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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 07/23/2026 has been entered.
Claim Status
Claims 3, 8, 10, 15, 19, 21, 33, 35, and 39-78 were previously canceled.
Claims 1-2, 4-7, 9, 11-14, 16-18, 20, 22-32, 34 and 36-38 are pending and examined on the merits.
Claims 1, 37, and 38 are independent claims.
Priority
The instant application claims priority to US Provisional Application 63/590,386, filed 10/13/2023. The claim to US Provisional Application 63/654,665, filed 05/31/2024 is acknowledged. As such, the effective filing date assigned to instant claims is 10/13/2023.
The following rejections and/or objections are either maintained or newly applied. They constitute the complete set presently being applied to the instant application.
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 1-2, 4-7, 9, 11-14, 16-18, 20, 22-32, 34 and 36-38 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1-2,4-7,9,11-14,16-18,20,22-32,34 and 36 being representative) is directed to a method and (claims 37-38 being representative) a system. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claim(s) 1-2, 4-7, 9, 11-14, 16-18, 20, 22-32, 34 and 36-38 recite the following steps which fall under the mathematical concepts, mental processes, and/or certain methods of organizing human activity groupings of abstract ideas:
Claims 1, 37, and 38 recite a naturally occurring relationship between DNA and molecular residue status for a cancer condition, and as such, claims recite a law of nature and natural phenomenon.
Claims 1, 37, and 38 recite determining a corresponding number of circulating-tumor DNA (ctDNA) fragments mapping to each respective region in a plurality of regions of one or more first reference sequences of the species of the subject using a methylation pattern wherein the plurality of regions comprises 1000 or more regions; the limitation determining, given the plain meaning of “determining”, can be practically performed in human mind (mental process), since human mind is capable of aligning/placing a set of data onto a reference structure.
Claims 1, 37 and 38 further recite determining a corresponding expected number of noise fragments based on a corresponding region-specific background emission distribution that has been learned from prior methylation sequencing data from a plurality of healthy subjects and an observed sequencing depth for the respective region from the first sequence reaction; the limitation determining is considered a mathematical calculation, as disclosed in instant specification [00157] the expected number of noise fragments 118 for a given region (noise) is determined by sampling a Binomial distribution with the observed depth and the learned Beta background emission rate, and as discloses in claims 1, 37-38, the determining is based on a learned algorithm. As such, said limitation falls into mathematical concepts groupings of abstract ideas.
Claims 1, 37 and 38 further recite that the expected number of noise fragments for the respective region is determined by combining the region-specific background emission distribution with the observed sequencing depth, such that the expected number of fragments reflects the likelihood of observing ctDNA- like fragments in the absence of cancer based on the learned distribution for the respective region; the limitation determining by combining such that the expected number of fragments reflects a likelihood is considered a mathematical calculation, and as such falls within mathematical concepts groupings of abstract ideas.
Claims 1, 37 and 38 further recite determining an excess fragment per million value for the first liquid biopsy sample from the corresponding number of ctDNA fragments; the limitation determining an excess fragments per million value is considered a mathematical calculation, and as such, falls within mathematical concepts groupings of abstract ideas.
Claims 1, 37 and 38 further recite correcting the excess fragments per million value for the first liquid biopsy sample by an observed CHG methylation level; the limitation correcting is considered a mathematical calculation (see instant specification [00160] correcting using quantitative estimate, and correction calculations of [00166]), and as such, falls within mathematical concepts groupings of abstract ideas.
Claims 1, 37 and 38 further recite applying a first threshold to the corrected excess fragments per million value; the limitation applying a threshold is considered a mathematical relationship between variables and numbers, and as such falls within mathematical concepts groupings of abstract ideas.
Claim 2 recites filtering by removing data; the limitation filtering, given the plain meaning of “filtering”, can be practically performed in human mind (mental process), since human mind is capable of selecting a subset of data that meets a specific criteria/condition.
Claim 2 further recites providing: a second call for molecular residual disease when there remains a candidate variant in the set of candidate variants after application of the procedure; the limitation providing a second call can be practically performed in human mind (mental process), since human mind is capable of providing a call/indication based on the result of an analysis.
Claim 4 recites removing from the set of candidate variants each respective candidate somatic variant in the set of candidate somatic variants (metal process of selecting a subset of data that meets a specific criteria/condition).
Claim 5 recites the providing G) provides the indication that the subject has negative molecular residual disease status for the cancer condition (mental process, see above).
Claim 22 recites generating a report for the subject comprising the identity of candidate variants remaining in the set of candidate variants after running the procedure (mental process of putting data into a structured format).
Claims 29-32 recite removing data (mental process).
Claim 34 recites determining that the subject has positive molecular residual disease status for the cancer condition in accordance with the providing G); and adjusting the adjuvant therapy; the limitation determining and adjusting can be practically performed in human mind (mental process of determining a status and adjusting).
Claim 36 recites increasing a dosage of the adjuvant therapy, decreasing a dosage of the adjuvant therapy, or ceasing the adjuvant therapy (mental process of adjusting a dosage).
Claims 6-7, 9, 11-14, 16-17, 18, 20, and 23-26 provide more information about the abstract ideas.
Additionally, claims 1-2, 4-7, 9, 11-14, 16-18, 20, 22-32, 34 and 36-38 recite a correlation between cf DNA and an MRD status, and as such, falls into judicial exception of Laws of nature and natural phenomena. See MPEP 2106(b) I.
The identified claims recite a law of nature, a natural phenomenon (product of nature) or fall into one of the groups of abstract ideas of mathematical concepts, mental processes, and/or certain methods of organizing human activity for the reasons set forth above. See MPEP 2106.04 (a)(2) III and MPEP 2106.04 (b) I. Therefore, claims are directed to a judicial exception and require further analysis in Prong Two. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
The additional elements of claim(s) 11-2, 4-7, 9, 11-14, 16-18, 20, 22-32, 34 and 36-38 include the following.
Claims 1, 37, 38 recite a computer system, a processor, and a memory; obtaining a corresponding nucleic acid sequence of each cell-free DNA fragment in a first plurality of cell-free DNA fragments; a non-transitory computer-readable medium including computer-executable instructions; a methylation sequencing.
Claim 2 recites obtaining, from a second sequencing reaction, a corresponding sequence of each cell-free DNA fragment in a second plurality of cell-free DNA fragments.
Claim 13 recites the second sequencing reaction is a panel-based sequencing reaction.
Claim 17 recites the first sequencing reaction is a whole genome methylation sequencing.
The additional elements of a system comprising a processor, a non-transitory computer-readable storage medium, a memory, and instructions are generic computer components and/or processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general-purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
Furthermore, the additional elements of sequencing reactions and obtaining data serve to collect the information for use by the abstract idea.
Therefore, these additional elements amount to insignificant extra-solution activity, which is not sufficient to integrate the recited judicial exception into a practical application. See MPEP 2106.05(g). [Step 2A, Prong 2: NO]
Response to Arguments
Applicant's arguments filed 07/23/2026 have been considered, but they are not yet persuasive. Applicant states (pg. 13, last para):
Step (B) does not broadly recite placing generic data into a generic structure. It requires determining a corresponding number of ctDNA fragments mapping to each respective region in a plurality of at least 1000 regions of one or more reference sequences, using the methylation pattern of each nucleic acid sequence obtained from the methylation sequencing reaction.
The August 4, 2025, memorandum titled Reminders on Evaluating Subject Matter Eligibility of Claims Under 35 U.S.C. 101 likewise cautions examiners not to expand the mental-process grouping to limitations that the human mind is not equipped to perform.
