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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10/16/2025 has been entered.
Office Action Overview
Claim Status
Canceled:
2, 10, 17-98
Pending:
1, 3-9, 11-16, and 99-101
Withdrawn:
none
Examined:
1, 3-9, 11-16, and 99-101
Independent:
1
Amended:
1, 8-9, 11
New:
99-101
Allowable:
none
Objected to:
1, 3
Rejections applied
Abbreviations
X
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
X
102, 103
JE
Judicial Exception
X
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed in the 09/17/2021 filing receipt, this application claims priority to U.S provisional application 62/968,507, filed on 01/31/2020.
Overview of Withdrawal/Revision of Objections/Rejections
In view of the amendment and remarks received 10/16/2025:
• The objection to claim 1 in the Office action mailed 04/21/2025 is withdrawn. A new objection to claim 1 is asserted.
• The 112(a) and 112(b) rejections of claims 1, 3-9, and 11-16 in the Office action mailed 04/21/2025 are withdrawn. The limitations for "wherein the determination that the first target nucleic acid variant is not absent at the first genetic locus indicates the presence of colorectal cancer in a subject" and " administering Cetuximab and/or Panitumumab to the subject based on the presence of colorectal cancer in a subject" have been deleted.
• The 101 rejection in the Office action mailed 04/21/2025 is maintained with revision to reflect the amendment.
• The 103 rejections in the Office action mailed 04/21/2025 are withdrawn and a new 103 rejection is asserted.
Claim Objections
Claims 1 and 3 is objected to because of the following informalities:
For ease of discerning the steps and sub-steps in claim 1, there should be indentations of the sub-step designations (i) and (ii), which occur under both the "generating an additional" step and the "determining at least two…" step.
Claim 3 is dependent on claim 2, which has been canceled. Claim 3 should be amended to depend from claim 1.
Appropriate correction is required.
Claim Interpretation
Claim 1 recites the term "clonal level" three times; and claims 6 and 13 recite the term "clonal level" once each. Specification paragraph [61] states "as used herein, ‘clonal’ in the context of nucleic acids refers to a population of nucleic acids that comprises nucleotide sequences that are substantially or completely identical to each other at least at a given locus of interest ( e.g., a target variant)"; therefore the term "clonal level" will be interpreted as referring to "clonal" as defined in Specification para.[61].
Regarding claims 99-101, because the equations themselves are not recited in the claims, claims 99-101 are interpreted as not further limiting claim 1. (The equation issue of claims 99-101 is further discussed in the 112(b) rejection below.)
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 3-9, 11-16, and 99-101 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted, and any amendments in response to the following rejections should be applied throughout the claims, as appropriate.
In claim 1, sub-step (ii) of the "determining at least two" step recites: "an additional first likelihood value and an additional second likelihood value." It is not clear if these values are the same values of the "generating an additional" step of claim 1, which also recites: "an additional first likelihood value and an additional second likelihood value." The rejection could be overcome by amending sub-step (ii) of the "determining at least two" step to recite: "the additional first likelihood value and the additional second likelihood value."
In claim 12, the connection between the likelihood values and the quantitative value is unclear in that it is not certain if the quantitative value is supposed to be based on the ratio of likelihood values, or on the ratio of likelihood values which have been log transformed.
Claims 99-101 are indefinite as referencing equations because a claim should be complete without reference to the specification. Claims 99-101 respectively recite the terms "Equation 11"; "Equation 17, 18, and/or 19"; and "Equation 20 and/or 21." These equations are disclosed at paragraphs [132] and [142-146]. MPEP 2173.05(s) explains that where possible, claims are to be complete in themselves. Incorporation by reference is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. It is not clear that the instant claim recitations constitute "exceptional circumstances." The claims may be amended to incorporate the particular equations. Because the equations are not recited in the claims, claims 99-101 are interpreted as not further limiting claim 1.
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, 3-9, 11-16, and 99-101 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 details the following framework to analyze Subject Matter Eligibility:
• Step 1: Are the claims directed to a category of statutory subject matter (a process, machine, manufacture, or composition of matter)? (see MPEP § 2106.03)
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. an abstract idea, a law of nature, or a natural phenomenon? (see MPEP § 2106.04(a)). Note, the MPEP at 2106.04(a)(2) & 2106.04(b) further explains that abstract ideas and laws of nature are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people);
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information)
laws of nature and natural phenomena are naturally occurring principles/ relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature.
