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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 09/24/2025 has been entered.
Applicant’s amendments and remarks, filed on 09/24/2025, are acknowledged. Applicant’s arguments have been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application. Rejections and/or objections not reiterated from the previous office actions are hereby withdrawn.
Status of Claims
Claims 21, 24-28, 31-35, 38-42 are under examination.
Claims 1-20, 22-23, 29-30, 36-37 are cancelled.
Priority
This application claims priority under 35 U.S.C. § 120 and is a continuation of U.S.
Application No. 14/517,419, filed October 17, 2014, which claims priority under 35 U.S.C. § 119(e) to U.S. Patent Application No. 61/892,666, filed October 18, 2013.
Withdrawn Rejections
The rejection of claims 21, 24-28, 31-35, 38-40 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112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is withdrawn in view of applicant’s amendments.
The rejection of claims 21, 28, 35 under 35 U.S.C. 103(a) as being unpatentable over Yanovsky et al. (International Workshop on Algorithms in Bioinformatics, 2008, Algorithms in Bioinformatics, pp 38-49) is withdrawn in view of applicant’s amendments.
The rejection of claims 21, 28, 35 is/are provisionally rejected under the judicially created doctrine of obviousness-type double patenting as being unpatentable over claims 21, 23, 25, 30, 32-34 of copending application 17/359338 is withdrawn in view of applicant’s amendments.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.
The following rejection has been modified in view of applicant’s amendments.
Claims 21, 24-28, 31-35, 38-42 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 United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Guidance Step 1:
Regarding claim(s) 21, 28, 35 the claimed invention is directed to a system for performing a series of process steps and therefore falls within one of the four statutory categories. Thus, the claim is directed to one of the statutory categories of invention. MPEP 2106.03.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. In this case, the claimed steps that are part of the abstract idea are as follows:
aligning the sequence read to the reference dag data structure…by: creating…a matrix for each of the…nodes to obtain a set of matrices…;
determining… a plurality of scores; determining…an overlap value indicative of a number of overlapping symbols..;
genotyping the genetic sample…when the overlap value exceeds a threshold.
Mental Processes
Under the broadest reasonable interpretation, the claimed steps listed in italics above mimic human thought processes of aligning different types of information, i.e., evaluation, determining relationships and scores, perhaps with paper and pencil, perceptible only in the human mind, i.e. analysis, and making determinations based on said analysis and/or criteria. 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 include only data analysis methods [pages 6, 7]. Accordingly, but for the recitation of a computer processor, the above steps clearly fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III [Step 2A, Prong 1: YES].
Mathematical Concept
In addition, the following steps require mathematically relating data and/or mathematical calculations. In particular, the aligning step requires creating a matrices (which are a mathematical concept) and determining scores amounts to mathematical calculations (based on degrees of overlap). Notably, a mathematical relationship is a relationship between variables or numbers, and may be expressed in words or using mathematical symbols. See MPEP 2106.04(a)(2). Moreover, the specification specifically teaches specific algorithms for aligning sequence data and DAGs includes creating matrices using mathematical equations [pages 3-4]. Therefore, when read in light of applicant’s own specification, the claims are directed to manipulating information through a mathematical concept. See MPEP 2106.04 and 2106.05(II) [Step 2A, Prong 1: YES].
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 or whether the claim is “directed to” the judicial exception. This evaluation is performed by (1) identifying whether there are any additional steps/elements recited in the claim beyond the judicial exception, and (2) evaluating those additional steps/elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. See MPEP 2106.04(d).
In this case, the additional steps/elements recited in the claim beyond the judicial exception are as follows:
obtaining…a reference directed acyclic graph (DAG) data structure comprising a plurality of nodes……wherein the nodes represent a nucleotide sequence…;
Under the BRI, the step of “obtaining…a reference DAG data structure…” is recited at a high level of generality and encompasses obtaining a particular data source of type of data to be manipulated by the abstract idea, i.e. necessary data gathering. Accordingly, this step amounts to “insignificant extra-solution activity” and does not integrate the judicial exception into a practical application. See MPEP 2106.05(g). With regards to the “DAG data structure”, this element is also recited at a high level of generality (merely comprising nodes and edges representing sequence information) and generally amounts to information being stored in a database. As such, this element also does not impose any other meaningful limits on the beyond generally linking the use of the abstract idea to a particular technological environment, i.e. a computer. MPEP 2016.05(e).