The complexity of the sequence-alignment operation recited in step (B) places it outside that grouping. A person cannot practically compare the assay-generated nucleic acid sequences and their methylation patterns against the reference sequences, resolve where the fragments map among at least 1000 genomic regions, and maintain the corresponding regional ctDNA-fragment counts in the human mind. The limitation requires manipulation of digital biological sequence data and reference-sequence structures at a scale and level of detail that is qualitatively different from a person observing a value or making a judgment. It is analogous to the network-packet analysis discussed in SRI International, Inc. v. Cisco Systems, Inc., 930 F.3d 1295, 1304 (Fed. Cir. 2019), and the pixel-by-pixel manipulation of digital image data discussed in Research Corp. Technologies, Inc. v. Microsoft Corp., 627 F.3d 859, 97 (Fed. Cir. 2010), which the MPEP identifies as operations that cannot practically be performed in the human mind.
These arguments are not yet persuasive. Applicant remarks are directed to Step 2A Prong One of 101 analysis, specifically to whether the claims recite a judicial exception.
Whether the human mind is equipped to perform a task is not linked to the scope of the task. There is not a threshold at which point determining a number of ctDNA fragments mapping to 1,000 genomic regions using methylation pattern graduates from what can be performed by the mind to not performable by the human mind. While this may take a long time, the use of physical aid, such as pen-and-paper or computer, may accelerate this process, and this does not negate the mental nature of the limitation. Applicant will further note that complexity of operations does not equate to eligibility. The fact remains that the step is directed to operations that are mental as above. See MPEP 2106.04(a)(2) III. B. & C.
With regards to Applicant referring to Cisco Systems, Claims of SRIInt'l, Inc. v. Cisco Systems, Inc., are directed to detecting suspicious activity by using network monitors and analyzing network packets, which human mind is not equipped to do. Applicant will note that the instant claims do not include the same type of limitations as are indicated in the above court cases.
The claims of Research Corp. Technologies, Inc. v. Microsoft Corp. are directed to rendering a halftone image of a digital image by comparing, pixel by pixel, the digital image against a blue noise mask, where the method required the manipulation of computer data structures, which human mind is not equipped to do. Applicant will note that the instant claims do not include the same type of limitations as are indicated in the above court cases.
Further, in contrast to SRIInt'l, Inc. v. Cisco Systems, Inc. and Research Corp. Technologies, Inc. v. Microsoft Corp., instant claims as a whole are directed to determining MRD status, comprising the steps of determining a number of fragments, determining expected number of noise fragments, determining excess fragment per million, correction the EFPM, applying thresholds to provide status, which are mental and/or mathematical processes.
Applicant further states (pg. 16-31):
The Office Action Conflates Limitations That May Involve Mathematics With Limitations That Recite Mathematical Concepts
Step (C) Does Not Recite a Mathematical Concept
The Office Action reasons that the Specification describes an implementation in which the expected number may be determined by sampling a Binomial distribution using observed depth and a learned Beta background emission rate. Office Action at 5, citing the specification at paragraph [0157]. But step (C) does not recite sampling a Binomial distribution, a Beta
distribution, a Beta-Binomial model, multiplication of a rate by a depth, or any formula or equation. It recites the use of a learned, region-specific biological-background data structure and a sample-specific observed sequencing depth to produce an expected regional background count. Selecting one mathematical implementation from the Specification and importing that
implementation into the claim would erase the distinction between involving mathematics and reciting mathematics.
Step (D) Does Not Recite a Mathematical Concept
The limitation identifies the biological counts from which the sample-level assay metric is derived and gives the output metric a defined name. It does not recite subtracting one count from another, summing regional differences, dividing by a total count, multiplying by one million, or any other mathematical formula or calculation.
The Office Action treats the phrase "excess fragments per million value" as though the name of a numerical assay output were itself a recited calculation. Office Action at 5-6. That is the same error addressed by Examples 39 and 47. A claim does not recite every mathematical operation that might be used to generate a named output. Step (D) is analogous to Example 39's generic model-training limitation: implementation may involve arithmetic, but the claim does not identify the arithmetic by words or symbols. It is unlike Example 47, which expressly named backpropagation and gradient descent as required mathematical calculations.
Step (E) Does Not Recite a Mathematical Concept
Step (E) requires correcting the excess fragments per million value by an observed CHG methylation level to obtain a corrected excess fragments per million value. The Office Action cites Specification paragraphs [0160] and [0166] as disclosing quantitative estimates and correction calculations. Office Action at 6. Those possible implementations do not appear in the claim
Step (F) Does Not Recite a Mathematical Concept
Step (F) requires applying a first threshold to the corrected excess fragments per million value to provide a first call for molecular residual disease when the corrected value satisfies the threshold and a first call against molecular residual disease when it does not. The Office Action alleges this is a mathematical relationship between variables and numbers. Office Action at 6.
But step (F) does not recite an inequality, equation, mathematical formula, or calculation. It does not state that the corrected value must be greater than, less than, equal to, or a specified mathematical distance from the threshold. It identifies a decision criterion applied to a particular assay metric and the two assay calls that follow from the criterion. The limitation may be implemented with a numerical comparison, just as the model training in Example 39 may be implemented with mathematical optimization, but the possible implementation is not itself set forth or described in the claim.
A claim that recites a mathematical calculation, when the claim is given its broadest reasonable interpretation in light of the specification, will be considered as falling within the "mathematical concepts" grouping. MPEP 21006.04 (a)(2) C.
It is important to note that a mathematical concept need not be expressed in mathematical symbols, because "[w]ords used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). MPEP 2106.04(a)(2) I.
The mathematical concept is recited in the claim. The limitation determining expected number of noise fragments…such that the expected number of noise fragment reflects the likelihood… in step C) is a recitation of a mathematical calculation/mathematical concept.
Similarly, the limitation determining an excess fragment per million value/ numerical ratio in step D) is a recitation of a mathematical calculation/mathematical concept.
Likewise, the limitation correcting an excess fragment per million value/numerical ratio in step E) is a recitation of a mathematical calculation/mathematical concept.
Similarly, the limitation applying a threshold to the corrected fragment per million value/ numerical ratio … to satisfy … or … fail to satisfy the …threshold in step F) is a recitation of a mathematical relationship/mathematical concept.
Furthermore, in contrast to Example 39, instant claim steps C) - F) do not recite a neural network nor do the claims include any analogous steps directed to analyzing facial images.
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. An inventive concept cannot be furnished by an abstract idea itself. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
The additional elements of claims 1-2, 4-7, 9, 11-14, 16-18, 20, 22-32, 34 and 36-38 include the following.
Claims 1, 37, 38 recite a computer system, a processor, and a memory; obtaining a corresponding nucleic acid sequence of each cell-free DNA fragment in a first plurality of cell-free DNA fragments; a non-transitory computer-readable medium including computer-executable instructions; a methylation sequencing.
Claim 2 recites obtaining, from a second sequencing reaction, a corresponding sequence of each cell-free DNA fragment in a second plurality of cell-free DNA fragments.
Claim 13 recites the second sequencing reaction is a panel-based sequencing reaction.
Claim 17 recites the first sequencing reaction is a whole genome methylation sequencing.
The additional elements of a system comprising a processor, a non-transitory computer-readable storage medium, a memory, and instructions are conventional computer components and/or processes. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general-purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TU Communications LLC v. AV Auto, LLC, 823 F.3d 607,613,118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
Furthermore, the additional elements of obtaining data amount to necessary data gathering and outputting. See MPEP 2106.05(g).
Furthermore, the additional elements of methylation sequencing, whole genome sequencing and panel-based sequencing amount to well-understood, routine, and conventional methods and systems for performing sequencing. This position is supported by Semenkovich et al. (Genomic approaches to cancer and minimal residual disease detection using circulating tumor DNA, 06/22/2023, Journal for Immunotherapy for Cancer, pages 1-12; as cited in the 04/16/2025 892 form). Semenkovich reviews approaches to cancer and MRD detection using circulating DNA (abstract). Semenkovich further teaches that methylation states, and epigenetic modifications, can be used to identify tumor-derived fragments (pg.6, col. 1, para. 2). Semenkovich further teaches that methylation sequencing of cfDNA and whole-genome bisulfite sequencing of cfDNA is used in cancer detection (pg. 6, col. 2, para.2). Semenkovich further teaches using sequencing panels to detect residual cancer (pg. 3, col.1, last para.).
