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 .
Please note: The examiner handling this application has changed. The new examiner on this case is Kailey Cash (kailey.cash@uspto.gov) in AU1683. Any correspondence relating to the instant application should be directed to this examiner.
Election/Restrictions
Applicant's election with traverse of the genera of “bacteria” and the species of “MRSA” in the reply filed on 5/11/2026 is acknowledged. The traversal is on the ground(s) that “there is no undue search burden as all genera (i)-(iv) have nucleic acids that are used in the independent method claims 1 and 22”. This is not found persuasive because merely being composed of nucleic acids does not make the species/genera obvious variants of one another. Each separate genera (i)-(iv) and species require different reagents necessary for their detection given the differing compositions of said nucleic acids. Additionally, each separate genera and species require different search terms in terms of prior art given their separate classifications, biological functions, and mechanisms of action.
The requirement is still deemed proper and is therefore made FINAL.
Claims 1-26 are pending and being examined on the merits.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement (e.g., US 2023/0042422 in paragraph [0064] and US 2020/0263244 in paragraph [0368]). 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Drawings
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted (most submitted figures contain color). Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.831-1.834 because it does not contain a “Sequence Listing XML” as a separate part of the disclosure. A “Sequence Listing XML” is required because there are sequences present in Figure 57.
Required response - Applicant must provide:
• A “Sequence Listing XML” part of the disclosure, as described above in item 1. or 2.; together with
o A statement that indicates the basis for the amendment, with specific references to particular parts of the application as originally filed, as required by 37 CFR 1.835(a)(3);
o A statement that the “Sequence Listing XML” includes no new matter as required by 37 CFR 1.835(a)(4)
AND
• A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph as required by 37 CFR 1.835(a)(2), consisting of:
o A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
o A copy of the amended specification without markings (clean version); and
o A statement that the substitute specification contains no new matter.
Specific deficiency - Sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.831(c) (see Figure 57). Sequence identifiers for sequences (i.e., “SEQ ID NO:X” or the like) must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Amended drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers (i.e., “SEQ ID NO:X” or the like) into the Brief Description of the Drawings, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities: There are several references to colors in the Figures throughout the specification (e.g., paragraphs [0071, 0078-0079, 0101, 0370]). As noted above, a petition to include color drawings must be filed for color to be included in the submitted figures. If no petition is filed, the drawings will only be available in black and white. Therefore, references to color in the figures for describing the content should be avoided.
Appropriate correction is required.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see paragraph [0166], references 9, 22, and 25). 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.
The use of the terms Sybr (as in “Sybrgreen”; paragraph [0152]) and “FilmArray” and “Verigene” (paragraph [0218]), which are trade names or marks used in commerce, have been noted in this application. These terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM, or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The examples above are not an exhaustive list of unmarked trade names or marks used in commerce throughout the specification. Please carefully read through and properly notate each instance.
Claim Objections
Claims 6 and 8-12 are objected to because of the following informalities:
Claims 6 and 10-12 recite “the target analyte” and should recite “the one or more target [[analyte]]analytes” to maintain consistent claim terminology with claim 1, from which these claims depend.
Claim 8 reads “the supernatant” and should read “the supernatant liquid” to maintain consistent claim terminology.
Claim 9 reads “the amplified step” and should read “the [[amplified]]amplification step” to be grammatically correct.
Appropriate correction is required.
Claim Rejections - 35 USC § 112b - Indefiniteness
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 9, 16-17, 19, 21, and 26 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 9: A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 9 recites the broad recitation “isothermal reaction”, and the claim also recites “a loop-mediated isothermal amplification reaction or a recombinase polymerase amplification (RPA)” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. The use of the term “including” does not make it clear whether these forms of isothermal reactions are required by the claim or merely exemplary.
Claim 16: A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 16 recites the broad recitation “a pathogen”, and the claim also recites “a bacteria” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 17 recites the limitation “diffusion of an amplified target nucleic acid from an interior of the dried blood sample”. However, no amplification step is present in claim 1, from which claim 17 depends, so it is unclear how an amplified target nucleic acid is being obtained or what the source of said amplified target nucleic acid is. Clarification is required.
Additionally for claim 17, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 17 recites the broad recitation “between 30% and 85%”, and the claim also recites “between 50% and 65%” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Claim 19 recites the limitation “a substrate” which the first electrode is positioned underneath. However, claim 1, from which claim 19 ultimately depends, already defines a substrate which the blood sample is applied to. It is unclear if the substrate defined in claim 19 is a different substrate as that noted in claim 1 or is the same substrate. If it is the same substrate, claim 19 should be amended to recite “the substrate”. For the purposes of examination, the substrate of claim 19 is being treated as the same substrate as in claim 1, however further clarification is required.
Claim 21 is directed to the method of claim 1 “wherein the detecting the one or more target analytes is used to select an antibiotic treatment therapy in an individual requiring treatment of a blood stream infection”. However, there is no practical step provided/added to the methodology of claim 1 that is provided to achieve the intended use recited in the claim. Therefore, it is unclear how this methodology is being used to perform the claimed selection of an antibiotic treatment therapy.
Claim 26 recited the limitation “further comprising the step of chemically lysing at least a portion of the whole blood sample and/or the dried blood sample”. It is unclear when in the methodology of claim 22 this step would occur. Is it occurring during the same lysing step as defined in claims 22 and 25 (from which this claim depends) or is this a separate lysing step that is occurring at a different step of the process? Clarification is required.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-2, 4-13, 16-17, 21-24, and 26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ganguli (Ganguli et al., PNAS, published on 9/26/2022; cited on IDS of 7/12/2024, C37).
