DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
The amended claim set received 12 September has been entered into the application.
Claims 1 and 11 are amended.
Claim 6 is cancelled.
Claim 2-5, 8, 10, and 12-14 are previously cancelled.
Claim(s) 1, 7, 9, 11, and 15 are pending.
Priority
This Application is 371 of PCT/KR2018/014079 filed 16 November 2018 which claims foreign priority to KR10-2018-0139875 filed 14 November 2018 and KR10-2018-0116410 filed 28 September 2018.
Claim Objections
The objection to claim 1 in the Office Action mailed 13 June 2025 is withdrawn in view of the amendments received 12 September 2025.
Claim Rejections - 35 USC § 101
The instant rejection is maintained for reason for record in the Office Action mailed 13 June 2025 and modified in view of the amendments filed 12 September 2025.
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, 7, 9, 11, and 15 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Following the flowchart of MPEP 2106
Step I - Process, Machine, Manufacture or Composition
Claims 1, 7, and 9 are directed towards a method, so a process. Claims 11 and 15 are drawn to an apparatus, so a machine.
2A Prong II - Identification of an Abstract Idea
Claim 1 recites:
determining, by the computer apparatus, k-mer reads in the sample sequence data
This step can be performed in the human mind by observing and evaluating sample sequence data to determine k-mers reads and is therefore an abstract idea.
wherein the k-mer reads are present in the k-mer table
This step is a description of the data that is being analyzed by the abstract idea/mental process.
determining, by the computer apparatus, a breakpoint and a candidate region of a structural variation by mapping the at least one target k-mer read to standard reference genome data
This step can be performed in the human mind by observing and evaluating mapped k-mers to a standard reference genome data to determine a breakpoint and a candidate region of a structural variation and is there an abstract idea.
predicting, by the computer apparatus, a structural variation type for the sample sequence data on the basis of a sequence mapping pattern and the breakpoint in the mapping result
This step can be performed in the human mind by observing and evaluating sequence mapping patterns and the breakpoint in the mapping result to predict a structural variation type and is therefore an abstract idea.
wherein the predicted structural variation type is an indicator for cancer diagnosis
The step describes the predicted structural variation type as an indicator for cancer diagnosis.
wherein the k-mer table comprises (i) multi-reference genome data including reference genomes of the plurality of races, (ii) published single nucleotide polymorphism (SNP) data, (iii} published small insertions/deletions (INDEL) data and (iv) normal genome data of a normal person
This step is a description of the table that is being analyzed by the abstract idea/mental process.
wherein the standard reference genome data is single reference genome data for a specific race.
This step is a description of the data that is being analyzed by the abstract idea/mental process.
wherein the data structure of the k-mer table is a hash table.
This step describes the data structure of the k-mer table as a hash table.
Claim 11 recites:
predict the structural variation type on the basis of a sequence mapping pattern and a breakpoint determined by mapping the at least one target k-mer read to the standard reference genome data
This step can be performed in the human mind by observing and evaluating the sequence mapping pattern and the breakpoint of the target k-mer read that is mapped to the standard reference genome data to predict the structural variation and is therefore an abstract idea.
wherein the predicted structural variation type is an indicator for cancer diagnosis
The step describes the predicted structural variation type as an indicator for cancer diagnosis.
wherein the k-mer table comprises (i) multi-reference genome data including reference genomes of a plurality of races, (ii) published single nucleotide polymorphism (SNP) data, (iii) published small insertions/deletions (INDEL) data and (iv) normal genome data of a normal person
This step is a description of the data that is being analyzed by the abstract idea/mental process.
wherein the standard reference genome data is single reference genome data for a specific race
This step this is a description of the data that is being analyzed by the abstract idea/mental process.
wherein the data structure of the k-mer table is a hash table.
This step describes the data structure of the k-mer table as a hash table.
Claims 6-7, 9, and 15 are further drawn to limitations that describe the abstract ideas of claims 1 and 11 are therefore also abstract ideas.
2A Prong II - Consideration of Practical Application
Claim 1 does not recite any additional element which integrates the judicial exception into a practical application. Here, in the instant case, the claims merely set forth a method of data analysis for analyzing sequence reads (i.e., k-mers) in a table to determine k-mers and determine breakpoints and candidate structural variations for predicting a structural variation type. Such a result only produces information (i.e., structural variation data) and does not provide for a practical application in the physical realm of physical things and acts, i.e., the claims do not utilize the data generated by the judicial exception to affect any type of change. See MPEP 2106.04(a)(2)(A)(iv). Therefore, the claims do not utilize the received sequence data, loaded k-mer table, determined k-mer reads, determined breakpoint and candidate structural variation, and predicted structural variation and abstract ideas to construct a practical application such as treating a subject, transformation of matter, or improving upon an existing technology.
