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 .
Response to Amendment
The Amendment filed 11/24/2025 has been entered. Claims 1-13 and 21-27 remain pending in the application. Applicant’s amendments to the claims have overcome each and every objection and rejection under 35 U.S.C. 112(b) previously set forth in the Final Office Action mailed 07/23/2025.
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.
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 1-2, 4-5, 12-13, and 21-26 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. (WO 2012031234 A2; cited in the IDS filed 08/27/2020) in view of Tsai et al. (KR 20130047550 A, see machine translation) and further in view of Merrill (US 5965875 A; cited in the IDS filed 08/27/2020).
Regarding claim 1, Li teaches a device (abstract; Fig. 3) comprising:
a transparent layer (Fig. 3; transparent layer 304) defining a surface (Fig. 3, surface 304) exposed to a flow volume (Fig. 3 shows surface 304 capable of being exposed to a flow volume; paragraph [0008] teaches flowing a solution over a surface layer of the device) and to secure a target polynucleotide template (interpreted as an intended use, see MPEP 2114; Fig. 1 shows an embodiment of the surface capable of securing a nucleic acid strand, thus the surface of Fig. 3 is structurally capable of securing a target polynucleotide template at a later time); and
a detector structure (Fig. 3 shows detectors 308) in optical communication with and secured to the transparent layer (Fig. 3 shows detectors 308 in optical communication with and secured to transparent layer 304) and including a plurality of detectors (detectors 308) configured to detect a fluorescent signal emitted during nucleotide incorporation during template-dependent nucleic acid synthesis (paragraph [0049] teaches detectors capable of sensing light, such as fluorescent emissions), wherein the detector structure includes a plurality of pixels (paragraph [0009] and Fig. 3 teaches a plurality of detectors 308, wherein “plurality of pixels” has a broadest reasonable interpretation as groupings of the detectors), each pixel of the plurality of pixels including a set of detectors of the plurality of detectors (Fig. 3 shows a set of detectors 308; wherein each “pixel” or grouping is being interpreted as comprising a set of light detectors of the array of light detectors; paragraph [0034] teaches detectors can include CMOS detectors or CCD);
and circuitry (paragraph [0053], “controllers or circuitry 514”).
While Li teaches: CMOS or CCD detectors (paragraph [0034]); detecting fluorescent emissions, wherein nucleotides can have a fluorescent label that emits a uniquely recognizable signature or wavelength (paragraphs [0066]-[0067]); and detectors can include multilayer semiconductor structures (paragraph [0055]), Li fails to explicitly teach: wherein the set of detectors is formed by a semiconductor structure including a substrate, a deep n-type implant, a shallow n-type implant, a p-type implant disposed between the deep n-type implant and the shallow n-type implant, and a p-type layer disposed over the shallow n-type implant and having a top surface coplanar with a top surface of the substrate, the deep n-type implant coupled to a first read column, the shallow n-type implant couple to a second read column, the p-type implant coupled to a third read column, wherein electron-hole pairs are created at depths in the substrate dependent on wavelength of radiation, with blue photons creating electron-hole pairs near the surface of the substrate and red photons creating electron-hole pairs deeper in the substrate, wherein the set of detectors includes at least two confinement wells at different depths within the substrate, including a shallow confinement well comprising the shallow n-type implant and centered around 1 micrometer depth and a deep confinement well comprising the deep n-type implant and centered around 2 micrometers depth, the substrate constituting a p-type material; and the circuitry to read each of the first, second, and third read columns in response to a row select.
Tsai teaches a semiconductor structure related to a photodiode array compatible with a CMOS manufacturing process (paragraph [0001]; Figs. 1a-1b). Tsai teaches a multi-junction photodiode that allows for low dark current and high sensitivity, which allows for fluorescence detection of biochemical reactions (paragraph [0059]). Tsai teaches the structure including a p-type substrate (Figs. 1a-1b; elements 102, 104; element 104 is p- and element 102 is p+, i.e. p-type material), a deep n-type implant (106), a shallow n-type implant (110), a p-type implant (108) disposed between the deep n-type implant (106) and the shallow n-type implant (110), and a p-type layer (112) disposed over the shallow n-type implant (110) and having a top surface coplanar with a top surface of the substrate (see below annotated Fig. 1b showing a top surface of p-type layer 112 coplanar with a top surface of the substrate 104; wherein the substrate comprises elements 102, 104), the deep n-type implant coupled to a first read column (elements 118, 126 are coupled to deep n-type implant 106), the shallow n-type implant couple to a second read column (elements 116 and 126 are coupled to shallow n-type implant 110), the p-type implant coupled to a third read column (element 124 is coupled to p-type implant 108), and the substrate constituting a p-type material (Fig. 1a-1b, element 104 is p- and element 102 is p+, i.e. p-type material); and circuitry (paragraph [0031], “circuit design”; paragraph [0039], “external circuits”). Tsai teaches wherein the detector (Fig. 1a-1b) includes at least three confinement wells at different depths within the p-type substrate (Figs. 1a-1B shows at least three confinement wells 114, 112, 110, 108, 106 within the p-type substrate 104), including a shallow confinement well comprising the shallow n-type implant (Fig. 1b, e.g. element 110) and a deep confinement well comprising the deep n-type implant (Fig. 1b, e.g. element 106). Tsai teaches multi-junction structure exhibits different quantum efficiencies within photodiodes located at different depths for blue, green, and red light (paragraph [0003]), and through the design of specific stacked structures, i.e. confinement wells, various depths of junction structures, and changes in doping concentration of junctions/layers the multi-junction photodiode is formed to allow for discrimination of various wavelengths, high detection sensitivity, and low noise (paragraph [0018]).
