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 .
DETAILED ACTION
Status of the Application
1. Claims 1-18 and 20-21 are pending and are considered for examination. Claims 19 and 22-50 are canceled.
Priority
2. This application filed on June 07, 2024 claims priority to US 63/507,029 filed on June 08, 2023.
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.
Claims 3-5 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 3 recites the limitation "the region" in line 1 of the claim. There is insufficient antecedent basis for this limitation in the claim because claim 1 upon which the claim 3 depends lack support for said limitation and it is not clear what the limitation is referring to.
Claim Rejections - 35 USC § 103
4. 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art. 2. Ascertaining the differences between the prior art and the claims at issue. 3. Resolving the level of ordinary skill in the pertinent art. 4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-18 and 20-21 are rejected under 35 U.S.C. 103 as being unpatentable over Yin et al. (US 2021/0285036) in view of So et al. (US 2018/0245142).
Yin et al. teach a method of claim 1, sequencing a polynucleotide, the method comprising: hybridizing the polynucleotide to a first oligonucleotide coupled to a particle (dissolvable, or degradable particle) (para 1121-1122, 1326-1327, 1353-1553-1558, 0980-0982, 0644-0655, 0693, 0830-0844, 0726); amplifying the hybridized polynucleotide using additional oligonucleotides coupled to the particle, to generate amplicons coupled to the particle (para 1121-1122, 1326-1327, 1353-1553-1558, 0980-0982, 0693, 0830-0844, 0726); after the amplifying, disposing the particle, having the amplicons coupled thereto, within a flowcell; after disposing the particle within the flowcell, dissolving the particle and using the flowcell to sequence the amplicons (para 1121-1122, 1166-1168, 1553-1558, 0980-0982, 1326-1327, 0644-0655, 0159, 0337, 0424-0425, 0830-0844, para 0159).
With reference to claim 2, Yin et al. teach that disposing the particle, having the amplicons coupled thereto, within the flowcell comprises electrostatically attracting the particle or the amplicons to a region of the flowcell (para 0466-0467).
With reference to claims 3-5, Yin et al. teach that the region of the flowcell comprises a recess wherein the recess (wells, ridges, features, projections or markings) comprises a hydrogel and the recess comprises a plurality of positively charged moieties (para 0583-0584, 0568, 0617, 0371, 1166).
With reference to claims 6-7, 9-10, Yin et al. teach that the particle is dissolved while using the flowcell to sequence the amplicons or the particle is dissolved before using the flowcell to sequence the amplicons (para 1166, 0844, 0337).
With reference to claim 8, Yin et al. teach that wherein the oligonucleotides are coupled to a polymer that is coupled to the particle (para 0673-0678, 0726-0730).
With reference to claim 11, 18, Yin et al. teach that the polymer and the amplicons are removed using a basic solution (organic solvent) (para 0337).
With reference to claim 12, Yin et al. teach that the polymer is coupled to the particle via a siloxane (-Si-O-Si-) bond (para 1210).
With reference to claim 13, Yin et al. teach that the polymer comprises polyacrylamide (para 0573-0576, 0583-0584, 0617,0677-0678, 0726-0727).
With reference to claims 14-16, Yin et al. teach that both before and after the particle is dissolved, the polymer is covalently coupled to the amplicons is non-covalently coupled to the flowcell (para 1478-1479, 0573).
With reference to claim 17, Yin et al. teach that the particle comprises silica (para 0644-0647, 0712, 0726).
Yin et al. teach a method of Claim 20, sequencing a polynucleotide using a particle having a plurality of oligonucleotides coupled thereto, the method comprising: using the plurality of oligonucleotides to generate amplicons of the polynucleotide that are coupled to the particle; disposing the particle, having the amplicons coupled thereto, within a flowcell; after disposing the particle within the flowcell, dissolving the particle; and using the flowcell to sequence the amplicons (para 1353-1359, 1470-1476, 1656-1661, 0830-0844, 0337).
With reference to claim 21, Yin et al. teach that a method of using a flowcell, the method comprising: disposing a first particle, having a first set of polynucleotide amplicons coupled thereto, within the flowcell; dissolving the first particle, leaving the first set of polynucleotide amplicons within the flowcell; using the flowcell to sequence the first set of polynucleotide amplicons; after sequencing the first set of polynucleotide amplicons, removing the first set of polynucleotide amplicons from the flowcell; and after removing the first set of polynucleotide amplicons from the flowcell, disposing a second particle, having a second set of polynucleotide amplicons coupled thereto, within the flowcell (para 1353-1359, 0830-0844, 0337).
Although Yin et al. teach dissolvable particle (para 0644-0655, 0844, 0337), Yin et al. specifically did not teach leaving amplicons within a flowcell.
So et al. teach a method of sequencing a polynucleotide in a flowcell, the method comprising: hybridizing the polynucleotide to a first oligonucleotide coupled to a particle; amplifying the hybridized polynucleotide using additional oligonucleotides coupled to the particle, to generate amplicons coupled to the particle (para 0195-0197, 0156, 0162, 0575-0579, 0627, 0540); after the amplifying, disposing the particle, having the amplicons coupled thereto, within a flowcell; after disposing the particle within the flowcell, and leaving the amplicons within the flowcell; and sequencing the amplicons in the flow cell (para 0195-0203, 0575-0579, 0627, 0156, 0162-0163, 0540).
It would have been prima facie obvious to a person of ordinary skill in the art before the effective filling date of the invention to combine the method of Yin et al. with the method as taught by So et al. to develop an improved method for sequencing a polynucleotide. The ordinary person skilled in the art would have motivated to combine the method as taught by Yin et al. with the amplicon with a flow cell as taught by So et al. and have a reasonable expectation of success that the combination would result in
improved method for detecting a target nucleic acid because So et al. explicitly taught
amplification in a flowcell and leaving the amplicon anchored within the flowcell for sequencing the amplicons in the flow cell (para 0195 -0197) and such a modification of the method is considered obvious over the prior art.
Conclusion
No claims are allowable.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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