Additionally, Melton (US12580051B2) identifying methylation patterns discriminating or indicating a cancer condition and teaches obtaining a corresponding fragment methylation pattern of each respective fragment, wherein the corresponding fragment methylation pattern of each respective fragment is determined by a methylation sequencing of nucleic acids from a respective biological sample obtained from a corresponding subject in a first set of subjects; state interval maps for one or more corresponding genomic regions; filtering, using the one or more processors, the one or more first state interval maps and the one or more second state interval maps to remove one or more nodes or corresponding genomic sub-regions that satisfy one or more exclusion criteria, and indicating a state of the cancer condition in the test subject (claim 1).
Therefore, these additional elements are not sufficient to amount to significantly more than the judicial exception. See MPEP 2106.05(g).
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]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more.
Response to Arguments
Applicant's arguments filed 07/23/2026 have been considered but they are not yet persuasive. Applicant states:
Claim 1 Recites Significantly More Than Any Alleged Judicial Exception.
The Office must support that conclusion with an express admission, an applicable court decision, a publication demonstrating widespread or common use, or properly taken official notice. MPEP §§ 2106.05(d), 2106.07(a). Merely locating an individual element in a publication does not establish that the element, much less the claimed combination, was well-understood, routine, and conventional.
The Office Action relies on Semenkovich et al. to show that circulating tumor DNA analysis, methylation states, methylation sequencing, whole-genome bisulfite sequencing, and sequencing panels were known. Office Action at 11. Even assuming those individual tools were conventional, Semenkovich does not establish that the claimed arrangement was widely prevalent or in common use. A review showing that researchers used ctDNA, methylation information, sequencing, and panels does not demonstrate conventional use of a separate healthy-subject- trained background emission distribution for each of at least 1000 regions, scaled to the observed test-sample sequencing depth, followed by regional excess-fragment aggregation and an observed CHG methylation correction before an MRD threshold is applied
These arguments are not yet persuasive. Applicant remarks are directed to Step 2B of 101 analyses, specifically evaluating additional elements to determine whether they amount to an inventive concept by considering them both individually and in combination to ensure that they amount to significantly more than the judicial exception itself.
Semenkovich in his review (a publication demonstrating widespread or common use) teaches that the additional elements of methylation sequencing, whole genome sequencing and panel-based sequencing amount to well-understood, routine, and conventional methods and systems for performing sequencing. Semenkovich teaches that liquid biopsies using cell- free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings to detect MRD and predict response to therapy (abstract). Semenkovich further teaches that to address high risk of false negative results, researchers have developed ever- more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part- per- million range and boost assay sensitivity and specificity by reducing sources of low- level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA (abstract). Semenkovich further teaches that panel- based mutation detection in cfDNA is ultimately limited by the number of ctDNA fragments possessing each on- panel variant. Semenkovich further teaches that several groups have now shown that broader sequencing to survey beyond focal recurrent mutations can improve the ctDNA limit of detection, with important implications for early cancer diagnostics and emerging applications to MRD detection. Targets of these broader approaches include methylated DNA, genome- wide copy number alterations (CNAs), and fragment- level sequencing features (fragmentomics) (pg. 5, co. 2, para.1). Semenkovich further teaches that whole- genome bisulfite sequencing of cfDNA at 30× coverage had higher sensitivity than targeted sequencing for SNVs across several cancer types and generatinge a 17.2 Mb panel covering over 100,000 informative regions which they applied using targeted bisulfite sequencing (pg. 6, col. 2, para.2).
Additionally, specification [0082] discloses that sequence reads refer to nucleotide sequences produced by any sequencing process described herein or known in the art.
Specification [0170] discloses that plurality of sequence reads is acquired by any methodology known in the art. For example, next generation sequencing (NGS) techniques such as sequencing-by-synthesis technology (Illumina), pyrosequencing (454 Life Sciences), ion semiconductor technology (Ion Torrent sequencing), single-molecule real-time sequencing (Pacific Biosciences), sequencing by ligation (SOLiD sequencing), or nanopore sequencing (Oxford Nanopore Technologies) is performed… In some embodiments, sequencing is performed using next generation sequencing technologies, such as short-read technologies. In other embodiments, long-read sequencing or another sequencing method known in the art is used.
Applicant further states (pg. 19-21):
The Rejection Does Not Address the Ordered Combination
Claim 1 requires the following ordered combination:
- obtaining methylation-pattern-bearing nucleic acid sequences for cell-free DNA fragments from a methylation sequencing reaction performed on a liquid biopsy sample of the subject;
- using the sequence and methylation pattern of each fragment to determine a corresponding number of ctDNA fragments mapping to each of at least 1000 genomic regions;
- for each region, using a region-specific background emission distribution learned from methylation sequencing data of healthy subjects, together with the learned regional background emission rate and the sequencing depth actually observed for the test sample in that region, to determine an expected number of ctDNA-like noise fragments;
- determining a sample-level excess fragments per million value from regional ctDNA- fragment counts observed above their corresponding expected regional background counts;
- correcting that sample-level excess-fragment value using the observed CHG methylation level of the same test sample; and
- applying a threshold to the corrected value to generate a positive or negative molecular residual disease call and providing the corresponding status indication.
The inventive concept resides in this arrangement and interaction, not in methylation sequencing, a processor, a numerical value, or a threshold viewed in a vacuum.
Moreover, because steps (B)-(F) do not themselves recite a mathematical concept as alleged by the Office Action, those limitations must be evaluated as additional elements at Step 2B rather than assigned wholesale to the alleged exception. The Office Action instead assigns nearly every limitation that defines the claimed assay architecture to the alleged exception, leaves only generic computer and data-acquisition recitations, and asks whether those residual elements are conventional. Regardless, the question at Step 2B is whether the additional elements, in combination with any alleged exception, provide an inventive concept.
In step 2B analysis, when making a determination whether the additional elements in a claim amount to significantly more than a judicial exception, the examiner should evaluate whether the elements define only well-understood, routine, conventional activity.
The additional elements a system comprising a processor, a non-transitory computer-readable storage medium, a memory, and instructions are well-understood, routine, and conventional computer components and/or processes and are recited at a high level of generality, therefore these additional elements don not favor eligibility. See MPEP 2106.05(d).
Furthermore, the additional elements of obtaining data amount to necessary data gathering and outputting. These additional elements are considered insignificant extra-solution activities and does not integrate the judicial exception into a practical application in Step 2A Prong Two or recites significantly more in Step 2B. As explained by the Supreme Court, the addition of insignificant extra-solution activity does not amount to an inventive concept. See MPEP 2106.05(g)(3).
Furthermore, the additional elements of methylation sequencing, whole genome sequencing and panel-based sequencing amount to well-understood, routine, and conventional methods and systems for performing sequencing, as taught by Semenkovich above and specification, as above.
Furthermore, the claim arrangement is conventional and can not provide the inventive concept. Semenkovich and Melton (see above) teach the arrangement. Semenkovich teaches that liquid biopsies using cell- free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings to detect MRD and predict response to therapy (instant claim 1 Step A) ). Semenkovich further teaches that to address high risk of false negative results, researchers have developed ever- more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part- per- million range and boost assay sensitivity and specificity by reducing sources of low- level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA addressing instant steps B) – E) (Semenkovich: abstract).