Since Tsai teaches a semiconductor structure as a photodetector, similar to Li, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the set of detectors of Li to incorporate the teachings of the semiconductor structure that include confinement wells at different depths, such as shallow and deep p-type and n-type implants within a p-type substrate, of Tsai (Fig. 1b) to provide: wherein the set of detectors is formed by a semiconductor structure including a substrate, a deep n-type implant, a shallow n-type implant, a p-type implant disposed between the deep n-type implant and the shallow n-type implant, and a p-type layer disposed over the shallow n-type implant and having a top surface coplanar with a top surface of the substrate, the deep n-type implant coupled to a first read column, the shallow n-type implant couple to a second read column, the p-type implant coupled to a third read column, wherein the set of detectors includes at least two confinement wells at different depths within the substrate, including a shallow confinement well comprising the shallow n-type implant and a deep confinement well comprising the deep n-type implant, the substrate constituting a p-type material. Doing so would improve analysis of molecules through discrimination of various wavelengths, high detection sensitivity, and low noise as taught by Tsai (paragraph [0018]) and have a reasonable expectation of successfully improving sensitivity of a signal to be analyzed.
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. the claimed pixel structure of Tsai and Li’s device) by known methods with no change in their respective functions (e.g. detecting fluorescent signal), and the combinations yielded nothing more than predictable results (i.e. providing the specific pixel structure as claimed and taught by Tsai would yield nothing more than the obvious and predictable result of enabling discrimination of various wavelengths, high detection sensitivity, and low noise). See MPEP 2143(A).
Modified Li fails to teach: wherein electron-hole pairs are created at depths in the substrate dependent on wavelength of radiation, with blue photons creating electron-hole pairs near the surface of the substrate and red photons creating electron-hole pairs deeper in the substrate; the shallow confinement well centered around 1 micrometer depth and the deep confinement well centered around 2 micrometers depth; and the circuity to read each of the first, second, and third read columns in response to a row select.
Merrill teaches an imaging array based upon a three-color pixel sensor using a triple-well structure (abstract, Figs. 6-7), wherein the array results in elimination of color aliasing (abstract). Merrill teaches a singular pixel comprises a semiconductor structure (Fig. 6); including by a p-type substrate (100), a deep n-type implant (102), a shallow n-type implant (106), and a p-type implant (104) disposed between the deep n-type implant and the shallow n-type implant (Fig. 6), the deep n-type implant coupled to a first read column (interpreted as the wiring from element 102 to element 110), the shallow n-type implant coupled to a second read column (interpreted as the wiring from element 106 to element 114), the p-type implant coupled to a third read column (interpreted as the wiring from element 104 to element 112). Merrill teaches circuitry to read each of the first, second, and third read columns in response to a row select (column 9, lines 13-47; Fig. 6 shows current meters 110, 112, 114). Merrill teaches that the structure of the pixel also eliminates the complex process steps associated with color filter arrays (column 3, lines 25-30) and that the overall efficiency of use for available photons are increased and quantum efficiency is improved overall in excess of three times (column 3, lines 30-37). Merrill discusses known imaging arrays such as CCD devices and CMOS integrated circuits (columns 1-2, section 2), wherein the present imaging array has an advantage of using a triple-well pixel cell structure to take advantage of the differences in absorption length in silicon of light of different wavelengths to measure different colors in the same location with sensitive areas almost as large as their spacing (column 2, lines 53-58).
Since Merrill teaches a photodetector, similar to modified Li, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have altered the circuitry of modified Li to incorporate the teachings of circuitry of a pixel sensor including current meters of Merrill (column 9, lines 13-47; Fig. 6 shows current meters 110, 112, 114) to provide the circuitry to read each of the first, second, and third read columns in response to a row select. Doing so would have a reasonable expectation of successfully allowing signals to be analyzed from the semiconductor structure as taught by Merrill (column 9, lines 13-47).
Modified Li fails to teach: wherein electron-hole pairs are created at depths in the substrate dependent on wavelength of radiation, with blue photons creating electron-hole pairs near the surface of the substrate and red photons creating electron-hole pairs deeper in the substrate; the shallow confinement well centered around 1 micrometer depth and the deep confinement well centered around 2 micrometers depth.
