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 .
Election/Restrictions
2. Applicant’s election of 1) agar as the “polymer” species (thus claim 2 is withdrawn as being drawn to non-elected species) and 2) the species of claim 7 (thus claim 8 is withdrawn as being drawn to non-elected species) in the reply filed on 6/30/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
3. Claims 1-8 are pending in the application. Claims 2 and 8 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Claims 1 and 3-7 are currently under examination.
Claim Rejections - 35 USC § 102
4. In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
5. 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.
6. Claims 1 and 4 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Ramirez et al. (WO 2018/208561 A1).
Regarding claim 1
Ramirez et al. teach, throughout the whole document (e.g., see Abstract; paragraphs [0005]-[0007], [0038]-[0041], [0059]-[0060] and [0253]; Figures 1-4; claims 1, 4-5 and 9), a sequencing kit comprising: (1) a flow cell including: a plurality of chambers (e.g., depressions separated by interstitial regions), and primers attached within each of the plurality of chambers (see paragraphs [0005]-[0007] and [0038]-[0041]; Figures 1-4; claims 1 and 4-5); and (2) an encapsulation matrix precursor composition (e.g., encapsulation matrix precursor aqueous solution that is used to form a protective coating on the primer) consisting of: a fluid (e.g., water), and a polymer (e.g., a natural polysaccharide or derivative thereof, such as agar, agarose, alginate, pectin, dextran, or cellulose) selected from the group consisting of agar, agarose, alginate, heparin, alginate sulfate, dextran sulfate, hyaluronan, pectin, carrageenan, gelatin, chitosan, cellulose, a collagen polymer, and combinations thereof (see paragraphs [0059]-[0060]).
Regarding claim 4
The sequencing kit according to Ramirez et al., further comprising a sample fluid including genetic material (e.g., DNA to be sequenced) (see paragraphs [0253]-[0254] and [0357]).
Claim Rejections - 35 USC § 103
7. 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 of this title, 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.
8. 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.
9. Claims 1 and 4 are rejected under 35 U.S.C. 103 as being unpatentable over Tsay et al. (WO 2018/119101 A1) in view of Barnard et al. (WO 2014/133905 A1).
Regarding claim 1
Tsay et al. disclose a sequencing kit comprising a flow cell including: a plurality of chambers, and primers attached within each of the plurality of chambers (see the whole document, particularly Abstract; paragraphs [0035]-[0037] and [00164]-[00165]; claims 17 and 20; Figures 3A and 3B). Tsay et al. do not specifically disclose the use of an encapsulation matrix precursor composition to encapsulate target nucleic acids to be sequenced.
However, Barnard et al. disclose, throughout the whole document, an array in a structured substrate such as a flow cell (see page 24, line 20 – page 25, line 8), comprising a solid support comprising a surface, the surface comprising a plurality of wells, the wells containing a gel material; and a library of target nucleic acids in the gel material (see Abstract; claim 1). The formation of the gel material involves the use of a gel-forming precursor composition (i.e., encapsulation matrix precursor composition) in a liquid state that is subsequently converted to a gel, wherein the gel-forming precursor composition consists of a fluid/liquid and a polymer such as agar, agarose, or gelatin (see page 21, line 23 – page 22, line 21). The array can be used in a sequencing procedure, such as a sequencing-by-synthesis (SBS) technique (see page 36, lines 12-30).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to encapsulate target nucleic acids by using a gel-forming precursor composition (i.e., encapsulation matrix precursor composition), as taught by Barnard et al., in the sequencing kit of Tsay et al. thus arriving at the instantly claimed invention, because encapsulating target nucleic acids by using an encapsulation matrix precursor composition was an art-recognized way of producing an array of target nucleic acids in a flow cell for high-throughput sequencing. In addition, combining prior art elements according to known methods to yield predictable results is considered prima facie obvious (see MPEP 2143.I.A). Given the teachings of the prior art and the level of the ordinary skilled artisan at the time of the application’s effective filing date, it must be considered, absent evidence to the contrary, that said skilled artisan would have had a reasonable expectation of success in practicing the claimed invention.
Regarding claim 4
The sequencing kit according to Tsay et al. in view of Barnard et al., further comprising a sample fluid including genetic material (e.g., target nucleic acid) (see Tsay et al., paragraphs [00164]-[00165]. Also see Barnard et al., page 3, lines 4-13; paragraph bridging pages 7-8.).
10. Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Tsay et al. (WO 2018/119101 A1) in view of Barnard et al. (WO 2014/133905 A1) as applied to claim 1 above, and further in view of Fisher et al. (US 2015/0176071 A1).
Tsay et al. in view of Barnard et al. teach the sequencing kit of claim 1 as discussed above. Tsay et al. in view of Barnard et al. do not specifically disclose the use of a library preparation solution including adapter sequences and transposomes.
However, Fisher et al. teach that, to generate the target nucleic acid fragments for sequencing analysis (see the whole document), a library preparation solution including adapter sequences and transposomes may be used (see paragraphs [0093]-[0097] and [0171]).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to use a library preparation solution including adapter sequences and transposomes, as taught by Fisher et al., in the sequencing kit of Tsay et al. in view of Barnard et al. thus arriving at the instantly claimed invention, because a library preparation solution including adapter sequences and transposomes would enable simultaneously attachment of sequencing adapters while generating the target nucleic acid fragments during library preparation, thus making the library preparation more efficient with less steps (i.e., without an additional step to attach sequencing adapters). Given the teachings of the prior art and the level of the ordinary skilled artisan at the time of the application’s effective filing date, it must be considered, absent evidence to the contrary, that said skilled artisan would have had a reasonable expectation of success in practicing the claimed invention.
11. Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Ramirez et al. (WO 2018/208561 A1) as applied to claim 1 above, and further in view of Fisher et al. (US 2015/0176071 A1).
Ramirez et al. teach the sequencing kit of claim 1 as discussed above. Ramirez et al. do not specifically disclose the use of a library preparation solution including adapter sequences and transposomes.
However, Fisher et al. teach that, to generate the target nucleic acid fragments for sequencing analysis (see the whole document), a library preparation solution including adapter sequences and transposomes may be used (see paragraphs [0093]-[0097] and [0171]).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to use a library preparation solution including adapter sequences and transposomes, as taught by Fisher et al., in the sequencing kit of Ramirez et al. thus arriving at the instantly claimed invention, because a library preparation solution including adapter sequences and transposomes would enable simultaneously attachment of sequencing adapters while generating the target nucleic acid fragments during library preparation, thus making the library preparation more efficient with less steps (i.e., without an additional step to attach sequencing adapters). Given the teachings of the prior art and the level of the ordinary skilled artisan at the time of the application’s effective filing date, it must be considered, absent evidence to the contrary, that said skilled artisan would have had a reasonable expectation of success in practicing the claimed invention.
Allowable Subject Matter
12. Claims 5-7 are allowed because the prior art of record does not teach the feature of “flushing the flow cell with a liquid external immobilization agent at a temperature ranging from about 40°C to about 80°C” as required by the method of claim 5.
Conclusion
13. Claims 1 and 3-4 are rejected; claims 5-7 are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAIJIANG ZHANG whose telephone number is (571)272-5207. The examiner can normally be reached Monday - Friday, 8:30 am - 5 pm.
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/KAIJIANG ZHANG/Primary Examiner, Art Unit 1684
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