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 . Applicant’s preliminary amendment filed 10/23/2023 is acknowledged and has been entered. The claims 1-20 have been canceled. The claims 21-40 have been added and under examination.
Priority
This application is a CON of 16/372,186 filed 04/01/2019 now US PAT 11,834,699 which is a CON of 15/421,979 filed 02/01/2017 now US PAT 10,267,804 which is a CON of 14/378,613 filed 08/13/2014 now US PAT 9,574,226 which is a 371 of PCT/EP2013/054517 filed 03/06/2013 which claims benefit of 61/607,418 filed 03/06/2012.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 10/23/2023 is acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Applicant’s amendment to the specification filed 10/23/2023 is acknowledged and has been entered.
Drawings
The drawings were received on 10/23/2023. These drawings are found acceptable by the Examiner.
Claim Objections
Claim 25 is objected to because of the following informalities: the claim recites “and/or molecular of biochemical manipulation.” It is clear from page 10, line 14 of the specification that the phrase “molecular of biochemical” should be “molecular or biochemical.” 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 24 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.
(a) Claim 24 is indefinite at the recitation of “wherein the transferred strand comprises a tag 5’ of the transposon sequence” because it is unclear as to which of the transposon sequence comprise of the tag 5’ of it. It cannot be determined if applicant is making reference to the “first transposon sequence” or the “second transposon sequence” or if both transposon sequences. A clear interpretation cannot be ascertained. Clarification is required.
Claim Rejections - 35 USC § 102
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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 21-40 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Shendure et al (US Patent No. 10,457,936 B2; see the entire reference), as evidenced by Voelkerding et al (Clinical Chemistry, Vol. 55, No. 4, pages 641-658, 2009) and Vyawahare et al (Chemistry & Biology, Vol. 17, pages 1052-1065, 2010) (All citations made of record on IDS filed 10/23/2023).
Regarding claims 21, 33-35 and 40, Shendure et al teach a composition comprising a DNA:DNA duplex in the form of a target DNA molecule immobilized on a flowcell, and a transposome comprising a transposase loaded with compatible adaptors (e.g., column 2, lines 31-47; column 11, lines 30-40; column 12, lines 48-55; Example 3). Shendure et al teach loading the transposase with synthetic DNA oligonucleotides containing transposase mosaic end (ME), primer sites, and flowcell adapter sequence, which are annealed to form a double-stranded nucleic acid (e.g., column 31, lines 38-43). Shendure et al teach that the transposase is a Tn5 transposase (e.g., column 32, lines 46-49). Shendure et al teach that transposition will result in one of the adaptors (ME at the 3’ end) being directly linked (i.e., the transferred strand of the claims), and the other remaining bound via hybridization (i.e., the non-transferred strand of the claims) (e.g., column 22, lines 29-36).
Regarding claim 22, Shendure et al teach that during transposition, the transposase is associated with the target DNA molecule (i.e., DNA:DNA duplex of the claim) (e.g., Example 3).
Regarding claim 23, Shendure et al teach the composition where the double-stranded nucleic acid molecule of the claim is the ME, and the double-stranded nucleic acid molecule comprises other nucleotide sequences on one or both strands, which are primer sites and a flowcell adaptor sequence (e.g., paragraph bridging columns 22-23, lines column 31, lines 38-43).
Regarding claims 24-29 and 40, Shendure et al teach the composition where the transposon comprises DNA sequence with an outer flowcell primer (capture tag domain of claims), a degenerate barcode (tags amplification products; amplification tag domain), and inner sequence primer (sequencing tag domain), and the transposase recognition sequence, such that the sequence is added by the transposase and wherein the transposon comprises of a biotin (e.g., col. 21, line 67, column 22, line 64 to column 23, line 21 and Figure 17) .
Regarding claim 30, Shendure et al teach that the target DNA (DNA:DNA duplex of the claim) are immobilized on the flowcell via immobilized primers on the flowcell (e.g., column 2, lines 31-47; paragraph bridging columns 2-3; paragraph bridging columns 16-17).
Regarding claim 31, Shendure et al teach wherein the immobilized primer each comprises a poly T sequence (col. 15, lines 48-49 and col. 16, lines 5-6, 44 and section 2.I. at col. 27).
