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 .
Priority
This application is a CON of 18/085,180 filed 12/05/2022, now U.S. Patent No. 12,571,034. 18/085,180 is a CON of 17/494,726 filed 10/05/2021, now U.S. Patent No. 11,519,028.
17/494,726 is a CON of 16/418,104 filed 05/21/2019, now U.S. Patent No. 11,530,442.
16/418,104 is a CON of 15/716,331 filed 09/26/2017, now U.S. Patent No. 10,577,650.
15/716,331 is a DIV of 15/372,279 filed 12/07/2016, now U.S. Patent No. 10,011,870.
Election/Restrictions
Applicant’s election of the following species with traverse in the reply filed on 06/23/2026 is acknowledged.
Concerning species group A. Type of selective enrichment to apply the instant method,
Applicant elects: choice (2) using a plurality of hybrid capture probes to capture at least a portion of the amplified adapted DNA (claims 1, 14, 17).
Concerning species group B. sequence reads grouping to apply the instant method,
Applicant elects: choice (5) grouping sequence reads having the same target locus, the same pair of MITs in the same relative positions to the target locus, and the same start and end genomic coordinates of the extracted cfDNA or DNA fragment derived therefrom when mapped to a reference genome (claims 9-10, 12-13).
Concerning species group C. Molecular index tag (MIT) features to apply the instant method, Applicant elects: (6) choice 50 and 1,000 different MITs, each comprising 3-8 nucleotides in length are to be attached to cfDNA or DNA fragments (claim 5).
Concerning species group D. Number of target loci for selective enrichment,
Applicant elects: choice (8) 50-5,000 target loci (claim 14).
Applicant’s traversal is on the grounds that species groups B, C, and D are not mutually exclusive embodiments. As explained in MPEP 806.04(f):
"Where two or more species are claimed, a requirement for restriction to a single species may be proper if the species are mutually exclusive. Claims to different species are mutually exclusive if one claim recites limitations disclosed for a first species but not a second, while a second claim recites limitations disclosed only for the second species and not the first. This may also be expressed by saying that to require restriction between claims limited to species, the claims must not overlap in scope."
This argument is not found persuasive since a single prior-art reference that teaches the non-elected choice (3) of species group B corresponding to
“grouping the sequence reads comprise the same target locus, the same MIT in the same relative position to the target locus” (claims 2, 11), may not teach/anticipate the elected choice (5) corresponding to
“grouping sequence reads having the same target locus, the same pair of MITs in the same relative positions to the target locus, and the same start and end genomic coordinates of the extracted cfDNA or DNA fragment derived therefrom when mapped to a reference genome”.
The scope of the choices (3), (4) (5) for species group B are distinct and the search for each species is not co-extensive.
The Office disagrees with Applicant’s argument that species 3, 4, 5 substantially overlap in scope and not mutually exclusive under MPEP 806.04(f).
Claims 6, 11 and 15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention(s), there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 06/23/2026.
Status of the claims
Claims 1-20 are pending. Claims 1-5, 7-10, 12-14 and 16-20 are currently under examination.
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 1-5, 7-8, 14 and 16-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-11 of U.S. Patent No. 12,571,034.
Although the claims are not identical, they are not patentably distinct from each other.
Both the method of the instant claims and the claims of U.S. Patent No. 12,571,034 are directed to method(s) for preparing a cfDNA fraction from a biological sample of a subject having cancer or suspected of having cancer for cancer mutations analysis.
Both methods of the instant claims and claims of U.S. Patent No. 12,571,034 comprise the steps of
(a) extracting cell-free DNA from the biological sample,
(b) attaching at least one adaptor comprising a molecular index tag (MIT) to at least one end of the extracted cfDNA or DNA fragment derived therefrom to produce adapted DNA,
(c) performing universal amplification on the adapted DNA to produce amplified adapted DNA,
(d) selectively enriching amplified adapted DNA performing one-sided PCR using a universal primer and a plurality of target-specific primers to amplify at least a portion of the amplified adapted DNA; or using a plurality of hybrid capture probes to capture at least a portion of the amplified adapted DNA,
(e) analyzing the enriched DNA, wherein the analyzing comprises:
(i) performing massively parallel sequencing on the enriched DNA to obtain sequence reads, wherein the sequence reads comprise sequencing the MIT and a sequence of the extracted cfDNA or DNA fragment derived therefrom,
identifying one or more cancer mutations in the biological sample of the subject.
The claims of U.S. Patent No. 12,571,034 are found to anticipate the instant claims as the claims of U.S. Patent No. 12,571,034 uses the sequence reads of the MIT and one or more preselected loci to identify one or more cancer mutations.
Conclusion
No claims are currently allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OLAYINKA A OYEYEMI whose telephone number is (571)270-5956. The examiner can normally be reached Monday -Thursday: 9:00 am - 5:00 pm, EST.
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OLAYINKA A. OYEYEMI
Examiner
Art Unit 1681
/OLAYINKA A OYEYEMI/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681
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