DETAILED ACTION
The Applicant’s response, received 04 December 2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 1-26 are pending.
Claims 1-26 are rejected.
Priority
This application is a CON of PCT/US2019/039749, filed 28 June 2019, which claims benefit of provisional application number 62/692,495m, filed 29 June 2018.
Claim Objections
The objection to claim 1 in the Office action mailed 04 June 2025 is withdrawn in view of the amendment received 04 December 2025.
Claim Rejections - 35 USC § 112
The rejection of claims 1-27 in the Office action mailed 04 June 2025 is withdrawn in view of the amendment received 04 December 2025.
The rejection of claim 27 under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, in the Office action mailed 04 June 2025 is withdrawn in view of the amendment to delete the claim as received 04 December 2025.
Claim Rejections - 35 USC § 101
The amendment received 04 December 2025 has been fully considered, however after further consideration the rejection of claims 1-27 under 35 U.S.C. 101 in the Office action mailed 04 June 2025 is maintained with modification in view of the amendment.
The rejection of claim 27 under 35 U.S.C. 101 in the Office action mailed 04 June 2025 is withdrawn in view of this claim having been cancelled in the amendment received 04 December 2025.
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 1-26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea and a law of nature without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion); and (c) a law of nature (naturally occurring relationships).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 1-26 are directed to a method (i.e., a process) for determining a presence or absence of a genetic aberration in deoxyribonucleic acid (DNA) molecules from a cell-free DNA biological sample.
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
constructing a distribution of the sequence information over a plurality of base positions of a set of one or more genetic loci of a genome (i.e., mental processes and mathematical concepts);
wherein the sequence information has been aligned to a reference genome (i.e., mental processes); and
without taking into account a base identity of each base position in the set of one or more genetic loci, processing the distribution over the set of one or more genetic loci comprising the CTCF binding regions of the genome to determine the presence or absence of the genetic aberration in the subject (i.e., mental processes); and
wherein the presence or absence of the genetic aberration is indicative of the presence or absence of cancer in the subject that is the source of the biological sample (i.e., mental processes).
Independent claim 1, and those claims dependent therefrom, further recite a law of nature by associating genomic loci comprising CTCF binding regions with phenotypes (i.e., the presence or absence of cancer in a subject), which is a genotype-phenotype correlation (MPEP 2106.04(b)).
Dependent claims 6-26 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 6 further recites:
wherein the distribution comprises quantitative measures indicative of one or more of: (i) a number of the DNA molecules having a start point, a mid-point, or an end-point at each of the plurality of base positions of the genome; (ii) a length of the DNA molecules that align with each of the plurality of base positions of the genome; and (iii) a number of the DNA molecules that align with each of the plurality of base positions of the genome (i.e., mental processes and mathematical concepts).
Dependent claim 7 further recites:
wherein the distribution comprises quantitative measures indicative of one or more of:
(i) a number of short molecules having a start point, a mid-point, or an end-point at each of the plurality of base positions of the genome (i.e., mental processes and mathematical concepts);
(ii) a number of mono-nucleosomal molecules having a start point, a mid-point, or an end-point at each of the plurality of base positions of the genome (i.e., mental processes and mathematical concepts); and
(iii) a number of di-nucleosomal molecules having a start point, a mid-point, or an end-point at each of the plurality of base positions of the genome (i.e., mental processes and mathematical concepts).
Dependent claim 8 further recites:
wherein the distribution comprises quantitative measures indicative of one or more of:
(i) a number of the short molecules having a mid-point at each of the plurality of base positions of the genome (i.e., mental processes and mathematical concepts);
(ii) a number of the mono-nucleosomal molecules having a mid-point at each of the plurality of base positions of the genome (i.e., mental processes and mathematical concepts);
(iii) a number of the di-nucleosomal molecules having a start point at each of the plurality of base positions of the genome (i.e., mental processes and mathematical concepts); and
(iv) a number of the di-nucleosomal molecules having an end point at each of the plurality of base positions of the genome (i.e., mental processes and mathematical concepts).
Dependent claim 9 further recites:
wherein the distribution comprises quantitative measures indicative of two or more of (i), (ii), (iii), and (iv) (i.e., mental processes and mathematical concepts).
Dependent claim 10 further recites:
wherein the distribution comprises quantitative measures indicative of three or more of (i), (ii), (iii), and (iv) (i.e., mental processes and mathematical concepts).
Dependent claim 11 further recites:
wherein the distribution comprises quantitative measures indicative of (i), (ii), (iii), and (iv) (i.e., mental processes and mathematical concepts).
Dependent claim 12 further recites:
wherein each of the CTCF binding regions comprises a region within a set number of nucleotides from a CTCF binding site (i.e., mental processes and mathematical concepts).
Dependent claim 13 further recites:
wherein the set number is about 100 (i.e., mental processes and mathematical concepts).
