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 .
Election/Restrictions
Applicant’s election without traverse of Group I in the reply filed on March 13, 2026 is acknowledged.
The Office acknowledges the cancelation of claims 39-49, 50-61, 80-86, and 93 drawn to nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on March 13, 2026.
Information Disclosure Statement
The IDS received on November 17, 2023 and December 8, 2023are proper and are being considered by the Examiner.
The IDS filed on April 4, 2025 is deemed non-compliant as the requirements under 37 CFR 1.98(a)(4). The IDS has been filed but the cited references therein have not been considered.
Drawings
The drawings received on November 17, 2023 are acceptable.
Claim Rejections - 35 USC § 112
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.
Claims 19, 25, 26-29, 31-38, 65, 70-72, and 87-92 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.
Claim 19 is indefinite because it is unclear what the difference between claim 19 and the parent claim 18 is. Claim 18 is drawn to a composition comprising, inter alia, “two or more probe oligonucleotides.” Claim 19 recites the phrase, “the two or more probe oligonucleotides comprises a plurality of probe oligonucleotides,” which is no different than two or more in scope. While the claim recites an additional functional language of, “capable of specifically hybridizing to a plurality of nucleic acid targets under hybridization condition,” the parent claim 18 already recites that the two or more probe oligonucleotides (i.e., plurality) comprises, “target-binding region” implying that the probe oligonucleotides anneal to their targets specifically under a hybridization condition.
Therefore, it is indeterminable what differences exist between claims 18 and 19.
Claim 25 recites the phrase, “each strand of the first primer-binding region and the second primer-binding region”. It is unclear what this means because the phrase could be referring to a first primer-binding region and a second primer-binding region on the same strand of a probe oligonucleotide; or a first primer-binding region of a probe oligonucleotide and to a second primer-binding region of a different probe oligonucleotide. For the purpose of prosecution, the former interpretation is adopted.
Claim 26 is indefinite for the following reasons.
Claim 26 depends from claim 24. Claim 24 recites that the enhancer oligonucleotides comprise a mixture of oligonucleotides capable of hybridizing to the first primer binding region and the second primer binding region. Claim 26, then recites that the mixture comprises a mixture of four oligonucleotides, each capable of hybridizing to a strand of the first primer binding site or the second primer binding site. This is indefinite because the parent claim requires that mixture of enhancer oligonucleotides must anneal to both the first and second primer binding sequences while a dependent claim appears to now broaden that to an alternative (i.e., anneal to first or second primer binding sequences).
Claims 27, 37, 38, 71, and 72 are indefinite for the same reason.
Claims 28, 29, and 31-38 are indefinite because the claims appear to be duplicate to that of claims 18-27 for the following reasons.
Claim 28 is directed to a composition comprising two or more probe oligonucleotides, each probe oligonucleotide comprising a target-binding region, and a first primer-binding region and a second primer-binding region, which is no different than claim 18. The composition of claim 28 also comprises one or more enhancer oligonucleotides capable of hybridizing to at least one of the primer-binding regions, and while slightly different in wording, is identical to element (b) of claim 18.
Claims 29, 31, 32, 33, 34, 35, 36, 37, and 38 are then identical in breadth to claims 19, 20, 21, 22, 23, 24, 25, 26, and 27.
Claims 35 and 70 are also indefinite for the same reason as claim 25 discussed above.
Claim 65 recites the limitation, “wherein hybridization conditions are”. There is an insufficient antecedent basis for this limitation in the claim. For the purpose of prosecution, the claim has been construed to depend from claim 63.
Claim 87 recites the phrase, “each enhancer oligonucleotide is capable of hybridizing to the first primer-binding region and/or the second primer-binding region.” It is unclear how a single enhancer oligonucleotide is annealing to both primer binding regions. The application does not appear to support for this embodiment and therefore, the claim has also been rejected under New Matter.
Claims 88-92 are rejected by way of their dependency on claim 87.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 87-92 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new matter rejection.
Claim 87 recites the phrase, “each enhancer oligonucleotide is capable of hybridizing to the first primer-binding region and/or the second primer-binding region.” These claims have been filed in a post-filing claim set and does not appear to find support. Applicants are requested to point to the application where such support can be found.
Claims 88-92 are rejected by way of their dependency on claim 87.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 18-20, 22-31, 33-38, 62-65, and 67-72 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Juneau, Kara (US 2021/0054451 A1, published February 25, 2021, priority August 19, 2019).
