DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Claims 1-30 are pending.
Claims 1-30 are rejected.
Claims 2, 6, 11-14, 16-17, 21, and 26-29 are objected to.
Priority
Applicant’s claim for the benefit of a prior-filed application, PCT/EP2020/077158 filed 28 Sept. 2020 and U.S. Provisional App. No. filed 01 Oct. 2019 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Accordingly, the effective filing date of the claimed invention is 01 Oct. 2019.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 21 March 2022, 01 Oct. 2024, and 15 May 2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered in full by the examiner.
Drawings
The drawings filed 21 March 2022 are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description:
#662 in FIG. 6.
Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
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 filed 18 July 2022 is objected to because:
The abstract contains 237 words, which is over 150 words.
A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Objections
Claims 2, 6, 11-14, 16-17, 21, and 26-29 are objected to because of the following informalities:
Independent claim 16 recites “…instructions for instructions for identifying variations…”, which is a typographical error and should have the duplicate “instructions for” removed.
Claims 2 and 17 recite “…generating for each generated edge graph a length…”, which is grammatically incorrect, and should be amended to include commas on either side of “for each generated edge graph”, thus reciting “generating, for each generated edge graph, a length…”.
Claims 2 and 17 recite “generating for each generated graph edge…of the sequence”, which should be amended to recite “the sequence of the current edge”, to increase clarity and use consistent language with claim 1.
Claims 6 and 21 recite “a position indicating…a chromosome identifier; the edge identifier, and a base position”, which recites a list separated by both a “;” (after chromosome identifier) and “,” (after edge identifier). The claims should be amended to consistently use commas in the list, thus reciting “a position indicating…a chromosome identifier[[;]], the edge identifier, and a base position”.
Claims 11 and 26 recite “adding the additional data fields: the edge identifier…”, which is grammatically incorrect and should recite “adding the additional data fields of: the edge identifier…”, or a similar amendment.
Claims 12 and 27 recite “adding the additional data fields: a trail…”, which is grammatically incorrect and should recite “adding the additional data fields of: a trail…”, or a similar amendment.
Claims 13 and 28 recite “adding the additional data fields: a coordinate_scheme field…” which is grammatically incorrect and should recite “adding the additional data fields of: a coordinate_scheme…”, or a similar amendment. Furthermore, each limitation pertaining to the additional data fields being added (i.e. a coordinate_scheme field” and “ a trail field”) should be indented further relative to the step of “adding the additional data fields” to increase readability.
Claims 13 and 28 recite “a trail field in each genomic record to indicate for each alignment position in mapping_pos the sequence of edge transitions to which all template segments in the same record are aligned”, which is grammatically incorrect and should include a comma between “mapping_pos” and “the sequence of edge transitions”, to recite “in mapping_pos, the sequence…”.
Claims 13 and 28 recites the steps of “adding the additional data fields….; using the MPEG-G file…”, which should be separated by an “and”, such that the claims recite “a trail field…are aligned; and using the MPEG-G file…”.
Claims 13 and 28 recite various substeps after the “using the MPEG-G file data field” step, which should be indented further with respect to the “using the MPEG-G” step to increase readability.
Claims 14 and 29 recite “from one of the endpoints of specified edge”, which is grammatically incorrect and is missing an article, “the”, before “specified edge” to refer to the previously recited “a specified edge”.
Claims 14 and 29 recite “…using a number of bases in between connecting nodes as distance”, which is missing an article before “distance”, and should recite “as a distance”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 2-3, 5-8, 10-15, 17-18, 20-23, and 25-30 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claims 2 and 17, and claims dependent therefrom, recite “storing the length in the data storage”. However, claims 2 and 17 previously recite “generating for each generated graph edge a length indicating the length of the sequence”. Therefore, it is unclear if “the length” being stored in claims 17 is intended to refer to the length for a single generated graph edge or refer to the length for each generated graph edge. If Applicant intends for the length to refer to the length of a single generated graph edge, it is further unclear what edge “the length” corresponds to. For purpose of examination, the limitation is interpreted to mean the length for each generated graph edge is stored.
Claims 5 and 20 are indefinite for recitation of “concatenating the sequences for each of the generated edges and storing them in a sequence data structure…”. Thus, claims 5 and 20 involve concatenating sequences for each of the generated edges, thus forming a concatenated sequence, and then later stores “them” in a data structure. It is unclear if “storing them” in claims 5 and 20 is intended to: (1) require storing the resulting concatenated sequence in the data structure (i.e. storing a singular concatenated sequence), given the claim has a single concatenating step; (2) if claims 5 and 20 intend to simply store “the sequences for each of the generated edges” after concatenation; or (3) if the claims intend to store multiple concatenated sequences, as suggested by the use of the plural “them”. If Applicant intends for a single concatenated sequence for all edges to be stored, given the edges include branching sequences representing variants of a graph reference, it is further unclear in what way this would be performed. Clarification is requested via claim amendment to specify what element or elements “them” is referring to. It is noted that Applicant’s specification discloses the sequences of edges belonging to a same group representing an individual sample may be concatenated and stored as one merged sequence ([0031]; [0051]). Therefore, for purpose of examination, claims 50 and 20 will be interpreted to mean multiple concatenated sequences are stored.
