DETAILED ACTION
Status of the Claims
Claims 1-20 are currently pending
Claims 1, 6, 16, and 20 are amended.
Claims 1-20 are the subject of this Office Action.
The following Office Action is in response to Applicant’s communication dated 02/10/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. Specifically, the objection to claim 6 for the misspelling of “ubiquitination” is withdrawn in light of amendment to the claim by Applicant. The following rejection(s) and/or objection(s) are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Modified Claim Rejections – 35 U.S.C. 102
Necessitated by Amendments
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Mitra et al.
Claims 1-20 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Mitra et al. (U.S. PGPub 2015/0160204 A1, cited in IDS of 10/01/2025, of record).
Regarding claim 1, Mitra discloses a method for characterizing modified forms of a first type of polypeptide in a sample (e.g., “characterizing structural properties of a polypeptide using analytical laboratory methods” as per [0006]), comprising
providing the first type of polypeptide on an array, wherein each of a plurality of individual polypeptide molecules of the first type of polypeptide are individually located at individually addressable locations on the array (e.g., such “methods comprise immobilizing, on a solid support, individual protein or polypeptide strands comprised by the sample, such that each polypeptide strand to be analyzed is separated by an optically resolvable distance from other protein or polypeptide strands comprised by the sample” as per [0016] and/or [0053]),
contacting the array with a plurality of different types of affinity reagents, wherein each of the plurality of different types of affinity reagents has binding specificity for a different single epitope within the first type of polypeptide having a different modification, and wherein each different single epitope comprises a specific post translational modification (e.g., probes can recognize one to six amino acids with one or more of several types of post-translational modifications as detailed in [0008]),
characterizing one or more modified forms of the first type of polypeptide on the array based upon detection of the types of different affinity reagents that bind or do not bind to each different single epitope of the plurality of individual polypeptide molecules of the first type of polypeptide on the array (e.g., “[i]n various configurations of the present teachings, presence or absence of a binding pool target in a protein or polypeptide to be identified can be considered binary property” as per [0014]).
Regarding claim 2, Mitra discloses the above method, wherein the modified forms of the first type of polypeptide comprise post translationally modified forms of the first type of polypeptide (e.g., probes can recognize various post-translational modifications as detailed in [0008] and/or [0040]).
Regarding claim 3, Mitra discloses the above method, comprising characterizing a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per [0008] and [0017]).
Regarding claim 4, Mitra discloses the above method, comprising quantifying each of a plurality of the different modified forms of the first type of polypeptide on the array (e.g., as per [0008] and [0017]).
Regarding claim 5, Mitra discloses the above method, wherein the one or more modified forms of the first type of polypeptide comprises one or more phosphate modified forms of the first type of polypeptide, the one or more phosphate modified forms of the first type of polypeptide comprising a phosphate group attached at one or more amino acid residues in the individual molecules of the first type of polypeptide (e.g., probes which can recognize several modifications including “a phosphorylated amino acids such as phosphotyrosine, phosphoserine and phosphothreonine” as per [0008] and/or [0040]).
Regarding claim 6, Mitra discloses the above method, wherein the modified forms of the first type of polypeptide comprise a modification at one or more of a plurality of amino acid residues in the individual molecules of the first type of polypeptide, wherein such modifications are independently selected from an acetate, an amide group, a methyl group, a lipid, ubiquitination, myristoylation, palmitoylation, isoprenylation, prenylation, farnesylation, geranylation, glypiation, lipoylation, flavin moiety attachment, phosphopantetheinylation, and retinylidene Schiff base formation (e.g., “a glycosyl moiety Such as an N-linked or an O-linked glycosyl moiety, a GPI anchor, a disulfide linkage, a pyroglutamic acid, a nitrotyrosine or a combination thereof” and/or “a phosphorylated amino acids such as phosphotyrosine, phosphoserine and phosphothreonine, a methylated amino acid, an acylated amino acid such as an amino acid comprising a farnesyl, a myristoyl, or a palmitoyl moiety, a hydroxyproline or a sulfated amino acid such as a sulfotyrosine” as per [0008]).
Regarding claim 7, Mitra discloses the above method, wherein each of a plurality of the affinity reagents has a binding specificity for a first type of polypeptide that comprises a phosphate group at a different amino acid residue or set of amino acid residues in the polypeptide (e.g., probes which can recognize several modifications including “a phosphorylated amino acids such as phosphotyrosine, phosphoserine and phosphothreonine” as per [0008] and/or [0040]).
Regarding claim 8, Mitra discloses the above method, wherein the one or more phosphate modified forms of the first type of polypeptide in the sample comprise a plurality of different phosphate modified forms of the first type of polypeptide (e.g., probes which can recognize several modifications including “a phosphorylated amino acids such as phosphotyrosine, phosphoserine and phosphothreonine” as per [0008] and/or [0040]).
Regarding claim 9, Mitra discloses the above method, further comprising quantifying different phosphate modified forms of the fist type of polypeptide in the sample from the quantity of different phosphate modified forms in the polypeptides on the array (e.g., “these aspects afford both relative and absolute quantification of protein or polypeptide strands comprising a sample” as per [0016]).
Regarding claim 10, Mitra discloses the above method, treating the individual polypeptide molecules on the array to remove one or more of the modifications of the first type of polypeptide on the array after the characterizing step, and repeating the contacting and characterizing steps to identify the first type of polypeptides on the array having the modifications removed (e.g., removal of modifications as per [0046] and/or [0049]).
Regarding claim 11, Mitra discloses the above method, wherein one or more of the modifications comprise a phosphate group attached to one or more amino acid residue in the first type of polypeptide, and the treating step comprises contacting the individual molecules of the first type of polypeptide with a phosphatase enzyme (e.g., phosphatase treatment as per [0045]).