Tsai teaches wherein the detector (Fig. 1a-1b) includes at least three confinement wells at different depths within the p-type substrate (Figs. 1a-1B shows at least three confinement wells 114, 112, 110, 108, 106 within the p-type substrate 104), including a shallow confinement well (Fig. 1b, e.g. elements 114, 112) and a deep confinement well (Fig. 1b, e.g. elements 110, 108, 106). Tsai teaches multi-junction structure exhibits different quantum efficiencies within photodiodes located at different depths for blue, green, and red light (paragraph [0003]), and through the design of specific stacked structures, i.e. confinement wells, various depths of junction structures, and changes in doping concentration of junctions/layers the multi-junction photodiode is formed to allow for discrimination of various wavelengths, high detection sensitivity, and low noise (paragraph [0018]).
Merrill teaches regions, i.e. confinement wells, formed at different depths of a p-type silicon substrate that are sensitive to desired light wavelengths, such as red, green, and blue light (column 2, line 59 – column 3, line 10). Merrill teaches the invention provides advantages of reducing of color aliasing, efficiency of use for available photons is increased, and the colors are separated by absorption depth are all collected and used, which can result in an overall improvement in quantum efficiency in excess of three times (column 3, lines 25-37). Merrill teaches it is well known that the greater the wavelength of light incident upon a silicon substrate, the deeper the light will penetrate into the silicon before it is absorbed (column 4, lines 33-35), where green light will be absorbed in the silicon substrate at a depth of about 0.5-1.5 microns and red light will be absorbed in the silicon at a depth of about 1.5-3.0 microns (column 4, lines 37-44); therefore, taking advantage of these differences in absorption depth in silicon of light of different wavelengths: the junction depth of the N-doped region is between about 1.5-3.0 microns, and preferably about 2 microns, i.e. the approximate absorption depth of red light (column 4, lines 52-55); and the pn junction between the P-doped region and the N-doped is formed at a depth between about 0.5-1.5 micron, the approximate absorption length of green light in silicon (column 4, lines 61-64). Merrill teaches the sensitive depletion region of the diodes described above extends somewhat above and below the junction depth (column 5, lines 8-10).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the substrate of modified Li to incorporate Tsai’s teachings of multi-junction structure exhibits different quantum efficiencies within photodiodes located at different depths for blue, green, and red light (paragraph [0003]) and the design of specific stacked structures, i.e. confinement wells, such as various depths of junction structures (paragraph [0018]), and Merrill’s teachings of regions, i.e. confinement wells, formed at different depths of a p-type silicon substrate that are sensitive to desired light wavelengths, such as red, green, and blue light (column 2, line 59 – column 3, line 10), such as green light will be absorbed at a depth of about 0.5-1.5 microns and red light will be absorbed at a depth of about 1.5-3.0 microns (column 4, lines 37-44), and providing the junction depth of the N-doped region is between about 1.5-3.0 microns, i.e. the approximate absorption depth of red light (column 4, lines 52-55); and the pn junction between the P-doped region and the N-doped is formed at a depth between about 0.5-1.5 micron, the approximate absorption length of green light in silicon (column 4, lines 61-64) to provide: wherein electron-hole pairs are created at depths in the substrate dependent on wavelength of radiation, with blue photons creating electron-hole pairs near the surface of the substrate and red photons creating electron-hole pairs deeper in the substrate; the shallow confinement well centered around 1 micrometer depth and the deep confinement well centered around 2 micrometers depth. Doing so would have a reasonable expectation of successfully allowing for discrimination of various wavelengths, high detection sensitivity, and low noise (Tsai, paragraph [0018]), reduction of color aliasing, increasing efficiency of use of available photons and allowing the desired colors (e.g. blue photons, red photons, green photons) separated by absorption depth, to be all collected and used, which can result in an overall improvement in quantum efficiency in excess of three times (Merrill, column 3, lines 25-37).
Additionally, since Merrill teaches a junction depth of a confinement well is between about 0.5-1.5 micron for green light (column 4, lines 61-64) and a junction depth of a confinement well is between about 1.5-3.0 microns for red light (column 4, lines 52-55), wherein the claimed depths of 1 micrometer and 2 micrometer lie inside the ranges disclosed by Merrill, it would have been a prima facie case of obviousness to one of ordinary skill in the art to have modified the substrate of modified Li to provide wherein the shallow confinement well centered around 1 micrometer depth and the deep confinement well centered around 2 micrometers depth (MPEP 2144.05 (I); In reWertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In reWoodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990)).
Note that the functional recitations that describe the transparent layer, the plurality of detectors, and the circuitry are given patentable weight to the extent which effects the structure of the claimed apparatus. The prior art structure is capable of performing these functional limitations as discussed above. If the prior art structure is capable of performing the functional limitations, then it meets the claim. Please see MPEP 2114.
