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 .
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.
Status of the Claims
Applicant’s election without traverse of Group I (claims 1, 2, 4-9, 11, 14, and 17-19) in the reply filed on 05/26/2026 is acknowledged. Claims 20-24 (Group II) and claims 25 and 28-30 (Group III) have been withdrawn from consideration. Claims 3, 10, 12, 13, 15, 16, 26, and 27 have been canceled. Claims 9, 11, 14, and 25 have been amended. Claims 1, 2, 4-9, 11, 14, and 17-19 are pending and examined herein.
Priority
This application, 18/284,993, filed 09/29/2023, is a 371 of PCT/US22/22762 filed on 03/31/2022, and claims benefit of provisional application 63/168,588 filed on 03/31/2021. This priority is acknowledged and the claims examined herein are treated as having an effective filing date of 03/31/2021.
Information Disclosure Statement
The Information Disclosure Statement filed 03/31/2022 is acknowledged and has been considered.
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 1, 2, 4-9, 11, 14, and 17-19 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 1 recites “…a member of a binding pair with the analyte linked to a surface of the hole.”. The claim is indefinite because there are multiple possible interpretations based on the claim language. For example, it is unclear if the claim language is to be interpreted as it is the analyte that is linked to a surface of the hole, or if it is to be interpreted as the binding pair member and analyte together are linked to a surface of the hole. Additionally, these interpretations represent a “used apparatus”, e.g. the function of the crystal for the detection of an analyte is not possible due to the analyte already being linked to the hole surface. Furthermore, an additional interpretation of the claim language would be that a member of a binding pair, that binds to the analyte, is linked to a surface of the hole. As there are multiple potential conflicting interpretations of the claim language, these claims are indefinite.
Appropriate correction is required.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 19 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 19 depends upon claim 1 and recites “…at least one of the one or more additional holes comprises a different member of a binding pair as compared to the member of a binding pair with the analyte bound to its surface, or no member of a binding pair bound to its surface”.
As discussed in the rejection above, one interpretation of the claim 1 language “…a member of a binding pair with the analyte linked to a surface of the hole.”, is that it is the analyte that is linked to a surface of the hole. Under this interpretation, there is no member of a binding pair discrete from the analyte that is linked to the surface of the hole. Therefore, the recitation in claim 19 of “…or no member of a binding pair bound to its surface” fails to further limit the subject matter of claim 1 upon which it depends.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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.
(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.
Claims 1, 4-9, 11, 14, 17, and 19 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Rothberg et al. (US 20170350818 A1).
Regarding claim 1, Rothberg teaches photonic structures and an integrated device used for analyzing single molecules and performing nucleic acid sequencing, where the device may include multiple pixels with sample wells configured to receive a sample, and the integrated device includes a surface having a trench region recessed from a portion of the surface and an array of sample wells, disposed in the trench region (Title; abstract). Rothberg teaches that the device is made of several layers, with a first layer (4-102) comprising silicon oxide having a first refractive index (paragraph [0122]; Fig. 4-1A), a second layer region (4-120) positioned above the first layer (4-102), and the second layer region is made of silicon oxide dielectric (4-116) having a second refractive index larger than the first refractive index of first layer (4-102) (paragraphs [0127, 0128, 0155]; Fig. 4-1A); wherein the second layer region (4-120) comprises a trench hole having a first diameter between upper and lower portions of second layer region 4-120 (Fig. 4-1A; paragraph [0156]); a second diameter of a second hole diameters along the X axis between the plurality of sample well (4-108) walls, the second wells holes having dimensions hW in the range of 0 nm to 400 nm (paragraph [0157]; Fig. 4-1A); wherein the first diameters along the X axis at the upper portion of second layer region (4-120) are larger than the second diameters along the X axis, wherein a plurality of second diameters of sample wells (4-108) are within the first diameter of (4-120) (Fig. 4-1A).
Rothberg also teaches that the biomolecule being detected may be extracted from a bodily fluid or tissue of the subject, such as breath, saliva, urine or blood (e.g., whole blood or plasma), and that the subject may be suspected of having a health condition, such as a disease ([0064]). Rothberg also teaches that the described device described may be used for diagnostic tests of blood, urine and/or saliva that may be used by individuals in their home, or by a doctor in a remote clinic in a developing country ([0056]). Rothberg also teaches that the photonic crystal biosensor could dramatically improve the health and well-being of patients through use in a remote clinic in a developing country, and or/by producing a diagnostic test that is cost-effective and readily transportable ([0056]).
Regarding claim 4, Rothberg teaches a third layer (4-105) positioned below the first layer (4-102), where the third layer comprises silicon and thus has a higher refractive index than the first layer (4-102) silicon oxide (Figure 4-1A; paragraph [0122]).
