DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 01/12/2026 has been entered.
Applicant's amendments and remarks, filed, 01/12/2026, are acknowledged. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Status of Claims
Claims 1, 3-5, 7, 8, 10-14, 16-19, 21 are under examination.
Claims 2, 6, 9, 15, 20 are cancelled.
Priority
This application claims the benefit of US Provisional Patent Application Serial No. 62/410,244, filed October 19, 2016.
Withdrawn Rejections
The rejection of claims 1-5, 7, 8, 10-14, 16-19 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is withdrawn in view of applicant’s amendments (which removes the language that necessitated the new matter rejection).
The rejection of claims 1-5, 7, 8, 10-14, 16-19 under 35 U.S.C. 103 as being unpatentable over Heber et al. (Bioinformatics, Vol. 18, Suppl. 1, 2002, Pages S181–S188) is withdrawn in view of applicant’s amendments.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 3-5, 7, 8, 10-14, 16-19, 21 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and ‘as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355).
Step 1
The instantly claimed invention (claim 1 being representative) is directed to a computer system for generating a reconstructed coding genome contig. Thus, the claim is directed to one of the statutory categories of invention. MPEP 2106.03.
A. Guidance Step 2A, Prong 1
As discussed in the MPEP, abstract ideas include mathematical concepts (mathematical relationships, mathematical formulas or equations, mathematical calculations; see MPEP § 2106.04(a)(2), subsection I); certain methods of organizing human activity (see MPEP § 2106.04(a)(2), subsection II); and mental processes (concepts performed in the human mind including an observation, evaluation, judgment, opinion; see MPEP § 2106.04(a)(2), subsection III). In this case, the claims recite the following abstract ideas:
instructions…for obtaining the set of full-length transcript sequences from a data repository…;
instructions…for constructing an undirected weighted graph of…transcript sequences comprising nodes and edges…;
instructions…for partitioning the set of full-length transcript sequences into at least one eukaryotic gene family based on the undirected weighted graph;
instructions…for building a directed weighted graph for the full-length transcripts…;
instructions…for simplifying each directed weighted graph to generate a reconstructed coding genome contig for each of the at least one gene eukaryotic family…;
Mental Processes
In this case, the above steps are nominally recited and embrace activities directed to observing data, analyzing data, and making a determination based on said analysis. As such, these steps can be reasonably performed by the human mind of a scientist or engineer and fall within the “mental processes” grouping of abstract idea. See MPEP 2016.04(a)(2). In addition, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks only involve data reception and analysis [see e.g. para. 0058, which shows that methods for constructing a “directed graph” involves algorithmic processes]. Applicant is also reminded that the Office's eligibility guidance does not set limit on the number of calculations that can or cannot be performed mentally. With regards to the recited “processor”, this still does not negate the mental nature of these limitations because the claims are merely using the computer as a tool to perform the otherwise mental processes. See also Intellectual Ventures I LLC v. Capital One Fin. Corp., 850 F.3d 1332, 1340 (Fed. Cir. 2017) (“[A]n invention directed to collection, manipulation, and display of data was an abstract process”). As such, the above steps also fall within the “mental processes” grouping of abstract idea set forth in the 2019 PEG (Section I, 84 Fed. Reg. at 52).
Mathematical Concept
In addition, the building step requires producing directed graphs and the simplifying step requires unipath reduction (i.e. dimensional reduction). Accordingly, these steps require mathematical relationships and/or calculations. This position is further supported by the specification, which clearly shows that these steps require using mathematical calculations and/or algorithms, e.g. hashing procedures, percentage matching, path representation [0058-0065, 0100]. Furthermore, Medvedev (Genome Graphs, 2010, pp.1-100) teaches the use of directed graphs are well known for genome assembly [Section 2.2] and require a clearly defined mathematical function as well as vertices and edges for relating data. Similarly, Chin et al. (US 2015/0302144) teaches the use of algorithms for performing sequence alignment and comparison that specifically include directed graphs [0031, 0061, 0122]. Applicant is also reminded that a mathematical concept need not be expressed in mathematical symbols, because "[w]ords used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). Therefore, when read on light of specification and the teachings of the art, the above limitations clearly encompass a mathematical concept.