Furthermore, steps (B)-(F) recite mathematical concepts/abstract ideas, as such, these steps are not considered additional elements. See above.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-2, 4-7, 9, 11, 13-14, 16-17, 20, 24-25, 29-32, and 37-38 are rejected under 35 U.S.C. 103 as being unpatentable over Hubbell (US-20190316209-A1; as cited in 04/16/2025 892 form) in view of Rifatbegovic et al. (Neuroblastoma cells undergo transcriptomic alterations upon dissemination into the bone marrow and subsequent tumor progression, 20 November 2017, International Journal of Cancer, pages 297-307; as cited in 04/16/2025 892 form), and further in view of Ong Abdullah hereinafter, Abdullah (BR112016025562B1; as cited in the attached 892 form).
Regarding claims 1, 37, and 38, Hubbell discloses a method of generating a cancer prediction, such as a presence or absence of cancer, for an individual based on cfDNA in a test sample obtained from the individual [0004], comprising a processor, a non-transitory computer-readable storage medium with encoded instructions (claim 27); reading on limitations of a method comprising: at a computer system having one or more processors, and memory storing one or more programs for execution by the one or more processors.
Hubbell further discloses obtaining a dataset associated with cell-free nucleic acids in a test sample obtained from the subject, the dataset comprising sequence reads generated from one or more sequencing assays on the cell-free nucleic acids (claim 1). Hubbell further discloses one or more methylation features derived from a methylation sequencing assay on the cell-free nucleic acids in the test sample (claim 2) where the test sequences include liquid cancer sequences [0596] and that the cell-free nucleic acids includes cf-DNA from white blood cells (for example, liquid biopsy) [0010]; reading on limitations of obtaining a corresponding nucleic acid sequence of each cell-free DNA fragment in a first plurality of cell-free DNA fragments, from a first plurality of sequence reads of a first sequencing reaction, wherein the first sequencing reaction is a methylation sequencing of the first plurality of cell-free DNA fragments from a first liquid biopsy sample of the subject, and wherein each respective nucleic acid sequence in the first plurality of nucleic acid sequences comprises a methylation pattern for a corresponding cell-free DNA fragment in the first plurality of cell-free DNA fragments;
Hubbell further discloses using hybridization probes designed to target and hybridize with targeted nucleic acid sequences to pull down and enrich targeted nucleic acid fragments that may be informative for the presence or absence of cancer (or disease), cancer status, or a cancer classification (for example, circulating tumor DNA). Hubbell further discloses that the hybridization probes are designed to target and pull-down nucleic acid fragments that derive from exon sequences in a reference genome [0179]. Hubbell further discloses aligning K-mers from reads to a k-mer represented by a node or edge in the directed graph ([0204-0205]. Hubbell further discloses performing or having performed a computational analysis on the sequence reads to generate values for one or more features derived from the sequence reads, where methylation features (e.g., features derived from sequence reads that were generated by a methylation sequencing assay) can include a total number hypermethylated or hypomethylated regions (claim 1; [0005]). Hubbell further discloses mapping/aligning to a reference genome that corresponds to a region that is associated with a gene or segment of gene [0187]. Hubbell further discloses designing targeted gene panels to analyze specific sets of genes or genomic regions, ranging in size from hundreds of genes to thousands of genes [0196]. Hubbell further discloses generating reads from generation of methylation sequencing assay ([0159], claim 65). Hubbell further discloses Hubble further discloses quantifying hypomethylated and hypermethylated counts and determining presence or absence of abnormally methylated fragments; Methylation features can be a fragment methylation pattern, which can be determined, e.g., by counting fragments satisfying a set of criteria ((claim 3); [0498] – [0502]); reading on limitations of determining a corresponding number of circulating-tumor DNA (ctDNA) fragments mapping to each respective region in a plurality of regions of one or more first reference sequences of the species of the subject using a methylation pattern of each nucleic acid sequence in the first plurality of nucleic acid sequences, wherein the plurality of regions comprises 1000 or more regions.
Hubbell further discloses identifying features of sequence reads that are informative for generating a cancer prediction while accounting for interfering signals (e.g., noise); candidate variants can be filtered to remove false positive variants that may arise due to an artifact and therefore are not indicative of cancer in the individual ([0004] [0192], FIG. 4D).
Hubbell further discloses using a Bayesian hierarchical model to determine expected noise rates for sequence reads from a subject; position-specific noise information in order to improve the sensitivity/specificity of variant calling; the processing system trains the model using samples from healthy individuals to model the expected noise rates per position of sequence reads [0207].
Hubbell further discloses example noise models that combine position-specific distribution with observed sequencing depth for the respective regions that reflects the likelihood of observing mutation-like fragments in the absence of cancer based on the learned distribution for the respective region ([0215-0217]; FIG 3B, 3C and 3Y; see also, a Poisson distribution given a depth [0225-0241]).
Hubbell further discloses modeling noise of sequence reads of nucleic acid sample ([0206], FIG 3B). Hubbell further discloses analyzing data from a test sample based on information learned from data with reduced dimensionality ([0078], FIG. 6).
Hubbell further discloses that one of many possible model architectures that may be used to generate candidate variants and which are related to each other in that they all model position-specific noise information in order to improve the sensitivity/specificity of variant calling. More specifically, the processing system trains the model using samples from healthy individuals to model the expected noise rates per position of sequence reads [0207]. Additionally, Hubble discloses identifying anomalously methylated fragments (segments of DNA where the methylation pattern that deviates from the typical or expected pattern, for example, noise) from a subject while minimizing computational overhead, the system leverages a noise distribution learned from healthy subjects as a baseline. It achieves this by calculating p-value scores for methylation state vectors, quantifying how likely an observed methylation pattern is to occur naturally (i.e., within the healthy subject distribution) or by chance [0508-0523]; reading on limitations of determining a corresponding expected number of noise fragments in each respective region of the plurality of regions of the one or more first reference sequences of the species of the subject based on a corresponding region-specific background emission distribution that has been learned from prior methylation sequencing data from a plurality of healthy subjects and an observed sequencing depth from the first sequence reaction, wherein the expected number of noise fragments for the respective region is determined by combining the region-specific background emission distribution with the observed sequencing depth, such that the expected number of fragments reflects the likelihood of observing ctDNA- like fragments in the absence of cancer based on the learned distribution for the respective region.
Hubbel further discloses normalization techniques to adjust count using a depth quality score [0280].
Hubbell does not teach determining an excess fragment per million values from ctDNA in excess of the corresponding expected number of noise fragments.
Rifatbegovic discloses a method of determining the presence of disseminated tumor cells (DTCs) in the bone marrow (BM) of metastatic (M)stage patients (abstract), where the DNA was extracted from the primary tumor, the BM-derived DTCs and a tumor cell-free BM or peripheral blood sample (pg. 299, col. 2, subsection: sample preparation and DNA extraction for qPCR). Rifatbegovic further discloses that in the enrichment analysis, after read mapping and counting, DESeq2 20 was used to call differentially expressed genes and DESeq2 was used to generate a normalized (function “fpm”, robust 5 TRUE) and variance-stabilized (function “vst”) gene expression matrix for import into and further analysis (pg. 299, col. 1, para. 3). Rifatbegovic further discloses identification of MRD markers based on a threshold (page. 302, FIG. 4a and 4b); reading on limitations of correcting the excess fragments per million value for the first liquid biopsy sample by an observed CHG methylation level to obtain a corrected excess fragments per million value and applying a first threshold to the corrected excess fragments per million value to provide: a first call for molecular residual disease when the corrected excess fragments per million value satisfies the first threshold or a first call against molecular residual disease when the corrected excess fragments per million value fails to satisfy the first threshold.
Further regarding claims 1, 37, and 38, Hubbell discloses that DNA methylation occurs in the context of CHG [0155]. Rifatbegovic teaches correcting FPM by an observed methylation (Figure 5).
Hubbell and Rifatbegovic do not teach correcting FPM by observed CHG methylation levels.