Regarding claims 5 and 6, Rothberg teaches a second layer region (4-120) comprising second silicon material (4-116), and third layer (4-105) comprising silicon (paragraph [0122, 0128]).
Regarding claim 7, Rothberg teaches a second layer region (4-120) comprising a plurality of sample wells (4-108n) (Figure 4-1A; paragraph [0140]).
Regarding claim 8, Rothberg teaches that each of the plurality of sample wells (4-108n) that have inverted cone shaped walls, wherein the second diameters at a top portion of sample wells (4-108n) along an X axis direction is larger than the third diameters across a bottom portion of each cone along an X axis direction (Figure 4-1A; paragraph [0157]).
Regarding claim 9, Rothberg teaches that the first diameter of the trench hole region may have a dimension along the x-direction of Wt in the range of 300 nm to 2000 nm or any value or range of values within that range (Figures 4-1A, B; paragraph [0162]).
Regarding claim 11, Rothberg teaches that the first hole depth comprises the difference between the dimensions hC - hM, wherein hC may be in the range of 200 nm to 2000 nm and hM may have a value in the range of 150 nm to 600 nm, and thus the first hole depth may be 400 nm or 0.4 um for example (Figure 4-1A; paragraphs [0141, 0155]).
Regarding claim 14, Rothberg teaches that the third diameters are less than 0.33 um, for a third diameter may be for example 0.32 µm, along an X axis direction across a bottom portion of each of the inverted cone shaped walls of each of the plurality of sample wells 4-108-n, as best shown in figure 4-1A, when a first diameter is 2000 nm and exemplary six wells 4-108 positioned therein each have a second diameter of about 330nm, or .33 µm (Figure 4-1A; paragraphs [0156, 0157]).
Regarding claim 17, Rothberg teaches that individual subunits of biomolecules may be identified using markers, and that such exogenous markers may be conjugated to a probe or functional group (e.g., molecule, ion, and/or ligand) that specifically binds to a particular target or component and that the combination of an exogenous marker and a functional group may form any suitable probes, tags, and/or labels used for detection, including molecular probes, labeled probes, hybridization probes, antibody probes, protein probes (e.g., biotin-binding probes), enzyme labels, fluorescent probes, fluorescent tags, and/or enzyme reporters ([0067]).
Regarding claim 19, Rothberg teaches that a trench region includes functionalization and/or modification of one or more surfaces of a sample well wherein a surface of a sample well may be modified and/or functionalized to provide a certain type and/or level of interaction with another type of molecule, e.g., an interaction that improves the association of a polymerase to a surface, or functionalizing a surface of a sample well using particles that have a dimension that allows the particles to reside within a trench region of the integrated device, the particles may carry one or more chemical species configured to functionalize and/or modify a surface of the sample well, and the surface topography of the trench regions may act to retain the particles in proximity to surfaces of the integrated device where chemical functionalization and modification is desired, and thus discretely addressable in arrays (Figures 4-1A, 4-1C and 4-1D; paragraphs [0164, 0165]).
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 2 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg as applied to claims 1, 4-9, 11, 14, 17, and 19 above, in view of Miller et al. (US 10215753 B2), (herein referred to as Miller), and Gong et al. (2010). “Photonic crystal cavities in silicon dioxide”. Applied physics letters, 96(3), (herein referred to as Gong).
The teachings of Rothberg are incorporated herein.
Regarding claims 2 and 18, Rothberg teaches all the limitations of claim 1 of the instant application, as well as a first material comprising silicon oxide, but does not specifically teach that the first material comprises silicon dioxide, nitride, indium phosphide, lithium niobite, sapphire, or a combination thereof, or where the analyte is a pathogen or an antibody specific to a pathogen.
Miller teaches a biosensor comprising a substrate including a surface having a topographical pattern formed at one or more sites on or in the surface, a coating on the substrate comprising hydrogel particles, and one or more capture molecules disposed to one or more sites on the biosensor (abstract). Miller teaches a 2-dimensional photonic crystal biosensor for detecting proteins and virus-like particles (column 17, lines 13-17). Miller also teaches that the active sensing area of this device is approximately 7 μm by 10 μm and contains 509 cylindrical wells in silicon with a diameter of 220 nm and a single cylindrical well 150 nm in diameter, with all wells etched to depths of ˜400 nm (column 17, lines 19-23). Miller also teaches that the photonic crystal is in a layer form where a p-type silicon-on-insulator wafer with a 450 nm silicon device (second layer) on top of 1 μm thick buried silicon oxide (first layer) was used as the starting substrate for the photonic crystals, and that silicon oxide (SiO2) has a lower refractive index than the silicon layer (column 13, lines 20-23; column 17, lines 25-28). Miller teaches that the hydrogel particles effectively mask the outer surface of the photonic crystal array, but leave the pore structures formed in the substrate exposed and accessible for subsequent binding of capture molecules to the interior pore surfaces (column 4, lines 57-61). Miller also teaches that target molecules may include, without limitation, proteins (including without limitation enzymes, antibodies or fragments thereof), glycoproteins, and nucleic acids which are expressed by certain pathogens (e.g. bacteria, viruses, multicellular fungi, yeasts, protozoans, etc.) (column 12, lines 21-27).