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception. In this case, the claimed steps that are not part of the abstract idea are as follows:
outputting the reconstructed coding genome contig for each of the at least one eukaryotic gene family to a user
In this case, the outputting step is generically recited and does not impose any limits on how the data is output or require any particular components that are used to output the information. As such, this step amounts to insignificant post-solution activity and is not indicative of an integration into a practical application. See MPEP 2106.05(g).
With regards to the generically recited processor and various “modules”, these limitations are recited at high level of generality and read on a computer and generic databases. Accordingly, they are merely being used as tools to perform generic computer functions or the abstract idea, as discussed above in Step 2A, Prong One, and therefore amount to no more than mere instructions to apply the exception using a generic computer. See MPEP 2106.05(f). Even when viewed in combination, these additional elements do not integrate the recited judicial exception into a practical application. [Step 2A, Prong 2: NO].
C. Guidance Step 2B:
Under the 2019 PEG, a conclusion that an additional element is insignificant extra-solution activity in Step 2A should be re-evaluated in Step 2B. In this case, the claims do not include additional steps and/or elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons:
As discussed above, the non-abstract steps/elements are recited at a high level of generality and amounts to nothing more than insignificant extra-solution activity. Moreover, applicant’s own specification teaches conventional computer system elements for outputting genomic data [0027, 0044-0046]. Accordingly, this step amounts to well-understood, routine, conventional activity. See MPEP 2106.05(d), subsection II. As discussed in Step 2A, Prong Two above, the recitation of a computer processor to perform the above limitations amounts to no more than mere instructions to apply the exception using a generic computer component. Even when considered in combination, these additional steps/elements represent mere instructions to implement an abstract idea or other exception on a computer and insignificant extra-solution activity, which do not provide an inventive concept. (Step 2B: NO). Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
Dependent Claims
The dependent claims have been considered under the two-part analysis, but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception. Regarding claim(s) 2-5, 7, 8, 10-14, 16-19, 21, these have been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. In particular, claims 2-5, 7, 8, 10-13, 17-19, 21 are all directed to limitations that further limit the specificity of the abstract idea set forth above, and therefore are also encompass a mental processor and/or mathematical concepts for reasons discussed above in the Step 2A (prong 1) analysis. Claims 14 and 16 further limit the nature or specificity of the data used by the abstract idea, and therefore are also part of the abstract idea for reasons discussed above in the Step 2A (prong 1) analysis. Therefore, the claims as a whole are not patent eligible. For additional guidance, applicant is directed generally to the October 2019 Revised Patent Subject Matter Eligibility Guidance.
Response to Arguments
Applicant’s arguments, filed 01/12/2026, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the claimed invention integrates the abstract into a practical application by using data structure elements for improving the functioning of computer technology (by optimizing performance, reducing storage capacity, and system complexity), asserting that the claims mirror the logic applied in Ex Parte Desjardis.
In response, as explained in MPEP 2106.04(d)(1), first the specification should be evaluated to determine if the disclosure provides sufficient details such that one of ordinary skill in the art would recognize the claimed invention as providing an improvement. Second, if the specification sets forth an improvement in technology, the claim must be evaluated to ensure that the claim itself reflects the disclosed improvement.
In this case, a review of Table 4 shows a comparison of two different algorithms running on the same data sets and on the same generic computer processor. While Table 4 does show an “improvement” (namely a decrease in runtime and memory usage), it appears to be found in the algorithm being used to process data. Accordingly, it is event that the computer itself has not been improved. Instead, the improvement is in the algorithm, i.e. the judicial exception itself. In other words, the invention is directed to an improved method of genomic sequence reconstruction but that is not a “technology”---it’s just data processing. It is well settled that mere computer-based efficiency does not save an otherwise abstract method. Bancorp Servs. L.L.C. v. Sun Life Assur. Co. of Canada (US.), 687 F.3d 1266, 1277-78 (Fed. Cir. 2012) (explaining that performance by computer of operations that previously were performed manually or mentally, albeit less efficiently, does not convert a known abstract idea into eligible subject matter). In addition, the Federal Circuit has previously addressed the issue of whether performing data analysis on genetic sequences entails a mental process and determined that it does. In re BRCAJ- and BRCA2-Based Hereditary Cancer Test Patent Litigation, 774 F.3d 755, 763 (Fed. Cir. 2014). As such, the Examiner maintains that Applicant’s claims fail to recite any limitations directed to an improvement in a particular machine, computer, or computer functionality (as in Enfish).