Abdullah teaches a classification method based on presence or absence of abnormality and teaches determining abnormality by the density of methylation (e.g., CHG methylation density) within a differential methylation region (DMR) in a sample [082] and calculating and plotting Fragments per kilobase of normalized expression values (FPKM) per mapped reads per million [115-118].
Further regarding claims 1, 37, and 38, Hubbell discloses a system for determining a cancer prediction for a subject, the system comprising: a processor; and a non-transitory computer-readable storage medium with encoded instructions that, when executed by the processor, cause the processor to accomplish the steps (claim 27).
Regarding claim 2, Hubbell discloses small variant computational analysis of sequence reads [0191], where the cell-free nucleic acids includes cf-DNA from white blood cells [0010]; reading on limitations of obtaining, from a second sequencing reaction, a corresponding sequence of each cell-free DNA fragment in a second plurality of cell-free DNA fragments in a second liquid biopsy sample of the subject, thereby obtaining a second plurality of sequence reads.
Hubbell further discloses that the small variant sequencing assay may be a sequencing-based assay that generates sequence reads, typically through targeted gene sequencing panels that can be used to determine small variants, examples of which include single nucleotide variants (SNVs) [0191]; reading on limitations of using the second plurality of sequence reads to identify each candidate somatic variant in a set of candidate somatic variants, wherein each candidate somatic variant in the set of candidate somatic variants is a single nucleotide variant (SNV).
Hubble further discloses that candidate variants can be filtered to remove false positive variants that may arise due to an artifact and therefore are not indicative of cancer in the individual [0192]; reading on limitations of filtering the set of candidate somatic variants
Hubbell further discloses process flow for noise models where they collect samples from a database of sequence reads and exclude sequence reads of healthy individuals that have suspected germline mutations that are not indicative of target noise in sequence reads. further, the processing system may determine which positions are likely to contain germline variants and selectively exclude such positions using thresholds [0236]; reading on limitations of removing from the set of candidate somatic variants each respective candidate somatic variant in the set of candidate somatic variants that is present in a repository of known germline variants.
Hubbell further discloses using ranges and/or values of variant allele frequencies that is only represented by the values of the top Nvariant allele frequencies. An example of the ranked order feature for the top 5 allele frequencies can be represented as: [0.1, 0.08, 0.05, 0.03, 0.02] which indicates that the 5 highest allele frequencies, independent of the somatic variants, range from 0.02 up to 0.1 [0200]. Hubbell further discloses determining, using the likelihoods, a probability that the true AF of the cfDNA sample is greater than a function of the true AF of the gDNA sample ([0250], FIG. 3Y); reading on limitations of removing from the set of candidate somatic variants each respective candidate somatic variant in the set of candidate somatic variants that maps to a variant interval in a plurality of variant intervals, wherein each respective variant interval in the plurality of variant intervals is identified as having a pre-test odds of a positive variant call that is less than a pre-test odds threshold value based upon a prevalence of a corresponding one or more training variants, which are each above a limit of detection and map to the respective variant interval, in a plurality of tumor-normal matched samples for the cancer condition obtained from a first cohort of training subjects having the cancer condition with the proviso that no variant detected in a second cohort of healthy samples maps to the respective variant interval;
Hubbell further discloses that candidate variants can be filtered to remove false positive variants that may arise due to an artifact and therefore are not indicative of cancer in the individual [0200]; reading on limitations of removing from the set of candidate somatic variants each respective candidate somatic variant in the set of candidate somatic variants that is identified as an artifactual variant,
Hubbell further discloses that both positive and negative strands of the originating nucleic acid molecule is captured; otherwise, the collapsed read is designated “non-duplex.” [0202]. Hubbell further discloses that examples of small variant features 154 include any of: a total number of somatic variants in a subject's cfDNA [0191], and that cfDNA is extracted from the test sample through a purification process (only cfDNA is used in the analysis) ([0176], FIG. IC); reading on limitations of removing from the set of candidate somatic variants each respective candidate somatic variant in the set of candidate somatic variants that fails to be represented by at least one cell-free DNA fragment in the second plurality of cell-free DNA fragments in which both strands of the at least one cell-free DNA fragment are identified in one or more sequence reads of the second plurality of sequence reads.
Hubbell further discloses that the small variant computational analysis 140C identifies candidate variants present in cfDNA that are likely to be derived from a somatic source in view of interfering signals such as noise and/or variants that can be attributed to a genomic source (e.g., from gDNA or WBC DNA) and that somatic variants, and features thereof, that remain following the filtering out of false positive variants can be used to determine the small variant features ([0192], Fig. 1C); reading on limitations of providing: a second call for molecular residual disease when there remains a candidate variant in the set of candidate variants after application of the procedure, or a second call against molecular residual disease when no candidate variant remains in the set of candidate variants after application of the procedure
Hubbell further discloses that the small variant features and methylation features along with whole genome and baseline features can be used to predict cancer in an asymptomatic individual (FIG. 1C). Hubbell further discloses that variant can lead to development and/or progression (for example, indication of molecular residual disease) of cancer in an individual. Further Hubbell discloses that the method detects presence and absence of cancer in an asymptomatic subject (for example, the presence of a very small number of cancer-derived cfDNA that remain in circulation during or after cancer treatment/Minimal residual disease)[0007-0008]; reading on limitations of the providing G) provides the indication that the subject has positive molecular residual disease status for the cancer condition when the applying F) provides the first call for molecular residual disease or the providing K) provides the second call for molecular residual disease.
Regarding claim 4, Hubbell discloses comparing alignment position information between a first sequence read and a second sequence read to determine whether nucleotide base pairs of the first and second sequence reads overlap in the reference genome (for example, database of known somatic mutations). Hubbell further discloses that a first and second sequence read are stitched if the overlap is greater than the threshold length and if the overlap is not a sliding overlap. For example, a sliding overlap may include a homopolymer run (e.g., a single repeating nucleotide base), a dinucleotide run (e.g., two-nucleotide base sequence), or a trinucleotide run (e.g., three-nucleotide base sequence), where the homopolymer run, dinucleotide run, or trinucleotide run has at least a threshold length of base pairs [0203]; reading on limitations of removing from the set of candidate variants each respective candidate somatic variant in the set of candidate somatic variants that (a) maps to a repeat region in the one or more second reference sequences of the species and (b) is not annotated as a known somatic mutation in a database of known somatic mutations for the species of the subject.
Regarding claim 5, Hubbell discloses that Embodiments of the invention provide for a method of generating a cancer prediction, such as a presence or absence of cancer, for an individual based on cfDNA in a test sample obtained from the individual ([0004] [0160], claim 62; FIG. 1C); reading on limitations of the indication that the subject has negative molecular residual disease status for the cancer condition when the applying F) provides the first call against molecular residual disease and the providing K) provides the second call against molecular residual disease.
Regarding claim 6, Hubbell discloses that the first and second biopsy samples are the same (FIG. 1C); reading on limitations of the first liquid biopsy sample and the second liquid biopsy sample are the same liquid biopsy sample.
Regarding claim 7, Hubbell discloses using training and test samples [0170-0176]; reading on limitations of the first liquid biopsy sample and the second liquid biopsy sample are different liquid biopsy samples.
Regarding claims 9 and 11, Hubbell discloses that the sample is selected from the group consisting of blood, plasma, serum, urine, fecal, saliva, whole blood, a blood fraction, a tissue biopsy, pleural fluid, pericardial fluid, cerebral spinal fluid, and peritoneal fluid sample (claim 21) and that training data can include cfDNA and/or WBC DNA obtained from training samples[0170]; reading on limitations of the first liquid biopsy sample comprises blood, whole blood, peripheral blood, plasma, serum, or lymph of the subject.