Claims 1 and 22: Ganguli teaches determining a presence or an absence of a pathogen (target nucleic acids corresponding to a pathogen) in a blood sample from an individual that may have a blood stream infection comprising obtaining a whole blood sample from the individual and applying it to a substrate (“we demonstrate the efficacy of our biphasic reaction to identify circulating pathogens in blood from clinical whole-blood samples using the process currently fol-lowed in clinical practice as a control. From February 2022 to April 2022, we collected a total of 724 samples, of which 63 samples (15 negative and 48 positive) were tested using our biphasic approach.”, pg 7, col 2, paragraph 2). Ganguli teaches lysing RBCs in the whole blood sample and mechanically lysing a pathogen if present in the whole blood sample (Figure 4A). Ganguli teaches thermally treating the whole blood sample to generate a dried blood sample island having a fluidic network inside the dried blood sample (Figure 4A). Ganguli teaches performing a biphasic reaction by introducing a liquid buffer having amplification reagents to the dried blood sample, allowing the amplification reagents to diffuse through the fluid network to contact an interior portion of the dried blood sample, amplifying the target nucleic acids within the interior portion and then diffusing the amplicons into the liquid supernatant surrounding the dried blood sample (“The generated porosity and the microfluidic and nanofluidic network allow for enzymes to access DNA in the liquid phase and initiate amplification with single-molecule sensitivity inside the dried blood matrix…. the fluorescent amplicons after amplification are concentrated in the clear supernatant phase, giving an extraordinary signal to noise and fluorescence change”, pg 3, col 1, paragraph 2). Ganguli teaches optically detecting the presence or absence of the pathogen based on the fluorescent signal in the supernatant (Figure 1F, H).
Claims 2 and 24: Ganguli teaches that the blood samples can be “pixelated” into a “pixelated Petri-dish” cartridge (pg 9, col 1, paragraph 3).
Claim 4: Ganguli teaches that detection is via optical detection (“fluorescent amplicons after amplification are concentrated in the clear supernatant phase, giving an extraordinary signal to noise and fluorescence change”, pg 3, col 1, paragraph 2; Figure 1H).
Claim 5: Ganguli teaches that the heme background interference is confined to the dried blood sample island (“the dried blood solid phase does not re-mix with the supernatant and keeps the high heme locked in the background in red blood cells(RBCs)”, pg 3, col 1, paragraph 2).
Claim 6: Ganguli teaches that the reagent comprises amplification enzymes and primers selected to amplify a target nucleic acid sequence of the target analyte(s) (Figure 2A).
Claim 7: Ganguli teaches that the amplicons are amplified within the dried blood island and then diffuse into the supernatant liquid covering the dried blood island (“The generated porosity and the microfluidic and nanofluidic network allow for enzymes to access DNA in the liquid phase and initiate amplification with single-molecule sensitivity inside the dried blood matrix…. the fluorescent amplicons after amplification are concentrated in the clear supernatant phase, giving an extraordinary signal to noise and fluorescence change”, pg 3, col 1, paragraph 2).
Claim 8: Ganguli teaches that the amplicons are detected by a change in fluorescence of the supernatant (“fluorescent amplicons after amplification are concentrated in the clear supernatant phase, giving an extraordinary signal to noise and fluorescence change”, pg 3, col 1, paragraph 2; Figure 1H).
Claim 9: Ganguli teaches that the amplification step is an isothermal reaction (“We couple this biphasic blood-processing module with a robust Bst polymerase, which we have previously shown to perform amplification in tissue matrices and loop-mediated isothermal amplification (LAMP) reaction, minimizing the need for a thermocycler”, pg 3, col 1, paragraph 2).
Claim 10: Ganguli teaches that the one or more target analytes corresponds to one or more pathogens (Detection of MRSA and E. coli Cell-Free DNA in Whole Blood in Biphasic Format, Figure 3).
Claim 11: Ganguli teaches achieving an LOD of the target in whole blood as small as 1 cfu per blood sample starting volume (“We first demonstrate our plat-form by efficiently amplifying cell-free methicillin-resistant Staphylococcus aureus (MRSA) and E. coli DNA in microliters of dried whole blood with single-molecule sensitivity (1 copy/4 μL of blood), pg 3, col 1, paragraph 2).
Claim 12: Ganguli teach a total test time less than 2.5 hours (“The sample-to-answer time of our platform is less than 2.5 h”, pg 3, col 2, paragraph 1).
Claim 13: Ganguli teaches that the blood sample is from unprocessed whole blood (“we have taken a materials approach to whole-blood processing, which minimizes sample preparation and simultaneously offers unprecedented sensitivity.”, pg 3, col 1, paragraph 2, Figure 1 and Figure 2A).
Claim 16: Ganguli teaches lysing the RBCs by applying an RBC lysis buffer and mechanically lysing a pathogen present in the whole blood sample (Figure 1C and D).
Claim 17: Ganguli teaches thermally treating the sample at 95C for 10min to generate the porosity that allows for access of reagents to diffusion into the interior of the dried blood sample (“The drying is performed by heating the sample at 95 °C for 10 min”, pg 6, col 2, paragraph 1). Ganguli teaches that this achieves a porosity of ∼63.8% (“It is important to note that for high-volume (0.8 to 1 mL) blood processing, we were able to rapidly dry 30 μL of blood lysate after bead beating at 95 °C while retaining the higher porosity after thermal lysis (∼63.8%).”, pg 6, col 2, paragraph 2).