Claims 6 and 21, and claims dependent therefrom, are indefinite for recitation of “the path is defined by:…a position indicating the starting point of the path including a chromosome identifier, the edge identifier…”. However, claims 1 and 16, from which claims 6 and 21 respectively depend, recite “…generating for each generated graph edge: an edge identifier”, such that there are multiple edge identifiers (i.e. one for each generated edge). As a result, it is unclear which edge identifier “the edge identifier” in claims 6 and 21 are referring to, given a path may include multiple edges in a graph as stated in the following limitation “a trail including a cascade of edge identifiers traversed by the path”. Clarification is requested via claim amendment. For purpose of examination, “the edge identifier” will be interpreted to mean “an edge identifier”.
Claims 8 and 23 are indefinite for recitation of “assumptions of the default priorities of the next edges”. There is insufficient antecedent basis for this limitation in the claims because claims 6 and 21, from which claims 8 and 23 respectively depend, do not recite any default priorities of next edges. In addition it is unclear what set of edges, “the next edges” is referring to with respect to the trail of edge identifiers. For example, are the next edges within the trail and “next” with respect to an edge identifier within the trail or are the edge identifiers of edges after the trail. Furthermore, would “the next edges” refer to the next 2 edges or all following/next edges. Last, the metes and bounds of “assumptions of default priorities” are unclear because it is not clear in what way a default priority is “assumed” rather than simply assigned. Clarification is requested. For purpose of examination, the limitation is interpreted to mean edge identifiers are removed based on priorities of next edges.
Claims 10 and 25 are indefinite for recitation of “identifies a group of edges from a same origin, such as an individual sample”. The phrase "such as" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d). Specifically, it is unclear if the “same origin” is required to be an individual sample or not. For purpose of examination, the limitation following “such as” are not interpreted to be part of the same invention, and thus the “same origin” is interpreted to be any same origin.
Claims 11 and 26 are indefinite for recitation of “…the beginning of the read is aligned” in line 3. There is insufficient antecedent basis for “the read”, because the claims do not previously recite any particular read. While it is noted claims 11 and 26 refer to “a sequence read alignment file (SAM)”, a SAM file includes alignment information for all reads in any given sequencing experiment, and thus it is not clear which read “the read” would be referring to. For purpose of examination, the limitation is interpreted to mean “the beginning of a read is aligned”.
Claims 11 and 26 are indefinite for recitation of “the next read of the template” because the claims do not previously recite a next read or a template, and thus it is unclear what template and what read are being referenced. For purpose of examination, the limitation is interpreted to mean “a next read of a template”.
Claims 11 and 26 are indefinite for recitation of “a trail indicating the delimited sequence of edge transitions taken by the path to which the read is aligned” and also “the delimited sequence of edge transitions taken by the path to which the next read of the template is primarily aligned”. As discussed above, it is not clear what read “the read” or “the next read” is referring to, and similarly what template “the template” is referring to. Furthermore, there is insufficient antecedent basis for “the delimited sequence of edge transitions” and “the path” in the claims. Claims 1 and 16, from which claims 11 and 26 depend, do not recite “a delimited sequence” or a path, let alone a path in which a read was aligned. For purpose of examination, the limitation is interpreted to mean “a trail indicating a delimited sequence of edge transitions taken by a path to which a read is aligned”.
Claims 12 and 27 are indefinite for recitation of “a trail indicating sequence of edge transitions that lead to the location of the variant”. There is insufficient antecedent basis for “the variant” in the claims, and as a result, “the location of the variant”, because the claims do not previously recite any particular variant. While claims 12 and 27 do recite “a variant call file (VCF)”, given a VCF files contains information on all variants called in a given sequencing experiment, it is unclear what variant, “the variant” is referring to. Furthermore, the claims are missing an article of “a” or “the” before “sequence of edge transitions”, and thus it is not clear if the limitation means “a trail indicating a sequence of edge transitions” (i.e. any sequence of edges leading to the variant) or if the limitation means “the sequence of edge transitions…”. If Applicant intends for the claims to recite “the sequence of edge transitions”, it would further be unclear what sequence of edge transitions leading to the variant are being referenced, given different paths (i.e. different edge sequences) in a graph genome may lead to a variant. For purpose of examination, the claims are interpreted to mean “a trail indicating a sequence of edge transitions that lead to the location of a variant”.
Claims 12 and 27 are indefinite for recitation of “…a distance…from the upstream anchor point to the variant”. First, “the variant” is indefinite for the same reasons discussed above. Furthermore, there is insufficient antecedent basis for “the upstream anchor point” in the claim, because claims 1 and 16, from which claims 12 and 27 depend, do not previously recite any anchor point, let alone an upstream anchor point. For purpose of examination, the limitation is interpreted to mean “a distance…form an upstream anchor point to a variant”.
Claims 13 and 28 are indefinite for recitation of “…the genomic coordinates” in the 3rd and 4th line respectively. There is insufficient antecedent basis for this limitation in the claim, because claims 1 and 16 do not previously recite the term genomic coordinates. As a result, it is unclear what genomic coordinates are being referenced.
Claims 13 and 28 are indefinite for recitation of “a trail field in each genomic record to indicate for each alignment position in mapping_pos[,] the sequence of edge transitions to which all template segments in the same record are aligned”. First, the claims do not recite any “genomic records” and therefore it is unclear what set of genomic records are required to have “a trail field” as claimed. Similarly, because the claims do not previously recite any alignment positions, let alone any alignment positions in mapping_pos, it is unclear what set of alignment positions “each alignment position in mapping_pos” is referring to. Last, there is insufficient antecedent basis for “the same record”, and it is unclear what record “the same record” is referring to. For example, it is unclear if “the same record” is referring to a same genomic record, or if this is intending to refer to some other same record (e.g. all template segments in a same SAM record are aligned). Clarification is requested via claim amendment.
