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 May 21, 2026 is acknowledged.
Claims 18-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on May 21, 2026.
Information Disclosure Statement
The IDS received on July 15, 2024 and May 21, 2026 are proper and are being considered by the Examiner.
Patent document 9, US 2003/008259, having the inventor name, “Kuo et al.” has been lined-through as the patent has nothing to do with the subject matter of the application (Kuo et al. patent is directed to “Dental Decals”).
Drawings
The drawings received on December 20, 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 7 and 10 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 7 recites the phrase, “primer is hybridized to the extension product”.
There is an insufficient antecedent basis for the “extension product,” but rather for the “amplification product.”
Claim 10 contains a period between the word, “tissue” and “said” in the preamble. This appears to be a typographical error.
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 1-17 are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al. (WO 2019/199579 A1, published October 17, 2019) in view of Yamada et al. (Environmental Microbiology, January 2008, vol. 10, no. 4, pages 978-987).
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With regard to claims 1, 8, and 9, Wang et al. teach an assay named, “SNAIL,” depicted in Fig. 1A (reproduced below):
As seen, Wang et al. teach a method of generating an amplification product, the method comprising the steps of: (a) contacting a target polynucleotide in a cell or tissue with an oligonucleotide comprising a target hybridization sequence, a first hybridization sequence and a second hybridization sequence (see, “contacting a fixed and permeabilized intact tissue with a pair of oligonucleotide primers … the pair of primers comprise a first oligonucleotide … comprises a first complementarity region, a second complementarity region, and a third complementarity region; wherein the first complementarity region of the first oligonucleotide is complementary to a first portion of the target nucleic acid, wherein the second complementarity region of the first oligonucleotide is complementary to the first complementarity region of the second oligonucleotide, wherein the third complementarity region of the first oligonucleotide is complementary to the third complementarity region of the second oligonucleotide” [0004]), wherein said target hybridization sequence is complementary to a target sequence of said target polynucleotide; (b) hybridizing a circularizable oligonucleotide, wherein said circularizable oligonucleotide comprises a first sequence complementary to the first hybridization sequence and (equivalent to the second complementarity region above) and a second sequence complementary to the second hybridization sequence (equivalent to the third complementarity region above); (c) extending the second sequence with a polymerase to generate a complementary region (i.e., ligate the gap of the padlock) and ligating said complementary sequence to the first sequence, thereby generating a circular oligonucleotide (see below from Fig. 1A, also “adding
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ligase to ligate the second oligonucleotide and generate a closed nucleic acid circle”, section [0004]); and (e) amplifying the circular oligonucleotide, thereby generating an amplification product (see left-figure).
With regard to claim 10, the method is performed in a cell or tissue that has been permeabilized or immobilized to a solid support (see above).
With regard to claim 2, the artisans also teach using a plurality of oligonucleotides having specificity to different target nucleic acids (see section [00137], “method … wherein the contacting the fixed and permeabilized intact tissue comprises hybridizing a plurality of oligonucleotide primers having specificity for different target nucleic acids”).
With regard to claim 3, the amplification product is detected (“amplification product can be readily detected by binding to a detection probe”, section [0070]).
With regard to claim 4, the amplicons are detected with detectable label (“a detectable label can be used to detect one or more amplicons”, section [0086]).
With regard to claims 5 and 6, the amplicon is sequenced (“the disclosed method … include integrating an improved sequencing-by-ligation process”, section [0032]; “imaging the one or more hydrogel-embedded amplicons to determine in situ gene sequencing of the target nucleic acid in the cell in the intact tissue”, section [0045]).
With regard to claim 11, the polymerase is phi29 DNA polymerase and incubation at 30oC for two hours (see section [0072], a known strand-displacement polymerase, “samples were washed … incubated with RCA mixture … Phi29 DNA polymerase … at 30oC for two hours under agitation”, section [00146]).
With regard to claim 14, the target hybridization sequence is about 5 to about 35 nucleotides in length (“the first complementarity region of the first oligonucleotide may have a length of 19-25 nucleotides”, section [0056]).