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application? (see MPEP § 2106.04(d))
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? (see MPEP § 2106.05)
Step 1 Analysis:
Step 1: Yes, the claims are directed to a method, and therefore to a category of statutory subject matter. (See MPEP § 2106.03).
Step 2A, Prong One Analysis:
The claims recite judicial exceptions in the form of abstract ideas as follows:
Independent claim 1 recites mental processes of: considering the data of the sequence reads from sequence analysis of a cfDNA sample of a subject; determining a first variant at the first locus is not detected in the sample based on the sequence reads; generating first and second likelihood values respectively based on a probability that the first variant is absent and not absent at the clonal level (also considered a mathematical concept); determining a tumor fraction estimate of the sample (also considered a mathematical concept); determining a quantitative value based on the first and second likelihood values (also considered a mathematical concept); comparing the quantitative values to a threshold; determining, based on the comparison, that the first variant is absent at the first genetic locus in the cfDNA sample and is wild type, or that the variant is not absent at the first genetic locus, wherein the first genetic locus is KRAS, BRAF, or NRAS.
Claim 3 recites a mental process of: determining a maximum mutant allele frequency (MAX MAF) of a tumor mutation in the sample (also considered a mathematical concept). Claim 4 recites a mental process of: determining a molecule count associated with the tumor mutation based on the plurality of sequence reads (also considered a mathematical concept). Claim 5 recites mental processes of: determining an allele frequency of at least a second variant (also considered a mathematical concept); and considering the first likelihood value and the second likelihood value are based further on the allele frequency and the MAX MAF. Claim 6 recites mental processes of: comparing the allele frequency with a second threshold that is based on the MAX MAF; and determining that the first variant of interest at the first locus is absent at the clonal level is based further on the comparison of the MAF with the second threshold (also considered a mathematical concept). Claim 7 recites a mental process of: determining a first molecule count associated with the first variant based on the plurality of sequence reads (also considered a mathematical concept). Claim 8 recites mental processes of: considering the data of the covariable information indicating a historical prevalence of one or more variants exhibiting co-occurrence and/or mutual exclusivity with the first variant; and considering the quantitative value is based on the covariable information. Claim 9 recites mental processes of: determining a prevalence of at least a second variant in the cfDNA sample (also considered a mathematical concept); and considering the quantitative value is based further on the covariable information.
Claim 11 recites mental processes of: determining a prevalence of at least a second variant in the cfDNA sample (also considered a mathematical concept); and further limits the quantitative value as based further on the prevalence of the second variant. Claim 12 further limits the quantitative value as based on the ratio of the first likelihood value to the second likelihood value (considered a mathematical concept). Claim 13 recites a mental process of: determining a level of confidence that the first variant is absent at the clonal level in the cfDNA sample based on the quantitative value (also considered a mathematical concept). Claim 14 recites a mental process of: determining a treatment plan to treat a disease in the human subject. Claim 15 further limits the disease in claim 14 to cancer. Claim 16 recites mental processes of determining a prevalence of at least a second variant in the cfDNA sample (also considered a mathematical concept); and adjusting the quantitative value based on the prevalence of at least a second variant in the cfDNA sample (also considered a mathematical concept).
Claims 99-101 are considered to recite mathematical concepts of log transformation.
Step 2A Prong One Summary: The claims recite abstract ideas, characterized as mental processes and mathematical concepts. Considering the broadest reasonable interpretation (BRI) of the claims, the mental processes recited in independent claim 1 (e.g., "determining the first variant has not been detected at the first locus in the sample based on the plurality of sequence reads", "generating likelihoods", "determining a quantitative value", "comparing values", determining the first variant is absent", etc.) are directed to processes that may be performed in the human mind, or with pen and paper, because in the simplest embodiment of the claims, there could be two reads for which it would be feasible to mentally perform the processes listed above, as there are no limitations put on the number of reads besides "a plurality". Additionally, the limitations of generating likelihoods, determining quantitative values, adjusting quantitative values, etc., inherently recite mathematical concepts, such as those described throughout the Specification, and at [026], [033], [110-147]. Such analysis performed mentally, or with paper and pencil, may take considerable time and effort, and although a general-purpose computer can perform these calculations at a rate and accuracy that can far exceed the mental performance of a skilled artisan, the nature of the activity is essentially the same, and therefore constitutes an abstract idea. Therefore, the claims recite elements that constitute a judicial exception in the form of an abstract idea. (Step 2A, Prong One: Yes.)