Claims 13 and 28 are indefinite for recitation of, “the first read” and “the beginning edges of any split segment alignments”. There is insufficient antecedent basis for any of these limitations in the claim, given claims 1 and 16, from which claims 13 and 28 depend do not previously recite a first read or beginning edges of split segment alignments. As a result, it is unclear what read, “the first read” is referring to, and what set of edges “the edges” are referring to.
Claims 14 and 29 are indefinite for recitation of “…determining anchor points on a specified edge by extending a MPEG-G file by running Dijkstra’s algorithm…”. Overall, the relationship between the steps of “determining anchor points”, “extending a MPEG-G file” and “running Dijkstra’s algorithm” are unclear. First, it is unclear if “by running Dijkstra’s algorithm” is modifying the step of “determining anchor points” or “extending a MPEG-G file”. One of ordinary skill in the art understands Dijkstra’s algorithm to be an algorithm for finding the shortest path between nodes in a graph. Therefore, while it is understood in which anchor points of an edge can be identified using Dijkstra’s algorithm, it is unclear in what way the MPEG-G file is intended to be extended “by running Dijkstra’s algorithm”. Second it is further unclear in what way the anchor points are intended to be determined by “extending a MPEG-G file”. It is noted that Applicant’s specification at para. [0056]-[0057] explains that the GetAnchorInfo function finds the anchor points and the corresponding shortest paths by running Dijkstra’s algorithm, and then that the proposed coordinate system and data structure may be used to extend existing genomic data formats based on linear coordinates to support graph genome references with simple modifications, suggesting the determined anchor points are used to extend the MPEG-G file, while Dijkstra’s algorithm is used to identify the anchor points. For purpose of examination, the claims will be interpreted accordingly.
Claims 14 and 29 are indefinite for recitation of “among all leaf nodes, except for those that cannot be extended further”. The metes and bounds of the claims are unclear because it is not clear which leaf nodes can or cannot be extended further. Given a leaf node is understood to refer to an end-most node in a tree (nodes that presumably cannot be extended, given the designation “leaf” node), it is unclear what nodes, “leaf nodes, except those that cannot be extended further”, are referring to . Clarification is requested. For purpose of examination, the limitation is interpreted to mean “with a shortest distance among leaf nodes”.
Claims 15 and 30 are indefinite for recitation of “along a path in the genome sequence”. There is insufficient antecedent basis for the genome sequence in the claims, because claims 1 and 16 do not previously recite “a genome sequence”. Furthermore, because claims 1 and 16 recite both “a reference genome” and “a first genome”, in addition to “a genomic graph” in the preamble, it is further unclear if “the genome sequence” is intending to refer to the sequence of the reference genome, the first genome, or the genomic graph. Clarification is requested.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-30 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1 and 16 being representative) is directed to a method and product. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claims 1 and 16 recite the following steps which fall under the mental processes grouping of abstract ideas:
identifying variations in the first genome from the reference genome;
generating graph edges for each variation in the first genome from the reference genome;
generating for each generated edge graph:
an edge identifier that uniquely identifies the current edge in the genome graph;
a start edge identifier that identifies the edge from which the current edge branches out;
a start position that indicates the position on the start edge that serves as an anchoring point for the current edge;
an end edge identifier that identifies the edge into which the current edge joins in;
an end position that indicates the position on the end edge that serves as an anchoring point for the current edge;
a sequence indicating the nucleotide sequence of the current edge.
The identified claim limitations falls into one of the groups of abstract ideas of mental processes, for the following reasons. First, identifying variations in the first genome relative to the reference merely requires comparing two sequences to identify a different in sequences, similar to the claims to "comparing BRCA sequences and determining the existence of alterations," where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014). Furthermore, generating graph edges for each identified variation can be practically performed in the mind aided with pen and paper by identifying the corresponding location of a given variant in the reference genome, and drawing a separate edge from the location way from a reference base, to produce a bubble within the graph indicating the presence of the given variant. Generating the recited identifiers and data for each generated edge involves merely collecting and analyzing information pertaining to the reference genome locations/sequences and the variant for each edge to record a unique identifier, where the respective edge branches from, wherein the edge starts, where the edge ends, and the sequence corresponding to the edge. That is, other than reciting the steps are carried out by a processor in claim 16, nothing in the claims precludes the steps from being practically performed in the mind. Therefore, these limitations recite a mental process. See MPEP 2106.04(a)(2) III.