Claim 11 does not recite any additional element which integrates the recited judicial exception into a practical application. Here, in the instant case, the claims merely set forth a method of data analysis for analyzing sequence reads (i.e., k-mers) in a table by extracting and filtering k-mer data for predicting a structural variation type. Such a result only produces information (i.e., structural variation data) and does not provide for a practical application in the real-world realm of physical things and acts, i.e., the claims do not utilize the data generated by the judicial exception to affect any type of change. See MPEP 2106.04(a)(2)(A)(iv). Therefore, the claims do not utilize input device configured to receive sequence data, stored k-mer table and computer configured to extract target k-mer from sample sequence data loaded k-mer table and predicted structural variation and abstract ideas to construct a practical application such as treating a subject, transformation of matter, or improving upon an existing technology.
The recited additional element of data gathering of claim 1 does not integrate the recited judicial exception into a practical application because receiving sequence data that is subsequently analyzed by abstract ideas is deem an extra-solution activity. See MPEP 2106.05(g).
The recited additional element of receiving and inputting data of claim 1 does not integrate the recited judicial exception into a practical application because receiving/inputting data of a table into a computer is deemed an extra-solution activity. See MPEP 2106.05(g).
The recited additional element of extracting data of claims 1 and claim 11 does not integrate the recited judicial exception into a practical application because extracting data that is subsequently filtered and analyzed by abstract ideas is a tangential computer function for gathering data from files or documents. See MPEP 2106.05(d)(II)(v).
The recited additional element of using computers processes, components, and equipment of claim 11 does not integrate the recited judicial exception into a practical application because using computers to process, store, load, and extract sequence data that is subsequently analyzed by abstract ideas are a tangential to the claimed process. See MPEP 2106.05(b) and 2106.05(d).
The recited additional element of storing data of claim 11 does not integrate the recited judicial exception into a practical application because storing sequence data that is subsequently analyzed by abstract idea is tangential to the claimed process. See MPEP 2106.05(d).
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses 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.
2B Analysis - Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea.
The recited additional element of data gathering of claim 1 does not add significantly more to the recited judicial exception because receiving sequence data, that is subsequently analyzed by abstract ideas, is deem a well-known and conventional extra-solution activity. See MPEP 2106.05(g).
The recited additional element of receiving and inputting data of claim 1 does not add more than the recited judicial exception because receiving/inputting data of a table into a computer is deemed a well-known and conventional extra-solution activity. See MPEP 2106.05(g) regarding extra solution activity.
The recited additional element of extracting data of claims 1 and claim 11 does not add significantly more than the recited judicial exception because extracting data that is subsequently filtered and analyzed by abstract ideas is well-known and conventional. See MPEP 2106.05(d)(II)(v).
The recited additional element of using computers processes, components, and equipment of claim 11 does not add significantly more than the recited judicial exception because using computers to process, store, load, and extract sequence data that is subsequently analyzed by abstract ideas is well-known and conventional. See MPEP 2106.05(b) and 2106.05(d).
The recited additional element of storing data of claim 11 does not add significantly more than the recited exception because storing sequence data that is subsequently analyzed by abstract idea is well-known and conventional. See MPEP 2106.05(d).
In conclusion and when viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Response to Arguments
Applicant's arguments filed 12 September 2025 have been fully considered but they are not persuasive.
The Applicant states “previously pointed out, the effect of the present invention is described in Figures 5 to 7 of the specification. Specifically, the presently claimed method and apparatus (using "multi reference genome") demonstrate better performance Fl-score of 0.78 compared to the other tested methods even at sequencing depth of I Ox as shown in Figure 5A; better performance FIscore of 0.59 compared to the other tested methods even when tumor purity is 10% as shown in Figure SB; and overall superior performance compared to conventional technologies including novoBreak disclosed in Chong as shown in Figures 6 and 7. The Examiner appears to simply dismiss these results without any substantiation.” [remarks, pages 5-6].