Note that “target polynucleotide template”, “electron-hole pairs”, “blue photons”, and “red photons” are not positively recited structurally. The limitation of “wherein electron-hole pairs are created at depths in the substrate dependent on wavelength of radiation, with blue photons creating electron-hole pairs near the surface of the substrate and red photons creating electron-hole pairs deeper in the substrate” is interpreted as a functional limitation of the claimed detector structure. A functional recitation 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 functional limitation, then it meets the claim. MPEP 2114. The apparatus of modified Li is identical to the presently claimed structure. Since modified Li discloses the device comprising the substrate as claimed and therefore, would have the ability to perform the use recited in the claim. See MPEP 2112.01 (I). Additionally, as evidenced by Merrill, it is well known that the greater the wavelength of light incident upon a silicon substrate, the deeper the light will penetrate into the silicon before it is absorbed (column 4, lines 33-35). Therefore, modified Li’s substrate would be structurally capable of having electron-hole pairs created at various depths depending on the wavelength, such as blue photons and red photons created at respective depths, during radiation of the device.
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Annotated Fig. 1b of Tsai: A p-type layer (third well region 112) is disposed over a shallow n-type implant (second well region 110) and having a top surface coplanar with a top surface of the substrate (arrows pointing to top surfaces of the p-type layer 112 and substrate 104 that are coplanar).
Regarding claim 2, Li further teaches wherein each pixel of the plurality of pixels includes at least two detectors of the plurality of detectors (Fig. 3 shows two detectors 308; wherein each “pixel” or grouping is being interpreted as comprising a set of at least two light detectors of the array of light detectors).
Regarding claim 4, Li further teaches wherein each pixel includes at least four detectors (paragraphs [0009]-[0010] teaches a plurality of detectors; paragraph [0049] teach each detector is associated with a reaction volume; Fig. 2 shows at least four reaction regions; thus Li teaches at least four detectors which are interpreted as “each pixel”; wherein each “pixel” or grouping is being interpreted as comprising at least four detectors of the plurality of detectors).
Regarding claim 5, modified Li fails to teach wherein the transparent layer (Li; Fig. 3, layer 304) includes an energy propagation layer.
Li teaches an embodiment wherein the substrate can be formed of a transparent material or includes a layer formed of the transparent material adjacent to the major surface (paragraph [0034]), wherein transparent material or layer permits substantial propagation of electromagnetic radiation having a wavelength of an excitation light provided to the transparent material or layer (paragraph [0034]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the transparent layer of modified Li to incorporate the teachings of an embodiment of a substrate formed of transparent material of Li (paragraph [0034]) to provide wherein the transparent layer includes an energy propagation layer. Doing so would have a reasonable expectation of successfully allowing for substantial propagation of light through the transparent layer, thus improving analysis of the plurality of reaction volumes or wells.
Regarding claim 12, Li further teaches the device further comprising a well structure defining wells (Fig. 3, wells 310 formed from layer 306) disposed on the transparent layer opposite the detector structure (Fig. 3).
Regarding claim 13, modified Li fails to teach the device (Fig. 3) further comprising a lid, the flow volume defined between the lid and the transparent layer.
Li teaches an embodiment (Fig. 10), wherein a device comprises a lid (layer 1006) that can be applied over surface layer 1004 to cap the channels 1008 to allow fluid to flow through the channels (Fig. 10).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the device of modified Li to incorporate the teachings of an embodiment comprising a lid and flow volume between the lid and a layer of Li (Fig. 10) to provide the device further comprising a lid, the flow volume defined between the lid and the transparent layer. Doing so would have a reasonable expectation of successfully capping or covering a channel to improve fluid control and allow for fluid to flow through the channels.
Regarding claim 21, modified Li fails to teach wherein the p-type implant is couple to the third read column through a read transistor and a row select transistor.
Merrill teaches the p-type implant is couple to the third read column through a read transistor and a row select transistor (Fig. 7). Merrill teaches that the structure of the pixel also eliminates the complex process steps associated with color filter arrays (column 3, lines 25-30) and that the overall efficiency of use for available photons are increased and quantum efficiency is improved overall in excess of three times (column 3, lines 30-37).
Since Merrill teaches a photodetector, similar to modified Li, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the p-type implant of modified Li to incorporate the teachings of an implant coupled to a read column of Merrill (Fig. 7) to provide wherein the p-type implant is couple to the third read column through a read transistor and a row select transistor. Doing so would have a reasonable expectation of successfully improving analysis of molecules that produce different colors by eliminating color aliasing, reducing complex processing steps, and improve overall efficiency of measurement as taught by Merrill (column 3, lines 25-37).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. the p-type implant is couple to the third read column through a read transistor and a row select transistor) by known methods with no change in their respective functions (i.e. electrical coupling of components of the pixel for detection), and the combinations yielded nothing more than predictable results (i.e. providing the p-type implant is couple to the third read column through a read transistor and a row select transistor would yield nothing more than the obvious and predictable result of enabling proper electrical connections of pixel components for detection of reactions). See MPEP 2143(A).
Regarding claim 22, modified Li fails to teach wherein the p-type implant is couple to a reset voltage through a reset transistor.