Regarding claim 32, Shendure et al teach that the target DNA (DNA:DNA duplex of the claim) comprises an adaptor that is complementary to a plurality of immobilized primers (e.g., column 2, lines 31-47; column 11, lines 30-40; column 12, lines 48-55; Example 3, see also ). The adaptor contains the target of the claim, and the immobilized primer is target-specific to the adaptor sequence. Shendure et al teach that the target DNA (DNA:DNA duplex of the claim) comprises an adaptor that is complementary to a plurality of immobilized primers (e.g., column 2, lines 31-47; column 11, lines 30-40; column 12, lines 48-55; Example 3).
Regarding claim 34-37, Shendure while teaching a flow cell, the reference also teaches the use of a magnetic beads (see e.g., col. 36, line 60, col. 42, lines 7 and 20). Shendure further teaches that the solid support may comprise of an array platform comprises of plurality of bead bound oligos (col.13, lines 48-49; col. 26-28 and col. 48, lines 3-4). Shendure et al further teach the transposon composition comprises a transposase and a double-stranded nucleic acid comprising a mosaic end sequence and its reverse complement (e.g., column 26, lines 47-59). Shendure et al teach the association of the immobilized transposon composition with genomic DNA (DNA:DNA duplex), whereby the genomic DNA becomes immobilized with the transposon composition during the transposition reaction (e.g., column 26, lines 34-59).
Regarding claim 38, Shendure et al teach that the flowcell is a standard GAIIx flowcell (e.g., column 5, lines 49-50; column 32, lines 43-52).
Regarding claim 38, Shendure et al teach that the flowcell is a standard GAIIx flowcell (e.g., column 5, lines 49-50; column 32, lines 43-52). Shendure does not teach that the flow cell reactor comprises multiple microfluidic channels.
However, Voelkerding et al is cited to show that the Illumina genome analyzer (GA) was purchased from Solexa in 2006 (e.g., paragraph bridging pages 642-643). Voelkerding et al teach that the GA uses a flow cell consisting of an optically transparent slide with 8 individual lanes of the surfaces of which are bound oligonucleotide anchors (e.g., paragraph bridging pages 642-643).
Vyawahare et al teach that the Solexa GAII uses a microfluidic flow cell split into eight lanes (e.g., paragraph bridging pages 1055-1056). Thus, the GAIIx flowcell of Shendure et al comprises multiple microfluidic channels and meets the limitations of claim 38.
Regarding claim 39, Shendure et al teach wherein the least one strand of the duplex comprises a ssDNA target nucleic acid sequence (col. 8, lines 48-52; see also Example 1).
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 21-40 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 11834699 (US Pat ‘699 used interchangeably herein). Although the claims at issue are not identical, they are not patentably distinct from each other because both the claims of the instant invention and the clams 1-18 of US Pat ‘699 are directed to a composition comprising duplex immobilized on a support wherein the duplex is immobilized on the support via an immobilized primer, and wherein at least one strand of the duplex comprises a sequence complementary to at least a portion of the immobilized primer; and a transposome complex, wherein the transposome complex comprises a transposase and a transposon composition, wherein the transposon composition comprises a double-stranded nucleic acid comprising a transferred strand comprising a first transposon sequence and a non-transferred strand comprising a second transposon sequence that is complementary to the first transposon sequence. The claims 22-40 of the instant invention are embodied in the limitations of the claims 2-18 of US Pat ‘699. The claims of the instant invention only slightly differ in wording from the claims 1-18 of US Patent ‘699 and further recite wherein the duplex is a DNA:DNA duplex which the instant specification defines that DNA:RNA duplex is amendable for DNA:DNA duplex (page 6 and Figure 8). Thus, the claims of the instant invention fall entirely within the scope of the claims of US Pat ‘699.
Thus, the claims 21-40 of the instant invention falls entirely within the scope of the claims 1-18 of US patent ‘699. As the court stated in In re Goodman, 29 USPQ2d 2010 (CAFC 1993), "a second application-- "containing a broader claim, more generical in its character than the specific claim in the prior patent"--typically cannot support an independent valid patent. Miller, 151, U.S. at 198; See Stanley, 214 F.2d at 153. Thus, the generic invention, as noted above is "anticipated" by the species of the patented invention. Cf., Titanium metal corp. v. Banner, 778 F.2d 775, 227 USPQ 773 (Fed. Cir. 1985) (holding that an earlier species disclosure in the prior art defeats any generic claims). This court's predecessor has held that, without a terminal disclaimer, the species claims preclude issuance of the generical application. "In re Van Ornum, 686 F.2d 937, 944, 214 USPQ 761, 767 (CCPA 1982); Schneller, 397 F.2d at 354".
Conclusion
No claims are allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681