Claim 21: Ganguli teaches that this method can be used to select an antibiotic treatment therapy following diagnosis within 3 hours of the individual initially presenting with a blood infection symptom (pg 1-2, col 1, paragraph 1).
Claim 23: Ganguli teaches the pathogen is a bacteria (e.g., MRSA, MSSA, E. coli, Figure 5).
Claim 26: Ganguli teaches chemically lysing a portion of the whole blood sample (Figure 4A).
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 3, 14-15, 18-19 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Ganguli (Ganguli et al., PNAS, published on 9/26/2022; cited on IDS of 7/12/2024, C37) in view of Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53).
Claims 3 and 14: The teachings of Ganguli as they apply to claim 1, from which claims 3 and 14 depend, are detailed above. Relevant to the instantly rejected claim, Ganguli teaches lysis of the pathogen via mechanical lysis.
Ganguli does not teach applying an electric field to the dried blood sample island to electrically lyse a biological material. However, use of electric fields to lyse biological material is known in the art, as taught by Islam.
Islam teaches that electrical lysis is a popular method of lysis of biological material (cells) in the microfluidic community (4.6. Electrical Lysis).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Ganguli, to use electrical lysis as taught by Islam. One would be motivated to do so given the teaching by Islam that electrical lysis is “fast and reagentless” as compared to mechanical, chemical, or enzymatic means of lysis. One would have a reasonable expectation of success given that Islam teaches of several examples of experiments in which various types of cells are able to be lysed (such as RBCs, hamster kidney cells, leukemia cells, M. smegmatis, etc.; 4.6. Electrical Lysis).
Claim 15: As noted above, Ganguli teaches pixelating the blood sample into a plurality of blood sample islands, wherein the plurality of blood sample islands are provided in an array configuration. Islam teaches that electrical lysis/an electric field can be applied to arrays (4.6. Electrical Lysis, Figure 13).
Claim 18 and 25: Ganguli teaches applying liquid to the dried liquid sample before performing lysis. Islam teaches that one such form of lysis can be electrical.
Claim 19: Islam teaches an example in which an electrode pair is energized in which the first electrode is beneath the substrate and the second electrode is positioned above the substrate (Figure 13).
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Ganguli (Ganguli et al., PNAS, published on 9/26/2022; cited on IDS of 7/12/2024, C37) in view of Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53), as applied to claims 3, 14-16, and 18-19 above, and further in view of Ameri (Ameri et al., Biosensors and Bioelectronics 2014).
The teachings of Ganguli in view of Islam as they apply to claim 18, from which claim 20 depends, are detailed above. Relevant to the instantly rejected claim, Ganguli in view of Islam teach applying an electric field to a dried blood sample with a liquid supernatant applied to lyse biological material.
Ganguli in view of Islam do not teach that there are one or more localized regions resulting in high electric field to increase lysing efficiency as compared to fluid regions without the dried blood sample. However, localized increase in electric field within areas occupied by biological material is known in the art, as taught by Ameri.
Ameri teaches a lab-on-a-chip device for lysis of cells in microwells in which there is one electrode positioned below the substrate which the cells rest on and one positioned above the substrate (Abstract and Figure 1). Ameri teaches that wells that contain biological material (cells) exhibit an increase in current density when compared to wells that do not contain cells (4.1. Experimental and simulation results; Figure 4a).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, that the modification of Ganguli with the electric field lysis teaching of Islam, would result in the areas containing the biological material (the dried blood sample with the fluidic network within) would generate a localized region of higher electric field, as taught by Ameri. Ameri teaches that the cells within microwells decrease the impedence between the electrode pair and thus results in localized regions of high electric field where the biological material is present as opposed to regions where biological material is not present (4.1. Experimental and simulation results).
Claims 1-2, 4, 6-13, and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Bashir (Bashir et al., WO2019/071142A1) in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88).
Claim 1: Bashir teaches a method of detecting one or more target analytes in a fluid sample (such as a blood sample (paragraph [0015])) wherein the method comprises applying the blood sample to a substrate, drying the blood sample to create a dried blood sample island having a fluidic network inside the dried blood sample island (paragraphs [0010 and 0013]), applying a liquid having a reagent suspended in a liquid buffer to the dried sample island, wherein the reagent is used for nucleic acid detection and the liquid transits the fluidic network to access a nucleic acid in the dried blood sample island (paragraphs [0010 and 0012-0013]); diffusing a nucleic acid from the dried blood sample island to a supernatant liquid having the applied reagent (paragraph [0011]), and detecting a presence or absence of the nucleic acid in the dried blood sample island by a bi-phasic reaction which occurs in both the dried blood sample island and in the supernatant liquid having the reagent suspended in the liquid buffer (paragraph [0010]).
While Bashir teaches drying the liquid sample and then performing a thermal lysis step at 95ºC which lyses the cells, Bashir does not teach thermally treating the liquid sample to perform the drying step (i.e., thermally treating the blood sample to dry the blood sample). However, thermally treating a liquid sample to dry it is known in the art, as taught by Mostafa.
Mostafa teaches a method of detecting target analytes from a liquid sample in which a liquid sample is first dried and lysed through thermal treatment and then a biphasic amplification reaction is performed on said dried and lysed sample (Abstract and Figure 1). Mostafa teaches performing drying/thermal lysis at 95C for 20min (Figure 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Bashir to perform the thermal drying step, rather than drying and then thermally lysing, as taught by Mostafa. One would be motivated to only perform the single thermal treatment given the teaching by Mostafa that adding a thermal lysis step after thermally drying the sample “does not improve matrix porosity” and “also increases false positive amplification” (Biphasic assay tolerance of complex food matrix, paragraph 2). One would have a reasonable expectation of success given that Mostafa is applying the drying and bi-phasic amplification reaction on a liquid sample, similar to the methodology as employed by Bashir.
