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 .
Inventor’s Oath or Declaration
At the time of writing this Office Action, it appears that an inventor’s oath or declaration has not been received.
Drawings
The drawings are objected to because Fig. 19 of the drawing set dated 08/08/2023 contains text that appears illegible. Please ensure that all letters measure at least 1/8 inch in height (MPEP 608.02). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see pp. 97 and 171 of the specification as-filed). 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.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 03/05/2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Objections
Claim 1 is objected to because of the following informalities:
In claim 1, it is believed the claim should read “…the substrate; and an image sensor…”.
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.
Claims 15 and 20 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.
Claim 15 recites the limitation "the substrate constructs" in line 1. There is insufficient antecedent basis for this limitation in the claim. Claim 1, from which claim 15 depends, does not recite substrate constructs.
Claim 20 recites the limitation "the one or more spots" in line 2. There is insufficient antecedent basis for this limitation in the claim. Claim 1, from which claim 20 ultimately depends, does not recite one or more spots.
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.
Claims 1-3, 6, 10-11, and 14-16 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Nordman et al. (US Patent Application Publication 2009/0305909).
Regarding claim 1, Nordman et al. discloses an imaging device (para. 44, 88, 98) comprising:
a reservoir (called sample chamber, comprising space 118) having an interior lower surface (para. 50) (Fig. 1, sheet 1 of 27);
a substrate (112) arranged below the reservoir (para. 50) (Fig. 1, sheet 1 of 27), wherein at least a portion of an upper surface of the substrate forms the interior lower surface of the reservoir (para. 50) (Figs. 1 and 3, sheets 1 and 3 of 27);
a first light source (120) arranged proximate the substrate (para. 44) (Fig. 1, sheet 1 of 27) and configured to direct light into the substrate (para. 50, 52) (Fig. 1, sheet 1 of 27); and
an image sensor (CCD detector of optical assembly 130) arranged below the substrate and configured to receive emission light produced within the reservoir (para. 46-48, 88) (Fig. 1, sheet 1 of 27).
Regarding claim 2, Nordman et al. discloses wherein the upper surface of the substrate comprises one or more spots each comprising a pool of substrate constructs immobilized to the surface (para. 46, 49, 52-56).
Regarding claim 3, Nordman et al. discloses wherein the substrate (112) is arranged between the reservoir (sample chamber, comprising space 118) and the image sensor (CCD detector of optical assembly 130) such that the emission light passes through the substrate prior to being received by the image sensor (para. 48-50) (Fig. 1, sheet 1 of 27).
Regarding claim 6, Nordman et al. discloses an optical filter positioned between the reservoir and the image sensor (para. 90-91) (Figs. 1 and 14A-14B, sheets 1 and 19 of 27).
Regarding claim 10, Nordman et al. discloses wherein the reservoir comprises one or more reagents that include sequencing reagents (para. 47, 50-54).
Regarding claim 11, Nordman et al. discloses wherein the sequencing reagents comprise a sequencing primer (para. 57), a pool of nucleotides (para. 50), and a polymerase (para. 57).
Regarding claim 14, Nordman et al. discloses wherein the reservoir and substrate are coupled to a common structure (para. 50), and wherein the reservoir, substrate, and common structure are configured to be removably inserted into the imaging device (para. 66).
Regarding claim 15, Nordman et al. discloses wherein the substrate constructs each comprise a substrate polynucleotide (para. 46, 49, 52-56).
Regarding claim 16, Nordman et al. discloses wherein the substrate polynucleotide comprises a DNA template (para. 49, 57) (reads on a sequence with identity or complementarity to a target nucleic acid that may be present in the sample).
Claim Rejections - 35 USC § 103
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.
Claims 4-5 are rejected under 35 U.S.C. 103 as being unpatentable over Nordman et al. (US Patent Application Publication 2009/0305909) in view of Nimse et al. (Immobilization Techniques for Microarray: Challenges and Applications).
Regarding claim 4, Nordman et al. discloses wherein each of the one or more spots comprise a nucleic acid molecule (para. 46) immobilized to the surface of the substrate (para. 49, 52-53). The device comprises an array of the spots (para. 51) for the detection of a target nucleic acid molecule (para. 46-47).
Nordman et al. is silent as to a gold layer beneath at least one of the one or more spots.
Nimse et al. discloses that it was known in the art to immobilize nucleic acid molecules on a surface for the purpose of forming a DNA microarray chip (p. 22209 para. 1) by providing a gold layer beneath the nucleic acid molecules such that the molecules bind thereto (p. 22212 para. 1). Nimse et al. further discloses that this technique is used “frequently” and provides a “strong interaction” between DNA and the gold surface (p. 22212 para. 1-2).
It would have been obvious to one of ordinary skill in the art at the time before the effective filing date of the claimed invention to modify the device disclosed by Nordman et al. to comprise a gold layer beneath at least one of the one or more spots, based on the teachings of Nimse et al., as the skilled artisan would have been motivated to use a common immobilization technique recognized in the art to provide a strong bond between the substrate and the nucleic acid molecules of the one or more spots.
