DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Specification
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because it is not limited to a single paragraph on a separate sheet.
Appropriate correction is required.
Claim Rejections - 35 USC § 102
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.
Claims 1-3, 5-7, 9-10, 14, 17, 33-39, 41-42, and 44-48 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Locke (US 20170199959 A1).
Regarding Claim 1, Locke discloses a method of generating a graph comprising connections between a first set of gene variants associated with a first species and a second set of gene variants associated with a second species different than the first species ([Abstract]: Genomes of different species may be embodied as a graph; [0042]: The objects are connected 115 in order to create paths through the connected blocks such that there is a path to represent each of the plurality of known sequences from the plurality of different species), the method comprising:
using at least one computer hardware processor to perform (Fig. 4; [0052]: Each computer in the system 401 includes a processor coupled to a memory device):
obtaining data generated by first genomic studies of the first species and second genomic studies of the second species, the data comprising a plurality of datasets comprising two or more data formats (Fig. 1; [0042]-[0045]: The method 101 includes obtaining 105 a plurality of known sequences from a plurality of different species from an online sequence database; [0073]: Reads may be stored in any suitable format);
storing a subset of the data in a cache (Figs. 3-4; [0052]-[0056]: It should be noted that FIG. 3 depicts an example of several simplified chromosomes in order to highlight that certain regions, subsets, or portions of genomes (or combinations thereof) may be conserved across species… For example, conserved regions may comprise… subsets of these regions… Preferably the reference graph 331 is stored in the memory subsystem 475; [0060]-[0062]: Preferably, each pointer identifies a physical location in the memory subsystem);
accessing the subset of the data in the cache ([0061]: In the preferred embodiments, the pointer or native pointer… permits access to the intended data by means of pointer dereference) and
transforming the subset of the data into a database having a uniform data format, the database describing graph objects and connections between the graph objects ([0021]: FIG. 2 shows transforming a plurality of known sequences from different species into a multi-species reference graph.; [0045]: The known sequences 303 may be retrieved from a database);
storing the database in non-transient computer-readable memory ([Abstract]: Genomes of different species may be embodied as a graph in which conserved parts of multiple genomes are stored at a fixed location in memory and accessed via spatial addressing); and
generating the graph using the database (Figs. 2-3; [0045]: FIG. 2 illustrates obtaining 105 a plurality of known sequences 303 from a plurality of different species and transforming 109 the known sequences 303 into a multi-species reference graph 331).
Regarding Claim 2, Locke discloses the method of claim 1, wherein determining the graph objects and the connections comprises:
determining first gene objects and first gene variant objects associated with the first species; determining second gene objects and second gene variant objects associated with the second species (Fig 1; [0042]-[0050]: The method 101 includes obtaining 105 a plurality of known sequences from a plurality of different species. Places where those species match when aligned—i.e., matching homologous segments—define blocks that are transformed 109 into objects);
determining first connections between a gene object of the first gene objects and one or more gene variant objects of the first gene variant objects; determining second connections between a gene object of the second gene objects and one or more gene variant objects of the second gene variant objects; and determining third connections between the first gene objects and the second gene objects (Fig. 1; [0042]-[0050]: The objects are connected 115 in order to create paths through the connected blocks such that there is a path to represent each of the plurality of known sequences from the plurality of different species).
Regarding Claim 3, Locke discloses the method of claim 2, wherein determining the first and/or second connections comprises determining expression quantitative trait loci (eQTL) (Fig. 3; [0063]: the capabilities of a given computer, e.g., any modern consumer-grade desktop computer, are extended to allow for full operation of a genomic-scale graph (i.e., a multi-species reference graph 331 that represents all loci in a substantial portion of the genome),
gene variant regulatory elements ([0124]: As discussed above briefly in connection with FIG. 8, optionally, systems and methods of the invention may be used for variant calling 807 to produce genotype information 831 about an organism),
chromatin contact regions, and/or intragenic mapping connections (Fig. 3; [0052]: For example, conserved regions may comprise intergenic regions, intragenic regions, and
wherein determining the third connections comprises determining homolog and/or orthologue connections between the first and second species ([0003]-[0005]: The graph branches into plural paths, each defined by pointers to other objects in the memory, where the genomes diverge due to either divergent homology or non-homologous portions); [0052]: the system 401 is perable to obtain a sequence generated by sequencing nucleic acid from a genome of a patient).