Regarding claim 12, Mitra discloses the above method, wherein the contacting step comprises sequentially contacting the individual molecules of the first type of polypeptide on the array with each of the plurality of different types of affinity reagents (e.g., “a polypeptide to be identified can be contacted with the binding pools sequentially” as per [0012]).
Regarding claim 13, Mitra discloses the above method, wherein at least two of the plurality of different affinity reagents are contacted with the array simultaneously (e.g., “each probe comprised by a binding pool can recognize and bind one structure” as per [0010]).
Regarding claim 14, Mitra discloses the above method, further comprising the step of identifying individual locations on the array occupied by the first type of polypeptides (e.g., as per [0053]-[0055]).
Regarding claim 15, Mitra discloses the above method, wherein the step of identifying individual locations on the array occupied by the first type of polypeptide comprises sequentially contacting the polypeptides on the array with a plurality of different affinity reagents, each different affinity reagent having affinity for a different epitope of amino acids, and identifying the polypeptides based upon a pattern of binding of the different affinity reagents to the epitopes in the polypeptides on the array (e.g., “a polypeptide to be identified can be contacted with the binding pools sequentially” as per [0012]).
Regarding claim 16, Mitra discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising providing polypeptides from the sample immobilized on an array, wherein individual molecules of the polypeptides from the sample are immobilized in locations on the array where the individual molecules are individually addressable, and wherein the polypeptides immobilized on the array comprise a plurality of individual molecules of the first type of polypeptide, iteratively contacting the individual molecules of the first type of polypeptide on the array with a plurality of different affinity reagents, each of the plurality of different affinity reagents having a binding affinity for a different single epitope in the first type of polypeptide, each single epitope comprising a specific post translational modification to the first type of polypeptide, detecting binding of each of the different affinity reagents to different single epitopes of the individual molecules of the first type of individual molecules of the first type of polypeptide on the array, and characterizing modified forms of the first type of polypeptides in the sample based upon the individual polypeptides on the array that are bound or not bound by each of the plurality of different affinity reagents (e.g., “a polypeptide to be identified can be contacted with the binding pools sequentially” using “cycles if testing binding of each binding pool of a plurality of binding pools” as per [0012] and probes can recognize one to six amino acids with one or more of several types of post-translational modifications as detailed in [0008]).
Regarding claim 17, Mitra discloses the above method, further comprising quantifying a plurality of different modified forms of the first type of polypeptide on the array (e.g., “these aspects afford both relative and absolute quantification of protein or polypeptide strands comprising a sample” as per [0016]).
Regarding claim 18, Mitra discloses the above method, further comprising a step of identifying individually addressable locations on the array at which the first type of polypeptide is immobilized (e.g., as per [0053]-[0055]).
Regarding claim 19, Mitra discloses the above method, wherein the identifying step comprises contacting individual polypeptide molecules on the array with one or more affinity reagents having binding specificity for the first type of polypeptide (e.g., “each probe comprised by a binding pool can recognize and bind one structure” as per [0010]).
Regarding claim 20, Mitra discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising:
providing polypeptides from the sample, wherein a plurality of individual molecules of the polypeptides from the sample are each immobilized at an individually detectable address on one or more solid supports, and wherein the individual molecules of the polypeptides immobilized on the one or more solid supports comprise a plurality of individual molecules of the first type of polypeptide (e.g., such “methods comprise immobilizing, on a solid support, individual protein or polypeptide strands comprised by the sample, such that each polypeptide strand to be analyzed is separated by an optically resolvable distance from other protein or polypeptide strands comprised by the sample” as per [0016] and/or [0053]);
contacting the individual molecules of the polypeptides on the one or more solid supports with a plurality of different affinity reagents, each of the plurality of different affinity reagents having binding affinity for a different single epitope in the first type of polypeptide, each single epitope comprising a specific post translational modification to the first type of polypeptide (e.g., “a polypeptide to be identified can be contacted with the binding pools sequentially” as per [0012] and probes can recognize one to six amino acids with one or more of several types of post-translational modifications as detailed in [0008]);
detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the one or more solid supports (e.g., “a polypeptide to be identified can be contacted with the binding pools sequentially” as per [0012]); and
characterizing modified forms of the first type of polypeptide in the sample based upon a pattern of binding of the plurality of different affinity reagents at each of a plurality of different individually detectable addresses on the one or more solid supports (e.g., “[i]n various configurations of the present teachings, presence or absence of a binding pool target in a protein or polypeptide to be identified can be considered binary property” as per [0014]).
***
Response to Arguments
The 02/10/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
RE: “A careful reading of … paragraph [0008] indicates that Mitra teaches the use of probes within a binding pool, where the probes are specific for a particular motif or modification within a protein or peptide. There is no teaching of using affinity reagents each type of which has binding specificity for a single epitope within the polypeptide, as recited in the independent claims” (emphasis in original) and “For example, the claimed method could be useful for determining proteins or peptides with multiple methylation sites within the protein since each methylation site would be bound by an affinity agent specific for a particular methylation site. For example, if the protein had three different methylation sites, then three different types of antibodies would bind to the protein in the claimed method. In contrast, the probes of Mitra would bind to any methylation site in the protein, and be unable to distinguish proteins with three methylation sites from proteins with 1, 2, 4 or more methylation sites.”
These remarks at pages 6-8 argue that the probes of Mitra are “specific for a particular motif or modification within a protein or peptide” with no teaching that “each type of which has binding specificity for a single epitope within the polypeptide”. Further, the remarks imply that the probes of the presently claimed invention could distinguish between, for example, three different methylated sites in different contexts, but that the probes of Mitra would “bind to any methylation site in the protein”.