A product is defined by its physical attributes and not by its intended usage, absent said usage necessarily confers/implies a structural limitation. The present rejection is based on the product by its structural limitations as the intended usage does not appear to necessarily confer a structural limitation.
With regard to claims 18 and 22, Juneau teaches a composition for nucleic acid hybridization, comprising the below structure (reproduced from FIG. 1A and B):
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As seen, Juneau teaches a composition comprising: a) two or more oligonucleotides (101 and 102, Fig. 1A), wherein each probe comprises a target-binding region (see 3’ ends of the two oligonucleotides that anneal to the target 107), a first primer binding-region (see regions 104 and 110, respectively), and a second primer-binding region (see regions 103 and 111, respectively); and b) one or more enhancer oligonucleotides, wherein the enhancer oligonucleotides are capable of hybridizing to at least one of the primer binging regions (see 112 and 113 of Fig. 1B annealing to regions 103 and 111, respectively).
With regard to claims 19 and 20, the two or more oligonucleotides (101 and 102) are capable of specifically annealing to a plurality of nucleic acid targets under hybridization conditions (“target DNA binding sites”, section [0058]).
With regard to claims 23-27, 34-38, and 68-72, the region 103 (or 111) can be construed as having a first and second primer binding domain. This is because the claim does not explicitly require a structural distinction of how a first and a second primer binding sequence are present on the two or more oligonucleotides. And the oligonucleotide 113 binds to both of such regions found on region 103 of the oligonucleotide probe 101 (and similarly applied for oligonucleotide probe of 102).
With regard to claims 26 and 27, the composition comprises a plurality of the SP2 oligonucleotides (therefore more than 4), capable of hybridizing to first or second primer binding region via base complementarity (that requires Watson-Crick base pairing).
Claims 28, 29, 31, and 33 are rejected as they are duplicates of the above rejected claims.
Claim 30 is also rejected because the above-discussed oligonucleotides are contacted with a sample that comprises target and non-target nucleic acids (“preparing a sample for SBS”, section [0009]; “target DNA for 107 for amplification by SP1 … may be DNA amplificons”, section [0066]).
With regard to claim 62, the amplification reaction employing the above oligonucleotides would necessarily be in a reaction mixture.
Claims 63, 65, 67, 71, and 72 are rejected as the limitations of the probe oligonucleotides and enhancer oligonucleotides are addressed above and because they are used in a reaction, they are necessarily present in a “reaction mixture.”
With regard to claim 64, the target nucleic acid is from a genomic DNA of an organism (“target sequence can be a genomic locus or extrachromosomal locus”, section [0046]).
Therefore, Juneau anticipates the invention as claimed.
Claims 18, 21 and 66 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kim, D. H. (US 2015/0051116 A1, published February 19, 2015).
A product is defined by its physical attributes and not by its intended usage, absent said usage necessarily confers/implies a structural limitation. The present rejection is based on the product by its structural limitations as the intended usage does not appear to necessarily confer a structural limitation.
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With regard to claim 18, Kim teaches a composition comprising the below reproduced configuration (from Figs. 9 and 10):
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As seen, Kim teaches a composition comprising two or more probe oligonucleotides (see two double-stranded oligonucleotides appended at each of the ends of the target amplicon), wherein each oligonucleotide comprises a target binding region (the “right-side” of the oligonucleotide probe that get ligated to the target nucleic acid), a first primer binding region and a second primer-binding region (see universal sequence_C and Universal sequence A); and one or more enhancer oligonucleotides, wherein the enhancer oligonucleotides are capable of hybridizing to at least one of the primer-binding regions (see ST-PCR-R-v1 and PCR1 primers that anneal).
With regard to claims 21 and 66, the probes are double-stranded.
Therefore, Kim anticipates the invention as claimed.
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 62, 73, 74, 79, 87-92 are rejected under 35 U.S.C. 103 as being unpatentable over Juneau, Kara (US 2021/0054451 A1, published February 25, 2021, priority August 19, 2019).
The teachings of Juneau have already been discussed above.