Merrill teaches wherein the p-type implant is couple to a reset voltage through a reset transistor (Fig. 7). Merrill teaches that the structure of the pixel also eliminates the complex process steps associated with color filter arrays (column 3, lines 25-30) and that the overall efficiency of use for available photons are increased and quantum efficiency is improved overall in excess of three times (column 3, lines 30-37).
Since Merrill teaches a photodetector, similar to modified Li, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the p-type implant of modified Li to incorporate the teachings of an implant coupled to a reset voltage through a reset transistor of Merrill (Fig. 7) to provide wherein the p-type implant is couple to a reset voltage through a reset transistor. Doing so would have a reasonable expectation of successfully improving analysis of molecules that produce different colors by eliminating color aliasing, reducing complex processing steps, and improve overall efficiency of measurement as taught by Merrill (column 3, lines 25-37).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. the p-type implant is couple to a reset voltage through a reset transistor) by known methods with no change in their respective functions (i.e. electrical coupling of components of the pixel for detection), and the combinations yielded nothing more than predictable results (i.e. providing the p-type implant is couple to a reset voltage through a reset transistor would yield nothing more than the obvious and predictable result of enabling proper electrical connections of pixel components for detection of reactions). See MPEP 2143(A).
Regarding claim 23, modified Li fails to teach wherein the deep n-type implant is couple to the first read column through a read transistor and a row select transistor.
Merrill teaches wherein the deep n-type implant is couple to the first read column through a read transistor and a row select transistor (Fig. 7). Merrill teaches that the structure of the pixel also eliminates the complex process steps associated with color filter arrays (column 3, lines 25-30) and that the overall efficiency of use for available photons are increased and quantum efficiency is improved overall in excess of three times (column 3, lines 30-37).
Since Merrill teaches a photodetector, similar to modified Li, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the deep n-type implant of modified Li to incorporate the teachings of an implant coupled to a read column of Merrill (Fig. 7) to provide wherein the deep n-type implant is couple to the first read column through a read transistor and a row select transistor. Doing so would have a reasonable expectation of successfully improving analysis of molecules that produce different colors by eliminating color aliasing, reducing complex processing steps, and improve overall efficiency of measurement as taught by Merrill (column 3, lines 25-37).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. the deep n-type implant is couple to the first read column through a read transistor and a row select transistor) by known methods with no change in their respective functions (i.e. electrical coupling of components of the pixel for detection), and the combinations yielded nothing more than predictable results (i.e. providing the deep n-type implant is couple to the first read column through a read transistor and a row select transistor would yield nothing more than the obvious and predictable result of enabling proper electrical connections of pixel components for detection of reactions). See MPEP 2143(A).
Regarding claim 24, modified Li fails to teach wherein the deep n-type implant is couple to a reset voltage through a reset transistor.
Merrill teaches wherein the deep n-type implant is couple to a reset voltage through a reset transistor (Fig. 7). Merrill teaches that the structure of the pixel also eliminates the complex process steps associated with color filter arrays (column 3, lines 25-30) and that the overall efficiency of use for available photons are increased and quantum efficiency is improved overall in excess of three times (column 3, lines 30-37).
Since Merrill teaches a photodetector, similar to modified Li, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the deep n-type implant of modified Li to incorporate the teachings of an implant coupled to a reset voltage and reset transistor of Merrill (Fig. 7) to provide wherein the deep n-type implant is couple to a reset voltage through a reset transistor. Doing so would have a reasonable expectation of successfully improving analysis of molecules that produce different colors by eliminating color aliasing, reducing complex processing steps, and improve overall efficiency of measurement as taught by Merrill (column 3, lines 25-37).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. the deep n-type implant is couple to a reset voltage through a reset transistor) by known methods with no change in their respective functions (i.e. electrical coupling of components of the pixel for detection), and the combinations yielded nothing more than predictable results (i.e. providing the deep n-type implant is couple to a reset voltage through a reset transistor would yield nothing more than the obvious and predictable result of enabling proper electrical connections of pixel components for detection of reactions). See MPEP 2143(A).
Regarding claim 25, modified Li fails to teach wherein the shallow n-type implant is couple to the second read column through a read transistor and a row select transistor.
Merrill teaches the shallow n-type implant is couple to the second read column through a read transistor and a row select transistor (Fig. 7). Merrill teaches that the structure of the pixel also eliminates the complex process steps associated with color filter arrays (column 3, lines 25-30) and that the overall efficiency of use for available photons are increased and quantum efficiency is improved overall in excess of three times (column 3, lines 30-37).
Since Merrill teaches a photodetector, similar to modified Li, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the shallow n-type implant of modified Li to incorporate the teachings of an implant coupled to a read column of Merrill (Fig. 7) to provide wherein the shallow n-type implant is couple to the second read column through a read transistor and a row select transistor Doing so would have a reasonable expectation of successfully improving analysis of molecules that produce different colors by eliminating color aliasing, reducing complex processing steps, and improve overall efficiency of measurement as taught by Merrill (column 3, lines 25-37).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. the shallow n-type implant is couple to the second read column through a read transistor and a row select transistor) by known methods with no change in their respective functions (i.e. electrical coupling of components of the pixel for detection), and the combinations yielded nothing more than predictable results (i.e. providing the shallow n-type implant is couple to the second read column through a read transistor and a row select transistor would yield nothing more than the obvious and predictable result of enabling proper electrical connections of pixel components for detection of reactions). See MPEP 2143(A).
