CTNF 17/924,948 CTNF 100270 DETAILED ACTION Notice of AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. 07-06 AIA 15-10-15 In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. Status of the Claims Claims 1-17,19 and 21-22 are pending. Claims 18, 20, and 23 are cancelled. Claims 1, 4, 10, 15, and 17 are objected to. Claims 1-17,19 and 21-22 are rejected. Priority This US Application 17/924,948 (11/11/2022) is a 371 of PCT/US2021/031957 (05/12/2021), which claims benefit of 63/025,498 (05/15/2020), as reflected in the filing receipt mailed on 03/14/2023. The claims to the benefit of priority are acknowledged; and the effective filing date of claims 1-17,19 and 21-22 is 05/15/2020 . Information Disclosure Statement The information disclosure statements (IDS) submitted on 11/11/2022, 05/16/2024, and 12/22/2025 were considered. Claim objections Claims 1, 4, 10, 15 and 17 are objected to because of the following informalities related to grammar/punctuation. Appropriate correction is required. In claim 1 , the recited "patters" should read patterns" In claim 4 , the recited "trans-fragment targeting TFT" should read "trans-fragment targeting (TFT)" In claim 10 , the recited "discarding ones of the sequence reads" should read "discarding one of the sequence reads" or "discarding one or more of the sequence reads." Claims 15 and 17 repeat the issue above. In claim 17 , the recited "and/or or" should read "and/or" 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 10-11 and 15-17 are rejected under 35 U.S.C. 112(b)as being indefinite for failing to particularly point out and distinctly claim the subject matter the invention. Dependent claims are rejected similarly, unless otherwise noted below. The following issues cause the respective claims to be rejected under 112(b) as indefinite: In claim 10 , the recited "the sequence reads" should read "the multiple sequence reads" for proper antecedent basis. Claims 11 and 15-17 repeat the issue above. In claim 15 , the relationship is unclear between the recited "having segments mapped onto" and the previously recited "segments of the multiple sequence reads." To overcome this rejection the claim may be amended to "having the subsets of the segments mapped onto" for proper antecedent basis . Claim Rejections - 35 USC § 101 07-04-01 AIA 07-04 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 1-17,19 and 21-22 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 §I). Abstract ideas include mathematical concepts and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). 101 background MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials. Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)? Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e ., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))? Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))? Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)? Analysis of instant claims Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)? The instant claims are directed to a method ( claims 1-12, 19, and 21-22 ) and a CRM ( claims 13-17 ); each of which falls within one of the categories of statutory subject matter. [Step 1: claims 1-17,19 and 21-22: Yes] Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))? Background With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as: • mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations) (MPEP 2106.04(a)(2)(I)); • certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or • mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)). Analysis of instant claims With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows: "mapping/map … multiple sequence reads from the output genome onto one or more reference sequences, wherein the one or more reference sequences are representative of the input genome" ( independent claims 1, 13, and 21 ); • "identifying/identify … from a data structure, the at least one edit based on one or more reference edit patterns matching a pattern associated with the at least one edit, wherein the one or more reference edit patters are defined by segments of the multiple sequence reads of the output genome mapped onto the one or more reference sequences" ( independent claims 1, 13, and 21 ); • "reporting/report, by the computing device, the identified at least one edit in response to the request"; ( independent claims 1, 13, and 21 ); • "searching, by the computing device, in the data structure, for the one or more reference edit patterns, in order to identify the at least one edit" ( claim 9 ); • "discarding ones of the sequence reads, prior to mapping the sequence reads onto the one or more reference sequences, based on the ones of the sequence reads being located apart from one or more target sites of the one or more reference sequences and/or or the output genome; and wherein mapping the sequence reads includes mapping the non-discarded ones of the sequence reads onto the one or more reference