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 .
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 December 2, 2025 has been entered.
Applicant’s amendment filed on December 2, 2025 is acknowledged and has been entered. Claim 2 has been canceled. Claims 1 and 3 have been amended. Claims 1 and 3-10 are pending.
Claims 1 and 3-10 are discussed in this Office action.
All of the amendments and arguments have been thoroughly reviewed and considered but are not found persuasive for the reasons discussed below. Any rejection not reiterated in this action has been withdrawn as being obviated by the amendment of the claims. The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
This action is made NON-FINAL as necessitated by Amendment.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on December 2, 2025 was filed in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Prior Grounds of Rejection
Priority
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 61448547, 61462972, 61426208, 61398159, 61395850, US Patent 8825412 and 61516996 fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application. While each of these priority documents include support for multiplex, universal adaptors or universal amplification and mutation detection, none of these priority documents include sufficient (or any) support for the inclusion of barcodes or barcode primers, or the inclusion of cancer or tumor or that polymorphic loci are associated with tumor or cancer.
Therefore, as the priority documents of US Patent 10017812, for example, provide support, the claims are afforded an earliest priority of November 18, 2011.
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 and 3-10 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-2, 4-9, 12-13 and 15-16 of copending Application No. 18620822 (reference application, ‘822 application herein). Although the claims at issue are not identical, they are not patentably distinct from each other because the steps of the method are not the same. The first amplification step of the ‘822 method recites multiplex amplification while the primary step of the instant claims are drawn more broadly to a step of amplifying one or more times. Additionally, the 20-2000 polymorphic loci associated with cancer of the instant claims is recited in the final sequencing step of the method, as claimed where those 20-2000 polymorphic loci associated with cancer are recited in the step of multiplex amplification in the ‘822 application. However, both methods share steps of amplification that encompasses 20-2000 polymorphic loci associated with cancer followed by ligating, tagging or appending adaptors to the amplified nucleic acids followed by amplification with universal adaptors followed by sequencing.
Further, while the steps of the instant claims and the claims of the ‘822 application are not identical, the claims share overlapping subject matter. For example, the molecular barcode is incorporated in claim 1 of the ‘822 application where the barcode is included in instant claims 1 and 4 of the instant application. However, while the methods include different specific steps, the claims are not patentably distinct.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
New Grounds of Rejection
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1 and 3-10 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Deciu et al. (US 20130338933 A1; December 2013).
With regard to claim 1, Deciu teaches a method for amplifying and sequencing DNA, comprising:
amplifying isolated cell-free DNA or DNA derived therefrom one or more times to generate amplification products, wherein the isolated DNA is isolated from a blood sample collected from a subject who is not a pregnant woman, wherein one of the amplification steps comprises targeted amplification of a plurality of single nucleotide polymorphism or variant loci in a single reaction volume (paragraph 5-6, 8, where cell free nucleic acid is isolated from blood; see also paragraph 177, 195, 214, 630, where the sample is focused on cell free DNA and cancer; p 209-210, paragraph 1170-1177, see especially Fig 165, in paragraph 1171, where the sample is subject to loci specific amplification followed by universal amplification);
tagging the amplification products with one or more universal tail adaptors to generate tagged products, and amplifying the tagged products using adaptor-specific primers to generate final amplification products, wherein the final amplification products comprise a barcode and one or more sequencing tags (p 209-210, paragraph 1170-1177, see especially Fig 166, in paragraph 120, paragraph 1171 and Table 13, where the sample is subject to loci specific amplification followed by universal amplification);
and sequencing the plurality of single nucleotide polymorphism or variant loci on the DNA by conducting massively parallel sequencing on the final amplification products, wherein the plurality of single nucleotide polymorphism or variant loci comprises 50-2,000 loci associated with cancer (p 209-210, paragraph 1170-1177, see especially Fig 166, in paragraph 120, paragraph 1171 and Table 13, where the sample is subject to loci specific amplification followed by universal amplification).
With regard to claim 3, Deciu teaches a method of claim 2, wherein the one or more universal tail adaptors each comprise a first strand and a second strand, wherein a first end of each of the universal tail adaptors comprises a double-stranded section comprising the 5' portion of the first strand and the 3' portion of the second strand, wherein the first end is appended to the amplification products (p 209-210, paragraph 1170-1177, see especially Fig 166, in paragraph 120, paragraph 1171 and Table 13, where the sample is subject to loci specific amplification followed by universal amplification).
With regard to claim 4, Deciu teaches a method of claim 1, wherein the one or more universal tail adaptors comprise the barcode (paragraph 356 and 362 where barcodes are included).
With regard to claim 5, Deciu teaches a method of claim 1, wherein the one or more universal tail adaptors comprise the one or more sequencing tags (paragraph 288, 296 and 352, for example, where sequence tagging is described).
With regard to claim 6, Deciu teaches a method of claim 1, wherein the one or more universal tail adaptors comprise a first universal tail adaptor and a second universal tail adaptor (p 209-210, paragraph 1170-1177, see especially Fig 166, in paragraph 120, paragraph 1171 and Table 13, where the sample is subject to loci specific amplification followed by universal amplification).
With regard to claim 7, Deciu teaches a method of claim 6, wherein amplifying the tagged products comprises a single amplifying step (p 209-210, paragraph 1170-1177, see especially Fig 166, in paragraph 120, paragraph 1171 and Table 13, where the sample is subject to loci specific amplification followed by universal amplification).
With regard to claim 8, Deciu teaches a method of claim 7, wherein amplifying the tagged products comprises using a first adaptor-specific primer and a second adaptor-specific primer, wherein the first adaptor-specific primer comprises a first sequencing tag and wherein the second adaptor-specific primer comprises a second sequencing tag (p 209-210, paragraph 1170-1177, see especially Fig 166, in paragraph 120, paragraph 1171 and Table 13, where the sample is subject to loci specific amplification followed by universal amplification).
With regard to claim 9, Deciu teaches a method of claim 1, wherein at least one amplicon in the amplification products comprises two or more nearby single nucleotide polymorphisms or variants loci (p 9, paragraph 134, p 10, paragraph 143-144, p 19, paragraph 215, p 23, paragraph 257-259, 264, where SNPs are analyzed).
With regard to claim 10, Deciu teaches a method of claim 1, wherein the isolated cell-free DNA is isolated from a plasma portion of the blood sample (paragraph 5-6, 8, where cell free nucleic acid is isolated from blood; see also paragraph 177, 195, 214, 630, where the sample is focused on cell free DNA and cancer).
Citation of Pertinent Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Ganova-Raeva et al. (Chapter 6, A. Buzdin and S. Lukyanov (eds.), Nucleic Acids Hybridization, 125–165. © 2007 Springer). Wang et al. (Appl Environ Microbiol, 2007, 73(15):5048-5051). Sparks et al. (US Patent 10,308,981; June 2019). Van Eijk (US 20130137587; May 2013).
Conclusion
No claims are allowed. All claims stand rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEPHANIE KANE MUMMERT whose telephone number is (571)272-8503. The examiner can normally be reached M-F 9:00-5:30.
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/STEPHANIE K MUMMERT/Primary Examiner, Art Unit 1681