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 .
Claim Status
Claims 1-2, 4-5, and 8-23 are pending. Claims 3, 6, and 7 are canceled.
Information Disclosure Statement
The information disclosure statement (IDS) filed 24 January 24 is considered, initialed, and is attached hereto. The non-patent literature document Mokros et al. was not considered because it was not provided.
Election/Restrictions
Restriction to one of the following inventions is required under 35 U.S.C. 121:
Group I. Claims 1-2 and 4-5, drawn to a multiplex method for detecting different analytes in a sample beyond the diffraction limit by sequential signal-encoding of said analytes, classified in C12Q 1/6825 and 2600/112.
Group II. Claim 3, drawn to a kit for multiplex analyte encoding beyond a diffraction limit, classified in Y10S 435/81.
Group III. Claim 6, drawn to an optical multiplexing system, classified in G01N 21/6458.
Group IV. Claim 7, drawn to a method of screening, identifying and/or testing a substance and/or drug, classified in C12Q 2600/136.
The inventions are independent or distinct, each from the other because:
Inventions I and II are related as product and process of use. The inventions can be shown to be distinct if either or both of the following can be shown: (1) the process for using the product as claimed can be practiced with another materially different product or (2) the product as claimed can be used in a materially different process of using that product. See MPEP § 806.05(h). In the instant case the product as claimed can be used in a materially different process of using that product, such as the probes and oligonucleotides of the kit having their length and/or molecular weight determined and then used as markers in gel electrophoresis.
Inventions I and III are related as process and apparatus for its practice. The inventions are distinct if it can be shown that either: (1) the process as claimed can be practiced by another and materially different apparatus or by hand, or (2) the apparatus as claimed can be used to practice another and materially different process. (MPEP § 806.05(e)). In this case the apparatus as claimed can be used to practice another and materially different process, such as being used to detect fluorescence of a single probe binding to an analyte.
Inventions I and IV are directed to related processes. The related inventions are distinct if: (1) the inventions as claimed are either not capable of use together or can have a materially different design, mode of operation, function, or effect; (2) the inventions do not overlap in scope, i.e., are mutually exclusive; and (3) the inventions as claimed are not obvious variants. See MPEP § 806.05(j). In the instant case, the inventions as claimed have a materially different effect, with Invention I having the effect of detecting different analytes and Invention IV having the effect of screening the effect of a substance and/or drug on analytes. Furthermore, the inventions as claimed do not encompass overlapping subject matter and there is nothing of record to show them to be obvious variants.
Inventions II and III are directed to related products. The related inventions are distinct if: (1) the inventions as claimed are either not capable of use together or can have a materially different design, mode of operation, function, or effect; (2) the inventions do not overlap in scope, i.e., are mutually exclusive; and (3) the inventions as claimed are not obvious variants. See MPEP § 806.05(j). In the instant case, the inventions as claimed have a materially different mode of operation, since Invention II is a kit that is operated by performing an assay on a sample, while Invention III is an optical system that operates by capturing an image of a sample. Furthermore, the inventions as claimed do not encompass overlapping subject matter and there is nothing of record to show them to be obvious variants.
Inventions II and IV are related as product and process of use. The inventions can be shown to be distinct if either or both of the following can be shown: (1) the process for using the product as claimed can be practiced with another materially different product or (2) the product as claimed can be used in a materially different process of using that product. See MPEP § 806.05(h). In the instant case the kit of Invention II could be used in another materially different process, such as being used to detect the localization of analytes in disease conditions compared to control conditions without the subject being contacted by any substance and/or drug as in Invention IV.
Inventions III and IV are related as process and apparatus for its practice. The inventions are distinct if it can be shown that either: (1) the process as claimed can be practiced by another and materially different apparatus or by hand, or (2) the apparatus as claimed can be used to practice another and materially different process. (MPEP § 806.05(e)). In this case the apparatus of Invention III could be used in another materially different process, such as observing cell morphology without any analytes being labeled or detected.
Restriction for examination purposes as indicated is proper because all the inventions listed in this action are independent or distinct for the reasons given above and there would be a serious search and/or examination burden if restriction were not required because one or more of the following reasons apply: The inventions have each acquired a separate status in the art in view of their different classification.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
The examiner has required restriction between product or apparatus claims and process claims. Where applicant elects claims directed to the product/apparatus, and all product/apparatus claims are subsequently found allowable, withdrawn process claims that include all the limitations of the allowable product/apparatus claims should be considered for rejoinder. All claims directed to a nonelected process invention must include all the limitations of an allowable product/apparatus claim for that process invention to be rejoined.
In the event of rejoinder, the requirement for restriction between the product/apparatus claims and the rejoined process claims will be withdrawn, and the rejoined process claims will be fully examined for patentability in accordance with 37 CFR 1.104. Thus, to be allowable, the rejoined claims must meet all criteria for patentability including the requirements of 35 U.S.C. 101, 102, 103 and 112. Until all claims to the elected product/apparatus are found allowable, an otherwise proper restriction requirement between product/apparatus claims and process claims may be maintained. Withdrawn process claims that are not commensurate in scope with an allowable product/apparatus claim will not be rejoined. See MPEP § 821.04. Additionally, in order for rejoinder to occur, applicant is advised that the process claims should be amended during prosecution to require the limitations of the product/apparatus claims. Failure to do so may result in no rejoinder. Further, note that the prohibition against double patenting rejections of 35 U.S.C. 121 does not apply where the restriction requirement is withdrawn by the examiner before the patent issues. See MPEP § 804.01.
A telephone call was made to Garrett H. Anderson on 13 November 2025 to request an election to the above restriction requirement. Applicant elected by filing a preliminary amendment with their elected claims. Applicant’s election without traverse of Group I, consisting of claims 1-2 and 4-5 along with newly presented claims 8-23 that are consistent with Group I, in the reply filed on 20 November 2025 is acknowledged.
Drawings
The drawings are objected to because the views in pages 3-5 are numbered “Fig. 3 continued”, the views in pages 8-13 are numbered “FIG. 5 continued”, the views in pages 22-24 are numbered “FIG. 13 continued”, and the views in pages 28-30 are numbered “FIG. 16 (continued)”. The numbering of views must comply with 37 C.F.R. 1.84 (u):
(u) Numbering of views.
(1) The different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. View numbers must be preceded by the abbreviation "FIG." Where only a single view is used in an application to illustrate the claimed invention, it must not be numbered and the abbreviation "FIG." must not appear.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 1, 3, 6, 7, 11, and 15 are objected to because of the following informalities:
Claim 1, line 33: “of first set” should be corrected to “of the first set”.
Claim 1, line 39: “of the for the” should be corrected to “for the”.
Claim 1, lines 46 and 56: “connect” should be corrected to “connector”.
Claim 1, line 48: “analyte of each” should be corrected to “analyte each”
Claim 1, lines 3, 18, 34-37, 39, 42, 47, 49, 52, 57, 63-64, 67, and 69; claim 2, lines 1-3; and claim 8, 1-2: steps are presented in inconsistent formats “(X)”, “X)”, “X”, and “(X, Y)”. Consistency of a chosen format is required.
Claim 1, lines 17, 36, 46, 56, 62, 63, 66: both “;” and “; and” are used inconsistently to delimit steps of the method. Consistency of a chosen format is required. As examples, using just “;” to delimit steps, just “; and” to delimit steps, or “;” to delimit all steps except for using “; and” to delimit step (E) from step (F) would satisfy this requirement.
Claims 3, 6, and 7: “Cancelled.” should be corrected to either “(Canceled)” or an acceptable alternative as laid out in MPEP §714 II. C. within a parenthetical expression. 37 C.F.R. 1.21 states:
In the claim listing, the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered).
Claim 11, line 1: “set of signal oligonucleotides” should be corrected to “the set of signal oligonucleotides”
Appropriate correction is required.
Claim Interpretation
In Claim 1, line 61, the phrase “comprised in a decoding oligonucleotide” is interpreted to mean the same as the more standard phrase “of a decoding oligonucleotide”. Correction to more standard phraseology is suggested but not required.
In Claim 15, line 1, the phrase “The method according to claim 15” appears to be intended to be “The method according to claim 14”, since a claim cannot depend on itself and claim 14 is the only preceding claim that provides antecedent basis for “the cancer fusion gene first portion” and “the cancer fusion gene second portion” in lines 1-2 of claim 15.
In Claim 21, line 2, the phrase “cancer activating mutations in DNA” is interpreted to not be limited to strictly point mutations, but also insertions, deletions, copy number gains, and rearrangements of DNA that lead to a cancer activating effect.
Claim Rejections - 35 USC § 112(b)
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, 4-5, and 8-23 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 describes “analyte-specific probes” with conflicting definitions. The phrase “each analyte-specific probe interacting with a different analyte” in lines 4 and 19 defines every single analyte-specific probe as targeting a different analyte (herein Interpretation 1). In contrast, both the phrase “each set of analyte-specific probes comprises analyte-specific probes which specifically interact with different sub-structures of the same analyte” in lines 5-6 and 20-21 and the phrase “the analyte-specific probes in each set of analyte-specific probes binds to the same analyte” in lines 15-16 and lines 30-31 defines ‘sets’ of analyte-specific probes wherein within a set the analyte-specific probes target the same analyte but the analyte-specific probes of different sets target different analytes (herein Interpretation 2). This conflict in the definition of analyte-specific probes renders the claim indefinite. For the purpose of examination, Interpretation 2 will be used as it appears to be most parsimonious with the specification. Amendment of claim 1 in lines 4 and 19 to read “each set of analyte-specific probes” would remedy this rejection and align the claim with Interpretation 2. Claims 2, 4-5, and 8-23 are rejected based on their dependency on claim 1, thereby inheriting the conflicting definitions that render the claims indefinite.