Dependent claim 14 further recites:
applying a smoothing filter to the distribution (i.e., mental processes and mathematical concepts).
Dependent claim 15 further recites:
wherein the smoothing filter is a box filter (i.e., mental processes and mathematical concepts).
Dependent claim 16 further recites:
normalizing the distribution (i.e., mental processes and mathematical concepts).
Dependent claim 17 further recites:
truncating the distribution to a subset of the plurality of base positions of the genome (i.e., mental processes).
Dependent claim 18 further recites:
wherein the genetic aberration comprises a sequence aberration or a copy number variation (CNV), wherein the sequence aberration is selected from the group consisting of: (i) a single nucleotide variant (SNV), (ii) an insertion or deletion (indel), and (iii) a gene fusion (i.e., mental processes).
Dependent claim 19 further recites:
processing the distribution to determine a distribution score, wherein the distribution score is indicative of a mutation burden of the genetic aberration (i.e., mental processes and mathematical concepts).
Dependent claim 20 further recites:
processing the distribution with one or more reference distributions to determine the distribution score, wherein the distribution score indicates a difference between the distribution and the one or more reference distributions (i.e., mental processes and mathematical concepts).
Dependent claim 21 further recites:
wherein the difference is a Euclidian distance (i.e., mental processes and mathematical concepts).
Dependent claim 22 further recites:
estimating the mutation burden of the genetic aberration (i.e., mental processes and mathematical concepts).
Dependent claim 23 further recites:
wherein the set of one or more genetic loci comprises at least about 500 distinct CTCF binding regions of the genome (i.e., mental processes and mathematical concepts).
Dependent claim 24 further recites:
wherein the set of one or more genetic loci comprises at least about 1,000 distinct CTCF binding regions of the genome (i.e., mental processes and mathematical concepts).
Dependent claim 25 further recites:
wherein the set of one or more genetic loci comprises at least about 2,000 distinct CTCF binding regions of the genome.
Dependent claim 26 further recites:
wherein the plurality of base positions of the set of one or more genetic loci include at least one base position associated with one or more of genes AKT1, ALK, APC, AR, ARAF, ARID1A, AR, ATM, BRAF, BRCA1, BRCA2, CCND1, CCND2, FGFR2, CCNE1, CDH1, CDK4, CDK6, CDKN2A, CDKN2B, CCNE1, CDK4, FGFR3, CTNNB1, EGFR, ERBB2, ESR1, EZH2, FBXW7, CDK6, FGFR1, FGFR2, FGFR3, GATA3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KIT, KRAS, MAP2K1, MAP2K2, MET, MLH1, MPL, MYC, NF1, NFE2L2, NOTCH1, NPM1, NRAS, NTRK1, PDGFRA, PIK3CA, PTEN, PTPN11, RAF1, RB1, RET, RHEB, RHOA, RIT1, ROS1, SMAD4, SMO, SRC, STK11, TERT, TP53, TSC1, and VHL (i.e., mental processes).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pencil and paper (e.g., processing the distribution over the set of one or more genetic loci comprising the CTCF binding regions of the genome to determine the presence or absence of the genetic aberration in the subject), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., constructing a distribution of the sequence information over a plurality of base positions of a set of one or more genetic loci of a genome) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind. Furthermore, a law of nature correlating a genotype-phenotype association is identified at Eligibility Step 2A: Prong One.
Therefore, claims 1-26 recite an abstract idea and a law of nature.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
Dependent claims 6-18, and 21-26 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claim 1 include:
a computer;
step (a) enriching the cell-free DNA biological sample for DNA molecules comprising a CTCF binding site, using oligonucleotide probes;
step (b) sequencing at least the DNA molecules comprising the CTCF binding site enriched in (a) to generate sequencing information;
the DNA molecules comprising the CTCF binding site are sequenced to an average reading depth of at least 3000 reads per base; and
the set of one or more genetic loci comprises CTCF binding regions of the genome.
The additional elements in dependent claims 2-5, 19, and 20 include:
the DNA molecules comprise a set of di-nucleosomal molecules having a first range of lengths, a set of mono-nucleosomal molecules having a second range of lengths less than the first range of lengths, and a set of short molecules having a third range of lengths less than the second range of lengths (claim 2); wherein the first range of lengths is about 240 base pairs to about 400 base pairs (claim 3); wherein the second range of lengths is about 120 base pairs to about 240 base pairs (claim 4); wherein the third range of lengths is about 1 base pair to about 120 base pairs (claim 5); and
a computer (claims 19 and 20).
The additional element of a computer (claims 1, 19, and 20) invokes a computer and/or computer-related components merely as a tool for use in the claimed process, and therefore is not an improvement to computer functionality itself, or an improvement to any other technology or technical field, and thus, does not integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(1)).