With regards to Ex Parte Desjardins, those claims were directed to solving a problem intrinsic to machine learning using a method for training a machine learning model comprising a plurality of different active method steps directed to model training. Conversely, the instant claims are concerned with using machine learning to solve a problem in genomic sequence reconstruction. Accordingly, applicant’s argument is not persuasive because the instant claims do not recite any limitations directed to training and are directed to an entirely different fact pattern. Similar to Recentive v. Fox, applicant is reminded that AI and machine learning claims need to demonstrate a genuine technological advancement beyond merely applying generic ML to a new use case or achieving increased speed and efficiency to be considered patent-eligible under Section 101. See also MPEP 2106.04(d)(1) for a list of considerations for evaluating whether additional elements integrate a judicial exception into a practical application.
With regard to Enfish, the instant claims are unlike the claims at issue in Enfish because the instant claims are directly to an entirely different fact pattern and do not improve or change the way a computer functions. Indeed, a review of the instant specification teaches only conventional computer processors for performing the claimed method [0044]. Accordingly, there is nothing in the specification to support applicant’s position that the claimed invention is directed to an improvement in a particular machine, computer, or computer functionality (as in Enfish). Therefore, for reasons set forth above, the Examiner maintains that Applicant’s claims fail to recite any limitations that purport to improve the functioning of a specific machine. See Enfish LLC v. Microsoft Corp., 822 F.3d 1327, 1335—6 (Fed. Cir. 2016).
Applicant additionally argues that the claims are directed to a specific technological problem and solution. In response, this argument essentially mirrors the argument set forth above for improving the functioning of computer technology (by optimizing performance, reducing storage capacity, and system complexity). Accordingly, this argument is also not persuasive for reasons set forth above. For the reasons set forth above, the rejection is maintained.
Claim rejections - 35 USC § 112, 2nd Paragraph
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-5, 7, 8, 10-14, 16-19, 21 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1 is/are also rejected due to said dependency.
Claim 1 recites “the memory”. It is unclear as to the metes and bounds of the term "memory” such that one of skill in the art would recognize what limitation is intended based on common knowledge in the art. In this case, the specification fails to provide any limiting definition for this term, which could encompass signals. Clarification is requested via amendment. The Examiner suggests that the instant claims be amended to replace the term memory with a non-transitory computer-readable medium (encoded with a program).
Claim 5 recites “wherein the partitioning the set of full-length transcript sequences into the at least one eukaryotic gene family based on the constructed undirected weighted graph comprised identifying nodes in the undirected weighted graph and then plurality applying a normalized cut technique.” Firstly, the above limitation recites the term “comprised”, which is past tense language that raises questions as to what limiting effect is intended. Secondly, it is unclear what is meant by “plurality applying a normalized cut technique” such that the artisan would know how what limiting effect is intended, i.e. what is “plurality applying”. The examiner believes this to be a grammatical error. In each case, clarification is requested via amendment.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis 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, 3-5, 7, 8, 10-14, 16-19, 21 are rejected under 35 U.S.C. 103 as being unpatentable over Grabherr et al. (Nat Biotechnol., 2013, 29(7): 644–652, pp.1-25; Author Manuscript Version) in view of Wijfjes (Improving transcriptome reconstruction by connecting genomic contigs through RNA-seq read alignments; Student report, Wageningen University, Bioinformatics; 2015, pp.1-15).
Grabherr teaches a method and modular computational algorithm (Trinity) for reconstructing a full-length transcriptome without a genome from RNA-Seq data.
Regarding claim(s) 1, Grabherr teaches obtaining sequence data via pooling a plurality of libraries and obtaining a set of full-length transcript sequences with different isoforms [pages 13-14; Figure 1], wherein the sequence data is from the S. pombe transcriptome (i.e. eukaryotic microorganism) [page 5, ¶3].