Gong teaches the use of photonic crystal cavities in silicon dioxide (abstract). Gong also teaches that the photonic crystal PC cavity is one type of optical cavity that allows for both high quality factors and low mode volumes, having ubiquitous use in cavity quantum electrodynamics, low threshold lasers, and optical control (page 1, 1st paragraph). Gong teaches that silicon is transparent in the near infrared regime, but that it absorbs heavily in the visible wavelength range, and would be difficult to employ in light emitting and waveguiding devices at the visible wavelengths (page 1, 1st paragraph). Furthermore, Gong teaches that silicon dioxide (SiO2), on the other hand, is transparent at the visible wavelengths, and similar to silicon, is a promising material due to its low cost, compatibility with electronics and established fabrication techniques (page 1, 2nd paragraph).
It would have been obvious to person of ordinary skill in the art before the effective filing date of the claimed invention to have modified the photonic crystal as taught by Rothberg, to use silicon dioxide as the first material, as disclosed by Miller, as a matter of using a known technique to improve a similar device in the same way. Both references teach multi-layered photonic crystal devices where the layers have different refractive indexes, with the purpose of analyzing molecules, with silicon-based layers.
A skilled artisan would have been motivated to make these modifications to the method taught by Rothberg, because Gong teaches that silicon dioxide provides the advantages of being transparent at the visible wavelengths, is a promising material due to its low cost, has compatibility with electronics, and has established fabrication techniques. A person of ordinary skill would have had a reasonable expectation of success in making these modifications because all three references are in the same field of silicon-based photonic crystals with cavities; Gong teaches that silicon dioxide is similar to silicon used by Rothberg; both Miller and Rothberg both use etching to create the holes/trenches/wells on the silicon layers which is a well-understood, routine, and conventional activity in the art, and also teach an embodiment where the layers are silicon-based and use an antibody to bind the analyte.
Additionally, it would have been obvious to person of ordinary skill in the art before the effective filing date of the claimed invention to have modified the photonic crystal as taught by Rothberg, for the analyte detected to be a pathogen or an antibody specific to a pathogen, as disclosed by Miller, as a matter of applying a known technique to a known device ready for improvement to yield predictable results. While Rothberg does not specifically teach that the detected analyte is a pathogen, they do teach that the biomolecule being detected may be extracted from a bodily fluid or tissue of the subject and that the subject may be suspected of having a health condition, such as a disease ([0064]). Photonic crystals with cavities and binding agents to measure analytes is a known base device as demonstrated by Rothberg and Miller, and Miller demonstrates that the measurement of pathogens is applicable to such a base device.
A person of ordinary skill in the art would have recognized that applying the known technique would have yielded predictable results and an improved device, because Rothberg teaches that the biomolecule being detected can be from the sample of a patient having a disease, and that their device can be used for diagnostic tests of blood, urine and/or saliva that may be used by individuals in their home. Furthermore, the use of assay devices to detect disease caused by pathogens specifically is a well-understood, routine, and conventional activity in the art. Applying the modification taught by Miller to the device of Rothberg, the predictable result would be a photonic crystal biosensor that acts as a point-of-care device for the detection of pathogens. A skilled artisan would have been motivated to make these modifications to the device taught by Rothberg, because Rothberg teaches that the photonic crystal biosensor could dramatically improve the health and well-being of patients through use in a remote clinic in a developing country, and or/by producing a diagnostic test that is cost-effective and readily transportable ([0056]).
Conclusion
For all the reasons discussed above, claims 1, 2, 4-9, 11, 14, and 17-19 are rejected and therefore no claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALEXANDER JOSEPH HOFFMAN whose telephone number is (571)272-9080. The examiner can normally be reached 10:00-6:30 M-F.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bao-Thuy Nguyen can be reached at (571) 272-0824. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ALEXANDER J. HOFFMAN/ Examiner, Art Unit 1677
/BAO-THUY L NGUYEN/ Supervisory Patent Examiner, Art Unit 1677 August 5, 2026
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