Regarding claim 13, Hubbell discloses that using targeted gene sequencing panels to determine small variants [0191]; reading on limitations of the second sequencing reaction is a panel-based sequencing reaction of a plurality of loci.
Regarding claim 14, Hubbell discloses generating candidate variants based on the sequencing depth of a target region. In particular, the processing system may be more confident in identifying variants in target regions that have greater sequencing depth, for example, because a greater number of sequence reads help to resolve (e.g., using redundancies) mismatches or other base pair variations between sequences.
Hubbell further discloses the experimental details (e.g., gene panel, sequencing depth, etc.) used to determine values of features for each respective predictive cancer model where the sequencing depth is at least 250x by the second sequencing reaction of [0089], FIG 9B); reading on limitations of the plurality of loci is sequenced at an average sequence depth of at least 250x by the second sequencing reaction.
Regarding claim 16, Hubbell discloses comparing alignment position information between a first sequence read and a second sequence read to determine whether nucleotide base pairs of the first and second sequence reads overlap in the reference genome ([0203], FIG, 5B and C).
Hubbell further discloses that nucleic acid sequence reads can be aligned to regions of a reference genome [0438].
Hubbell further discloses that any suitable size can be used to define genomic regions. For example, a genomic region can include 10 kb -250 kb [0439]. Hubbell further discloses a human haploid reference genome includes over three billion bases that can be divided into about 30,000 regions (or bins). [0441]. Hubbell further discloses that a reference genome can be divided into any number of genomic regions, or genomic regions of any sizes [0449]. Hubbell further discloses that sequence reads can be aligned to a plurality of chromosomal regions of reference genome [0457]. Hubbell further discloses that determining a bin sequence read count of a reference genome were each bin is between 10 kilobases (kb) and 1 megabase (mb) [0375]; reading on limitations of the one or more first reference sequences is a human reference genome, the one or more second reference sequences is the human reference genome, the plurality of regions comprises 1000 or more regions cumulatively mapping to between four megabases and ten megabases of the human reference genome, and the plurality of loci comprises 50 or more loci cumulatively mapping to between 0.1 megabase and 1 megabase of the human reference genome.
Regarding claim 17, Hubbell discloses that the nucleic acid sequencing data is whole genome methylation sequencing data (abstract, [0481]); reading on limitations of wherein the first sequencing reaction is a whole genome methylation sequencing.
Regarding claim 20, Hubbell discloses that the first and/or second score represents one of: a presence or an absence of cancer in the subject, a severity or a grade of cancer in the subject, a type of cancer; reading on limitations of the cancer condition is a particular type of cancer or a particular stage of a particular type of cancer (claim 31); reading on limitations of the cancer condition is a particular type of cancer or a particular stage of a particular type of cancer.
Regarding claim 24, Hubbell discloses variant calling and quality control to extracted DNA or RNA ([0037] [0175], FIG. 3R-3S). Hubbell further discloses that the value of a variant allele frequency can be between 0 to 1, where a variant allele frequency of 0 indicates no sequence reads that possess the alternate allele at the position and where a variant allele frequency of 1 indicates that all sequence reads possess the alternate allele at the position [0200]; reading on limitations of applying a variant caller to the second plurality of sequence reads with a restriction that the variant caller determines that each respective candidate somatic variant in the set of candidate somatic variants has a variant allele frequency of at least 0.1 in the second plurality of sequence reads and that at least one cell-free DNA fragment in the second plurality of cell-free DNA fragments exhibits the respective candidate somatic variant.
Regarding claim 25, Hubbell discloses that candidate variants can be filtered to remove variants that are not indicative of cancer in the individual [0192] and that CNVs can refer to copy number changes in white blood cells that can arise due to clonal hematopoiesis [0145].
Hubbell further discloses that low probability that the true AF of the cfDNA sample is greater than a function of the true AF of the gDNA sample indicates that nucleotide mutations observed in cfDNA likely did not originate from potential cancer cells or other diseased cells of the subject. Instead, the nucleotide mutations may be attributed to naturally occurring mutations in healthy individuals, due to factors such as germline mutations, clonal hematopoiesis and that the probability represents a confidence level that at least some nucleotide mutations from the sequence reads of cfDNA are not found in sequence reads of reference tissue [0250].
Hubbell further discloses filtering out ALTs observed in cfDNA samples due to the low confidence of the source of the ALTs [0268]; reading on limitations of removing from the set of candidate somatic variants each respective candidate somatic variant in the set of candidate somatic variants that maps to a region of clonal hematopoiesis of indeterminate potential (CHIP).
Regarding claim 29, Hubbell discloses a process for extracting an allele fraction ([0053] [0309], FIG. 4E-4G). Hubble further discloses that any sequence read that includes an alternative allele that is located greater than a threshold number of base pairs from an edge of a sequence read is categorized as non-artifact training data [0300], FIG. 4B-C); reading on limitations of removing from the set of candidate allele variants each candidate variant in the set of candidate allele variants that has a variant allele fraction exceeding an upper threshold fraction in the second plurality of sequence reads.
Regarding claim 30, Hubbell discloses that the example data in the following FIGS. 4S-Z were generated using sequence reads obtained from a sample set of individuals of a cell free genome study and processed using one or more of the methods described herein (e.g., noise modeling, joint modeling, edge filtering, non-synonymous filtering, etc.). The sample set includes healthy individuals from which blood samples (e.g., cfDNA) were obtained [0357]. Hubbell further discloses observed counts of variants in samples from healthy individuals [0260]; reading on limitations of removing from the set of candidate allele variants each candidate variant in the set of candidate allele variants that is observed in a cohort of healthy subjects.
Regarding claim 31, Hubbell discloses that the processing system filters a candidate variant responsive to determining that the candidate variant is an edge variant artifact, has less than a threshold cfDNA depth (e.g., 200 sequence reads), has less than a threshold cfDNA quality score (e.g., 60); reading on limitations of removing from the set of candidate allele variants each respective candidate variant in the set of candidate allele variants in which the second sequencing reaction produced a coverage depth of less than a threshold amount for the respective locus in one or more second reference sequences of the species of the subject that the candidate somatic variant maps to.
Regarding claim 32, Hubbell discloses that in order to identify which of the fragments are anomalously methylated, the processing system may filter the set of methylation state vectors based on their p-value scores. In one embodiment, filtering is performed by comparing the p-values scores against a threshold and keeping only those fragments below the threshold (0511); reading on limitations of removing, from the first plurality of cell-free DNA fragments, each cell-free DNA fragment that fails to satisfy a methylation rate threshold.
In KSR Int 'l v. Teleflex, the Supreme Court, in rejecting the rigid application of the teaching, suggestion, and motivation test by the Federal Circuit, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Applying the KSR standard to Hubbell, Rifatbegovic, and Abdullah examiner concludes that this combination represents the use of known techniques to improve similar methods. Hubbell, Rifatbegovic and Abdullah are directed to predicting abnormality from methylation analysis. Hubbell only disclosed obtaining and determining cfDNA and noise determination and normalization and methylation in the context of CHG. In the same field of research, Rifatbegovic provided normalization of sample using fragment per million values by differentially methylated regions. Abdullah provided per million normalization/correction in the context of CHG by differentially methylated regions. Combining the cancer prediction of Hubbell with the known sample quantification/normalization of Rifatbegovic and Abdullah would have allowed for accounting for differences in sequencing depth and would make data more comparable across different samples. One ordinary skilled in the art before he effective filing data of the claimed invention would have had a reasonable expectation of success at combining these methods. This combination would have been expected to have provided a more accurate measurement of low-level disease, improving sensitivity, consistency and comparability in detecting residual cancerous cells. Therefore, the invention would have been prima facie obvious to one of skill in the art before the effective filing date of the claimed invention, absent evidence to the contrary.
Response to Arguments
Applicant's arguments filed 07/23/2026 have been considered but they are not persuasive.