Regarding Claim 5, Locke discloses the method of claim 1, wherein generating the graph comprises generating a weighted undirected graph (Fig. 3; [0121]: A reference graph 331 can be given edge weights that reflect empirically derived or otherwise estimated allele frequencies in a population).
Regarding Claim 6, Locke discloses the method of claim 2, further comprising:
obtaining data generated by third genomic studies of a third species, the third species being different than the first species or the second species ([0004]- [0005]: Aspects of the invention provide a method for analyzing genetic information. The method includes obtaining a genetic sequence from an organism… Optionally, the method may include, prior to the aligning step: obtaining the known sequences from the plurality of different species from an online sequence database);
determining third gene objects and third gene variant objects associated with the third species ([0074]: FIG. 8 also illustrates an optional variant calling 807 step to identify a subject genotype 831);
determining fourth connections between a gene object of the third gene objects and one or more gene variant objects of the third gene variant objects; and determining fifth connections between the third gene objects and the first or second gene objects (Fig. 3; [0048]: The objects 305 are connected 115 to create paths such that there is a path for each of the original known sequences 303… The connections creating the paths can themselves be implemented as objects so that the blocks are represented by vertex objects 305 and the connections are represented by edge objects 309).
Regarding Claim 7, Locke discloses the method of claim 2, further comprising identifying, using the graph and a gene variant object associated with the first species, one or more genomic studies associated with the second species ([0004]- [0005]: Aspects of the invention provide a method for analyzing genetic information. The method includes obtaining a genetic sequence from an organism… Optionally, the method may include, prior to the aligning step: obtaining the known sequences from the plurality of different species from an online sequence database), wherein using the graph to identify the one or more genomic studies comprises:
identifying, using the gene variant object associated with the first species, a gene object of the first gene objects using the first connections ([0124]-[0125]: As discussed above briefly in connection with FIG. 8, optionally, systems and methods of the invention may be used for variant calling 807 to produce genotype information 831 about an organism… wherein each pointer identifies a physical location in the memory subsystem at which the adjacent object is stored);
identifying a gene object of the second gene objects using the third connections ([0125]-[0126]: Objects of the reference graph may include vertex objects connected by edge objects and an adjacency list for each vertex object and edge object, wherein the adjacency list for a vertex object or edge object lists the edge objects or vertex objects to which that vertex object or edge object is adjacent);
identifying a gene variant object associated with the second species using the second connections ([0124]-[0126]: A variant in the genetic sequence, relative to the reference graph is identified and “called” (e.g., reported out as a variant in the genetic sequence)); and
identifying the one or more genomic studies using the gene variant associated with the identified gene variant object ([0033]-[0035]: For example, a gene may be studied that codes for something that appears across multiple species with little or no variation appearing across those species… The invention provides tools for the study of interaction at a distance in the genome and in the ways that function supervenes on spatially distant parts of the genome).
Regarding Claim 9, Locke discloses the method of claim 7, wherein the gene variant object associated with the first species is associated with a disease, and wherein the method further comprises identifying a treatment modality for a patient having the disease using the identified one or more genomic studies ([0031]-[0033]: Graphs may be used as a tool in answering bioinformatic questions from metagenomics, phylogenetics, population genetics, comparative genomics, basic organismal biology and other fields; [0123]-[0124]: FIG. 11 illustrates a report 1101 that may be produced using systems and methods of the invention… As discussed above briefly in connection with FIG. 8, optionally, systems and methods of the invention may be used for variant calling 807 to produce genotype information 831).