Regarding claim 26, modified Li fails to teach wherein the shallow n-type implant is couple to a reset voltage through a reset transistor.
Merrill teaches the shallow n-type implant is couple to a reset voltage through a reset transistor (Fig. 7). Merrill teaches that the structure of the pixel also eliminates the complex process steps associated with color filter arrays (column 3, lines 25-30) and that the overall efficiency of use for available photons are increased and quantum efficiency is improved overall in excess of three times (column 3, lines 30-37).
Since Merrill teaches a photodetector, similar to modified Li, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the shallow n-type implant of modified Li to incorporate the teachings of an implant coupled to a reset voltage through a reset transistor of Merrill (Fig. 7) to provide wherein the shallow n-type implant is couple to a reset voltage through a reset transistor. Doing so would have a reasonable expectation of successfully improving analysis of molecules that produce different colors by eliminating color aliasing, reducing complex processing steps, and improve overall efficiency of measurement as taught by Merrill (column 3, lines 25-37).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. shallow n-type implant is couple to a reset voltage through a reset transistor) by known methods with no change in their respective functions (i.e. electrical coupling of components of the pixel for detection), and the combinations yielded nothing more than predictable results (i.e. providing the shallow n-type implant is couple to a reset voltage through a reset transistor would yield nothing more than the obvious and predictable result of enabling proper electrical connections of pixel components for detection of reactions). See MPEP 2143(A).
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Li in view of Tsai and Merrill as applied to claim 2 above, and further in view of Lee (US 20090085136 A1).
Regarding claim 3, modified Li fails to teach wherein the at least two detectors are disposed one over the other when viewed in cross-section.
Lee teaches an image sensor comprising a photodiode region (abstract). Lee teaches a vertical-type photodiode providing photodiodes at different depths for receiving different wavelengths of light (paragraph [0017]). Lee teaches at least two detectors disposed one over the other when viewed in cross-section (Fig. 1; color didoes 111, 112, 113). Lee teaches that the vertical-type photodiode inhibits light loss and signal distortion (paragraph [0038]). Lee teaches that by including the vertical-type photodiode, a color filter layer can be omitted, therefore reducing the number of processes for manufacturing an image sensor (paragraph [0020]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the at least two detectors of modified Li to incorporate the teachings of the configuration of detectors of Lee (Fig. 1) to provide where the at least two detectors are disposed one over the other when viewed in cross-section. Doing so would utilize know types of photodiodes in the art, i.e. a vertical-type photodiode as taught by Lee, which would have a reasonable expectation of successfully reducing manufacturing processes and thus costs while allowing for multiple wavelengths to be detected.
Claims 6-8 are rejected under 35 U.S.C. 103 as being unpatentable over Li in view of Tsai and Merrill as applied to claim 1 above, and further in view of Su et al. (US 20100330553 A1).
Regarding claim 6, Li teaches an embodiment wherein the substrate can be formed of a transparent material or includes a layer formed of the transparent material adjacent to the major surface (paragraph [0034]), wherein transparent material or layer permits substantial propagation of electromagnetic radiation having a wavelength of an excitation light provided to the transparent material or layer (paragraph [0034]). Modified Li fails to explicitly teach the device further comprising an energy propagation layer disposed between the transparent layer and the detector structure.
Su teaches a method for sequencing nucleic acids (abstract) and optical detection of the products of nucleic acid sequencing reactions (paragraph [0003]). Su teaches a device for analyzing DNA sequencing (Fig. 8) comprising a reaction substrate (610), a light source (605) and an imager (615), wherein the substrate comprises a transparent layer (Fig. 7; paragraph [0030], low refractive index functional layer 520), chelators (525) attached to the transparent layer, an energy propagation layer (510; paragraph [0030], planar waveguide 510) disposed between the transparent layer (520) and a total internal reflection layer (515; paragraph [0030], low refractive index material 515). Su teaches that evanescence from the propagating light is created in the region of the chelators, which is used to detect chelation of reaction products from DNA sequencing reactions (paragraph [0030]). Su teaches that total internal reflection occurs when the dielectric index of a middle layer is larger than that of surrounding layers (paragraph [0030]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the device of modified Li to incorporate the teachings of an energy propagation layer of Su (Fig. 8) to provide the device further comprising an energy propagation layer disposed between the transparent layer and the detector structure. Doing so which would have a reasonable expectation of successfully being used to detect reaction products of nucleic acids (Su, paragraph [0030]).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. an energy propagation layer disposed between the transparent layer and the detector structure) by known methods with no change in their respective functions (i.e. detecting reaction products), and the combinations yielded nothing more than predictable results (i.e. adding an energy propagation layer between the transparent layer and the detector structure would yield nothing more than the obvious and predictable result of enabling detection of reactions). See MPEP 2143(A).
