2144.04 IV C., the claimed order of steps is an obvious variant of the steps of the cited prior art.
Regarding claim 176, Gross teaches that the template nucleic acid is cell-free DNA ([0014]).
Regarding claim 177, Gross teaches that the template nucleic acid molecule is methylated ([0018]).
Gross does not teach the limitations of steps (a) and (b), i.e., hybridizing a first target specific region of a first bridge probe to a first target sequence of a template nucleic acid molecule, hybridizing a second target specific region of a second bridge probe to a second target sequence of the template nucleic acid molecule, and hybridizing a first landing sequence of the first bridge probe and a second landing sequence of the second bridge probe to a first and second bridge binding sequence of an anchor probe, thereby forming a complex comprising the template nucleic acid molecule, the first bridge probe, the second bridge probe, and the anchor probe. Additionally, Gross does not teach the limitation wherein the anchor probe does not hybridize directly to the template nucleic acid molecule.
However, Karadeema teaches hybridizing an R probe (i.e., a first bridge probe) and a P probe (i.e., a second bridge probe) to a target nucleic acid via a first and second target specific region, and then hybridizing a molecular beacon (i.e., an anchor probe) to the first and second bridge probes via a first and second landing sequence, respectively, forming a complex comprising a template nucleic acid, a first bridge probe, a second bridge probe, and an anchor probe (Fig. 2A, Owl Sensor). Karadeema teaches that in this complex the anchor probe does not hybridize directly to the nucleic acid template but associates with the template through the R and P probes, that the anchor probe is not covalently attached to the template nucleic acid molecule (Fig. 2A), and that the formation of the complex occurs in solution in the absence of a solid support (Supporting information, pg. 2 ¶ 2).
It would have been obvious to one having ordinary skill in the art to have modified the target capture and enrichment method taught by Gross to have incorporated the bridging probes taught by Karadeema to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this modification because Gross specifically teaches that off-target interactions with hybridization probes must be considered and that probes with unacceptably high off-target risks are filtered out ([0162]), while Karadeema specifically teaches that the dual-adapter design of the ‘owl structure’ was able to significantly reduce off-target binding of even single nucleotide variations (pg. 10117 and Fig. 2). Additionally, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the formation of hybridized nucleic acid complexes.
Regarding claim 178, without additional limitations to the claim the unpaired arm of the R probe (i.e., the first bridge probe) taught by Karadeema is considered an adapter (Fig. 1A and Fig 2A).
Regarding claim 190, Karadeema teaches that the first and second bridge probes (i.e., the R and P probes) comprises a target specific region that hybridizes to an analyte (i.e., a target sequence), an adapter landing sequence that hybridizes to an anchor probe (e.g., the capture probe taught by Gross), and a linker region connecting the target specific region and the adapter landing sequence (e.g., the unpaired regions of the R and P probes; Fig. 1A).
Regarding claims 191 and 192, without additional limitation to these claims the “3' portion” is being interpreted as any portion that is not at the immediate 5' end of the bridge probe, and the “5' portion” is interpreted as any portion that is not immediately at the 3' end of the bridge probe. Therefore, Karadeema’s teaching of the TSR in the middle of the bridge probe meets these limitations.
8. Claims 179-182 are rejected under 35 U.S.C. 103 as being unpatentable over Gross et al (United States Patent Application No. US20210238694, with valid priority to 27 September 2018) in view of Karadeema et al (The owl sensor: a ‘fragile’ DNA nanostructure for the analysis of single nucleotide variations, Nanoscale, 21, published 26 April 2018) as applied to claim 178 above, and further in view of Guoliang et al (International Patent Application No. WO2018193233, published 25 October 2018).
Regarding claim 179, the method of claim 178 is discussed fully above and incorporated here. Neither Gross nor Karadeema teach that the complex is contacting with a 3' to 5' exonuclease.