Regarding Claim 10, Locke discloses the method of claim 1,
wherein the first species and the second species comprise two species selected from a list including: Mus musculus, Homo sapiens, Rattus norvegicus, Danio rerio, Drosophilia melanogaster, Macaca mulatta, Caenorhabditis elegans, Saccharomyces cervisiae, Gallus gallus, and Canis familiaris ([0041]: A multi-species genome graph of the invention may be used for any suitable inquiry… An example here would be with non-homo-sapiens human species, where this kind of analysis could be used to better sequence newly discovered species… Such graphs may be sometimes intraspecies and sometimes interspecies (e.g., two species of orangutan)).
Regarding Claim 14, Locke discloses the method of claim 1, further comprising regenerating the graph based on updated data ([Abstract]: Newly obtained sequences such as output from NGS instruments can be mapped onto the graph for assembly or identification), the regenerating comprising:
obtaining the updated data generated by first genomic studies of the first species and second genomic studies of the second species, the updated data comprising a plurality of datasets comprising two or more data formats (Fig. 1; [0042]-[0045]: The method 101 includes obtaining 105 a plurality of known sequences from a plurality of different species from an online sequence database; [0073]: Reads may be stored in any suitable format);
storing a subset of the updated data in a cache Figs. 3-4; [0052]-[0056]: It should be noted that FIG. 3 depicts an example of several simplified chromosomes in order to highlight that certain regions, subsets, or portions of genomes (or combinations thereof) may be conserved across species… For example, conserved regions may comprise… subsets of these regions… Preferably the reference graph 331 is stored in the memory subsystem 475; [0060]-[0062]: Preferably, each pointer identifies a physical location in the memory subsystem);
accessing the subset of the updated data in the cache ([0061]: In the preferred embodiments, the pointer or native pointer… permits access to the intended data by means of pointer dereference) and
transforming the subset of the updated data into a uniform data format, the uniform data format describing graph objects and connections between the graph objects ([0021]: FIG. 2 shows transforming a plurality of known sequences from different species into a multi-species reference graph.; [0045]: The known sequences 303 may be retrieved from a database);
storing, in non-transient computer-readable memory, the transformed subset of the updated data in a database ([Abstract]: Genomes of different species may be embodied as a graph in which conserved parts of multiple genomes are stored at a fixed location in memory and accessed via spatial addressing); and
regenerating the graph using the database ([0003]: Newly obtained sequences such as output from NGS instruments can be mapped onto the graph for assembly or identification).
Regarding Claim 17, Locke discloses at least one non-transitory computer readable storage medium storing processor-executable instructions ([0052]-[0054]: FIG. 4 illustrates a computer system 401 suitable for performing methods of the invention… Preferably, each computer includes a non-transitory memory device) that, when executed by at least one processor, cause the at least one processor to perform a method of generating a graph comprising connections between a first set of gene variants associated with a first species and a second set of gene variants associated with a second species ([Abstract]: Genomes of different species may be embodied as a graph; [0042]: The objects are connected 115 in order to create paths through the connected blocks such that there is a path to represent each of the plurality of known sequences from the plurality of different species), the method comprising:
obtaining data generated by first genomic studies of the first species and second genomic studies of the second species, the data comprising a plurality of datasets comprising two or more data formats (Fig. 1; [0042]-[0045]: The method 101 includes obtaining 105 a plurality of known sequences from a plurality of different species from an online sequence database; [0073]: Reads may be stored in any suitable format);
storing a subset of the data in a cache (Figs. 3-4; [0052]-[0056]: It should be noted that FIG. 3 depicts an example of several simplified chromosomes in order to highlight that certain regions, subsets, or portions of genomes (or combinations thereof) may be conserved across species… For example, conserved regions may comprise… subsets of these regions… Preferably the reference graph 331 is stored in the memory subsystem 475; [0060]-[0062]: Preferably, each pointer identifies a physical location in the memory subsystem);
accessing the subset of the data in the cache ([0061]: In the preferred embodiments, the pointer or native pointer… permits access to the intended data by means of pointer dereference) and
transforming the subset of the data into a database having a uniform data format, the uniform data format describing graph objects and connections between the graph objects ([0021]: FIG. 2 shows transforming a plurality of known sequences from different species into a multi-species reference graph.; [0045]: The known sequences 303 may be retrieved from a database);
storing the database in non-transient computer-readable memory ([Abstract]: Genomes of different species may be embodied as a graph in which conserved parts of multiple genomes are stored at a fixed location in memory and accessed via spatial addressing); and
generating the graph using the database (Figs. 2-3; [0045]: FIG. 2 illustrates obtaining 105 a plurality of known sequences 303 from a plurality of different species and transforming 109 the known sequences 303 into a multi-species reference graph 331).