Claim 1 recites “wherein (optionally)” in line 33. This phrase renders claim 1 indefinite because the parentheses around the word ‘optionally’ make it unclear whether the limitation that follows this phrase is required by the claim or is optional and not required. For the purpose of examination, this will be treated as an optional limitation that is not required for art to read on the claim. Removal of the parentheses would obviate this rejection. Claims 2, 4-5, 8, and 10-23 are rejected based on their dependency on claim 1, thereby inheriting this unclear limitation. Though claim 9 is also dependent on claim 1, it is not rejected because it cures the unclear limitation by adding a limitation that is narrower than either reasonable interpretation of the unclear limitation.
Claim 1 recites the limitation “the number of […] targets” in line 33. There is insufficient antecedent basis for this limitation in the claim. Claims 2, 4-5, and 8-23 are rejected based on their dependency on claim 1, thereby inheriting this limitation that has insufficient antecedent basis.
Claim 1 recites the limitation "the corresponding analyte-specific probe set A1" in line 42. There is insufficient antecedent basis for this limitation in the claim. For the purpose of examination, this limitation will be interpreted as referring to the analyte-specific probe set of step (A1). Claims 2, 4-5, and 8-23 are rejected based on their dependency on claim 1, thereby inheriting this limitation that has insufficient antecedent basis.
Claim 1 recites the limitation "the corresponding analyte-specific probe set A2" in line 52. There is insufficient antecedent basis for this limitation in the claim. For the purpose of examination, this limitation will be interpreted as referring to the analyte-specific probe set of step (A2). Claims 2, 4-5, and 8-23 are rejected based on their dependency on claim 1, thereby inheriting this limitation that has insufficient antecedent basis.
Claim 1 recites a step labeled “(C)” in line 57 and then also uses it to define “a translator connector element (C)” in line 59. The reuse of the same label for different aspects of this claim renders this claim indefinite. Claims 2, 4-5, and 8-23 are rejected based on their dependency on claim 1, thereby inheriting the reuse of the same label for different aspects.
Claim 1 recites the limitation "the signal" in line 63. There is insufficient antecedent basis for this limitation in the claim. Claims 2, 4-5, and 8-23 are rejected based on their dependency on claim 1, thereby inheriting this limitation that has insufficient antecedent basis.
Claim 1 recites the limitation "the specific binding of the analyte-specific probes to the analytes to be encoded" in lines 65-66. There is insufficient antecedent basis for this limitation in the claim. Claims 2, 4-5, and 8-23 are rejected based on their dependency on claim 1, thereby inheriting this limitation that has insufficient antecedent basis.
Claim 1 recites the limitation "steps B)" in line 67. There is insufficient antecedent basis for this limitation in the claim, as no step B) is recited but both steps (B1) and (B2) are recited. For the purpose of examination, this limitation will be interpreted as each further cycle comprising steps (B1), (B2), (C), (D), and (E). Claims 2, 4-5, and 8-23 are rejected based on their dependency on claim 1, thereby inheriting this limitation that has insufficient antecedent basis.
Claim 2 recites the limitation "n" in the phrases "(A1, B1, C, D, E and F)n" and "A2, B2, C, D, E and F)n" in lines 2-3. There is insufficient antecedent basis for this limitation in the claim. For the purpose of examination, this claim will be interpreted as requiring that the steps are performed in the order (A1), (B1), (C), (D), (E), (F) (step (F) here requiring 3 further cycles comprising steps (B1) to (E)), (A2), (B2), (C), (D), (E), (F) (step F here requiring 3 further cycles comprising steps (B2) to (E)).
Claims 4 and 5 are rejected in that they fail to point out what is included or excluded by the claim language because they use the phrase “comprising the use of the multiplex method according to the present disclosure”. This claim is an omnibus type claim (MPEP §2173.05(r)) as there are no specific structural limitations provided in the claim to further define the method.
Claim 8 recites the limitation "wherein n is the number of " in line 3. There is insufficient antecedent basis for this limitation in the claim because claim 1, which claim 8 depends on, recites in line 67 “[step] (F) performing at least three (3) cycles comprising steps B) to E)” and claim 8 recites “interwoven cycles of the steps in the order (A1, A2, B1, B2, C, D, E and F)”, so it is unclear what instance of “cycles” is being modified by this limitation. For the purpose of examination, the number of cycles denoted by n is interpreted to be the number of cycles recited in step (F) of claim 1. Under this interpretation, the phrase “wherein n is the number of cycles and at least 3” in claim 8 does not further limit claim 1, but claim 8 as a whole further limits claim 1 because it adds a limitation requiring a specific order of steps (A1), (A2), (B1), (B2), (C), (D), (E), and (F) (step (F) here interpreted as requiring 3 further cycles comprising steps (B1), (B2), (C), (D), and (E)).
Claim 12 recites the limitations "the signal generated from the first set of analyte-specific probes for encoding different analytes" and "the signal generated from the second set of analyte-specific probes for encoding different analytes" in lines 1-2 and 2-3, respectively. There is insufficient antecedent basis for these limitations in the claim as the only signal given at this point is “the signal caused by the signal element” (Claim 1 line 63). Claim 13 is rejected based on its dependency on claim 12, thereby inheriting these limitations that have insufficient antecedent basis.
Claim 15 recites the limitation “The method according to claim 15” in line 1. There is insufficient antecedent basis for this limitation in the claim. For the purpose of examination, this limitation is interpreted as “The method according to claim 14” as discussed in the claim interpretation section above.
Claim 15 recites the limitation "the cancer fusion" in line 3. There is insufficient antecedent basis for this limitation in the claim.
Claim 17 recites the limitations “a high abundance analyte-specific probe” in line 2 and “a low abundance analyte-specific probe” in lines 3-4. It is unclear whether the level of abundance in these limitations describes the abundance of the analyte or the abundance of the probe, thereby rending the claim indefinite. For the purpose of examination, these limitations are interpreted as referring to the abundance of the analyte that the probe is specific for, not the abundance of the probe itself.
The terms “high" and "low” in claim 17, lines 2 and 3 respectively, are relative terms which render the claim indefinite. The terms “high" and "low” are not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The relative abundance.
The term “usually” in claim 19 line 3 and claim 20 line 2 is a relative term which renders the claims indefinite. The term “usually” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The relative frequency of high spatial overlap is therefore rendered indefinite. Claim 20 is also rejected based on its dependency on claim 19, thereby inheriting the indefinite limitation.
The term “high” in claim 19 line 3 and claim 20 line 3 is a relative term which renders the claims indefinite. The term “high” is not defined by the claims, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The relative degree of spatial overlap is therefore rendered indefinite. Claim 20 is also rejected based on its dependency on claim 19, thereby inheriting the indefinite limitation.
Claim Rejections - 35 USC § 112(d)
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 15 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 15 states that colocalization of the cancer fusion gene first and second portion indicates an increased risk of cancer associated with the cancer fusion. This does not add or change any additional step or action in the method, such as a step of making a determination of cancer risk, and it does not limit any material component of the method. Therefore, claim 15 fails to further limit the subject matter of claim 14, which it is interpreted as depending upon.
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 § 112(a) - Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 11-17 and 21-23 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claims contain subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Regarding claim 11, lines 1-4 add new matter by distinguishing between a set of signal oligonucleotides used to detect the first set of analyte-specific probes for encoding different analytes and a set of signal oligonucleotides used to detect the second set of analyte-specific probes for encoding different analytes. The original disclosure does not disclose the separation of signal oligonucleotides into sets based on being used to detect either the first or second set of analyte-specific probes. The closest disclosure is on page 25 lines 9-11 of the specification filed on 28 November 2023, where it discloses “at least two different sets of signal oligonucleotides, wherein the signal oligonucleotides in each set comprise a different signal element and comprise a different connector element”. However, this disclosure still fails to disclose different sets of signal oligonucleotides that are specifically distinguished based on their detection of either the first or second set of analyte-specific probes.
Regarding claims 12 and 13, lines 1-3 of claim 12 add new matter by combining the signal generated from the two sets of analyte-specific probes into a single image. The original disclosure does not disclose combining the signals into an image. The closest disclosure is on page 4 line 32 and page 54 line 14 of the specification filed on 28 November 2023, which both read “both runs generate independent datasets that can be combined in-silico afterwards”. However, while this discloses the combining being performed in silico, as claimed in claim 13, it only discloses that datasets are combined which would imply that the resulting combination would be a dataset, not an image. Claim 13 is rejected for failing to comply with the written description requirement because of its dependency on claim 12.