In response, the claims, in view of the specification, do not set forth evidence that the claimed process causes a computer to operate differently than it ordinarily would. It appears that the claims are drawn to an abstract idea that results in a computational process that is more efficient as compared to selected others known in the art. However, the computer is not improved by way to the claimed process. As such and as described by the MPEP 2106.05(a)(II), for example, in Trading Technologies Int’l v. IBG, 921 F.3d 1084, 1093-94, 2019 USPQ2d 138290 (Fed. Cir. 2019), the court determined that the claimed user interface simply provided a trader with more information to facilitate market trades, which improved the business process of market trading but did not improve computers or technology. Therefore, even though there is a change in the FIscore, it is insufficient to show an improvement to a computer or computer technology. Thus, the claim(s) must include more than mere instructions to perform the method on a generic component or machinery to qualify as an improvement to an existing technology. Here, the claims are drawn to data filtering and data selection by prediction. As such, these data filtering and data selection by prediction steps are abstract ideas for selecting and reducing information. Therefore, the claims do not recite additional elements that reflect an improvement to technology such as an improvement to a computer or computer technology, for example. See MPEP 2106.04(d)(1). Furthermore, and as noted in Step 2A Prong II of the 101 analyses above, the instant claims are drawn to gathering and analyzing information (i.e., sequence data: A, T, G, C) using conventional techniques (i.e., hash table storage) and displaying the result (i.e., predicted structural variation) which is insufficient to show an improvement to technology. See MPEP 2106.05(A)(II)(iii).
The Applicant states the claims are not drawn to conventional techniques. The Applicant points to figures 5-7 for guidance [remarks, page 5-6]. The Applicant points to Enfish for guidance. The Applicant states “In Enfish, the court concluded the claims were not directed to an abstract idea, but rather an improvement to computer functionality, because the invention improved the way the computer stores and retrieves data in memory in combination with the specific data structure. Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1339 (Fed. Cir. 2016). The court stated that the claim was not simply the addition of general-purpose computers added post-hoc to an abstract idea, but a specific implementation of a solution to a problem in the software arts. Id at 1339.” [remarks, page 6].
In response and with respect to Enfish, the court determined that claims related to a database architecture that used a new, self-referential logical table were non-abstract because they focused on “an improvement to computer functionality itself, not on economic or other tasks for which a computer is used in its ordinary capacity.” Id. at 1336. Indeed, the self-referential database found patent eligible in Enfish did more than allow computers to perform familiar tasks with greater speed and efficiency; it permitted users to launch and construct databases in a new way. While deployment of a traditional relational database involved “extensive modeling and configuration of the various tables and relationships in advance of launching the database,” Enfish’ s self-referential database could be launched “with no or only minimal column definitions” and configured and adapted “on-the-fly.” Id. at 1333. Additionally, the claims of Enfish were found not to contain abstract ideas because they focused on “an improvement to computer functionality itself, not on economic or other tasks for which a computer is used in its ordinary capacity.” Compared to the instant claims, where the computer functionality and elements are merely tangential to the claimed steps. Furthermore, the instant claims are drawn to merely storing structural genetic sequence data of races in a hash table which doesn’t provide an improvement to technology because the claims are drawn to receiving sequence data, loading a k-mer, determining k-mer reads, determining a breakpoint predicting structural variation which is merely gathering and analyzing information (i.e., sequence data: A, T, G, C) using conventional techniques (i.e., hash table storage) and displaying the result (i.e., predicted structural variation). See MPEP 2106.05(A)(II)(iii). The claims, in view of the specification, do not set forth evidence that the claimed process causes a computer to operate differently than it ordinarily would. Thus, the computer is not improved by way to the claimed process. Therefore, the claims do not provide an improvement under Enfish.
The Applicant points to McRo for guidance. The Applicant states “In McRO, the court indicated that it was the incorporation of the particular claimed rules in computer animation that "improved [the] existing technological process", unlike cases such as Alice where a computer was merely used as a tool to perform an existing process. McRO, Inc. v. Bandai Namco Games America, Inc., 837 F.3d 1299, 1314 (Fed. Cir. 2016).” [remarks, page 6].