Juneau, while explicitly teaching that the target DNA are from various sources (“‘target sequence’, or ‘genomic target locus’ refer to any locus in vitro or in vivo, or in a nucleic acid (e.g., genome or episome) of a cell or population of cells, in which sequencing is desired …”, section [0046]), do not explicitly teach that the plurality of nucleic acids comprising the target nucleic acid and non-target nucleic acids constitutes genomic DNA of an organism, a library formed from a genomic DNA of an organism (claims 73 and 74), or that the oligonucleotides are enclosed in a kit (claims 87 and 88), with reagents for separation of nucleic acids (claim 89), reagents for forming a library (claim 90), amplifying (claim 91) and sequencing (claim 92), or having a capture moiety (claim 79).
However, 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 apply the teaching of Juneau and the conventionally available application in the diagnostics, thereby arriving at the invention as claimed for the following reasons.
As far as the claims directed to a kit, packaging the oligonucleotides into a kit as a commercially available product would have been an obvious application of providing pre-packaged, pre-weighed solution of the disclosed assay.
As regard to packaging reagents, such as isolation of nucleic acids, buffers for stabilizing nucleic acids, substrates utilized in a polymerase reaction base addition, and sequencing, doing so would have been obvious because the assay disclosed by Juneau required sample preparation, isolation, and extension reactions with a polymerase in the presence of buffers and reagents (see section [0086], [0087], [0090]), and packaging such reagents together with the oligonucleotides would have been a convenient way of providing a kit which provides all the necessary elements of the assay.
As regard to the sources of the target DNA which could be assayed by the method of Juneau, while the artisan did not explicitly list all types of organism from which the method could be utilized, applying the method of Juneau to process samples from various organisms have been obvious as doing so have been routine in the field of research, diagnostics.
As to conjugating a capture moiety to the oligonucleotides of Juneau, doing so would have been obvious for the purpose of isolating the products so that the produced products could be used in a sequence read, via biotin-streptavidin capture, or bead/column capture which are routine in the art of molecular biology, yielding no more than a predictable outcome.
In KSR, the Supreme Court particularly emphasized “the need for caution in granting a patent based on the combination of elements found in the prior art,” Id. at 415, 82 USPQ2d at 1395, and discussed circumstances in which a patent might be determined to be obvious. Importantly, the Supreme Court reaffirmed principles based on its precedent that “[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” Id. at 415-16, 82 USPQ2d at 1395. The Supreme Court stated that there are “[t]hree cases decided after Graham [that] illustrate this doctrine.” Id. at 416, 82 USPQ2d at 1395. (1) “In United States v. Adams, . . . [t]he Court recognized that when a patent claims a structure already known in the prior art that is altered by the mere substitution of one element for another known in the field, the combination must do more than yield a predictable result.”
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
Claims 75-78 are free of prior art, but are objected to for being dependent on a rejected base claim.
Juneau nor Kim (or record) provide a sufficient motivation to apply the respective teachings to a library of nucleic acids which already comprise a plurality of adapters (or “at least adapters”) because the method of Juneau and Kim was for the purpose of generating a sequencing read from a target DNA by attaching primer/tag sequences at the respective ends of the target DNA. Because the oligonucleotides employed by the artisans served as “adapters” which were attached to the target DNA molecules, there wouldn’t have been any motivation to utilize them to target DNA molecules which already contained additional adapters.
Inquiries
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Young J. Kim whose telephone number is (571) 272-0785. The Examiner can best be reached from 7:30 a.m. to 4:00 p.m (M-F). The Examiner can also be reached via e-mail to Young.Kim@uspto.gov. However, the office cannot guarantee security through the e-mail system nor should official papers be transmitted through this route.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner's supervisor, Gary Benzion, can be reached at (571) 272-0782.
Papers related to this application may be submitted to Art Unit 1681 by facsimile transmission. The faxing of such papers must conform with the notice published in the Official Gazette, 1156 OG 61 (November 16, 1993) and 1157 OG 94 (December 28, 1993) (see 37 CFR 1.6(d)). NOTE: If applicant does submit a paper by FAX, the original copy should be retained by applicant or applicant’s representative. NO DUPLICATE COPIES SHOULD BE SUBMITTED, so as to avoid the processing of duplicate papers in the Office. All official documents must be sent to the Official Tech Center Fax number: (571) 273-8300. Any inquiry of a general nature or relating to the status of this application should be directed to the Group receptionist whose telephone number is (571) 272-1600.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/YOUNG J KIM/Primary Examiner
Art Unit 1637 July 11, 2026
/YJK/
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