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 28 March 2022 filing receipt, the application claims priority as early as 02 April 2021. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Withdrawn Objection
The objection to the specification due to a misspelling is withdrawn in view of amendment.
The rejection under 35 USC 103 is withdrawn in view of amendment reciting modification of a call based on a bubble detected by the machine learning model. Previously cited art, such as Sikora (US 20130090860 A1; previously cited on the 28 November 2025 PTO-892 form) and Chou (WO 2020/047177 A1; previously cited on the 29 September 2022 IDS form), do not teach or fairly suggest the recited combination of a model-based determination of bubbles in a nucleotide slide and subsequent modification of a basecall in view of the bubble determination. Therefore, the claims are considered free of the prior art.
The following objections and/or rejections are either maintained or newly applied, and constitute to the complete set of objections and/or rejections to the instant application.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-16 and 19 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites a system comprising at least one processor and non-transitory computer-readable medium. The body of the claim instantiates a sequencing device. It is not clear that the sequencing device is part of the system or whether it is outside the metes and bounds of the claimed invention (MPEP 2173.02). Similarly, claim 11 recites a non-transitory computer readable medium executed by a processor and causing a computer system to perform the steps of claim 1, and a sequencing device is also instantiated in the body of the claim rather than coupled to the medium. Dependent claims 2-9 and 12-16 are rejected on similar grounds. Amendment clearly reciting whether the sequencing device is part of the system or coupled to the medium for claims 1 and 11 respectively may overcome this rejection.
Claim 19 recites “additional tube sensors.” It is unclear how many sensors are required and what additional sensors would constitute, as “sensors” does not occur elsewhere in the claims. Amendment to more specifically recite “detecting the presence of the bubble without a tube sensor for bubble detection” or a similar amendment may overcome this rejection.
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 detecting a bubble in nucleotide data.
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 (claim 1-10), a non-transitory computer-readable medium (claims 11-16), and a method (claims 17-18 and 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)).
Mental processes, defined as concepts practically performed in the human mind such as steps of observing, evaluating, or judging information, recited in claims 1, 11, and 17 include determining a first and second subset of base calls satisfying a quality metric, where the step is interpreted as comparing values, which the human mind is practically equipped to do; and detecting the presence of a bubble based on a model informed by the quality score, where the human mind can interpret model output. Also recited in modifying a quality metric. The modification is broadly recited and as such is interpreted as changing a number, which can be practically performed in the human mind.
The independent claims also recite a mathematical concept in the form of a machine learning model, which is used as part of the detecting step. The specification discloses use of various types of machine learning models, including (pg. 8-9, paragraph [25]), including a support vector machine or adaptive boosting. Under a broadest reasonable interpretation, a support vector machine is a mathematical concept. 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 (MPEP 2106.04(a)(2)). Also recited in modifying a quality metric. The modification is broadly recited and as such is interpreted as changing a number, where modifying numerical values can be interpreted as a mathematical concept.
Claims 2-3, 5-6, 14-15, and 20 recite further aspects of detecting the bubble, which is performed mathematically as explained above.
Claims 4 and 18 recites further aspects of determining the subsets of data, where subsetting data is a mental process.
Claim 8 recites generating a probability and comparing a probability to a threshold, which is interpreted as numerical comparison and thus a mathematical concept.
Claims 10 and 16 recite determining a bubble during a sequencing cycle, which is interpreted as further information about the time at which point the mathematical step of the detecting takes place.
Claim 12 recites at least a support vector machine and adaptive boosting, which are interpreted as mathematical concepts.
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))?
Elements in addition to the abstract ideas recited in the claims include a system comprising at least one processor (claim 1) and a non-transitory computer readable medium (claims 1 and 11), which together are a computer (claim 17), and receiving call data and quality data for a sample slide (claims 1, 11, and 17). Also claimed is a sequencing device (claims 1, 11, and 17) and omitting additional tube sensors (claim 19).
Claims 2 and 14 recite receiving call and quality data.
Claim 7 recites the machine learning model is a convolutional neural network comprising feature extraction layers, classification layers, and an adaptive max pooling layer, where the model is interpreted as a mathematical concept.
Claim 9 recites additional details regarding the data received by the system.
Claim 13 recites displaying an alert.
Claims 1, 2 9, and 14 recite data collection steps required to perform the abstract step of determining the presence of a bubble. These steps are interpreted as insignificant extra-solution activity that does not integrate the abstract ideas into a practical application (MPEP 2016.05(g)). Similarly, the sequencing device is used for generating data to perform the abstract steps on and as such is also related to insignificant extra-solution activity, which does not integrate the abstract ideas into a practical application (MPEP 2016.05(g)).
Claim 1, 7, 11, and 17 recite computer elements performing the recited steps. 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)). Although the additional element using a convolutional neural network limits the identified judicial exception of detecting a bubble based on the first and second subsets of base calls, this type of limitation merely confines the use of the abstract idea to a particular technological environment (neural networks) and thus fails to add an inventive concept to the claims. See MPEP 2106.05(h).