sequences" ( claim 10 ); • "selecting the output genome based on the identified at least one edit" ( claim 12 ); • "keeping ones of the sequence reads having segments mapped onto different ones of the one or more reference sequences or onto two locations in opposite orientations of one of the one or more reference sequences" ( claim 15 ); • "map only non-discarded ones of the sequence reads onto the one or more reference sequences" ( claim 17 ); • "discard ones of the sequence reads, prior to mapping the sequence reads onto the one or more reference sequences, based on the ones of the sequence reads being located apart from one or more target sites of the one or more reference sequences and/or or the output genome ( claim 17 ); and • "identifying … the one or more edits in the output genome based on at least one reference pattern identified by mapping multiple sequence reads of the output genome onto a reference sequence of an unedited version of the genome" ( claim 19 ). Dependent claims 2-8, 10-11, 14, 22and 16 recite further steps that limit the judicial exceptions in independent claims 1 and 13 and, as such, also are directed to those abstract ideas. For example, claims 2, 11, 14, 22 and 16 further limit the one or more reference edit patterns identified; claim 3 further limits the one or more reference sequences mapped; claims 4-8 further limit the at least one edit identified; and claim 10 further limits the mapping step. The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation. Without further detail as to the methodology involved in "identifying and mapping genome edits", under the BRI, one may simply, for example, use pen and paper to perform the recited identifying, mapping searching, selecting and discarding steps using sequence reads and reference reads data. [Step 2A Prong One: claims 1-17,19 and 21-22: Yes ] Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))? Background MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application: An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a); Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2); Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b); Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e). Analysis of instant claims Instant claims 1, 9, 12-13, 19, and 21 recite additional elements that are not abstract ideas: • "computing device" ( claims 1, 9, 19, and 21 ); • "processor" ( claims 13, 15, and 17 ); • "receiving/receive, by a computing device, a request to identify at least one edit in an output genome, the output genome based on an input genome and one or more edits to the input genome" ( independent claims 1, 13, and 21 ); and • "planting an organism consistent with the selected output genome in a growing space" ( claim 12 ). Considerations under Step 2A, Prong Two The recited limitations in claims 1, 9, 13, 15, 17, 19, and 21 are interpreted as requiring the use of a computer. Hence, the claims explicitly recite steps executed by computers and therefore can be described as computer functions or instructions to implement on a generic computer. Further steps directed to additional non-abstract elements of a computing device/computer do not describe any specific computational steps by which the "computer parts" perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Claims directed to "receiving" data ( claims 1, 13, and 21 ) read on receiving data over a network -Symantec, 838 F.3d at 1321 - MPEP 2106.05(a) pertains; which constitutes just necessary data gathering and therefore correspond to insignificant extra-solution activity. The recited claims read on data gathering activities; not amounting to a practical application. The type of data doesn’t change that it is mere data gathering or conventional computer receiving means The recited "planting an organism consistent with the selected output genome in a growing space" ( claim 12 ) read on a generic "apply it" step because the claim recites an idea of a solution or outcome without any indication of how the judicial exception impacts or influences this step. There are no additional limitations to indicate details of exactly how the judicial exception is being integrated into the recited step of "planting." There are no additional limitations to indicate that the claimed computer, processor, or computer readable medium require anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(b). Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)). None of the dependent claims recite any additional non-abstract elements; they are all directed to further aspects of the information being analyzed, the manner in which that analysis is performed, or the mathematical operations performed on the information. In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs). In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements . Additional elements are further discussed in Step 2B below. Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application. [Step 2A Prong Two: claims 1-17,19 and 21-22: No] Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)? According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s). Claims 1, 9, 13, 15, 17, 19, and 21 recite a computer or computer functions, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions; which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)). Further, the courts have found that receiving data well-understood, routine, and conventional functions of a computer when claimed in a generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versa ta Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(Il)(i)). When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h). With respect to the instant claims, the prior art review to Songstad ("Genome editing of plants." Critical Reviews in Plant Sciences 36(1):1-23 (2017)) discloses genome editing of plants to screen through mutant populations to identify specific genes of interest is routine, well-understood and conventional in the art. Said portions of the prior art are, for example, pg. 6 col. 2 para. 4; wherein studies performed were able to conclude effects such as early flowering and shorter roots following the use of mutant genes identified by genome editing steps (i.e. reading on planting an organism consistent with the selected output genome in a growing space ) (pg. 6 col.1 para. 2). The instant claims constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)). [Step 2B: claims 1-17,19 and 21-22: No] Conclusion: Instant claims are directed to non-statutory subject matter For the reasons above, the claims in this instant application, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept not clearly anything significantly more. Claim Rejections - 35 USC § 103 07-20-fti The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action: (a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made. 07-23-fti The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) are summarized as follows: 1. Determining the scope and contents of the prior art. 2. Ascertaining the differences between the prior art and the claims at issue. 3. Resolving the level of ordinary skill in the pertinent art. 4. Considering objective evidence present in the application indicating obviousness or nonobviousness. A. Claims 1-10, 13-17, and 21-22 are rejected under 35 U.S.C. 103(a) as being unpatentable over Kim ("GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies." BMC genomics 19(2):89 (2018)) in view of Bingmann ("COBS: a compact bit-sliced signature index." International Symposium on String Processing and Information Retrieval . Cham: Springer International Publishing, 2019)) in view of Boel ("BATCH-GE: Batch analysis of Next-Generation Sequencing data for genome editing assessment." Scientific reports 6(1)30330 (2016)), as cited on the attached Form PTO-892. Bullet points indicate the teachings of the instant features over the prior art. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims. Claim 1 recites: mapping, by the computing device, multiple sequence reads from the output genome onto one or more reference sequences, wherein the one or more reference sequences are representative of the input genome; identifying, by the computing device, from a data structure, the at least one edit based on one or more reference edit patterns matching a pattern associated with the at least one edit, wherein the one or more reference edit patters are defined by segments of the multiple sequence reads of the output genome mapped onto the one or more reference sequences Claim 13 recites: non-transitory computer-readable storage medium including executable instructions for identifying edits in output genomes, which, when executed by at least one processor, cause the at least one processor to perform the steps recited in claim 1. • Kim teaches a method for 1) cutting the genome into many short reads, 2) identifying the DNA sequence of each read, and 3)mapping each read against the reference genome to analyze the variations in the sequenced genome (pg. 24 col. 1para. 1); wherein a seed location filter exploits the high memory bandwidth and processing-in-memory capabilities of 3D-stacked dynamic random access memory (DRAM) (i.e. computing device and non-transitory computer-readable storage medium including executable instructions ) to improve the performance of DNA read mappers (pg. 24 col. 2 para. 5); wherein billions of DNA fragments (reads) sampled from a donor are mapped (i.e. mapping … multiple sequence reads from the output genome onto one or more reference sequences ) onto a reference human genome to identify genomic variants of the donor (i.e. identifying edits ) (pg. 23 para. 1); wherein the mapper indexes a data structure (i.e. identifying data structures ) with each seed to obtain a list of possible locations within the reference genome that could result in a match (pg. 24 col. 1 para. 2); wherein the mapper aligns the read sequence to the