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 1-13, 15-21, and 23 are pending and examined herein.
Claims 14, 22, and 24 are canceled.
Priority
As detailed on the date filing receipt, the application claims priority as early 24 March 2022 as found on provision application 63/323,314. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Information Disclosure Statement
An information disclosure statement (IDS) was filed on 16 May 2026. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the references are being considered by the examiner.
Withdrawn Objections and/or Rejections
The objection to claim 1 is withdrawn in view of amendment regarding the indentation of “enumerating.”
The rejection of claim 24 under 35 USC 101 is withdrawn in view of cancelation of the claim.
The rejection under 35 USC 103 is withdrawn in view of amendments incorporating dependent claims reciting enumerating the first and second partition count and using the enumerated values from the first and second partitions as input for a prediction algorithm which determines the length of a fragment population. Related art such as Basu (SLAS Technology 22(4): 369-386, 2017; previously cited on the 22 January 2026 PTO-892 form) and Didelot (Molecular Diagnostics and Genetics 59(5): 815-812, 2013; previously cited on the 22 January 2026 PTO-892 form) do not teach this limitation.
The following objections and/or rejections are maintained from the previous office action(s) and constitute the complete set of objections and/or rejections applied to the instant claims.
Claim Objections
Claim 1 is objected to because the phrase “using results of enumerating” is missing articles and should read “using the results of the enumerating”. This objection is maintained from the previous office action.
Appropriate correction is required.
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 1-13, 15-21, and 23 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 both individually and in combination, do not amount to significantly more than the abstract idea of predicting a length characteristic of nucleic acid fragments.
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 methods (claims 1-13, 15-21, and 23), 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 claims 1 and 20-21 include enumerating target-defined subsets of the partitions and predicting at least one characteristic of the population of nucleic acid fragments using results of enumerating. The enumerating is interpreted as a verbal description of a mathematical concept which may be as simple as counting or determining ratios, which is supported in light of the specification (pg. 19, paragraph [77]). The predicting is also interpreted as a mathematical step, where the predicting is disclosed as using the results of the enumerating steps as inputs for a predicting algorithm (pg. 19, paragraph [79]), which is further disclosed as generated by logistic regression (pg. 27, Subsection D). Similarly, estimating values for coefficients and an intercept are related to the mathematical values for the algorithm. 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)). These claims may also take the form of mental processes as enumerating and predicting a length characteristic describe observation and evaluation steps which are practically performed by the human mind. Selection of nucleotides a given distance from each other in the genome (claim 20), as a selection step, can be performed by the human mind.
Claims 2-13, 15-20, and 23 recite further limitations on the predicting step, which is a mathematical concept, such as predicting length (claim 2), classifying length (claim 3), predicting a percentage meeting a criterion (claim 4) such as threshold length (claim 5), confidence interval (claim 6), measures of central tendency (claims 7-8), confidence interval of the median (claim 9), and further details of the predictor function (claims 10-13 and 15-18) and generating the size prediction algorithm (claim 23), where the predictor function is disclosed as “any function that provides an output value for a dependent variable, based on one or more input values for one or more independent variables, where the output value represents a prediction from the one or more input values,” having variables, coefficients, and constants(pg. 9, paragraph [41]), having a mathematical form (pg. 10, paragraph [42]), and fitting the function results in a linear regression model (pg. 10, paragraph [43]) or logistic regression model (pg. 10-11, paragraph [44]), and as such the claims are interpreted as directed to a mathematical concept.
Claim 19 recites additional information about the targets, including their lengths (claim 19), where selection of the lengths of the targets is performed by the human mind.
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 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)).
Claims 1 and 20-21 recite forming partitions of the sample wherein each target of at least two targets is present in only a fraction of the nucleic acid fragments, performing amplification reactions of the targets, and collecting amplification data, where the amplification data collection is derived from fluorescence. These steps are data collection steps required to perform the enumerating and predicting using the prediction algorithm. Clam 21 also recites providing a standard and measuring the length of the standards, which is interpreted as further data collection for generating the size prediction. Therefore, they are considered to be insignificant extra-solution activity, which does not integrate the abstract ideas into a practical application (MPEP 2106.05(g)).