Step 2A, Prong Two Analysis:
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs). Here at Step 2A, Prong Two, any remaining steps and/or elements not identified as JEs are therefore in addition to the identified JE(s), and are considered additional elements. Because the claims have been interpreted as being directed to judicial exceptions (abstract ideas in this instance) then Step 2A, Prong Two provides that the claims be examined further to determine whether the judicial exception is integrated into a practical application [see MPEP § 2106.04(d)]. A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception.
MPEP § 2106.04(d)(I) lists the following five example considerations for evaluating whether a judicial exception is integrated into a practical application:
(1) An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a).
(2) Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2).
(3) Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b).
(4) Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c).
(5) Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
The additional element(s) of the instant claims are as follows:
Additional elements of data gathering: Claims 1 and 8 recite additional elements of accessing data. These limitations represent data gathering steps, and are additional elements which perform functions of inputting, collecting, and/or outputting data needed to carry out the abstract idea. These steps are considered insignificant extra-solution activity, and are not sufficient to integrate an abstract idea into a practical application as they do not impose any meaningful limitation on the abstract idea or how it is performed, nor do they provide an improvement to technology [see MPEP § 2106.04(d)(I)].
Additional element of therapy: Claim 1 recites an additional element of "administering Cetuximab and/or Panitumumab to the subject," which is informed by the abstract idea of sequence data analysis. Because the claim further recites "or that the variant is not absent at the first genetic locus" there is an embodiment in which the administration of Cetuximab and/or Panitumumab does not occur. As such, instant claim 1 does not recite a particular therapy, and therefore is insufficient to integrate the abstract idea into a practical application (see MPEP § 2106.04(d)(2)). However, If claim 1 were to be amended, possibly by deleting the phrase "or that the variant is not absent at the first genetic locus", it might be a step toward reciting a particular therapy and therefore a practical application at Step 2A Prong Two. However, because the
Step 2A Prong Two summary: The claims have been further analyzed with respect to Step 2A, Prong Two, and no additional elements have been found, alone or in combination, that would integrate the judicial exception into a practical application. (Step 2A, Prong Two: No).
Step 2B analysis:
Because the additional claim elements do not integrate the JE (in this case, the abstract ideas) into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept. An inventive concept is furnished by an element or combination of elements that is recited in the claim in addition to the judicial exception, and is sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself (see MPEP § 2106.05).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions because the claims recite additional elements that are well-understood, routine, and conventional. Those additional elements are as follows:
The additional elements of data gathering (accessing data, and a human cfDNA sample) of claims 1 and 8 do not cause the claims to rise to the level of significantly more than the judicial exception. The courts have recognized receiving or transmitting data over a network; storing and retrieving information in memory; analyzing DNA to provide sequence information or detect allelic variants, using polymerase chain reaction to amplify and detect DNA, etc., [see MPEP§2106.05(d)(II)], as well-understood, routine, conventional activity when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity. The well-understood, routine, conventional aspects are also shown by the following reference:
Bai, (Molecular and cellular probes, vol. 49: 101480, pages 1-8 (Nov. 2019); cited in the 06/18/2024 form PTO-892) , presents a review on sequence analysis of circulating tumor DNA (ctDNA) in cancer patients (p.1, col.2; p.2, col.1-2; and throughout entire document), showing analysis of the input data to be well-understood, routine, and conventional.
The additional element of administering Cetuximab and/or Panitumumab to the subject of claim 1 does not cause the claims to rise to the level of significantly more than the judicial exception, as the additional elements are shown to be routine and conventional in the art as follows:
Pietrantonio, (European journal of cancer, vol. 51(5), pages 587-594 (2015); cited in the 06/18/2024 form PTO-892), presents a review of clinical trials focusing on use of wild type BRAF status to predict response to Cetuximab and Panitumumab treatment in colorectal cancer patients.
