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 .
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 .
Status of the Claims
Claims 1-14 are pending. Claims 1-12 are the subject of this FINAL Office Action.
Election/Restrictions
Applicant’s election of interaction species of Figure 2 in the reply filed on 07/15/2026 is acknowledged. Applicants fail to provide a traversal rationale based on the reasons provided by the Examiner. Instead, they state “[o]ne reason for the traverse is that Applicant does not wish to be bound by the Examiner's reasoning in requiring election of species and Applicant believes that examination of all claims can be conducted without undue burden on the Examiner.” Applicants may not wish to be bound by the Examiner’s reasoning, nonetheless they must address that reasoning. And as is abundantly clear below, the very broad claims encompass hundreds of possible assays, each different from each other. In this context, a burden is clear. Yet, this is not the standard for Section 371/PCT national stage entries. Rather, it is unity. Applicants fail to address this basis. Thus, the election is treated without traverse. Claims 13-14 are withdrawn as directed to a different species from Figure 2.
Claim Rejections - 35 USC § 112- Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(B) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-12 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Applicants’ claims are full of confusing language. In claim 1, the “candidate interacting entities” are “assumed to interact with one or more candidate interacting entities of the second candidate entity library (and vice versa).” It is unclear who assumes this and how this affects the claimed method. Moreover, parentheses introduce confusion because they can introduce different things: an example; a suggestion; an acronym; a definition; or many other things. At the least, the scope of claim 1 is unclear due to this confusing language.
At step c of claim 1, “any entity” and “entities” lack antecedent basis because the claim only states types of “candidate entity.” It is unclear what “entity” is referenced.
In claims 1-2 and 7, all uses of “preferably” and “such as” introduce confusion as to whether what follows is required or optional.
In claims 1 and 7, “means for identifying of one or more labelling portion encapsulated within a compartment” is not clear linked to any particular structure in the specification. The specification vaguely references “the means for identifying of one or more labelling portion comprises components sufficient for conducting the PCR amplification, preferably the fusion PCR” (para. 0053). However, these vague and undefined “components” are not clear.
Claim 2 is a confusing attempt at a Markush group. It reads:
wherein the interacting-portion is selected from the group consisting of a polypeptide, peptide, glycoprotein, a peptidomimetic, an antibody or antibody-like molecule; a nucleic acid such as a DNA or RNA, a peptide nucleic acid (PNA), a carbohydrate such as a polysaccharide or oligosaccharide, including variants or derivatives thereof; a lipid such as a fatty acid and the like, including variants or derivatives thereof; or a small organic molecules including but not limited to small molecule ligands, small cell-permeable molecules, and peptidomimetic compounds.
First, “antibody-like” is never defined; and is a vague, boundary-less term. It is impossible to determine how much like an antibody, and in what ways, something has to be to meet this limitation. Second, “variants or derivatives thereof” is very expansive, overwhelming any limitations on any of the Markush group members. For example, what are “variants or derivatives” of a DNA? Does this include an Okazaki fragment? How about a single nucleotide? Or maybe a phosphate? Third, “including but not limited to,” just like “preferably” introduces confusion as to the scope. Fourth, between some, but not all, Markush group members, there are semicolons, yet between others only commas. It is unclear what role these two different grammatical marks play, and whether they affect the scope of the Markush group. Finally, Applicants are reminded that Markush group members must have a common structure or function. It is hard indeed to see how an antibody has a common structure or function with a carbohydrate, for example.
Claim 3 has a parenthesis with confusing language within it, as spelled out above.
In claim 5, “the amino acid sequence of the proteinaceous interacting-portion” lacks antecedent basis.
Claim 6 has a parenthesis with confusing language within it, as spelled out above.
In claim 6, “each primer binding sequence” lacks antecedent basis.
In claim 9, “the first- and the second hybridization sequence” lacks antecedent basis.
In claim 10, the “the subsequent nested PCR” lacks antecedent basis.
In claim 10, “nested PCR” is unclear in light of the specification and its commone meaning in the art. The specification discloses this as an example of nested PCR:
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However, this is not a nested PCR as commonly understood in the art because none of the second primers lie nested between the outer limits of the first pair. Nested PCR as commonly understood is this:
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The Polymerase Chain Reaction, in Molecular Biology and Genomics, Ch. 4, pgs. 65-94, Cornel Mülhardt, E.W. Beese M.D., Available online 2 September 2007, Fig. 4-3.