Regarding claims 14 and 15, lines 1-3 of claim 14 add new matter by requiring that the first set of analyte-specific probes for encoding different analytes comprises a cancer fusion gene first portion and the second set of analyte-specific probes for encoding different analytes comprises a cancer fusion gene second portion. The original disclosure does not disclose using the method to detect a first and a second portion of a cancer fusion gene. The closest disclosure is on page 54 line 18 of the specification filed on 28 November 2023, which discloses the method allowing for detection of “fusion genes (cancer)”. However, this does not disclose the manner in which a cancer fusion gene is detected or that two distinct portions of a cancer fusion gene would be detected by the first and second sets of analyte-specific probes. Claim 15 is rejected because of its dependency on claim 14. Lines 1-3 of claim 15 also add new matter by stating that the colocalization of the cancer fusion gene first and second portions indicates an increased risk of cancer associated with the cancer fusion. The original disclosure does not disclose that colocalization of cancer fusion genes indicates an increased risk of cancer. The closest disclosure is on page 14 lines 2-7 of the specification filed on 28 November 2023, which disclose that the analytical sets may be directed toward different targets associated with cancer and that their colocalization may indicate activated promoters in genes associated with cancer. However, it does not disclose that these targets are portions of a cancer fusion gene or that activated promotors in genes associated with cancers indicates an increased risk of cancer associated with a cancer fusion.
Regarding claim 16, lines 4-5 add new matter by stating that the first and second analyte-specific probes are expected to co-localize in a patient condition. The original disclosure does not disclose a patient and so cannot disclose a patient condition wherein the probes are expected to co-localize. The closest disclosure is on page 14 lines 5-7 of the specification filed on 28 November 2023, which disclose that a colocalization of signals may indicate activated promotors in genes associated with cancer. However, this does not disclose a patient.
Regarding claim 17, lines 1-4 add new matter by limiting the first set of analyte-specific probes to comprising a high abundance analyte-specific probe and limiting the second set of analyte-specific probes to comprising a low abundance analyte-specific probe. The original disclosure does not disclose a high abundance analyte-specific probe or a low abundance analyte-specific probe. The closest disclosure is on page 55 lines 2-3 of the specification filed on 28 November 2023, which disclose that the method allows transcripts with higher expression levels to be analyzed because the “signal spread” of the high number of abundant signals vs. the detection of other lowly expressed genes is improved. However, this does not disclose probes specific to high abundance analytes and probes specific to low abundance analytes, and further fails to disclose that the high abundance analytes are detected by the first probe set while the low abundance analytes are detected by the second probe set.
Regarding claims 21-23, lines 1-2 of claim 21 add new matter by limiting the first set of analyte-specific probes to probes directed to cancer activating mutations in DNA. The original disclosure does not disclose probes directed to cancer activating mutations in DNA. The closest disclosure is on page 14 lines 3-4 of the specification filed on 28 November 2023, which disclose that the first analytical set may be directed to known activating mutations in promotor-structures with a high prevalence for cancer. However, cancer activating mutations is a broader class of mutations than the disclosed mutations in promotor-structures with a high prevalence for cancer, including additional undisclosed embodiments such as cancer activating mutations in coding regions, so the claimed probes directed to cancer activating mutations in DNA is not disclosed in the original disclosure. Claims 22 and 23 are rejected for failing to comply with the written description requirement because of their dependency on claim 21.
Regarding claim 22, lines 1-2 add new matter by limiting the seconding set of analyte-specific probes to probes directed to transcripts associated with cancer. The original disclosure does not disclose probes directed to transcripts associated with cancer. The closest disclosure is on page 14 lines 4-5 of the specification filed on 28 November 2023, which disclose that the second analytical set may be directed to genes associated with cancer development when over-expressed. However, genes are sequences of DNA, while transcripts are sequences of RNA that are based on sequences of DNA, so this fails to disclose probes directed to transcripts associated with cancer.
Regarding claim 23, lines 1-2 add new matter by limiting the seconding set of analyte-specific probes to probes directed to proteins associated with cancer. The original disclosure does not disclose probes directed to proteins associated with cancer. The closest disclosure is on page 14 lines 4-5 of the specification filed on 28 November 2023, which disclose that the second analytical set may be directed to genes associated with cancer development when over-expressed. However, genes are sequences of DNA, while proteins are made of peptides based on sequences of DNA, so this fails to disclose probes directed to proteins associated with cancer.
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, 8-13, and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Eng et al. ("Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+", Nature 568, 235-239 (2019)), herein Eng.
Regarding claim 1, Geipel teaches a multiplex method for detecting different analytes in a sample (method for specific detection of many different analytes in parallel [0068]) by sequential signal-encoding of said analytes ([0001]) and steps (A1) and (A2) in the following teachings. Geipel teaches contacting the sample with a first set of analyte-specific probes for encoding different analytes (page 38, D: each target-specific probe set was added to the mixture), each set of analyte-specific probes interacting with a different analyte (page 34, Table 2, target transcript column lists different analytes, such as DDX5), wherein if the analyte is a nucleic acid each set of analyte-specific probes comprises analyte-specific probes which specifically interact with different sub-structures of the same analyte (SEQ ID No. 1, from 5’ to 3’, consists of 24 bases that have 100% identity with the DDX5 mRNA transcript variant 2 [see BLAST Alignment 1 below], followed by the spacer sequence ‘gtaac’ and the unique identifier sequence ‘gattaccgacttatcc’ and SEQ ID No. 2, from 5’ to 3’, consists of 21 bases that have 100% identity with the DDX5 mRNA transcript variant 2 [see BLAST Alignment 2 below] followed by the spacer sequence ‘gtaac’ and the unique identifier sequence ‘gattaccgacttatcc’ – SEQ ID Nos. 1 and 2 are defined in [00123] and the sequence listing).
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BLAST Alignment 1: Query is first 24 bases of Geipel’s SEQ ID No. 1
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BLAST Alignment 2: Query is first 21 bases of Geipel’s SEQ ID No. 2
Giepel further teaches that each analyte-specific probe comprises (aa) a binding element (S) that specifically interacts with one of the different analytes to be encoded ([0073-0074]; Fig. 3 views 1-3) and (bb) an identifier element (T) comprising a nucleotide sequence which is unique to the analyte to be encoded (unique identifier sequence) ([0073-0074]; Fig. 3 views 1-3), wherein the analyte-specific probes of a particular set of analyte-specific probes (Fig. 5 view 2, probes on nucleic acid sequence A) differ from the analyte-specific probes of another set of analyte-specific probes (Fig. 5 view 2, probes on nucleic acid sequence B) in the nucleotide sequence of the identifier element (T) ([0092]; Fig. 5 view 2, distinguished as T1 and T2), wherein the analyte-specific probes in each set of analyte-specific probes binds to the same analyte and comprises the same nucleotide sequence of the identifier element (T) which is unique to said analyte (Fig. 5 view 2). Step (A2) recites nearly identical language to (A1) with the difference being that the sample is contacted with a second set of analyte-specific probes. Geipel teaches step (A2) because in Experiments 1 and 2 they use 50 different target specific probe sets ([00115]; pages 34-37 Tables 2 and 3).
Geipel further teaches steps (B1) and (B2) in the following teachings. Geipel teaches contacting the sample with decoding oligonucleotides for the sets of analyte-specific probes of steps (A1) and (A2) wherein each decoding oligonucleotide comprise (aa) an identifier connector element (t) comprising a nucleotide sequence which is essentially complementary to at least a section of the unique identifier sequence of the identifier element (T) of the corresponding analyte-specific probe set of either step (A1) or (A2), and (bb) a translator element (c) comprising a nucleotide sequence allowing a specific hybridization of a signal oligonucleotide ([0076-0077], [00115]; page 34-36 Table 2; page 39 E.; Fig. 3 views 4-6 and Fig. 5 view 3), wherein the decoding oligonucleotides of a set for an individual analyte differ from the decoding oligonucleotides of another set for a different analyte in the first connector element (t) (Fig. 5 view 3, t1-t3 are specific to the analyte nucleic acid sequences A-C).
Geipel further teaches contacting the sample with at least a set of signal oligonucleotides, each signal oligonucleotide comprising (aa) a translator connector element (C) comprising a nucleotide sequence which is essentially complementary to at least a section of the nucleotide sequence of a translator element (c) of a decoding oligonucleotide, and (bb) a signal element ([0079-0080]; page 39 F.; Fig. 3 views 7-9, F is the signal element); detecting a signal caused by the signal element ([0082]; pages 39-40 G.; Fig. 3 view 10); selectively removing the decoding oligonucleotides and signal oligonucleotides from the sample ([0084]; page 40 H.; Fig. 3 views 11-12); and performing at least three further cycles comprising steps (B1), (B2), (C) to generate an encoding scheme with a code word per analyte wherein the last cycle stops at step (D) ([00117], 4 additional rounds are performed).
However, regarding claim 1, Geipel does not disclose the use of this method for detecting different analytes in a sample beyond the diffraction limit by sequential signal-encoding. This deficiency is provided for in Eng.