Step 2B summary: All limitations of claims 1, 3-9, 11-16, and 99-101 have been analyzed with respect to Step 2B, and none provides a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception, and thus do not transform the judicial exception into a patent eligible application of the exceptions. (Step2B: NO).
Therefore, claims 1, 3-9, 11-16, and 99-101, when the limitations are considered individually and as a whole, are rejected under 35 U.S.C. § 101 as being directed to non patent-eligible subject matter.
Response to Applicant Arguments - 35 USC § 101
Applicant's arguments filed 10/16/2025 have been fully and respectfully considered, but they are not yet persuasive.
Applicant asserts (p.7-8):
• …the presently amended claims at issue are integrated in providing a practical application (p.7, ¶ 3).
• …the presently claimed methods refer to a determination step where: (1) wildtype KRAS, BRAF, or NRAS is identified and administration of a drug is provided or (2) a non-wild type KRAS, BRAF, or NRAS is identified. In either scenario, the determination step will always occur (p.7, ¶ 3).
• …the administration of the recited Cetuximab and/or Panitumumab is in relation to wildtype genes ( e.g., KRAS, NRAS)… If non-wildtype variants are present "RAS is activated, inhibiting EGFR will have minimal or no impact, so the Cetuximab or Panitumumab treatment will be administered inappropriately." Para. 0196 of the Specification (bridging p.7-8).
• …the presently amended claims are directed to a specific treatment (i.e., EGFR inhibition) for a specific genetic status (e.g., wild-type KRAS, NRAS). This use arises directly from the aforementioned mechanism of action, in determining administration of treatment when appropriate, and so the determination and use are inexorably linked (p.8, ¶ 1).
• As "the goal may be to avoid non-effective treatments", the presently amended claims are much more than simply a nominal relationship to a judicial exception (p.8, ¶ 1).
The argument is not yet persuasive, because at present, instant claim 1 does not yet recite a particular therapy for the following two reasons:
First, claim 1includes an embodiment in which the administering step does not occur when the variant is present; this might be remedied through possibly amending claim 1 by deleting the recitation of "or that the first variant is not absent at the first genetic locus."
Second, claim 1 does not recite a disease for which the subject is being treated. As such, claim 1 does not recite a particular therapy, and therefore the additional element of administering Cetuximab and/or Panitumumab to the subject does not integrate the judicial exception into a practical application. One way to demonstrate such integration into a practical application is when the additional elements apply or use the recited judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition. See MPEP 2106.04(d)(2). This issue might move toward overcoming the 101 by possibly amending claim 1 to recite "colorectal cancer patient" instead of "human subject" and "subject." It is noted that if the suggestion is taken regarding "colorectal cancer patient", then claims 14 and 15 should be amended or canceled as appropriate.
Applicant is encouraged to request an interview if it would be helpful to advance prosecution.
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.
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, 3-9, 11-16, and 99-101 are rejected under 35 U.S.C. 103 as being unpatentable over Lanman, (PloS one, vol. 10(10):e0140712, pages 1-27, plus supplementary table S3 (2 pages, p.28-29 of document); 29 pages total (2015); cited in the 06/18/2024 form PTO-892), in view of Odegaard, (Clinical Cancer Research, vol. 24(15), pages 3539-3549 (2018); cited in the 06/18/2024 form PTO-892), in view of Pietrantonio, (European journal of cancer, vol. 51(5), pages 587-594 (2015); cited in the 06/18/2024 form PTO-892), in view of Zill, (Clinical Cancer Research, vol. 24(15), pages 3528-3538 (11 pages), plus Zill supplemental material (36 pages), document total: 47 pages; (2018); cited in the attached form PTO-892).