None of the dependent claims recite any additional non-abstract elements; they are all directed
to further aspects of the information being analyzed, the manner in which that analysis is performed, or
the mathematical operations performed on the information. [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).
Claims 1 and 20-21 recite forming partitions of the sample wherein each target of at least two targets is present in only a fraction of the nucleic acid fragments, performing amplification reactions of the targets, and collecting amplification data, where the amplification data collection is derived from fluorescence. Clam 21 also recites providing a standard and measuring the length of the standards, which is interpreted as further data collection for generating the size prediction
Regarding claim 1, Basu (SLAS Technology 22(4): 369-386, 2017; previously cited on the 22 January 2026 PTO-892 form) teaches digital assay in which the sample is partitioned (pg. 369, col. 1, first paragraph) where there may be two or more targets (Fig. 1), amplified (pg. 370, col. 1, last paragraph), and data is collected on the amplification results by “spectrophotometry, fluorimetry, or nonoptical methods. For example, fluorescence intensity emitted from a probe may be used to quantify the concentration of DNA” (pg. 370, col. 1, last paragraph). Using such a method, it is taught “approximate distribution of nucleotide sequence lengths could be digitally quantified by counting the number of amplified species resulting from each probe” (pg. 381, col. 2, last paragraph).
Regarding claim 21, the further limitations of providing and measuring a standard are taught by Basu as quantitation of standards by commercial sources (pg. 381, col. 2, first paragraph), where quantitation is interpreted as measuring the standards which are commercially provided.
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 17 April 2026 Applicant Remarks
Applicant remarks state the abstract ideas found in the claims at Step 2A Prong One of the 101 analysis are integrated into a practical application at Step 2A Prong Two of the 101 analysis because the calculation forms part of the workflow for analyzing fragments (pg. 10, second paragraph), and using measuring and using standards are part of a technological process (pg. 10, fourth paragraph). This argument is unpersuasive. At Step 2A Prong Two, it is determined whether the abstract ideas are integrated into a practical application by an additional element (MPEP 2106.04(d)). Here, the elements in addition to the abstract ideas are partitioning a sample, performing amplification reactions, and collecting amplification data, which is also asserted in the remarks (pg. 10, third paragraph). These steps are interpreted as data collection steps for the enumeration and prediction steps, which are abstract, which is why they are interpreted as insignificant extra-solution activity (MPEP 2106.05(g)). These steps are not providing the improvement but rather are directed to data gathering such that the predictor algorithm can predict fragment length, which is an abstract, mathematical step.
Applicant remarks assert analogy to Vanda Pharmaceuticals Inc. v. West-Ward Pharmaceuticals International Ltd., 887 F.3d 1117 (Fed. Cir. 2018) and lllumina Inc. v. Ariosa Diagnostics Inc., 967 F.3d 1319 (Fed. Cir. 2020) in that these situations apply biological measurements in a specific technological procedure (pg. 10, fifth paragraph). The analogy is not persuasive. In Vanda, a judicial exception in the form of a natural relationship is applied to a treatment, which is an element in addition to the abstract ideas. In the instant claims, the abstract ideas are applied to a mathematical concept, which is not an element in addition to the abstract ideas much less a particular treatment, and thus cannot integrate the abstract ideas into a practical application. In Illumina v. Ariosa, the claim elements are directed to DNA preparation realized by elements in addition to the abstract ideas – DNA extraction, physical size discrimination by removing fragments, and analysis – whereas the instant claims are directed to the abstract step of fragment length prediction using an algorithm based on additional elements known within the state of the art and conventionally found alone or in combination at Step 2B.
Therefore, the rejection under 35 USC 101 is maintained.
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.
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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