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 1-20 are pending and examined herein.
No claims are canceled.
Priority
As detailed on the 01 December 2023 filing receipt, the application claims priority as early as 29 June 2021. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Information Disclosure Statement
Information disclosure statement (IDS) was filed on 12 March 2026. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the reference is being considered by the examiner.
Claim Rejections - 35 USC § 112(a)
The rejections of claims 1-14 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112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement are withdrawn in view of amending reciting a sequencing device as part of the system in claim 1 and operatively coupled to the computer-readable medium in claim 11.
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 1-20 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 determining base calls and base call quality.
MPEP 2106 organizes JE 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 1-10), a non-transitory computer-readable medium (claims 11-14), and method (claims 15-20), 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)).
The claims recite to “deconstruct… a scaling factor and a noise level” (claims 1 and 11), where a scaling factor is disclosed as coefficient (pg. 16, paragraph [41]) determined by a least squares algorithm (pg. 10, paragraph [28]) and a noise level is a value based on signal variation (pg. 16, paragraph [41]) which forms part of a ratio and is thus a mathematical concept.
The claims recite to “generate... a nucleotide base call” and to “generate a signal-to-noise-ratio metric” (claims 1 and 11), where generating a base call is a data evaluation or interpretation step and thus a mental process, and generating a ratio and/or metric is interpreted as a verbal description of a mathematical concept.
The claims recite to “generate, utilizing a base-call-quality model, a quality metric” (claim 1), where the step is interpreted as a mathematical concept in view of the specification, which discloses the model uses the ratio as an input into a Phred algorithm to generate a Q-score of accuracy (pg. 45, paragraph [111]).
The claims recite to determine a noise level by “determining… corrected intensity values” and “determining the noise level… based on the corrected intensity values” (claim 2). This claim is interpreted as modifying a value using another value based on the mathematical concepts discussed related to the independent claims and thus also a mathematical concept.
The claims recite to “determine… the corrected intensity values… the scaling factor… and correction offset factors” (claims 3), which are all interpreted as determining numerical values and thus mathematical concepts.
The claims recite to “determine the noise level” by “determining centroid intensity values” and “determining distances between the centroid intensity values and the corrected intensity values” (claim 4); determining a centroid and measuring distances between that value and intensity vales are mathematical concepts.
The claims recite to “determine… an average noise level” and “determine… the noise level corresponding to the signal” (claim 5), which are mathematical concepts related to determining and comparing an average.
The claims recite “determining a relationship” between values, “determining an error function,” and “determining the scaling factor by generating a partial derivative” (claim 6), all of which are verbal descriptions of mathematical concepts.
The claims recite to “generate the signal-to-noise-ratio metric” for different sections of the slide (claim 7), where determining the metric is already determined to be a mathematical concept.
The claims recite to “generate the quality metric estimating the error… by generating a Phred quality score” (claim 8), where generate a metric based on Phred is a mathematical concept.
The claims recite to “determine a chastity value” based on centroid differences and to “generate, utilizing the base-call-quality model, the quality metric” based on the values (claim 9), which are verbal descriptions of mathematical concepts.
The claims recite further aspects of determining noise levels, weighting noise levels, and using the weighted noise levels (claim 10), which are verbal descriptions of mathematical concepts.
The claims recite to “include or exclude a… call” (claim 11), which is a data evaluation or selection step practically performed by the human mind and thus a mental process.
The claims recite to “exclude… calls… based on determining that the signal-to-noise-ratio metric is lower than” the threshold (claim 12), which is a mental step of data selection and comparison.
The claims recite to “generate the signal-to-noise-ratio metric by equating the scaling factor to the signal to determine a ratio” (claim 13), which is a verbal description of mathematical steps.
The claims recite to “generate the signal-to-noise-ratio” for a given position (claim 14), which is a mathematical concept for the reasons explained above.
The claims recite “separating... associated noise based on intensity values” where intensity values are, as disclosed by the specification, wavelength or brightness values (paragraph [40])
The claims recite “generating signal-to-noise-ratio metrics” based on the signals and determining ranges from the metrics (claim 15), where generating a metric is considered a mathematical step.
The claims recite “generating… intensity-value boundaries… according to one or more base-call models” (claim 15), where the step can be interpreted as a mental step of observing differences in data distributions.
The claims recite generating different boundaries corresponding to different nucleotide bases (claim 16), which is a mental step for the same reasons as its parent claim.