Independent claim 1 recites a method for accessing sequence reads from sequence analysis of a human cfDNA sample; determining a first variant at the first locus is not detected in the sequence reads; generating first and second likelihood values respectively based on a probability that the first variant is absent and not absent at the clonal level; determining a tumor fraction estimate of the sample, wherein the first and second likelihood values are based on the tumor fraction estimate; generating additional first and second likelihood values based on mutual exclusivity and/or co-occurrence of the variants; determining quantitative values based on the log transformation of the first and second likelihood values and/or the additional first and second likelihood values; comparing the quantitative values to a threshold; determining that the first variant is absent at the first genetic locus in the cfDNA sample and is wild type, and administering Cetuximab and/or Panitumumab to the subject based on the presence of colorectal cancer in a subject or that the first variant is not absent at the first genetic locus, wherein the first genetic locus is KRAS, BRAF, or NRAS.
Dependent claim 3 further recites determining the tumor fraction estimate comprises: determining a maximum mutant allele frequency (MAX MAF) of a tumor mutation in the sample. Dependent claim 4 further recites determining the MAX MAF comprises determining a molecule count associated with the tumor mutation based on the sequence reads. Dependent claim 5 further recites generating the first likelihood value and the second likelihood value comprises: determining an allele frequency of at least a second variant, wherein the first likelihood value and the second likelihood value are based further on the allele frequency and the MAX MAF. Dependent claim 6 further recites comparing the allele frequency with a second threshold that is based on the MAX MAF, where determining that the first variant of interest at the first locus is absent at the clonal level is based further on the comparison of the MAF with the second threshold. Dependent claim 7 further recites determining a first molecule count associated with the first variant based on the plurality of sequence reads.
Dependent claim 8 further recites accessing covariable information indicating a historical prevalence of one or more variants exhibiting co-occurrence and/or mutual exclusivity with the first variant, wherein the quantitative value is based on the covariable information. Dependent claim 9 further recites determining a prevalence of a second variant in the cfDNA sample, wherein the quantitative value is based further on the covariable information. Dependent claim 11 further recites determining a prevalence of a second variant in the cfDNA sample, where the quantitative value is based further on the prevalence of the second variant.
Dependent claim 12 further recites the quantitative value is based on the ratio of the first likelihood value to the second likelihood value. Dependent claim 13 further recites determining a level of confidence that the first variant is absent at the clonal level in the cfDNA sample based on the quantitative value. Dependent claim 14 further recites determining a treatment plan to treat a disease in the human subject. Dependent claim 15 further recites the disease is cancer.
Dependent claim 16 further recites determining a prevalence of a second variant in the cfDNA sample; and adjusting the quantitative value based on the prevalence of a second variant in the cfDNA sample.
Dependent claims 99-101 further recite log transformation comprises equations. (Because the equations themselves are not recited in the claims, claims 99-101 are interpreted as not further limiting claim 1. The equation issue of claims 99-101 is further discussed in the 112(b) rejection above.)
Lanman shows analyzing sequence reads from cfDNA sequence analysis (p.4, para.2; and p. 19, para.1), and workflow for the Guardant360 cell-free circulating DNA NGS genomic profile (p.5, Fig.1). Lanman shows accuracy and analytic specificity for SNVs in stating: (the method) "defines analytic specificity as the probability that the assay will not detect a sequence variation when none are present" (p.20). Lanman shows comparing the binary presence or absence of a single nucleotide variant/point mutation or focal gene amplification (p.14, para.2). Lanman shows analytic sensitivity of the Guardant360 digital sequencing method, where twenty nine SNV samples were diluted serially until they could no longer be measured with the assay; the limit of detection (LOD) was 0.25% mutant allele frequency or fraction) (MAF) (p./8, fig.4). Lanman shows Mutant Allele Frequency measurement accuracy; quantification uncertainty varies inversely with single nucleotide variant MAF, with the highest relative uncertainty at lower MAF and least percent relative uncertainty at higher MAF (p.8, table 2). ). Lanman shows the Guardant360 test has the potential to evaluate the multiple genomic alterations cited in NCCN guidelines, to act as a "summary" of the different tumor clones in patients with tumor heterogeneity (p.3, above "Results"). (Showing accessing sequence reads, determining a 1st variant not detected, probability first variant absent/present, generating values based on probability first variant absent or present at clonal level, determining (and comparing) a quantitative value based on the first likelihood value and the second likelihood value of claim 1, and determining allele frequency of claim 5).