Dependent claims 2, 5-15, 17, 20-25, and 29-30 further recite an abstract idea and/or further limit the abstract idea identified above. Dependent claims 2 and 17 further recite the mental process of generating, for each generated graph edge, a length indicating the length of the sequence. Dependent claims 5 and 20 further recite the mental process of concatenating the sequences for each of the generated edges. Dependent claims 6 and 21 further recite specifying a path in the genome graph, wherein the path is specified/defined by a position, a path length, and a trail, as claimed. Dependent claims 7 and 22 further limit the mental process of specifying the path to use a branch-out delimiter and an endpoint delimiter (e.g. 2; 3; 5-7). Dependent claims 8 and 23 further recite the mental process of simplifying the trail by removing edge identifiers from the trail based upon assumptions of default priorities of next edges. Dependent claims 9-10 and 24-25 further limit the mental process of generating the edge identifier for each edge, to include a group identifier and an edge index, wherein the group identifier identifies a group of edges from a same source origin. Dependent claims 11 and 26 further recite the mental process of adding additional data fields including the edge identifier, an ENEXT identifier, a trail indicating the delimited sequence of edge transitions taken by the path the read is aligned, and TNEXT indicating the delimited sequence of edge transitions taken by the path to which the next read is aligned. Dependent claims 12 and 27 further recite the mental process of adding additional data fields of a trail indicating a sequence of edge transitions and a distance between the upstream anchor point to the variant. Dependent claims 13 and 28 further recite the mental process of adding the data fields of a coordinate_scheme field indicting how to interpret genomic coordinates, a trail field to indicate the sequence of edge transitions, and a seq_ID indicating a position a first read is mapped, and further recite using (i.e. analyzing) data fields including the seq_ID indicating where a first read is mapped, a split_seq_ID indicating a beginning edges of any split segment alignments, and the positions mapping_pos and split_pos from the beginning of the edges in seq_ID and split_seq_ID. Overall, the limitations pertaining to adding data fields in claims 11-13 and 26-28 involve a mental analysis of information pertaining to a the graph reference and aligned reads to determine the additional data fields (e.g. the edge where a read starts, the edge transitions to the variant, a distance, etc.). Dependent claims 14 and 28 further recite the mental process of determining anchor points by running Dijkstra’s algorithm from one endpoint of the specified edges using a number of bases between nodes as a distance until the specified edge is on a tree with a shortest distance among leaf nodes. Dependent claims 15 and 30 further recite the mental process of determining a sequence along a path in a genome sequence comprising traversing a trail including edge identifiers defining the path and concatenating the sequences of the edges identified along the path. Therefore, claims 1-30 recite an abstract idea. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Claims 6-10, 15, 21-25, and 30 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements of claims 1 and 16 include:
a non-transitory machine-readable storage medium (claim 16 only);
storing a linear representation of a reference genome in a data storage;
receiving a first genome;
storing the edge identifier, start edge identifier, start position, end edge identifier, end edge position, and sequence for each generated graph edge in the data storage.
The additional elements of claims 2-5, 11-14, 17-20, and 26-29 include:
storing the length in the data storage (claims 2 and 17).
wherein the edge identifier, start edge identifier, start position, end edge identifier, end edge position, sequence, and length for each generated graph edge are stored as a row in a data table (claims 3 and 18);
wherein the edge identifier, start edge identifier, start position, end edge identifier, end edge position, and sequence, for each generated graph edge are stored as a row in a data table (claims 4 and 19);
extending a sequence read alignment file (SAM) (claims 11 and 26);
extending a variant call file (VCF) (claims 12 and 27)
storing them in a sequence data structure separate from the data table (claims 5 and 20);
extending a MPEG-G file (claims 13-14 and 28-29).
The additional elements of a non-transitory machine-readable medium storing instructions, and simply storing the various data in a data storage (e.g. memory) are generic computer components and functions. Dependent claims 2-4 and 17-19 further limit the data being stored. Dependent claims 5 and 20 similarly require broadly storing sequences in a separate data structure. The additional elements of extending various data files (SAM, VCF, and MPEG-G) in dependent claims 11-14 and 26-29, also only store additional data in the various file types. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
Further regarding the extension of the SAM, VCF, and MPEG-G files in claims 11-13 and 26-28, the claims only serve to store additional information pertaining to reads aligned to a graph reference in the files. However, these additional elements do not appear to actually improve any particular technology, such as improving computer memory requirements for storing a graph genome and/or improved computer data structures, and instead only serve to record information generated by the abstract idea.
Therefore, the additionally recited elements amount to mere instructions to apply an exception, and, as such, the claims as a whole do no integrate the abstract idea into practical application.
Thus, claims 1-30 are directed to an abstract idea. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
Claims 6-10, 15, 21-25, and 30 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements of claims 1 and 16 include:
a non-transitory machine-readable storage medium (claim 16 only);
storing a linear representation of a reference genome in a data storage;
receiving a first genome;
storing the edge identifier, start edge identifier, start position, end edge identifier, end edge position, and sequence for each generated graph edge in the data storage.
The additional elements of claims 2-5, 11-14, 17-20, and 26-29 include:
storing the length in the data storage (claims 2 and 17).
wherein the edge identifier, start edge identifier, start position, end edge identifier, end edge position, sequence, and length for each generated graph edge are stored as a row in a data table (claims 3 and 18);
wherein the edge identifier, start edge identifier, start position, end edge identifier, end edge position, and sequence, for each generated graph edge are stored as a row in a data table (claims 4 and 19);
extending a sequence read alignment file (SAM) (claims 11 and 26);
extending a variant call file (VCF) (claims 12 and 27)
storing them in a sequence data structure separate from the data table (claims 5 and 20);
extending a MPEG-G file (claims 13-14 and 28-29).
The additional elements of a non-transitory machine-readable medium storing instructions, and simply storing the various data in a data storage (e.g. memory) are conventional computer components and functions. Dependent claims 2-4 and 17-19 further limit the data being stored. Dependent claims 5 and 20 similarly require broadly storing sequences in a separate data structure. The additional elements of extending various data files (SAM, VCF, and MPEG-G) in dependent claims 11-14 and 26-29, also only store additional data in the various file types. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Therefore, the additional element is not sufficient to amount to significantly more than the judicial exception.