The remarks seem to allege that “a particular motif or modification within a protein or peptide” is materially different from “a single epitope within [a] polypeptide”, and that while the probes of the presently claimed invention could distinguish between, for example, three different methylated sites in different contexts, that the probes of Mitra would “bind to any methylation site in the protein”. This is not persuasive for at least the reason that there is no limitation in the claim (nor the specification) that specifically limits the claimed “affinity reagents” to be able to, for example, distinguish between multiple methylation sites in different contexts. Secondly, even if such a limitation were present (it is not), there is nothing in Mitra that limits their probes to only bind to, for example, methylation sites regardless of context. On the contrary, paragraph [0008] of Mitra states that:
Examples of protein or polypeptide structures which can be recognized and bound by a probe include epitopes of an antibody, a peptide motif comprising at least one amino acid up to about six amino acids, a glycosyl moiety such as an N-linked or an O-linked glycosyl moiety, a GPI anchor, a disulfide linkage, a pyroglutamic acid, a nitrotyrosine or a combination thereof. Examples of amino acids which can be recognized or contribute to a structure recognized by a probe include a phosphorylated amino acids such as phosphotyrosine, phosphoserine and phosphothreonine, a methylated amino acid, an acylated amino acid such as an amino acid comprising a farnesyl, a myristoyl, or a palmitoyl moiety, a hydroxyproline or a sulfated amino acid such as a sulfotyrosine (emphasis added).
The phrase “or a combination thereof” reasonably includes, for example, a peptide motif with one to six amino acids and a specific post-translational modification. Furthermore, the same paragraph makes it clear that phosphorylated/methylated/acetylated amino acids “can be recognized or contribute to a structure recognized by a probe”, that is, a post-translational modification can be in the context of a larger peptide motif and still be differentially detected by the probes of Mitra. Therefore, the probes of Mitra could reasonably distinguish between, for example, multiple methylation sites in a protein even when they are in differing contexts.
In conclusion, the rejection is proper and is maintained.
Maintained 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 obviousness-type 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); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
U.S. 19/180,024
Claim 1, 3, and 12-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 192-226 of copending Application No. 19/180,024 (the ‘024 application). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 1, the claims of the ‘024 application discloses a method for characterizing modified forms of a first type of polypeptide in a sample, comprising providing the first type of polypeptide on an array, wherein each of a plurality of individual polypeptide molecules of the first type of polypeptide are individually located at individually addressable locations on the array, contacting the array with a plurality of different types of affinity reagents, wherein each of the plurality of different types of affinity reagents has binding specificity for the first type of polypeptide having a different modification, characterizing one or more modified forms of the first type of polypeptide on the array based upon detection of the types of different affinity reagents that bind or do not bind to each of the plurality of individual polypeptide molecules of the first type of polypeptide on the array (e.g., as per claim 192 of the ‘024 application).
Regarding claim 3, the claims of the ‘024 application discloses the above method, comprising characterizing a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 205 of the ‘024 application).
Regarding claim 12, the claims of the ‘024 application discloses the above method, wherein the contacting step comprises sequentially contacting the individual molecules of the first type of polypeptide on the array with each of the plurality of different types of affinity reagents (e.g., as per claim 192 of the ‘024 application).
Regarding claim 13, the claims of the ‘024 application discloses the above method, wherein at least two of the plurality of different affinity reagents are contacted with the array simultaneously (e.g., as per claim 192 of the ‘024 application).
Regarding claim 14, the claims of the ‘024 application discloses the above method, further comprising the step of identifying individual locations on the array occupied by the first type of polypeptides (e.g., as per claim 212 of the ‘024 application).
Regarding claim 15, the claims of the ‘024 application discloses the above method, wherein the step of identifying individual locations on the array occupied by the first type of polypeptide comprises sequentially contacting the polypeptides on the array with a plurality of different affinity reagents, each different affinity reagent having affinity for a different epitope of amino acids, and identifying the polypeptides based upon a pattern of binding of the different affinity reagents to the epitopes in the polypeptides on the array (e.g., as per claim 192 of the ‘024 application).
Regarding claim 16, the claims of the ‘024 application discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising providing polypeptides from the sample immobilized on an array, wherein individual molecules of the polypeptides from the sample are immobilized in locations on the array where the individual molecules are individually addressable, and wherein the polypeptides immobilized on the array comprise a plurality of individual molecules of the first type of polypeptide, iteratively contacting the individual molecules of the first type of polypeptide on the array with a plurality of different affinity reagents, each of the plurality of different affinity reagents having a binding affinity for a different modification to the first type of polypeptide, detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the array, and characterizing modified forms of the first type of polypeptides in the sample based upon the individual polypeptides on the array that are bound or not bound by each of the plurality of different affinity reagents (e.g., as per claim 192 and 217 of the ‘024 application).
Regarding claim 18, the claims of the ‘024 application discloses the above method, further comprising a step of identifying individually addressable locations on the array at which the first type of polypeptide is immobilized (e.g., as per claim 212 of the ‘024 application).
Regarding claim 19, the claims of the ‘024 application discloses the above method, wherein the identifying step comprises contacting individual polypeptide molecules on the array with one or more affinity reagents having binding specificity for the first type of polypeptide (e.g., as per claim 192 of the ‘024 application).
