DETAILED ACTION
Applicant’s response, filed 29 April 2026, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 6 and 21 are cancelled.
Claims 1-5, 7-20, and 22-30 are pending.
Claims 1-5, 7-20, and 22-30 are rejected.
Claims 2-5, 7-15, 17-20, and 22-30 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.
Drawings
The objection to the drawings in the Office action mailed 29 Dec. 2025 has been withdrawn in view of the amendments to the specification received 29 April 2026.
The drawings filed 21 March 2022 are accepted.
Specification
The objection to the abstract in the Office action mailed 29 Dec. 2025 has been withdrawn in view of the replacement abstract received 29 April 2026.
Claim Objections
The objection to clams 2, 6, 11-14, 16-17, 21, and 26-29 in the Office action mailed 29 Dec. 2025 has been withdrawn in view of claim amendments and cancellations received 29 April 2026.
Claims 2-5, 7-15, 17-20, and 22-30 are objected to because of the following informalities. This objection is newly recited after further consideration of the claims.
Claims 2-5 and 7-15 should be amended to recite “The method of claim…”, instead of “The method claim..” to correct grammar.
Claims 17-20 and 22-30 should be amended to recite “The non-transitory machine-readable storage medium of claim…”, instead of “The non-transitory machine-readable storage medium claim…” to correct grammar.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The rejection of claims 6 and 21 under 35 U.S.C. 112(b) in the Office action mailed 29 Dec. 2025 has been withdrawn in view of the cancellation of these claims received 29 April 2026.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1-5, 7-20, and 22-30 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. Any newly recited portion is necessitated by claim amendment.
Claims 1 and 16, and claims dependent therefrom, are indefinite for recitation of “repeating the process until the edges of all individual genomes are generated and incorporated into the result genome graph”. It is unclear what step or steps, “the process” is referring to, and therefore, it is not clear which step(s) are required to be repeated. For example, it is not clear if “repeating the process” only requires generating graph edges and then creating an expanded graph reference, or if “the process” refers to additional steps such as storing the various identifiers for each generated edge graph in the data storage. Clarification is requested via amendment.
Claims 1 and 16, and claims dependent therefrom, are indefinite for recitation of “the edges of all individual genomes are generated..”. There is insufficient antecedent basis for “the edges of all individual genomes” in the claim. Claims 1 and 16 only previously recite “a genomic graph representing a plurality of individual genomes” in the preamble, but then only generate graph edges for variations in the first genome (i.e. a single individual).
Claim 7 is indefinite for recitation of “The method [of] claim, wherein…”. The metes and bounds of the claim are not clear because it is not clear which claim, claim 7 is intended to depend from. For purpose of examination, claim 7 is interpreted to defined from claim 1. Clarification is requested via claim amendment.
Claims 8 and 23 are indefinite for recitation of “the next edge belongs to a foundation group”. The metes and bounds of the term “foundation group” are unclear, and as a result, one of ordinary skill in the art cannot ascertain the metes and bounds of which next edges belong to “a foundation group” as claimed. A review of Applicant’s specification does not provide a definition of the term “foundation group” that serves to clarify the metes and bounds of the term. Clarification is requested via claim amendment. It is noted that Applicant’s specification does provide an example of a foundation group as a backbone sequence ([0064])- if Applicant intends for the foundation group to simply refer to a backbone sequence, then the claims should be amended accordingly. Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. See MPEP 2111.01. For purpose of examination, the foundation group will be interpreted to refer to a backbone sequence.
Claims 8 and 23 are indefinite for recitation of “(iii)…and none of the edges reachable from the endpoint belonging to a same group as the current edge”…”. There is a lack of antecedent basis for “the endpoint belonging to a same group as the current edge” because claims 1 and 16, from which claims 8 and 23 depend, do not recite an endpoint belonging to a same group as the current edge. Furthermore, given each group or section of a graph presumably has more than one endpoint (i.e. one on each side), it is further unclear which endpoint is being referenced. As a result, it is further unclear which edges “the edges reachable from the endpoint…” are referring to.