reference sequence (i.e. reference sequences are representative of the input genome defined by segments of the multiple sequence reads of the output genome mapped onto the one or more reference sequences ) (pg. 24 col. 1 para. 2); wherein an verification sequence alignment algorithm to determine the similarity between the read sequence and the reference sequence (pg. 24 col. 1 para. 2). • Kim does not teach the identification of edit patterns. However, Bingmann teaches an algorithm namely COmpact Bit-sliced Signature index to generate DNA data structure from sequencing experiments (pg. 1 para. 2); wherein the creation of k-mers for DNA string allows pattern matching (pg. 5 para. 2); wherein each filter is represented bit arrays with possibly different parameters to perform approximate matching for a pattern of DNA (pg. 5 para. 4). Claim 1 recites: receiving, by a computing device, a request to identify at least one edit in an output genome, the output genome based on an input genome and one or more edits to the input genome; reporting, by the computing device, the identified at least one edit in response to the request Claim 13 recites: non-transitory computer-readable storage medium including executable instructions for identifying edits in output genomes, which, when executed by at least one processor, cause the at least one processor to perform the steps recited in claim 1. • Kim does not teach the recitation above. However, Boel teaches a method that detects and reports indel mutations and other precise genome editing events (pg. 1 para. 1) by mapping reads against complete genomic sequence of the organism of interest (i.e. multiple sequence reads of the output genome mapped onto the one or more reference sequences ) (pg. 7 Table 3); wherein input files define the genomic coordinates for the user-defined region of interest (i.e. receiving a request to identify at least one edit in an output genome) (pg. 2 para. 2); wherein a list of variants is generated (i.e. reporting the identified at least one edit in response to the request ) (pg. 7 Table 3); wherein the tool is implemented as a freely available Perl script and can be run on any Linux-based server or personal computer (i.e. computing device and non-transitory computer-readable storage medium including executable instructions ). Claim 2 recites: wherein the one or more reference edit patterns are further defined by locations and/or orientations of the segments of the multiple sequence reads of the output genome mapped onto the one or more reference sequences • Kim does not teach the recitation above. However, Bingmann teaches an “ensemble” of encoding techniques for compressing the occurrence maps of k-mers in the document set (i.e. locations of the segments of the multiple sequence reads of the output genome mapped ), in which the occurrence maps are grouped depending on their density and encoding into disjoint buckets (pg. 4 para. 2). Claim 3 recites: wherein each of the one or more reference sequences is representative of an input wild type genome • Kim does not teach an input wild type genome. However, Boel teaches the incorporation of a control sample (e.g. non-injected zebrafish embryos from the same clutch – wild type control ) in the genomic analysis to identify these polymorphisms, or to examine the reads (pg. 4 para. 2). Claim 4 recites: wherein the at least one edit includes: a deletion edit, an inversion edit, a homolog fragment targeting (HFT) edit, and/or a trans-fragment targeting TFT edit; and wherein the one or more reference edit patterns include one or a combination of simple edits including: a deletion edit, an inversion edit, a homolog fragment targeting (HFT) edit, and/or a trans-fragment targeting TFT edit • Kim does not teach the recitation above. However, Bingmann teaches a method for pattern matching including searching within the stored datasets to find important genes or mutations, or combinations of mutations (i.e. DNA deletion and DNA inversion edits ) (pg. 2 para. 2). Claim 5 recites: determining whether the at least one edit is associated with only one target site of the output genome; and wherein the at least one edit includes a simple edit in response to the at least one edit being associated with the only one target site • Kim does not teach the recitation above. However, Boel teaches a system applied in a range of organisms to achieve either gene knock-out or knock-in (i.e. gene edit comprising a simple edit) including the combined use of a customizable target-specific single-guide RNA (sgRNA) (i.e. edit associated with only one target site of the output genome ) (pg. 2 para. 1); wherein for each gene, a sgRNA target sequence was selected (i.e. simple edit in response to the at least one edit being associated with the only one target site ), guided by a number of criteria, which are based on current knowledge on optimal sgRNA design (pg. 7 para. 5). Claim 6 recites: wherein the target site is