Regarding claim 20, the claims of the ‘024 application discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising:
providing polypeptides from the sample, wherein a plurality of individual molecules of the polypeptides from the sample are each immobilized at an individually detectable address on one or more solid supports, and wherein the individual molecules of the polypeptides immobilized on the one or more solid supports comprise a plurality of individual molecules of the first type of polypeptide;
contacting the individual molecules of the polypeptides on the one or more solid supports with a plurality of different affinity reagents, each of the plurality of different affinity reagents having binding affinity for a different modification to the first type of polypeptide;
detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the one or more solid supports; and
characterizing modified forms of the first type of polypeptide in the sample based upon a pattern of binding of the plurality of different affinity reagents at each of a plurality of different individually detectable addresses on the one or more solid supports (e.g., as per claim 192 of the ‘024 application).
U.S. 19/391,598
Claim 1-4 and 12-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 31-58 of copending Application No. 19/391,598 (the ‘598 application). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 1, the claims of the ‘598 application discloses a method for characterizing modified forms of a first type of polypeptide in a sample, comprising
providing the first type of polypeptide on an array, wherein each of a plurality of individual polypeptide molecules of the first type of polypeptide are individually located at individually addressable locations on the array, contacting the array with a plurality of different types of affinity reagents, wherein each of the plurality of different types of affinity reagents has binding specificity for the first type of polypeptide having a different modification, characterizing one or more modified forms of the first type of polypeptide on the array based upon detection of the types of different affinity reagents that bind or do not bind to each of the plurality of individual polypeptide molecules of the first type of polypeptide on the array (e.g., as per claims 31 and/or 57 of the ‘598 application).
Regarding claim 2, the claims of the ‘598 application discloses the above method, wherein the modified forms of the first type of polypeptide comprise post translationally modified forms of the first type of polypeptide (e.g., as per claim 57 of the ‘598 application).
Regarding claim 3, the claims of the ‘598 application discloses the above method, comprising characterizing a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 57 of the ‘598 application).
Regarding claim 4, the claims of the ‘598 application discloses the above method, comprising quantifying each of a plurality of the different modified forms of the first type of polypeptide on the array (e.g., as per claims 31 and 51-52 of the ‘598 application).
Regarding claim 12, the claims of the ‘598 application discloses the above method, wherein the contacting step comprises sequentially contacting the individual molecules of the first type of polypeptide on the array with each of the plurality of different types of affinity reagents (e.g., as per claims 31 and/or 57-58 of the ‘598 application).
Regarding claim 13, the claims of the ‘598 application discloses the above method, wherein at least two of the plurality of different affinity reagents are contacted with the array simultaneously (e.g., as per claims 31 and/or 57-58 of the ‘598 application).
Regarding claim 14, the claims of the ‘598 application discloses the above method, further comprising the step of identifying individual locations on the array occupied by the first type of polypeptides (e.g., as per claims 31 and/or 57-58 of the ‘598 application).
Regarding claim 15, the claims of the ‘598 application discloses the above method, wherein the step of identifying individual locations on the array occupied by the first type of polypeptide comprises sequentially contacting the polypeptides on the array with a plurality of different affinity reagents, each different affinity reagent having affinity for a different epitope of amino acids, and identifying the polypeptides based upon a pattern of binding of the different affinity reagents to the epitopes in the polypeptides on the array (e.g., as per claims 31 and 39 of the ‘598 application).
Regarding claim 16, the claims of the ‘598 application discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising providing polypeptides from the sample immobilized on an array, wherein individual molecules of the polypeptides from the sample are immobilized in locations on the array where the individual molecules are individually addressable, and wherein the polypeptides immobilized on the array comprise a plurality of individual molecules of the first type of polypeptide, iteratively contacting the individual molecules of the first type of polypeptide on the array with a plurality of different affinity reagents, each of the plurality of different affinity reagents having a binding affinity for a different modification to the first type of polypeptide, detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the array, and characterizing modified forms of the first type of polypeptides in the sample based upon the individual polypeptides on the array that are bound or not bound by each of the plurality of different affinity reagents (e.g., as per claims 31 and/or 51-52 of the ‘598 application).
Regarding claim 17, the claims of the ‘598 application discloses the above method, further comprising quantifying a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claims 31 and/or 57 of the ‘598 application).
Regarding claim 18, the claims of the ‘598 application discloses the above method, further comprising a step of identifying individually addressable locations on the array at which the first type of polypeptide is immobilized (e.g., as per claims 31 and/or 57 of the ‘598 application).
Regarding claim 19, the claims of the ‘598 application discloses the above method, wherein the identifying step comprises contacting individual polypeptide molecules on the array with one or more affinity reagents having binding specificity for the first type of polypeptide (e.g., as per claims 31 and/or 57 of the ‘598 application).
Regarding claim 20, the claims of the ‘598 application discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising:
providing polypeptides from the sample, wherein a plurality of individual molecules of the polypeptides from the sample are each immobilized at an individually detectable address on one or more solid supports, and wherein the individual molecules of the polypeptides immobilized on the one or more solid supports comprise a plurality of individual molecules of the first type of polypeptide;
contacting the individual molecules of the polypeptides on the one or more solid supports with a plurality of different affinity reagents, each of the plurality of different affinity reagents having binding affinity for a different modification to the first type of polypeptide;
detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the one or more solid supports; and
characterizing modified forms of the first type of polypeptide in the sample based upon a pattern of binding of the plurality of different affinity reagents at each of a plurality of different individually detectable addresses on the one or more solid supports (e.g., as per claims 31 and/or 57 of the ‘598 application).
