DETAILED ACTION
Applicant’s response, filed May 26 2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn.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.
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 .
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.
Claim Status
Claims 16-25 and 27-34 are pending.
Claims 1-15 and 26 are canceled.
Claims 16-25 and 27-34 are rejected.
Priority
This application is a CON of 16/057,357 filed Aug 7 2018 (now USP 11,894,106), which claims priority to provisional application 62/542,203, filed Aug 7 2017.
Accordingly, each of claims 16-25 and 27-34 are afforded the effective filing date of Aug 7 2017.
Claim Rejections- 35 USC § 112
The outstanding rejections to the claims are withdrawn in view of the amendments submitted herein.
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 16-25 and 27-34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portions are necessitated by claim amendment.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows 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.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
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;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to a method, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
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) are as follows:
Independent claim 16: reconstructing… the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication.
Dependent claim 20: reconstructing… at least an approximation of the quality score curve based on the quality score parameter information.
Dependent claims 27-34 recite further steps that limit the judicial exception of reconstructing the unaligned genomic sequence read data in independent claim 16 and, as such, also are directed to those abstract ideas.
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 because the method only requires a user to manually reconstruct sequence read data based on a reference sequence and a variant list. Without further detail as to the methodology involved in “reconstructing”, under the BRI, one may simply, for example, use pen and paper to perform such an action.
Therefore, claim 16 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they 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).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claim 16: receiving, by the first computing system from a second computing system, an initiation of a transfer of unaligned genomic sequence read data;
receiving, by the first system from the second computing system, a variant list representative of the unaligned genomic sequence read data, a first indication of a first reference motif included in the unaligned genomic sequence read data, and a second indication of a second reference motif included in the unaligned genomic sequence read data, the variant list indicating differences between at least a first portion of the unaligned genomic sequence read data and at least a portion of a first reference sequence associated with the first reference motif and differences between at least a second portion of the unaligned genomic sequence read data and at least a portion of a second reference sequence associated with the second reference motif, the first reference sequence being different than the second reference sequence;
wherein reconstructing the unaligned genomic sequence read data further comprises: accessing, using the first indication, the at least a portion of the first reference sequence; and accessing, using the second indication, the at least a portion of the second reference sequence.
Dependent claim 17: receiving, by the first computing system from the second computing system, quality score curve parameter information.
Dependent claims 18-19 and 21-25 recite steps that further limit the recited additional elements in the claims. For example, claims 18-19 and 21-24 further limits the received quality score curve parameter information; and claim 25 further limits the received first indication.
The claims also include non-abstract computing elements. For example, independent claim 16 includes a first computing system comprising a processor and a non-transitory computer-readable medium storing instructions that, when executed by the processor, cause the first computing system to perform the method and a second computing system.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “receiving” and “accessing” data, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering and outputting do not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering and outputting steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
Further steps directed to additional non-abstract computing elements 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, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
The specification as published discloses that the instant invention allows for the communication of unaligned sequence read data to a system with greater computational resources to perform the alignment process without communicating all of the unaligned sequence read data at [0006-0007], but does not provide a clear explanation for how the additional elements provide these improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
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 prosecution 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).
With respect to the instant claims, 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, as discussed in MPEP 2106.05(d)(II)(i)). As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claims 16 and those claims dependent therefrom, the computer-related elements or the general purpose computer do not rise to the level of significantly more than the judicial exception. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, which the courts have found to not provide significantly more when recited in a claim with a judicial exception (Alice Corp., 573 U.S. at 225-26, 110 USPQ2d at 1984; see MPEP 2106.05(A)). The specification as published also notes that computer processors and systems, as example, are commercially available or widely used at [0035]. The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Response to Applicant Arguments
At p. 7-9, par. 2, Applicant submits that the claims do not recite a judicial exception at Step 2A, Prong 1 because the claims recite a computer implemented method for efficiently communicating genomic information between computer systems by reconstructing unaligned genomic sequence read data based on a variant list and first and second indications. Applicant submits that the claimed invention is dissimilar to the examples of general “observations, evaluations, judgments, and opinions” detailed in MPEP 2106.04(a)(2)(III), and that certain elements of the claimed method cannot be practically performed in the mind.