Regarding claim 1, Eng teaches a method of detection of analytes beyond the diffraction limit (Main Body paragraph 4: “super-resolution imaging”, “allows each mRNA dot to be localized below the diffraction limit”) through sequential signal-encoding (Main Body paragraph 4: “sequential hybridizations”). Eng accomplishes this detection using 60 “pseudocolors” in 3 channels wherein analyte-specific probes are bound to analytes and then labels that only apply to a subset of the analyte-specific probes are hybridized, detected, removed, and then the process is repeated with new labels that apply to a different subset of analyte-specific probes, such that there are 20 sets of analyte-specific probes that are imaged separately and sequentially (Main Body paragraph 4, Figure 1a). By combining the images, analytes closer than the diffraction limit can be distinguished due to being labeled by in different detection rounds. This is analogous to the division of sets of analyte-specific probes between (A1) and (A2) in the instant application that are detected by the series of steps (B1), (C), (D) and (B2), (C), (D) separately which are then combined to identify analytes of (A1) and (A2) that are closer than the diffraction limit would normally allow. This method is also combined with barcoding. Eng also teaches that previous barcoding-based methods of multiplexed in situ analyte detection have a major challenge because each mRNA occupies a diffraction limited spot in an image, leading to optical crowding that prevents some mRNAs from being resolved (Main Body paragraph 2). Eng teaches that their method of modifying the seqFISH multiplex RNA in situ detection technique with pseudocolors solves this challenge while also not having the flaws of existing super-resolution localization microscopy techniques that rely on the detection of single dye molecules and only work robustly in optically thin samples (Main Body paragraphs 2 and 4).
Regarding claim 8, Geipel teaches the steps (A1), (A2), (B1), (B2), (C), (D), (E), and (F), as described above, in the claimed order (pages 38-40, D., E., F., G., H., and [00117]). However, the claimed order prevents Eng’s method of using pseudocolors from functioning to detect different analytes in a sample beyond the diffraction limit because both analyte sets would be labeled and detected simultaneously in the claimed order of the steps, while the pseudocolor system requires sequentially detecting different sets of analytes. Despite this, Eng teaches that an alternative to the pseudocolor system that they have conceived of is to “combine super-resolution microscopy with [fluorescence in situ hybridization]” in order to overcome the crowding problem and detect different analytes in a sample beyond the diffraction limit (Main Body paragraph 2). Therefore, the combination of Geipel and Eng teach performing the method according to claim 1 to detect different analytes in a sample beyond the diffraction limit with the order of steps (A1), (A2), (B1), (B2), (C), (D), (E), and (F).
Regarding claim 9, neither Geipel nor Eng teach the first set of analyte-specific probes encoding at least 10x more analytes than the second set of analyte-specific probes encode. However, one of ordinary skill in the art would understand that the number of analytes encoded in either set of analyte-specific probes can be changed and the effect of the method to detect different analytes in a sample beyond the diffraction limit by signal encoding would be maintained so long as the analytes encoded for in a set of analyte-specific probes do not usually spatially overlap. This limitation is a change in size/proportion of the sets of analyte-specific probes that is common practice for one ordinary skill in the art (MPEP §2144.04 IV. A.). Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Regarding claim 10, Geipel teaches using a fluorophore as the signal element ([0029], [00115]).
Regarding claim 11, Geipel teaches the sets of signal oligonucleotides used to detect the first and second sets of analyte-specific probes comprise the same signal oligonucleotides (page 39 F. “signal oligonucleotide hybridization mixture was the same for all rounds of experiments 1 to 4” and each experiment included multiple analyte-specific probe sets, see Tables 2 and 3 on pages 34-37).
Regarding claims 12 and 13, Eng teaches combining the signal generated from one set of analyte-specific probes with the signal generated from another set of analyte-specific probes into a single image (Main Body paragraph 4: “recombining the images to reconstruct a super-resolution image”, Methods, seqFISH+ encoding strategy paragraph 3: “all of the genes are sampled every 20 rounds of readout hybridization [i.e. are split between 20 sets of analyte-specific probes] and collapsed into super-resolved images”) and teaches performing this combining step in silico (Methods, Image analysis: “all image analysis was performed in Matlab”).
Regarding claim 18, Geipel teaches that in a single embodiment one set of analyte-specific probes may comprise a protein-specific probe (probe set binds specifically to the protein analyte) and another set of analyte-specific probes may comprise a nucleic acid-specific probe (probe set binds to the nucleic acid sequence) ([0071]).
In view of Eng’s teaching that splitting analyte detection with their pseudocolor system obtains the advantage of allowing multiplexed RNA in situ detection assays to detect different mRNAs in a sample beyond the diffraction limit with the further advantage of not being limited to the detection of single dye molecules or optically thin samples, one of ordinary skill in the art would have found it obvious to modify Geipel by splitting the detection of sets of analyte-specific probes to detect different analytes in a sample beyond the diffraction limit. One of ordinary skill in the art would have a reasonable expectation of success because Eng teaches that their method is advantageous for multiplexed RNA in situ detection assays and Geipel teaches a method of performing a flexible multiplexed in situ detection assay wherein nucleic acids such as RNA are potential analytes. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claims 1-2, 9-11, and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Walch et al. ("Sequential Multilocus Fluorescence In Situ Hybridization Can Detect Complex Patterns of Increased Gene Dosage at the Single Cell Level in Tissue Sections", Lab Invest 81, 1457-1459 (2001)), herein Walch.
Regarding claim 1, the teachings of Geipel are set forth above in the prior 103 rejection. However, Geipel does not disclose the use of this method for detecting different analytes in a sample beyond the diffraction limit by sequential signal-encoding. This deficiency is provided for in Walch.
Regarding claim 1, Walch teaches a method of detecting different analytes in a sample beyond the diffraction the limit (when limited optical resolution can result in complex signal overlays, paragraph 4). This is accomplished by sequentially applying fluorescently labeled probes one at a time, detecting and then removing a probe before adding the next probe (paragraph 2). Walch also teaches an advantage to using their sequential detection approach instead of a simultaneous detection approach is that the simultaneous detection approach results in complex signal overlays in multiple scenarios that confound interpretation, while their sequential detection approach avoids this problem by detecting only one target at a time.
Regarding claim 2, Walch teaches performing fluorescence in situ hybridization sequentially by first using a probe targeting one analyte and detecting it (analogous to steps (A1) and (D) in the first series of steps (A1), (B1), (C), (D), (E), (F)), then washing out the probe by heating and denaturing the sample, confirming the deletion of the probe, and then repeating the process with a different probe targeting a different analyte (analogous to steps (A2) and (D) in the second series of steps (A2), (B2), (C), (D), (E), (F)) (paragraph 2). Because Geipel teaches, as described above, detecting an analyte-specific probe with decoding oligonucleotides and signal oligonucleotides in at least 3 cycles to encode the detected analyte (steps (A#), (B#), (C), (D), (E), (F)), the modification of Geipel with Walch would teach one of ordinary skill in the art to perform steps (A1), (B1), (C), (D), (E), and (F) before then performing steps (A2), (B2), (C), (D), (E), and (F).
Regarding claim 9, neither Geipel nor Walch teach the first set of analyte-specific probes encoding at least 10x more analytes than the second set of analyte-specific probes encode. However, one of ordinary skill in the art would understand that the number of analytes encoded in either set of analyte-specific probes can be changed and the effect of the method to detect different analytes in a sample beyond the diffraction limit by signal encoding would be maintained so long as the analytes encoded for in a set of analyte-specific probes do not usually spatially overlap. This limitation is a change in size/proportion of the sets of analyte-specific probes that is common practice for one ordinary skill in the art (MPEP §2144.04 IV. A.). Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Regarding claim 10, Geipel teaches using a fluorophore as the signal element ([0029], [00115]).
Regarding claim 11, Geipel teaches the sets of signal oligonucleotides used to detect the first and second sets of analyte-specific probes comprise the same signal oligonucleotides (page 39 F. “signal oligonucleotide hybridization mixture was the same for all rounds of experiments 1 to 4” and each experiment included multiple analyte-specific probe sets, see Tables 2 and 3 on pages 34-37).
Regarding claim 18, Geipel teaches that in a single embodiment one set of analyte-specific probes may comprise a protein-specific probe (probe set binds specifically to the protein analyte) and another set of analyte-specific probes may comprise a nucleic acid-specific probe (probe set binds to the nucleic acid sequence) ([0071]).
In view of Walch’s teaching that splitting detection of multiple analytes sequentially obtains the advantage of allowing the detection of different analytes for which their nearness would otherwise confound simultaneous detection due to the optical resolution, one of ordinary skill in the art would have found it obvious to modify Geipel by splitting the detection of sets of analyte-specific probes that are likely to overlap into the two sets of analyte-specific probes of steps (A1) and (A2). One of ordinary skill in the art would have a reasonable expectation of success because Walch teaches using their method in an RNA in situ detection assay and Geipel teaches a method of performing an in situ detection assay wherein nucleic acids such as RNA are potential analytes. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claims 1, 8-11, and 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Zhuang et al. (WO 2021138078, published 08 July 2021), herein Zhuang.
Regarding claim 1, the teachings of Geipel are set forth above in the prior 103 rejection. However, Geipel does not disclose the use of this method for detecting different analytes in a sample beyond the diffraction limit by sequential signal-encoding. This deficiency is provided for in Zhuang.