Regarding claim 7, modified Li fails to explicitly teach wherein the energy propagation layer includes a total internal reflection layer.
Su teaches that total internal reflection occurs when the dielectric index of a middle layer is larger than that of surrounding layers (paragraph [0030]). Su teaches an energy propagation layer (510; paragraph [0030], planar waveguide 510) disposed between the transparent layer (520) and a total internal reflection layer (515; paragraph [0030], low refractive index material 515).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the energy propagation layer of modified Li to further incorporate the teachings of the energy propagation layer of Su (paragraph [0030]) to provide wherein the energy propagation layer includes a total internal reflection layer. Doing so would have a reasonable expectation of successfully being used to detect reaction products of nucleic acids (Su, paragraph [0030]).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. a total internal reflection layer) by known methods with no change in their respective functions (i.e. detecting reaction products), and the combinations yielded nothing more than predictable results (i.e. adding an energy propagation layer between the transparent layer and the detector structure would yield nothing more than the obvious and predictable result of enabling detection of reactions). See MPEP 2143(A).
Regarding claim 8, Li further teaches the device further comprising an energy emitting component (Fig. 3, light source 312) to provide energy to the energy propagation layer (interpreted as an intended use, see MPEP 2114; the light source is capable of providing energy, i.e. light, at a later time).
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Li in view of Tsai and Merrill as applied to claim 1 above, and further in view of Sanfilippo et al. (US 20110272561 A1).
Regarding claim 9, Li further teaches the device further comprising a separator structure extending from the detector structure toward the transparent layer (Fig. 3, see structure between elements 308). Modified Li fails to explicitly teach the separator structure is opaque to the fluorescent signal.
Sanfilippo teaches a photodiode (abstract), wherein detector arrays are used in a variety of scientific applications (paragraph [0002]). Sanfilippo teaches a metal structure of each photodiodes may surround either a resistive anode or a resistive cathode regions of the photodiode and effectively acts also as a metal shield that reduces cross-talk (paragraphs [0018] and [0029]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the separator structure of modified Li to incorporate the teachings of a metal shield for photodiodes of Sanfilippo (paragraphs [0018],[0029]) to provide the separator structure extending from the detector structure toward the transparent layer, the separator structure opaque to the fluorescent signal. Doing so would have a reasonable expectation of successfully reducing cross-talk between the detectors as discussed by Sanfilippo (paragraphs [0018],[0029]), thus improving overall detection.
Claims 10-11 and 27 are rejected under 35 U.S.C. 103 as being unpatentable over Li in view of Tsai and Merrill as applied to claim 1 above, and further in view of Chen et al. (US 20100256918 A1).
Regarding claim 10, while Li teaches fluorescent emissions may be filtered (paragraph [0049]), modified Li fails to teach the device further comprising a filter layer disposed between the device structure and the transparent layer.
Chen teaches a device for detecting objects capable of emitting fluorescence, such as from DNA sequencing (abstract; paragraphs [0091], [0138]). Chen teaches a long-pass interference thin-film optical filter may be placed between the detection zone and the photodiode to partially block the scattered excitation light (paragraph [0175]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the device of modified Li to incorporate the teachings of an optical filter of Chen (paragraph [0175]) to provide the device further comprising a filter layer disposed between the device structure and the transparent layer. Doing so would have a reasonable expectation of successfully improving analysis by improving selectivity of a desired light and reduce noise from scattered excitation light (Chen, paragraph [0175]).
Regarding claim 11, modified Li further teaches wherein the filter layer is configured to limit transmission of excitation energy (see above claim 10; Chen, paragraph [0175] teaches a filter is capable of blocking scattered excitation light).
Regarding claim 27, modified Li further teaches wherein the filter layer is configured to permit the transmission of a wavelength spectrum associated with a dye (see above claim 10; Chen, paragraph [0175] a long-pass interference thin-film optical filter may be placed between the detection zone and the photodiode to partially block the scattered excitation light; thus the filter layer is capable of permitting a transmission of a wavelength at a later time).
Note that the dye is not positively recited structurally and the specific wavelength spectrum is not claimed. A claim is only limited by positively recited elements (MPEP 2115), and thus, inclusion of the material or article (dye) worked upon by a structure (filter layer) being claimed does not impart patentability to the claims."
Response to Arguments
Applicant’s arguments, see pages 5-6, filed 11/24/2025, with respect to the drawing objection, claim objection, and rejections under 35 U.S.C. 112(b) have been fully considered and are persuasive. The drawing objection, claim objection, and rejections under 35 U.S.C. 112(b) of 07/23/2025 have been withdrawn.
Applicant’s arguments, see pages 6-8, filed 11/24/2025, with respect to the rejection(s) of claims 1-13 and 21-27, specifically regarding claim 1, under 35 U.S.C. 103, have been fully considered but they are not persuasive.