defined by guide RNA (gRNA) • Kim does not teach the recitation above. However, Boel teaches a system applied in a range of organisms to achieve either gene knock-out or knock-in (i.e. gene edit ) including the combined use of a customizable target-specific single-guide RNA pg. 2 para. 1). Claim 7 recites: determining whether the at least one edit is associated with more than one target site of the output genome; and determining whether the at least one edit is associated with only one gene or locus; wherein the at least one edit includes multiple edits selected from simple edits, inversion edits, and/or HFT edits, but not TFT edits, in response to the at least one edit being associated with more than one target site and being associated with only one gene or locus Claim 8 recites: determining whether the at least one edit is associated with more than one gene or locus; and wherein the one or more edit includes multiple edits selected from simple edits, inversion edits, HFT edits, and TFT edits, in response to the at least one edit being associated with more than one target site and being associated with more than one gene or locus • Kim does not teach the recitation above. However, Boel teaches that specific base pair alterations in the repair template can be marked, allowing the simultaneous detection of single and multiple intended base pair substitutions (i.e. reading on at least one edit includes multiple edits selected from simple edits – wherein substitutions are simple edits but not TFT edits ) (pg. 7 para. 1); sequence reads (indicated by a tick) are screened for insertions and deletions (i.e. reading on claims 7-8 ) initiated within the same user-defined region of interest (pg. 3 Fig. 1); wherein for each entry in the experiment file, a folder with four output files is generated, containing genome editing data for every sample analysed for the user-defined region of interest, where Fig. 2 shows multiple entries related to multiple regions of interest (i.e. reading on claims 7-8 ) (pg. 2 para. 3 and pg. 5 Fig. 2). Claim 9 recites: searching, by the computing device, in the data structure, for the one or more reference edit patterns, in order to identify the at least one edit • Kim does not teach the recitation above. However, Bingmann teaches an algorithm namely COmpact Bit-sliced Signature index to generate DNA data structure from sequencing experiments (pg. 1 para. 2); wherein the creation of k-mers for DNA string allows pattern matching (pg. 5 para. 2); wherein each Bloom filters bit arrays with possibly different parameters to perform approximate matching for a pattern (pg. 5 para. 4); wherein search queries can be expressed in terms of exact or approximate matching of strings (pg. 2 para. 2). Claim 10 recites: discarding ones of the sequence reads, prior to mapping the sequence reads onto the one or more reference sequences, based on the ones of the sequence reads being located apart from one or more target sites of the one or more reference sequences and/or or the output genome; and wherein mapping the sequence reads includes mapping the non-discarded ones of the sequence reads onto the one or more reference sequences • Kim teaches billions of DNA fragments (reads) sampled from a donor are mapped (i.e. mapping … multiple sequence reads from the output genome onto one or more reference sequences ) onto a reference human genome to identify genomic variants of the donor (i.e. reading on identifying edits ) (pg. 23 para. 1); wherein an optimized seed location filter executed before alignment (i.e. reading on discarding prior to mapping the non-discarded ones of the sequence reads ) during DNA read mapping, discarding seed locations that alignment would deem a poor match ( reading on discarding sequence reads being located apart from one or more target sites ) (pg. 1 para. 1). Claim 14 recites: wherein the one or more reference edit patterns are further defined by locations and/or orientations of the segments of the multiple sequence reads of the output genome mapped onto the one or more reference sequences • Kim does not teach the recitation above. However, Bingmann teaches an “ensemble” of encoding techniques for compressing the occurrence maps of k-mers in the document set (i.e. locations of the segments of the multiple sequence reads of the output genome mapped as in claims 14 and 21 ), in which the occurrence maps are grouped depending on their density and encoding into disjoint buckets (pg. 4 para. 2). Claim 15 recites: after mapping the multiple sequence reads from the output genome onto the one or more reference sequences and before identifying the at least one edit, keeping ones of the sequence reads having segments mapped onto different ones of the one or more reference sequences or onto two locations in opposite orientations of one of the one or more reference sequences • Kim teaches a seed location filter exploits the high memory bandwidth and processing-in-memory