However, Guoliang teaches an embodiment wherein a target nucleic acid is hybridized to a 3' hairpin capture probe, and the template nucleic acid is “trimmed” at the 3' end to remove any excess material not hybridized to the capture probe ([Page 21, lines 9-11]) and that this trimming is performed by a polymerase having 3' to 5' exonuclease activity (i.e., a 3' to 5' exonuclease [Page 28, lines 17-19]).
It would have been obvious to one having ordinary skill in the art to have modified the method taught by Gross in view of Karadeema to have trimmed the 3' end of the target nucleic acid with a 3' to 5' exonuclease as taught by Guoliang to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this substitution in order to clean-up/end repair the 3' end of the target nucleic acid in preparation for an extension assay as taught by Guoliang. In addition, it would have been obvious to one having ordinary skill in the art that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the preparation of nucleic acid molecules for sequencing.
Regarding claim 180, Guoliang teaches extending the end of the target nucleotide using the ATO (i.e., the adapter) as a template (FIG. 1C and pg. 10 ¶ 3).
Regarding claim 181, Gross teaches that an extension primer is hybridized to a sequence included in the adapter is used to form a double stranded DNA molecule (i.e., a second extension product is generated; [0256]).
Regarding claim 182, Gross teaches that the captured nucleic acid fragments are amplified by PCR enrichment ([0258]). This process inherently comprises hybridizing a target specific primer to the second extension product and extending the target specific primer to generate a third extension product.
Response to Arguments
9. Applicant's arguments filed 23 June 2026 have been fully considered but they are not persuasive.
Applicant’s amendments to claims 191 and 192 have addressed the previously applied rejections under U.S.C. § 112(b) in the Office Action dated 06 April 2026, however these amendments have necessitated new grounds of rejection as applied above.
On pg. 6 ¶ 2 and pg. 7 ¶ 2 of applicant’s remarks, applicant makes arguments related to the teachings of Gross and Karadeema individually. 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). Applicant further argues that even in combination, Gross and Karadeema do not teach forming the claimed bridge-probe/anchor-probe complex in solution and then subsequently coupling the indirect anchor probe to a solid support. This argument is not found persuasive because, as discussed fully above, Gross teaches that the captured cfDNA is coupled to a solid support after hybridization ([0008] and [0258]) and Karadeema teaches a complex corresponding to the bridge-probe/anchor-probe complex is formed in solution (supporting information pg. 2 ¶ 2). Therefore, the combination of these references teaches the formation of the claimed complex prior to coupling it to a solid support.
In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, Karadeema specifically teaches a dual adapter design that significantly reduces off-target binding of even single nucleotide variations (pg. 10117 and Fig. 2) and Gross specifically teaches that off-target interactions with hybridization probes must be considered ([0162]). The ordinary artisan would have been motivated by the teachings of Gross to have explored methods to reduce off-target binding, such as those taught by Karadeema, to arrive at the instantly claimed invention with a reasonable expectation of success.
Applicant additionally argues on pg. 6 ¶ 3 that “Karadeema is a fundamentally different system than the present claims.” However, the MPEP states that in order for a reference to be relied upon in an obviousness rejection it must be ‘analogous art’ to the claimed invention, either within ‘same/relevant field of endeavor’ or ‘reasonably pertinent’ to the problem faced by the inventor (MPEP 2141.01(a)(I)). In order to determine if a reference meets the criteria for the ’relevant field of endeavor,’ the MPEP states that “the field of endeavor is ‘not limited to the specific point of novelty, the narrowest possible conception of the field, or the particular focus within a given field.’” Karadeema is considered to be analogous art because it is in a relevant field of endeavor (i.e., the use of nucleic acid hybridization strategies for the highly specific detection of nucleic acid targets via the formation of nucleic acid complexes) for the instantly claimed invention (i.e., the formation of structured nucleic acid complexes to pull down specific nucleic acid targets).
For these reasons, applicant’s arguments are not found persuasive and the rejections under U.S.C. § 103 are maintained.
10. 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.
Conclusion
11. No claims are allowed.
12. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-T 0800 - 1630.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached on (571) 272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
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