The additional elements of enriching the cell-free DNA biological sample for DNA molecules comprising a CTCF binding site, using oligonucleotide probes (claim 1); sequencing at least the DNA molecules comprising the CTCF binding site enriched in (a) to generate sequencing information (claim 1); the DNA molecules comprising the CTCF binding site are sequenced to an average reading depth of at least 3000 reads per base (claim 1); and the set of one or more genetic loci comprises CTCF binding regions of the genome (claim 1); are merely pre-solution activities used in the gathering of data for use in the claimed process – nominal additions to the claims that do not meaningfully limit the claims, and therefore do not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional elements of DNA molecules that comprise a set of di-nucleosomal molecules having a first range of lengths, a set of mono-nucleosomal molecules having a second range of lengths less than the first range of lengths, and a set of short molecules having a third range of lengths less than the second range of lengths (claim 2); wherein the first range of lengths is about 240 base pairs to about 400 base pairs (claim 3); wherein the second range of lengths is about 120 base pairs to about 240 base pairs (claim 4); wherein the third range of lengths is about 1 base pair to about 120 base pairs (claim 5); further limit the DNA molecules in the cell-free DNA biological sample, and therefore are merely part of the pre-solution activities used in the gathering of data for use in the claimed process – nominal additions to the claims that do not meaningfully limit the claims, and therefore do not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Thus, the additionally recited elements merely invoke a computer as a tool, and/or amount to insignificant extra-solution data gathering activity, and as such, when all limitations in claims 1-26 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-26 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Dependent claims 6-18, and 21-26 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claim 1 and dependent claims 2-5, 19, and 20 are identified above, and carried over from Step 2A: Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A: Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional element of a computer (claims 1, 19, and 20) is conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional element of sequencing cell-free DNA (claim 1) is conventional. Evidence for conventionality is shown by Snyder et al. (Prenatal Diagnosis, 2013, Vol. 33, pp. 547-554, as cited in the Office action mailed 06 December 2023). Snyder et al. reviews noninvasive fetal genome sequencing (Title; and Abstract) and shows an overview of noninvasive fetal whole genome sequencing including cell-free DNA sample collection and processing (page 549, Figure 1).
The additional element of DNA molecules sequenced to an average reading depth of at least 3,000 reads per base (claim 1), is conventional. Evidence for conventionality is shown by Lennon et al. (Genome Medicine, 2016, Vol. 8, No. 112, pp. 2-10, as cited in the Office action mailed 27 August 2024). Lennon et al. reviews technological considerations for genome-guided diagnosis and management of cancer (Title; and Abstract), and shows that variant sensitivity is a function of the depth of unique, high quality sequence reads at a site (read depth), and that tests that seek to assay known cancer driver genes or hotspots typically aim for high sensitivity to call these specific variants, and to achieve acceptable sensitivity (>99%) for clinical use in liquid biopsies, these tests are commonly run at far greater read depths (>5000x mean coverage) as compared to use in solid tumor fresh frozen FFPE samples (page 4, column 2, para. 1).
The additional element of enriching a cell-free DNA biological sample for DNA molecules using oligonucleotide probes (claim 1) is conventional. Evidence for conventionality is shown by Volckmar et al. (Genes Chromosomes Cancer, 2018 (First published 05 December 2017), Vol. 57, pp. 123-139; as cited in the Office action mailed 04 June 2025). Volckmar et al. reviews cancer diagnostics using cell-free DNA (Title; and Abstract), and discusses separation and enrichment of ctDNA from non-neoplastic cfDNA molecules to overcome sensitivity limitations in the detection of somatic alterations, and that enrichment of ctDNA alleles may improve the detection of genetic alterations with higher sensitivity and potentially lower tumor stages (page 126, col. 2, para. 3); and further discusses targeted approaches for detection of ctDNA frequencies, including dPCR and BEAMing, as well as a targeted NGS approach termed “cancer personalized profiling by deep sequencing” (CAPP-Seq) for accurate detection of somatic alterations (page 127, col. 2, para. 2), and using locked nucleic acid probes to enhance the sensitivity for mutations during amplification (page 129, col. 1, Section 5.3, para. 1). Volckmar et al. further discusses NGS or massive parallel sequencing (Section 5.4) and shows that targeted sequencing approaches utilize enrichment of recurrently altered loci by PCR amplification or hybrid capture and permits deep sequencing of up to several hundred kilobases (page 129, col. 2, para. 1), and further discusses whole-exome sequencing or whole-genome sequencing (Section 5.5) and shows that besides focused panels for massively parallel sequencing, hybrid-capture allows for coverage of large fractions of the genome, illustrating the utility of whole-exome sequencing (WES) to characterize the molecular tumor representation in cfDNA (page 129, col. 2, para. 2), and further shows that hybridization-based enrichment of recurrently mutated regions across various entities enables the detection of somatic alterations down to 0.01% (Section 6, para. 1), and further shows that a liquid biopsy might be used for mutational profiling (Section 7.2, para. 1) and targeted error correction sequencing (TEC-Seq) for the evaluation of tumor tissue and corresponding plasma samples (page 131, col. 2, para. 1). Volckmar et al. further discusses liquid biopsy in diagnostic reporting and shows that the minimal required information includes the testing method and the assay (i.e., the mutation spectrum covered by the test or the panel with complete information on screened genes and exons) (Section 8, para. 2).