Claim 13 recites alerting on a display. This is interpreted as outputting information and thus also insignificant extra-solution activity that does not integrate the abstract ideas into a practical application (MPEP 2016.05(g)).
The recited detection without additional tube sensors (claim 19). While an improvement may be argued based such a change in the detection apparatus, it is unclear in view of the rejection under 35 USC 112(b) what constitutes additional sensors as claimed.
[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 a 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 data using a computer is a conventional computer activity (buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014)). Storing data on a computer is a conventional computer function (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93; MPEP 2106.05(d)). Display steps are interpreted as insignificant extra-solution activity (MPEP 2106.05(g)) which do not impose meaningful limits on the claim, here displaying an output of the analysis (Ameranth, 842 F.3d at 1241-42, 120 USPQ2d at 1854-55; MPEP 2106.05(g)).
The details of the convolutional neural network recited in claim 7 are taught in the review by Aslam (IEEE 2019 International Conference on Smart Systems and Inventive Technology (ICSSIT), Tirunelveli, India, pg. 709-714, 2019; newly cited), which teaches CNNs in a comprise feature extractors, max pooling, and classifier layers (pg. 710, col. 2, second paragraph) and similar CNN architectures have been applied with “great success” in a biomedical context (pg. 710, col. 1, second paragraph).
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.
Claim 19 recites detecting the presence of a the bubble without additional tube sensors on the sequencing device. If interpreted as performing bubble detection without a dedicated sensor for bubble detection, thus improving efficiency and accuracy (specification: paragraphs [27-28]) compared to existing systems which require such additional hardware (paragraphs [5, 29-30]), this element is interpreted as an improvement to sequencing technology at Step 2A Prong Two of 101 analysis (MPEP 2106.04(d)(1)), pending clarification under 35 USC 112(b) above.
Response to the 24 February 2026 Applicant Remarks
Applicant remarks state the rejection under 35 USC 101 is overcome. The arguments are not persuasive.
Applicant remarks state the claims do not recite an abstract idea at Step 2A Prong One of analysis (pg. 11, last paragraph) but this argument does not appear to be supported (pg. 12, first and second paragraphs). Instead, it is argued that, at Step 2A Prong Two, while an abstract idea is recited, the claims integrate the abstract ideas into a practical application.
Applicant remarks assert analogy to XY, LLC v. Trans Ova Genetics, LC, 968 F.3d 1323 (Fed. Cir. 2020), recently summarized in the 2024 Guidance Update, wherein a claim is patent eligible when
the claimed subject matter "yield[s] an improved result" from operating a specialized machine (pg. 12, last paragraph). The analogy between XY and the instant claims is unpersuasive. In XY, the claims culminate in an element in addition to the abstract ideas: sorting particles into a desired receptacle. The analogy within XY to Diehr, in which the calculations are used to monitor and produce rubber cured at an optimal temperature, is also directed to an element in addition to the abstract ideas: producing cured rubber. This is different from the instant claims. The instant claims collect data, possibly from a sequencing device, and performs determinations of base calls and quality, detecting a bubble based on a model, and modifies a metric, which are all abstract steps. Therefore, unlike XY and Diehr, any improvement is realized from the abstract steps. The instant remarks and XY decision also references Thales Visionix (remarks: pg. 13, last paragraph), where the improvement was provided by additional elements in the form of non-conventional sensors. The additional elements provided the improvement and were unconventionally arranged, thus overcoming a rejection under 35 USC 101 at Steps 2A Prong Two and 2B. The XY decision notes accomplishing a physical process is important to overcoming the rejection, and a physical process is not accomplished in the instant claims. The remarks specifically state the algorithm used provides the improvement by accessing the data and metrics from the various file types (pg. 14, last paragraph to pg. 15, first paragraph), exemplifying it is an abstract process.
Applicant remarks state the abstract steps reduce the physical resources (e.g., fluids, tubing, sensors, cameras) required to detect such bubbles relative to traditional or then-existing sequencing devices (pg. 16, penultimate paragraph). This negative limitation is on only claimed in claim 19, but may overcome the rejection if clarified what “additional” means in the context of the sequencing device and compared to a baseline number of sensors as discussed in the rejection under 35 USC 112(b) above and if applied to the non-method claims.
Applicant remarks state real-time analysis of call data is performed (pg. 17, second paragraph), but this is not clearly recited in the claims. Applicant remarks point to paragraphs [26-29] of the specification but these paragraphs do not clearly recite real-time analysis.
At Step 2B, it is determined whether the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05). Applicant remark assert reducing re-sequencing cycles and eliminating hardware requirements are elements in addition to the abstract ideas providing significantly more (pg. 18). However, at least the independent claims do not close the claims to omitting a sensor for bubble detection.
Therefore, the rejection under 35 USC 101 is maintained.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert J Kallal whose telephone number is (571)272-6252. The examiner can normally be reached Monday through Friday 8 AM - 4 PM EST.
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/R.J.K./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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