Applicant states (pg. 27; pg. 28):
The Office Action improperly combines unrelated Hubbell pipelines and yet does not teach element C.
Hubbell’s methylation p-value does not determine an expected number of noise fragment per region.
As stated above, Hubbell discloses example noise models that combine position-specific distribution with observed sequencing depth for the respective regions that reflects the likelihood of observing mutation-like fragments in the absence of cancer based on the learned distribution for the respective region ([0215-0217]; FIG 3B, 3C and 3Y; see also, a Poisson distribution given a depth [0225-0241]).
Hubbell further discloses that one of many possible model architectures that may be used to generate candidate variants and which are related to each other in that they all model position-specific noise information (for example, region-specific background distribution) in order to improve the sensitivity/specificity of variant calling. More specifically, the processing system trains the model using samples from healthy individuals to model the expected noise rates per position of sequence reads [0207].
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Hubbell in view of Rifatbegovic, in view of Abdullah, as applied to claims 1-2, 4-7, 9, 11, 13-14, 16-17, 20, 24-25, 29-32, and 37-38 above, and further in view of Du (CN-118974282-A).
Claim 12 depends on claim 1. Limitations of claim 1 have been taught in the above rejections.
Regarding claim 12, Hubbell discloses that the sample is selected from the group consisting of blood, plasma, serum, urine, fecal, saliva, whole blood, a blood fraction, a tissue biopsy, pleural fluid, pericardial fluid, cerebral spinal fluid, and peritoneal fluid sample ([0018], claim 82). Hubbell is silent on the volume of the sample.
Du discloses a Minimal Residual Disease (MRD) detection method comprising sequencing cell free DNA, detecting biomarkers, and determining MRD, where methylation status can be determined using methylation status (claim 1; pg. 3, para. 4).
Du further teaches that the cell-free DNA (cfDNA) in blood or urine may be used to perform a customized liquid biopsy NGS assay specific to the patient to detect MRD and monitor therapeutic response or redevelopment (pg. 2, last para.).
Du further teaches that at each MRD monitoring point in time, 2 tubes of blood (20 ml in total) are drawn and sequenced to obtain high detection sensitivity (pg. 3, last para.)
Applying the KSR standard to Hubbell, Rifatbegovic, Abdullah and Du, examiner concludes that the combination of Hubbell, Rifatbegovic, Abdullah and Du represent the use of known techniques to improve similar methods. Hubbell, Rifatbegovic, and Abdullah only disclosed obtaining sample and determining cfDNA and noise determination and normalization of sample using fragment per million values. In the same field of research, Du taught that MRD monitoring can be effectively done for low blood volumes of biopsy samples. Combining the cancer prediction of Hubbell and Rifatbegovic with sample volume of Du would have allowed retrieval of enough cfDNA to be captured. One ordinary skilled in the art before he effective filing data of the claimed invention would have had a reasonable expectation of success at combining the method of Hubbell, Rifatbegovic, and Abdullah with the method of Du. This combination would have been expected to have provided a more accurate measurement of low-level disease, improving clinical outcomes in residual cancerous cells. Therefore, the invention would have been prima facie obvious to one of skill in the art before the effective filing date of the claimed invention, absent evidence to the contrary.
Response to Arguments
Applicant's arguments filed 07/23/2026 have been considered but they are not persuasive. Applicant states (pg. 17):
Wang… does not remedy the missing region-specific methylation background model, excess fragment calculation, or CHG correction.
Wang concerns immunoaffinity capture of circulating tumor cells, not claimed cell-free DNA methylation workflow.
With regards to Applicant stating that Wang does not remedy missing limitations, Hubbell teaches region-specific methylation background noise model and Rabinovic and Abdullah teach excess fragment calculation and CHG correction.
Applicant argument regarding Wang not disclosing cell free DNA methylation workflow is found persuasive. As stated above, Du teaches the blood volume of biopsy sample in a methylation workflow.
Claims 18 and 22-23 are rejected under 35 U.S.C. 103 as being unpatentable over Hubbell in view of Rifatbegovic, in view of Abdullah, as applied to claims 1-2, 4-7, 9, 11, 13-14, 16-17, 20, 24-25, 29-32, and 37-38 above, and further in view of Mortimer (US11345968B2; ; as cited in 04/16/2025 892 form).
Claims 18 and 22-23 depend on claim1 and claim 2, respectively. Limitations of claims 1 and 2 have been taught in the above rejections.
Regarding claim 18, Hubbell discloses obtaining sequence reads directly from millions of individual nucleic acid (e.g., DNA such as cfDNA or gDNA) molecules in parallel. Such techniques can be suitable for performing any of targeted gene panel sequencing, whole exome sequencing, whole genome sequencing, targeted gene panel bisulfite sequencing, and whole genome bisulfite sequencing [0181]. Hubbell further discloses that the sequence reads are generated from a next generation sequencing (NGS) procedure. In some embodiments, the sequence reads are generated from a massively parallel sequencing procedure using sequencing-by-synthesis [0010].
Hubbell and Rifatbegovic are silent on at least 50,000 sequence reads for the first plurality of sequence reads.
Mortimer discloses methods for use in detection of molecular residual disease (abstract). Mortimer further discloses obtaining a plurality of cell-free deoxyribonucleic acid (cfDNA) molecules obtained or derived from the subject to generate amplified cfDNA molecules, enriching cfDNA for a sequencing panel with plurality of genomic regions from cancer tumor biopsy of the subject, sequencing enriched amplified cfDNA molecules at a sequence read depth of at least about fifty thousand sequence reads per base to generate sequence reads, aligning reads to a reference genome to detect a variant, and therefore, determining the molecular residual disease in the subject, where the bodily fluid sample is a blood sample, a plasma sample, or a serum sample (claims 1 and 11).
Regarding claims 22 and 23, Hubbell and Rifatbegovic are silent on generating a report for the subject comprising the identity of candidate variants and a therapeutic match.
Mortimer discloses a method for identifying treatment for a subject with non-small cell lung carcinoma (NSCLC), comprising: (a) sequencing cell-free DNA (cfDNA) molecules derived from a cell-free DNA (cfDNA) sample obtained from the subject; (b) analyzing sequence reads derived from the sequencing to identify (i) circulating tumor DNA (ctDNA) among the cfDNA molecules and (ii) a copy number amplification (CNA) of the MET gene in the ctDNA with a specificity of at least 99%; and (c) identifying, based at least on the identified CNA of the MET gene, an anti-MET therapy to be administered to the subject to treat the NSCLC (col. 7, para. 6); reading on limitations of generating a report for the subject comprising the identity of candidate variants and a therapeutic match.
Applying the KSR standard to Hubbell, Rifatbegovic, Abdullah, and Mortimer, examiner concludes that this combination represents the use of known techniques to improve similar methods. Hubbell, Rifatbegovic, and Abdullah only disclosed obtaining sample and determining cfDNA and noise determination and normalization of sample using fragment per million values. In the same field of research, Mortimer provided information about the least number of sequencing reads. Combining the cancer prediction of Hubbell, Rifatbegovic, and Abdullah with threshold reads of 50,000 of Mortimer would have allowed to detect rare mutations, genetic alterations, or biomarkers. One ordinary skilled in the art before he effective filing data of the claimed invention would have had a reasonable expectation of success at combining the method of Hubbell, Rifatbegovic, and Abdullah with the method of Mortimer. This combination would have been expected to have provided a more accurate detection of low-level disease, improving clinical outcomes in residual cancerous cells. Therefore, the invention would have been prima facie obvious to one of skill in the art before the effective filing date of the claimed invention, absent evidence to the contrary.
Response to Arguments
Applicant's arguments filed 07/23/2026 have been considered but they are not persuasive. Applicant states (pg. 30, last para):
Claims 18, 22-23, and 34-36 depend … from claim 1 or claim 2 and are patentable as set forth above.