Claim 2: Bashir teaches pixelating the blood sample into a plurality of blood sample islands, wherein the plurality of blood sample islands are provided in an array configuration (paragraphs 0007, 0010, 0016-0017, 0031, and 0146]).
Claim 4: Bashir teaches that detecting is by electrical or optical detection (paragraph [0010]).
Claim 6: Bashir teaches that the reagent comprises amplification enzymes and primers selected to amplify a target nucleic acid sequence of the target analyte (paragraphs [0028, 0065]).
Claim 7: Bashir teaches that the amplifying the target nucleic acid into amplicons in the dried blood sample island, wherein the amplicons diffuse from the dried blood sample island to the supernatant liquid that covers the dried blood sample island (paragraphs [0028, 0065]).
Claim 8: Bashir teaches that the amplicons are detected by a chain in fluorescence of the supernatant (Paragraphs [0029, 0031]).
Claim 9: Bashir teaches that the amplification is by an isothermal reaction (paragraphs [0027, 0063]).
Claim 10: Bashir teaches that the target analytes correspond to one or more pathogens (paragraph [0024]).
Claim 11: Bashir teaches achieving an LOD of the target analytes as small as 1 cfu per blood sample starting volume (paragraph [0023, 0061]).
Claim 12: Bashir teaches detection of the target analytes in a total test time that is less than 2.5 hours (paragraph [0022]).
Claim 13: Bashir teaches that tblood sample is from unprocessed (“raw”) whole blood (paragraphs [0012, 0015]).
Claim 17: Mostafa teaches that the thermally treating step is performed at 95ºC for 20 minutes to generate a porosity in the liquid sample which allows for access by the reagents and diffusion of the target nucleic acid from an interior of the dried sample to the liquid supernatant positioned outside the dried blood sample, and that the achieved porosity is 55.3% (Figure 1a-c).
Claims 3, 14-16, and 18-19 are rejected under 35 U.S.C. 103 as being unpatentable over Bashir (Bashir et al., WO2019/071142A1) in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88) as applied to claims 1-2, 4, 6-13, and 17 above, and further in view of Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53).
Claims 3 and 14: The teachings of Bashir in view of Mostafa as they apply to claim 1, from which claims 3 and 14 depend, are detailed above. Relevant to the instantly rejected claim, Bashir teaches lysis of cells in the sample by “any technique that can reliably release nucleic acid from the sample” (Bashir, paragraph [0011]).
Bashir in view of Mostafa do not teach applying an electric field to the dried blood sample island to electrically lyse a biological material. However, use of electric fields to lyse biological material is known in the art, as taught by Islam.
Islam teaches that electrical lysis is a popular method of lysis of biological material (cells) in the microfluidic community (4.6. Electrical Lysis).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Bashir in view of Mostafa, to use electrical lysis as taught by Islam. One would be motivated to do so given the teaching by Islam that electrical lysis is “fast and reagentless” as compared to mechanical, chemical, or enzymatic means of lysis. One would have a reasonable expectation of success given that Islam teaches of several examples of experiments in which various types of cells are able to be lysed (such as RBCs, hamster kidney cells, leukemia cells, M. smegmatis, etc.; 4.6. Electrical Lysis).
Claim 15: As noted above, Bashir teaches pixelating the blood sample into a plurality of blood sample islands, wherein the plurality of blood sample islands are provided in an array configuration (paragraphs 0007, 0010, 0016-0017, 0031, and 0146]). Islam teaches that electrical lysis/an electric field can be applied to arrays (4.6. Electrical Lysis, Figure 13).
Claim 16: Bashir in view of Mostafa teach applying an RBC lysis buffer to specifically lyse RBCs in the unprocessed whole blood sample (Bashir, paragraph [0023]). Islam teaches application of electrical lysis for lysing of other biological material which would enable release of nucleic acids from, for example, pathogens to enable analysis of analytes from pathogens, as taught by Bashir (Islam, 4.6. Electrical Lysis; Bashir, paragraph [0023-0024]).
Claim 18: Bashir in view of Mostafa teaches applying liquid to the dried liquid sample before performing lysis (Bashir, paragraph [0011]).
Claim 19: Islam teaches an example in which an electrode pair is energized in which the first electrode is beneath the substrate and the second electrode is positioned above the substrate (Figure 13).
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Bashir (Bashir et al., WO2019/071142A1) in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88), and Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53) as applied to claims 3, 14-16, and 18-19 above, and further in view of Ameri (Ameri et al., Biosensors and Bioelectronics 2014).
The teachings of Bashir in view of Mostafa and Islam as they apply to claim 18, from which claim 20 depends, are detailed above. Relevant to the instantly rejected claim, Bashir in view of Mostafa and Islam teach applying an electric field to a dried blood sample with a liquid supernatant applied to lyse biological material.
Bashir in view of Mostafa and Islam do not teach that that are one or more localized regions resulting in high electric field to increase lysing efficiency as compared to fluid regions without the dried blood sample. However, localized increase in electric field within areas occupied by biological material is known in the art, as taught by Ameri.