Regarding claim 1, Zhuang teaches a method of multiplexed fluorescence in situ hybridization (combinatorial FISH; page 68 lines 18-32) wherein different analytes in a sample are detected beyond the diffraction limit by sequential signal encoding (“Schematic of chromatin tracing of whole chromosomes by sequential hybridization and imaging. When the target chromatin structure is comparable to or smaller than the diffraction limited resolution, a single chromatin locus is imaged in each color channel per imaging round”; page 84 lines 2-8, Fig. 17A). This is accomplished by contacting a sample with a first set of analyte-specific probes (probes for genomic loci, analogous to those of step (A1); page 68 lines 5-12) and sequentially contacting those analyte-specific probes with signal oligonucleotides (readout probes, analogous to those of step (C); page 72 lines 7-15, page 72-73 lines 34-11), the signal oligonucleotides are detected by imaging and then removed before the next cycle (round) of applying new signal oligonucleotides for detection as it proceeds through at least 3 further cycles (50 rounds of hybridization, analogous to steps (D), (E), and (F); page 73 lines 23-25 and 27-28). Zhuang further teaches contacting the same sample with a second set of analyte-specific probes (probes for nascent RNA transcripts, analogous to those of step (A2); page 68 lines 13-17) and sequentially contacting those analyte-specific probes with signal oligonucleotides (readout probes, analogous to those of step (C); page 72 lines 7-15, page 73 lines 12-22), the signal oligonucleotides are detected by imaging and then removed before the next cycle (round) of applying new signal oligonucleotides for detection as it proceeds through at least 3 further cycles (18 rounds of hybridization, analogous to steps (D), (E), and (F); page 73 lines 23-25 and 29-30). Because the probe encoding is optimized for the largest genomic distance between targets with barcodes that result in them being detected in the same detection step (page 68 lines 18-32), signals that would be within the diffraction limit of each other are separated into detection steps that are performed sequentially, allowing the analytes encoded by the signals to be distinguished beyond the diffraction limit.
Zhuang also teaches that there is demand for methods that allow genome-scale measurements of both chromatin organization and transcriptional activity in the same cells, which their multiplexing method achieves by being able to distinguish different targets beyond the diffraction limit by splitting the detection of sets of analytes with sequential hybridization and imaging, because it is important to understand how chromatin organization regulates transcription and how transcription in turn impacts chromatin organization (pages 1-2 lines 33-3).
Regarding claim 8, Geipel teaches the steps (A1), (A2), (B1), (B2), (C), (D), (E), and (F), as described above, in the claimed order (pages 38-40, D., E., F., G., H., and [00117]). However, the claimed order prevents Zhuang’s method of optimizing probe encoding for the largest genomic distance between targets with barcodes that are detected in the same detection step from functioning to detect different analytes in a sample beyond the diffraction limit because both analyte sets would be labeled and detected simultaneously in the claimed order of the steps, while the method of Zhuang requires sequentially detecting different sets of analytes. Despite this, Zhuang teaches that in some embodiments of their method the spatial position of labels may be determined at resolutions better than the diffraction limit using super-resolution microscopy techniques such as STORM and STED (page 43 lines 5-21). Therefore, the combination of Geipel and Zhuang teach performing the method according to claim 1 to detect different analytes in a sample beyond the diffraction limit with the order of steps (A1), (A2), (B1), (B2), (C), (D), (E), and (F).
Regarding claim 9, neither Geipel nor Zhuang teach the first set of analyte-specific probes encoding at least 10x more analytes than the second set of analyte-specific probes encode. However, one of ordinary skill in the art would understand that the number of analytes encoded in either set of analyte-specific probes can be changed and the effect of the method to detect different analytes in a sample beyond the diffraction limit by signal encoding would be maintained so long as the analytes encoded for in a set of analyte-specific probes do not usually spatially overlap. This limitation is a change in size/proportion of the sets of analyte-specific probes that is common practice for one ordinary skill in the art (MPEP §2144.04 IV. A.). Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Regarding claim 10, Geipel teaches using a fluorophore as the signal element ([0029], [00115]).
Regarding claim 11, Geipel teaches the sets of signal oligonucleotides used to detect the first and second sets of analyte-specific probes comprise the same signal oligonucleotides (page 39 F. “signal oligonucleotide hybridization mixture was the same for all rounds of experiments 1 to 4” and each experiment included multiple analyte-specific probe sets, see Tables 2 and 3 on pages 34-37).
Regarding claim 18, Geipel teaches that in a single embodiment one set of analyte-specific probes may comprise a protein-specific probe (probe set binds specifically to the protein analyte) and another set of analyte-specific probes may comprise a nucleic acid-specific probe (probe set binds to the nucleic acid sequence) ([0071]).
Regarding claims 19 and 20, Zhuang teaches a method of multiplex fluorescence in situ hybridization, of a which in a specific embodiment (page 68, Example 5) a first set of analyte-specific probes comprises probes directed to a first subgroup of targets which do not usually show a high spatial overlap among one another (probes were made for target genomic loci that were chosen in each chromosome and assigned barcodes for sequential imaging rounds – the barcodes were optimized for the largest minimal genomic distance between loci that are imaged simultaneously [i.e. so that they usually would not show a high spatial overlap]; page 68 lines 5-12 and 18-32; these probes were hybridized with the sample; page 71 lines 16-19; and sequentially imaged; page 73 lines 27-28). Zhuang further teaches in the same embodiment a second set of analyte-specific probes comprises probes directed to a subgroup of targets which usually show a high spatial overlap with the first subgroup of targets (nascent RNA transcript targets were chosen for genes that completely or partially overlap [i.e. usually show a high spatial overlap] the targeted genomic loci [the first subgroup of targets]; page 68 lines 13-17; these probes were hybridized with the sample; page 71 lines 16-19; and sequentially imaged separately from the first set of probes; page 73 lines 29-30).
In view of Zhuang’s teaching that their method of multiplexed fluorescence in situ hybridization fulfills the need for a method that allows genome-scale measurements of both chromatin organization and transcriptional activity in the same cells by splitting the detection of sets of analyte-specific probes to detect different analytes in a sample beyond the diffraction limit, one of ordinary skill in the art would have found it obvious to modify Geipel by splitting the detection of sets of analyte-specific probes to detect different analytes in a sample beyond the diffraction limit. One of ordinary skill in the art would have a reasonable expectation of success because Zhuang teaches that their method is advantageous for multiplexed RNA in situ detection assays and Geipel teaches a method of performing a flexible multiplexed in situ detection assay wherein nucleic acids such as RNA are potential analytes. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claims 4 and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Eng et al. ("Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+", Nature 568, 235-239 (2019)), herein Eng, as applied to claims 1, 8-13, and 18 above, and further in view of Markey et al. ("Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ", PLoS One 9(3): e93488 (2014)), herein Markey.
Regarding claim 4, Geipel in view of Eng does not teach the method according to claim 1 for in vitro diagnosis of a disease. This deficiency is provided for in Markey.
Regarding claim 4, Markey teaches using a method of fluorescence in situ hybridization for in vitro diagnosis of cancer (“cancer cells identified by Fusion FISH will be displayed in a different color than normal cells. These digital views will greatly improve cancer diagnosis” Discussion paragraph 1).
Regarding claim 14, Markey teaches a method of fluorescence in situ hybridization wherein one probe set targets exon 11 of mRNA of the Abelson (ABL) gene (cancer fusion gene first portion) and a second probe set targets exon 1 of the Breakpoint Cluster Region (BCR) gene (cancer fusion gene second portion), which are brought together in a well-characterized gene fusion that occurs in chronic myeloid leukemia (Results, Detection of BCR-ABL transcripts in chronic myeloid leukemia, paragraph 1).
Regarding claim 15, Markey teaches that the BCR-ABL gene fusion is well-characterized and occurs in chronic myeloid leukemia, so one of ordinary skill in the art would recognize that the colocalization of the BCR-ABL gene fusion indicates an increased risk of chronic myeloid leukemia.
Regarding claim 16, Markey teaches that the a first and a second analyte specific probes would be expected to co-localize in a patient condition (employing Fusion FISH imaging to detect fusion transcripts [i.e. co-localization of probes] in the serum of Ewing’s sarcoma patients [i.e. a patient condition] to enable sensitive diagnosis) (Discussion paragraph 3).
In view of Markey’s teaching that the identification of cancer cells based on gene fusions detected by fluorescence in situ hybridization will greatly improve cancer diagnosis, one of ordinary skill in the art would be motivated to combine the teachings of Geipel in view of Eng with Markey in order to use the method of detecting analytes in situ of Geipel in view of Eng for detecting cancer fusion genes and diagnosing cancer. One of ordinary skill in the art would have a reasonable expectation of success because Markey teaches the use of a fluorescence in situ hybridization method and Geipel in view of Eng teaches a fluorescence in situ hybridization method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claims 4 and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Walch et al. ("Sequential Multilocus Fluorescence In Situ Hybridization Can Detect Complex Patterns of Increased Gene Dosage at the Single Cell Level in Tissue Sections", Lab Invest 81, 1457-1459 (2001)), herein Walch, as applied to claims 1-2, 9-11, and 18 above, and further in view of Markey et al. ("Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ", PLoS One 9(3): e93488 (2014)), herein Markey.