With regards to the computer processor and computer readable medium, these fail to impose any meaningful limits on the claim’s scope and are merely used as a tool to perform generic computer functions, as discussed above in Step 2A, Prong One. Therefore, the above step amounts to no more insignificant extra-solution activity and/or mere instructions to apply the exception using a generic computer. See MPEP 2106.05(f).
Accordingly, the claims fail to recite any non-abstract elements that apply the information in practical manner, such as treating a specific disease or disorder, improve the functioning of a specific claimed device, effect an improvement to the technology, or provide meaningful limitations beyond generally linking the use of an abstract idea to a particular technological environment. See Enfish LLC v. Microsoft Corp., 822 F.3d 1327, 1335—6 (Fed. Cir. 2016). Consequently, the claimed invention does not integrate the abstract idea 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 amount to nothing more than insignificant extra-solution activity or field of use. Moreover, a review of the prior art teaches that the above non-abstract limitations were routine and conventional in the art.
Sorenson et al. (US 2010/0169026; Pub. Date: July 1, 2010) teaches a computer algorithm/program for the alignment of genomic sequences using directed acyclic graphs (DAGs) for storing sequence data [ref. claims 1 18, 19].
Ma et al. (Int. J. Bioinformatics Research and Applications, 2010, vol. 6, no 4, pp366-383) teaches a computer system and programs that includes representing genomic sequence data using directed acyclic graphs (DAGs) [Section 3, page 371-72, Figure 2, page 376-77, Table 1, and Table 2].
Bondy et al. (Graph Theory With Applications, 1976, pp.1-115, see at least Sections 1.1 through 1.6), teaches that directed acyclic graphs (DAGs) are well understood, routine, and conventional in the art of graph theory and comprise vertices and edges that are associated with data. In other words, there is nothing unconventional with regards to the use of DAGs for storing sequence data and applicant has not presented any evidence to the contrary.
With regards to the claimed processor and storage medium, as explained with respect to Step 2A Prong 2, this limitation is at best the equivalent of merely adding the words “apply it” to the judicial exception. In addition, to the extent that the DAG is stored on the computer (which is not readily apparent), the courts have held that a claim defining storing data in a "data structure" does not define a "particular machine," and does not distinguish from "manipulation of abstract ideas" and therefore does not satisfy the requirements of 35 USC 101. See Ex Parte Wasynczuk, No. 2008-1496 (2 June 2008) and Ex Parte Langemyr, No. 2008-1495 (28 May 2008). Mere instructions to apply an exception cannot provide an inventive concept, and the courts have also explained that the use of generic computer elements do not alone transform an otherwise abstract idea into patent-eligible subject matter. See DDR Holdings (Fed. Cir. 2014). Therefore, there is nothing unconventional with regards to the above steps/elements and applicant has not provide any evidence to the contrary.
Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea 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.
D. Dependent Claims
Dependent claims 24-27, 31-34, 38-42 have also 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. Regarding claims 24-27, 31-34, 38-40, these claims further limit the specificity of the abstract idea set forth above (by reciting additional mental processes and/or mathematical concepts), or further limit the nature of the data being analyzed by the abstract idea. Accordingly, these claims are also directed to an abstract idea for reasons set forth above (Step 2A, prong 1 analysis). Consequently, the claimed invention does not integrate the abstract idea into a “practical application.” Regarding claim(s) 41 and 42, these claims further comprise generically recited limitations are directed to tagging data and outputting results. Accordingly, these steps amount to “insignificant extra-solution activity” and do not integrate the judicial exception into a practical application. See MPEP 2106.05(g). These limitations also do not provide any meaningful limitation(s) to transform the abstract idea into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. For additional guidance, applicant is directed generally to the 2019 Revised Patent Subject Matter Eligibility Guidance published in the Federal Register (84 FR 50) on January 7, 2019.
Response to Arguments
Applicant’s arguments, filed 09/24/2025, have been fully considered but are not persuasive for the following reasons.
