Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Priority
The instant application is a continuation of 18151794, filed 01/09/2023, now U.S. patent 11,767,550 which is a continuation of 17825719, filed 05/26/2022, now U.S. patent 11,549,138, which is a continuation of 17/030,230, filed 09/23/2020, now U.S. patent 11,384,386, which is a continuation of 16/988,284, filed 08/07/2020, now U.S. patent 10/961,566, which is a continuation of 16/414,213, filed 05/16/2019, now U.S. patent 10,787,701, which is a continuation of 16/402,098, filed 05/02/2019, now U.S. patent 10,472,669, which is a continuation of 16/276,235, filed 02/14/2019, now U.S. patent 10,480,022 , which is a continuation of 15/187,661 , filed 06/20/2016, now U.S. patent 10,308,982, which is a continuation of 13/080,616, filed 04/05/2011, now U.S. patent 9,371,598, which claims priority from provisional application 61321124, filed 04/05/2010.
Claim Status
Claim 1 has been canceled prior to examination. Claims 2-21 are pending and under examination. Claim 2 is the only independent claim.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claim 2-21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-30 of U.S. Patent No. 11,767,550, (‘550 henceforward). Although the claims at issue are not identical, they are not patentably distinct from each other because:
Claim 2 of the instant application recites a method for spatially associating a protein and a nucleic acid in a biological sample comprising the steps of (a) contacting the biological sample with a binding agent that specifically binds to the protein wherein the binding agent is coupled to an oligonucleotide comprising a sequence; (b) contacting the biological sample with an array comprising a first capture probe and a second capture probe, wherein the first capture probe comprises a first target-binding domain that hybridizes to the oligonucleotide coupled to the binding agent and a nucleic acid sequence identifying a unique location of the first capture probe on the array, and the second capture probe comprises a second target-binding domain that hybridizes to the nucleic acid of the biological sample and a nucleic acid sequence identifying a unique location of the second capture probe on the array; (c) generating a sequence complementary to the oligonucleotide coupled to the binding agent using the first target binding domain of the first capture probe hybridized to the oligonucleotide as a primer; and (d) generating a cDNA using the second target-binding domain of the second capture probe hybridized to the nucleic acid of the biological sample as a primer thereby spatially associating the protein and the nucleic acid in the biological sample.
Claim 1 of ‘550 recites a method for determining a location of a protein and a nucleic acid in a biological sample comprising the steps of: (a) contacting the biological sample with a binding agent that specifically binds to the protein, wherein the binding agent is coupled to an oligonucleotide comprising a sequence; (b) contacting the biological sample with an array comprising a first capture probe and a second capture probe, wherein the first capture probe comprises a first target-binding domain that hybridizes to the oligonucleotide coupled to the binding agent and a nucleic acid sequence identifying a unique location of the first capture probe on the array, and the second capture probe comprises a second target-binding domain that hybridizes to the nucleic acid of the biological sample and a nucleic acid sequence identifying a unique location of the second capture probe on the array; (c) determining the sequence of the oligonucleotide coupled to the binding agent and the nucleic acid sequence identifying the unique location of the first capture probe on the array and using those determined sequences to determine the location of the protein in the biological sample; and (d) determining all or a portion of the sequence of the nucleic acid of the biological sample and the nucleic acid sequences identifying the unique location of the second capture probe on the array, and using those determined sequences to determine the location of the nucleic acid in the biological sample.
Comparing the two claims, steps (a) and (b) are identical between them. The only differences reside in steps (c) and (d). In claim 2 of the instant application, step (c) recites generating a sequence complementary to the oligonucleotide couple to the binding agent using the first target-binding domain of the first capture probe hybridized to the oligonucleotide as a primer, and step (d) recites generating a cDNA using the second target-binding domain of the second capture probe hybridized to the nucleic acid of the biological sample as a primer. These limitations are not patentably distinct from claim 1 of ‘550 for the following reasons.
First, dependent claim 2 of ‘550 expressly recites that “the second target binding domain of the second capture probe, when bound to the nucleic acid of the biological sample, can function as a primer,” directly encompassing the primer function recited in step (d) of claim 2 of the instant application. The recitation in claim 2 of the instant application that the second target-binding domain actually functions as a primer to generate cDNA is merely an obvious implementation of the primer functionality expressly disclosed and claimed in dependent claim 2 of ‘550. Using a hybridized oligonucleotide probe as primer for extension or cDNA synthesis is a fundamental and well-known technique in molecular biology that person of ordinary skill in the art would have recognized as the natural and routine application of primer functionality recited in dependent claim 2 of ‘550.
