DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
The claims dated 6/24/2026 are under consideration.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-18, in the reply filed on 6/24/2026 is acknowledged.
Claims 19-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 6/24/2026.
Priority
The present application is a continuation of 16/949,159 (filed 10/15/2020; issued as 11,851,703),
which is a continuation of 15/965,595 (filed 04/27/2018; issued as 10,829,811),
which is a continuation of 13/458,739 (filed 4/27/2012; issued as 9,957,558),
which claims benefit of US provisional application 61/479,952 (filed 4/28/2011) and
claims benefit of US provisional application 61/531,583 (filed 9/06/2011) and
claims benefit of US provisional application 61/531,574 (filed 9/06/2011) and
claims benefit of US provisional application 61/538,079 (filed 9/22/2011) and
claims benefit of US provisional application 61/564,763 (filed 11/29/2011) and
claims benefit of US provisional application 61/578,192 (filed 12/20/2011) and
claims benefit of US provisional application 61/594,160 (filed 2/02/2012) and
claims benefit of US provisional application 61/598,881 (filed 2/14/2012) and
claims benefit of US provisional application 61/598,892 (filed 2/14/2012) and
claims benefit of US provisional application 61/625,596 (filed 4/17/2012) and
claims benefit of US provisional application 61/639,017 (filed 4/26/2012).
Priority is recognized.
Information Disclosure Statement
The listing of references in the specification or the citation of references throughout the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892 or cited on a submitted IDS, they have not been considered.
Specification
The disclosure is objected to because of the following informalities: the patent number for application 16/949,159 is not provided in paragraph 2. The ‘159 application issued as 11,851,703.
Appropriate correction is required.
Claim Rejections - 35 USC § 103
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.
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, 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 negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-6, 8 and 10-18 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS) in view of Mitra (US 2010/0129874; cited on the 11/21/2023 IDS).
Regarding claims 1, 12 and 13, Schroeder teaches amplifying a plurality of different target sequences within a single amplification reaction mixture by contacting the plurality of different target sequences with a plurality of target-specific primers and a polymerase under amplification conditions, where at least one of the plurality of target-specific primers and at least one of the amplified target sequences including a cleavable group (Fig. 2; para. 7; para. 10; para. 32; and para. 33). The amplification is a multiplex reaction (para. 32 and 33).
Schroeder further teaches cleaving a cleavable group of at least one amplified target sequence (para. 11).
Schroeder further teaches producing one or more adapter-ligated amplified target sequences by ligating at least one adapter to at least one amplified target sequence in a ligation reaction (para. 11), in a blunt end ligation reaction (para. 24 and 28).
Regarding claims 2 and 3, Schroeder teaches adapters that are not complementary to the target DNA (para. 39, where BRCA gene is taught, and para. 56, where adaptors with M13 sequences are taught).
Regarding claim 4, Schroeder teaches primers with a length between 15 and 40 bases (para. 39 and 57).
Regarding claims 5 and 6, Schroeder teaches primers and adaptors without protecting groups (para. 39 and 56), therefore they inherently teach primers susceptible to exonuclease digestion.
Regarding claim 8, Schroeder teaches the amplicons are purified prior to ligation (para. 48-56), satisfying the conditions of claim 8.
Regarding claim 10, Schroeder teaches an isothermal ligation reaction at 25O C (para. 57).
Regarding claim 11, Schroder teaches two different double-stranded adaptors are used (para. 56).
Regarding claim 14, Schroeder teaches blunt end ligation as described above. In blunt end ligation reaction, the ends of the ligating nucleotides are not complementary to one another as there is not overhanging or “sticky” ends.
Regarding claim 15, Schroeder teaches the cleavable group, i.e. MmeI site, is within 15 terminal of the ends of the primers (para. 39-40).
Regarding claim 16, Schroeder teaches reamplifying the adaptor ligated amplicons using M13 primers (para. 57).
Schroeder does not specifically teach the number of different targets in the multiplexed amplification reaction or the elements specific to claims 12, 13, 17 and 18.
However, Mitra demonstrates that conditions for multiplex PCR were known.
Regarding claims 1, 12 and 13, Mitra teaches that a multiplex PCR may include 40, 100, 500 or 1200 primer pairs (para. 42).
It would have been prima facie obvious to the ordinary artisan to have used 40, 100, 500 or 1200 primer pairs in the generic multiplex assay of Schroeder. The modification has a reasonable expectation of success as it adds specific and known details to the generic multiplex method of Schroeder.
Regarding claim 17, Mitra teaches steps of amplifying, cleaving and ligating may occur in a single tube via an addition-only reaction (para. 85).
It would have been prima facie obvious to have modified the method of Schroeder such that it is an assay carried out in a single tube. A single tube assay simplifies the process as it eliminates the need to purify, isolate and extract nucleic acids between steps.