Lanman shows the fractional concentration or mutant allele fraction for a given mutation is calculated as the fraction of circulating tumor DNA harboring that mutation in a background of wild-type cfDNA fragments at the same nucleotide position (p.19, para.1). Lanman shows maximum mutant allele fraction (fig.6); and by their low concentrations, somatic mutations (far left-hand small peak) can be generally distinguished from heterozygous germline SNVs around 50% MAF (middle peak) and homozygous germline SNVs around 100% MAF (right-hand peak); cell-free DNA is both leukocyte-derived and tumor-derived, with the germline DNA generally representing the bulk of the cfDNA; the molecular tumor board of the Guardant360 panel filters out the germline SNVs and only the somatic mutations are reported (p.11, fig.6). Lanman shows software utilized includes CASAVA (version 1.8.4), the open source BWA-MEM aligner, and a custom read pile-up process that utilizes information encoded by digital-sequencing oligonucleotides to reconstruct the set of unique cfDNA molecules. First, 150bp paired-end reads are aligned to the reference genome. Lanman shows a statistical z-score for each gene is calculated by comparing the normalized gene fragment number to that derived from the Normal Set to estimate the likelihood of the gene exhibiting amplification and remove any remaining region specific bias. Gene amplifications with a z-score > 2.5758 (the inverse of the cumulative distribution function of a Gaussian distribution at 99.5% confidence level) are called as truly amplified. The numerical result of the above procedure expresses the absolute copy number of a gene in plasma-derived cfDNA samples, which Ultra-Accurate Circulating Tumor DNA Profiling is a combination of both normal cfDNA (mainly leukocyte-derived) and tumor-derived gene copy number (bridging page 19-20). (Showing determining (and comparing) a quantitative value based on the first likelihood value and the second likelihood value of claim 1, a tumor fraction of claim 1 and 3, a MAX MAF of claim 3, a molecular count based on reads of claim 4 and 7, comparing allele frequencies of claim 6, the ratio of claim 12, confidence level of claim 13, and wild-type (genotype) of claim 1).
Lanman does not explicitly recite "a threshold" of claims 1 and 6. Lanman does not explicitly recite a "ratio" of claim 12. Lanman does not recite adjusting the quantitative value of claim 16.
Lanman does not show co-occurrence and/or mutual exclusivity with the first variant of claim 1; covariable information indicating a historical prevalence of claim 8, prevalence of a second variant based on covariable information of claim 9; prevalence of at least a second variant of claim 11.
While Lanman discusses wild-type as stated above (p.19, para.1), Lanman does not specifically show the determination that the first target nucleic acid variant is absent at the first genetic locus in the cfDNA sample indicates that the first genetic locus is wild type of claim 1.
Lanman does not show a treatment plan of claim 14; cancer of claim 15; colorectal cancer, wild type KRAS, BRAF, or NRAS of claim 32; or administering Cetuximab and/or Panitumumab of claim 1.
Odegaard shows reporting thresholds were event-specific as determined by performance in training samples but were most commonly at least one unique molecule for clinically actionable indels, which in an average sample corresponds to a detection limit of approximately 0.02% VAF (p.3541, col.1). Odegaard shows a likelihood ratio score (p.3541, col.1). (Showing thresholds of claim 1 and 6.)
Odegaard shows prevalence adjusted PPV (positive predictive value) as a function of allelic frequency was defined using per-sample frequency of somatic calls in clinical samples within VAF range, per-sample frequency of false positive calls in known negative samples in allelic range (p.3541, col.1). (Considered to show adjusting the quantitative value of claim 16.)
Odegaard shows SNVs and indels were quantified using variant-specific PCR primer pairs and wild-type or mutant-specific fluorescent hydrolysis probes (p.6541, col.2). (Considered to show when the variant is absent at the first genetic locus in the cfDNA sample a wild type (genotype) is indicated of claim 1.)