U.S. 16/972,341
Claim 1-4 and 13-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 43-44, 47-55, 56-61, 63-64, and 67 of copending Application No. 16/972,341 (the ‘341 application). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 1, the claims of the ‘341 application discloses a method for characterizing modified forms of a first type of polypeptide in a sample, comprising providing the first type of polypeptide on an array, wherein each of a plurality of individual polypeptide molecules of the first type of polypeptide are individually located at individually addressable locations on the array, contacting the array with a plurality of different types of affinity reagents, wherein each of the plurality of different types of affinity reagents has binding specificity for the first type of polypeptide having a different modification, characterizing one or more modified forms of the first type of polypeptide on the array based upon detection of the types of different affinity reagents that bind or do not bind to each of the plurality of individual polypeptide molecules of the first type of polypeptide on the array (e.g., as per claims 43 and 50-51 of the ‘341 application).
Regarding claim 2, the claims of the ‘341 application discloses the above method, wherein the modified forms of the first type of polypeptide comprise post translationally modified forms of the first type of polypeptide (e.g., as per claims 43 and 50-51 of the ‘341 application).
Regarding claim 3, the claims of the ‘341 application discloses the above method, comprising characterizing a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 43 of the ‘341 application).
Regarding claim 4, the claims of the ‘341 application discloses the above method, comprising quantifying each of a plurality of the different modified forms of the first type of polypeptide on the array (e.g., as per claim 43 of the ‘341 application).
Regarding claim 13, the claims of the ‘341 application discloses the above method, wherein at least two of the plurality of different affinity reagents are contacted with the array simultaneously (e.g., as per claim 43 of the ‘341 application).
Regarding claim 14, the claims of the ‘341 application discloses the above method, further comprising the step of identifying individual locations on the array occupied by the first type of polypeptides (e.g., as per claim 44 of the ‘341 application).
Regarding claim 15, the claims of the ‘341 application discloses the above method, wherein the step of identifying individual locations on the array occupied by the first type of polypeptide comprises sequentially contacting the polypeptides on the array with a plurality of different affinity reagents, each different affinity reagent having affinity for a different epitope of amino acids, and identifying the polypeptides based upon a pattern of binding of the different affinity reagents to the epitopes in the polypeptides on the array (e.g., as per claims 43-44 of the ‘341 application).
Regarding claim 16, the claims of the ‘341 application discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising providing polypeptides from the sample immobilized on an array, wherein individual molecules of the polypeptides from the sample are immobilized in locations on the array where the individual molecules are individually addressable, and wherein the polypeptides immobilized on the array comprise a plurality of individual molecules of the first type of polypeptide, iteratively contacting the individual molecules of the first type of polypeptide on the array with a plurality of different affinity reagents, each of the plurality of different affinity reagents having a binding affinity for a different modification to the first type of polypeptide, detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the array, and characterizing modified forms of the first type of polypeptides in the sample based upon the individual polypeptides on the array that are bound or not bound by each of the plurality of different affinity reagents (e.g., as per claim 43 of the ‘341 application).
Regarding claim 17, the claims of the ‘341 application discloses the above method, further comprising quantifying a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 43 of the ‘341 application).
Regarding claim 18, the claims of the ‘341 application discloses the above method, further comprising a step of identifying individually addressable locations on the array at which the first type of polypeptide is immobilized (e.g., as per claim 44 of the ‘341 application).
Regarding claim 19, the claims of the ‘341 application discloses the above method, wherein the identifying step comprises contacting individual polypeptide molecules on the array with one or more affinity reagents having binding specificity for the first type of polypeptide (e.g., as per claim 43 of the ‘341 application).
Regarding claim 20, the claims of the ‘341 application discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising:
providing polypeptides from the sample, wherein a plurality of individual molecules of the polypeptides from the sample are each immobilized at an individually detectable address on one or more solid supports, and wherein the individual molecules of the polypeptides immobilized on the one or more solid supports comprise a plurality of individual molecules of the first type of polypeptide;
contacting the individual molecules of the polypeptides on the one or more solid supports with a plurality of different affinity reagents, each of the plurality of different affinity reagents having binding affinity for a different modification to the first type of polypeptide;
detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the one or more solid supports; and
characterizing modified forms of the first type of polypeptide in the sample based upon a pattern of binding of the plurality of different affinity reagents at each of a plurality of different individually detectable addresses on the one or more solid supports (e.g., as per claim 43 of the ‘341 application).