Regarding Claim 33, Locke discloses a system for generating a graph comprising connections between a first set of gene variants associated with a first species and a second set of gene variants associated with a second species ([0052]-[0054]: FIG. 4 illustrates a computer system 401 suitable for performing methods of the invention; ([Abstract]: Genomes of different species may be embodied as a graph; [0042]: The objects are connected 115 in order to create paths through the connected blocks such that there is a path to represent each of the plurality of known sequences from the plurality of different species), the system comprising:
at least one processor; and at least one non-transitory computer readable storage medium storing processor-executable instructions that, when executed by the at least one processor, cause the at least one processor to perform a method comprising ([0052]-[0054]: Each computer in the system 401 includes a processor… Preferably, each computer includes a non-transitory memory device):
obtaining data generated by first genomic studies of the first species and second genomic studies of the second species, the data comprising a plurality of datasets comprising two or more data formats ([0004]- [0005]: Aspects of the invention provide a method for analyzing genetic information. The method includes obtaining a genetic sequence from an organism… Optionally, the method may include, prior to the aligning step: obtaining the known sequences from the plurality of different species from an online sequence database; [0073]: Reads may be stored in any suitable format);
storing a subset of the data in a cache (Figs. 3-4; [0052]-[0056]: It should be noted that FIG. 3 depicts an example of several simplified chromosomes in order to highlight that certain regions, subsets, or portions of genomes (or combinations thereof) may be conserved across species… For example, conserved regions may comprise… subsets of these regions… Preferably the reference graph 331 is stored in the memory subsystem 475; [0060]-[0062]: Preferably, each pointer identifies a physical location in the memory subsystem);
accessing the subset of the data in the cache ([0061]: In the preferred embodiments, the pointer or native pointer… permits access to the intended data by means of pointer dereference) and
transforming the subset of the data into a database having a uniform data format, the uniform data format describing graph objects and connections between the graph objects ([0021]: FIG. 2 shows transforming a plurality of known sequences from different species into a multi-species reference graph.; [0045]: The known sequences 303 may be retrieved from a database);
storing the database in non-transient computer-readable memory ([Abstract]: Genomes of different species may be embodied as a graph in which conserved parts of multiple genomes are stored at a fixed location in memory and accessed via spatial addressing); and
generating the graph using the database (Figs. 2-3; [0045]: FIG. 2 illustrates obtaining 105 a plurality of known sequences 303 from a plurality of different species and transforming 109 the known sequences 303 into a multi-species reference graph 331).
Regarding Claim 34, Locke discloses the system of claim 33, wherein determining the graph objects and the connections comprises:
determining first gene objects and first gene variant objects associated with the first species; determining second gene objects and second gene variant objects associated with the second species (Fig 1; [0042]-[0050]: The method 101 includes obtaining 105 a plurality of known sequences from a plurality of different species. Places where those species match when aligned—i.e., matching homologous segments—define blocks that are transformed 109 into objects);
determining first connections between a gene object of the first gene objects and one or more gene variant objects of the first gene variant objects; determining second connections between a gene object of the second gene objects and one or more gene variant objects of the second gene variant objects; and determining third connections between the first gene objects and the second gene objects (Fig. 1; [0042]-[0050]: The objects are connected 115 in order to create paths through the connected blocks such that there is a path to represent each of the plurality of known sequences from the plurality of different species).