Regarding claim 4, Geipel in view of Walch does not teach the method according to claim 1 for in vitro diagnosis of a disease. This deficiency is provided for in Markey.
Regarding claim 4, Markey teaches using a method of fluorescence in situ hybridization for in vitro diagnosis of cancer (“cancer cells identified by Fusion FISH will be displayed in a different color than normal cells. These digital views will greatly improve cancer diagnosis” Discussion paragraph 1).
Regarding claim 14, Markey teaches a method of fluorescence in situ hybridization wherein one probe set targets exon 11 of mRNA of the Abelson (ABL) gene (cancer fusion gene first portion) and a second probe set targets exon 1 of the Breakpoint Cluster Region (BCR) gene (cancer fusion gene second portion), which are brought together in a well-characterized gene fusion that occurs in chronic myeloid leukemia (Results, Detection of BCR-ABL transcripts in chronic myeloid leukemia, paragraph 1).
Regarding claim 15, Markey teaches that the BCR-ABL gene fusion is well-characterized and occurs in chronic myeloid leukemia, so one of ordinary skill in the art would recognize that the colocalization of the BCR-ABL gene fusion indicates an increased risk of chronic myeloid leukemia.
Regarding claim 16, Markey teaches that the a first and a second analyte specific probes would be expected to co-localize in a patient condition (employing Fusion FISH imaging to detect fusion transcripts [i.e. co-localization of probes] in the serum of Ewing’s sarcoma patients [i.e. a patient condition] to enable sensitive diagnosis) (Discussion paragraph 3).
In view of Markey’s teaching that the identification of cancer cells based on gene fusions detected by fluorescence in situ hybridization will greatly improve cancer diagnosis, one of ordinary skill in the art would be motivated to combine the teachings of Geipel in view of Walch with Markey in order to use the method of detecting analytes in situ of Geipel in view of Walch for detecting cancer fusion genes and diagnosing cancer. One of ordinary skill in the art would have a reasonable expectation of success because Markey teaches the use of a fluorescence in situ hybridization method and Geipel in view of Walch teaches a fluorescence in situ hybridization method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claims 4 and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Zhuang et al. (WO 2021138078, published 08 July 2021), herein Zhuang, as applied to claims 1, 8-11, and 18-20 above, and further in view of Markey et al. ("Fusion FISH Imaging: Single-Molecule Detection of Gene Fusion Transcripts In Situ", PLoS One 9(3): e93488 (2014)), herein Markey.
Regarding claim 4, Geipel in view of Zhuang does not teach the method according to claim 1 for in vitro diagnosis of a disease. This deficiency is provided for in Markey.
Regarding claim 4, Markey teaches using a method of fluorescence in situ hybridization for in vitro diagnosis of cancer (“cancer cells identified by Fusion FISH will be displayed in a different color than normal cells. These digital views will greatly improve cancer diagnosis” Discussion paragraph 1).
Regarding claim 14, Markey teaches a method of fluorescence in situ hybridization wherein one probe set targets exon 11 of mRNA of the Abelson (ABL) gene (cancer fusion gene first portion) and a second probe set targets exon 1 of the Breakpoint Cluster Region (BCR) gene (cancer fusion gene second portion), which are brought together in a well-characterized gene fusion that occurs in chronic myeloid leukemia (Results, Detection of BCR-ABL transcripts in chronic myeloid leukemia, paragraph 1).
Regarding claim 15, Markey teaches that the BCR-ABL gene fusion is well-characterized and occurs in chronic myeloid leukemia, so one of ordinary skill in the art would recognize that the colocalization of the BCR-ABL gene fusion indicates an increased risk of chronic myeloid leukemia.
Regarding claim 16, Markey teaches that the a first and a second analyte specific probes would be expected to co-localize in a patient condition (employing Fusion FISH imaging to detect fusion transcripts [i.e. co-localization of probes] in the serum of Ewing’s sarcoma patients [i.e. a patient condition] to enable sensitive diagnosis) (Discussion paragraph 3).
In view of Markey’s teaching that the identification of cancer cells based on gene fusions detected by fluorescence in situ hybridization will greatly improve cancer diagnosis, one of ordinary skill in the art would be motivated to combine the teachings of Geipel in view of Zhuang with Markey in order to use the method of detecting analytes in situ of Geipel in view of Zhuang for detecting cancer fusion genes and diagnosing cancer. One of ordinary skill in the art would have a reasonable expectation of success because Markey teaches the use of a fluorescence in situ hybridization method and Geipel in view of Zhuang teaches a fluorescence in situ hybridization method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Eng et al. ("Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+", Nature 568, 235-239 (2019)), herein Eng, as applied to claims 1, 8-13, and 18 above, and further in view of Fang and Ramasamy ("Current and Prospective Methods for Plant Disease Detection", Biosensors 5, 537-561 (2015)), herein Fang.
Regarding claim 5, Geipel in view of Eng does not teach the method according to claim 1 for diagnosis of a disease in plants. This deficiency is provided for in Fang.
Regarding claim 5, Fang teaches using fluorescence in situ hybridization technology for diagnosis of plant diseases caused by biotic stress, particularly infection by bacterial, fungal, and viral pathogens (“In addition to bacterial pathogens, [fluorescence in situ hybridization] could also be used to detect fungi and viruses and other endosymbiotic bacteria that infect the plant” 2.1.2 Fluorescence in situ Hybridization). Fang also discloses that an advantage of using fluorescence in situ hybridization for diagnosis of plant diseases is that the high affinity and specificity of probes provide high single-cell sensitivity.
In view of Fang’s teaching that it is advantageous to use fluorescence in situ hybridization technologies for diagnosis of plant disease due to the high single-cell sensitivity, one of ordinary skill in the art would be motivated to combine the teachings of Geipel in view of Eng with Fang in order to use the method of detecting analytes in situ of Geipel in view of Eng for diagnosing plant disease. One of ordinary skill in the art would have a reasonable expectation of success because Fang teaches the use of fluorescence in situ hybridization technologies and Geipel in view of Eng teaches a fluorescence in situ hybridization method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Walch et al. ("Sequential Multilocus Fluorescence In Situ Hybridization Can Detect Complex Patterns of Increased Gene Dosage at the Single Cell Level in Tissue Sections", Lab Invest 81, 1457-1459 (2001)), herein Walch, as applied to claims 1-2, 9-11, and 18 above, and further in view of Fang and Ramasamy ("Current and Prospective Methods for Plant Disease Detection", Biosensors 5, 537-561 (2015)), herein Fang.
Regarding claim 5, Geipel in view of Walch does not teach the method according to claim 1 for diagnosis of a disease in plants. This deficiency is provided for in Fang.
Regarding claim 5, Fang teaches using fluorescence in situ hybridization technology for diagnosis of plant diseases caused by biotic stress, particularly infection by bacterial, fungal, and viral pathogens (“In addition to bacterial pathogens, [fluorescence in situ hybridization] could also be used to detect fungi and viruses and other endosymbiotic bacteria that infect the plant” 2.1.2 Fluorescence in situ Hybridization). Fang also discloses that an advantage of using fluorescence in situ hybridization for diagnosis of plant diseases is that the high affinity and specificity of probes provide high single-cell sensitivity.
In view of Fang’s teaching that it is advantageous to use fluorescence in situ hybridization technologies for diagnosis of plant disease due to the high single-cell sensitivity, one of ordinary skill in the art would be motivated to combine the teachings of Geipel in view of Walch with Fang in order to use the method of detecting analytes in situ of Geipel in view of Walch for diagnosing plant disease. One of ordinary skill in the art would have a reasonable expectation of success because Fang teaches the use of fluorescence in situ hybridization technologies and Geipel in view of Walch teaches a fluorescence in situ hybridization method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Zhuang et al. (WO 2021138078, published 08 July 2021), herein Zhuang, as applied to claims 1, 8-11, and 18-20 above, and further in view of Fang and Ramasamy ("Current and Prospective Methods for Plant Disease Detection", Biosensors 5, 537-561 (2015)), herein Fang.
Regarding claim 5, Geipel in view of Zhuang does not teach the method according to claim 1 for diagnosis of a disease in plants. This deficiency is provided for in Fang.
Regarding claim 5, Fang teaches using fluorescence in situ hybridization technology for diagnosis of plant diseases caused by biotic stress, particularly infection by bacterial, fungal, and viral pathogens (“In addition to bacterial pathogens, [fluorescence in situ hybridization] could also be used to detect fungi and viruses and other endosymbiotic bacteria that infect the plant” 2.1.2 Fluorescence in situ Hybridization). Fang also discloses that an advantage of using fluorescence in situ hybridization for diagnosis of plant diseases is that the high affinity and specificity of probes provide high single-cell sensitivity.