Regarding the steps of extending a MPEG-G file, VCF file, and SAM file, these limitations require storing additional information in particular file formats. However, storing information in these file formats was well-understood, routine, and conventional before the effective filing date of the claimed invention in view of Applicant’s specification and Hernaez et al. (Genomic Data Compression, March 2019, Annu. Rev. Biomed. Data Sci. 2, pg. 19-37). First, Applicant’s specification at para. [0029] discloses existing genomic data file formats used for genomic data, including SAM files, VCF files, and MPEG-G files, demonstrating the conventionality of storing data in such formats. Hernaez reviews general guidelines for storing genomic data (Abstract), and discloses that MPEG-G is a new open standard for genomic information representation (pg. 32, para. 4). Hernaez also discloses that genomic data is still largely stored using compressed algorithms such as gzip for SAM files (pg. 32, para. 3) and GTC is a current-state of the art for compressing genotype information contained in VCF files (pg. 31, para. 3), which demonstrates the conventionality of SAM and VCF files for storing genomic information.
Therefore, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-2, 6-10, 15-17, 21-25, and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Semenyuk (2018) in view of Rand (2017).
Cited references:
Semenyuk, US 2018/0373839 A1; cited in IDS filed 21 March 2022; and
Rand et al., Coordinates and intervals in graph-based reference genomes, 2017, BMC Bioinformatics, 18:263, pg. 1-8; cited in IDS filed 21 March 2022.
Regarding claims 1 and 16, Semenyuk discloses a method for encoding information of a genomic graph, and a non-transitory memory for carrying out the method, (Abstract; [0069]), wherein the method comprises the following steps:
Semenyuk discloses incorporating a first reference sequence as a backbone branch ([0088]), wherein the backbone branch represents a particular linear reference sequence ([0085]; FIG. 10, linear backbone branch #102). Semenyuk discloses the reference sequence is stored in memory ([0155]; [0159]).
Semenyuk discloses subsequent sequences representing variations from the reference can be inserted as new branches connected to the backbone branch (i.e. identifying variations…from the reference genome) ([0085]; [0088]; FIG. 10), thereby generating graph edges for each variation.
Semenyuk discloses generating, for each graph edge ([0068]), the following:
Semenyuk discloses a unique identifier for the edge ([0068]; [0071]) and an associated identifier indicating the order in which the edges were added (i.e. a start and end edge identifier identifying the edge from which the current edge branches out) ([0071]).
Semenyuk discloses edges are described by a starting coordinate and an end coordinate ([0009]). Semenyuk discloses the starting coordinate of the edge includes an offset, branch pair (i.e. a start position, edge pair) that identifies a particular start position and edge from which the current edge starts (branches out) (i.e. a start edge identifier and start position) ([0076]; FIG. 6; [0089], e.g. offset, branch pairs separated by period; [0092], e.g. complicate coordinate system that identifies a particular offset/position and the edge; [0095], e.g. coordinate 1.21; [0140], e.g. start coordinate 10.2.5 indicating start at edge 5);
Semenyuk discloses the end coordinate of the edge representing an offset, branch pair that identifies a particular end position and end edge from which the current edge joins (i.e. an end edge identifier and end position) ([0009], e.g. end coordinate in addition to start coordinate; [0089]; [0100], e.g. coordinate 3.2.2. [0140], e.g. end coordinate at 10.2.7, with start coordinate of 10.2.5; FIG. 10)
Semenyuk discloses the nucleotide sequence of the edge ([0076]; FIG. 6, #601 “A”).
Semenyuk discloses storing the identifiers, start and end coordinates including the offset branch pairs (i.e. the start/end edge identifiers and start/end positions), and sequence in the data storage ([007]-[0008], e.g. graph built within memory [0155]; [0159]; FIG. 6)
Regarding claims 1 and 16, Semenyuk does not disclose the following limitations:
Regarding claims 1 and 16, Semenyuk does not explicitly disclose the process of generating the graph includes receiving a fist genome, or that the identified variations from the reference are in the first genome.
However Rand discloses a coordinates system for storing graph-based reference genomes (Abstract), and discloses that the GRCh38 reference genome contains alternate loci and regions with significantly different sequences between individuals, and can be represented as a graph reference. Rand discloses the sequence graph represents genomes from one or more individuals along with their variation data (pg. 1, col. 2, para. 3 to pg. 2, col. 1, para. 1), which demonstrates a first genome of an individual is received and variations in a graph reference are with respect to an individual’s genome. Rand discloses this allows for the representation of features from an individual that are very different from a linear reference genome (pg. 1, col. 2, para. 2).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the method of Semenyuk to have obtained an individual’s genome and included variants in the genome relative to the reference as edges in a graph reference, as shown by Rand (pg. 2, col. 1, para. 1). One of ordinary skill in the art would have been motivated to combine the methods of Semenyuk and Rand to represent features of an individual that are not represented in a linear reference genome, as shown by Rand (pg. 1, col. 2, para. 2). This modification would have had a reasonable expectation of success given Semenyuk discloses sequences representing variations from the reference are inserted as new branches connected to the backbone branch (linear reference) ([0085]; [0088]; FIG. 10), such that the addition of variants of an individual into a reference graph as shown by Rand is applicable to the method of Semenyuk.
Regarding the dependent claims:
Regarding claims 2 and 17, Semenyuk discloses generating a length of the sequence for each edge ([0076]; FIG. 6, #601 “1”). Semenyuk discloses the length is stored in memory (FIG. 6; [0155]; [0159]).
Regarding claims 6 and 21, Semenyuk discloses specifying a path in the genome graph to identify a position in the reference genome relative to a source vertex ([0095]; [0098]), wherein the path is defined by the following.