10,473,654 B2
Claims 1-4 and 12-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 10,473,654 B2 (the ‘654 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, the claims of the ‘654 patent discloses a method for characterizing modified forms of a first type of polypeptide in a sample, comprising providing the first type of polypeptide on an array, wherein each of a plurality of individual polypeptide molecules of the first type of polypeptide are individually located at individually addressable locations on the array, contacting the array with a plurality of different types of affinity reagents, wherein each of the plurality of different types of affinity reagents has binding specificity for the first type of polypeptide having a different modification, characterizing one or more modified forms of the first type of polypeptide on the array based upon detection of the types of different affinity reagents that bind or do not bind to each of the plurality of individual polypeptide molecules of the first type of polypeptide on the array (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 2, the claims of the ‘654 patent discloses the above method, wherein the modified forms of the first type of polypeptide comprise post translationally modified forms of the first type of polypeptide (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 3, the claims of the ‘654 patent discloses the above method, comprising characterizing a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 4, the claims of the ‘654 patent discloses the above method, comprising quantifying each of a plurality of the different modified forms of the first type of polypeptide on the array (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 12, the claims of the ‘654 patent discloses the above method, wherein the contacting step comprises sequentially contacting the individual molecules of the first type of polypeptide on the array with each of the plurality of different types of affinity reagents (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 13, the claims of the ‘654 patent discloses the above method, wherein at least two of the plurality of different affinity reagents are contacted with the array simultaneously (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 14, the claims of the ‘654 patent discloses the above method, further comprising the step of identifying individual locations on the array occupied by the first type of polypeptides (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 15, the claims of the ‘654 patent discloses the above method, wherein the step of identifying individual locations on the array occupied by the first type of polypeptide comprises sequentially contacting the polypeptides on the array with a plurality of different affinity reagents, each different affinity reagent having affinity for a different epitope of amino acids, and identifying the polypeptides based upon a pattern of binding of the different affinity reagents to the epitopes in the polypeptides on the array (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 16, the claims of the ‘654 patent discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising providing polypeptides from the sample immobilized on an array, wherein individual molecules of the polypeptides from the sample are immobilized in locations on the array where the individual molecules are individually addressable, and wherein the polypeptides immobilized on the array comprise a plurality of individual molecules of the first type of polypeptide, iteratively contacting the individual molecules of the first type of polypeptide on the array with a plurality of different affinity reagents, each of the plurality of different affinity reagents having a binding affinity for a different modification to the first type of polypeptide, detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the array, and characterizing modified forms of the first type of polypeptides in the sample based upon the individual polypeptides on the array that are bound or not bound by each of the plurality of different affinity reagents (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 17, the claims of the ‘654 patent discloses the above method, further comprising quantifying a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 18, the claims of the ‘654 patent discloses the above method, further comprising a step of identifying individually addressable locations on the array at which the first type of polypeptide is immobilized (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 19, the claims of the ‘654 patent discloses the above method, wherein the identifying step comprises contacting individual polypeptide molecules on the array with one or more affinity reagents having binding specificity for the first type of polypeptide (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
Regarding claim 20, the claims of the ‘654 patent discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising:
providing polypeptides from the sample, wherein a plurality of individual molecules of the polypeptides from the sample are each immobilized at an individually detectable address on one or more solid supports, and wherein the individual molecules of the polypeptides immobilized on the one or more solid supports comprise a plurality of individual molecules of the first type of polypeptide;
contacting the individual molecules of the polypeptides on the one or more solid supports with a plurality of different affinity reagents, each of the plurality of different affinity reagents having binding affinity for a different modification to the first type of polypeptide;
detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the one or more solid supports; and
characterizing modified forms of the first type of polypeptide in the sample based upon a pattern of binding of the plurality of different affinity reagents at each of a plurality of different individually detectable addresses on the one or more solid supports (e.g., as per claims 1-6 and 8-9 of the ‘654 patent).
11,579,144 B2
Claims 1-4 and 12-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 11,579,144 B2 (the ‘144 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, the claims of the ‘144 patent discloses a method for characterizing modified forms of a first type of polypeptide in a sample, comprising providing the first type of polypeptide on an array, wherein each of a plurality of individual polypeptide molecules of the first type of polypeptide are individually located at individually addressable locations on the array, contacting the array with a plurality of different types of affinity reagents, wherein each of the plurality of different types of affinity reagents has binding specificity for the first type of polypeptide having a different modification, characterizing one or more modified forms of the first type of polypeptide on the array based upon detection of the types of different affinity reagents that bind or do not bind to each of the plurality of individual polypeptide molecules of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 2, the claims of the ‘144 patent discloses the above method, wherein the modified forms of the first type of polypeptide comprise post translationally modified forms of the first type of polypeptide (e.g., as per claim 13 of the ‘144 patent).
Regarding claim 3, the claims of the ‘144 patent discloses the above method, comprising characterizing a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 4, the claims of the ‘144 patent discloses the above method, comprising quantifying each of a plurality of the different modified forms of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 12, the claims of the ‘144 patent discloses the above method, wherein the contacting step comprises sequentially contacting the individual molecules of the first type of polypeptide on the array with each of the plurality of different types of affinity reagents (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 13, the claims of the ‘144 patent discloses the above method, wherein at least two of the plurality of different affinity reagents are contacted with the array simultaneously (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 14, the claims of the ‘144 patent discloses the above method, further comprising the step of identifying individual locations on the array occupied by the first type of polypeptides (e.g., as per claim 5 of the ‘144 patent).
Regarding claim 15, the claims of the ‘144 patent discloses the above method, wherein the step of identifying individual locations on the array occupied by the first type of polypeptide comprises sequentially contacting the polypeptides on the array with a plurality of different affinity reagents, each different affinity reagent having affinity for a different epitope of amino acids, and identifying the polypeptides based upon a pattern of binding of the different affinity reagents to the epitopes in the polypeptides on the array (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 16, the claims of the ‘144 patent discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising providing polypeptides from the sample immobilized on an array, wherein individual molecules of the polypeptides from the sample are immobilized in locations on the array where the individual molecules are individually addressable, and wherein the polypeptides immobilized on the array comprise a plurality of individual molecules of the first type of polypeptide, iteratively contacting the individual molecules of the first type of polypeptide on the array with a plurality of different affinity reagents, each of the plurality of different affinity reagents having a binding affinity for a different modification to the first type of polypeptide, detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the array, and characterizing modified forms of the first type of polypeptides in the sample based upon the individual polypeptides on the array that are bound or not bound by each of the plurality of different affinity reagents (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 17, the claims of the ‘144 patent discloses the above method, further comprising quantifying a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 18, the claims of the ‘144 patent discloses the above method, further comprising a step of identifying individually addressable locations on the array at which the first type of polypeptide is immobilized (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 19, the claims of the ‘144 patent discloses the above method, wherein the identifying step comprises contacting individual polypeptide molecules on the array with one or more affinity reagents having binding specificity for the first type of polypeptide (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 20, the claims of the ‘144 patent discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising:
providing polypeptides from the sample, wherein a plurality of individual molecules of the polypeptides from the sample are each immobilized at an individually detectable address on one or more solid supports, and wherein the individual molecules of the polypeptides immobilized on the one or more solid supports comprise a plurality of individual molecules of the first type of polypeptide;
contacting the individual molecules of the polypeptides on the one or more solid supports with a plurality of different affinity reagents, each of the plurality of different affinity reagents having binding affinity for a different modification to the first type of polypeptide;
detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the one or more solid supports; and
characterizing modified forms of the first type of polypeptide in the sample based upon a pattern of binding of the plurality of different affinity reagents at each of a plurality of different individually detectable addresses on the one or more solid supports (e.g., as per claim 1 of the ‘144 patent).
