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 .
MAINTAINED REJECTION
2. 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.
3. 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 1-8, 11-14, and 16-18 are rejected under 35 U.S.C. 103 as being unpatentable over Chen et al. (US 2006/0134633).
Regarding independent claims 1 and 18, Chen discloses a method comprising: hybridizing a first primer to a single-strand polynucleotide, incorporating into the first primer via a polymerase one or more nucleotides to form an extension strand, identifying the incorporated nucleotides in the extension strand thus carrying out sequencing, contacting the extension strand with a blocking element forming a blocked extension strand, and repeating the previous steps by hybridizing different primers to different portions of the single-strand polynucleotide. See paragraph 0073 and claims 36-38.
Regarding claim 1, Chen does not explicitly disclose using a ‘terminal sequencing primer’ as the final sequencing primer.
Regarding claim 18, Chen does not explicitly disclose using second and third sequencing primers.
One of ordinary skill in the art would have been motivated to modify the method of Chen by using a ‘terminal sequencing primer’ or specifically second and third sequencing primers because this would have followed merely from straightforward logical scientific reasoning. In paragraph 0073, Chen recites ‘repeating steps (a) to (c) on the same strand of nucleic acid…until a desired amount of sequence is determined’, which was clearly suggestive of using second, third, or more sequencing primers to determine the desired amount of sequence. A ‘terminal sequencing primer’ is reasonably interpreted as the last in the series of sequencing primers necessary to determine the desired amount of sequence. 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.
Regarding claims 2-3, the length of the single-stranded polynucleotide to be sequenced would have been determined merely by 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).
Regarding claim 4, Chen discloses the use of a modified nucleotide triphosphate which lacks a 3’-OH. See paragraph 0100.
Regarding claim 5, choice of conventional blocking elements would have also pertained to routine optimization.
Regarding claim 6, repeating the steps three of more times would have also pertained to routine optimization.
Regarding claim 7, length of each extension strand would have also pertained to routine optimization.
Regarding claim 8, using three or more different primer binding sites on the single-stranded polynucleotide to be sequenced would have also pertained to routine optimization.
Regarding claims 11-14, Chen discloses the use of amplification in paragraph 0057. Choice of amplification method would have also pertained to routine optimization.
Regarding claim 16, use of a solid support would have also pertained to routine optimization, as solid phase and liquid phase nucleic acid assays were both conventional assay formats, each having known advantages and limitations.
Regarding claim 17, producing, grouping, and aligning sequence reads would have also pertained to routine optimization, as this merely involves conventional bioinformatics analysis.
REPLY TO ARGUMENTS
4. With respect to the above rejection, the arguments of the response filed 06/29/26 on pages 8-10 have been fully considered, but are not found persuasive. The response argues that independent claims 1 and 18 require serial interrogation of a single-strand polynucleotide, whereas Chen’s approach is to hybridize multiple primers up front. In other words, it is argued that the claims require a ‘hybridize, sequence, block; then hybridize, sequence, block; then hybridize’ workflow, whereas Chen hybridizes multiple primers in advance and controls later sequencing by deblocking pre-hybridized primers. However, the Office disagrees because here the arguments relate to teachings or embodiments of Chen not relied upon in the rejection. The rejection points to paragraph 0073 and claims 36-38 of Chen, which disclose an embodiment comprising the same ‘hybridize, sequence, block; then hybridize, sequence, block; then hybridize’ workflow as required in the pending claims. Although the response alleges that in pointing to paragraph 0073 and claims 36-38 of Chen, the rejection ‘reads Chen at an unduly high level of generality and does not account for the claimed method as a whole’, the response offers no convincing reason for this assertion. Thus, the rejection is maintained.
ALLOWABLE SUBJECT MATTER
5. Claims 9-10 and 15 are free of the prior art, but they are objected to as being based on a rejected base claim. No prior art has been found teaching or suggesting modifying the method of Chen by forming the single-stranded polynucleotide to be sequenced using two or more interposing oligonucleotide probes in the manner required by claim 9.
CONCLUSION
6. No claims are allowable.
7. THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
8. 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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08/20/26
/KENNETH R HORLICK/ Primary Examiner, Art Unit 1681
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