Regarding claim 5, Nordman et al. discloses wherein each of the one or more spots comprise a nucleic acid molecule (para. 46) immobilized to the surface of the substrate (para. 49, 52-53). The device comprises an array of the spots (para. 51) for the detection of a target nucleic acid molecule (para. 46-47).
Nordman et al. is silent as to a gold layer beneath each of the one or more spots.
Nimse et al. discloses that it was known in the art to immobilize nucleic acid molecules on a surface for the purpose of forming a DNA microarray chip (p. 22209 para. 1) by providing a gold layer beneath the nucleic acid molecules such that the molecules bind thereto (p. 22212 para. 1). Nimse et al. further discloses that this technique is used “frequently” and provides a “strong interaction” between DNA and the gold surface (p. 22212 para. 1-2).
It would have been obvious to one of ordinary skill in the art at the time before the effective filing date of the claimed invention to modify the device disclosed by Nordman et al. to comprise a gold layer beneath each the one or more spots, based on the teachings of Nimse et al., as the skilled artisan would have been motivated to use a common immobilization technique recognized in the art to provide a strong bond between the substrate and the nucleic acid molecules of the one or more spots.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Nordman et al. (US Patent Application Publication 2009/0305909) in view of Kramer (The Right Filter Set Gets the Most out of a Microscope).
Regarding claim 7, Nordman et al. discloses the optical filter between the reservoir and the image sensor, as set forth above, and further discloses wherein the optical filter directs the emission light to the image sensor (para. 90-91).
However, Nordman et al. discloses wherein the optical filter is a bandpass filter (para. 90-91) rather than a longpass filter.
Nonetheless, Kramer discloses that “Emission filters can be bandpass or long-pass filters” (p. 3 col. 2) and longpass filters have the advantage of maximizing the amount of signal passing through to the detector (p. 3 col. 2-3).
It would have been obvious to one of ordinary skill in the art at the time before the effective filing date of the claimed invention to modify the optical filter disclosed by Nordman et al. to be a longpass filter, based on the teachings of Kramer, as the skilled artisan would have been motivated to use a filter type that allows maximum passage of emission signal.
Claims 8-9 are rejected under 35 U.S.C. 103 as being unpatentable over Nordman et al. (US Patent Application Publication 2009/0305909).
Regarding claim 8, Nordman et al. discloses wherein the substrate has a refractive index of about 1.46 (para. 77).
Nordman et al. is silent as to wherein the substrate has a refractive index of at least 1.48.
Nonetheless, it has been held that in the case where a claimed range approaches/is similar to the prior art range, a prima facie case of obviousness exists (MPEP 2144.05). In this case, the prior art value of 1.46 approaches the claim value of at least 1.48 so closely that one of ordinary skill in the art would expect only negligible differences between the two. Therefore, a prima facie case of obviousness exists, absent any evidence of criticality of the claimed value.
Regarding claim 9, Nordman et al. discloses wherein the substrate has a refractive index of about 1.46 (para. 77).
Nordman et al. is silent as to wherein the substrate has a refractive index of at least 1.7.
Nonetheless, it has been held that where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation, when the particular parameter is recognized as a result-effective variable (MPEP §2144.05). Nordman et al. discloses general conditions, as discussed above, and further discloses that the refractive index of the substrate impacts which fluids can effectively be used in the sample chamber during device operation (para. 77). Therefore, it would have been obvious to one of ordinary skill in the art at the time before the effective filing date of the claimed invention to discover an optimum or workable range for the refractive index through routine experimentation.
Claims 12-13 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Nordman et al. (US Patent Application Publication 2009/0305909) in view of Wimberger-Friedl et al. (US Patent Application Publication 2015/0079585).
Regarding claim 12, Nordman et al. discloses wherein the reservoir comprises sequencing reagents including a pool of nucleotides, as set forth above. Nordman et al. further discloses wherein fluorescent labels of newly incorporated nucleotides can be cleaved (e.g. via a photo-cleavable linker) throughout sequencing (para. 48).
Nordman et al. does not expressly teach wherein the pool of nucleotides is a pool of protected nucleotides.
Wimberger-Friedl et al. discloses a device for DNA sequencing (Abstract) comprising a substrate comprising DNA bound thereto and a reservoir above the substrate, the reservoir comprising a pool of nucleotides (para. 75) (Fig. 1, sheet 1 of 9). Specifically, the nucleotides are protected nucleotides (Abstract, para. 10, 75). Wimberger-Friedl et al. discloses that using protected nucleotides provides the advantage of increasing efficiency of the sequencing process (para. 17).
It would have been obvious to one of ordinary skill in the art at the time before the effective filing date of the claimed invention to modify the pool of nucleotides disclosed by Nordman et al. to be a pool of protected nucleotides, based on the teachings of Wimberger-Friedl et al., in order to enhance efficiency during sequencing operations of the device.