Grabherr teaches assembling k-mer reads into the unique sequences of transcripts and constructing a graph of the set of full-length transcript sequences comprising nodes and edges [page 4, ¶4, and Figure 1a], wherein the algorithm uses a default k-mer size of 25 and weights each edge of the graph with the number of (k-1)-mers in the original read set that support it [page 4, ¶4, and Figure 1a, page 10, ¶4]. Grabherr does not specifically teach the use of an undirected weighted graph, as claimed. However, the choice of graph being used is considered a design choice that does not appear to change the function of the claimed process steps, as claimed, and Applicant has not disclosed that this particular feature provides an advantage, is used for a particular purpose, or solves a stated problem. Furthermore, Wijfjes teaches methods for improving transcriptome reconstruction using directed and undirected graphs [see at least page 6]. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to alter the method of Grabherr by alternatively using an undirected weighted graph, as claimed, since Wijfjes teaches such graphs were routinely used in the art. The rationale would have been to account for the reverse complements of contigs.
Grabherr additionally teaches clustering (i.e. partitioning) the related contigs that correspond to portions of alternatively-spliced transcripts or otherwise unique portions of paralogous genes, and constructing (i.e. building) a de Bruijn graph (i.e. directed graph) for each cluster of related contigs, each reflecting the complexity of overlaps between variants [Figure 1b], which reads on partitioning and building as claimed.
Grabherr additionally teaches simplifying the graph by (1) merging consecutive nodes in linear paths in the de Bruijn graph to form nodes that represent longer sequences; and (2) pruning edges that represent minor deviations (supported by comparatively few reads), thereby generating a “reconstructed” graph with less sequencing errors [page 5, ¶2, page 12, and Figure 1c], which reads on simplifying and outputting as claimed.
Regarding claim(s) 3, 4, Grabherr teaches employing a hashing procedure for storing k-mers used on the process [page 10, ¶4, “Inchworm”, page 11, ¶1] and using a default k-mer size of 25 [ page 10, ¶4], which at a minimum suggests a locality-sensitive hashing procedure absent any limiting definition to the contrary.
Regarding claim(s) 5, Grabherr teaches partitioning sequences (as set forth above) and pruning edges that represent deviations [page 5, ¶2], which is broadly interpreted as a normalized cut technique absent any limiting definition to the contrary.
Regarding claim(s) 6, 10, 11, 12, 13, 14, Grabherr teaches that there simplifying process is recursive and includes: merging consecutive nodes into linear (i.e. continuous) paths in the de Bruijn graph to for at least one node that represents longer sequences [page 5 ¶2]; pruning edges that represent minor deviations (supported by comparatively few reads), which likely correspond to sequencing errors [page 5, ¶2]; and plausible path scoring which identifies those paths that are supported by actual reads and read pairs, using a dynamic programming procedure that traverses potential paths in the graph while maintaining the reads (and pairs) that support them [page 5, ¶2].
Regarding claim(s) 16, 18, 19, Grabherr teaches resolving ambiguities by examining individual introns and the combinations of introns (‘splicing patterns’) defined by mapping all the reconstructed transcripts (annotated or not) back to the reference genome [page 8, ¶2; page 12, last ¶; page 5, ¶2], wherein they additional display visualizations of transcripts with accuracy on par with 99% [Figure 6].
Regarding claim(s) 17, Grabherr teaches splitting gene families into sub-partitions, merging (i.e. combining) contigs, and reconstructing contigs to generate a combined contig, as set forth above [see at least Figure 1]. Grabherr does not specifically teach subjecting the combined contig to the reconstructing when a partitioned eukaryotic gene family of the at least one eukaryotic gene families is above a threshold size. However, Grabherr reasonably suggests this feature since they teach splitting gene families into sub-partitions and merging (i.e. combining) contigs if they are more than 95% identical [page 12, ¶5], wherein the percentage reads on a threshold.
Regarding claim(s) 21, Grabherr teaches their algorithm accurately resolved the sequences of closely-related paralogous transcripts, recovering at full length all members of 33 families (68 genes) out of 77 families [page 6, ¶4] and teaches performing algorithms on a server in parallel [page 16, ¶2].
Cited Prior Art
The following prior art made of record and not relied upon is considered pertinent to applicant' s disclosure.
Lee et al. (BMC Genomics (2015) 16:1033, pp.1-11), which teaches a method for de novo transcriptome reconstruction and annotation of the Egyptian rousette bat.
BingXin et al. (Science China, February 2013 , Vol.56, No.2, pp.143–155), which teaches a comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619