In response, claim 1 of McRo is limited to a specific process for automatically animating characters using particular information and techniques and does not preempt approaches that use rules of a different structure or different techniques. Claim 1 of McRo used these rules in a process specifically designed to achieve an improved technological result in conventional industry practice for lip synchronization animation. By using and incorporating the claimed rules, the method of McRo led to an improvement that allowed computers to produce “accurate and realistic lip synchronization and facial expressions in animated characters” that previously could only be produce by human animators. Therefore, the claims of McRO were found to be a patentable, technological improvement over the existing, manual 3-D animation techniques. The claims of McRo used limited rules in a process specifically designed to achieve an improved technological result of a computer product, i.e. lip synchronization animation which was found not to encompass abstract ideas. Whereas, the instant claims are drawn to merely storing structural genetic sequence data of races in a hash table for predicting genetic structural variation which doesn’t provide an improvement to technology because the claims are drawn to receiving sequence data, loading a k-mer, determining k-mer reads, determining a breakpoint predicting structural variation which is merely gathering and analyzing information (i.e., sequence data: A, T, G, C) using conventional techniques (i.e., hash table storage) and displaying the result (i.e., predicted structural variation). See MPEP 2106.05(A)(II)(iii). The claims, in view of the specification, do not set forth evidence that the claimed process causes a computer or computer product to operate differently than it ordinarily would based on predicting structural genetic variation. Thus, the computer or a computer product is not improved by way to the claimed process. Therefore, the claims do not provide an improvement under McRo.
The Applicant points to Finjan for guidance. The Applicant states “ In Finjan, the court determined that the claims were eligible for a patent because the claimed method enabled more flexible virus filtering and greater user customization than the preexisting methods, which reflected improvement to the computer function. Finjan Inc. v. Blue Coat Systems, Inc., 879 F.3d 1299, 1286-87 (Fed. Cir. 2018).” [remarks, page 6].
In response, claim 1 of Finjan from U.S. Patent 6,615,844 is drawn to a method comprising receiving by an inspector a Downloadable, generating by the inspector a first Downloadable security profile that identifies suspicious code in the received Downloadable, and linking by the inspector the first Downloadable security profile to the Downloadable before a web server makes the Downloadable available to web clients. In Finjan, the method of claim 1 employs a new kind of file that enables a computer security system to do things it could not do before. The security profile approach allows access to be tailored for different users and ensures that threats are identified before a file reaches a user’s computer. The fact that the security profile “identifies suspicious code” allows the system to accumulate and utilize newly available, “behavior-based” information about potential threats. The asserted claims are therefore directed to a non-abstract improvement in computer functionality, rather than the abstract idea of computer security writ large. Whereas, the instant claims are drawn to merely storing structural genetic sequence data of races in a hash table and making predictions regarding genetic structural variation which doesn’t provide an improvement technology because the claims are drawn receiving sequence data, loading a k-mer, determining k-mer reads, determining a breakpoint for predicting structural variation which is merely gathering and analyzing information (i.e., sequence data: A, T, G, C) using conventional techniques (i.e., hash table storage) and displaying the result. See MPEP 2106.05(A)(II)(iii). The claims, in view of the specification, do not set forth evidence that the claimed process causes a computer to operate differently than it ordinarily would based on predicting genetic structural variation. Thus, the computer is not improved by way to the claimed process. Therefore, the claims do not provide an improvement under Finjan.
The Applicant states “The court's rationale articulated in these cases is fully applicable to the present claims. Applicant demonstrated that the claimed method and apparatus provide tangible improvements in several parameters related to data processing and analysis. Further, the present claims provide a specific data structure as a k-mer table and enable large-scale computation using the hash table data structure. These computations cannot be performed in a human mind. Thus, the present claims are directed to an improvement in computer technology and in genomic analysis technology as demonstrated by measuring specific performance parameters.”[remarks, page 7].
In response, as noted in Step 2A Prong I of the above 101 analyses, the claims encompass abstract ideas. Furthermore, under step 2A Prong II of the above 101 analyses, the claims do not encompass any additional elements that integrate the recited judicial exception into a practical application. Additionally, the claims do not provide an improvement to technology because the claims are drawn receiving sequence data, loading a k-mer, determining k-mer reads, determining a breakpoint predicting structural variation which is merely gathering and analyzing information (i.e., sequence data: A, T, G, C) using conventional techniques (i.e., hash table storage) and displaying the result (i.e., predicted structural variation) which is in sufficient to show an improvement to technology. See MPEP 2106.05(III)(iii).
Conclusion
Claims 1, 7, 9, 11, and 15 are rejected.
No claims are allowed.
Finality
THIS ACTION IS MADE FINAL. 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.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH C PULLIAM whose telephone number is (571)272-8696. The examiner can normally be reached 0730-1700 M-F.
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/J.C.P./Examiner, Art Unit 1687
/Anna Skibinsky/
Primary Examiner, AU 1635