Semenyuk discloses defining an initial offset, which is identified based on a base position in a chromosome of a genome in addition to an edge identifier of the position (i.e. a position including a chromosome identifier, an edge identifier, and a base position) ([0093], e.g. “a SNP on chromosome 1 at position 203,422,877 could be identified by the coordinates: 203422877.2, representing a traversal that position along a second outgoing edge (2)”.
Semenyuk discloses defining the length of the associated nucleotide sequence of the path ([0074], e.g. longest path identified; [0140]).
Semenyuk discloses defining a path by a trail of coordinates containing edge identifiers traversed by the path, wherein the coordinates may be combined by delimiters ([0090], e.g. coordinate 1.2 uses edge identifier 2 [0098], [0100]; FIG. 10, e.g. 0..1.2.1; [0130], e.g. see path with coordinate components).
Regarding claims 7 and 22¸ Semenyuk discloses using a delimiter “..” to combine a start and end coordinate defining a path including branches (i.e. a branch-out delimiter) ([0098], and a delimiter “.” which is used in the end coordinate (i.e. an endpoint delimiter) ([0089]; [0009]; [0140], e.g. 10.2.7).
Regarding claims 8 and 23, Semenyuk discloses simplifying the path (i.e. trail) by omitting the second integer in a coordinate representing a diverging branch (i.e. removing an edge identifier) if no divergent paths from the current branch are required to reach the desired position (i.e. a priority of next edges to reach a position) ([0091]).
Regarding claims 9 and 24¸ Semenyek discloses the edge identifier includes an edge index that uniquely identifies an edge ([0068]).
Semenyuk does not disclose the edge identifier includes a group identifier wherein the group identifier identifies a group of related edges.
Regarding claims 10 and 25¸ Semenyuk further does not disclose the group identifier identifies a group of edges from a same origin.
However, regarding claims 9-10 and 24-25, Rand discloses a coordinates system in graph-based reference genomes (Abstract), and defines each edge of a graph reference genome based on a “region identifier” (i.e. group identifier identifying edges from a same origin/region) and an offset that is counted from the start of the region in addition to offsets counted from the beginning of each region (pg. 2, col. 2, para. 3; FIG. 1). Rand discloses this class of coordinate systems has intuitive and readable coordinates and makes determining a distance between two coordinates with a same region simple (pg. 2, col. 2, para. 3).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the method of Semenyuk to have utilized group identifiers with each edge identifier, as shown by Rand (pg. 2, col. 2, para. 3; Fig. 3). One of ordinary skill in the art would have been motivated to combine the methods of Semenyuk and Rand in order improve readability and intuitiveness of the graph reference genome and facilitate simple analysis of edges within a same region, as shown by Rand (pg. 2, col. 2, para. 3). This modification would have had a reasonable expectation of success given Semenyuk also uses edge identifiers in a graph reference genome, such that the group identifier of Rand is applicable to the edges of Semenyuk.
Regarding claims 15 and 30, Semenyuk discloses converting a portion of the genomic graph into a linear string of bits representing a plurality of edges in a path ([0016]; [0072]), by traversing the graph to identify a linear path of edges for encoding and removal ([0072]), and then the remaining set of linear edges are selected together as a single edge for serialization and encoding, forming a single concatenated sequence ([0077]; FIG. 8, e.g. see linear sequence).
Therefore, the invention is prima facie obvious.
Claims 3-5 and 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Semenyuk in view of Rand, as applied to claims 1-2 and 16-17 above, and further in view of Duke 2014.
Cited reference: Duke, Graph Data, 2014, Everything Data CompSci 290.01, pg. 1-35.
Regarding claims 3-4 and 18-19, Semenyuk in view of Rand disclose the method and product of claims 1-2 and 16-17 as applied above.
Further regarding claims 3-4 and 18-19, Semenyuk in view of Rand, as applied to claims 1-2 and 16-17 above, does not disclose the edge identifier, start edge identifier, start position, end edge identifier, end edge position, sequence, and length for each generated graph edge are stored as a row in a data table. Instead, Semenyuk discloses in embodiment in which the graph may be stored using adjacency lists ([0159]).
However, Duke overviews graph data structures including nodes and edges connecting two nodes (pg. 3 and 8), and then discusses various methods of representing graphs on a computer (pg. 31-35). Duke discloses graph data structures may be stored in a relational representation by storing edges in a table, with rows providing information on the edge, including a source node, a target node, and edge properties. (pg. 32).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Semenyuk to have stored the edges and various edge properties as a row in a data table, as shown by Duke (pg. 32). One of ordinary skill in the art would have been motivated to combine the method of Semenyuk and Duke based on the simple substitution of the known adjacency lists of Semenyuk and with the known element of a relational table storing edge and edge properties as rows, as shown by Duke (pg. 32). Given the functions of both the adjacency lists and relational table are to store a graph data structure, as shown by Semenyuk and Duke, one of ordinary skill in the art would have recognized the results of the substitution would predictably result in the storage of the graph reference genome edges using a relational table.
Regarding claims 5 and 20, Semenyuk further discloses a process of copying portions of a genome graph and moving the portions to another location, resulting in rapid transfer and compact storage of portions of the reference in computer systems ([0007]). Semenyuk discloses the process involves converting a portion of the genomic graph into a linear string of bits representing a plurality of edges in a path ([0016]; [0072]), by traversing the graph to identify a linear path of edges for encoding and removal ([0072]), and then the remaining set of linear edges are selected together as a single edge for serialization and encoding into a string of bits, forming a concatenated sequence for the portion ([0007]; [0077]; FIG. 8, e.g. see linear sequence). Semenyuk discloses this process can be performed on all portions of a graph to create a serialized data structure for each portion ([0007]), demonstrating each generated edge is concatenated to a larger sequence for a portion of the graph and stored in a sequence data structure (e.g. the serialized data structure) separate from the stored reference graph (the data table), given the portions are copied ([0007]).