A trick to demonstrate even the smallest of template concentrations involves the use of nested PCR. You perform a PCR and use the product as a template for a second amplification with other primers. The second primer pair lies nested between the outer limits of the first pair (Figure 4-3)
(pg. 76). Applicants fail to clearly redefine nested PCR. Thus, the phrase “nested PCR” is confusing based on the single example in the specification in contrast to the common meaning in the art.
Claim Rejection - 35 USC § 112 – Written Description
The following is a quotation 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.
Claims 1-12 are rejected under 35 U.S.C. 112(a) 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, at the time the application was filed, had possession of the full scope of the claimed invention.
The specification fails to demonstrate possession of the full scope of any and all methods of identifying any two interacting entities using any “labelling portion” and any detection technique. Claim 1 generically states that “a first candidate entity library and a second candidate entity” interact using an “interacting-portion,” and after any encapsulation/compartmentalization, they are detected in the compartments using the generic “labelling portions.” This encompasses any and all “candidate entity” (e.g. carbohydrate, lipid, protein, small molecule, etc.; see claim 2); any and all “labelling portion” (e.g. fluorescent label, dye, radiolabel, antibody, GFP, etc.); any and all encapsulation/compartmentalization (e.g. microwell, emulsion droplet, water droplet, slipchip, etc.); and any and all detection techniques (e.g. sequencing, PCR, overlap extension PCR, RCA, HRP detection; fluorescent label detection, etc.). Despite this vast breadth, the specification discloses a single, very specific assay:
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That is, two interacting candidate entities each with attached barcoded oligonucleotides flanked by primer binding sites; then encapsulated in emulsion droplets; then a fusion PCR is performed with primers that hybridize to the flanking primer binding sites, and include overlapping hybridization regions to allow overlap extension PCR between the oligos on each candidate entity. No other assay is disclosed. Yet, claim 1 clearly encompasses innumerable other assays from the generic “labelling portion.” A single example cannot define an entire genus of vastly different species. Applicants fail to disclose the full scope of their claimed invention with “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.”
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. § 102 that form the basis for the rejections under this section made in this Office action:
(A) A person shall be entitled to a patent unless –
(1)the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention; or
(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-12 are rejected under 35 U.S.C. § 102(a)(1) as being anticipated by ROTH (US20090098555).
As to claim 1, ROTH teaches a method for the identification of at least two interacting entities comprised in at least two separated libraries of candidate interacting entities, the method comprising the steps of:
(a) Providing at least a first candidate entity library (first cell with first mutation; Figs. 13-14) and a second candidate entity library (first cell with second mutation; id.) each library comprising a plurality of candidate interacting entities each of which is composed of at least an interacting-portion and a labelling-portion, wherein one or more candidate interacting entities of the first candidate entity library are assumed to interact with one or more candidate interacting entities of the second candidate entity library (and vice versa) (each cell interacts via cellular interactions, and each cell contains TAG1 and TAG2 barcodes with flanking primer sites, and when cells combine or interact yield overlap extension amplification of each tag/barcode oligo; id.);
(b) Bringing into contact the candidate interacting entities of the first candidate entity library with the candidate interacting entities of the second candidate entity library under conditions that allow for the formation of an interaction-complex between at least two interacting entities (id.);
(c) Encapsulating any entity and any interaction-complex from (b) in a plurality of microfluidic compartments under at least the conditions:
(i) A ratio of entities to compartments which is larger than 0 and less 1, and preferably is about 0.1; and
(ii) Optionally, a presence of one or more means for identifying of one or more labelling portion encapsulated within a compartment (poisson distribution; id.; paras, 0041, 0058);
(d) Detecting subsequent to step (c) within the plurality of compartments, which comprise encapsulated entities, a presence of, and preferably an identity of, at least two labelling-portions encapsulated within a single compartment, wherein the presence of two labelling portions within a single compartment is indicative for an interaction between the two candidate interacting entities encapsulated within said compartment (Figs. 13 & 14).
As to claim 2, ROTH teaches the interacting-portion is selected from the group consisting of a polypeptide, peptide, glycoprotein, a peptidomimetic, an antibody or antibody-like molecule; a nucleic acid such as a DNA or RNA, a peptide nucleic acid (PNA), a carbohydrate such as a polysaccharide or oligosaccharide, including variants or derivatives thereof; a lipid such as a fatty acid and the like, including variants or derivatives thereof; or a small organic molecules including but not limited to small molecule ligands, small cell-permeable molecules, and peptidomimetic compounds (id.)