Ameri teaches a lab-on-a-chip device for lysis of cells in microwells in which there is one electrode positioned below the substrate which the cells rest on and one positioned above the substrate (Abstract and Figure 1). Ameri teaches that wells that contain biological material (cells) exhibit an increase in current density when compared to wells that do not contain cells (4.1. Experimental and simulation results; Figure 4a).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, that the modification of Bashir in view of Mostafa with the electric field lysis teaching of Islam, would result in the areas containing the biological material (the dried blood sample with the fluidic network within) would generate a localized region of higher electric field, as taught by Ameri. Ameri teaches that the cells within microwells decrease the impedence between the electrode pair and thus results in localized regions of high electric field where the biological material is present as opposed to regions where biological material is not present (4.1. Experimental and simulation results).
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Bashir (Bashir et al., WO2019/071142A1) in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88) as applied to claims 1-2, 4, 6-13, and 17 above, and further in view of Al-Soud (Al-Soud et al., Journal of Clinical Microbiology 2001; cited on IDS of 7/12/2024, C2).
The teachings of Bashir in view of Mostafa as they apply to claim 1, from which claim 5 depends, are detailed above. Relevant to the instantly rejected claim, Bashir teaches that drying liquid samples reduces the interaction between inhibitory contaminants within crude samples and the amplification enzymes in the liquid within biphasic reactions (paragraph [0145]).
Bashir in view of Mostafa do not explicitly teach that one such inhibitory compound contained in dried samples such as whole blood includes heme. However, heme being a component of whole blood which is a known inhibitor of amplification reactions is known in the art, as taught by Al-Soud.
Al-Soud teaches that heme, a natural component of whole blood, is an inhibitor of amplification-based diagnosis of pathogenic infection (Introduction, paragraph 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, that the inhibitory compounds within crude hwole blood samples that are contain within the dried sample, as taught by Bashir in view of Mostafa, includes the known inhibitor of amplification reactions, heme (as taught by Al-Soud).
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Bashir (Bashir et al., WO2019/071142A1) in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88) as applied to claims 1-2, 4, 6-13, and 17 above, and further in view of Sinha (Sinha et al., Clinical Microbiology Reviews 2018; cited on IDS of 7/12/2024, C123).
The teachings of Bashir in view of Mostafa as they apply to claim 1, from which claim 21 depends, are detailed above. Relevant to the instantly rejected claim, Bashir teaches detection of pathogens in blood samples (paragraph [00143]). Bashir also teaches that the problem in current diagnostics is that diagnosis of a bacterial infection of the blood relies on bacterial detection from cultures that take days or weeks to grow (paragraph [0004]). This delays diagnosis and means that physicians are often relying on “experience and guesswork” and potentially an “overreliance on antibiotics” even when unnecessary for the infection (paragraph [0003]). Additionally, in the case of blood stream infections such as sepsis, in the time it takes for diagnosis the patient may already have progressed into advanced stages of the disease (paragraph [0004]).
Bashir does not explicitly teach that the detecting of analytes is within 1-3 hours of the individual initially presenting with a blood infection symptom. However, the critical period of identification for a blood stream infection being 1-3 hours is known in the art, as taught by Sinha.
Sinha teaches that the “swift initiation of precise and targeted antibiotic therapies depends on the ability of a sepsis diagnostic test to capture clinically relevant organisms along with antimicrobial resistance within 1 to 3 h”, which is critically important for the administration of the appropriate, narrow-spectrum antibiotics in clinical decision-making (Abstract).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Bashir in view of Mostafa to perform the diagnostic test within 1 to 3 hours of the subject presenting with symptoms to enable the selection of the correct antibiotic treatment therapy for a blood stream infection, as taught by Sinha. One would be motivated to do so given the teaching by Sinha that “studies suggest that there is a 1- to 3-h diagnostic window, from symptom-based sepsis recognition to the initiation of antimicrobial treatment, before the mortality rate increases” (Introduction, paragraph 6). One would have a reasonable expectation of success given that the diagnostic test as taught by Bashir takes less than 2.5 hours.
Claims 22-26 are rejected under 35 U.S.C. 103 as being unpatentable over Bashir (Bashir et al., WO2019/071142A1) in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88) and Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53).
Claim 22: Bashir teaches a method of detecting one or more target analytes in a fluid sample (such as a blood sample (paragraph [0015])) wherein the method comprises applying the blood sample to a substrate, drying the blood sample to create a dried blood sample island having a fluidic network inside the dried blood sample island (paragraphs [0010 and 0013]), applying a lysis buffer to specifically lyse RBCs (paragraph [0023]), applying amplification reagents suspended in a liquid buffer to the dried sample island, wherein the amplification reagents diffuse through the fluidic network to access a nucleic acid in the dried blood sample island (paragraphs [0010 and 0012-0013]); amplifying the target nucleic acid to generate amplicons (paragraphs [0014, 0027]); diffusing an amplicon from the dried blood sample island to a supernatant liquid having the applied reagent (paragraph [0011]), and optically detecting a presence or absence of the nucleic acid corresponding to the pathogen in the dried blood sample island by a bi-phasic reaction which occurs in both the dried blood sample island and in the supernatant liquid having the reagent suspended in the liquid buffer (paragraph [0010]). Bashir teaches that the target analyte can be a pathogen in a bodily fluid sample (whole blood) from an individual that may have a blood stream infection (paragraphs [0025, 00143-00146]).
While Bashir teaches drying the liquid sample and then performing a thermal lysis step at 95ºC which lyses the cells, Bashir does not teach thermally treating the liquid sample to perform the drying step (i.e., thermally treating the whole blood sample from the individual). However, thermally treating a liquid sample to dry it is known in the art, as taught by Mostafa.
