DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 30, 36, 42, 47, 49, 52, and 54, in the reply filed on July 9th, 2025 is acknowledged.
Claim 67 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on July 9th, 2025.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on November 8th, 2022 and July 9th, 2025 are acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Claim Summary
Claims 3, 4, 6, 8, 11, 15, 20, 22, 25, 27, 30, 36, 42, 47, 49, 52, and 54 have been amended. Claims 5, 7, 10, 12-14, 16-19, 21, 23-24, 26, 28-29, 31-35, 37-41, 43-46, 48, 50-51, 53, 55-66, and 68 have been canceled. Claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 30, 36, 42, 47, 49, 52, 54, and 67 are pending. Claim 67 is withdrawn from consideration as being drawn to a non-elected invention/species. Claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 30, 36, 42, 47, 49, 52, and 54 are under examination and discussed in this Office action.
Drawings
The drawings are objected to due to the spelling errors in Figure 1. As outlined in red below, the word “Barcode(s)” and “Sequence” have been misspelled in the top box.
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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 Interpretation
Claims 1 and 22 recite the limitations “generating a plurality of monomers by cleaving the concatemer at the restriction site.” In general, it is understood that use of a restriction site is indicative of combined use with a restriction enzyme. This idea is supported by paragraph [0008] in the specification, wherein it is stated “the cleaving of the concatemer at the restriction site can comprise contacting the biological sample with a restriction endonuclease that recognizes the restriction site”. As such, mentions of cleaving or cleavage in the claims are interpreted as being accomplished by a restriction enzyme.
Claim Objections
Claims 6, 11, and 22 are objected to because of the following informalities:
Claim 6 recites “wherein the target nucleic acid comprises a messenger RNA (mRNA) molecules”. This recitation should be amended to reflect either the target nucleic acid comprises a messenger RNA molecule (remove the “s” at the end of molecules) or the target nucleic acids comprise messenger RNA molecules (pluralize target nucleic acids and remove the “a”), depending on if the Applicant intended for this recitation to be singular or plural. Claim 6 further recites “at or near the a labeling agent”. This recitation should be amended to remove the “a”.
Claim 11 recites “wherein the target nucleic acid comprises mRNA molecules that comprises a polyA tail”. This recitation should also be amended to reflect either a singular or plural target nucleic acid as it currently states a singular target nucleic acid is a plurality of mRNA molecules. Furthermore, once the tense has been decided on, the second instance of “comprises” should be amended to reflect the change in tense.
Claim 22 recites “(2)(a) generating, in a biological sample a target nucleic acid”. A comma should be inserted between “sample” and “a”. This same issue is noted at the recitation of “(3)(a) generating, in a biological sample a target nucleic acid”, where a comma should also be inserted between “sample” and “a”.
Appropriate correction is required.
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 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 30, 36, 42, 47, 49, 52, and 54 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites the limitation “allowing the monomer to hybridize to a target nucleic acid in the biological sample via the complement”. It is unclear from this recitation how a monomer will hybridize to a target nucleic acid in the biological sample when there is no claimed step for the release of nucleic acids from the biological sample. It is generally understood that nucleic acids are contained within cells and not immediately accessible for probes that are intended to hybridize to a nucleic acid. Therefore, without a release step, there would be no nucleic acids available for the monomers to hybridize with, rendering the method as claimed indefinite. It is further unclear from this recitation if there is meant to be a plurality of monomers binding to target nucleic acids, or if one monomer from the plurality goes on to bind with a single target sequence. If one monomer from the plurality goes on to bind with a single target sequence, it is further unclear how the rest of the plurality of monomers does not then hybridize to target nucleic acids supposing the same conditions that allow the one monomer to bind allow all of the plurality of monomers to bind. Claims 2-4, 6, 8-9, 11, 15, 20, 25, 27, 30, 36, 42, 47, 49, 52, and 54 are also rejected here for their dependence on claim 1 and further lack of clarity regarding the issues at hand. Claim 22, while having a more detailed method than claim 1, also suffers from the same identified issues and is also rejected here.