Second, dependent claim 11 of ‘550 expressly recites that “the determining in step (d) includes generation of a cDNA using the second target-binding domain of the second capture probe, bound to the nucleic acid of the biological sample, as a primer,” which is identical in substance to step (d) of claim 2 of the instant application. The recitation of cDNA generation using the second capture probe as a primer in step (d) of claim 2 of the instant application therefore does not distinguish claim 2 of the instant application from the subject matter already claimed in claims 1 and 11 of ‘550.
Third, with respect to step (c) of claim 2 of the instant application, which recites generating a sequence complementary to the oligonucleotide coupled to the binding agent using the first target-binding domain of the first capture probe as a primer, this limitation represents an obvious corollary to the primer extension chemistry already expressly claimed in dependent claims 2 and 11 of ‘550 with respect to the second capture probe. A person of ordinary skill in the art would have recognized that the same primer extension chemistry applicable to the second capture probe in the context of nucleic acid capture is equally and obviously applicable to the first capture probe in the context of capturing the oligonucleotide coupled to the binding agent. Extending the first capture probe using the antibody-coupled oligonucleotide as a templated it the functional mirror image of the second capture probe extension recited in claims 2 and 11 of ‘550,and applying this chemistry to the first capture probe requires no more than routine skill in the art. Accordingly, the differences between step (c) of claim 2 of the instant application and the claims of ‘550 do not give rise to a patentably distinct invention.
Furthermore, the preamble of claim 2 of the instant application recites “spatially associating” the protein and nucleic acid, whereas claim 1 of ‘550 recites determining a location” of the protein and nucleic acid. Theses phrases are not patentably distinct. Spatially associating a protein and a nucleic acid in a biological sample is the result of determining the location of both the protein and the nucleic acid in that sample using the same spatially barcoded array as recited in claim 1 of ‘550. A method that determine the spatial location of both a protein and a nucleic acid in a biological sample using a common array with spatial location identifiers necessarily spatially associates those two analytes, as the location of both are resolved with reference to the same spatial coordinate system defined by the array. The difference in preamble language therefore does not reflect a patentably distinct method.
For the foregoing reasons, claim 2 of the instant claim is not patentably distinct from claims 1, 2, and 11 of ‘550.
Claim 3 of the instant application depends on claim 2 and adds steps (e) and (f), which recite: (e) determining the sequence of the oligonucleotide coupled to the binding agent and the nucleic acid sequence identifying the unique location of the first capture probe on the array and using those determined sequences to determine the location of the protein in the biological sample and (f) determining all or a portion of the sequence of the nucleic acid of the biological sample and the nucleic acid sequence identifying the unique location of the second capture probe on the array, and using those determined sequences to determine the location of the nucleic acid in the biological sample.
Steps (e) and (f) of claim 3 of the instant application are identical in all material respects to steps (c) and (d) of claim 1 of ‘550. Claim 3 of the instant application therefore incorporates the full substantive scope of claim 1 of ‘550 including its determination and location-mapping steps, while also incorporating the primer extension limitations of dependent claims 2 and 11 of ‘550 through its dependence on claim 2 of the instant application. Claim 3 of the instant application thus claims a method is wholly encompassed within the scope of claims 1, 2, and 11 of ‘550, with no limitation that is not already expressly claimed or that would not have been obvious to a person of ordinary skill in the art in view of those claims.
For the foregoing reasons, claim 3 of the instant application is not patentably distinct from claims 1, 2, and 11 of ‘550.
Since independent claim 2 and dependent claim 3 map to the independent claim of ‘550 as outlined above, the following claims map directly to claims ‘550 with word-for-word accuracy.
Claim 4 maps directly to claims 3 and 16 of ‘550 (“wherein the determining in step (#) comprises nucleic acid amplification”.
Claim 5 maps directly to claim 4 of ‘550.
Claim 6 maps directly to claim 18 of ‘550.
Claim 7, maps directly to claim 19 of ’550.
Claim 8, maps directly to claim 7 of ‘550.
Claim 9, maps directly to claim 9 of ‘550.
Claim 10, maps directly to claim 10 of ‘550.
Claim 11, maps directly to claim 12 of ‘550.
Claim 12, maps directly to claim 14 of ‘550.
Claim 13, maps directly to claim 15 of ‘550.
Claim 14, maps directly to claim 17 of ‘550.
Claim 15, maps directly to claim 22 of ‘550.
Claim 16, maps directly to claim 23 of ‘550.
Claim 17, maps directly to claim 24 of ‘550.
Claim 18, maps directly to the combination of claims 25 and 26 of ‘550.
Claim 19, maps directly to claim 29 of ‘550.