The additional element of enriching DNA molecules comprising a CTCF binding site (claim 1) is conventional. Evidence for conventionality is shown by Deng (Information Science and Management Engineering IV (ISME 2016), pp. 318-324; as cited in the Office action mailed 04 June 2025). Deng reviews high-throughput sequencing (HTS) technology and its applications in human disease (Title) and in particular exome sequencing and ChIP (chromatin immunoprecipitation) to summarize the application of HTS in human disease (Abstract). Deng further shows that exome sequencing is a high-throughput sequencing method using special means to enrich the whole exome, and the basic processes include enrichment of exome region sequences, high throughput sequencing, and bioinformatics analysis of the sequencing data (page 321, col. 2, para. 3), and that exome sequencing is an effective method to detect pathogenicity genes and susceptibility loci at the genomic level (page 322, col. 1, para. 1). Deng further shows that ChIP uses an immune reagent specific for a DNA binding factor to enrich target DNA sites to which the factor is bound, and then the enriched DNA sites are identified and quantified (page 322, col. 2, para. 2), and ChIP-seq (i.e., ChIP followed by high-throughput sequencing) can be applied to any species with a known genome sequence to study the interaction between any kind of DNA-related protein and its target DNA (page 322, col. 2, para. 3), and in particular CTCF (i.e., CCCTC-binding factor) (page 323, col. 1, para. 1).
The additional elements of DNA molecules that comprise a set of di-nucleosomal molecules having a first range of lengths, a set of mono-nucleosomal molecules having a second range of lengths less than the first range of lengths, and a set of short molecules having a third range of lengths less than the second range of lengths (claim 2); wherein the first range of lengths is about 240 base pairs to about 400 base pairs (claim 3); wherein the second range of lengths is about 120 base pairs to about 240 base pairs (claim 4); wherein the third range of lengths is about 1 base pair to about 120 base pairs (claim 5); are conventional. Evidence for conventionality is shown by Jiang et al. (Trends in Genetics, June 2016, Vol. 32, No. 6, pp. 360-371, as cited in the Office action mailed 04 June 2025). Jiang et al. reviews the technologies that have been used for analyzing the size profiles of cfDNA in plasma, and further reviews the size profiles of cfDNA in different clinical scenarios, including cancer, pregnancy, transplantation, and autoimmune diseases, and discusses the potential diagnostic applications of plasma DNA size profiling (Title; and Abstract). Jiang et al. further shows a schematic illustration of the determination of cell-free DNA sizes using nucleic acid electrophoresis that depicts different sizes of DNA fragments including dinucleosomal DNA fragments and mononucleosomal DNA fragments (Figure 1). Jiang et al. further discusses the overall sizes of cfDNA ranging from relatively short cfDNA fragments at 143 bp and shorter to larger than 10,000 bp (pages 363-364: Overall Sizes of cfDNA).
Therefore, when taken alone, all additional elements in claims 1-26 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-26 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments/remarks received 04 December 2025 have been fully considered, but they are not persuasive.
The Applicant states on page 7 of the Remarks that the claims recite a method for detecting genetic aberrations by analyzing the distribution of cell-free DNA (cfDNA) rather than the identity of each base position. The Applicant further states that a notable feature of the claimed method is the physical enrichment of the cfDNA sample specifically for DNA molecules comprising a CTCF binding site using oligonucleotide probes, and that following this targeted enrichment, the method involves sequencing to an average read depth of at least 3,000 reads per base to construct a distribution of sequence information from the enriched DNA. The Applicant further states that in step (c), the method processes this distribution to determine the presence of a genetic aberration “without taking into account a base identity of each base position” and that this represents a significant departure from methods which either employ whole genome sequencing (WGS) to look at broad nucleosome patterns or employ targeted enrichment to look for specific sequence mutations (SNVs/Indels). The Applicant further states that the references pointed to in the Office action for conventionality fail to take into account the features as recited in the claims (e.g., the approaches described in Volckmar et al. relate to the use of base identity for the detection of somatic mutations, such as CAPP-SEQ). The Applicant further states on page 8 of the Remarks that the claimed method uniquely combines physical enrichment using oligonucleotide probes and sequencing with a distribution analysis, yielding a high-resolution view of chromatin organization at specific regulatory regions (CTCF sites), which can be used to detect cancer without taking into account base identity of each base position, and further states that this combination of steps was neither routine nor conventional and is an improvement over the other cfDNA-based liquid biopsy assays, and for at least these reasons, the claimed method as a whole recites patentable subject matter.