Claims 8 and 23 are indefinite for recitation of “(iii)…none of the edges reachable from the endpoint…”. The term “reachable” is a relative term which renders the claim indefinite. The term “reachable” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. In other words, it is unclear what distance from an endpoint an edge becomes “unreachable” rather than reachable.
Claims 8 and 23 are indefinite for recitation of “(iv)…the next edge traversed by the path”. It is unclear which path, “the path” in (iv) is referring to because claims 1 and 16, from which claims 8 and 23 depend, recite “specifying a path…” and claims 8 and 23 also previously recite “a path” in each of (i), (ii), and (iii). Therefore, it is unclear if “the path” in (iv) is referring to the path recited in claims 1 and 16 or a path in (i), (ii), or (iii) of claims 8 and 23. Furthermore, given it is not clear which path “the path” is referring to, it is also unclear which edge, “the next edge traversed by the path” is referring to.
Claims 8 and 23 are indefinite for recitation of “wherein the one or more rules for edge identifier removal comprise: (i) omitting…; (ii) omitting…; (iii) omitting…; (iv) substitution”, because the claim is missing a conjunction “and” or “or” between (iii) and (iv). As a result, it is not clear if the claims intend to require the one or more rules comprise all of (i), (ii), (iii), and (iv), or comprise (i), (ii), (iii), or (iv). For purpose of examination, the claim is interpreted to mean the one or more rules comprise (i), (ii), (iii), or (iv). Clarification is requested via claim amendment.
Claims 11 and 26 are indefinite for recitation of “TNEXT indicating…the path to which the next read of the template is primarily aligned”. There is antecedent basis for “the path to which the next read of the template is primarily aligned”. Claims 1 and 16, from which claims 1 and 26 depend, do recite “specifying a path”, but do not require that the path is “to which the next read of the template is primarily aligned”. It is noted that this rejection is previously recited. For purpose of examination, the limitation is interpreted to mean “a path to which the next read….”.
Claims 14 and 29 are indefinite for recitation of “determining anchor points on a specified edge by extending a MPEG-G file, comprising determining anchor points by running Dijkstra’s algorithm…”. It is unclear if determining the determining anchor points is intended to be performed by extending a MPEG-G file, by running Dijkstra’s algorithm, and/or both extending a MPEG-G file and running Dijkstra’s algorithm. 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 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. It is noted this rejection is previously recited.
Claims 15 and 30 are indefinite for recitation of “the path” in lines 3-5 and 4-6 respectively. Claims 1 and 16, from which claims 15 and 30 depend, recite “specifying a path in the genome graph”, and claims 15 and 30 also previously recite “a path in the genome graph”. As a result, it is unclear if “the path” in lines 3, 4, and 5 of claims 15 and 30 is referring to the path recited in claims 1 and 16, the path recited in lines 3-5 and 4-6 of claims 15 and 30, or if these are all intended to be the same path. Clarification is requested via claim amendment.
Response to Arguments
Applicant's arguments filed 29 April 2026, regarding 35 U.S.C. 112(b), have been fully considered but they are not persuasive.
Applicant remarks that the claims have been amended to clarify the claim language and facilitate prosecution, and thus the 112(b) rejection should be withdrawn (Applicant’s remarks at pg. 18, para. 2).
This argument is not persuasive. First, this argument is not persuasive because it does not pertain to the new grounds of rejection under 35 U.S.C. 112(b) set forth above in view of the claim amendments. Furthermore, the claim amendments did not address the previous 112(b) rejection relating to determining anchor points in claims 14 and 29 and relating to “the path” in claims 11 and 26.
Claim Rejections - 35 USC § 101
The rejection of claims 6 and 21 under 35 U.S.C. 101 in the Office action mailed 29 Dec. 2025 has been withdrawn in view of the cancellation of these claims received 29 April 2026.
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 1-5, 7-20, and 22-30 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. Any newly recited portion herein is necessitated by claim amendment.