Therefore, the invention is prima facie obvious.
Claims 11 and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Semenyuk in view of Rand, as applied to claims 1 and 16 above, and further in view of Zarate (2017).
Cited references: Quiroz Zarate et al., WO 2017024138 A1 (hereinafter, Zarate).
Regarding claims 11 and 26, Semenyuk in view of Rand disclose the method and product of claims 1 and 16, as applied above.
Further regarding claims 11 and 26, Semenyuk in view of Rand, as applied to claims 1 and 16 above, do not disclose: extending a sequencing read alignment file (SAM) by adding the additional data fields: the edge identifier of the specific edge to which the beginning of the read is aligned; an ENEXT identifier of the specific edge to which the next read of the template is primarily aligned; a trail indicating the delimited sequence of edge transitions taken by the path to which the read is aligned; and TNEXT indicating the delimited sequence of edge transitions taken by the path to which the next read of the template is primarily aligned.
However, Zarate provides a method for aligning sequence reads with a graph reference ([007]), which comprises characterizing the graph alignment of the read by reporting additional information in the form of read tags in a SAM format (i.e. extending a SAM file by adding additional data fields), by adding a read tag indicating the start and end of the aligned read relative to a coordinate of a variant path in the graph (i.e. an edge identifier of the specific edge to which the beginning of the read is aligned) and a read tag detailing the alternate paths the read passed through, an alternate path referring to non-reference sequences or bubbles on the graph (e.g. edges) (i.e. a trail indicating a delimited sequence of edge transitions taken by a path a read is aligned) ([0033]-[0034]; [00144]; [00196]; FIG. 5, e.g. see VL tag indicating alternate paths the read crossed). Zarate discloses these read tags are provided for each read ([00144]), which shows the recited ENEXT identifier and TNEXT identifier (e.g. an identifier of the specific edge for a next read and a sequence of edge transitions taken by a path for the next read).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Semenyuk in view of Rand, as applied to claims 1 and 16 above, to have extended a SAM file with the additional data fields of Zarate, as discussed above, thus arriving at the invention of claims 11 and 26. One of ordinary skill in the art would have been motivated to combine the methods of Semenyuk in view of Rand with Zarate, in order to write alignment information of a graph reference in a SAM format that is compatible with the SAM format reads aligned to a linear reference, while conveying additional information, as shown by Zarate ([00144]). This modification would have had a reasonable expectation of success given Semenyuk discloses the graph reference can be used for read alignment ([0097]), such that the generated file format and data fields of Zarate are applicable to Semenyuk.
Last, while Zarate does not explicitly disclose identifiers named “ENEXT” or “TNEXT”, the specific data field names are interpreted as a matter of design choice, and Applicant has not disclosed that this feature provides an advantage, is used for a particular purpose, or solves a stated problem when compared to using tag names such as “NL”, “VL”, VN”, etc. to provide the information regarding a start edge and a trail of edges for each read, as shown by Zarate (FIG. 5; [0144]; [0196]). Therefore, the above data fields of Zarate would perform equally as well in representing the various data fields specifying an identifier of a start edge and sequence of edges, and such a modification fails to patentably distinguish over Zarate.
Therefore, the rejection is prima facie obvious.
Claims 14 and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Semenyuk in view of Rand, as applied to claims 1 and 16 above, and further in view of Brown (2017) and Alberti (2018).
Cited references:
Brown, US 20170242958 A1; cited in IDS filed 21 March 2022; and
Alberti et al., An introduction to MPEG-G, the new ISO standard for genomic information representation, 2018, bioRxiv, pg. 1-18.
Regarding claims 14 and 29, Semenyuk in view of Rand disclose the method and product of claims 1 and 16 as applied above.
Further regarding claims 14 and 29, Semenyuk in view of Rand, as applied to claims 1 and 16 above, do not disclose determining anchor points on a specified edge by extending a MPEG-G file by running Dijkstra's algorithm beginning from one of the endpoints of a specified edge using a number of bases in between connecting nodes as distance until the specified edge is on a spanning tree with a shortest distance among all leaf nodes, except for those that cannot be extended further.
However, these limitations were obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention as shown by Brown and Alberti below.
First, regarding claims 14 and 29, Brown discloses a method for traversing a graph reference genome to determine a genotype of an organism by mapping reads to the reference graph (Abstract), which comprises applying Dijkstra’s algorithm by identifying a starting node (i.e. one of the endpoints of an edge), determining a distance of a node from the initial node based on a length of the edges connecting the nodes (i.e. a number of bases, given the length of an edge is the sequence length in Semenyuk para. [0076]), and then finding a shortest path between two nodes in the graph by iteratively visiting unvisited nodes ([0051]). Brown discloses the algorithm steps if a destination node is already marked as visited or if the smallest tentative distance among nodes in the unvisited set is infinity, meaning there is no connection between the initial and remaining unvisited node (i.e. the specified edge is on a tree with a shortest distance among leaf nodes) ([0051]). The two ends of the identified shortest path are interpreted as the determined “anchor points”. Brown discloses this algorithm is used to map a read to the reference graph ([0057]; claims 10-11). Brown discloses Dijkstra’s algorithm allows for genotyping larger portions of a reference graph, such as multiple deletions, comprising multiple consecutive positional nodes ([0053]).