Claim 30 recites the limitation “wherein the RCA is performed using a circularized nucleic acid probe as a template and the reporter oligonucleotide as a primer or using a circularized nucleic acid probe as a template and a second oligonucleotide as a primer”. It is unclear from this recitation whether the circularized nucleic acid probe is meant to be or contain the aspects of the nucleic acid probe presented in claim 1, or if it is an entirely different probe. If it is meant to be a different probe, it is further unclear, without further limitations related to the circularized probe, how this probe could function in the method as claimed without the aspects of the nucleic acid probe detailed in claim 1.
Claim Rejections - 35 USC § 112(a)
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.
Enablement
Claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 30, 36, 42, 47, 49, 52, and 54 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
There are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “undue.” See MPEP § 2164. These factors include, but are not limited to: the breadth of the claims, the nature of the invention, the state of the prior art, the level of one of ordinary skill, the level of predictability in the art, the amount of direction provided by the inventor, the existence of working examples, and the quantity of experimentation needed to make or use the invention based on the content of the disclosure.
The office has analyzed the specification in direct accordance to the factors outlines in In re Wands. MPEP 2164.04 states: “[W]hile the analysis and conclusion of a lack of enablement are based on factors discussed in MPEP 2164.01(a) and the evidence as whole, it is not necessary to discuss each factor in written enablement rejection.” These factors will be analyzed, in turn, to demonstrate that one of ordinary skill in the art would have had to perform “undue experimentation” to make and/or use the invention and therefore, applicant’s claims are not enabled.
(A) With respect to the breadth of the claims: Claim 1 as currently drafted encompasses a method for analyzing a biological sample, comprising a labeling agent and a nucleic acid probe. The probe comprises a cassette comprising a restriction site, a nucleic acid capture sequence, and a barcode sequence, and hybridizes to a reporter oligonucleotide conjugated to the labeling agent. The probe is amplified to generate a concatemer of monomers complementary to the cassette. The concatemer is then cleaved at the restriction site to generate a plurality of monomers that hybridize to target nucleic acids in the biological sample. However, this broad method of analyzing biological samples does not include a step of creating double stranded DNA at the restriction sites in the concatemer, which is generally necessary for cleavage at restriction sites. Concatemers produced in this way, as will be discussed below, are single stranded nucleic acids and thus generally cannot be cleaved at what would be a single stranded restriction site. A further issue in this broad method is nucleic acids in the biological sample that are accessible to the restriction enzyme will also be cleaved if they contain a restriction site for that restriction enzyme. It is generally understood that a restriction enzyme will cleave at any restriction site it is capable of binding to, as will be discussed below. If this restriction site appears in a target nucleic acid, it is then unclear how the target would remain intact and available for hybridization with the monomer if it happens to be cleaved where the monomer would hybridize. Claims 2-4, 6, 8-9, 11, 15, 20, 25, 27, 30, 36, 42, 47, 49, 52, and 54 encompass the same breadth as claim 1, and therefore suffer from the same issue. Claim 22 as currently drafted encompasses more detailed methods of claim 1, all of which have target nucleic acids that are single stranded or can reasonably be single stranded, and therefore will not experience off target effects of cleaving target nucleic acids with a restriction enzyme. However, claim 22 does not address a step of creating double-stranded DNA at the restriction sites in the concatemer, which is generally necessary for cleavage at restriction sites and an issue as detailed for claim 1.
(B) The nature of the invention: The invention “relates in some aspects to methods and compositions for analyzing the presence and location of target nucleic acids, such as mRNA molecules, in a biological sample (e.g., in situ), in connection with an analyte in the biological sample” (Paragraph [0002] of the instant specification).