Regarding claim 13, Nordman et al. in view of Wimberger-Friedl et al. teaches the polymerase and the protected nucleotides, as set forth above, and furthermore, neither reference makes any mention of the polymerase exhibiting any incorporation bias against the nucleotides. Therefore, the prior art reads on the claimed subject matter.
Regarding claim 17, Nordman et al. discloses wherein the device can be used for nucleic acid sequencing (para. 10), wherein the sequencing is performed by using the first light source to provide excitation light to cause fluorescence emission of fluorescence-labeled nucleotides within the device (para. 47). Nordman et al. further discloses wherein fluorescent labels of newly incorporated nucleotides can be cleaved (e.g. via a photo-cleavable linker) throughout sequencing (para. 48).
Nordman et al. is silent as to a second light source arranged proximate to the substrate and configured to direct light into the substrate, wherein light produced by the second light source has a different wavelength spectrum different from light produced by the at least one first light source.
Wimberger-Friedl et al. discloses a device for DNA sequencing (Abstract), wherein the device uses fluorescence-labeled nucleotides (para. 75) and a substrate having DNA bound thereto (para. 75). Wimberger-Friedl et al. further discloses wherein the device comprises a first light source arranged proximate the substrate configured to direct excitation light into the substrate to induce fluorescence (para. 14, 75, 83) (Fig. 1, sheet 1 of 9) and a second light source arranged proximate the substrate to direct cleavage light into the substrate for cleavage of fluorescence labels (para. 76, 83) (Fig. 1, sheet 1 of 9), wherein the excitation light and the cleavage light have different wavelength spectrums (para. 14, 20).
It would have been obvious to one of ordinary skill in the art at the time before the effective filing date of the claimed invention to modify the device disclosed by Nordman et al. to comprise a second light source arranged proximate to the substrate and configured to direct light into the substrate, wherein light produced by the second light source has a different wavelength spectrum different from light produced by the at least one first light source, in order to achieve the light-activated cleavage of fluorescence labels as envisioned by Nordman et al., using a configuration known in the prior art as embodied by Wimberger-Friedl et al. to be suitable for providing both excitation and cleavage light.
Claims 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Nordman et al. (US Patent Application Publication 2009/0305909) in view of Liu et al. (Integrated optical waveguide-based fluorescent immunosensor for fast and sensitive detection of microcystin-LR in lakes: Optimization and Analysis).
Regarding claim 18, Nordman et al. discloses the substrate, as set forth above, wherein the substrate comprises a plurality of discrete analysis points (para. 43, 50-51) which in operation emit light to be sensed by a detector (para. 84).
Nordman et al. is silent as to a transparent isolation layer arranged on the upper surface of the substrate.
Liu et al. discloses that it was known in the art to provide a transparent isolation layer on the upper surface of a substrate of a biosensor, wherein the isolation layer covers the substrate except for openings over discrete sensing locations, to isolate the substrate from an analyte except for at the sensing locations (p. 2 para 4-5) (Fig. 1, p. 3). Specifically, the transparent isolation layer has is a transparent material having a thickness of 1 µm (p. 2 para. 5).
It would have been obvious to one of ordinary skill in the art at the time before the effective filing date of the claimed invention to modify the device disclosed by Nordman et al. to comprise a transparent isolation layer arranged on the upper surface of the substrate, e.g., a 1 µm thick layer covering the substrate except for the discrete analysis points on the substrate, based on the teachings of Liu et al., in order to provide isolation and prevent reactions between an analyte and the substrate except as desired on analysis points of the substrate.
Regarding claim 19, Nordman et al. in view of Liu et al. teaches the transparent isolation layer having a thickness of 1 µm (falls within the claim range), as set forth above.
Regarding claim 20, Nordman et al. in view of Liu et al. teaches the transparent isolation layer covering the upper surface of the substrate (i.e., the interior lower surface of the reservoir as discussed in the rejection of claim 1, above) except for the one or more spots (analysis points), as set forth above.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Nordman et al. (US Patent Application Publication 2009/0305909) in view of Sugimura et al. (US Patent Application Publication 20120316087).
Regarding claim 21, Nordman et al. discloses the substrate, as set forth above, wherein the substrate is made of a material such as silica (para. 70) and comprises DNA immobilized thereon (para. 52-54).
Nordman et al. is silent as to wherein the substrate comprises sapphire.
Sugimura et al. discloses a device comprising a substrate upon which nucleic acids are immobilized (para. 37), wherein the substrate may be made of materials such as glass or sapphire.
It would have been obvious to one of ordinary skill in the art at the time before the effective filing date of the claimed invention to modify the substrate disclosed by Nordman et al. to comprise sapphire, as such a modification represents simple substitution of one known element for another to obtain predictable results (MPEP § 2143), in this case, substitution of sapphire for silica to obtain the predictable result of a substrate compatible with nucleic acid handling.
Citation of Pertinent Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Klunder et al. (US Patent Application Publication 2010/0252751) is directed to device for evanescent wave imaging comprising a sample chamber.
Conclusion
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/HOLLY KIPOUROS/Primary Examiner, Art Unit 1799