Mostafa teaches a method of detecting target analytes from a liquid sample in which a liquid sample is first dried and lysed through thermal treatment and then a biphasic amplification reaction is performed on said dried and lysed sample (Abstract and Figure 1). Mostafa teaches performing drying/thermal lysis at 95ºC for 20min (Figure 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Bashir to perform the thermal drying step, rather than drying and then thermally lysing, as taught by Mostafa. One would be motivated to only perform the single thermal treatment given the teaching by Mostafa that adding a thermal lysis step after thermally drying the sample “does not improve matrix porosity” and “also increases false positive amplification” (Biphasic assay tolerance of complex food matrix, paragraph 2). One would have a reasonable expectation of success given that Mostafa is applying the drying and bi-phasic amplification reaction on a liquid sample, similar to the methodology as employed by Bashir.
Bashir in view of Mostafa do not teach applying an electric field to the dried blood sample island to electrically lyse a pathogen. However, use of electric fields to lyse pathogens is known in the art, as taught by Islam.
Islam teaches that electrical lysis is a popular method of lysis of biological material (cells or pathogens) in the microfluidic community (4.6. Electrical Lysis).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Bashir in view of Mostafa, to use electrical lysis as taught by Islam. One would be motivated to do so given the teaching by Islam that electrical lysis is “fast and reagentless” as compared to mechanical, chemical, or enzymatic means of lysis. One would have a reasonable expectation of success given that Islam teaches of several examples of experiments in which various types of cells are able to be lysed (such as RBCs, hamster kidney cells, leukemia cells, M. smegmatis, etc.; 4.6. Electrical Lysis). Additionally, Bashir teaches that “any method that can reliably release nucleic acid from the sample” is compatible with their methodology (paragraph [0011]).
Claim 23: Bashir teaches that the pathogen corresponds to a bacteria (paragraph [0024]).
Claim 24: Bashir teaches pixelating the blood sample into a plurality of blood sample islands, wherein the plurality of blood sample islands are provided in an array configuration (paragraphs 0007, 0010, 0016-0017, 0031, and 0146]).
Claim 25: Bashir in view of Mostafa and Islam teaches applying liquid to the dried liquid sample before performing lysis (Bashir, paragraph [0011]) and then applying an electrical field to perform lysis (Islam, 4.6. Electrical Lysing).
Claim 26: Bashir teaches performing chemical lysis as a method of lysing cells (paragraph [0011]). Bashir does not mention performing multiple types of lysis (other than the chemical lysis of RBCs prior to further lysis, paragraph [0011, 0023]). However, Islam notes that performing combinations of types of lysis methods often yields superior results (3.1.1. High Pressure Homogenizer, paragraph 3; 3.3. Combination of Mechanical and Non-Mechanical Methods). Therefore, one would be motivated to combine multiple methods of lysis in order to increase the efficiency of nucleic acid release.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-2, 4-13, 16-17, 21-24 and 26 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Ganguli (Ganguli et al., PNAS, published on 9/26/2022; cited on IDS of 7/12/2024, C37).
Regarding instant claims 1, 2, and 4: Claim 1 of ‘293 teaches:
A method of detecting one or more target analytes from a liquid sample, the method comprising the steps of:
applying a liquid sample to a substrate, wherein the substrate has an array of wells (relevant to instant claim 2);
drying the liquid sample to generate a plurality of dried sample islands, with each sample island confined to a unique well;
applying a liquid having a reagent suspended in a liquid buffer to each well, wherein the reagent is used for nucleic acid detection;
eluting a nucleic acid from the dried sample islands with a liquid phase having the applied reagent;
detecting a target nucleic acid if present in a dried sample island by a bi-phasic reaction, that occurs in both the dried sample islands and in the liquid having the reagent suspended in the liquid buffer, wherein the detecting is by electrical or optical detection (relevant to instant claim 4); thereby detecting the one or more target analytes from the liquid biological sample.
Claim 20 of ‘293 teaches that the liquid sample is whole blood.
The claims of ‘293 do not teach thermally treating the liquid sample to perform the drying step (i.e., thermally treating the blood sample to dry the blood sample). However, thermally treating a liquid sample to dry it is known in the art, as taught by Ganguli.
Ganguli teaches heating the sample at 95C for 10min to dry the sample (pg 6, col 2, paragraph 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘293 to perform the thermal drying step as taught by Ganguli. One would be motivated to do so given the assertion by Ganguli that this drying step provides a high porosity (~64%) to the blood matrix and enables efficient biphasic reaction (pg 6, col 2, paragraph 2). One would have a reasonable expectation of success given that Ganguli is also performing this methodology on a liquid blood sample specifically for the performance of a biphasic amplification reaction.
Regarding instant claim 5: Ganguli teaches that the heme background interference is confined to the dried blood sample island (“the dried blood solid phase does not re-mix with the supernatant and keeps the high heme locked in the background in red blood cells(RBCs)”, pg 3, col 1, paragraph 2).
Regarding instant claim 12: Ganguli teach a total test time less than 2.5 hours (“The sample-to-answer time of our platform is less than 2.5 h”, pg 3, col 2, paragraph 1).
Regarding instant claim 16: Ganguli teaches lysing the RBCs by applying an RBC lysis buffer and mechanically lysing a pathogen present in the whole blood sample (Figure 1C and D).
Regarding instant claim 17: Ganguli teaches thermally treating the sample at 95C for 10min to generate the porosity that allows for access of reagents to diffusion into the interior of the dried blood sample (“The drying is performed by heating the sample at 95 °C for 10 min”, pg 6, col 2, paragraph 1). Ganguli teaches that this achieves a porosity of ∼63.8% (“It is important to note that for high-volume (0.8 to 1 mL) blood processing, we were able to rapidly dry 30 μL of blood lysate after bead beating at 95 °C while retaining the higher porosity after thermal lysis (∼63.8%).”, pg 6, col 2, paragraph 2).