(C), (D), (E) With respect to the state of the art, the level of one of ordinary skill and predictability of the art: Promega (How to Use Restriction Enzymes: A Resource Guide. Promega, [2025] [retrieved on September 26th, 2025]. Retrieved from: https://www.promega.com/resources/guides/nucleic-acid-analysis/restriction-enzyme-resource/) generally teaches on the known aspects of restriction enzymes and how they function (whole document). As stated in the first sentence of the article, “[r]estriction enzymes recognize short DNA sequences and cleave double-stranded DNA at specific sites within or adjacent to these sequences” (Page 1, first paragraph). This is further reiterated later in the article where it is stated that restriction endonucleases bind dsDNA specifically and nonspecifically, and that restriction enzymes can diffuse along DNA to locate target sites (Page 11, last paragraph). It can reasonably be assumed from the recitations in Promega that a restriction enzyme will cleave at any restriction site it comes across. In regards to single-stranded DNA, Promega states that this function has been reported for a few restriction enzymes (Pages 27-28, section of Single-Stranded DNA). However, further research has shown that several of the restriction enzymes thought to cleave single-stranded DNA actually instead recognize folded back duplex regions and cleave at these double-stranded DNA sites in the single-stranded DNA (Pages 27-28, section of Single-Stranded DNA). Therefore, it is unpredictable as to whether any restriction enzyme is truly capable of cleaving single-stranded DNA.
NEB Enzymes (Products [online]. New England Biolabs, [2025] [retrieved on September 27th, 2025]. Retrieved from: https://www.neb.com/en-us/products) provides product pages for a number of different restriction enzymes, which include their recognition sites. Looking at a small selection of these product pages, like for DraI and MseI, both of these enzymes have double-stranded recognition sites (see screenshots below).
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Furthermore, based on the teachings of Promega, the restriction enzymes exemplified above can reasonably cleave any restriction site that they recognize in a sample containing nucleic acids.
Ali (Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine, Chemical Society Reviews, March 2014, 43, 3324-3341) generally teaches on the rolling circle amplification (RCA) method and its capability of producing concatemers from circular templates (Introduction). Ali teaches that RCA continuously adds nucleotides to a primer annealed on the circular template to produce long single-stranded DNA with a plurality of repeats (e.g. concatemer) (Page 3324, column 1, paragraph 1). Figure 1F in Ali generally teaches the splitting of an RCA concatemer into monomers using what appears to be an oligonucleotide complementary to a restriction site in the concatemer.
Goransson (Rapid Identification of Bio-Molecules Applied for Detection of Biosecurity Agents Using Rolling Circle Amplification, PLOS One, February 2012, 7, 1-9) teaches on an application of RCA generated concatemers for detecting pathogens (Introduction). The generated concatemers are digested by restriction enzymes to form monomers that are further subject to RCA for the purpose of amplifying a detection signal (Figure 1B). As shown in Figure 1B, an oligonucleotide referred to as a replication oligonucleotide is used to bind to the single-stranded restriction sites in the concatemer to make them double-stranded and available for digestion.
Taken together, the art is unpredictable in regards to single-stranded cleavage of restriction sites with restriction enzymes. Instead, the art indicates that, when making a concatemer, it is necessary to form double-stranded DNA for to cut at restrictions sites if they are included in the concatemers. The art also indicates that restriction enzymes reasonably cleave any restriction site that they recognize in a sample containing nucleic acids.
The invention is drawn to biological molecules, and is therefore in a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001). The level of skill in the art is therefore deemed to be high.