With regard to claims 15-17, the barcode is at least 5 bases (see section [00179], “[a] 5-base barcode (library size of 1,024) was designed and built into each padlock probe as a gene-unique identifier to be sequenced, thus enabling multiplexed gene detection”).
The barcode of Wang et al. is designed into the second primer that ligates to a circular probe, and not on the first primer that anneals to a target nucleic acid (claims 1 and 10, in-part).
Wang et al. do not explicitly teach all types of sequencing means which could be employed for sequencing the RCA product, such as incorporation of a labeled nucleotide/analogue to a sequencing primer (claim 7), or that the oligonucleotide (or first primer) comprises LNA (claim 12), or the size of the circular probe (claim 13).
Yamada et al. teach a well-known advantage of utilizing LNA analogs in a primer in an RCA which improves sensitivity:
“we demonstrate that the sensitivity of IPCR dramatically increased when target DNA sequences were pre-amplified by RCA using LNA-containing site-specific primers”, page 979, 1st column, bottom paragraph to 2nd column, 1st paragraph)
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 combine the teachings of Wang et al. with Yamada et al., thereby arriving at the invention as claimed for the following reasons.
With regard to moving the barcode sequence from the circularizable primer of Wang et al. to the first primer (as presently claimed), doing so would have been prima facie obvious because the movement of the barcode from one primer to the other primer does not produce an appreciable difference other than that which yields a predictable outcome, that is, generating an RCA product which contains a barcode that is specific to the target gene. The barcode of Wang et al. that is moved to the first primer of Wang et al. instead of the second primer which is circularized (as presently claimed) would have resulted in an RCA product produced from a barcode sandwiched between the sequence of the two ends of the circularized probe (see side-by-side comparison), yielding a same predictable outcome of generating a sequenceable RCA product which comprises a barcode that is specific and identifies the target from which it was produced:
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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.”
As to the utilization of LNA bases into the first primer of Wang et al. that anneals specifically to the target nucleic acid, doing so would have been well-within the purview of the ordinarily skilled artisan based on the well-recognized advantage provided by LNA bases which allow for enhanced target-specificity in primers/probes. In view of such well-known advantage, as well as Yamada’s demonstration of using LNA incorporated primer in an RCA reaction, one of ordinary skill in the art would have also had a reasonable expectation of success at realizing the same advantage by incorporating LNA bases into the first primer of Wang et al.
With regard to the size of the circular oligonucleotide probe when ligated being about 100 to about 1000 bases in length, one of ordinary skill in the art would have been capable of adjusting the size of the various sections of the second primer that forms the circular probe accordingly to yield an RCA product for sequencing for optimal purposes.
Wang et al. explicitly teach that each of the sections of the second primer (which forms the circular probe) results in approximately 55 nucleotides without the length of the barcode:
“the second complementarity region of the first oligonucleotides has a length of 3-10 nucleotides … the third complementarity region of the first oligonucleotide has a length of about 3-10 nucleotides” (section [0056])
“the target site of the second oligonucleotide may refer to the second complementarity region … the second complementarity region of the second oligonucleotide may have a length of 19-25 nucleotides … the first complementarity region of the … [second]1 oligonucleotide has a length of 3-10 nucleotides … the third complementarity region of the second oligonucleotide has a length of 3-10 nucleotides …” (section [0057])
While the artisans did not explicitly teach all possible lengths of the regions including the barcode that may result in the total length of circular probe being in the range of 100-1000 nucleotides, doing so would have been well-within the purview of the ordinarily skilled artisan for the purpose of generating a sequenceable product that is of optimum characteristis.
Lastly, with regard to utilizing any of conventional means of sequencing the RCA product such as sequencing-by-synthesis (i.e., incorporation of labeled/detectable nucleotides), doing so has been routine and conventional and given the artisans express suggestion to sequence the RCA product, employing any such sequencing means would have been an obvious alternative to use for the ordinarily skilled artisan.
Therefore, the invention as claimed is deemed prima facie obvious over the cited references.
Conclusion
No claims are allowed.
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 August 6, 2026
/YJK/
1 The document appears to contain a typo referring to first oligonucleotide again, but in context, it is clear that the section is referring to the second oligonucleotide.
Prosecution Insights