Regarding Claim 35, Locke discloses the system of claim 34, wherein determining the first and/or second connections comprises determining
expression quantitative trait loci (eQTL) (Fig. 3; [0063]: the capabilities of a given computer, e.g., any modern consumer-grade desktop computer, are extended to allow for full operation of a genomic-scale graph (i.e., a multi-species reference graph 331 that represents all loci in a substantial portion of the genome),
gene variant regulatory elements ([0124]: As discussed above briefly in connection with FIG. 8, optionally, systems and methods of the invention may be used for variant calling 807 to produce genotype information 831 about an organism),
chromatin contact regions, and/or intragenic mapping connections (Fig. 3; [0052]: For example, conserved regions may comprise intergenic regions, intragenic regions).
Regarding Claim 36, Locke discloses the system of claim 34, wherein determining the third connections comprises determining homolog and/or orthologue connections between the first and second species ([0003]-[0005]: The graph branches into plural paths, each defined by pointers to other objects in the memory, where the genomes diverge due to either divergent homology or non-homologous portions); [0052]: the system 401 is perable to obtain a sequence generated by sequencing nucleic acid from a genome of a patient).
Regarding Claim 37, Locke discloses the system of claim 33, wherein generating the graph comprises generating a weighted undirected graph (Fig. 3; [0121]: A reference graph 331 can be given edge weights that reflect empirically derived or otherwise estimated allele frequencies in a population).
Regarding Claim 38, Locke discloses the system of claim 34, the method further comprising:
obtaining data generated by third genomic studies of a third species, the third species being different than the first species or the second species ([0004]- [0005]: Aspects of the invention provide a method for analyzing genetic information. The method includes obtaining a genetic sequence from an organism… Optionally, the method may include, prior to the aligning step: obtaining the known sequences from the plurality of different species from an online sequence database);
determining third gene objects and third gene variant objects associated with the third species ([0074]: FIG. 8 also illustrates an optional variant calling 807 step to identify a subject genotype 831);
determining fourth connections between a gene object of the third gene objects and one or more gene variant objects of the third gene variant objects; and determining fifth connections between the third gene objects and the first or second gene objects (Fig. 3; [0048]: The objects 305 are connected 115 to create paths such that there is a path for each of the original known sequences 303… The connections creating the paths can themselves be implemented as objects so that the blocks are represented by vertex objects 305 and the connections are represented by edge objects 309).
Regarding Claim 39, Locke discloses the system of claim 38, the method further comprising
identifying, using the graph and a gene variant object associated with the first species, one or more genomic studies associated with the second species ([0035]: The invention provides tools for the study of interaction at a distance in the genome and in the ways that function supervenes on spatially distant parts of the genome), wherein using the graph to identify the one or more genomic studies comprises:
identifying, using the gene variant object associated with the first species, a gene object of the first gene objects using the first connections; identifying a gene object of the second gene objects using the third connections; identifying a gene variant object associated with the second species using the second connections (Fig. 3; [0048]-[0052]: The objects 305 are connected 115 to create paths such that there is a path for each of the original known sequences 303); and
identifying the one or more genomic studies using the gene variant associated with the identified gene variant object ([0041]: A multi-species genome graph of the invention may be used for any suitable inquiry. Exemplary types of inquiries that may be addressed using a multi-species genome graph include identifying relationships among related species and newly identified species (e.g., from recent fossils).
Regarding Claim 41, Locke discloses the system of claim 39, wherein the gene variant object associated with the first species is associated with a disease, and wherein the method further comprises identifying a treatment modality for a patient having the disease using the identified one or more genomic studies ([0031]-[0033]: Graphs may be used as a tool in answering bioinformatic questions from metagenomics, phylogenetics, population genetics, comparative genomics, basic organismal biology and other fields; [0123]-[0124]: FIG. 11 illustrates a report 1101 that may be produced using systems and methods of the invention… As discussed above briefly in connection with FIG. 8, optionally, systems and methods of the invention may be used for variant calling 807 to produce genotype information 831).