It is respectfully submitted that this is not persuasive. As set forth in MPEP 2106.04(II), Step 2A is a two-prong inquiry, in which examiners determine in Prong 1 whether a claim recites a judicial exception. MPEP 2106.04(I) sets forth that when determining whether a claim recites a judicial exception, it is sufficient to identify the claimed concept which aligns with at least one judicial exception, or, in other words, the specific claim limitations that the examiner believes may recite an exception. That the claim recites limitations which are in addition to those which recite judicial exceptions (i.e., additional elements) does not alter the analysis to determine whether a claim recites a judicial exception performed at Step 2A, Prong 1 (see MPEP 2106.04(II)(A)(1)). Those additional elements are examined at Step 2A, Prong 2, to determine whether the claim is directed to the judicial exceptions (see MPEP 2106.04(II)(A)(2)), which is discussed further below. As set forth in the above rejection, those limitations which are considered to recite a judicial exception are identified at Step 2A, Prong 1, and why they are considered to recite a judicial exception is explained, as is required by the eligibility analysis as outlined in MPEP 2106.04.
The instant claims recite “reconstructing… the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication” in claim 16 and “reconstructing… at least an approximation of the quality score curve based on the quality score parameter information” in claim 20, which are considered to recite a mental process as described in the above rejection. It is considered that a person could use an indication to retrieve a part of a reference sequence and compare that sequence with a variant to identify what the entire sequence would be. A person could then substitute the variant into the reference sequence to reconstruct the original unaligned sequence. Therefore, “reconstructing” is considered to recite a mental process, rather than merely involve an exception. That the MPEP provides no examples which are similar in scope to the claimed act of “reconstructing” does not mean that “reconstructing” does not recite a mental process. Further, Applicant has provided no specific arguments for why “reconstructing” cannot be performed mentally.
At p. 9, par. 3 through p. 10, par. 2, Applicant submits that the combination of elements in the claim apply any abstract idea in a meaningful way because, when properly giving weight to all additional elements, whether or not they are conventional, there is a practical application that imposes meaningful limits and which do not seek to monopolize any judicial exception. Applicant submits that the claims recite an improved method for efficiently communicating genomic information between computer systems.
It is respectfully submitted that this is not persuasive. Conventionality of the additional elements is not examined at Step 2A, Prong 2. In the above rejection, each additional element is properly examined in relation to the recited judicial exception (i.e., the claims as a whole) to ascertain whether there is a practical application. The claims merely recite receiving, by a computer, data which is required by the judicial exception for its performance. Therefore, the additional elements of “receiving” and “accessing”, which are the only additional elements in the claims, function as data gathering steps, and therefore do not provide a practical application of the judicial exception, similar to the example of an improved particular method of digital data compression.
While preemption is the concern underlying the judicial exceptions, it is not a standalone test for determining eligibility (Rapid Litig. Mgmt. v. CellzDirect, Inc., 827 F.3d 1042, 1052, 119 USPQ2d 1370, 1376 (Fed. Cir. 2016)). It is necessary to evaluate eligibility using the Alice/Mayo test, because while a preemptive claim may be ineligible, the absence of complete preemption does not demonstrate that a claim is eligible (Diamond v. Diehr, 450 U.S. 175, 191-92 n.14, 209 USPQ 1, 10-11 n.14 (1981); “We rejected in Flook the argument that because all possible uses of the mathematical formula were not pre-empted, the claim should be eligible for patent protection”; see MPEP 2106.04).
Regarding the supposed improvement, it is maintained that the claims merely recite a computer receiving data. The type of data which is received by the computer does not alter the function of the computer while it is receiving data or while it is performing the reconstruction. Therefore, the function of the computer in the claims is not changed, and the claims do not reflect an improvement in the functioning of a computer.
Regarding Applicant’s assertion that the claims are similar to the improved particular method of digital data compression described in MPEP 2106.05(a)(II), it is noted that the example pointed to by Applicant is the case of DDR Holdings, LLC v. Hotels.com, L.P., 773 F.3d 1245, 1258, 113 USPQ2d 1097, 1106 (Fed. Cir. 2014). In DDR Holdings, the claims were found patent eligible because they specified how interactions with the Internet are manipulated to yield a desired result‐‐a result that overrides the routine and conventional sequence of events ordinarily triggered by the click of a hyperlink, providing an example that computer-implemented processes can be significantly more than an abstract idea (and thus eligible), when generic computer components are able in combination to perform functions that are not merely generic (see MPEP 2106.05(d)(II)). The courts found that the modification of conventional internet hyperlink protocol in DDR Holdings provided an improvement in computer functionality (see MPEP 2106.05(a)(I)). However, the instant claims are not analogous to the claims at issue in DDR Holdings because they do not recite modification of conventional internet hyperlink protocol which provides an improvement to computer functionality. The instant claims, as described above, are not considered to recite an improvement in computer functionality because they merely require a computer to receive data in a normal manner.