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;
creating an expanded graph reference genome by merging the generated edges into the existing reference genome;
repeating the process until the edges of all individual genomes are generated and incorporated into the resulting genome graph;
specifying a path in the genome graph, wherein the path is defined by: (i) a position indicating the starting point of the path including at least a chromosome identifier, and a base position; (ii) a path length indicating the total number of nucleotides in the path; and (iii) a trail including a cascade of one or more edge identifiers traversed by the path using delimiters; and
simplifying the trail by removing one or more edge identifiers from the trail using one or more rules for edge identifier removal.
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. Creating an expanded graph reference genome by merging edges into the existing reference genome can be practically performed in the mind aided with pen and paper by organizing edges into corresponding locations of the reference genome and drawing the edges from the corresponding locations on the reference genome via pen and paper. Repeating this process for the edges of all individual genomes can be practically performed in the mind for the same reasons discussed above for each limitation, but repeating the mental steps for edges of additional genomes. Specifying a path in the graph can be practically performed in the mind by identifying a region of the genome graph with a particular starting position, identifying the chromosome of the region, determining the length of the region, and identifying edge identifiers that are part of the graph, which amounts to a mere analysis of data. Last, removing one or more edge identifiers from the trail using a rule for edge identifier removal can be practically performed in the mind by determining a path traverses the full length of a current edge and then removing an identifier of the next edge, as discussed in dependent claim 8. 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, 7-15, 17, 20, 22-25, 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 to generate one or more concatenated sequences. 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 limit the mental process of removing edge identifiers using the recited one or more rules for removal. 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 1-5, 7-20, and 22-30 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 7-10, 15, 22-25, 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 each generated 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);
storing the one or more concatenated sequences in a sequence data structure separate from the table (claims 5 and 20);
extending a sequence read alignment file (SAM) (claims 11 and 26);
extending a variant call file (VCF) (claims 12 and 27)
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 1-5, 7-20, and 22-30 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 7-10, 15, 22-25, 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 each generated 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);
storing the one or more concatenated sequences in a sequence data structure separate from the table (claims 5 and 20);
extending a sequence read alignment file (SAM) (claims 11 and 26);
extending a variant call file (VCF) (claims 12 and 27)
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; previously cited). 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.
Response to Arguments
Applicant's arguments filed 29 April 2026, regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Step 2A, Prong 1:
Applicant remarks the claims require storing the generated identifiers in data storage, and the storage is not generic post-solution activity because it is the goal of generating these parameters of each edge graph since they are utilized to, inter alia, create an expanded reference graph by merging the stored generated edges with their associated stored parameters into the existing reference genome, and thus the claims are patent eligible under Step 2A, Prong 1 (Applicant’s remarks at pg. 19, para. 1 to pg. 20, para. 4).
This argument is not persuasive. Under Step 2A, Prong 1, examiners evaluate whether the claim recites a judicial exception. See MPEP 2106. II. A. Simply because the claims recite an additional element of “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” does not preclude the claim from reciting an abstract idea.
Furthermore, it is noted that the step of creating an expanded graph reference does not utilize the stored identifiers in any particular way, as alleged by Applicant. Regardless, the human mind can practically read stored information, including start/end positions, identifiers, and a sequence to then determine the appropriate locations to modify a linear reference genome and add edges aided with pen and paper. Storing information in data storage, does not preclude subsequent process steps that use that information from reciting a mental process. Therefore, the claims recite an abstract idea under Step 2A, Prong 1.
Step 2A, Prong 2:
Applicant remarks the amended claims requires storing the genome graph in a concrete data structure in which, for each generated graph edge, the edge identifier, start edge identifier, start position, end edge identifier and end position are stored, while the variable-length nucleotide sequence for the edge is stored separately, which are not generic limitations and define a specific way to organize genome-graph data in computer memory and file storage such that fixed-length metadata remains in regular table format while variable-length edge sequences are externalized and addressed by position (Applicant’s remarks at pg. 21, para. 1-4). Applicant remarks the specification explains this technical arrangement allows for efficient file storage by storing edge sequences of varying lengths separately while table structures are more efficiently stored and access when the fields in the table have a fixed size (Applicant’s remarks at pg. 21, para. 5 to pg. 22, para. 1). Applicant remarks this reflects an improvement in computer storage, analogous to the type of specific data-structure improvement in Enfish, and the claims improve how a computer stores and accesses such information (Applicant’s remarks at pg. 22, para. 2-3).