Regarding claim 18, Mitra teaches that barcodes are known and incorporated into oligonucleotides for sample identification (para. 8 and 75).
It would have been prima facie obvious to have modified the method of Schroeder by incorporating barcodes into the primers such that nucleic acids and samples may be readily identified from one another.
Claims 7 and 9 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS) in view of Mitra (US 2010/0129874; cited on the 11/21/2023 IDS), as applied to claim 1 above, and in further view of Taylor (US 2009/0068659 A1).
Regarding claims 7 and 9, the combination of Schroeder and Mitra renders obvious the method of claim 1 as described above.
The combination is silent regarding phosphorylating the 5’ end of the amplicon.
However, in the context of blunt end ligations, such as those taught by Schroeder, Taylor demonstrates it is known to dephosphorylate 3' ends and phosphorylate 5' ends of the double-stranded nucleic acids prior to ligating a double-stranded adaptor onto ends of the double-stranded nucleic acids (para. 12, 16, 17, 67 and 81; and claim 13).
It would have been prima facie obvious to have included at least the step of phosphorylating the 5’ end of the double stranded amplicon of Schroeder in order to carry out the blunt end ligation of Schroeder. One would be motivated to do so because it is a well-known step that is needed in order to ligate the two nucleic acids together.
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 1-18 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-9 of copending Application No. 18/340,581 in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS), Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘581 application. The two differ in that the present claims require blunt end ligation and the ‘581 claims are silent regarding the type of ligation.
However as noted above, Schroeder teaches that such a process is known and a variety of “sticky” end ligation.
The reminder of the elements not in the ‘581 claims or taught by Schroeder are rendered obvious by Mitra and/or Taylor.
This is a provisional nonstatutory double patenting rejection.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-26 of U.S. Patent No. 10,266,881 B2 in view of in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS) or in further combination with Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘881 patent. The two differ in that the present claims require blunt end ligation and the ‘881 claims are silent regarding the type of ligation.
However as noted above, Schroeder teaches that such a process is known and a variety of “sticky” end ligation.
The reminder of the elements not in the ‘881 claims or taught by Schroeder are rendered obvious by Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5 of U.S. Patent No. 10,100,354 B2 in view of in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS) or in further combination with Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘354 patent. The two claim sets differ in that the present claims require blunt end ligation and the ‘354 claims are silent regarding the type of ligation.
However as noted above, Schroeder teaches that such a process is known and a variety of “sticky” end ligation.
The reminder of the elements not in the ‘354 claims or taught by Schroeder are rendered obvious by Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-9 of U.S. Patent No. 8,673,560 B2 alone or in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS), Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘560 patent. The two claim sets differ in that the dependent claims include elements not found in the ‘560 claims.
The reminder of the elements not in the ‘560 claims are rendered obvious by Schroeder, Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 8,728,728 B2 alone or in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS), Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘728 patent. The two differ in that the dependent claims include elements not found in the ‘728 claims.
The reminder of the elements not in the ‘728 claims are rendered obvious by Schroeder, Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. 9,885,076 B2 alone or in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS), Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘076 patent. The two claim sets differ in that the dependent claims include elements not found in the ‘076 claims.
The reminder of the elements not in the ‘076 claims are rendered obvious by Schroeder, Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 9,95,380 B2 alone or Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS), Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘380 patent. The two differ in that the dependent claims include elements not found in the ‘380 claims.
The reminder of the elements not in the ‘380 claims are rendered obvious by Schroeder, Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 9,957,558 B2 alone or in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS), Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘558 patent. The two differ in that the dependent claims include elements not found in the ‘558 claims.
The reminder of the elements not in the ‘558 claims are rendered obvious by Schroeder, Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No.10,829,811 B2 alone or in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS), Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘811 patent. The two claim sets differ in that the dependent claims include elements not found in the ‘811 claims.
The reminder of the elements not in the ‘811 claims are rendered obvious by Schroeder, Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 10,837,052 B2 alone or in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS), Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘052 patent. The two claim sets differ in that the dependent claims include elements not found in the ‘052 claims.
The reminder of the elements not in the ‘052 claims are rendered obvious by Schroeder, Mitra and/or Taylor.
Claims 1-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 11,851,703 B2 in view of Schroeder (US 2008/0131937 A1; cited on the 11/21/2023 IDS) or in further combination with Mitra (US 2010/0129874; cited on the 11/21/2023 IDS) and/or Taylor (US 2009/0068659 A1).
The present claims are sufficiently broad so as to encompass the claims of the ‘703 patent. The two differ in that the present claims require blunt end ligation and the ‘703 claims are silent regarding the type of ligation.
However as noted above, Schroeder teaches that such a process is known and a variety of “sticky” end ligation.
The reminder of the elements not in the ‘703 claims or taught by Schroeder are rendered obvious by Mitra and/or Taylor.
Conclusion
No claims allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682
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