Regarding Claim 42, Locke discloses the system of claim 33, wherein the first species and the second species comprise two species selected from a list including: Mus musculus, Homo sapiens, Rattus norvegicus, Danio rerio, Drosophilia melanogaster, Macaca mulatta, Caenorhabditis elegans, Saccharomyces cervisiae, Gallus gallus, and Canis familiaris ([0041]: A multi-species genome graph of the invention may be used for any suitable inquiry… An example here would be with non-homo-sapiens human species, where this kind of analysis could be used to better sequence newly discovered species… Such graphs may be sometimes intraspecies and sometimes interspecies (e.g., two species of orangutan)).
Regarding Claim 44, Locke discloses the system of claim 33, wherein transforming the subset of data into a uniform data format comprises transforming the subset of data into one or more comma-separated values (CSV) files ([0073]: As shown in FIG. 7… Reads may be stored in any suitable format).
Regarding Claim 45, Locke discloses the system of claim 33, wherein obtaining the data comprising two or more data formats comprises obtaining data comprising two or more of a gene transfer file (GTF) format, a genome variation format (GVF), browser extensible data (BED) file format, an EXCEL binary file format (XLS), a comma-separate values (CSV) file format, a tab- separated values (TSV) file format, and/or a report (RPT) file format ([0073]: As shown in FIG. 7… Reads may be stored in any suitable format.
Regarding Claim 46, Locke discloses the system of claim 33, the method further comprising regenerating the graph based on updated data, the regenerating comprising:
obtaining the updated data generated by first genomic studies of the first species and second genomic studies of the second species, the updated data comprising a plurality of datasets comprising two or more data formats (Fig. 1; [0042]-[0045]: The method 101 includes obtaining 105 a plurality of known sequences from a plurality of different species from an online sequence database; [0073]: Reads may be stored in any suitable format);
storing a subset of the updated data in a cache (Figs. 3-4; [0052]-[0056]: It should be noted that FIG. 3 depicts an example of several simplified chromosomes in order to highlight that certain regions, subsets, or portions of genomes (or combinations thereof) may be conserved across species… For example, conserved regions may comprise… subsets of these regions… Preferably the reference graph 331 is stored in the memory subsystem 475; [0060]-[0062]: Preferably, each pointer identifies a physical location in the memory subsystem);
accessing the subset of the updated data in the cache ([0061]: In the preferred embodiments, the pointer or native pointer… permits access to the intended data by means of pointer dereference) and
transforming the subset of the updated data into a uniform data format, the uniform data format describing graph objects and connections between the graph objects ([0021]: FIG. 2 shows transforming a plurality of known sequences from different species into a multi-species reference graph.; [0045]: The known sequences 303 may be retrieved from a database);
storing, in non-transient computer-readable memory, the transformed subset of the updated data in a database ([Abstract]: Genomes of different species may be embodied as a graph in which conserved parts of multiple genomes are stored at a fixed location in memory and accessed via spatial addressing); and
regenerating the graph using the database ([0003]: Newly obtained sequences such as output from NGS instruments can be mapped onto the graph for assembly or identification).
Regarding Claim 47, Locke discloses the system of claim 33, wherein determining the graph objects and the connections comprises:
determining first transcript objects associated with the first species; determining sixth connections between the first transcript objects and the first gene objects; and determining seventh connections between the first transcript objects and the first gene variant objects (Fig. 1; [0042]-[0050]: The objects are connected 115 in order to create paths through the connected blocks such that there is a path to represent each of the plurality of known sequences from the plurality of different species).
Regarding Claim 48, Locke discloses the system of claim 33, wherein determining the graph objects and the connections comprises:
determining first peak objects associated with the first species; and determining eighth connections between the first peak objects and the first gene variant objects (Fig. 1; [0042]-[0050]: The objects are connected 115 in order to create paths through the connected blocks such that there is a path to represent each of the plurality of known sequences from the plurality of different species).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHIRLEY D. HICKS whose telephone number is (571)272-3304. The examiner can normally be reached Mon - Fri 7:30 - 4:00.
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/S.D.H./Examiner, Art Unit 2168
/CHARLES RONES/Supervisory Patent Examiner, Art Unit 2168