These arguments are not persuasive, because first, with regard to the Applicant’s argument that the claims recite a method for detecting genetic aberrations by analyzing the distribution of cell-free DNA (cfDNA) rather than the identity of each base position, it is noted that this argument comprises the limitations that are identified as judicial exceptions at Step 2A Prong One in the above rejection. Second, with regard to the Applicant’s argument that the step of constructing a distribution of sequence information from the enriched DNA, and further that in step (c), the method processes this distribution to determine the presence of a genetic aberration “without taking into account a base identity of each base position,” it is noted that these arguments comprise the limitations that are identified as judicial exceptions at Step 2A Prong One in the above rejection. Third, with regard to the Applicant’s argument that a notable feature of the claimed method is the physical enrichment of the cfDNA sample specifically for DNA molecules comprising a CTCF binding site using oligonucleotide probes, and that following this targeted enrichment, the method involves sequencing to an average read depth of at least 3,000 reads per base, it is noted that these limitations comprise additional elements identified at Step 2A Prong Two that are determined to not integrate the recited judicial exceptions because these additional elements are steps in the gathering of data for use in the claimed process, as noted and discussed in the above rejection. Fourth, with regard to the Applicant’s argument that references pointed to in the Office action for conventionality fail to take into account the features as recited in the claims (e.g., the approaches described in Volckmar et al. relate to the use of base identity for the detection of somatic mutations, such as CAPP-SEQ), it is noted that at Step 2B only the additional elements recited in the claimed process are evaluated, and therefore it is irrelevant Volckmar et al. discusses the use of base identity for the detection of somatic mutations, because for the purpose of showing conventionality at Step 2B in the above rejection, the Volckmar et al. reference was cited to show evidence of conventionality of the step of enriching a cell-free DNA biological sample for DNA molecules using oligonucleotide probes (claim 1). Fifth, with regard to the Applicant’s argument that the claimed method uniquely combines physical enrichment using oligonucleotide probes and sequencing with a distribution analysis, yielding a high-resolution view of chromatin organization at specific regulatory regions (CTCF sites), which can be used to detect cancer without taking into account base identity of each base position, and further states that this combination of steps was neither routine nor conventional and is an improvement over the other cfDNA-based liquid biopsy assays, it is noted that this argument combines aspects of the claimed process that are identified as judicial exceptions at Step 2A Prong One (i.e., a distribution analysis, yielding a high-resolution view of chromatin organization at specific regulatory regions (CTCF sites) which can be used to detect cancer without taking into account base identity of each base position) and identified as additional elements at Step 2A Prong Two (i.e., physical enrichment using oligonucleotide probes and sequencing), however at Step 2B of the eligibility analysis, the evaluation only considers the additional elements with regard to whether the combination of steps was routine or conventional, and as noted and discussed in the above rejection, the additional elements of physical enrichment using oligonucleotide probes and sequencing were conventional additional elements before the effective filing date of the claimed invention. Therefore, the instant claimed improvement over the other cfDNA-based liquid biopsy assays is a purported improvement to the abstract idea (data analysis), and not an improvement to computer functionality itself, or an improvement to another technology or technical field.
Claim Rejections - 35 USC § 103
The amendment received 04 December 2025 has been fully considered, however after further consideration, the rejection of claims 1-27 under 35 U.S.C. 103 as being unpatentable over Abdueva in view of Shendure et al. in view of Lanman et al. in the Office action mailed 04 June 2025 is maintained with modification in view of the amendment.
The rejection of claim 27 under 35 U.S.C. 103 in the Office action mailed 04 June 2025 is withdrawn in view of this claim having been cancelled in the amendment received 04 December 2025.
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.
Claims 1-26 are rejected under 35 U.S.C. 103 as being unpatentable over Abdueva (WO 2018/009723, as cited in the Information Disclosure Statement (IDS) received 09 February 2022, and as cited in the Office action mailed 04 June 2025) in view of Shendure et al. (US 2017/0211143, as cited in the Information Disclosure Statement (IDS) received 09 February 2022, and as cited in the Office action mailed 04 June 2025) in view of Lanman et al. (PLoS ONE, 2015, 10(10): e0140712, doi:10.1371/journal.pone.0140712, pp. 1-27, as cited in the Office action mailed 04 June 2025).
Independent claim 1 is broadly directed to determining a presence or absence of a genetic aberration that is indicative of the presence or absence of cancer by analyzing sequence read data generated from a cell-free DNA biological sample enriched for DNA molecules comprising a CTCF binding site.