(F), (G) With respect to the amount of direction and working examples provided by the applicant: The Applicants have provided minimal information regarding the nature of their restriction sites as they relate to the structure of their concatemer. The instant specification speaks on restriction sites with generality, as may be expected with a concept well-known in the art. However, as indicated by the state of the art above, it is well-known that specific restriction enzymes require specific recognition sequences, with those recognition sequences being double-stranded. The instant specification describes a number of restriction enzymes, all of which require a double stranded recognition site (see paragraph [0069] for described enzymes and NEB Enzymes file). There is no direction in the specification of how the concatemer produced by the method becomes double-stranded when it is well accepted in the art that a concatemer produced by similar methods will be single-stranded. The art also indicates that some type of oligonucleotide can be used to make a single-stranded concatemer double-stranded at the required restriction sites, which then also needs to be dissociated for further functionality of the digested monomers. In the instant case, there is a single mention of a restriction-site oligonucleotide in paragraph [0008]. As stated, “[i]n some of any of the provided embodiments, the cleaving can also involve a restriction-site oligonucleotide comprising nucleic acid sequences complementary to the restriction site.” From this simple description, there is no indication that this oligonucleotide is intended to interact with the concatemer. It would be improper to assume that, even if the oligonucleotide is complementary to the restriction site, it interacts with that restriction site as no further information has been provided in the instant specification regarding the structure and function of this oligonucleotide. Furthermore, while it is described that the cleaving can also involve this oligonucleotide, this is not claimed and it would be improper to read limitations from the specification into the claims. Finally, the working examples provided by the Applicant are all prophetic examples that detail the concept of the method, but again, do not provide direction on how the concatemer becomes double-stranded for restriction enzyme cleavage.
The Applicants have provided no information on how to contend with off-target effects when introducing a restriction enzyme to a biological sample. The instant specification speaks on restriction sites with generality, as may be expected with a concept well-known in the art. However, as indicated by the state of the art above, it can reasonably be assumed that a restriction enzyme will cleave at any restriction site it comes across. The instant specification describes a number of restriction enzymes (see paragraph [0069] for described enzymes and NEB Enzymes file), all of which would reasonably cleave every restriction site they recognize as indicated by the state of the art. The working examples provided by the Applicant are all prophetic examples that detail the concept of the method, but again, do not provide direction on how to contend with off-target effects when introducing a restriction enzyme to a biological sample.
Overall, the Applicants have not provided direction on how their concatemer becomes double-stranded for the purpose of cleavage by any restriction enzyme that has been specifically described in the instant specification. The Applicants have also not provided direction on how restriction enzyme off-target effects may be addressed. Therefore, the method as claimed could not be achieved.
(H) Undue experimentation would be required to practice the invention as claimed due to the amount of experimentation necessary because of the expansive breadth of the claims, the state of the art, and the lack of guidance in the form of varied working examples in the specification. A skilled artisan recognizes that a double-stranded DNA restriction site is generally required for cleavage by restriction enzymes and that restriction enzymes will have off-target effects when introduced to a biological sample. Thus the claimed method remains unpredictable, requiring undue experimentation.
In regards to the double-stranded restriction site, one of skill in the art would first need to develop a method by which to make double-stranded DNA at the restriction sites of the concatemer. This would require determining an optimal method, which may include aspects of introducing an oligonucleotide as described in the art and the instant specification, to form double-stranded DNA at the restriction sites in the concatemer. Taking the specific example of the oligonucleotide as described, this would require further investigation as to the optimal length of an oligonucleotide for this function, as shorter oligonucleotides are well known to experience greater off-target binding, as well as an optimal method to the release the digested halves of the oligonucleotide if the monomers are then intended to be used as primers as later claimed. This method would need to not affect the rest of the components of the method, and would therefore require experimentation with options like heat-induced and chemically-induced denaturation which may negatively affect the sample being tested. Experimentation would also be needed to determine the optimal time to introduce these oligonucleotides as premature binding may affect the creation of the concatemer itself if the oligonucleotide were to bind directly to the probe. Finally, a step removing the oligonucleotides may be necessary to prevent unintended binding with newly created monomers that may circularize them and prevent interaction with target nucleic acids. These suggestions are just the possible experimentation for one method. If it were to be unsatisfactory for use in the claimed method, one of skill in the art would then need to investigate further methods for forming double-stranded DNA at the restriction sites in the concatemer. This reasonably represents an undue amount of experimentation, and therefore the specification does not teach one skilled in the art how to perform the full scope of the method.