As to claim 3, ROTH teaches the labelling portion of each distinct candidate interacting entity comprises a nucleic acid molecule having at least one identification-sequence unique to the interacting-portion of the distinct candidate interacting entity (DNA-encoding library or DEL) (id.)
As to claim 4, ROTH teaches the identification sequence is flanked by an upstream primer binding sequence and a downstream primer binding sequence, which both are different and do not anneal to each other during an annealing phase of a PCR amplification cycle (id.)
As to claim 5, ROTH teaches the identification sequence comprises a nucleic acid sequence encoding at least parts of the amino acid sequence of the proteinaceous interacting-portion (id.)
As to claim 6, ROTH teaches each primer binding sequence of the labelling portion of the candidate interacting entity of the first candidate entity library differs from each primer binding sequence of the labelling portion of the candidate interacting entity of the second candidate entity library (and vice versa) (id.)
As to claim 7, ROTH teaches step (d) involves a PCR amplification, preferably a fusion PCR and wherein the means for identifying of one or more labelling portion comprises components sufficient for conducting the PCR amplification, preferably the fusion PCR (id.)
As to claim 8, ROTH teaches the means comprise a first and a second PCR primer pair, wherein the upstream primer of the first PCR primer pair anneals to the upstream primer binding sequence of each labelling-portion contained in the first candidate entity library, and the downstream primer of the first PCR primer pair anneals to the downstream primer binding sequence of each labelling-portion contained in the first candidate entity library; and wherein the upstream primer of the second PCR primer pair anneals to the upstream primer binding sequence of each labelling-portion contained in the second candidate entity library, and the downstream primer of the second PCR primer pair anneals to the downstream primer binding sequence of each labelling-portion contained in the second candidate entity library (id.)
As to claim 9, ROTH teaches the upstream- and the downstream primer of the first primer pair comprises a first cross-hybridization sequence and the upstream- and the downstream primer of the second primer pair comprises a second cross-hybridization sequence; wherein the first- and the second hybridization sequence hybridize to each other under annealing conditions during a PCR annealing step (id.)
As to claim 10, ROTH teaches a PCR amplification in step (c) comprises a fusion PCR immediately followed by the removal of residual primer oligonucleotides and the subsequent nested PCR using (i) an upstream primer which anneals to the upstream primer binding sequence of each labelling-portion contained in the first candidate entity library, and a downstream primer which anneals to the downstream primer binding sequence of each labelling-portion contained in the second candidate entity library; or (ii) an upstream primer which anneals to the upstream primer binding sequence of each labelling-portion contained in the second candidate entity library, and a downstream primer which anneals to the downstream primer binding sequence of each labelling-portion contained in the first candidate entity library; wherein step (d) involves the detection of the amplification product of the nested PCR and wherein the presence of an amplification product indicates the presence of two labelling portions within a single compartment (id.)
As to claim 11, ROTH teaches sequencing the amplification product of the nested PCR in order to determine the identity of the interacting-portions which were comprised within one compartment (id.)
As to claim 13, ROTH teaches a compartment is a droplet (id.)
Claims 1-12 are rejected under 35 U.S.C. § 102(a)(1) as being anticipated by GHADESSY (US20130143749).
As to claim 1, GHADESSY teaches a method for the identification of at least two interacting entities comprised in at least two separated libraries of candidate interacting entities, the method comprising the steps of:
(a) Providing at least a first candidate entity library and a second candidate entity library each library comprising a plurality of candidate interacting entities each of which is composed of at least an interacting-portion and a labelling-portion, wherein one or more candidate interacting entities of the first candidate entity library are assumed to interact with one or more candidate interacting entities of the second candidate entity library (and vice versa) (first (12) and a second (13) binding partner within a plurality of peptides and/or proteins (11, 12, 13) is identified, which are physically linked to a member encoding nucleic acid molecule (1, 2, 3); para. 0023, Figs. 2-3);
(b) Bringing into contact the candidate interacting entities of the first candidate entity library with the candidate interacting entities of the second candidate entity library under conditions that allow for the formation of an interaction-complex between at least two interacting entities (id.);
(c) Encapsulating any entity and any interaction-complex from (b) in a plurality of microfluidic compartments under at least the conditions:
(i) A ratio of entities to compartments which is larger than 0 and less 1, and preferably is about 0.1; and
(ii) Optionally, a presence of one or more means for identifying of one or more labelling portion encapsulated within a compartment (Fig. 3);
(d) Detecting subsequent to step (c) within the plurality of compartments, which comprise encapsulated entities, a presence of, and preferably an identity of, at least two labelling-portions encapsulated within a single compartment, wherein the presence of two labelling portions within a single compartment is indicative for an interaction between the two candidate interacting entities encapsulated within said compartment (Figs. 2-3).