Applicant argues that the claims do not recite a mental process because the human mind is not equipped to align a sequence reads to a reference DAG data structure as claimed. In response, as set forth above in Step 2A, the step for aligning sequence reads to a DAG are performed inside of a computer using generically recited mathematical techniques (i.e. creating matrix alignments and determining scores). The Office's eligibility guidance does not set limit on the number of calculations that can or cannot be performed mentally. MPEP § 2106.04(a)(2)III. Moreover, merely automating processes that can be performed manually or as mental processes does not transform an abstract idea into a patent-eligible invention. See Cellspin Soft, Inc. v. Fitbit, Inc., 927 F.3d 1306, 1316 (Fed. Cir. 2019). Therefore, absent any evidence to the contrary, the examiner maintains that the above steps clearly fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III [Step 2A, Prong 1: YES].
Applicant argues that the claims do not recite a mathematical concept because the recited “reference DAG data structure” is not a mathematical concept. In response, contrary to applicant’s assertion, the “reference DAG data structure” has not been interpreted as a mathematical concept. It has been interpreted as an “additional element” and evaluated under Step 2A (prong 2) and Step 2B. Notably, the “DAG data structure” element is recited at a high level of generality (merely comprising nodes and edges representing sequence information) and generally amounts to information being stored in a database. As such, this element also does not impose any other meaningful limits on the beyond generally linking the use of the abstract idea to a particular technological environment, i.e. a computer. MPEP 2016.05(e). For these reasons, applicant’s argument is not persuasive and the examiner maintains that the claims indeed recite a mathematical concept for reasons set forth above (Step 2A, prong 1).
Applicant argues that the claims are eligible under Step 2A (prong 2) because they recite an improvement to sequence alignment and genotyping technologies because it recites a reference DAG data structure and an alignment process that allows for efficient, multi-dimensional alignment of sequence reads to the reference DAG data structure, which in turn enables more efficient genotyping. In response, Applicant’s identified improvements are to the abstract idea itself (i.e. aligning a sequence read to a reference DAG data structure), not improvements to a technology or computer functionality. That is, the cited claim limitations result in generating additional information which does not improve the functionality of the general purpose computer, nor do they achieve an improved technological result. See MPEP § 2106.04(d). In other words, Applicant is essentially arguing that the inventive concept is the abstract idea, and that the abstract idea is being used to obtain “better data”. However, the courts have instructed that “[t]he different use of a mathematical calculation, even one that yields different or better results, does not render patent eligible subject matter.” Board Of Trustees Of Leland Stanford Junior University, 991 F.3d 1245, 1251 (Fed. Cir. 2021). While applicant’s particular algorithmic approach may achieve an alternative solution for improving the accuracy of sequence alignment, the claimed invention is, nevertheless, directed to an improved algorithmic analysis that results in generating additional information without any “real-world” practical application of said information.
Applicant additionally asserts that conventional sequence alignment techniques utilize linear methods, require "massive computing power," and are extremely inefficient, whereas the claimed techniques provide for "a multi-dimensional approach to sequence alignment" that "reduce[s] the computational resources required to make alignments while allowing for simultaneous comparison to multiple reference sequences." (pages 6-7). In response, after careful consideration, this amounts to setting forth an improvement but in a conclusory manner (i.e., a bare assertion of an improvement without the detail necessary to be apparent to a person of ordinary skill in the art). Moreover, there is also case law supporting the determination that claims that merely provide efficiency or accuracy increases over mental calculations do not recite eligible subject matter. See Bancorp Servs., L.L.C. v. Sun Life Assurance Co. of Can. (US.), 687 F.3d 1266, 1279 (Fed. Cir. 2012) ("Using a computer to accelerate an ineligible mental process does not make that process patent-eligible."). For at least these reasons, the rejection is maintained.
Nonstatutory Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the "right to exclude" granted by a patent and to prevent possible harassment by multiple assignees. See In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970);and, In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent is shown to be commonly owned with this application. See 37 CFR 1.130(b).
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Claims 21, 28, 35 is/are provisionally rejected under the judicially created doctrine of obviousness-type double patenting as being unpatentable over claims 21, 23, 25, 30, 32-34 of copending application 17/359338. Although the conflicting claims are not identical, they are not patentably distinct from each for the following reasons. In the present case, reference claim 21 of the ‘338 application recites all the limitations of those required by instant claims 21, 28, 35 plus additional limitations. Therefore, instant claim(s) 21, 28, 35 are anticipated by the narrower claims (i.e. species anticipates the genus). This is a provisional obviousness-type double patenting rejection because the conflicting claims have not in fact been patented.
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.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619