11,754,559 B2
Claims 1-10, 12-16, and 18-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 11,754,559 B2 (the ‘559 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, the claims of the ‘559 patent discloses a method for characterizing modified forms of a first type of polypeptide in a sample, comprising providing the first type of polypeptide on an array, wherein each of a plurality of individual polypeptide molecules of the first type of polypeptide are individually located at individually addressable locations on the array, contacting the array with a plurality of different types of affinity reagents, wherein each of the plurality of different types of affinity reagents has binding specificity for the first type of polypeptide having a different modification, characterizing one or more modified forms of the first type of polypeptide on the array based upon detection of the types of different affinity reagents that bind or do not bind to each of the plurality of individual polypeptide molecules of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 2, the claims of the ‘559 patent discloses the above method, wherein the modified forms of the first type of polypeptide comprise post translationally modified forms of the first type of polypeptide (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 3, the claims of the ‘559 patent discloses the above method, comprising characterizing a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 4, the claims of the ‘559 patent discloses the above method, comprising quantifying each of a plurality of the different modified forms of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 5, the claims of the ‘559 patent discloses the above method, wherein the one or more modified forms of the first type of polypeptide comprises one or more phosphate modified forms of the first type of polypeptide, the one or more phosphate modified forms of the first type of polypeptide comprising a phosphate group attached at one or more amino acid residues in the individual molecules of the first type of polypeptide (e.g., as per claim 3 of the ‘559 patent).
Regarding claim 6, the claims of the ‘559 patent discloses the above method, wherein the modified forms of the first type of polypeptide comprise a modification at one or more of a plurality of amino acid residues in the individual molecules of the first type of polypeptide, wherein such modifications are independently selected from an acetate, an amide group, a methyl group, a lipid, ubiquitination, myristoylation, palmitoylation, isoprenylation, prenylation, farnesylation, geranylation, glypiation, lipoylation, flavin moiety attachment, phosphopantetheinylation, and retinylidene Schiff base formation (e.g., as per claim 3 of the ‘559 patent).
Regarding claim 7, the claims of the ‘559 patent discloses the above method, wherein each of a plurality of the affinity reagents has a binding specificity for a first type of polypeptide that comprises a phosphate group at a different amino acid residue or set of amino acid residues in the polypeptide (e.g., as per claim 3 of the ‘559 patent).
Regarding claim 8, the claims of the ‘559 patent discloses the above method, wherein the one or more phosphate modified forms of the first type of polypeptide in the sample comprise a plurality of different phosphate modified forms of the first type of polypeptide (e.g., as per claim 3 of the ‘559 patent).
Regarding claim 9, the claims of the ‘559 patent discloses the above method, further comprising quantifying different phosphate modified forms of the fist type of polypeptide in the sample from the quantity of different phosphate modified forms in the polypeptides on the array (e.g., as per claim 3 of the ‘559 patent).
Regarding claim 10, the claims of the ‘559 patent discloses the above method, comprising treating the individual polypeptide molecules on the array to remove one or more of the modifications of the first type of polypeptide on the array after the characterizing step, and repeating the contacting and characterizing steps to identify the first type of polypeptides on the array having the modifications removed (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 12, the claims of the ‘559 patent discloses the above method, wherein the contacting step comprises sequentially contacting the individual molecules of the first type of polypeptide on the array with each of the plurality of different types of affinity reagents (e.g., as per claim 22 of the ‘559 patent).
Regarding claim 13, the claims of the ‘559 patent discloses the above method, wherein at least two of the plurality of different affinity reagents are contacted with the array simultaneously (e.g., as per claim 22 of the ‘559 patent).
Regarding claim 14, the claims of the ‘559 patent discloses the above method, further comprising the step of identifying individual locations on the array occupied by the first type of polypeptides (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 15, the claims of the ‘559 patent discloses the above method, wherein the step of identifying individual locations on the array occupied by the first type of polypeptide comprises sequentially contacting the polypeptides on the array with a plurality of different affinity reagents, each different affinity reagent having affinity for a different epitope of amino acids, and identifying the polypeptides based upon a pattern of binding of the different affinity reagents to the epitopes in the polypeptides on the array (e.g., as per claim 15 of the ‘559 patent).
Regarding claim 16, the claims of the ‘559 patent discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising providing polypeptides from the sample immobilized on an array, wherein individual molecules of the polypeptides from the sample are immobilized in locations on the array where the individual molecules are individually addressable, and wherein the polypeptides immobilized on the array comprise a plurality of individual molecules of the first type of polypeptide, iteratively contacting the individual molecules of the first type of polypeptide on the array with a plurality of different affinity reagents, each of the plurality of different affinity reagents having a binding affinity for a different modification to the first type of polypeptide, detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the array, and characterizing modified forms of the first type of polypeptides in the sample based upon the individual polypeptides on the array that are bound or not bound by each of the plurality of different affinity reagents (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 18, the claims of the ‘559 patent discloses the above method, further comprising a step of identifying individually addressable locations on the array at which the first type of polypeptide is immobilized (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 19, the claims of the ‘559 patent discloses the above method, wherein the identifying step comprises contacting individual polypeptide molecules on the array with one or more affinity reagents having binding specificity for the first type of polypeptide (e.g., as per claim 1 of the ‘559 patent).