capabilities of 3D-stacked dynamic random access memory (DRAM) (i.e. computing device ) to improve the performance of DNA read mappers (pg. 24 col. 2 para. 5); wherein billions of DNA fragments (reads) sampled from a donor are mapped (i.e. mapping … multiple sequence reads from the output genome onto one or more reference sequences ) onto a reference human genome to identify genomic variants of the donor (i.e. reading on keeping ones of the sequence reads having segments mapped onto different ones of the one or more reference sequences ) (pg. 23 para. 1). Claim 16 recites: wherein the pattern associated with the at least one edit is defined by at least one location and/or at least one orientation of the segments of the sequence reads mapped onto the one or more reference sequences, relative to target sites on the one or more reference sequences • Kim teaches billions of DNA fragments (reads) sampled from a donor are mapped onto a reference human genome to identify genomic variants of the donor (pg. 23 para. 1); wherein the mapper indexes a data structure with each seed to obtain a list of possible locations within the reference genome that could result in a match (i.e. reading on at least one edit is defined by at least one location relative to target sites ) (pg. 24 col. 1 para. 2). Claim 17 recites: discard ones of the sequence reads, prior to mapping the sequence reads onto the one or more reference sequences, based on the ones of the sequence reads being located apart from one or more target sites of the one or more reference sequences and/or or the output genome; and wherein the executable instructions, when executed by the at least one processor, in order to map the multiple sequence reads, cause the at least one processor to map only non-discarded ones of the sequence reads onto the one or more reference sequences • Kim teaches billions of DNA fragments (reads) sampled from a donor are mapped (i.e. mapping … multiple sequence reads from the output genome onto one or more reference sequences ) onto a reference human genome to identify genomic variants of the donor (i.e. reading on identifying edits ) (pg. 23 para. 1); wherein an optimized seed location filter executed before alignment (i.e. reading on discarding prior to mapping the non-discarded ones of the sequence reads ) during DNA read mapping, discarding seed locations that alignment would deem a poor match ( reading on discarding sequence reads being located apart from one or more target sites ) (pg. 1 para. 1). Claim 21 recites: receiving, by a computing device, a request to identify at least one edit in an edited genome, the edited genome based on an input wild type genome and one or more edits to the input wild type genome, wherein one or more reference sequences are representative of the input wild type genome; mapping, by the computing device, sequence reads from the edited genome to the one or more reference sequences; identifying, by the computing device, from a data structure, the at least one edit of the one or more edits, based on one or more reference edit patterns matching a pattern associated with the at least one edit; and reporting, by the computing device, the identified at least one edit in response to the request • Kim teaches a method for 1) cutting the genome into many short reads, 2) identifying the DNA sequence of each read, and 3)mapping each read against the reference genome to analyze the variations in the sequenced genome (pg. 24 col. 1para. 1); wherein a seed location filter exploits the high memory bandwidth and processing-in-memory capabilities of 3D-stacked dynamic random access memory (DRAM) (i.e. computing device and non-transitory computer-readable storage medium including executable instructions ) to improve the performance of DNA read mappers (pg. 24 col. 2 para. 5); wherein billions of DNA fragments (reads) sampled from a donor are mapped (i.e. mapping … multiple sequence reads from the output genome onto one or more reference sequences ) onto a reference human genome to identify genomic variants of the donor (i.e. identifying edits ) (pg. 23 para. 1); wherein the mapper indexes a data structure (i.e. identifying data structures ) with each seed to obtain a list of possible locations within the reference genome that could result in a match (pg. 24 col. 1 para. 2); wherein the mapper aligns the read sequence to the reference sequence (i.e. reference sequences are representative of the input genome defined by segments of the multiple sequence reads of the output genome mapped onto the one or more reference sequences ) (pg. 24 col. 1 para. 2); wherein an verification sequence alignment algorithm to determine the similarity between the read sequence and the reference sequence (pg. 24 col. 1 para. 2). • Kim does not teach the identification of edit patterns. However, Bingmann teaches an algorithm namely COmpact Bit-sliced Signature index to generate DNA data structure from sequencing