Regarding instant claim 21: Ganguli teaches that this method can be used to select an antibiotic treatment therapy following diagnosis within 3 hours of the individual initially presenting with a blood infection symptom (pg 1-2, col 1, paragraph 1).
Regarding instant claim 22: The claims of ‘293 teach the methodology of a biphasic reaction on a liquid sample (claim 1) and the liquid sample being a whole blood sample (claim 20). The claims of ‘293 also teach that the methodology can be used for detection of a pathogen from a bodily fluid sample such as for diagnosis of sepsis (which is a type of blood stream infection; claim 19).
The claims of ‘293 do not teach: thermally treating the sample to dry the sample, lysing RBCs, or mechanically lysing a pathogen. However, all of these steps in performed in on an individual that may have a blood stream infection is known in the art, as taught by Ganguli.
Ganguli teaches obtaining a whole blood sample from an individual that may have a blood stream infection and thermally treating said blood sample to dry it (pg 6, col 2, paragraph 1). Ganguli teaches lysing RBCs in the blood sample as well as mechanically lysing pathogens in the blood sample (Figure 1 and Figure 4A).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘293 to perform the thermal drying step, RBC lysis step, and mechanical pathogen lysis step as taught by Ganguli. One would be motivated to do the thermal drying step given the assertion by Ganguli that this drying step provides a high porosity (~64%) to the blood matrix and enables efficient biphasic reaction (pg 6, col 2, paragraph 2). One would be motivated to lyse the RBCs given the assertion by Ganguli that this allows for higher porosity after thermal lysis due to discarding of clotting proteins and factors in the RBC lysis step, leaving behind only intact cells and pathogens (pg 6, col 2, paragraph 2). One would be motivated to mechanically lyse the pathogens given the assertion by Ganguli that this enables for much more sensitive detection of pathogens in blood samples (below 10 CFU with and about 100 CFU without (pg 6, col 1-col 2). One would have a reasonable expectation of success given that Ganguli is also performing this methodology on a liquid blood sample specifically for the performance of a biphasic amplification reaction.
Regarding instant claim 23: Ganguli teaches the pathogen is a bacteria (e.g., MRSA, MSSA, E. coli, Figure 5).
Regarding instant claim 24: Ganguli teaches that the blood samples can be “pixelated” into a “pixelated Petri-dish” cartridge (pg 9, col 1, paragraph 3).
Regarding instant claim 26: Ganguli teaches chemically lysing a portion of the whole blood sample (Figure 4A).
Claims 3, 14-15, 18-19 and 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Ganguli (Ganguli et al., PNAS, published on 9/26/2022; cited on IDS of 7/12/2024, C37), as applied to claims 1-2, 4-13, 16-17, 21-24 and 26, and further in view of Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53) according to citations and rationales provided above.
Claim 20 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Ganguli (Ganguli et al., PNAS, published on 9/26/2022; cited on IDS of 7/12/2024, C37) and Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53), as applied to claims 1-19 and 21-26 above, and further in view of Ameri (Ameri et al., Biosensors and Bioelectronics 2014) according to citations and rationales provided above.
Claims 1-2, 4, 6-13, and 17 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88).
Regarding instant claims 1, 2, and 4: Claim 1 of ‘293 teaches:
A method of detecting one or more target analytes from a liquid sample, the method comprising the steps of:
applying a liquid sample to a substrate, wherein the substrate has an array of wells (relevant to instant claim 2);
drying the liquid sample to generate a plurality of dried sample islands, with each sample island confined to a unique well;
applying a liquid having a reagent suspended in a liquid buffer to each well, wherein the reagent is used for nucleic acid detection;
eluting a nucleic acid from the dried sample islands with a liquid phase having the applied reagent;
detecting a target nucleic acid if present in a dried sample island by a bi-phasic reaction, that occurs in both the dried sample islands and in the liquid having the reagent suspended in the liquid buffer, wherein the detecting is by electrical or optical detection (relevant to instant claim 4); thereby detecting the one or more target analytes from the liquid biological sample.
Claim 20 of ‘293 teaches that the liquid sample is whole blood.
The claims of ‘293 do not teach thermally treating the liquid sample to perform the drying step (i.e., thermally treating the blood sample to dry the blood sample). However, thermally treating a liquid sample to dry it is known in the art, as taught by Mostafa.
Mostafa teaches a method of detecting target analytes from a liquid sample in which a liquid sample is first dried and lysed through thermal treatment and then a biphasic amplification reaction is performed on said dried and lysed sample (Abstract and Figure 1). Mostafa teaches performing drying/thermal lysis at 95C for 20min (Figure 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘293 to perform the thermal drying step, rather than drying and then thermally lysing (“eluting”), as taught by Mostafa. One would be motivated to only perform the single thermal treatment given the teaching by Mostafa that adding a thermal lysis step after thermally drying the sample “does not improve matrix porosity” and “also increases false positive amplification” (Biphasic assay tolerance of complex food matrix, paragraph 2). One would have a reasonable expectation of success given that Mostafa is applying the drying and bi-phasic amplification reaction on a liquid sample, similar to the methodology as employed by ‘293.
Regarding instant claim 12: Mostafa teaches that the full reaction time is less than 2.5 hours (Significance).