This argument is not persuasive. First, this argument is not commensurate with the scope of the claims. Claims 1 and 16 simply require storing the various identifiers, position, and sequence in “the data storage”, which is the same place the linear representation of the reference genome is stored. The independent claims do not recite any details for how this information is stored, let alone in “regular table format” or that the “sequence for each generated graph edge” are stored in some separate structure.
It is noted that dependent claims 4 and 19 do recite “the edge identifier, start edge identifier…, and sequence for each generated graph edge are stored as a row in a data table”. However, this involves storing the sequence for each edge (variable length, as stated by Applicant) in the same data table as the identifiers and positions, rather than in some separate data structure. Therefore, the argument does not appear commensurate with the scope of the claims. Dependent claims 5 and 20 do recite storing “concatenated sequences in a sequence data structure separate from the data table”, which encompasses simply storing the concatenated sequence in another data table.
MPEP 2106.05(a) states in computer-related technologies, the examiner should determine whether the claim purports to improve computer capabilities or, instead, invokes computers merely as a tool. Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016). In the instant case, simply storing the recited information in separate data structures/tables does not clearly improve the capability of a computer, but rather invokes computers as a tool to store information in a conventional manner (e.g. storing data in two tables). Contrary to Applicant’s assertion, this is not analogous to the claims in Enfish, which involved a specifically recited data structure of a “self-referential database” that improved the way the computer stores and retrieves data in memory. In the instant case, it is not apparent that storing information in a “data table” and “data structure” improves the way a computer stores data or retrieves data from memory like the claims in Enfish. Instead, the claims store data in a conventional manner using a “data table” and “data structure”.
Applicant remarks the amended claims cannot be characterized as a process that could be performed mentally because a human mind cannot maintain the claimed row-based edge table together with externally stored group sequences and positional pointers in the manner required by the claims, and thus the judicial exception is integrated into a practical application, and thus the rejection should be withdrawn (Applicant’s remarks at pg. 22, para. 3 to pg. 23, para. 2).
This argument is not persuasive. First, it was not alleged that the steps of storing information recite a mental process. However, the claims still recite a mental process for the reasons discussed above and in the above rejection. Furthermore, the argument is not commensurate with the scope of the claims because the claims do not recite the use of any “pointers”, which is a memory-address variable. Last, the argument regarding the improvement to technology is not persuasive for the reasons already discussed above.
Claim Rejections - 35 USC § 103
The rejection of claims 6 and 21 under 35 U.S.C. 103 as being unpatentable over Semenyuk in view of Rand in the Office action mailed 29 Dec. 2025 has been withdrawn in view of the cancellation of these claims received 29 April 2026.
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, 7-10, 15-17, 22-25, and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Semenyuk (2018) in view of Rand (2017). Any newly recited portion is necessitated by claim amendment
Cited references:
Semenyuk, US 2018/0373839 A1; cited in IDS filed 21 March 2022 (previously cited); 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 (previously cited).
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).
Semenyuk discloses sequentially inserting (i.e. merging) each edge into the reference genome to construct a graph reference ([0066]-[0068]; FIG. 4).
Semenyuk discloses the insertion of edges representing variants is repeated until the genomic graph is complete ([0066]), and further discloses the graph genome can be built to represent genetic variation among populations of individuals ([0005]), demonstrating edges from all individual genomes of a plurality of individuals may be generated and incorporated into the genome graph.
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 indicating the starting point of the path 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 (i.e. a path length indicating the total number of nucleotides in the path) ([0074], e.g. longest path identified; [0140]); Semenyuk discloses defining the 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).
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 rule for edge identifier removal) ([0091]).
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. an identifier of a next edge) if no divergent paths from the current branch are required to reach the desired position (i.e. when a path traverses a full length of a current edge) ([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. This rejection is previously cited.