Dependent claims 2-26 further define the panel of genes used in the generation of sequence read data, and further define data analysis steps used for constructing a distribution of the sequence information and processing the distribution of data to determine the presence or absence of the genetic aberration.
Abdueva is directed to methods for fragmentome profiling of cell-free nucleic acid that uses sequence information in a macroscale and global manner, with or without somatic variant information, to assess a fragmentome profile that can representative of a tissue of origin, disease, progression, etc., and is further directed to determining a presence or absence of a genetic aberration in DNA fragments from cell-free DNA obtained from a subject, the method comprising steps for constructing a multi-parametric distribution of the DNA fragments over a plurality of base positions in a genome, and without taking into account a base identity of each base position in a first locus, using the multi-parametric distribution to determine the presence or absence of the genetic aberration in the first locus of the subject.
Shendure et al. is directed to methods of determining tissues and/or cell types giving rise to cell-free DNA, and methods of identifying a disease or disorder in a subject as a function of the determined tissues and/or cell types contributing to cfDNA in a biological sample from the subject.
Lanman et al. is directed to the analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA.
Regarding independent claim 1, Abdueva shows using cell-free DNA (cfDNA) sequence information to assess a fragmentome profile that can be representative of a tissue of origin, disease, progression, etc., and used for determining a presence or absence of a genetic aberration in DNA fragments from cfDNA obtained from a subject (Title; and Abstract). Abdueva further shows that the cfDNA fragments are sequenced to produce a plurality of sequence reads of the fragments, and that each sequence is mapped to reference sequences from the human genome (para. [00190]). Abdueva further shows that in some embodiments, the method further comprises performing one or more assays on a bodily sample from the subject including a transcription factor binding site (TFBS) occupancy analysis (para. [0022]); a modular gene panel configuration that allows for designs of a set of probes or baits that selectively enrich regions of the genome that are relevant for nucleosomal profiling (para. [00271]), e.g., changes in chromatin structure, e.g., nucleosomal re-positioning at transcription start sets, and transcription factor binding sites (para. [00272]). Abdueva further shows that the enriched genetic loci comprise genomic regions associated with one or more of the genes of interest listed in Table 1 (para. [00248]), many of which are genes that are listed in the Applicant’s Tables 1-3 (Applicant’s Specification: pages 40-44) and Applicant’s amended claim 26). Abdueva further shows constructing, by a computer, a multi-parametric distribution of the DNA fragments over a plurality of base positions in a genome; and without taking into account a base identity of each base position in a first locus, using the multi-parametric distribution to determine the presence or absence of the genetic aberration in the first locus in the subject (paras. [0005] & [0060]), wherein the condition is cancer (para. [0037]).
Abdueva does not explicitly show enriching for a DNA from the cell-free DNA biological sample for DNA molecules comprising a CTCF (i.e., a transcription factor) binding site (although see previous paragraph); wherein the set of one or more genetic loci comprises CTCF binding regions of the genome (although see previous paragraph); or computer processing the distribution over the set of one or more genetic loci comprising the CTCF binding regions of the genome (although see previous paragraph).
Shendure et al. shows determining normal/healthy tissue(s)-of-origin from cfDNA, and that by optimizing library preparation protocols to recover short fragments, it was discovered that the in vivo occupancies of transcription factors (TFs) such as CTCF are also directly footprinted by cfDNA (Example 4: para. [0176]); and the analysis of nucleosome spacing around CTCF binding sites, wherein the positions of 10 nucleosomes on either side of the binding site were extracted for each site, and distances calculated between all adjacent nucleosomes to obtain a distribution of inter-nucleosome distances for each set of sites (paras. [0222] & [0223]). Shendure et al. further discloses methods of determining tissues and/or cell types giving rise to cell-free DNA (cfDNA) and methods of identifying a disease or disorder (e.g., chromosomal or other genetic abnormalities (para. [0128])) using same (Title; and Abstract), and shows an overview of the processes giving rise to cfDNA fragments, wherein apoptic and/or necrotic cell death results in near-complete digestion of native chromatin, however protein-bound DNA fragments, typically associated with histones or transcription factors (TFs) (e.g., CTCF; para. [0176]), preferentially survive digestion and are released into the circulation, while naked DNA is lost (para. [0031]). Shendure et al. further shows measuring nucleosome occupancy relative to transcription binding sites with cfDNA sequencing data (Example 3: paras. [0151] – [0157]) demonstrating that the set of TF binding sites (TFBSs) occupied in vivo in a particular cell varies between tissues and cell types, such that if one were able to identify TFBS occupancy maps for tissues or cell types of interest, and repeated this process for one or more TFs, one could identify components of the mixture of cell types and tissues contributing to a population of cfDNA by identifying enrichment or depletion of one or more cell type- or tissue-specific TF binding site occupancy profiles (para. [0152]). Shendure et al. further shows that as a result of conventional library preparation, a substantial proportion of total cfDNA may be poorly recovered, and therefore minimal PCR amplification was performed to enrich for adapter-bearing molecules (para. [0180]); all libraries were sequenced on HiSeq 2000 instruments (para. [0163]); and sequence reads were aligned to the human reference genome (para. [0164]).