Regarding claim 20, the claims of the ‘559 patent discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising:
providing polypeptides from the sample, wherein a plurality of individual molecules of the polypeptides from the sample are each immobilized at an individually detectable address on one or more solid supports, and wherein the individual molecules of the polypeptides immobilized on the one or more solid supports comprise a plurality of individual molecules of the first type of polypeptide;
contacting the individual molecules of the polypeptides on the one or more solid supports with a plurality of different affinity reagents, each of the plurality of different affinity reagents having binding affinity for a different modification to the first type of polypeptide;
detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the one or more solid supports; and
characterizing modified forms of the first type of polypeptide in the sample based upon a pattern of binding of the plurality of different affinity reagents at each of a plurality of different individually detectable addresses on the one or more solid supports (e.g., as per claim 1 of the ‘559 patent).
11,768,201 B2
Claims 1-3 and 12-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 11,768,201 B2 (the ‘201 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, the claims of the ‘201 patent discloses a method for characterizing modified forms of a first type of polypeptide in a sample, comprising providing the first type of polypeptide on an array, wherein each of a plurality of individual polypeptide molecules of the first type of polypeptide are individually located at individually addressable locations on the array, contacting the array with a plurality of different types of affinity reagents, wherein each of the plurality of different types of affinity reagents has binding specificity for the first type of polypeptide having a different modification, characterizing one or more modified forms of the first type of polypeptide on the array based upon detection of the types of different affinity reagents that bind or do not bind to each of the plurality of individual polypeptide molecules of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 2, the claims of the ‘201 patent discloses the above method, wherein the modified forms of the first type of polypeptide comprise post translationally modified forms of the first type of polypeptide (e.g., as per claim 13 of the ‘201 patent).
Regarding claim 3, the claims of the ‘201 patent discloses the above method, comprising characterizing a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 12, the claims of the ‘201 patent discloses the above method, wherein the contacting step comprises sequentially contacting the individual molecules of the first type of polypeptide on the array with each of the plurality of different types of affinity reagents (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 13, the claims of the ‘201 patent discloses the above method, wherein at least two of the plurality of different affinity reagents are contacted with the array simultaneously (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 14, the claims of the ‘201 patent discloses the above method, further comprising the step of identifying individual locations on the array occupied by the first type of polypeptides (e.g., as per claims 1 and 5 of the ‘201 patent).
Regarding claim 15, the claims of the ‘201 patent discloses the above method, wherein the step of identifying individual locations on the array occupied by the first type of polypeptide comprises sequentially contacting the polypeptides on the array with a plurality of different affinity reagents, each different affinity reagent having affinity for a different epitope of amino acids, and identifying the polypeptides based upon a pattern of binding of the different affinity reagents to the epitopes in the polypeptides on the array (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 16, the claims of the ‘201 patent discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising providing polypeptides from the sample immobilized on an array, wherein individual molecules of the polypeptides from the sample are immobilized in locations on the array where the individual molecules are individually addressable, and wherein the polypeptides immobilized on the array comprise a plurality of individual molecules of the first type of polypeptide, iteratively contacting the individual molecules of the first type of polypeptide on the array with a plurality of different affinity reagents, each of the plurality of different affinity reagents having a binding affinity for a different modification to the first type of polypeptide, detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the array, and characterizing modified forms of the first type of polypeptides in the sample based upon the individual polypeptides on the array that are bound or not bound by each of the plurality of different affinity reagents (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 17, the claims of the ‘201 patent discloses the above method, further comprising quantifying a plurality of different modified forms of the first type of polypeptide on the array (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 18, the claims of the ‘201 patent discloses the above method, further comprising a step of identifying individually addressable locations on the array at which the first type of polypeptide is immobilized (e.g., as per claims 1 and 5 of the ‘201 patent).
Regarding claim 19, the claims of the ‘201 patent discloses the above method, wherein the identifying step comprises contacting individual polypeptide molecules on the array with one or more affinity reagents having binding specificity for the first type of polypeptide (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 20, the claims of the ‘201 patent discloses a method of characterizing modified forms of a first type of polypeptide in a sample, comprising:
providing polypeptides from the sample, wherein a plurality of individual molecules of the polypeptides from the sample are each immobilized at an individually detectable address on one or more solid supports, and wherein the individual molecules of the polypeptides immobilized on the one or more solid supports comprise a plurality of individual molecules of the first type of polypeptide;
contacting the individual molecules of the polypeptides on the one or more solid supports with a plurality of different affinity reagents, each of the plurality of different affinity reagents having binding affinity for a different modification to the first type of polypeptide;
detecting binding of each of the different affinity reagents to individual molecules of the first type of polypeptide on the one or more solid supports; and
characterizing modified forms of the first type of polypeptide in the sample based upon a pattern of binding of the plurality of different affinity reagents at each of a plurality of different individually detectable addresses on the one or more solid supports (e.g., as per claim 1 of the ‘201 patent).
***
Response to Arguments
Applicant does not offer further arguments regarding the above obviousness rejections beyond what was set forth with regard to the 35 U.S.C. § 102 rejection, above. To the extent that Applicant is merely repeating their previous argument, the Examiner contends that those issues were adequately addressed in the above sections, which are incorporated in their entireties herein by reference.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684