experiments (pg. 1 para. 2); wherein the creation of k-mers for DNA string allows pattern matching (pg. 5 para. 2); wherein each filter is represented bit arrays with possibly different parameters to perform approximate matching for a pattern of DNA (pg. 5 para. 4). • Kim does not teach an input wild type genome. However, Boel teaches the incorporation of a control sample (e.g. non-injected zebrafish embryos from the same clutch – wild type control ) in the genomic analysis to identify these polymorphisms, or to examine the reads (pg. 4 para. 2). Claim 22 recites: wherein the one or more reference edit patterns are defined by locations and/or orientations of the segments of the multiple sequence reads of the output genome mapped onto the one or more reference sequences • Kim does not teach the recitation above. However, Bingmann teaches an “ensemble” of encoding techniques for compressing the occurrence maps of k-mers in the document set (i.e. locations of the segments of the multiple sequence reads of the output genome mapped as in claims 14 and 21 ), in which the occurrence maps are grouped depending on their density and encoding into disjoint buckets (pg. 4 para. 2). Rationale for combining (MPEP §2142-2143) Regarding claims 1-10, 13-17, and 21-22, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Kim in view of Bingmann and Boel because all references disclose methods for the identification of genome edits. The motivation would have been to: • enable the index to be applied to corpora with highly varying document sizes when investigating DNA samples (pg. 2 para. 4 Bingmann ) and to incorporate an indexing method to enable approximate pattern matching due to its simple data structure (pg. 16 para. 2 Bingmann ); and • incorporate a faster, more informative and flexible analysis of multiple genome editing experiments for any organism of interest (pg. 7 para. 4 Boel ). Therefore it would have been obvious to one of ordinary skill in the art to substitute the identification of genome edits method of Kim to the methods by Bingmann and Boel because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for the identification of genome edits. B. Claim 11 is rejected under 35 U.S.C. 103(a) as being unpatentable over Kim , Bingmann and Boel as applied to claim 1 above further in view of Frizzi ("Small RNA profiles from virus-infected fresh market vegetables." Journal of Agricultural and Food Chemistry 62(49)12067-12074 (2014)), as cited on the attached Form PTO-892. Bullet points indicate the teachings of the instant features over the prior art. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims. Claim 11 recites: wherein the one or more reference edit patterns defined by the segments of the sequence reads mapped onto the one or more reference sequences includes: one of the segments of a first one of the sequence reads spaced apart from a second one of the segments of the first one of the sequence reads, and oriented in an opposite direction relative to the second one of the segments of the first one of the sequence reads • Kim teaches billions of DNA fragments (reads) sampled from a donor are mapped (i.e. mapping … multiple sequence reads from the output genome onto one or more reference sequences ) onto a reference human genome to identify genomic variants of the donor (i.e. reading on identifying edits ) (pg. 23 para. 1); wherein an optimized seed location filter executed before alignment during DNA read mapping, discarding seed locations that alignment would deem a poor match ( identifying sequence reads spaced apart from a second one of the segments of the first one of the sequence reads ) (pg. 1 para. 1). • Kim does not teach "oriented in an opposite direction relative to the second one of the segments of the first one of the sequence reads". However, Frizzi teaches segment reads matched in the tomato sample (Figure 3A), and the small reads in both the sense and antisense orientations come predominantly from the regions corresponding to the nonstructural and nucleocapsid protein coding sequences (pg. 12069 col.2 para. 2). Rationale for combining (MPEP §2142-2143) Regarding claim 11 , 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Kim , Bingmann and Boel in view of Frizzi because all references disclose methods for the identification of genome edits. The motivation would have been to incorporated studies of genetically engineered crops (pg. 12067 para. 1). Therefore it would have been obvious to one of ordinary skill in the art to substitute the identification of genome edits method of Kim, Bingmann and Boel to the methods by Frizzi because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for the identification of genome edits. C. Claim 12 is rejected under 35 U.S.C. 103(a) as being unpatentable over Kim, Bingmann and Boel as applied to claim 1 above further in view of Songstad ("Genome editing of plants." Critical Reviews in Plant Sciences 36(1):1-23 (2017)), as cited on the attached Form PTO-892. Bullet points indicate the teachings of the instant features over the prior art. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims. Claim 12 recites: selecting the output genome based on the identified at least one edit; and planting an organism consistent with the selected output genome in a growing space • Kim does not teach the recitation above. However, Songstad teaches genome editing of plants to screen through mutant populations to identify specific genes of interest (pg. 6 col. 2 para. 4); wherein studies performed were able to conclude effects such as early flowering and shorter roots following the use of mutant genes identified by genome editing steps (i.e. reading on planting an organism consistent with the selected output genome in a growing space ) (pg. 6 col.1 para. 2). Rationale for combining (MPEP §2142-2143) Regarding claim 12 , 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Kim Bingmann and Boel in view of Songstad because all references disclose methods for the identification of genome edits. The motivation would have been to incorporate the application of genome editing technology to plant genetic modification. (pg. 1 col. 1 para. 2 Songstad ). Therefore it would have been obvious to one of ordinary skill in the art to substitute identification of genome edits method of Kim, Bingmann and Boel to the methods by Songstad because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for identification of genome edits. D. Claim 19 is rejected under 35 U.S.C. 103(a) as being unpatentable over Kim in view of Bingmann, as cited on the attached Form PTO-892. Bullet points indicate the teachings of the instant features over the prior art. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims. Claim 19 recites: identifying, by a computing device, the one or more edits in the output genome based on at least one reference pattern identified by mapping multiple sequence reads of the output genome onto a reference sequence of an unedited version of the genome • Kim teaches a method for 1) cutting the genome into many short reads, 2) identifying the DNA sequence of each read, and 3)mapping each read against the reference genome to analyze the variations in the sequenced genome (pg. 24 col. 1para. 1); wherein a seed location filter exploits the high memory bandwidth and processing-in-memory capabilities of 3D-stacked dynamic random access memory (DRAM) (i.e. computing device ) to improve the performance of DNA read mappers (pg. 24 col. 2 para. 5); wherein billions of DNA fragments (reads) sampled from a donor are mapped (i.e. mapping … multiple sequence reads from the output genome onto one or more reference sequences ) onto a reference human genome to identify genomic variants of the donor (i.e. reading on identifying edits ) (pg. 23 para. 1); wherein the mapper indexes a data structure (i.e. identifying data structures ) with each seed to obtain a list of possible locations within the reference genome that could result in a match (pg. 24 col. 1 para. 2); wherein the mapper aligns the read sequence to the reference sequence (i.e. reference sequences are representative of the input genome defined by segments of the multiple sequence reads of the output genome mapped onto the one or more reference sequences ) (pg. 24 col. 1 para. 2); wherein an verification sequence alignment algorithm to determine the similarity between the read sequence and the reference sequence (pg. 24 col. 1 para. 2); wherein a series of analyses on the fundamental characteristics of the human reference genome to determine a range for the filter parameters to process the output (i.e. reading on reference sequence of an unedited version of the genome ) (pg. 9 col. 2 para. 6). • Kim does not teach the identification of sequence reads patterns. However, Bingmann teaches an algorithm namely COmpact Bit-sliced Signature index to generate DNA data structure from sequencing experiments (pg. 1 para. 2); wherein the creation of k-mers for DNA string allows pattern matching (pg. 5 para. 2); wherein each filter is represented bit arrays with possibly different parameters to perform approximate matching for a pattern of DNA (pg. 5 para. 4). Rationale for combining (MPEP §2142-2143) Regarding claim 19 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Kim in view of Bingmann because all references disclose methods for the identification of genome edits. The motivation would have been to enable the index to be applied to corpora with highly varying document sizes when investigating DNA samples (pg. 2 para. 4 Bingmann ) and to incorporate an indexing method to enable approximate pattern matching due to its simple data structure (pg. 16 para. 2 Bingmann ). Therefore it would have been obvious to one of ordinary skill in the art to substitute the identification of genome edits method of Kim to the methods by Bingmann because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these reference