In view of Fang’s teaching that it is advantageous to use fluorescence in situ hybridization technologies for diagnosis of plant disease due to the high single-cell sensitivity, one of ordinary skill in the art would be motivated to combine the teachings of Geipel in view of Zhuang with Fang in order to use the method of detecting analytes in situ of Geipel in view of Zhuang for diagnosing plant disease. One of ordinary skill in the art would have a reasonable expectation of success because Fang teaches the use of fluorescence in situ hybridization technologies and Geipel in view of Zhuang teaches a fluorescence in situ hybridization method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Eng et al. ("Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+", Nature 568, 235-239 (2019)), herein Eng, as applied to claims 1, 8-13, and 18 above, as evidenced by Shah et al. (“In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus”, Neuron 92(2), 342-357 (2016)), herein Shah 1, and Shah et al. (“seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus”, Neuron 94(4) 752-758 (2017)), herein Shah 2.
Regarding claim 17, Eng demonstrates an embodiment of the pseudocolor system of sequential detection in which a first set of analyte-specific probes comprises a probe for a high abundance analyte (Sox2) and a second set of analyte-specific probes comprises a probe for a low abundance analyte (Abca9). The respective probes for the high abundance analyte (Sox2) and low abundance analyte (Abca9) were in different sets of analyte-specific probes (sets of probes detected separately) because Sox2 was detected by pseudocolor detection cycles 12, 10, 6, and 16 (of barcoding rounds 1-4, respectively) and Abca9 was detected by pseudocolor detection cycles 2, 13, 16, and 19 (of barcoding rounds 1-4, respectively) (Supplementary Table 1, for each column indicating a barcoding round the number associated with the gene is the pseudocolor detection cycle it was assigned to). Shah 2 teaches that the 125 gene experiment of Figure S3 of Shah 1 includes both high and low abundance genes (Shah 2 Results and Discussion, paragraph 13). Figure S3A of Shah 1 shows the counts per cell of these genes, teaching that Sox2 has one of the highest counts per cell (therefore being interpreted as a high abundance gene) and that Abca9 has among the lowest counts per cell (therefore being interpreted as a low abundance gene) (Figure S3A).
Claims 21 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Eng et al. ("Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+", Nature 568, 235-239 (2019)), herein Eng, as applied to claims 1, 8-13, and 18 above, and further in view of Onozato et al. ("Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics" J Mol Diagn. 21(3), 390-407 (2019)), herein Onozato.
Regarding claim 21, Geipel in view of Eng does not teach probes directed to cancer activating mutations in DNA. This deficiency is provided for in Onozato.
Regarding claim 21, Onozato teaches using fluorescence in situ hybridization probes to that are directed to cancer activating mutations in DNA (probes designed for “five important cancer genes” PDGFRA, MET, EGFR, MYC, and RET; Results, Probe Development, paragraph 1; used the probes to detect the copy number of these and other cancer genes; Results, Validation, paragraphs 1-2, Figure 6B-G). Onozato also teaches that “the assessment of gene copy number is important in the management of cancer patients and is standard of care for the ERBB2 gene in breast and esophagogastric tumors”, as well as that a robust and reproducible multiplex fluorescence in situ hybridization assay has the potential to be clinically useful and therapeutically informative (Discussion, paragraph 1).
Regarding claim 22, Eng teaches a probe directed toward the transcript of EGFR (Supplementary Table 1), which Onozato teaches is a cancer-associated gene (Results, Probe Development, paragraph 1). Because Eng teaches using the pseudocolor system to separate sets of analyte-specific probes that may overlap in order to detect the respective analytes beyond the diffraction limit as discussed above, it would be obvious to one of ordinary skill in the art to place the EGFR copy number analyte-specific probe of Onozato and the EGFR transcript analyte-specific probe of Eng in separate sets because a transcript that is captured by the assay in the process of transcription or immediately after would be localized near to the EGFR gene, resulting in the two probes having potentially overlapping signals.
In view of Onozato’s teaching that multiplex fluorescence in situ assays will be useful for management of cancer patients and will be therapeutically informative, one of ordinary skill in the art would be motivated to combine the targeting of probes toward the cancer activating copy number gains taught by Onozato with the robust multiplex fluorescence in situ assay taught by Geipel in view of Eng. One of ordinary skill in the art would have a reasonable expectation of success because this combination applies a probe target for a multiplex fluorescence in situ assay taught by Onozato with a similar multiplex fluorescence in situ assay taught by Geipel in view of Eng. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Walch et al. ("Sequential Multilocus Fluorescence In Situ Hybridization Can Detect Complex Patterns of Increased Gene Dosage at the Single Cell Level in Tissue Sections", Lab Invest 81, 1457-1459 (2001)), herein Walch, as applied to claims 1-2, 9-11, and 18 above, and further in view of Onozato et al. ("Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics" J Mol Diagn. 21(3), 390-407 (2019)), herein Onozato.
Regarding claim 21, Geipel in view of Walch does not teach probes directed to cancer activating mutations in DNA. This deficiency is provided for in Onozato.
Regarding claim 21, Onozato teaches using fluorescence in situ hybridization probes to that are directed to cancer activating mutations in DNA (probes designed for “five important cancer genes” PDGFRA, MET, EGFR, MYC, and RET; Results, Probe Development, paragraph 1; used the probes to detect the copy number of these and other cancer genes; Results, Validation, paragraphs 1-2, Figure 6B-G). Onozato also teaches that “the assessment of gene copy number is important in the management of cancer patients and is standard of care for the ERBB2 gene in breast and esophagogastric tumors”, as well as that a robust and reproducible multiplex fluorescence in situ hybridization assay has the potential to be clinically useful and therapeutically informative (Discussion, paragraph 1).
In view of Onozato’s teaching that multiplex fluorescence in situ assays will be useful for management of cancer patients and will be therapeutically informative, one of ordinary skill in the art would be motivated to combine the targeting of probes toward the cancer activating copy number gains taught by Onozato with the robust multiplex fluorescence in situ assay taught by Geipel in view of Walch. One of ordinary skill in the art would have a reasonable expectation of success because this combination applies a probe target for a multiplex fluorescence in situ assay taught by Onozato with a similar multiplex fluorescence in situ assay taught by Geipel in view of Walch. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Zhuang et al. (WO 2021138078, published 08 July 2021), herein Zhuang, as applied to claims 1, 8-11, and 18-20 above, and further in view of Onozato et al. ("Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics" J Mol Diagn. 21(3), 390-407 (2019)), herein Onozato.
Regarding claim 21, Geipel in view of Zhuang does not teach probes directed to cancer activating mutations in DNA. This deficiency is provided for in Onozato.
Regarding claim 21, Onozato teaches using fluorescence in situ hybridization probes to that are directed to cancer activating mutations in DNA (probes designed for “five important cancer genes” PDGFRA, MET, EGFR, MYC, and RET; Results, Probe Development, paragraph 1; used the probes to detect the copy number of these and other cancer genes; Results, Validation, paragraphs 1-2, Figure 6B-G). Onozato also teaches that “the assessment of gene copy number is important in the management of cancer patients and is standard of care for the ERBB2 gene in breast and esophagogastric tumors”, as well as that a robust and reproducible multiplex fluorescence in situ hybridization assay has the potential to be clinically useful and therapeutically informative (Discussion, paragraph 1).
In view of Onozato’s teaching that multiplex fluorescence in situ assays will be useful for management of cancer patients and will be therapeutically informative, one of ordinary skill in the art would be motivated to combine the targeting of probes toward the cancer activating copy number gains taught by Onozato with the robust multiplex fluorescence in situ assay taught by Geipel in view of Zhuang. One of ordinary skill in the art would have a reasonable expectation of success because this combination applies a probe target for a multiplex fluorescence in situ assay taught by Onozato with a similar multiplex fluorescence in situ assay taught by Geipel in view of Zhuang. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Eng et al. ("Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+", Nature 568, 235-239 (2019)), herein Eng, and in view of Onozato et al. ("Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics" J Mol Diagn. 21(3), 390-407 (2019)), herein Onozato, as applied to claims 21 and 22 above, and further in view of Shangguan et al. ("Cell-Specific Aptamer Probes for Membrane Protein Elucidation in Cancer Cells", J Proteome Res. 7(5), 2133-2139 (2008)), herein Shangguan.
Regarding claim 23, Geipel in view of Eng and Onozato does not teach probes directed to proteins associated with cancer. This deficiency is provided for in Shangguan.
Regarding claim 23, Shangguan teaches a probe (the aptamer probe sgc8; Results and Discussion paragraph 1) directed to a protein associated with cancer (PTK7; Results and Discussion paragraph 3) that is used to fluorescently label PTK7 in situ (Results and Discussion paragraph 4, Figure 5 bottom row). Shangguan also teaches that aptamer probes are useful for the recognition of the target molecules that are biomarkers for disease conditions like cancer (Introduction, paragraph 2) and that the cost and complexity of generating aptamer probes is significantly lower than that of generating antibody-based probes (Discussion, paragraph 2).
Regarding claim 23, it would be obvious to one of ordinary skill in the art to try a version of the method of Geipel in view of Eng and Onozato in further view of Shangguan in which a first set of analyte-specific probes includes a probe directed to cancer activating mutations and a second set of analyte-specific probes includes a probe directed to a protein associated with cancer. One of ordinary skill in the art would have recognized a problem: whether those probes should be assigned to the same or different sets of analyte-specific probes. There would be only two possible options: assigning them to the same set or to different sets. There would be a reasonable expectation of success in trying a version of the method in which those probes are in separate sets because the sets would be detected separately, thereby avoiding the undesirable potential for overlapping signals of those probes. Therefore, the separation of those probes into separate sets of analyte-specific probes would be obvious to try (MPEP §2143 I. E.).