Further regarding claims 14 and 29, Alberti overviews a compressed data format enabling large scale genomic data to be processed, called MPEG-G (Abstract). Alberti discloses MPEG-G formats store aligned reads (pg. 2, para. 2), and includes genomic records split across descriptor streams, including mapping positions (e.g. the anchor points), numbers of substitutions, and read lengths (pg. 3, para. 3; pg. 5, para. 7, e.g. “start to end mapping position”, Figure 1), access unit headers containing metadata describing the genomic data encoded in blocks, such as genomic regions the reads are mapped to, and data structures containing SAM (e.g. sequence read alignment file) auxiliary fields (pg. 3, para. 5 to pg. 4, para. 1; Figure 2). Alberti further discloses the MPEG-G file overcomes shortcomings with widely used formats to represent genomic information, such as SAM/BAM files), and allows for genomic data to be accessed, processed, and shared, as simply as streaming an audio file or watching a movie, and stored with reduced file size (pg. 8, para. 1-3).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the method of Semenyuk in view of Rand, as applied to claims 1 and 16 above, to have determined anchor points on an edge using Dijkstra’s algorithm with a number of bases connecting nodes as a distance, as shown by Brown ([0051]). One of ordinary skill in the art would have been motivated to combine the methods of Semenyuk in view of Rand and Brown in order to genotype a large portion, such as a multiple deletion, of a reference graph in a read mapping, as shown by Brown ([0053]). This modification would have had a reasonable expectation of success given Semenyuk discloses reads can be aligned to a graph genome ([0097]), and thus the mapping algorithm of Brown is applicable to the graph genome of Semenyuk.
It would have been further prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Semenyuk in view of Rand and Brown, as applied above, to have further stored the determined anchor points (e.g. the alignment positions of the mapped read) in an MPEG-G file, thus extending an MPEG-G file, as shown by Alberti (pg. 3, para. 3 to pg. 4, para. 1; pg. 5, para. 7, e.g. “start to end mapping position”, Figure 1). One of ordinary skill in the art would have been motivated to combine the methods of Semenyuk in view of Rand and Brown with Alberti, in order to represent mapped reads in a file with reduced size and that can easily accessed, processed, and shared, as shown by Alberti (pg. 8, para. 1-3). This modification would have had a reasonable expectation of success because the method of storing aligned read information of Alberti is applicable to the mapped read shown by Semenyuk in view of Rand and Brown, discussed above.
Therefore, the invention is prima facie obvious.
Citation of Pertinent Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Garrison et al., Variation graph toolkit improves read mapping by representing genetic variation in the reference, 2018, Nat Biotechnol., 36(9), pg. 875-879; cited in IDS filed 21 March 2018
Conclusion
No claims are allowed.
Claims 12-13 and 27-28 are free of the prior art. Claims 12 and 27 require extending a VCF file by adding the additional data fields of a trail indicating a sequence of edge transitions that lead to a location of a variant and a distance indicating a distance in a number of bases from an upstream anchor point to the variant. Claims 13 and 28 require extending an MPEG-G file by adding additional data fields including a coordinate-scheme field and a trail field, in addition to using the MPEG-G data fields of a seq_ID to indicates beginning edges, a split_seq ID to indicate beginning edges of split segment alignments, and mapping_pos and split_pos to count from the beginning of edges in seq_ID and split_seq_ID.
Regarding claims 12 and 27, Garrison (cited above), discloses a variation graph (vg) toolkit for improving read mapping by representing variation in a reference (Abstract) comprising constructing graphs from VCF files by repeated read alignment and editing of the graph to include sequence variations in the graph as paths (pg. 8, para. 5-6). Garrison then explains that these actions are also invertible in that the vg toolkit can also generate a VCF file to describe the graph as a set of variants using an arbitrarily embedded path as a reference (pg. 8, para. 6). Thus Garrison describes how to create a standard VCF file from variants of an arbitrary path of a reference, but does not describe adding the particular fields of the trail of edges or distance to a VCF file, as claimed.
Regarding claims 13 and 28, Alberti overviews the MPEG-G format for genomic data (Abstract), and discloses the format includes genomic records split across descriptor streams, including mapping positions (e.g. the anchor points), numbers of substitutions, and read lengths (pg. 3, para. 3; pg. 5, para. 7, e.g. “start to end mapping position”, Figure 1), access unit headers containing metadata describing the genomic data encoded in blocks, such as genomic regions the reads are mapped to, and data structures containing SAM (e.g. sequence read alignment file) auxiliary fields (pg. 3, para. 5 to pg. 4, para. 1; Figure 2). Furthermore, Zarate discloses particular auxiliary fields relating to read alignment to graph genomes such as a read tag indicating the start and end of the aligned read relative to a coordinate of a variant path in the graph (i.e. an edge identifier of the specific edge to which the beginning of the read is aligned) and a read tag detailing the alternate paths the read passed through, an alternate path referring to non-reference sequences or bubbles on the graph (e.g. edges) (i.e. a trail field) that can be added to a SAM file ([0033]-[0034]; [00144]; [00196]; FIG. 5, e.g. see VL tag indicating alternate paths the read crossed). However, the prior art does not disclose or suggest adding additional data fields relating to a coordinate scheme indicating how a decoder should interpret genomic coordinates, or the particular use of the MPEG-G data fields as recited in claims 13 and 28.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685