At p. 10, par. 3-4, Applicant submits that the claims are neither anticipated nor rendered obvious over the art of record and are thus directed to inventive concepts at Step 2B.
It is respectfully submitted that this is not persuasive. Applicant is reminded that the standard for assessing the conventionality of the additional elements at Step 2B of the 35 USC 101 analysis is separate and distinct from the standard for applying prior art under 35 USC 102 or 103 (see MPEP 2106.05(I)). Because they are separate and distinct requirements from eligibility, patentability of the claimed invention under 35 U.S.C. 102 and 103 with respect to the prior art is neither required for, nor a guarantee of, patent eligibility under 35 U.S.C. 101. The difference between conventionality of the additional elements at Step 2B and novelty under 35 U.S.C. 102 and 103 partly stems from the fact that only the additional elements of the claim are considered at Step 2B, rather than the claims as a whole. MPEP 2106.05(d) sets forth that, at Step 2B, it is the additional elements which are examined to determine whether they are well-understood, routine, conventional activities previously known to the industry. The analysis at Step 2A, Prong 2, considers the claims as a whole, i.e., the additional elements in combination with the judicial exceptions (see MPEP 2106.05(a)), although the integration or improvement provided in the claim must flow from the additional elements and not the judicial exceptions to be considered persuasive. However, Step 2B requires examining only the additional elements, either alone or in combination with one another, for conventionality. An “inventive concept” is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception, and is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception itself (Alice Corp., 573 U.S. at 27-18, 110 USPQ2d at 1981 (citing Mayo, 566 U.S. at 72-73, 101 USPQ2d at 1966)). The limitations pointed to be Applicant are considered to recite a judicial exception as described above and are therefore not considered at Step 2B.
As set forth in the above rejection, the additional elements of the claims of “receiving” and “accessing” data recite conventional functions of a generic computer and do not provide significantly more at Step 2B.
Claim Rejections - 35 USC § 102
The outstanding rejections from the previous Office Action are withdrawn in view of the amendments submitted herein. Although Hahm et al. (US 2018/0121601 A1; priority Oct 28 2016) is considered to teach reconstructing, by the first computing system, the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication, Hahm does not teach a variant list indicating differences between at least a first portion of the unaligned genomic sequence read data and at least a portion of a first reference sequence associated with the first reference motif and differences between at least a second portion of the unaligned genomic sequence read data and at least a portion of a second reference sequence associated with the second reference motif and accessing the at least a portion of one or more reference sequences in order to reconstruct unaligned genomic sequence read data as recited in claim 16.
Claim Rejections - 35 USC § 103
The outstanding rejections from the previous Office Action are withdrawn in view of the amendments submitted herein. Although Hahm et al. (US 2018/0121601 A1; priority Oct 28 2016) is considered to teach reconstructing, by the first computing system, the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication, neither Hahm or Huang et al. (GigaScience, 2017, 6(5), pages 1–9; cited on the Dec 18 2023 IDS) teaches a variant list indicating differences between at least a first portion of the unaligned genomic sequence read data and at least a portion of a first reference sequence associated with the first reference motif and differences between at least a second portion of the unaligned genomic sequence read data and at least a portion of a second reference sequence associated with the second reference motif and accessing the at least a portion of one or more reference sequences in order to reconstruct unaligned genomic sequence read data as recited in claim 16.
Double Patenting
The terminal disclaimer filed on May 26 2026 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of U.S. Patent No. 11894106 has been reviewed and is accepted. The terminal disclaimer has been recorded.
The outstanding rejections from the previous Office Action is therefore withdrawn.
Conclusion
No claims are allowed.
The claims appear to be free of the prior art. Although the closest prior art to Hahm et al. (US 2018/0121601 A1; priority Oct 28 2016) is considered to teach reconstructing, by the first computing system, the unaligned genomic sequence read data based on the variant list, the first indication, and the second indication, neither Hahm or any other identified references fairly teach a variant list indicating differences between at least a first portion of the unaligned genomic sequence read data and at least a portion of a first reference sequence associated with the first reference motif and differences between at least a second portion of the unaligned genomic sequence read data and at least a portion of a second reference sequence associated with the second reference motif and accessing the at least a portion of one or more reference sequences in order to reconstruct unaligned genomic sequence read data as recited in claim 16.
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 JANNA NICOLE SCHULTZHAUS whose telephone number is (571)272-0812. The examiner can normally be reached on Monday - Friday 8-4.
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/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685
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