In regards to restriction enzymes potentially cleaving target nucleic acids, one of skill in the art would need to evaluate a range of reaction conditions that would allow for cleavage of the concatemer but not cleavage of target nucleic acids. There are a multitude of reaction conditions that can be altered for restriction enzyme reactions. These include the pH of the reaction, the concertation of Mg2+, the concentration of salts, the concentration of the stabilizer BSA, incubation temperature, and reaction volume. While there are general standards for restriction enzyme reactions of purified DNA, there are no guarantees that those standards will apply if the biological sample is a tissue sample or a blood sample. Given all of these conditions, there are a large number of parameters that would need to be tested in the course of determining which conditions would work for a method as claimed. This reasonably represents an undue amount of experimentation, and therefore the specification does not teach one skilled in the art how to perform the full scope of the method.
MPEP §2164.01(a), 4th paragraph, provides that, “A conclusion of lack of enablement means that, based on the evidence regarding each of the above factors, the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention without undue experimentation. In re Wright, 999 F.2d 1157, 1562; 27 USPQ2d 1510, 1513 (Fed. Cir. 1993).
Genentech Inc. v. Novo Nordisk A/S, 42 USPQ2d 1001, 1005 (CA FC), states that, “[p]atent protection is granted in return for an enabling disclosure of an invention, not for vague intimations of general ideas that may or may not be workable,” citing Brenner v. Manson, 383 U.S. 519, 536 (1966) (stating, in the context of the utility requirement, that “a patent is not a hunting license. It is not a reward for search, but compensation for its successful conclusion”). The Genentech decision continued, “tossing out the mere germ of an idea does not constitute enabling disclosure. While every aspect of a generic claim certainly need not have been carried out by an inventor, or exemplified in the specification, reasonable detail must be provided in order to enable members of the public to understand and carry out the invention.” Id. at p. 1005.
After applying the Wands factors and analysis to claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 30, 36, 42, 47, 49, 52, and 54, in view of the applicant’s entire disclosure, and considering the In re Wright, In re Fisher and Genentech decisions discussed above, it is concluded that the practice of the full scope of the invention as claimed would not be enabled by the written disclosure. Therefore, claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 30, 36, 42, 47, 49, 52, and 54 are rejected under 35 U.S.C. §112(a) for failing to disclose sufficient information to enable a person of skill in the art to practice the claimed invention to the full scope embraced by the claims.
Scope of Enablement
Claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 36, 42, 47, 49, 52, and 54 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method of analyzing a biological sample, comprising a circular nucleic acid probe comprising a cassette comprising (1) a restriction site, (2) a nucleic acid capture sequence, and (3) a barcode sequence, wherein the nucleic acid probe hybridizes to the reporter oligonucleotide and amplifying the nucleic acid probe with rolling circle amplification to generate a concatemer of monomer sequences, this does not reasonably provide enablement for a method of analyzing a biological sample, comprising any nucleic acid probe comprising a cassette comprising (1) a restriction site, (2) a nucleic acid capture sequence, and (3) a barcode sequence, wherein the nucleic acid probe hybridizes to the reporter oligonucleotide and amplifying the nucleic acid probe with any amplification method to generate a concatemer of monomer sequences as embraced by the claims.
Similarly, Claim 22 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method of analyzing a biological sample, comprising a circular nucleic acid probe comprising a cassette comprising (1) a restriction site, (2) a plurality of adenine (A) nucleotides, (3) a barcode sequence comprising an analyte-binding moiety- specific barcode sequence and a spatial barcode sequence and (4) an adapter sequence, wherein the nucleic acid probe hybridizes to the reporter oligonucleotide, this does not reasonably provide enablement for a method of analyzing a biological sample, comprising any nucleic acid probe comprising a cassette comprising (1) a restriction site, (2) a plurality of adenine (A) nucleotides, (3) a barcode sequence comprising an analyte-binding moiety- specific barcode sequence and a spatial barcode sequence and (4) an adapter sequence, wherein the nucleic acid probe hybridizes to the reporter oligonucleotide, wherein the nucleic acid probe hybridizes to the reporter oligonucleotide as embraced by the claims.