Abdueva in view of Shendure et al. does not show wherein the DNA molecules from the biological sample are sequenced to an average reading depth of at least 3000 reads per base.
Lanman et al. shows analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA (Title; and Abstract), and further shows characteristics of the Guardant360 panel and clinical diagnostic assay (Materials and Methods) and in particular shows that each base was sequenced at average raw coverage depth of 8,000X with a minimum average base coverage of 3,000X (page 17, Materials and Methods, para. 2).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method shown by Abdueva by incorporating data of the distribution of sequence read-starts around CTCF binding sites as disclosed by Shendure et al., and discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Abdueva and Shendure et al. because Shendure et al. shows that CTCF is an insulator binding protein and plays a major role in transcriptional repression (para. [0155]). This modification would have had a reasonable expectation of success because both Abdueva and Shendure et al. provide methods for identifying a disease or disorder in a subject as a function of one or more determined tissues and/or cell types contributing to cell-free DNA (cfDNA) in a biological sample from the subject.
It would have been further obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method shown by Abdueva in view of Shendure et al. by incorporating an average sequencing read depth of at least 3,000 reads per base as shown by Lanman et al., and discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Abdueva in view of Shendure et al. and Lanman et al. because Shendure et al. shows that quality metrics are a function of sequencing depth (para. [0081]). This modification would have had a reasonable expectation of success given that Abdueva in view of Shendure et al. and Lanman et al. each disclose methods for quantitative analysis of cell-free DNA (cfDNA).
Regarding dependent claims 2-11, Abdueva further shows detecting a number of the DNA fragments with dinucleosomal proctection and/or mononucleosomal protection (para. [0023]); at least one of the localized genomic regions is a short region of DNA ranging from about 2 to about 200 base pairs (para. [0026]); dinucleosomal proctection (e.g., a fragment size of at least 240 base pairs) and mononucleosomal protection (e.g., a fragment size of less than 240 base pairs) (para. [00141]); the multi-parametric distribution comprises parameters indicative of one or more of: (i) a length of the DNA fragments that align with each of the plurality of base positions in the genome, (ii) a number of the DNA fragments that align with each of the plurality of base positions in the genome, and (iii) a number of the DNA fragments that start or end at each of the plurality of base positions in the genome (para. [0056]); and data sets selected from the group consisting of: (a) start position of DNA fragments sequenced, (b) end position of sequenced DNA fragments, (c) number of unique sequenced DNA fragments that cover a mappable position, (d) length of sequenced DNA fragments, (e) likelihood that a mappable base-pair position will appear at a terminus of a sequenced DNA fragment, (f) a likelihood that a mappable base-pair position will appear within a sequenced DNA fragment (para. [0060]).
Regarding dependent claim 16, Abdueva further shows that in some embodiments, the quantitative measure is a normalized measure (para. 0041]).
Regarding dependent claim 17, Abdueva further shows a sub-locus may be a plurality of contiguous base positions such that said plurality is a subset of a locus in a genome (para. [00217]); and the distribution model may be processed to define a subset of DNA fragments associated with a particular chromatin unit (para. [00336]).
Regarding dependent claim 18, Abdueva further shows that genetic aberrations may comprise SNVs, CNVs, indels, or fusions (paras. [0056] & [00165]).
Regarding dependent claim 19, Abdueva further shows using the multi-parametric distribution to determine a distribution score, wherein the distribution score is indicative of a mutation burden of the genetic aberration (para. [0056]).
Regarding dependent claim 20, Abdueva further shows determining a disease score of a disease, wherein the disease score is determined as a function of one or more healthy reference multi-parametric models associated with a cohort not having the disease (para. [0029]).
Regarding dependent claim 22, Abdueva further shows using the multi-parametric distribution to determine a distribution score, wherein the distribution score is indicative of a mutation burden of the genetic aberration (para. [0056]).
Regarding dependent claim 26, Abdueva further shows the plurality of base positions or regions of a genome include at least one base position or region associated with one or more of the genes listed in Table 1 (paras. [0060] & [00248]).
Abdueva does not show the limitations recited in dependent claims 12-15, 21, and 23-25.
Regarding dependent claims 12 and 13, Shendure et al. further shows that nucleosomes are symmetrically and regularly spaced around a given binding site, with an approximate period of 185 base pairs (para. [0155]).
Regarding dependent claims 14 and 15, Shendure et al. further shows parameters to smooth and detrend the data, e.g., moving averages (para. [0169]).