Claim 20, maps directly to claim 30 of ‘550.
Claim 21, maps directly to claim 27 of ‘550.
Claims 2-5, 14, and 20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 of U.S. Patent No. 10,619,196. Although the claims at issue are not identical, they are not patentably distinct from each other because the differences are limited to obvious variations in claim terminology that do not reflect substantive distinctions in the claimed subject matter.
Claim 2 of the instant application recites a method A method for spatially associating a protein and a nucleic acid in a biological sample, the method comprising: (a) contacting the biological sample with a binding agent that specifically binds to the protein, wherein the binding agent is coupled to an oligonucleotide comprising a sequence; (b) contacting the biological sample with an array comprising a first capture probe and a second capture probe, wherein: the first capture probe comprises: (i) a first target-binding domain that hybridizes to the oligonucleotide coupled to the binding agent, and (ii) a nucleic acid sequence that identifies a unique location of the first capture probe on the array; and the second capture probe comprises: (i) a second target-binding domain that hybridizes to the nucleic acid of the biological sample, and (ii) a nucleic acid sequence that identifies a unique location of the second capture probe on the array; and (c) generating a sequence complementary to the oligonucleotide coupled to the binding agent using the first target-binding domain of the first capture probe hybridized to the oligonucleotide as a primer; and (d) generating a cDNA using the second target-binding domain of the second capture probe hybridized to the nucleic acid of the biological sample as a primer. Claim 1 of US 10,619,196 B1 is directed to a method for determining a location of a polypeptide and a nucleic acid in a biological sample comprising (a) contacting the biological sample with a binding agent attached to a coding identifier having an oligonucleotide sequence; (b) contacting the biological sample with an array comprising a first encoded probe having a binding agent that specifically binds to the oligonucleotide sequence of the coding identifier and a coding tag comprising an oligonucleotide sequence corresponding to a location in the array, and a second encoded probe having a binding agent that specifically binds to the nucleic acid and a coding tag comprising an oligonucleotide sequence corresponding to a location in the array; (c) determining the oligonucleotide sequence coding identifier and the coding tag of the first encoded probe to determine the location of the polypeptide; and (d) determining the sequence of the nucleic acid and the coding tag of the second encoded probe to determine the location of the nucleic acid.
The difference between claim 2 of the instant application and claim 1 of US 10,619,196 B1 are limited to cosmetic terminology. Specifically, “protein” and “polypeptide” are art recognized synonyms for the same class of biological molecules. “Capture probe” and “encoded probe” are functionally identical structural elements, bother are array immobilized oligonucleotide probes comprising a target-binding domain and a spatial location identifier. “Nucleic acid sequence that identifies a unique location” and “coding tag comprising an oligonucleotide sequence that corresponds to a location in the array” describe the same element. “Oligonucleotide comprising a sequence” coupled to the binding agent and “coding identifier having an oligonucleotide sequence” attached to the binding agent describe the same structural arrangement. The recitation of claim 2 of generating a sequence complementary to the oligonucleotide using the first capture probe as a primer, and generating a cDNA using the second capture probe as a primer represents an obvious implementation of the determination steps recited in claim 1 of ‘196, as extension from a hybridized oligonucleotide probe is a well-known and routine method for generating sequences reads from captured analytes. Claim 2 of ‘196 further expressly recites that the binding agent of the second encoded probe, when specifically bound to the nucleic acid, can function as a primer, confirming that this limitation is not patentably distinct from what is already claimed in ‘196.
Claim 3 of the instant application adds determination steps (e) and (f) reciting sequencing of the oligonucleotide coupled to the binding agent together with the spatial barcode of the first capture probe to determine protein location, and sequencing of the nucleic acid together with the spatial barcode of the second capture probe to determine nucleic acid location. These limitations are expressly recited in claim 1 of ‘196 at steps (c) and (d), which recite determining the oligonucleotide sequence of the coding identifier and the coding tag of the first encoded probe to determine polypeptide location, and determining the sequence of the nucleic acid and the coding tag of the second encoded probe to determine nucleic acid location. Claim 3 of the instant application is therefore not patentably distinct from claims 1 and 2 of ‘196.
Claim 4 of the instant application recites that the determining steps (e) and (f) comprises nucleic acid amplification. Claim 3 of ‘196 recites that the determining in step (d) comprises nucleic acid amplification. The extension of this limitation to encompass both determination steps (e) and (f) of claim 3 of the instant application is an obvious variation that a person of ordinary skill in the art would have had no reason to treat as a patentably distinct feature. Claim 4 of the instant application is therefore not patentably distinct from claims 1-3 of ‘196.
