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
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 1OCT2025 has been entered.
Claims pending: 1-2,4-30
Claims under consideration: 1-2,4-30
Priority
This application has a filing date of 11/07/2024 and is a CON of 18/388,735 11/10/2023
18/388,735 is a CON of 18/172,091 02/21/2023 ABN
18/172,091 is a CON of 17/852,994 06/29/2022 ABN
17/852,994 is a CON of 16/717,375 12/17/2019 PAT 11414688
16/717,375 is a CON of 16/228,362 12/20/2018 PAT 10557158
16/228,362 is a CON of 14/990,276 01/07/2016 PAT 10221436
14/990,276 has PRO 62/262,769 12/03/2015
14/990,276 has PRO 62/102,420 01/12/2015
Withdrawn Objection(s) and/or Rejection(s)
All rejections from the previous action are hereby withdrawn in light of Applicant’s amendments.
New Claim Rejection(s) – 35 USC § 112
The following is a quotation of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-6,9-30 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This rejection concerns new matter.
Claim 1 has been amended to add the limitation of a peptide nucleic acid (PNA) or a locked nucleic acid (LNA) nucleotide as an extension terminator, the present response proffering support therefor may be found at paragraphs [0120], [0289] and [0295] of the application as filed.
In reviewing such passages, however the examiner only finds description of PNAs or LNAs in primers (that are NOT terminated but rather extended).
The response does not point to where such material is disclosed in the priority documents. And accordingly, the original specification does not provide implicit or explicit description for such aforementioned changes that introduce new material.
Applicants are reminded that it is their burden to show where the specification supports any amendments to the disclosure. See MPEP 714.02, paragraph 5, last sentence and also MPEP 2163.06 I.
MPEP 2163.06 notes “If new matter is added to the claims, the examiner should reject the claims under 35 U.S.C. 112, first paragraph - written description requirement. In re Rasmussen, 650 F.2d 1212, 211 USPQ 323 (CCPA 1981).” MPEP 2163.02 teaches that “Whenever the issue arises, the fundamental factual inquiry is whether a claim defines an invention that is clearly conveyed to those skilled in the art at the time the application was filed...If a claim is amended to include subject matter, limitations, or terminology not present in the application as filed, involving a departure from, addition to, or deletion from the disclosure of the application as filed, the examiner should conclude that the claimed subject matter is not described in that application. MPEP 2163.06 further notes “When an amendment is filed in reply to an objection or rejection based on 35 U.S.C. 112, first paragraph, a study of the entire application is often necessary to determine whether or not “new matter” is involved. Applicant should therefore specifically point out the support for any amendments made to the disclosure.
New 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 may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
Claims 1,2,4-6,9-11,14-16,19-28,30 and 7,8,29 are rejected under 35 U.S.C. 103(a) as being unpatentable over Zhou et al (US AppPub 20160369334; of record) in view of Guo et al (2008 PNAS 105:9145-50; provided previously)
Zhou et al teach throughout the document and especially the abstract, long DNA sequencing. More particularly at paragraph 0210, 0211-0212 describing figures 1 and 2 taken with paragraphs 0227,0230,0007,0113,0107,0109,0150,0081 Zhou et al: provide a template nucleic acid molecule like gDNA or cDNA, dNTPs, a random hexamer primer, amplifying with a polymerase (e.g. Taq for 30 thermal cycles or phi29 DNA polymerase which has strand displacement and 3' to 5' proofreading activities), an extension terminator (optionally chemically reversible), and an oligonucleotide barcode molecule optionally with a functional sequence (e.g. 15 nucleotide primer) and thereby subjects the template nucleic acid molecule to a nucleic acid extension reaction under conditions sufficient to yield an extended nucleic acid fragment and render the extended nucleic acid fragment unextendible via terminator nucleotides; and after that, use the oligonucleotide barcode molecule and the terminated extended nucleic acid fragment to generate a barcoded nucleic acid molecule with an ATP independent enzyme such as a T4 DNA ligase and finally sequencing. In the passages, Zhou et al teach such reactions may be performed isothermally, in microwell arrays, on polystyrene beads with the aid of biotin-streptavidin chemistry, in emulsions, etc. The foregoing reads on claims 1 (in part),2,4,5,6 9,10,11,14,15,16,19,20, necessarily on claim 21 and claims 22,23,24,25, 26,27,28,30.
Zhou et al do not explicitly teach: dideoxynucleotide nor blocker oligonucleotide extension terminators as set forth in claims 1c,7,8; nor performing a releasing operation to remove a blocking group from an extension terminator derivative, wherein the releasing operation comprises applying a chemical stimulus to the extension terminator derivative of claim 29.
Guo et al teach throughout the document and especially the abstract, figures 5,2 & 1 and the Materials and Methods section, sequencing-by-synthesis with dideoxynucleotide and blocker oligonucleotide extension terminators (prepared in situ) as set forth in claims 1c,7,8 as well as performing a releasing operation to remove a blocking group from an extension terminator derivative, wherein the releasing operation comprises applying a chemical stimulus to the extension terminator derivative like claim 29.
It would have been prima facie obvious for one of ordinary skill in the art, before the effective filing date of the claimed invention to have performed long nucleic acid sequencing as in Zhou et al with the sequencing-by-synthesis approach of Guo et al.
One of ordinary skill in the art would have been motivated to have performed long nucleic acid sequencing as in Zhou et al with the sequencing-by-synthesis approach of Guo et al and had reasonable expectation of success in doing so since Zhou et al expressly suggest in paragraph 0237 and again paragraph 0227 that the approach is well suited therefor as well as its commercially availability.
Claims 1,4-6,9-11,14-16,19-28,30 and 7,8,29 and 12-13,17,18 are rejected under 35 U.S.C. 103 as being unpatentable over Zhou et al (US AppPub 20160369334; of record) in view of Guo et al (2008 PNAS 105:9145-50; provided previously) and further in view of Hindson et al (US AppPub 20140155295 – IDS entry 1/17/2025; of record) as evidenced by US AppPub 20170253923; of record; referred to again hereafter as '923)
Zhou et al in view of Guo et al is relied on as above. And, concerning claims 17 and 18, as interpreted in MPEP 2144.05, the courts have held substituting art-recognized equivalents for the same purpose is obvious. Here, as evidenced by '923 paragraph 0194, topoisomerases and 5' App DNA/RNA ligase each constitute an art-recognized equivalents for the same purpose of modifying a 3' end of RNA as Zhou's T4 DNA ligase.
Zhou et al in view of Guo et al do not teach chemically reducible disulfide cross-linkers such as recited in claims 12-13, however.
Hindson et al teach throughout the document and especially at least paragraphs 0005,0008 and 0115, gel beads degradable with chemically reducible disulfide crosslinkers such as set forth in claims 12-13.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized Hindson's gel beads to have prepared nucleic acids for sequencing as in Zhou et al in view of Guo et al.
One of ordinary skill in the art would have been motivated to have utilized Hindson's gel beads to have prepared nucleic acids for sequencing as in Zhou et al in view of Guo et al and had a reasonable expectation of success in doing so for the convenience of facilely removing bead polymers without extra physical manipulation(s) and Hindson et al expressly stating in the abstract that the invention therein described is, in fact, satisfies just such needs.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTOPHER M GROSS whose telephone number is (571)272-4446. The examiner can normally be reached M-F 10-6.
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.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached on (571)272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CHRISTOPHER M GROSS/Primary Examiner, Art Unit 1684