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 Claims
Claims 1-35 and 56-68 are cancelled.
Claims 36-55 are under examination.
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.
Claims 42, 43, and 46 are 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.
Claims 42, 43, and 46 are indefinite because it is not clear where the 2nd, 3rd, or 4th amplicon is coming from. It is not clear if it is produced from the first amplicon or if it is produced from a 2nd, 3rd, or 4th target polynucleotide. The claim is interpreted such that they are produced from a 2nd, 3rd, or 4th target polynucleotide.
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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention 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 35 U.S.C. 103 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 36, 37-44, and 46-55 are rejected under 35 U.S.C. 103 as being unpatentable over Sabot et al. (US 2012/0122737 A1).
Sabot et al. teach a method of amplifying polynucleotides on a solid support. (claim 1). Sabot et al. teach a solid support with a plurality of oligonucleotides immobilized on the it wherein the plurality of oligonucleotides comprises a plurality of capture oligonucleotides and a plurality of amplification oligonucleotides. (claim 1). Therefore, Sabot et al. teach an orthogonal probe because one set is different from the other. Sabot et al. teach that capture probes are longer than the amplification probes. (claim 6). Sabot et al. teach that different areas can be created on the solid support. [0024, 0039, “As such, a portion of the surface having a mixture of different immobilized sequences can be surrounded by an area of the surface having a mixture of the same immobilized sequences.”, 0096].
Sabot et al. teach template polynucleotides in a nucleic acid sample. (claim 1). Sabot et al. does not specifically state the template polynucleotides are comprised in a fluid, however, it does make reference to a flow cell application, dilution of the sample and elution of the sample, which are all indications that the sample is in a fluid. It would have been obvious to one of skill in the art to suspend nucleic acids in a sample for use in a flow cell application, for example.
Sabot et al. teach that adaptors can be added to one or both ends. Sabot et al. shows in figure 1 a DNA insert with a “seq primer” and “P7” attached to the DNA insert. The instant specification does not state what an adapter is and Sabot et al. show that the “seq primer” and the “P7” bind to the probes on the solid support. They are added to the DNA insert and are therefore adapters.
As discussed above, the “seq primer” and “P7” adapters hybridize to the probes on the solid support and the sequence is amplified. (figure 1, steps c-e of claim 1).
Sabot et al. do not explicitly teach wherein the capture probes and orthogonal capture probes are in discreet regions on the solid surface. However, one of skill in the art would have been motivated to arrange the probes in any particular pattern that suited their purpose because it was known in the art that probes could be placed in discreet locations. Sabot et al. teach arranging probes in different areas. Arranging the probes in specific locations would provide one of skill in the art greater control over the amplification process and knowledge of where amplification was located on the solid support.
Regarding claim 37, as shown in figure 1, the adapters are shorter than the probe on the solid support.
Regarding claim 38, Sabot et al. teach an ideal melting (denaturation) temperature from 60-65°C. [0078].
Regarding claim 39, Sabot et al. show in figure 1 that the amplicon is hybridized to the template. [0014]
Regarding claim 40, Sabot et al. show in figure 1 that the amplicon is then used for amplification. [0014]
Regarding claim 41, Sabot et al. teach that immobilization can be covalent and immobilization can occur via hybridization to a surface attached oligonucleotide or polynucleotide. [0026]. As stated above the template copy (amplicon) can hybridize to an amplification oligonucleotide and be extended. [0014].
Regarding claims 42, 43, and 46, based on the claim interpretation above under 35 USC 112, the second amplicon would result from a second target polynucleotide, which is taught by Sabot et al. because a plurality of template polynucleotides is provided. (claim 1). The inability to bind to a to capture primers of the first plurality of capture primers would depend on sequence or is the capture primers were blocked. [0045].
Regarding claims 44 and 47, Sabot et al. teach that blocking the amplification primer inhibits hybridization and/or extension. [0045].
Regarding claim 48, Sabot et al. teach P5 and P7 primers. [0021].
Regarding claim 49, Sabot et al. show in figure 1, the adapters are shorter than the probe on the solid support, therefore, one of ordinary skill in the art would make the primers to accommodate the probe length that is attached to the solid support so they can hybridize.
Regarding claim 50-52, Sabot et al. do not state how many bases shorter the probes are that are attached to the solid support or the approximate length of the probes compared to each other, however, it is known in the art to make them shorter and a specific number of bases shorter, or the same approximate length, would be a matter of design choice for one of ordinary skill in the art.
Regarding claims 53-55, Sabot et al. teach arranging probes in different areas. Arranging the probes in specific locations would provide one of skill in the art greater control over the amplification process and knowledge of where amplification was located on the solid support. One of skill in the art would have been motivated to arrange the probes in any particular pattern that suited their purpose because it was known in the art that probes could be placed in discreet locations.
Claim 45 is rejected under 35 U.S.C. 103 as being unpatentable over Sabot et al. (US 2012/0122737 A1) as applied to claims 36, 37-44, and 46-55 above, and further in view of Noll (Lablogatory, 2016).
The teachings of Sabot et al. are applied to claims 38 and 45 as they were applied to claims 36, 37-44, and 46-55. Sabot et al. does not teach the melting temperatures recited in claim 45. Claim 45 recites a melting temperature of 20°C between the second adapter and the third amplicon.
Sabot et al. teach an ideal melting (denaturation) temperature from 60-65°C. [0078]. Noll teaches that at the melting temperature, half of the sequence is double stranded and half of the sequence is single stranded. Therefore, a probe/primer with a low melting temperature will not bind in an assay using a higher temperature. One of ordinary skill in the art would know that designing a probe/primer with a low melting temperature and utilizing a high temperature in the assay will result in the probe/primer not binding.
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 36-55 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 11,913,067 B2.
The instant claims require a composition for a substrate to perform the method. That composition is recited in claims 1-20 of the 067 patent. Therefore, it would have been obvious to one of ordinary skill in the art to utilize the substrate of the 067 patent to perform the method of the instant claims.
Conclusion
No claims are allowed.
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/MINDY G BROWN/Patent Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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