Claim 5 of the instant application recites that the determining in step (f) comprises sequencing all or a portion of the nucleic acid sequence and the nucleic acid sequence identifying the unique location of the second capture probe. Claim 4 of ‘196 recites that the determining in step (d) comprises sequencing all or a portion of the oligonucleotide sequence of the coding identifier and the oligonucleotide sequence of the coding tag of the second encoded probe. These limitations are directed to the same subject matter expressed in different terminology. Claim 5 of the instant application is therefore not patentably distinct from claims 1 and 4 of ‘196.
Claim 14 of the instant application recites that the determining in step (e) comprises sequencing the oligonucleotide coupled to the binding agent and the nucleic acid sequence identifying the unique location of the first capture probe. This maps directly to the determination step (c) of claim 1 of ‘196, which recites determining the oligonucleotide sequence of the coding identifier and the oligonucleotide sequence of the coding tag of the first encoded probe. Claim 14 of the instant application is therefore not patentably distinct from claim 1 of ‘196.
Claim 20 of the instant application recites that the method further comprises generating a map of the location of the protein and/or the nucleic acid in the biological sample. This limitation is inherent in and an obvious implementation of the determination steps of claim 1 of ‘196 which recites using the determined sequences to determine the location of the polypeptide and the location of the nucleic acid in the biological sample. Generating a map from determined spatial locations is the necessary and obvious output of the claimed method and does not constitute a patentably distinct feature. Claim 20 of the instant application is therefore not patentably distinct from claim 1 of ‘196.
Potentially Allowable Subject Matter
Apart from the double patenting issues addressed above, the prior art of record has been considered and no single reference or combination of references discloses or suggests every limitation of claim 2.
The closest prior art reflects several independent lines of development, each solving different pieces of the problem addressed by claim 2, but none of which discloses the specific combination of elements required by the claim.
Schweitzer et al. (“Immunoassays with rolling circle DNA amplification: A versatile platform for ultrasensitive antigen detection”, PNAS, 2000, 97, 17, 10113-10119, on IDS 10/12/2023) discloses antibody-oligonucleotide conjugates capture on a microarray, with the capture oligonucleotides subsequently extended or amplified by rolling-circle amplification to generate a detectable signal. Schweitzer therefore discloses extension-based readout of an antibody-coupled oligonucleotide on an array surface, closely related to step (c) of claim 2. However, Schweitzer’s arrays are directed solely to protein detection; Schweitzer contains no disclosure of a second, structurally distinct capture probe directed to an endogenous nucleic acid target, no disclosure of a nucleic acid sequence identifying the location of the capture probe on the array, and no disclosure of simultaneous dual-analyte detection.
Konry et al. (“Microsphere-Based Rolling Circle Amplification Microarray for the Detection of DNA and Proteins in a Single Assay”, Anal. Chem., 2009, Vol. 81, 14, 5777-5782), discloses a microsphere-based array having two distinct capture probe populations (an antibody-based capture probe for a protein analyte and an oligonucleotide-based capture probe for a nucleic acid analyte) readout simultaneously on the same array using rolling-circle amplification chemistry. Konry therefore discloses the general concept of dual-analyte, dual-capture-probe detection on a single array. However, Konry’s capture probes are not disclosed as bearing a nucleic acid sequence that identifies their unique location on the array. Further, Konry’s array is microsphere based with optical/fluorescent readout rather than a spatially-organized sequence-barcoded array. Furthermore, Konry discloses padlock prober ligation and rolling circle amplification as its detection chemistry rather than primer extension directly from a capture probe into the captured oligonucleotide or nucleic acid as recited in steps (c) and (d) of claim 2.
Roth (US 2006/0046313 A1, on IDS 10/12/2023) similarly discloses an array having two or more capture probes of different specificity at defined locations, with position-associated signals correlated to analyte identity, extending Konry’s general architecture to a SERS/Raman-based optical readout. As with Konry, Roth’s location-identify mechanism is the known physical position of each array feature rather than a nucleic acid sequence identifying that location, and Roch discloses no primer-extension or cDNA generation chemistry.
Brenner (US 2007/0172873 A1, on IDS 10/12/2023) discloses methods for digital counting of target molecules using combinatorial oligonucleotides tags and sequence-based sorting, including general disclosure that antibody-oligonucleotide conjugates may be used to label protein targets for quantification. Brenner’s methodology is directed entirely to bulk solution-phase quantification of a homogenized sample and contains no disclosure of an array, no disclosure of contacting an intact biological sample with a capture surface and no teaching of any mechanism for preserving the spatial origin of a detected molecule.