Regarding dependent claim 21, Shendure et al. further shows using hierarchical clustering dendrograms of Euclidean distances of intensities measured at different base pair periodicities (paras. [0019], [0021], & [0027]; and FIGs. 5, 7, and 13).
Regarding dependent claims 23, 24, and 25, Shendure et al. further shows read-start density in 1 kbp window around 23,666 CTCF binding sites for a set of samples with at least 100M reads (para. [0028]; and FIG. 14).
Thus, the claims are prima facie obvious.
Response to Arguments
The Applicant’s arguments/remarks received 04 December 2025 have been fully considered, but are not persuasive.
The Applicant states on page 8 of the Remarks that the cited references, when combined, do not teach or suggest the method of claim 1. The Applicant further states that the Office action accepts that Abdueva does not teach enriching for DNA comprising a CTCF binding site, and instead turns to Shendure for this feature. The Applicant further states that the reference in Shendure to CTCF, however, refers to the bioinformatic analysis of data already generated via whole genome sequencing (WGS) and does not teach or suggest physical enrichment for such regions, e.g., as described in Shendure: page 14, para. [0155], the reference identifies transcription factor binding sites by “informatically scanning the genome” for binding motifs and intersecting these with public databases (e.g., ENCODE), and therefore Shendure uses CTCF only as a computational filter applied after the entire genome has been sequenced to identify patterns in the sequencing data. The Applicant further states that this is fundamentally different from step (a) of claim 1, which recites “enriching…for DNA molecules comprising a CTCF binding site” as a physical step before sequencing. The Applicant further states that there is no suggestion in any of the cited documents to enrich for DNA comprising CTCF binding sites from a cfDNA sample, as recited by claim 1, and therefore claim 1 is not obvious from this first reason alone.
These arguments are not persuasive, because with regard to the Applicant’s argument that Shendure uses CTCF only as a computational filter applied after the entire genome has been sequenced to identify patterns in the sequencing data, it is noted that at para. [0176] Shendure shows an example (Example 4) method for determining normal/healthy tissue(s)-of-origin from cfDNA wherein the cfDNA was deeply sequenced and the library preparation protocols were optimized to recover the short cfDNA fragments containing transcription factors (TFs) such as CTCF which are directly footprinted by the cfDNA. Therefore, at least the Shendure reference teaches and/or suggests the step of enriching cfDNA fragments for regions and/or sites containing the CTCF transcription factor prior to any bioinformatic analyses of the data generated from the DNA molecules.
The Applicant states on page 9 of the Remarks that the Office action further accepts that Abdueva in view of Shendure does not teach sequencing to an average read depth of at least 3,000 reads per base, and instead turns to Lanman for this feature. The Applicant further states that the claimed method relates to determining the sequencing information around CTCF binding sites, which are predominantly non-coding regions, whereas in contrast, Lanman is centered on determining somatic mutations in coding regions, and as such, a person having ordinary skill in the art (PHOSITA) would not gain any information from Lanman on how to profile chromatin structure in non-coding regions, as in the claimed method. The Applicant further states that in particular, the PHOSITA would not see the sequencing depth of Lanman being relevant to the method of Abdueva and Shendure, because Lanman teaches this sequencing depth for a purpose fundamentally distinct from and irrelevant to the chromatin structure analysis of Abdueva and Shendure, and further states that Lanman describes methods to detect somatic single nucleotide variants (SNVs) and copy number variants (CNVs) by overcoming sequencing noise to identify rare mutant alleles, and that the depth of sequencing is used to build “per-base noise models” to distinguish true somatic variants from sequencing errors at low mutant allele fractions. The Applicant further states that in contrast, the methods of Abdueva and Shendure analyze the distribution and positioning of fragments to infer chromatin structure, and that the PHOSITA reading Lanman would understand that the sequencing depth taught therein is tied to the specific considerations associated with detecting SNVs and CNVs, and thus is not relevant to the methods disclosed in Abdueva and Shendure, which do not target these mutations, and as such, the PHOSITA would not have combined these references in the manner suggested by the Office action.
These arguments are not persuasive, at least because Abdueva is directed to a method for determining a presence or absence of a genetic aberration in DNA fragments from cell-free DNA (Abstract) and further shows that aspects of the bioinformatics analytical method may be used to indicate a total mutation burden from the detection of variants including SNVs and CNVs by fragmentome analysis (para. [00332]); and that, e.g., the assessment of optimal PCR performance is measured by maximum depth of coverage of a probe associated with each of the genes (para. [00275]); and Shendure at least shows that sequence data metrics of quality are a function of sequencing depth (para. [0081]). Furthermore, a PHOSITA would understand that average sequence read depth is the average number of times each nucleotide in a genome or target region is sequenced, and directly dictates the accuracy (i.e., variant detection), confidence (i.e., reducing sequencing errors), and sensitivity (e.g., lowering false positives) of genomic data.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687