DETAILED ACTION
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 .
Claims 104-123 are pending and are being examined on the merits.
Information Disclosure Statement
The Information Disclosure Statement submitted March 18, 2025 has been considered.
Specification
The disclosure is objected to because of the following informalities: the “Cross-Reference to Related Application” paragraph (para. 1), should be updated to indicate that the parent application, US Serial No. 17/165,802, has issued into US Patent No. 12,110,548.
Appropriate correction is required.
Claim Objections
Claim 116 is objected to because of the following informalities:
In claim 116, the limitation “system of analyzing” in l. 1 should be “system for
analyzing”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
Claim 123 is 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 123 recites the limitation “an additional ligase”, the meaning of which is unclear.
Specifically, neither of claims 119 or 122, from which claim 123 indirectly or directly depends, recite “a ligase”. Thus, it is not clear what the “additional” language in claim 123 is intended to refer to. Since the ordinary artisan would not be able to determine the metes and bounds of the claim, it is indefinite.
Prior Art
Claims 104-123 are free of the art.
Independent claims 104 and 116 are each directed to a system that is capable of performing both sequencing-by-ligation and sequencing-by-synthesis on two different regions of interest in a target nucleic acid. More specifically, the system comprises, in part, a sample comprising a nucleic acid of interest which comprises non-overlapping first and second regions of interest and an adapter; an anchor capable of hybridizing to an adaptor on the nucleic acid of interest; a ligase; a plurality of detection probes, each comprising an interrogatory region and a detectable label; a polymerase capable of participating in a sequencing-by-synthesis reaction; and a pool of nucleotides and/or nucleotide analogs. Independent claim 119 is directed to similar subject matter, but the polymerase and ligase are optional.
Relevant prior art is Samusik1 (WO 2017/147483 A1), which is directed to methods and systems for multiplex single molecule RNA visualization using probes. Samusik specifically teaches “SNAIL” probes (i.e., padlock probes) for the polymerase extension part of the method (e.g., Example 1, Fig. 1). Samusik also teaches the use of such probes to detect target sequences, although Samusik does not teach sequencing by synthesis, per se. Samusik also does not teach the detection probe and ligase part of the system, nor does it teach sequencing by ligation. However, systems for sequencing by synthesis are known in the art (e.g., Banerjee2, US Patent No. 8,241,573), as are systems for sequencing by ligation (e.g., Bortner3, US Patent No. 9,404,155).
Thus, many individual parts of the systems of the independent claims are generally known in the art. However, there does not appear to be any motivation for the ordinary artisan to combine all of these different methods and corresponding system components into a single system embodiment. Therefore, the art does not reasonably teach or suggest the systems of the independent claims.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 104-123 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. 12,110,548 (hereinafter, the ‘548 patent).
Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-16 of the ‘548 patent teach or suggest methods which require components that correspond to the system components of instant claims 104, 110 and 114-123.
Further, regarding the limitations of instant claims 105-109 and 111-113, it would have been obvious for the ordinary artisan to arrive at these limitations through routine optimization.
It would have been prima facie obvious to modify the ‘548 method claims to assemble the required components into a system. The ordinary artisan would have been motivated to do so to achieve the expected advantage of, e.g., a kit or device with the capability of performing the claimed methods in a single, integrated unit. The ordinary artisan would have had an expectation of success as assembling nucleic acid components into various types of systems is well-known in the art.
It would have been further obvious to modify the ‘548 method claim components to optimize the various reagents and oligonucleotides in order to customize the system as desired using routine practices. The ordinary artisan would have had an expectation of success as the design and modification of various nucleic acid assays, and their corresponding systems, is well-known in the art.
Conclusion
Claims 104-123 are being examined and are rejected. Claim 116 is objected to. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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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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/CAROLYN L GREENE/Primary Examiner, Art Unit 1681
1 Samusik was cited in the Information Disclosure Statement submitted March 18, 2025.
2 Banerjee was cited in the Information Disclosure Statement submitted March 18, 2025.
3 Bortner was cited in the Information Disclosure Statement submitted Mach 18, 2025.