In view of Shangguan’s teaching that aptamer probes are a cost-efficient way to target proteins with fluorescently-labeled nucleic acid probes akin to those used in conventional fluorescence in situ hybridization assays that target complementary nucleic acid sequences, one of ordinary skill in the art would be motivated to combine the aptamer probe design for targeting proteins of Shangguan with the robust multiplex fluorescence in situ assay taught by Geipel in view of Eng and Onozato in order to efficiently expand the potential analytes of the multiplex assay. One of ordinary skill in the art would have a reasonable expectation of success because this combination merely changes the binding domain of the probe from being a complementary sequence specific to a nucleic acid target to an aptamer sequence specific to a protein target, which would not be expected to impact the function of the tails that are involved in the multiplexing of the method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Walch et al. ("Sequential Multilocus Fluorescence In Situ Hybridization Can Detect Complex Patterns of Increased Gene Dosage at the Single Cell Level in Tissue Sections", Lab Invest 81, 1457-1459 (2001)), herein Walch, and in view of Onozato et al. ("Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics" J Mol Diagn. 21(3), 390-407 (2019)), herein Onozato, as applied to claim 21 above, and further in view of Shangguan et al. ("Cell-Specific Aptamer Probes for Membrane Protein Elucidation in Cancer Cells", J Proteome Res. 7(5), 2133-2139 (2008)), herein Shangguan.
Regarding claim 23, Geipel in view of Walch and Onozato does not teach probes directed to proteins associated with cancer. This deficiency is provided for in Shangguan.
Regarding claim 23, Shangguan teaches a probe (the aptamer probe sgc8; Results and Discussion paragraph 1) directed to a protein associated with cancer (PTK7; Results and Discussion paragraph 3) that is used to fluorescently label PTK7 in situ (Results and Discussion paragraph 4, Figure 5 bottom row). Shangguan also teaches that aptamer probes are useful for the recognition of the target molecules that are biomarkers for disease conditions like cancer (Introduction, paragraph 2) and that the cost and complexity of generating aptamer probes is significantly lower than that of generating antibody-based probes (Discussion, paragraph 2).
Regarding claim 23, it would be obvious to one of ordinary skill in the art to try a version of the method of Geipel in view of Walch and Onozato in further view of Shangguan in which a first set of analyte-specific probes includes a probe directed to cancer activating mutations and a second set of analyte-specific probes includes a probe directed to a protein associated with cancer. One of ordinary skill in the art would have recognized a problem: whether those probes should be assigned to the same or different sets of analyte-specific probes. There would be only two possible options: assigning them to the same set or to different sets. There would be a reasonable expectation of success in trying a version of the method in which those probes are in separate sets because the sets would be detected separately, thereby avoiding the undesirable potential for overlapping signals of those probes. Therefore, the separation of those probes into separate sets of analyte-specific probes would be obvious to try (MPEP §2143 I. E.).
In view of Shangguan’s teaching that aptamer probes are a cost-efficient way to target proteins with fluorescently-labeled nucleic acid probes akin to those used in conventional fluorescence in situ hybridization assays that target complementary nucleic acid sequences, one of ordinary skill in the art would be motivated to combine the aptamer probe design for targeting proteins of Shangguan with the robust multiplex fluorescence in situ assay taught by Geipel in view of Walch and Onozato in order to efficiently expand the potential analytes of the multiplex assay. One of ordinary skill in the art would have a reasonable expectation of success because this combination merely changes the binding domain of the probe from being a complementary sequence specific to a nucleic acid target to an aptamer sequence specific to a protein target, which would not be expected to impact the function of the tails that are involved in the multiplexing of the method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Geipel et al. (WO 2020254519, published 24 December 2020), herein Geipel, in view of Zhuang et al. (WO 2021138078, published 08 July 2021), herein Zhuang, and in view of Onozato et al. ("Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics" J Mol Diagn. 21(3), 390-407 (2019)), herein Onozato, as applied to claim 21 above, and further in view of Shangguan et al. ("Cell-Specific Aptamer Probes for Membrane Protein Elucidation in Cancer Cells", J Proteome Res. 7(5), 2133-2139 (2008)), herein Shangguan.
Regarding claim 23, Geipel in view of Zhuang and Onozato does not teach probes directed to proteins associated with cancer. This deficiency is provided for in Shangguan.
Regarding claim 23, Shangguan teaches a probe (the aptamer probe sgc8; Results and Discussion paragraph 1) directed to a protein associated with cancer (PTK7; Results and Discussion paragraph 3) that is used to fluorescently label PTK7 in situ (Results and Discussion paragraph 4, Figure 5 bottom row). Shangguan also teaches that aptamer probes are useful for the recognition of the target molecules that are biomarkers for disease conditions like cancer (Introduction, paragraph 2) and that the cost and complexity of generating aptamer probes is significantly lower than that of generating antibody-based probes (Discussion, paragraph 2).
Regarding claim 23, it would be obvious to one of ordinary skill in the art to try a version of the method of Geipel in view of Zhuang and Onozato in further view of Shangguan in which a first set of analyte-specific probes includes a probe directed to cancer activating mutations and a second set of analyte-specific probes includes a probe directed to a protein associated with cancer. One of ordinary skill in the art would have recognized a problem: whether those probes should be assigned to the same or different sets of analyte-specific probes. There would be only two possible options: assigning them to the same set or to different sets. There would be a reasonable expectation of success in trying a version of the method in which those probes are in separate sets because the sets would be detected separately, thereby avoiding the undesirable potential for overlapping signals of those probes. Therefore, the separation of those probes into separate sets of analyte-specific probes would be obvious to try (MPEP §2143 I. E.).
In view of Shangguan’s teaching that aptamer probes are a cost-efficient way to target proteins with fluorescently-labeled nucleic acid probes akin to those used in conventional fluorescence in situ hybridization assays that target complementary nucleic acid sequences, one of ordinary skill in the art would be motivated to combine the aptamer probe design for targeting proteins of Shangguan with the robust multiplex fluorescence in situ assay taught by Geipel in view of Zhuang and Onozato in order to efficiently expand the potential analytes of the multiplex assay. One of ordinary skill in the art would have a reasonable expectation of success because this combination merely changes the binding domain of the probe from being a complementary sequence specific to a nucleic acid target to an aptamer sequence specific to a protein target, which would not be expected to impact the function of the tails that are involved in the multiplexing of the method. Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made.
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).
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Claims 1, 9, and 12-13 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 75 of copending Application No. 18/292,537 in view of any one of Eng et al. ("Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+", Nature 568, 235-239 (2019)), herein Eng, Walch et al. ("Sequential Multilocus Fluorescence In Situ Hybridization Can Detect Complex Patterns of Increased Gene Dosage at the Single Cell Level in Tissue Sections", Lab Invest 81, 1457-1459 (2001)), herein Walch, or Zhuang et al. (WO 2021138078, published 08 July 2021), herein Zhuang.
Regarding instant claim 1, claim 75 of ‘537 claims a multiplex method for detecting different analytes by sequential signal-encoding of said analytes, comprising contacting the sample with at least 20 different sets of analyte-specific probes that are not patentably distinct from the first and second set of analyte-specific probes claimed in steps (A1) and (A2) of instant claim 1. The differences are that claim 75 of ‘537 claims at least 20 sets of analyte-specific probes whereas instant claim 1 only claims at least the 2 sets of analyte-specific probes recited in steps (A1) and (A2), and that claim 75 of ‘537 recites “if the analyte is a nucleic acid each set of analyte-specific probes comprises at least five (5) analyte-specific probes which specifically interact with different sub-structures of the same analyte” whereas the instant claim 1 lacks the language “at least five (5)”. Because both of these differences merely further limit the language of instant claim 1, the descriptions of the analyte-specific probes are not patentably distinct. Claim 75 of ‘537 further claims contacting the sample with at least one set of decoding oligonucleotides per analyte (which means at least 20 sets of decoding oligonucleotides), which possess the same structural limitations as the decoding oligonucleotides of steps (B1) and (B2) in the instant claim 1. Claim 75 of ‘537 further claims steps (C), (D), (E), and (F) in identical language to instant claim 1. The only limitation of instant claim 1 that claim 75 of ‘537 does not explicitly teach is that the method is for detecting the different analytes in a sample beyond the diffraction limit. This deficiency is provided for in Eng as described in the 35 U.S.C. § 103 rejections above. It would be obvious to one of ordinary skill in the art to combine Eng with ‘537 for the same reasons given in the 35 U.S.C. § 103 rejections above that Eng would be obvious to combine with Geipel, because, like Geipel, claim 75 of ‘537 teaches a method of multiplex method of in situ analyte detection.
Instant claims 9 and 12-13 are obvious variants of claim 75 of ‘537 in view of Eng based on the further teachings of Eng, as described in the 35 U.S.C. § 103 rejections above.
This is a provisional nonstatutory double patenting rejection.
Conclusion
All claims are rejected.
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/JEFFREY BELLAH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683