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 .
2. The use of the term THERMINATOR, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
NON-PRIOR ART REJECTIONS
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 2, 4-5, and 13-24 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.
A) Claim 5 contains the trademark/trade name THERMINATOR. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a polymerase enzyme and, accordingly, the identification/description is indefinite.
B) Claim 2 is indefinite because ‘the 3’-unblocked protected nucleotide’ lacks proper antecedent basis. Correction is required.
C) Claim 4 is indefinite because ‘the photocleavable terminating group’ lacks proper antecedent basis. Correction is required.
D) Claims 13-18 are indefinite because of the language ‘any one of claim 1’ in claim 13. Correction is required.
E) Claims 19-20 are indefinite because of the language ‘a sequencing primers’ in claim 19, and also because ‘the photocleavable terminating moieties’ in claim 19 lacks proper antecedent basis. Correction is required.
F) Claims 21-24 are indefinite because ‘the detectable moieties’ in claim 21 (three occurrences) lacks proper antecedent basis. These claims are further indefinite because of the term ‘aincorporated’ near the end of claim 21. Correction is required.
G) Claim 23 is indefinite because ‘the first light’ lacks proper antecedent basis. Correction is required.
H) Claim 24 is indefinite because ‘the second light’ and ‘the detectable moieties’ lack proper antecedent basis. Correction is required.
PRIOR ART REJECTIONS
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 (i.e., changing from AIA to pre-AIA ) 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.
Claims 1-4, 7-10, and 13-16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wimberger-Friedl et al. (US 2015/0079585).
Regarding independent claim 1, Wimberger-Friedl discloses a sequencing method comprising: contacting a substrate polynucleotide immobilized to a substrate with a protected nucleotide and a sequencing primer and a polymerase, wherein the nucleotide comprises a detectable moiety and a photocleavable terminating moiety; using evanescent wave imaging to identify an incorporated nucleotide; and using evanescent wave imaging to cleave the photocleavable terminating moiety. See paragraphs 0010-0059, 0079-0080, and 0092.
Regarding claim 2, Wimberger-Friedl discloses the use of a 3’-unblocked protected nucleotide. See paragraph 0033.
Regarding claim 3, Wimberger-Friedl discloses the use of a fluorophore label. See paragraph 0014.
Regarding claim 4, Wimberger-Friedl discloses the use of a photocleavable terminating group comprising a 2-nitrobenzyl group. See paragraph 0092.
Regarding claim 7, Wimberger-Friedl discloses the use of excitation light using an evanescent wave produced by total internal reflection. See paragraph 0014.
Regarding claim 8, Wimberger-Friedl discloses that excitation light produces fluorescent emission. See paragraph 0014.
Regarding claims 9-10, Wimberger-Friedl discloses the use of excitation light in the visible or UV spectrum. See paragraph 0020.
Regarding claims 13-14, Wimberger-Friedl discloses detecting fluorescence to identify the nucleotide. See paragraph 0014.
Regarding claims 15-16, Wimberger-Friedl discloses photocleavage using an evanescent wave produced by total internal reflection using light in the UV spectrum. See paragraphs 0014 and 0016.
The claimed methods cannot be distinguished from the methods of Wimberger-Friedl.
6. 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.
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 6, 11-12, and 17-24 are rejected under 35 U.S.C. 103 as being unpatentable over Wimberger-Friedl.
The teachings of Wimberger-Friedl are discussed above.
This document does not disclose the further limitations of these claims.
Claim 6 further requires a polymerase having an incorporation bias of less than 10.
Claims 11 and 17 further require excitation light emitted at a power density of at least 20 W/cm2.
Claims 12 and 18 further require excitation light having a pulse duration of about 10 ms or less.
Claims 19-20 further require a ratio of at least 30:1 between a rate constant for nucleotide incorporation and a rate constant for photocleavage.
Claims 21-24 further require determining percentage of nucleotide incorporation into primers and/or percentage of cleavage of detectable moieties, and modifying a parameter of sequencing primer extension and/or protected nucleotide cleavage.
One of ordinary skill in the art would have been motivated to modify the method of Wimberger-Friedl in the manner of these claims because the further limitations would have merely involved straightforward, logical scientific reasoning and routine optimization of known-important reaction parameters, which as well established in U.S. patent practice does not support unobviousness (M.P.E.P. 2144.05). It would have been prima facie obvious to one of ordinary skill in the art at the time the application was filed to carry out the claimed methods.
8. Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Wimberger-Friedl in view of Stemple et al. (US 7,270,951).
The teachings of Wimberger-Friedl are discussed above.
Wimberger-Friedl does not disclose the use of Bst DNA polymerase in the context of sequencing.
Stemple discloses the use of Bst DNA polymerase in the context of sequencing. See column 6, line 58 to column 7, line 11.
One of ordinary skill in the art would have been motivated to use Bst DNA polymerase as the DNA polymerase in the method of Wimberger-Friedl because Stemple disclosed the advantages of using Bst DNA polymerase in sequencing. It would have been prima facie obvious to one of ordinary skill in the art at the time the application was filed to carry out the claimed method.
CONCLUSION
9. No claims are free of the prior art.
10. The following are made of record by the Office as references of interest: Wimberger-Friedl et al. (US 9,823,196 and US 10,564,104), Kato et al. (US 2011/0105358), Rigler (US 2007/0020626), and Gunn III (US 2011/0045472).
11. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENNETH R HORLICK whose telephone number is (571)272-0784. The examiner can normally be reached Mon. - Thurs. 8:30 - 6:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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09/30/25
/KENNETH R HORLICK/ Primary Examiner, Art Unit 1681