Claim 36 contains an additional deficiency… of the adjuvant therapycomprise increasing a dosage, decreasing a dosage, or ceasing the therapy.
As stated above, Hubbell, Rifatbegovic, and Abdullah teach all the limitations of claims 1 and 37-38. As such, the rejection of claims 18, 22-23 under U.S.C 103 is maintained.The argument regarding claim 36 is found persuasive. As such, claims 34 and 36 are separately rejected in view of Zhang below.
Claims 25-28 are rejected under 35 U.S.C. 103 as being unpatentable over Hubbell in view of Rifatbegovic, in view of Abdullah, as applied to claims 1-2, 4-7, 9, 11, 13-14, 16-17, 20, 24-25, 29-32, and 37-38 above, and further in view of Dai et al. (WO2023225175A1; as cited in 04/16/2025 892 form).
Claims 25-28 depend from claim 2. The limitations of claim 2 has been taught in the above rejection.
Regarding claims 25, 26, 27, and 28 Hubbell discloses that candidate variants can be filtered to remove variants that are not indicative of cancer in the individual [0192] and that CNVs can refer to copy number changes in white blood cells that can arise due to clonal hematopoiesis [0145].
Hubbell further discloses that low probability that the true AF of the cfDNA sample is greater than a function of the true AF of the gDNA sample indicates that nucleotide mutations observed in cfDNA likely did not originate from potential cancer cells or other diseased cells of the subject. Instead, the nucleotide mutations may be attributed to naturally occurring mutations in healthy individuals, due to factors such as germline mutations, clonal hematopoiesis and that the probability represents a confidence level that at least some nucleotide mutations from the sequence reads of cfDNA are not found in sequence reads of reference tissue [0250].
Hubbell further discloses filtering out ALTs observed in cfDNA samples due to the low confidence of the source of the ALTs [0268]; reading on limitations of removing from the set of candidate somatic variants each respective candidate somatic variant in the set of candidate somatic variants that maps to a region of clonal hematopoiesis. Hubbell and Rifatbegovic are silent on mapping to regions of clonal hematopoiesis of indeterminate potential (CHIP) where the region is DNMT3A, TET2, and ASXL1.
Dai discloses a cancer therapy monitoring method comprising (a) obtaining or deriving a biological sample from a subject, wherein said subject has cancer, has previously had cancer, or is suspected of having cancer; (b) assaying cell-free deoxyribonucleic acid (cfDNA) molecules obtained or derived from said biological sample, wherein said assaying comprises sequencing at least a portion of said cfDNA molecules or derivatives thereof to produce a set of sequencing reads, wherein said sequencing comprises at least one of whole-exome sequencing (WES) and whole-genome sequencing (WGS); and (c) determining at least one of a tumor mutational burden and a copy number burden of said subject, based at least in part on processing said set of sequencing reads. Dai further discloses that the sample is extracted from blood sample of the subject [0007-0009]. See also, liquid biopsy sample [00195].
Dai further discloses somatic coding SNVs including synonymous and nonsynonymous variants within panel target regions, where variants in common CHIP genes (DNMT3A, TET2, ASXL1 and JAK2) were excluded in score estimation [00290].
Applying the KSR standard to Hubbell, Rifatbegovic, Abdullah, and Dai, the examiner concludes that this combination represents the use of known techniques to improve similar methods. Hubbell, Rifatbegovic, and Abdullah only disclosed obtaining sample and determining cfDNA and noise determination and normalization of sample using fragment per million values. In the same field of research, Dai provided information about the exclusion of clonal hematopoiesis of indeterminate potential (CHIP) that maps to DNMT3A, TET2, and ASXL1. Combining the cancer prediction of . Hubbell, Rifatbegovic, and Abdullah with region exclusion of Dai would have allowed background noise reduction in somatic mutation analysis. One ordinary skilled in the art before he effective filing data of the claimed invention would have had a reasonable expectation of success at combining the method of . Hubbell, Rifatbegovic, and Abdullah with the method of Dai. This combination would have been expected to have allowed focusing on mutations that are more likely to be associated with disease development rather than benign, age-related changes. Therefore, the invention would have been prima facie obvious to one of skill in the art before the effective filing date of the claimed invention, absent evidence to the contrary.
Claims 34 and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Hubbell in view of Rifatbegovic, in view of Abdullah, as applied to claims 1-2, 4-7, 9, 11, 13-14, 16-17, 20, 24-25, 29-32, and 37-38 above, and further in view of Zhang (Molecular residual disease: A new clue for individualized approach in non-small cell lung cancer, Medicine Advances, Volume 1, Issue 1, 29 March 2023, pages 79-88; as cited in the attached 892 form).
Claims 34 and 36 depend on claim 1. Limitations of claim 1 have been taught in the above rejections.
Regarding claims 34 and 36, Hubbell, Rifatbegovic, and Abdullah do not disclose that the subject is taking an adjuvant therapy for the cancer condition and the method further comprises: determining that the subject has positive molecular residual disease status for the cancer condition in accordance with the providing G); and adjusting the adjuvant therapy, wherein the adjuvant therapy is chemotherapy, radiation therapy, hormone therapy, or immunotherapy, and adjusting the adjuvant therapy comprises increasing a dosage of the adjuvant therapy, decreasing a dosage of the adjuvant therapy, or ceasing the adjuvant therapy.
Zhang reviews molecular residual disease and discloses that MRD can direct individualized therapy, such as escalation or de-escalation of adjuvant therapy based on MRD (abstract).
Zhang further discloses that in their previous study, adjuvant therapy was given to 55 patients of whom 10 with detectable MRD after surgery. These 10 patients had significantly longer disease-free survival compared with all other patients who were MRD-positive immediately after surgery but did not receive adjuvant therapy. Conversely, patients with undetectable MRD after surgery cannot benefit from adjuvant therapy; Conversely, patients with undetectable MRD after surgery cannot benefit from adjuvant therapy (pg. 82, col. 2, para. 1).
Zhang further discloses that the adjuvant therapy if adjuvant chemotherapy (pg, 81, col. 2, first para.)
Applying the KSR standard to Hubbell, Rifatbegovic, Abdullah, and Zhang, the examiner concludes that this combination represents the use of known techniques to improve similar methods. Hubbell, Rifatbegovic, and Abdullah only disclosed obtaining sample and determining cfDNA and noise determination and normalization of sample using fragment per million values. In the same field of research, Zhang provided escalation or de-escalation of adjuvant therapy based on MRD. Combining the cancer prediction of Hubbell, Rifatbegovic, and Abdullah with adjuvant therapy adjustment of Zhang would have allowed complete monitoring of disease. One ordinary skilled in the art before he effective filing data of the claimed invention would have had a reasonable expectation of success at combining the method of Hubbell, Rifatbegovic, and Abdullah with the therapy technique of Zhang. Therefore, the invention would have been prima facie obvious to one of skill in the art before the effective filing date of the claimed invention, absent evidence to the contrary.
Citation of Pertinent Art
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Gross (US12497662B2; as cited in the attached 892 form) discloses systems and methods for cancer subject tumor fraction estimation comprise obtaining a first plurality of cell-free nucleic acid fragment sequences from the subject's liquid biological sample, sequencing, determining noise, determining methylation status, and modifying a treatment regimen for the subject based, at least in part, on a value of the tumor fraction f of the subject, wherein the treatment regimen comprises applying an agent for cancer to the subject, wherein the agent for cancer is a hormone, an immune therapy, radiography, or a cancer drug, and wherein the modification to the treatment regimen comprises intensifying or discontinuing the agent (claim 1).
Melton (US12580051B2 as cited in the attached 892 form) claims 1-3.
Conclusion
No claims are allowed.
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/G.S./Examiner, Art Unit 1686
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
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