Larsson et al. (“In situ genotyping individual DNA molecules by target-primed rolling circle amplification of padlock probes”, Nature Methods, 2004, 1, 227-232, on IDS 10/12/2023) discloses in situ genotyping of individual DNA molecules within fixed tissue sections using padlock probes and target-primed rolling circle amplification, achieving single-molecule spatial resolution directly within intact tissue. Larson’s spatial information, however is derived entirely from optical microscopy of the fixed tissue sample rather than from a sequence encoded positional barcode resolvable by sequencing.
Considered individually, each of these references addresses a different dimension of the problem solved by claim 2. Schweitzer extends established immuno-PCR literature that antibody-oligonucleotide conjugates can serve as a sequence encoded protein detection reagent, read on an array, but for protein detection only. Konry and Roth extend the architecture to simultaneous dual analyte detection on a single array with two distinct capture probe populations, but rely on optical or fluorescent decoding of physical array position rather than a sequence based positional barcode, and neither contemplated extension-based cDNA generation from the capture target. Brenner teaches digital sequence-based identification of molecules but sacrifices all spatial information entirely. Larsson teaches sequence-based , single-molecule spatial detection with high fidelity but is limited toa single nucleic acid analyte and lacks any array architecture of positional barcode.
No reference or record discloses the combination of (i) a fixed array bearing two distinct capture probe populations each carrying a nucleic acid sequence that identifies its unique location on the array, (ii) one capture probe directed to an oligonucleotide conjugated binding agent for protein detection ad the other directed to an endogenous nucleic acid, and (iii) primer extension from each capture probe to generate a sequence or cDNA that carries both the analyte information and the positional barcode in a single sequencing compatible product.
Considered in combination, the cited references do not remedy these individual deficiencies. There is no teaching or suggestion in any reference, nor would there have been any apparent reason for a person of ordinary skill in the art at the time of the invention to replace the optical or fluorescent position-decoding mechanism of Konry and Roth with a sequencing-based positional barcode, while simultaneously substituting their padlock-ligation/RCA or COIN based detection chemistry with the primer extension and cDNA generation chemistry taught by Schweitzer and Larsson.
Comments on the Cantor Reference (WO 2009/091934 A1)
In regards to the Cantor reference which was the subject of the Inter Partes Review concerning related claims in this patent family, the reference has been considered and does not anticipate or render obvious claim 2. The Board’s analysis in that proceeding is instructive and is adopted here: Cantor’s methods are directed to determining whether a target nucleic acid sequence is present in a sample and where present, identifying or counting it, not determining where that target is located within a biological sample.
Cantor’s core architecture requires that ta single molecule of sample nucleic acid hybridize to a single solid support molecule under dilute, single-molecule conditions. Cantor’s sample is necessarily extracted, purified, and in solution prior to contact with the solid support. Cantor contains no disclosure of contacting an intact biological sample with an array, and no disclosure of any spatial relationship being preserved between a detected target and its original location within a tissue or sample. Furthermore, Cantor’s array is not arranged in manner conducive for spatial detection of molecules. Cantor’s “identification sequence” identifies a solid support species within a population for the purpose of sequence reconstruction and single-molecule counting, it does not identify the spatial position within a biological sample.
Moreover, Cantor does not teach a capture probe, let alone a first and second capture probe, having a nucleic acid sequence that identifies a unique location of that capture probe on an array as recited in claim 2. No such spatial relationship exists or is preserved in Cantor’s method. While Cantor does state that solid supports may optionally be “provided in an array” for the limited purpose of organizing samples for processing or readout, but Cantor does not disclose using the array position itself , nor a sequence encoding that position, to determine where in a biological sample a target was located. Cantor’s stated applications, microbial identification, SNP detection, haplotyping, methylation analysis, resequencing, and the line, are uniformly directed to determining the presence, identity, or sequence of a target, not its spatial origin within an intact sample.
Cantor further contains no disclosure of a binding agent coupled to an oligonucleotide for detecting a protein analyte, nor any disclosure of a second capture probe directed to a different analyte class than the first.
For at least these reasons, Cantor does not teach or suggest determining the location of a protein or nucleic acid in a biological sample, does not teach a capture probe bearing a sequence that identifies a unique location on an array correlated toa position in a biological sample, and does not teach detection of a protein analyte via an oligonucleotide conjugated binding agent. Cantor is therefore directed to a different problem than that solved by claim 2 and does not anticipate of render obvious claim 2, alone or in combination with the other prior art of record.
Conclusion
No claim is allowed.
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/MATTHEW HAROLD RAYMONDA/Examiner, Art Unit 1684
/AARON A PRIEST/Primary Examiner, Art Unit 1681
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