As to claim 2, GHADESSY teaches the interacting-portion is selected from the group consisting of a polypeptide, peptide, glycoprotein, a peptidomimetic, an antibody or antibody-like molecule; a nucleic acid such as a DNA or RNA, a peptide nucleic acid (PNA), a carbohydrate such as a polysaccharide or oligosaccharide, including variants or derivatives thereof; a lipid such as a fatty acid and the like, including variants or derivatives thereof; or a small organic molecules including but not limited to small molecule ligands, small cell-permeable molecules, and peptidomimetic compounds (id.)
As to claim 3, GHADESSY teaches the labelling portion of each distinct candidate interacting entity comprises a nucleic acid molecule having at least one identification-sequence unique to the interacting-portion of the distinct candidate interacting entity (DNA-encoding library or DEL) (id.)
As to claim 4, GHADESSY teaches the identification sequence is flanked by an upstream primer binding sequence and a downstream primer binding sequence, which both are different and do not anneal to each other during an annealing phase of a PCR amplification cycle (id.)
As to claim 5, GHADESSY teaches the identification sequence comprises a nucleic acid sequence encoding at least parts of the amino acid sequence of the proteinaceous interacting-portion (id.)
As to claim 6, GHADESSY teaches each primer binding sequence of the labelling portion of the candidate interacting entity of the first candidate entity library differs from each primer binding sequence of the labelling portion of the candidate interacting entity of the second candidate entity library (and vice versa) (id.)
As to claim 7, GHADESSY teaches step (d) involves a PCR amplification, preferably a fusion PCR and wherein the means for identifying of one or more labelling portion comprises components sufficient for conducting the PCR amplification, preferably the fusion PCR (id.)
As to claim 8, GHADESSY teaches the means comprise a first and a second PCR primer pair, wherein the upstream primer of the first PCR primer pair anneals to the upstream primer binding sequence of each labelling-portion contained in the first candidate entity library, and the downstream primer of the first PCR primer pair anneals to the downstream primer binding sequence of each labelling-portion contained in the first candidate entity library; and wherein the upstream primer of the second PCR primer pair anneals to the upstream primer binding sequence of each labelling-portion contained in the second candidate entity library, and the downstream primer of the second PCR primer pair anneals to the downstream primer binding sequence of each labelling-portion contained in the second candidate entity library (id.)
As to claim 9, GHADESSY teaches the upstream- and the downstream primer of the first primer pair comprises a first cross-hybridization sequence and the upstream- and the downstream primer of the second primer pair comprises a second cross-hybridization sequence; wherein the first- and the second hybridization sequence hybridize to each other under annealing conditions during a PCR annealing step (id.; para. 0121, 0165, 0177)
As to claim 10, GHADESSY teaches a PCR amplification in step (c) comprises a fusion PCR immediately followed by the removal of residual primer oligonucleotides and the subsequent nested PCR using (i) an upstream primer which anneals to the upstream primer binding sequence of each labelling-portion contained in the first candidate entity library, and a downstream primer which anneals to the downstream primer binding sequence of each labelling-portion contained in the second candidate entity library; or (ii) an upstream primer which anneals to the upstream primer binding sequence of each labelling-portion contained in the second candidate entity library, and a downstream primer which anneals to the downstream primer binding sequence of each labelling-portion contained in the first candidate entity library; wherein step (d) involves the detection of the amplification product of the nested PCR and wherein the presence of an amplification product indicates the presence of two labelling portions within a single compartment (id.)
As to claim 11, GHADESSY teaches sequencing the amplification product of the nested PCR in order to determine the identity of the interacting-portions which were comprised within one compartment (id.)
As to claim 13, GHADESSY teaches a compartment is a droplet (id.)
Prior Art
The following prior art also teaches barcoded overlap extension PCR in droplets to detect interactions of molecules: US 20120245039; US 20130296535; US 20190085324; US 20180258422; US 20200362334; US 20230383283; US 20220390436; US10329557.
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/YUNG-SHENG M TSUI/ Primary Examiner, Art Unit 1684
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