In response to applicant's arguments against the references individually (Remarks, page 7, regarding Li, Tsai, an Merrill), one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
In response to applicant’s argument that Li does not teach the “specific structural arrangement as claimed” (Remarks, page 7), the examiner partially agrees. As discussed above in the rejection of claim 1 under 35 U.S.C. 103, Li fails to explicitly teach: wherein the set of detectors is formed by a semiconductor structure including a substrate, a deep n-type implant, a shallow n-type implant, a p-type implant disposed between the deep n-type implant and the shallow n-type implant, and a p-type layer disposed over the shallow n-type implant and having a top surface coplanar with a top surface of the substrate, the deep n-type implant coupled to a first read column, the shallow n-type implant couple to a second read column, the p-type implant coupled to a third read column, wherein electron-hole pairs are created at depths in the substrate dependent on wavelength of radiation, with blue photons creating electron-hole pairs near the surface of the substrate and red photons creating electron-hole pairs deeper in the substrate, wherein the set of detectors includes at least two confinement wells at different depths within the substrate, including a shallow confinement well comprising the shallow n-type implant and centered around 1 micrometer depth and a deep confinement well comprising the deep n-type implant centered around 2 micrometers depth, the substrate constituting a p-type material; and the circuitry to read each of the first, second, and third read columns in response to a row select. However, Li in view of Tsai and Merrill are used in combination to arrive at all of the limitations of claim 1.
In response to applicant’s argument that Tsai does not teach the claimed coplanar surface arrangement (Remarks, page 7), the examiner disagrees. As discussed above in the rejection of claim 1 under 35 U.S.C. 103, Tsai teaches a p-type layer (see below annotated Fig. 1b; third well region 112) is disposed over a shallow n-type implant (second well region 110) and having a top surface coplanar with a top surface of the substrate (arrows pointing to top surfaces of the p-type layer 112 and substrate 104 that are coplanar). Note that the BRI of “top surface of the substrate” includes Tsai’s substrate 104 having multiple top surfaces, such as the top surface that is coplanar with element 112.
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Annotated Fig. 1b of Tsai: A p-type layer (third well region 112) is disposed over a shallow n-type implant (second well region 110) and having a top surface coplanar with a top surface of the substrate (arrows pointing to top surfaces of the p-type layer 112 and substrate 104 that are coplanar).
In response to applicant’s argument that Merrill does not teach the “claimed layer structure” (Remarks, page 7), the examiner notes that Li in view of Tsai is used to arrive the claimed semiconductor structure. Merrill is used in combination with Li and Tsai to arrive at the claimed: “wherein electron-hole pairs are created at depths in the substrate dependent on wavelength of radiation, with blue photons creating electron-hole pairs near the surface of the substrate and red photons creating electron-hole pairs deeper in the substrate, wherein the shallow confinement well centered around 1 micrometer depth and the deep confinement well centered around 2 micrometers depth; and the circuity to read each of the first, second, and third read columns in response to a row select”.
In response to applicant’s argument that the combination fails to teach the integrated structure with the transparent layer as recited by claim 1, the additional references fail to cure the deficiencies of the base reference since they are directed to different technical fields and do not teach the claimed sequencing device architecture (Remarks, page 7), the examiner disagrees. Applicant’s argument is a mere conclusory statement and fails to specifically point out how the language of the claims patentably distinguishes them from the references. The examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In short, as discussed above in the rejection of claim 1 under 35 U.S.C. 103, Li, Tsai, and Merrill provides some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art to have arrived at the claimed invention.
Additionally in response to applicant’s argument that the references are directed to different technical fields, MPEP 2141.01(a) discusses that a reference is analogous art to the claimed invention if: (1) the reference is from the same field of endeavor as the claimed invention (even if it addresses a different problem); or (2) the reference is reasonably pertinent to the problem faced by the inventor (even if it is not in the same field of endeavor as the claimed invention). Li teaches sequencing devices (paragraph [0002]), which is in the same field of endeavor as the claimed invention (the instant specification, paragraph [0002], discusses the system is for genetic sequencing). Similarly, Tsai’s invention is related to sequencing of genomes (paragraph [0059]) that uses photodiode arrays (paragraph [0001]), which is in the same field of endeavor as the claimed invention (the instant specification, paragraph [0002], discusses the system is for genetic sequencing; paragraph [0045] discusses photodiodes). Merrill teaches an imaging array based upon a three-color pixel sensor using a triple-well structure involving a semiconductor including p-type and n-type implants (abstract, Figs. 6-7), which is in the same which is in the same field of endeavor as the claimed invention (the instant specification, paragraph [0045] discusses photodiodes including pixels). Therefore the references are analogous art.
Conclusion
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to HENRY H NGUYEN whose telephone number is (571)272-2338. The examiner can normally be reached M-F 7:30A-5:00P.
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/HENRY H NGUYEN/Primary Examiner, Art Unit 1758