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 .
Status of the Application
Applicant’s election without traverse of Group I ( claims 61-81) in the reply filed on 19 June 2025 is acknowledged.
Claims 82-84 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 19 June 2025.
Claim Interpretation
Claims 61-81 recite a kit, which is a product invention.
Regarding claims 70, 73, 77, 79 and 80:
Claims 70, 73, 77, 79 and 80 recite an intended use of the claimed kit.
See MPEP 2114.II: MANNER OF OPERATING THE DEVICE DOES NOT DIFFERENTIATE APPARATUS CLAIM FROM THE PRIOR ART
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"[A]pparatus claims cover what a device is, not what a device does." Hewlett-Packard Co. v. Bausch & Lomb Inc., 909 F.2d 1464, 1469, 15 USPQ2d 1525, 1528 (Fed. Cir. 1990) (emphasis in original). A claim containing a "recitation with respect to the manner in which a claimed apparatus is intended to be employed does not differentiate the claimed apparatus from a prior art apparatus" if the prior art apparatus teaches all the structural limitations of the claim. Ex parte Masham, 2 USPQ2d 1647 (Bd. Pat. App. & Inter. 1987) (The preamble of claim 1 recited that the apparatus was "for mixing flowing developer material" and the body of the claim recited "means for mixing ..., said mixing means being stationary and completely submerged in the developer material." The claim was rejected over a reference which taught all the structural limitations of the claim for the intended use of mixing flowing developer. However, the mixer was only partially submerged in the developer material. The Board held that the amount of submersion is immaterial to the structure of the mixer and thus the claim was properly rejected.).
Therefore, a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim.
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.
U.S. Patent No. 11,339,391
Claims 61-73 and 75-80 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 11,339,391.
Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
Claim 1 of U.S. Patent No. 11,339,391 recites a method comprising multiple reagents, including a double-stranded DNA (dsDNA) preadaptor comprises (i) a ligation strand oligonucleotide that is ligated to the 3' end of each strand of the end-repaired DNA fragments and comprises an anchor sequence; and (ii) a non-ligation partner strand oligonucleotide; a repair oligonucleotide, wherein the repair oligonucleotide is longer than the ligation strand oligonucleotide, and wherein the 3' end of the repair oligonucleotide is complementary to the 5' end of the ligation strand oligonucleotide.
Therefore, patented claim 1 of U.S. Patent No. 11,339,391 anticipates instant claim 61.
Furthermore, patented claims 1-23 of U.S. Patent No. 11,339391 recite at least the flowing reagents: one or more end-repair enzymes; a kinase; and two different ligases, including a thermostable ligase.
Furthermore, patented claims 1-23 of U.S. Patent No. 11,339391 recite very similar limitations to instant claims 62-73 and 75-80.
Therefore, claims 1-23 of U.S. Patent No. 11,339391 anticipate the requirements of instant claims 61-73 and 75-80.
U.S. Patent No. 11,339,391
Claims 61-81 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 11,339391 in view of Makarov et al. (WO2015134552; filed 03 March 2015; cited in IDS filed 11 February 2022) and Raymond et al. (US20140274731; filed 10 December 2013).
As noted above, claims 1-23 of U.S. Patent No. 11,339391 teach systems with very similar structural features to the kit of the instant invention, including a double-stranded DNA (dsDNA) preadaptor comprises (i) a ligation strand oligonucleotide that is ligated to the 3' end of each strand of the end-repaired DNA fragments and comprises an anchor sequence; and (ii) a non-ligation partner strand oligonucleotide; a repair oligonucleotide, wherein the repair oligonucleotide is longer than the ligation strand oligonucleotide, and wherein the 3' end of the repair oligonucleotide is complementary to the 5' end of the ligation strand oligonucleotide, as recited in instant claim 61.
Furthermore, patented claims 1-23 of U.S. Patent No. 11,339391 recite one or more end-repair enzymes; a kinase; and two different ligases, including a thermostable ligase.
Furthermore, patented claims 1-23 of U.S. Patent No. 11,339391 recite very similar limitations to instant claims 62-73 and 75-80.
Claims 1-23 of U.S. Patent No. 11,339391 do not expressly teach all the reagents recited in the claimed invention.
However, prior to the effective filing date of the claimed invention, Makarov et al. teach collections of reagents that are used to prepare target nucleic acid libraries for sequencing. Makarov et al. teach adaptor modules comprising ligatable and non-ligatable strands that are complementary as well as complementary repair oligonucleotides ( e.g. Entire Makarov reference and especially para 0012-0015, pg. 4-5; para 0104- 0148,pg. 27-36).