Regarding instant claim 17: Mostafa teaches that the thermally treating step is performed at 95ºC for 20 minutes to generate a porosity in the liquid sample which allows for access by the reagents and diffusion of the target nucleic acid from an interior of the dried sample to the liquid supernatant positioned outside the dried blood sample, and that the achieved porosity is 55.3% (Figure 1a-c).
Claims 3, 14-15, and 18-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88), as applied to claims 1-2, 4, 6-13, and 17 above, and further in view of Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53) according to citations and rationales provided above.
Claim 5 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88), as applied to claims 1-2, 4, 6-13, and 17 above, and further in view of Al-Soud (Al-Soud et al., Journal of Clinical Microbiology 2001; cited on IDS of 7/12/2024, C2) according to citations and rationales provided above.
Claim 16 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88) and Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53), as applied to claims 1-4, 6-15, and 17-19 above, and further in view of Bashir (Bashir et al., WO2019/071142A1).
Regarding instant claim 16: The claims of ‘293 do not teach applying a red blood cell lysis buffer to lyse RBCs in the unprocessed blood sample. However, application of a lysis buffer to specifically lyse RBCs within a whole blood sample is known in the art, as taught by Bashir.
Bashir teaches applying a lysis buffer to specifically lyse RBCs (paragraph [0023]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘293 in view of Mostafa and Islam to include a red blood cell lysis buffer as taught by Bashir. One would be motivated to do so given the teaching by Bashir that this reduces overall cellular debris from the sample (paragraph [0023]). One would have a reasonable expectation of success given that Bashir is teaching a methodology similar to that of the claims of ‘293.
Claim 20 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88) and Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53), as applied to claims 1-4, 6-15, and 17-19 above, and further in view of Ameri (Ameri et al., Biosensors and Bioelectronics 2014) according to citations and rationales provided above.
Claim 21 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88), as applied to claims 1-2, 4, 6-13, and 17 above, and further in view of Sinha (Sinha et al., Clinical Microbiology Reviews 2018; cited on IDS of 7/12/2024, C123) according to citations and rationales provided above.
Claims 22-26 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 5, 7-8, 18-23, and 26-27 of U.S. Patent No. 11,732,293 B2 in view of Mostafa (Mostafa et al., Biotechnology Bioengineering, published 8/6/2021; cited on IDS of 7/12/2024, C88), Bashir (Bashir et al., WO2019/071142A1), and Islam (Islam et al., Micromachines 2017; cited on IDS of 7/12/2024, C53).
Regarding instant claim 22 and 25: The claims of ‘293 teach the methodology of a biphasic reaction on a liquid sample (claim 1), the liquid sample being a whole blood sample (claim 20). The claims of ‘293 also teach that the methodology can be used for detection of a pathogen from a bodily fluid sample such as for diagnosis of sepsis (which is a type of blood stream infection; claim 19).
The claims of ‘293 do not teach thermally treating the whole blood sample to perform the drying step. However, thermally treating a liquid sample to dry it is known in the art, as taught by Mostafa.
Mostafa teaches a method of detecting target analytes from a liquid sample in which a liquid sample is first dried and lysed through thermal treatment and then a biphasic amplification reaction is performed on said dried and lysed sample (Abstract and Figure 1). Mostafa teaches performing drying/thermal lysis at 95C for 20min (Figure 1).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘293 to perform the thermal drying step, rather than drying and then thermally lysing (“eluting”), as taught by Mostafa. One would be motivated to only perform the single thermal treatment given the teaching by Mostafa that adding a thermal lysis step after thermally drying the sample “does not improve matrix porosity” and “also increases false positive amplification” (Biphasic assay tolerance of complex food matrix, paragraph 2). One would have a reasonable expectation of success given that Mostafa is applying the drying and bi-phasic amplification reaction on a liquid sample, similar to the methodology as employed by ‘293.
The claims of ‘293 in view of Mostafa do not teach applying a red blood cell lysis buffer to lyse RBCs in the unprocessed blood sample. However, application of a lysis buffer to specifically lyse RBCs within a whole blood sample is known in the art, as taught by Bashir.
Bashir teaches applying a lysis buffer to specifically lyse RBCs (paragraph [0023]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘293 in view of Mostafa and Islam to include a red blood cell lysis buffer as taught by Bashir. One would be motivated to do so given the teaching by Bashir that this reduces overall cellular debris from the sample (paragraph [0023]). One would have a reasonable expectation of success given that Bashir is teaching a methodology similar to that of the claims of ‘293.
The claims of ‘293 in view of Mostafa and Bashir do not teach applying an electric field to the dried blood sample island to electrically lyse a pathogen. However, use of electric fields to lyse pathogens is known in the art, as taught by Islam.
Islam teaches that electrical lysis is a popular method of lysis of biological material (cells or pathogens) in the microfluidic community (4.6. Electrical Lysis).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of ‘293 in view of Mostafa and Bashir, to use electrical lysis as taught by Islam. One would be motivated to do so given the teaching by Islam that electrical lysis is “fast and reagentless” as compared to mechanical, chemical, or enzymatic means of lysis. One would have a reasonable expectation of success given that Islam teaches of several examples of experiments in which various types of cells are able to be lysed (such as RBCs, hamster kidney cells, leukemia cells, M. smegmatis, etc.; 4.6. Electrical Lysis).
Regarding instant claim 23: Mostafa teaches that the pathogen is a bacteria (E. coli).
Conclusion
No claims are allowed.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571)272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KAILEY ELIZABETH CASH/ Examiner, Art Unit 1683
/ANNE M. GUSSOW/ Supervisory Patent Examiner, Art Unit 1683
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