Zill shows CfDNA landscape of resistance to on-label therapies across cancer types (p.3535, fig.5); and longitudinal monitoring analysis of an NSCLC patient with emerging resistance (T790M) in the third draw after presumptive EGFR inhibitor therapy indicated by the L858R mutation; colored lines track the VAF (cfDNA %) of each mutation across three consecutive blood draws. Zill teaches deriving an estimated cfDNA clonality metric using the VAF/maximum VAF ratio that would allow inferring the likely cancer-cell fraction of mutations present in the tumor (p.3531, col.2). Zill teaches their model takes into account nonlinearities by normalizing the VAF by log-transformed copy number for driver variants and by holding out variants that initially appear subclonal from the normalization procedure (p.3531 col.2; also see Zill supplemental material (3:74), p.14 of 47 total pages) . Zill teaches mutual exclusivity analysis on common cfDNA alterations in LUAD (lung adenocarcinoma), breast cancer, and colorectal cancer samples (p.3532, col.2). Zill shows in the colorectal cancer samples, mutual exclusivity was observed between KRAS and BRAF, ERBB2, and NRAS, similar to reports in tumor tissue. In the pre-filtered data, KRAS and PIK3CA tended to co-occur, but in the post-filtering data they showed a weak trend toward exclusivity, suggesting the presence of subclonal KRAS resistance alterations in the cfDNA colorectal cancer samples (p.3534, bridging cols.1-2; also see Zill supplemental material FIG. S12, p.40 of 47 total pages). Zill shows log odds ratios for the mutual exclusivity analysis (Showing mutual exclusivity and co-occurrence of the first variant of claim 1, covariable information indicating a historical prevalence of one or more variants exhibiting co-occurrence and/or mutual exclusivity with the first variant, wherein the quantitative value is based on the covariable information of claims 8; prevalence of a second variant based on covariable information of claim 9; and prevalence of at least a second variant of claim 11; and the ratio of claim 12.
Pietrantonio shows a study examining the impact of cetuximab (C) and panitumumab (P) on progression-free survival (PFS), overall survival (OS) and overall response rate (ORR) in advanced colorectal cancer (CRC) patients who have RAS-wt/BRAF-mutant (BRAF-mut) status (p.587, abstract, and entire document). Pietrantonio shows cetuximab (C) and panitumumab (P) monotherapy versus best supportive care (BSC) in KRAS-wt CRC patients, and patients were classified as BRAF wild type (BRAF-wt) if no mutation was detected; almost all patients had wild type KRAS (p.588, col.2). Pietrantonio concludes that BRAF and all-RAS mutation testing should be included in the initial diagnostic work-up of all patients with advanced CRC, in order to obtain valuable prognostic and predictive information that drive treatment decisions (p.593, col.2). (Showing a treatment plan of claim 14; cancer of claim 15; colorectal cancer, wild type KRAS, BRAF, or NRAS of claim 1; or administering Cetuximab and/or Panitumumab of claim 1.)
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the method for analyzing cell-free circulating tumor DNA, determining mutant allele fractions, and determining presence and absence of variants/ wild-type genotype of Lanman; with the related frequency ratios, thresholds, and determining presence and absence of variants/ wild-type genotype of Odegaard; with the method involving covariant information indicating longitudinal, historical prevalence of variants, to include variant co-occurrence and/or mutual exclusivity, in ctDNA of Zill; with the with the colorectal cancer treatment plan administering Cetuximab and/or Panitumumab in patients with wild type KRAS, BRAF, or NRAS of Pietrantonio, to come to a better method for analyzing cell-free circulating tumor DNA in determining absence of variants based on mutual exclusivity and co-occurrence, and administering therapy based on the determination of variants in colorectal cancer, because Lanman shows a differentiating characteristic from other "liquid biopsy" methods is their Guardant360 method’s ultra-high specificity, while Odegaard states "Guardant360's 73-gene design also allows interpretation of negative findings (required for effective biopsy prevention) and early detection of immunotherapy resistance" (p.3547, col.1). Zill states "cfDNA and other minimally invasive techniques address a real and unmet need, as it is essential to provide real-time tumor genotyping at the time of progression to guide subsequent therapeutic strategies" (p. 3537, col.2). Pietrantonio shows identification of "10 randomized trials that explored the outcome of RAS-wt /BRAF-mut treated with (or without) cetuximab (C) and panitumumab (P), in either upfront or pretreated setting; and showed that the addition of anti-EGFR agents to standard therapy is not associated with a significant overall survival (OS), progression-free survival (PFS), or overall response rate (ORR) benefit in RAS-wt but BRAF-mut patients, particularly in first-line setting" (p.590, col.2). One would have had a reasonable expectation of success in doing so because Lanman, Odegaard, Zill, and Pietrantonio are obviously drawn to related teaching, and one of ordinary skill in the art would have understood how to and would have been motivated to combine the related teachings of Lanman, Odegaard, Zill, and Pietrantonio and as such, the combination would have been obvious.
