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
Claims 1, 4-5, and 8-13 are pending and examined herein.
Claims 2-3 and 6-7 are canceled.
Priority
As detailed on the 08 April 2022 filing receipt, the application claims priority as early as 08 October 2019 to foreign patent JP 2019-185444. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Withdrawn Objections
The objection to the disclosure is withdrawn in view of amendment numbering the first paragraph.
The rejections under 35 USC 112(b) regarding the antecedence of the database filter and function prediction filter are withdrawn in view of amendment of their articles.
The follow objections and/or rejections are either maintained or newly applied, and constitute the complete set of objections and/or rejections applied to the instant claims.
Claim Interpretation
Claim 9 recites an “external apparatus” which is not disclosed in the specification. The specification discloses “an external server” (pg. 29, paragraph [102]). Therefore, the apparatus is interpreted as a server and thus a computer.
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, 4-5, and 8-13 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), 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)). The claims as a whole, considering all claim elements individually and in combination, are directed to a judicial exception at Step 2A, Prong 2, and the additional elements of the claims, considered individually and in combination, do not provide significantly more at Step 2B than the abstract idea of ranking possibility a mutation is pathologic.
MPEP 2106 organizes 101 analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
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)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to a computer system (claims 1, 4-5, and 8-11), a method (claim 12), and a non-transitory computer-readable medium (claim 13), each of which falls within one of the categories of statutory subject matter. [Step 1: 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))?
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)).
Mathematical concepts recited in the independent claims include determining a score and ranking a degree of possibility (claims 1 and 12-13). These steps are interpreted as numerical determinations and represent probability, which are mathematical concepts.
A mathematical relationship may be expressed in words and there is no particular word or set of words that indicates a claim recites a mathematical calculation. That is, a claim does not have to recite the word "calculating" in order to be considered a mathematical calculation. For example, a step of "determining" a variable or number using mathematical methods or "performing" a mathematical operation may also be considered mathematical calculations when the broadest reasonable interpretation of the claim in light of the specification encompasses a mathematical calculation (MPEP 2106.04(a)(2)).
Mental steps recited in claims and 12-13 include: determining if a mutation is in a database, which is a mental step of data comparison; determining if a mutation state affects protein coding, which is interpreted as determining amino acid translation and amino acid comparison, where comparison is a mental step; determining if a mutation is present in multiple species, where the step is interpreted as alignment and comparing amino acids at a given position; determining if a fusion gene is formed and whether the translation is sense or nonsense, where interpreting codons for continuity is a mental step of amino acid translation; determining if a fusion gene is functional is also based on its translation and is also a mental step; determining whether or not the mutation occurs in an enhancer region is a data evaluation step of determining the type and location of the mutation compared to a reference enhancer; and comparing to the time-series data is comparing two sequence for a change at a given position, and thus is data comparison and within the scope of what the human mind can perform,
Claims 4-8 recite additional information about determining the score, which is a mathematical concept as explained above.
Hence, the claims explicitly recite numerous elements that, individually and in combination,
constitute abstract ideas. The claims must therefore be examined further to determine whether they
integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A: 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))?
Because the claims recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they recite elements in addition to the abstract ideas which integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(III)).
The independent claims recite additional elements that are not abstract idea, including an apparatus comprising a non-transitory computer readable medium and a processor (claim 1), receiving sequence information and outputting the created rank information (claims 1 and 12-13), storing information (claim 1), and a storage medium storing a program in a non-transitory manner (claim 13).
Claims 1, 9, and 12-13 recites an external apparatus, interpreted as a computer. The external apparatus is not recited in the preamble of claims 1, 9, or 13 as coupled with the apparatus or memory and thus is interpreted as outside the required apparatus. Claims 1 and 12-13 recite storage of accumulated values of occurrence frequency and outputting a value for mutation state.
The claims recite use of at least one general purpose computer including memory and receiving and/or storing information. The claims comprising computer components do not describe any specific computational steps by which the computer performs or carries out the abstract idea, 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 that a generic computer performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; and MPEP 2106.05(f)). The specification discloses the output is to the control unit, which is interpreted as a computer or processor (pg. 6, paragraph [17]). The claim elements comprising storing records are mere instructions to apply an exception using a computer (MPEP 2106.05(f)) and insignificant extra solution activity (MPEP 2106.05(g)), and necessary data input and output do not integrate the abstract ideas into a practical application. Similarly, outputting data such as a value for a mutation state is insignificant extra solution activity (MPEP 2106.05(g)).
Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are directed to that abstract idea. Claims that are directed to abstract ideas must be examined further to determine whether the additional elements besides the abstract idea render the claims significantly more than the abstract idea. Claims that are directed to abstract ideas and that raise a concern of preemption of those abstract ideas must be examined to determine what elements, if any, they recite besides the abstract idea, and whether these additional elements constitute inventive concepts that are sufficient to render the claims significantly more than the abstract idea (MPEP 2106.05). [Step 2A Prong Two: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself. Step 2B of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05).
The claims recite an apparatus comprising a non-transitory computer readable medium and a processor (claim 1), receiving sequence information and outputting the created rank information (claims 1 and 12-13) and a storage medium storing a program in a non-transitory manner (claim 13). Claims 1 and 12-13 recite storage of accumulated values of occurrence frequency and outputting a value for mutation state.
The claims recite at least one computer, 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)). Receiving information, including over a network to/from an external computer, is a conventional computer function (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).
Finally, storage of sequence information in databases is disclosed as widely used (pg. 1, paragraph [2]). The courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely 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), Versata 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 (storing and retrieving information in memory), as discussed in MPEP 2106.05(d)(II)(i)).
