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 8/8/2023 is acknowledged. Claims 3-6 have been amended. Claims 10-16 have been added. Claims 1-16 are pending.
Priority
This application claims benefit of 63/337044 filed 04/29/2022.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 3/5/2024 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.
Drawings
The drawings were received on 8/8/2023 is acknowledged. However, the Figure 19 is objected to because the drawing is difficult to read, perhaps due to copy machine artifacts in that the shading makes interpretation difficult.
Applicant is required to submit a proposed drawing correction in reply to this Office action. However, formal correction of the noted defect may be deferred until after the examiner has considered the proposed drawing correction. Failure to timely submit the proposed drawing correction will result in the abandonment of the application.
Specification
The disclosure is objected to because of the following informalities:
(a) The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code at pages 97 and 170. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Appropriate correction 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) 1-6 and 10-13 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Trevisan et al {Travisan, used interchangeably herein} (Biosensors and Bioelectronics, 26, 1631-1637, 2010).
Regarding claim 1, Travisan teaches a method for detecting an analyte in a sample, comprising: contacting a substrate construct with a sample that may comprise the analyte, and using evanescent wave imaging to detect the analyte (page 1632, col. 2, last paragraph bridging top paragraph of page 1633, col. 1; see also Figure 1).
Regarding claim 2, Travisan teaches a method for diagnosing a disease in a subject, comprising: providing a sample that may comprise an analyte from the subject, contacting a substrate construct with the sample, using evanescent wave imaging to detect the presence of the analyte, and responsive to detecting the presence of the analyte, diagnosing the subject as having the disease (page 1632, col. 2, last paragraph bridging top paragraph of page 1633, col. 1; page 1636, col. 2, section 3.5 which teaches detection of a nosocomial infections; see also Figure 1).
Regarding claims 3 and 10, Travisan teaches wherein the substrate construct comprises a substrate polynucleotide (page 1632, col. 2, last paragraph bridging top paragraph of page 1633; page 1633, last paragraph under section 2.2.1)
Regarding claims 4 and 11, Travisan teaches absent a wash step prior detection (page 1632, col. 2, last paragraph bridging top paragraph of page 1633, col. 1 and section 3.5 on page 1636).
Regarding claims 5 and 12, Travisan teaches further comprising contacting the sample with a label that binds to the analyte, wherein the substrate construct binds to the label (page 1632, col. 2, last paragraph bridging top paragraph of page 1633, col. 1; see also Figure 1; see section 2.2.2).
Regarding claims 6 and 13, Travisan teaches wherein:1) the analyte comprises a target nucleic acid; and 2) the substrate construct comprises a substrate polynucleotide comprising a sequence having identity or complementarity with the target nucleic acid (page 1632, col. 2, last paragraph bridging top paragraph of page 1633, col. 1; see also Figure 1; see also section 3.2). Thus, Travisan meets the limitations of the claims recited above.
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.
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.
Claim(s) 7-9 and 14-16 is/are rejected under 35 U.S.C. 103 as being unpatentable over Travisan et al as previously applied above for the claims recited above, in view of Huertas (Frontiers in Chemistry, 7 (724), 1-18, 2019) and further in view of Mir et al (20180327829, Nov. 2018).
Regarding claims 7-9 and 14-16, Travisan teach a method comprising method for detecting an analyte in a sample, comprising: contacting a substrate construct with a sample that may comprise the analyte, and using evanescent wave imaging to detect the analyte (page 1632, col. 2, last paragraph bridging top paragraph of page 1633, col. 1; see also Figure 1).
Travisan does not expressly teach wherein the method comprising amplifying the target nucleic acid to produce a substrate polynucleotide amplicon and further contacting the substrate polynucleotide amplicon with sequencing reagents and sequencing the substrate polynucleotide amplicon.
In a similar embodiment, Huertas teach using evanescent-wave optical biosensor and imaging for screening of nucleic acids in clinical context (abstract). Huertas et al teach that sensitivity is one of the main challenges in the detection of nucleic acids. The reference teaches that the outstanding sensitivity required for nucleic acid analysis can be obtained by the combination of highly sensitive biosensor transducer and signal pre- and post-amplification approaches by PCR based methods or signal enhancers, such as nanomaterials or DNA/RNA binding proteins. Huertas et al teach that the bioreceptor layer must interact with sufficient specificity and selectivity with the target nucleic acid. It is highly dependent on both the proper covalent attachment to the surface and the hybridization event (page 6, last paragraph of col. 1). Huertas further teach that amplification strategies facilitate the identification and quantification of extremely low-concentrated samples or small targets which do not have enough mass, size and/or concentration to generate a significant change in the refractive index. The reference teaches that the amplification approach makes use of an enzyme (most often DNA polymerase) to create a large number of copies of a specific nucleic acid or isothermal PCR based strategies that is carried out at a constant temperature, increasing the speed of analysis, avoiding alternating temperature cycles (page 10, col. 2 “amplification strategies” to page 11). (see also Figure 2 and Figure 3).
Huertas does not expressly teach contacting the substrate polynucleotide amplicon with sequencing reagents and sequencing the substrate polynucleotide amplicon.
Mir provides a method of performing a super-resolution sequencing method, the method comprising (a) providing an array of target polynucleotides in a fluidic vessel; (b) contacting the array of polynucleotides with a solution comprising (i) polymerization complex and (ii) reversibly terminating and differently labeled A,C,G, and T/U nucleotides; (c) incorporating one of the differently labeled nucleotides, using the polymerization complex, into a chain complementary to at least one of the array of polynucleotides; (d) binding imaging tags to the differently labeled nucleotides of step (c); (e) imaging and storing the identity and position of the imaging tags of step (d); (f) reversing termination (b)-(e); (g) repeating steps (b)-(e) and assembling a sequence for each of the array of target polynucleotides from the stored identity and position of the imaging tags, optionally as a homogeneous or one pot reaction (abstract). Mir teaches wherein the method may encompass contacting the substrate polynucleotide amplicon with sequencing reagents and sequencing the substrate polynucleotide amplicon (see paragraphs [484] – [0490], [0504] – [0517]). Mir teaches wherein the imaging method may encompass evanescent wave imaging ([0541] and claim 17).
It would have been prima facie obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to have been motivated to have combined the method of Travisan in view of Heuertas and further in view of Mir. The ordinary artisan would have been motivated to do for improved advantages of detection of desired targets with increased speed without the need for any washing steps as suggested by Travisan.
Double Patenting
13. 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.
14. Claims 1, 8 and 9 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of copending Application No. 18/309752. 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 claims of copending application comprise the step of contacting the substrate polynucleotide with sequencing reagents and using evanescent wave imaging in the sequencing reaction.
The claims 1-2 of copending application 18/309752 differs from the claims 1, 8 and 9 of the instant invention in that the claims of the copending application are broader in scope. Likewise, the claims 1, 8 and 9 of the instant invention do not expressly recite that the identifying comprises 3’-unblocked protected nucleotide incorporated into a sequencing primer. However, the instant specification defines that the protected nucleotide recited in the claim 9 is a 3’-unblocked nucleotide (page 31). Thus, the claims 1-2 of copending application 18/309752 falls entirely within the scope of the claims 1, 8 and 9 of the instant invention.
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".
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
15. 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