Response to Applicant Arguments - 35 USC § 103
Applicant's arguments filed 10/16/2025 have been fully and respectfully considered, but they are not persuasive.
Applicant asserts, on p.9:
• …Figure 5 of Zill et al. does not teach, suggest, motivate or in any other way make obvious the presently claimed invention. Figure 5 of Zill et al. depicting variants (co-occurring and/mutually exclusive) is an observation of complex, advanced, treated cancers in a single NSCLC patient ex post facto …entirely missing from Zill et al. is how to particularly utilize any such prevalence of additional variants, in concert with a first variant to then determine a subject's genetic status and a suitable treatment ex ante (p.9, ¶ 2).
The argument is not persuasive because Zill is not relied upon for "how to particularly utilize any such prevalence of additional variants, in concert with a first variant to then determine a subject's genetic status and a suitable treatment ex ante." Zill is relied upon for teaching mutual exclusivity of the first variant and prevalence of one or more variants, and co-occurrence of the first variant and prevalence of one or more variants. Pietrantonio was relied upon for teaching administering cetuximab (C) and panitumumab (P) monotherapy versus best supportive care (BSC) in KRAS-wt CRC patients (Pietrantonio, p.588, col.2),
Applicant asserts, on p.9 (italicized portion added):
• …(the pursuit motivated by Zill) provides no particular direction towards the specific solution recited in the presently recited claims. That is, the use of combination of a first variant and additional variant (co-occurring, mutual exclusive, or both) each expressed as log likelihood ratios (LLRs) to generate a quantitative measurement for threshold comparison. These are expressly taught in the Specification… (p.9, ¶ 3).
The argument is not persuasive because there is no log-likelihood ratio (LLR) explicitly recited in the claims. The only ratio explicitly recited is in claim 12, and it is unclear if the values have been log transformed (there is a 112(b) rejection for this issue), as claim 12 recites "wherein the quantitative value is based on the ratio of the first likelihood value to the second likelihood value." As a step toward 103 withdrawal, claim 1 could possibly be amended to include log-likelihood ratio (LLR), as well as the actual equation for LLR from the Specification.
Additionally, Zill teaches deriving an estimated cfDNA clonality metric using the VAF/maximum VAF ratio that would allow inferring the likely cancer-cell fraction of mutations present in the tumor (p.3531, col.2). Zill teaches their model takes into account nonlinearities by normalizing the VAF by log-transformed copy number for driver variants and by holding out variants that initially appear subclonal from the normalization procedure (p.3531 col.2; also see Zill supplemental material (3:74), p.14 of 47 total pages) . Zill teaches mutual exclusivity analysis on common cfDNA alterations in LUAD (lung adenocarcinoma), breast cancer, and colorectal cancer samples (p.3532, col.2).
Applicant asserts, on p.10:
•… new claims 99-101…recite the particular algorithms described in the Specification. As LLR-based assessment is entirely absent in the combination of Lanman et al. in view of Odegaard et al., Pietrantonio et al., and Zill et al., so are the methods utilizing the particular algorithms for determining suitable treatment (p.10, ¶ 2).
The argument is not persuasive because the actual equations are not recited in the claims. Claims 99-101 do not recite the particular equations described in the Specification. (See the 112(b) rejection above regarding this issue.) As such, claims 99-101 are interpreted as not further limiting claim 1. The claims might be amended to include the equations from Specification paragraphs [132] and [142-146].
Conclusion
No claims are allowed. This is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Meredith A Vassell whose telephone number is (571)272-1771. The examiner can normally be reached 8:30 - 4:30.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, KARLHEINZ SKOWRONEK can be reached at (571)272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/M.A.V./Examiner, Art Unit 1687
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686