Therefore, the recited additional elements, alone or in combination with the judicial exceptions, do not appear to provide an inventive concept. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
Response to the 11 August 2026 Applicant Remarks
Applicant remarks state, regarding Step 2A of 101 analysis, that the processor and storage are not actions the human mind can perform (pg. 12, Section 1a). This is agreed to and reflected in the office action, as these are elements in addition to the abstract ideas.
Applicant remarks state that structural mutations across multiple genes refers to areas across potentially large genome regions and spanning chromosomes, and that a broadest reasonable interpretation is not short, adjacent genes (pg. 13, second and third paragraphs). While the claims are not limited to short, adjacent genes, they read on embodiments that do not require multiple genes of a given distance, or multiple chromosomes, or a complete genome. A limitation is not being imported from the specification, but merely highlighting embodiments where minimal sizes and distances are within the scope of the claims and would be mentally tractable.
Applicant remarks state the combination of filters modifying the score requires complex computational processing not performable by the human mind, where genomic data cannot be adjusted mentally (pg. 14). Each individual filter was determined to be an abstract idea because they require abstract steps such as determining if a sequence is present in a database, if it affects protein coding, if it is conserved, if it causes a fusion, if it is functional, if it encompasses multiple genes, if it affects regulation, and if it is present in a time series. All of these are considered to be within the scope of what can be performed by the human mind based on comparing data, and adding to or subtracting from the running score is arithmetic. Even if an entire genome of data was required for comparison, which does not seem to be the case, these would be data collection steps for determining the numerical score.
Applicant remarks state the comparison of temporal genetic data cannot be mentally performed (pg. 14, Section d). It is unclear why comparison of sites at two different points in time is any different than the other steps, as they are merely two data points. Active or real-time data collection is not required, only two data points which may have been collected at any point in the past.
Applicant remarks state the instant claim do not recite abstract ideas, but rather involve them because they are performed by a processor and storage (pg. 14, last paragraph) and are directed to a concrete solution of correctly assessing mutation pathogenicity (pg. 15, first paragraph). However, invoking a computer to perform abstract steps does not integrate the abstract ideas into a practical application (MPEP 2106.05(f)). Furthermore, assessing pathogenicity is an abstract step of data evaluation, not an additional elements which may integrate the abstract ideas into a practical application.
At Step 2A Prong Two of 101 analysis, applicant remarks state the instant claims reflect technical improvements in data storage and processing (pg. 15, Section 2a), improvements in pathogenicity determination accuracy (pg. 15, Section 2b), data processing (pg. 16, Section 2c), and actionable steps and advantages (pg. 16, Section 2d). Regarding Section 2a, enabling a processor and memory to perform abstract steps is merely invoking a general purpose computer, which does not integrate the abstract ideas into a practical application (MPEP 2106.05(f)). Regarding Section 2b, applicant analogizes to Ex Parte Desjardins, suggesting improvement to an AI model in the form of the filters. However, the problem addressed in Ex Parte Desjardins is a problem rooted in computer technology, whereas the instant claims use a general purpose computer to execute abstract steps to solve a biological issue. Therefore, the comparison is not persuasive as the improvement lies in the abstract steps. Regarding Section 2c, applicant remarks state the arrangement of filters, storage, and processor is unconventional and provides a technical advantage. This explanation appears to conflate Step 2A Prong Two and 2B, as the conventionality of an arrangement of elements in addition to the abstract ideas is the criterion at 2B. However, as the filters are abstract elements and the computer and data storage are conventional, the claims are not considered to overcome the rejection at Step 2B. Regarding Section 2d, applicant remarks state the rank information reflecting a mutation possibility is tangible and specific output which provides an advantage in allowing a user to determine a mutation state. However, outputting a value based on adding and subtracting scores is not tangible output but merely data. Therefore, it is not clear what element in addition to the abstract ideas is helping provide the improvement.
Applicant remarks state determining a score and ranking a degree of possibility, as stated in previous office actions, do not render the claim ineligible and must be considered with other elements such as the computer elements, data storage, filters, and output (pg. 16-17). It is agreed that the mere presence of mathematical steps does not preclude eligibility under 35 USC 101. However, the presence of abstract ideas necessitates further analysis at Step 2A Prong Two and 2B, where elements in addition to the abstract ideas – that is, those other than mathematical and mental steps – are analyzed to determine if they integrate the abstract ideas into a practical application at Step 2A Prong Two and, failing that, if they are unconventional and provide significantly more than the abstract ideas at Step 2B. The computer elements, data storage, and data input and output were not considered to integrate the abstract ideas into a practical application nor are they unconventional, and thus the rejection is interpreted as directed to abstract ideas.
Applicant remarks state, regarding Step 2B, applicant remarks state the previous office actions ignore the claims recite a specific combination of elements that is unconventional and not taught by the prior art (pg. 17). However, at Step 2B, claims are analyzed to determine whether they recite an inventive concept that provides significantly more than the judicial exception itself in the form of additional elements that amount to an inventive concept. An inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05). The claims recite an apparatus comprising a non-transitory computer readable medium and a processor (claim 1), receiving sequence information and outputting the created rank information (claims 1 and 12-13) and a storage medium storing a program in a non-transitory manner (claim 13). Claims 1 and 12-13 recite storage of accumulated values of occurrence frequency and outputting a value for mutation state. These elements amount to using a computer to perform the abstract ideas, plus input/output and storage, which are conventional computer functions which do not provide significantly more at Step 2B.
Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
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/Robert J. Kallal/Examiner, Art Unit 1685
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