The claims recite generating calls for signals based on their occurrence inside nucleotide-specific ranges (claims 17-19), which is a mental step of data evaluation.
The claims recite generating boundaries according to Gaussian distributions models (claim 20), which is application of a mathematical concept.
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 claims recite elements in addition to the abstract ideas: a system comprising at least one processor and non-transitory computer readable medium with our coupled to a sequencing device (claims 1 and 11), a computer with a sequencing device (claim 15), and detecting a signal from labeled nucleotide bases (claims 1, 11, 14-15, and 17-19).
The computer system is generically recited and amounts to 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 detecting of signals from labeled nucleotide bases is a data gathering step necessary to perform the abstract quality control step. Data gathering is interpreted as insignificant extra solution activity and therefore the claim does not integrate that abstract idea into a practical application. See MPEP 2106.05(g).
Hence, the claims recite additional elements that do not integrate the abstract ideas into a practical application. The claims must therefore be examined further to determine conventionality of the additional elements alone or in combination (MPEP 2105). [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 elements in addition to the abstract ideas: a system comprising at least one processor and non-transitory computer readable medium with our coupled to a sequencing device (claims 1 and 11), a computer with a sequencing device (claim 15), and detecting a signal from labeled nucleotide bases (claims 1, 11, 14-15, and 17-19).
The claims recite a computer for receiving information and performing calculations, which are conventional computer functions (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; Flook, 437 U.S. at 594, 198 USPQ2d at 199 (recomputing or readjusting alarm limit values); Bancorp Services v. Sun Life, 687 F.3d 1266, 1278, 103 USPQ2d 1425, 1433 (Fed. Cir. 2012). MPEP 2106.05(d)(II)(i)) pertains.
The step of detecting signals from labeled nucleotide bases, interpreted in light of the specification as using a camera in a sequencing-by-synthesis system to capture images of irradiated fluorophore tags (pg. 1, paragraph [2]) is conventional at the effective filing date of the instant application, and taught in a review by Gupta (Trends in Biotechnology 26(11): 602-611, 2008; previously cited on the 09 March 2026 PTO-892 form) as using camera imaging to obtain images of fluorescent dye tagged to nucleotides upon incorporation (pg. 604, col. 2, second and third paragraphs; Fig. 1).
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 09 June 2026 Applicant Remarks
Applicant remarks state similarity to Example 48, claim 3 directed to analyzing speech signals and separating desired speech from extraneous or background speech, and in particular using a deep neural network to extract features are based on but do not recite mathematical features and are also not practically performed in the human mind (pg. 13, last paragraph to pg. 14, first paragraph). It is agreed the human mind cannot detect light signals emitted as disclosed (pg. 14, last paragraph). The cited example notes that specific mathematical relationships are not cited; however, claim 1 recites at least generating a “variation-correction coefficient” which is interpreted as a mathematical concept, which is disclosed in the specification as determined using a least squares model (paragraph [75]). Therefore, the analogy to Example 48 is not persuasive. Instead, it is interpreted as akin to performing backpropagation as in Example 47, which is considered to be a judicial exception.
Applicant remarks state that even if abstract ideas are recited, the deconstructing/separating steps integrate the abstract ideas into a practical application similar to the speech separation of Example 48. However, for the reasons above, the separation/deconstruction step is not considered to be an element in addition to the abstract ideas. Determination regarding whether abstract ideas are integrated into a practical application 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)). Therefore, the separation/deconstruction step cannot integrate into a practical application.
Thus, the rejection under 35 USC 101 is maintained.
Claim Rejections - 35 USC § 102 and 35 USC § 103
The rejections of the claims in view of Tomaney (US 20110256631 A1; previously cited on the 13 November 2025 IDS form) and Tomaney further in view of Rothberg (US 20190237160 A1; previously cited on the 10 November 2022 IDS form) and Langlois (US 20180260940 A1; previously cited on the 10 November 2022 IDS form). Tomaney, while teaching background correction, does not teach the required a scaling factor comprising a variation-correction coefficient corresponding to the light signal and a noise level corresponding to the light signal based on intensity values for the light signal or generating a signal-to-noise-ratio metric for the section of the nucleotide-sample slide, based on the scaling factor as a substitute for the light signal and the noise level. Combination with Rothberg and Langlois does not remedy these deficiencies. Therefore, the claims are considered free of the prior art.
Conclusion
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.
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/R.J.K./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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