Cited reference: Duke, Graph Data, 2014, Everything Data CompSci 290.01, pg. 1-35 (previously cited).
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). This rejection is previously cited.
Cited references: Quiroz Zarate et al., WO 2017024138 A1 (hereinafter, Zarate) (previously cited).
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). This rejection is previously cited.
Cited references:
Brown, US 20170242958 A1; cited in IDS filed 21 March 2022 (previously cited); and
Alberti et al., An introduction to MPEG-G, the new ISO standard for genomic information representation, 2018, bioRxiv, pg. 1-18 (previously cited).
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.
Response to Arguments
Applicant's arguments filed 29 April 2026, regarding 35 U.S.C. 103 have been fully considered but they are not persuasive.
Applicant remarks that the independent claims 1 and 16 are amended to add the subject matter of claims 6, 8, 21, and 23 respectively, and neither Semenyuk nor Rand alone or in combination discloses the combination of added features (Applicant’s remarks at pg. 23, para. 3 to pg. 24, para. 2). Applicant remarks that Semenyuk does not disclose any trail formed as a cascade of edge identifiers with delimiters, does not start with a path with a chromosome identifier and base position, and does not simplify a trail, and similarly Rand does not disclose a starting position that includes an edge identifier, a path length field, or a cascade of edge identifiers (Applicant’s remarks at pg. 24, para. 3-4).
This argument is not persuasive. First, Rand is not relied upon to disclose these limitations in the above rejection. Furthermore, Applicant merely asserts that Semnyuk does not disclose the above features previously recited in claims 6, 8, 21, and 23, but does not address why the above and previously cited portions of Semenyuk fail to teach these limitations.
As previously discussed, Semenyuk discloses defining the 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 identifiers 1 and 2 [0098], [0100]; FIG. 10, e.g. 0..1.2.1; [0130], e.g. see path with coordinate components).The trail of coordinates “0..1.2.1” includes a trail of edge identifiers defining the path.
Furthermore, there is not requirement that a path “starts” with a chromosome identifier and base position. Claims 1 and 16 only require that a path “is defined by” a position indicating the starting point of the path including at least a chromosome identifier, and a base position; a path length; and a trail including a cascade. 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 indicating the starting point of the path 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 (i.e. a path length indicating the total number of nucleotides in the path) ([0074], e.g. longest path identified; [0140]).
Applicant further remarks that Semenyuk is coordinate/vertex-centric and lacks those stored edge fields and the per-individual merge loop, that Semenyuk does not teach a cascade of edge identifiers, and Rand lacks per-variation edge records and the per-individual receive-identify-generate-merge-repeat loop, and therefore the claims are free of the prior art (Applicant’s remarks at pg. 24, para. 5 to pg. 25, para. 2).
This argument is not persuasive. First, Rand is not relied upon to teach per-variation edge records and a per individual repeat loop. Furthermore, Semenyuk does teach a cascade of edge identifiers as discussed above.
Regarding the “per-individual…loop”, this argument is not commensurate with the scope of the claims. Claims 1 and 16 require “repeating the process until the edges of all individual genomes are generated and incorporated into the resulting genome graph”, but there is not requirement this is performed on a per-individual basis as alleged by Applicant. Semenyuk does disclose repeating the process of creating edges and merging generated edges into an existing graph reference for multiple individuals. For example, Semenyuk discloses sequentially inserting (i.e. merging) each edge into the reference genome to construct a graph reference ([0066]-[0068]; FIG. 4), describing that new generated edges are added sequentially/iteratively. Semenyuk discloses the insertion of edges representing variants is repeated until the genomic graph is complete ([0066]), and further discloses the graph genome can be built to represent genetic variation among populations of individuals ([0005]), demonstrating repeating the process of generating and incorporating edges from all individual genomes into the genome graph.
Conclusion
No claims are allowed.
Claims 12-13 and 27-28 are free of the prior art for the reasons discussed in the Office action mailed 29 Nov. 2025.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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