The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
There are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “undue.” See MPEP § 2164. These factors include, but are not limited to: the breadth of the claims, the nature of the invention, the state of the prior art, the level of one of ordinary skill, the level of predictability in the art, the amount of direction provided by the inventor, the existence of working examples, the quantity of experimentation needed to make or use the invention based on the content of the disclosure.
The office has analyzed the specification in direct accordance to the factors outlines in In re Wands. MPEP 2164.04 states: “[W]hile the analysis and conclusion of a lack of enablement are based on factors discussed in MPEP 2164.01(a) and the evidence as whole, it is not necessary to discuss each factor in written enablement rejection.” These factors will be analyzed, in turn, to demonstrate that one of ordinary skill in the art would have had to perform “undue experimentation” to make and/or use the invention and therefore, applicant’s claims are not enabled.
(A) With respect to the breadth of the claims: Claim 1 as currently drafted encompasses a method if analyzing a biological sample, comprising a nucleic acid probe comprising a cassette comprising (1) a restriction site, (2) a nucleic acid capture sequence, and (3) a barcode sequence, wherein the nucleic acid probe hybridizes to the reporter oligonucleotide and amplifying the nucleic acid probe to generate a concatemer of monomer sequences. “A nucleic acid probe” and “amplifying” do not limit the probe and the amplification method to a circular probe and rolling circle amplification as described in the specification. Consequently, the breadth of the claim is expansive. Claims 2-4, 6, 8-9, 11, 15, 20, 25, 27, 30, 36, 42, 47, 49, 52, and 54 encompass the same breadth as claim 1 since they do not limit the Cas protein to any specific Cas protein.
Claim 22 as currently drafted encompasses a method of analyzing a biological sample, comprising nucleic acid probe comprising a cassette comprising (1) a restriction site, (2) a plurality of adenine (A) nucleotides, (3) a barcode sequence comprising an analyte-binding moiety-specific barcode sequence and a spatial barcode sequence and (4) an adapter sequence, wherein the nucleic acid probe hybridizes to the reporter oligonucleotide. “A nucleic acid probe” and does not limit the probe to a circular probe as described in the specification. Consequently, the breadth of the claim is expansive.
(B) The nature of the invention: The invention “relates in some aspects to methods and compositions for analyzing the presence and location of target nucleic acids, such as mRNA molecules, in a biological sample (e.g., in situ), in connection with an analyte in the biological sample” (Paragraph [0002] of the instant specification).
(C), (D), (E) With respect to the state of the prior art, the level of one of ordinary skill and predictability of the art: Ali (Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine, Chemical Society Reviews, March 2014, 43, 3324-3341) generally teaches on the rolling circle amplification (RCA) method and its capability of producing concatemers from circular templates (Introduction). Ali teaches that RCA continuously adds nucleotides to a primer annealed on the circular template to produce long single-stranded DNA with a plurality of repeats (e.g. concatemer) (Page 3324, column 1, paragraph 1). Figure 1 provides a general schematic of the principles of rolling circle amplification, wherein a linear template is first ligated to become circular, before then undergoing continuous rolling circle amplification to produce the afore mentioned long single-stranded DNA with a plurality of repeats.
Goransson (Rapid Identification of Bio-Molecules Applied for Detection of Biosecurity Agents Using Rolling Circle Amplification, PLOS One, February 2012, 7, 1-9) teaches on an application of RCA generated concatemers for detecting pathogens (Introduction). A padlock probe is circularized before undergoing rolling circle amplification to produce a concatemer for the purpose of amplifying a detection signal (Figure 1B).