Furthermore, Makarov et al. teach their collection of reagents including kinase, phosphatases; end repair enzymes; enzymes for repairing damage; and several additional types of ligases, phosphatases and polymerases (e.g. Entire Makarov reference and especially PNK as in para 0104, pg. 27-28; phosphatases as in para 0012; para 0104, pg. 27-28; end repair enzymes as in para 0013; para 0105-0107, pg. 28-29; enzymes for repairing damage such as degradation endonuclease such as UDG, endonuclease V, RNase H, or their combination ... a nick-translation DNA polymerase or a 5'-flap endonuclease as in para 0148, pg. 36; additional types of ligases, phosphatases and polymerases as in Enzymes section, para 0171-0174,pg. 43-44).
Therefore, the teachings of Makarov et al. meet the requirements of claims 68,69,71,72 and 74-77.
Furthermore, prior to the effective filing date of the claimed invention, Raymond et al. teach systems for analysis of target DNA comprising multifunctional adaptors that are ligated to the target DNA , wherein the adaptors comprise a random tag region, a sample code region, and an anchor region (e.g. Entire Raymond reference and especially para 0009-0013,pg. 1; para 0031, pg. 3; para 0034, pg. 3; para 0222, pg. 14; anchor region as in para 0678, pg. 71).
Furthermore, Raymond et al. teach different adaptors or the identical adaptors may be ligated to the target DNA. Furthermore, Raymond et al. teach a plurality, i.e. 2 or more, of adaptor modules (e.g. Entire Raymond reference and especially multiple adaptor modules as in para 0226,pg. 14; Table 1, pg. 22; unique adaptors as in Example 10, pg. 39-41).
Furthermore, Raymond et al. teach a plurality of capture probe modules, wherein each module comprises a polynucleotide comprising a capture probe sequence, which is capable of hybridizing to target DNA, and a tail sequence (e.g. Entire Raymond reference and especially para 0227-0241, pg. 14-15; the term "multifunctional capture probe module" refers to a polynucleotide comprising: (i) a first region capable of hybridizing to a partner oligonucleotide; (ii) a second region capable of hybridizing to a specific target region; and optionally (iii) a third region comprising a tail sequence.... as in para 0227; multiple capture probe modules as in para 0255, pg. 17; para 0268, pg. 18; para 0282,pg. 19; Table 29, pg. 46-48; table 31, pg. 50-55).
Therefore, the teachings of Raymond et al. meet the requirements of claim 81.
Therefore, as claims 1-23 of U.S. Patent No. 11,339391, Makarov et al. and Raymond et al. all disclose systems of reagents comprising adaptor modules, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date to modify the system of reagents of claims 1-23 of U.S. Patent No. 11,339391 and to include the teachings of Makarov et al. and Raymond et al. as discussed above because a person of ordinary skill in the art would recognize that these claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions, and the combination would have yielded the predictable outcome of a kit comprising double stranded adaptors.
Therefore, claims 1-23 of U.S. Patent No. 11,339391 in view of Makarov et al. and Raymond et al. render obvious the requirements of instant claims 61-81.
Free of the Prior Art
Claims 61-81 are free of the prior art.
The closest art, Makarov et al.(WO2015134552), teach collections of reagents that are used to prepare target nucleic acid libraries for sequencing. Makarov et al. teach adaptor modules comprising ligatable and non-ligatable strands that are complementary as well as complementary repair oligonucleotides (e.g. Entire Makarov reference and especially para 0012-0015, pg. 4-5; para 0104- 0148,pg. 27-36).
Furthermore, Raymond et al. (US20140274731) teach a plurality of capture probe modules, wherein each module comprises a polynucleotide comprising a capture probe sequence, which is capable of hybridizing to target DNA, and a tail sequence (e.g. Entire Raymond reference and especially para 0227-0241, pg. 14-15; the term "multifunctional capture probe module" refers to a polynucleotide comprising: (i) a first region capable of hybridizing to a partner oligonucleotide; (ii) a second region capable of hybridizing to a specific target region; and optionally (iii) a third region comprising a tail sequence.... as in para 0227; multiple capture probe modules as in para 0255, pg. 17; para 0268, pg. 18; para 0282,pg. 19; Table 29, pg. 46-48; table 31, pg. 50-55).
However, the state of the art does not teach or fairly suggest the combination of features of the claimed kit, including a double-stranded DNA (dsDNA) preadaptor comprises (i) a ligation strand oligonucleotide that is ligated to the 3' end of each strand of the end-repaired DNA fragments and comprises an anchor sequence; and (ii) a non-ligation partner strand oligonucleotide; a repair oligonucleotide, wherein the repair oligonucleotide is longer than the ligation strand oligonucleotide, and wherein the 3' end of the repair oligonucleotide is complementary to the 5' end of the ligation strand oligonucleotide, as required by the claimed invention.
Conclusion
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SAHANA S KAUP whose telephone number is (571)272-6897. The examiner can normally be reached on M-F 7am-7pm EST.
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/SAHANA S KAUP/Primary Examiner, Art Unit 1684