Taken together, the art supports using rolling circle amplification to amplify a circular probe and produce a concatemer of that probe. However, methods comprising any amplification method and any probe as claimed in claim 1, or a method comprising any probe as claimed in claim 22, remain highly unpredictable.
The invention is drawn to biological molecules, and is therefore in a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001). The level of skill in the art is therefore deemed to be high.
(F), (G) With respect to the amount of direction and working examples provided by the applicant: The applicants have provided direction and description directed towards using rolling circle amplification with circularized nucleic acid probes in the method as claimed. For example, paragraph [0025] describes that the amplification to generate a concatemer can be carried out using rolling circle amplification, and that this may be performed with a circularized nucleic acid probe. In paragraphs [0062] and [0063], it is described that the reporter oligonucleotide that is conjugated to the labeling agent permits ligation (e.g. circularization) of the nucleic acid probe, and that the circularizable probe may be a padlock probe. In paragraph [0070], it is described that a circularizable probe such as a padlock probe is amplified through rolling circle amplification. These are representative of the many mentions of these aspects of the method in the instant specification. In terms of working examples, the Applicant has provided only prophetic examples, but these examples (Examples 1-3, also shown in Figures 1-3) similarly support a circularized probe amplified by rolling circle amplification.
The applicants have not provided working examples comprising any probe or any amplification method.
(H) Undue experimentation would be required to practice the invention as claimed due to the amount of experimentation necessary because of the expansive breadth of the claims, the state of the prior art and its high predictability, and the limited amount of guidance in the form of varied working examples in the specification. A skilled artisan recognizes that circular probes and rolling circle amplification are distinct from any probe and any amplification method and thus applicability of the claimed method to any probe or amplification method as embraced by the claims remains unpredictable, requiring undue experimentation.
For example, multiple other amplification methods would need to be evaluated for their ability to create a concatemer as claimed. While other methods do exist that can create a concatemer, one of skill in the art would then need to determine optimal reaction conditions for each of those methods to determine if they work in the environment of the method as claimed. Optimal reaction conditions include evaluation of a number of different parameters, including but not limited to reaction time, temperature, and polymerase. Thus, the quantity of experimentation in this area would be extremely large since there are a significant number of parameters that would have to be studied. Furthermore, the ultimate outcome of such experimentation is completely unpredictable.
MPEP §2164.01(a), 4th paragraph, provides that, “A conclusion of lack of enablement means that, based on the evidence regarding each of the above factors, the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention without undue experimentation. In re Wright, 999 F.2d 1157, 1562; 27 USPQ2d 1510, 1513 (Fed. Cir. 1993).
Genentech Inc. v. Novo Nordisk A/S, 42 USPQ2d 1001, 1005 (CA FC), states that, “[p]atent protection is granted in return for an enabling disclosure of an invention, not for vague intimations of general ideas that may or may not be workable,” citing Brenner v. Manson, 383 U.S. 519, 536 (1966) (stating, in the context of the utility requirement, that “a patent is not a hunting license. It is not a reward for search, but compensation for its successful conclusion”). The Genentech decision continued, “tossing out the mere germ of an idea does not constitute enabling disclosure. While every aspect of a generic claim certainly need not have been carried out by an inventor, or exemplified in the specification, reasonable detail must be provided in order to enable members of the public to understand and carry out the invention.” Id. at p. 1005.
After applying the Wands factors and analysis to claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 36, 42, 47, 49, 52, and 54, in view of the applicant’s entire disclosure, and considering the In re Wright, In re Fisher and Genentech decisions discussed above, it is concluded that the practice of the full scope of the invention as claimed would not be enabled by the written disclosure. Therefore, claims 1-4, 6, 8-9, 11, 15, 20, 22, 25, 27, 36, 42, 47, 49, 52, and 54 are rejected under 35 U.S.C. §112(a) for failing to disclose sufficient information to enable a person of skill in the art to practice the claimed invention to it the full scope embraced by the claims.
Conclusion
All claims are rejected.
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/ALLISON E SCHLOOP/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683