DETAILED ACTION
The Applicant’s response, received 20 January 2026, 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 1-4 and 7-10 are pending.
Claims 1-4 and 7-10 are rejected.
Priority
This application is a 371 of PCT/US2017/066210, filed 13 December 2017, which claims benefit of 62/433,737, filed 13 December 2016.
Claim Rejections - 35 USC § 112
The rejection of claims 1-4 and 7-10 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in the Office action mailed 17 July 2025 is withdrawn in view of the amendment received 20 January 2026.
The Applicant’s amendment received 20 January 2026 has been fully considered, however after further consideration, new grounds of rejection are raised under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, in view of the amendment.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-4 and 7-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 recites the limitation “an endpoint-resolved fragmentation profile,” however the Specification does not contain the terms “endpoint-resolved fragmentation profile,” “endpoint-resolved,” or “profile.” Therefore, this appears to be a new scope not contemplated nor supported by the present Specification.
Claims 2-4 and 7-10 are rejected under 35 U.S.C. 112(a) for depending from claim 1 and for failing to remedy the failure of claim 1 to comply with the written description requirement.
Claim Rejections - 35 USC § 101
The Applicant’s amendment received 20 January 2026 has been fully considered, however after further consideration, the rejection of claims 1-4 and 7-10 under 35 U.S.C. 101 in the Office action mailed 17 July 2025 is maintained with modification in view of the amendment.
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 1-4 and 7-10 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 1-4 and 7-10 are directed to a method (i.e., a process) of identifying cancer in a subject.
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:
mapping a plurality of cfDNA fragments (i.e., data) to a reference genome (i.e., mental processes);
assigning to each of a plurality of genomic positions, a first value corresponding to the number of cfDNA fragments having their leftmost endpoint at said position and a second value corresponding to the number of cfDNA fragments having their rightmost endpoint at said position (i.e., mental processes);
wherein the first value and the second value are determined by separately tallying the leftmost endpoints and the rightmost endpoints of cfDNA fragments at each of the plurality of genomic positions (i.e., mental processes and mathematical concepts),
wherein the first value and second value provide an endpoint-resolved fragmentation profile that is not detectable using a per genomic position aggregated single value (i.e., mental processes);
comparing, for each of the plurality of genomic positions, the first value and the second value from the subject to corresponding values in a reference dataset from one or more reference subjects (i.e., mental processes);
identifying a probability of the presence or absence of cancer in the subject based on the correlation of the first value to the corresponding value in the reference dataset and/or the correlation of the second value to the corresponding value in the reference dataset (i.e., mental processes and mathematical concepts); and
determining a presence or absence of the cancer in the subject by comparing the identified probability of the presence or absence of cancer to a threshold probability value, wherein the comparison classifies the subject as either having or not having cancer (i.e., mental processes and mathematical concepts).
Independent claim 1, and those claims dependent therefrom, recite a law of nature by correlating genomic data (i.e., cell-free DNA fragment endpoints) with a phenotype (i.e., a subject either having or not having cancer), i.e., a genotype-phenotype association (MPEP 2106.04(b)).
Dependent claims 2, 3, and 7-10 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
generating a report listing a plurality of scores comparing the first value and the second value from the subject to corresponding values in a reference dataset from one or more reference subjects (i.e., mental processes).
Dependent claim 3 further recites:
recommending treatment for the cancer in the subject determined to be present in the biological sample (i.e., mental processes).
Dependent claim 7 further recites:
wherein the first value and the second value assigned to each of a plurality of genomic positions is a statistical transformation of the number of cfDNA fragment leftmost and rightmost endpoints, respectively, observed at the position (i.e., mental processes and mathematical concepts).
Dependent claim 8 further recites:
where each of a plurality of genomic positions receives two values, the first value corresponding to the number of cfDNA fragments having their leftmost endpoint at said position and where the fragments were derived from the Watson strand, the second value corresponding to the number of cfDNA fragments having their rightmost endpoint at said position and where the fragments were derived from the Watson strand (i.e., mental processes and mathematical concepts).
Dependent claim 9 further recites:
where each of a plurality of genomic positions receives four values, the first value corresponding to the number of cfDNA fragments having their leftmost endpoint at said position and where the fragments were derived from the Watson strand, the second value corresponding to the number of cfDNA fragments having their rightmost endpoint at said position and where the fragments were derived from the Watson strand, the third value corresponding to the number of cfDNA fragments having their leftmost endpoint at said position and where the fragments were derived from the Crick strand, and the fourth value corresponding to the number of cfDNA fragments having their rightmost endpoint at said position and where the fragments were derived from the Crick strand (i.e., mental processes and mathematical concepts).
Dependent claim 10 further recites:
wherein at least one of the multiple values assigned to each of a plurality of genomic positions is/are a statistical transformation of the number of cfDNA fragment endpoints meeting the stated criteria.
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 pen and paper (e.g., assigning to each of a plurality of genomic positions, a first value corresponding to the number of cfDNA fragments having their leftmost endpoint at said position and a second value corresponding to the number of cfDNA fragments having their rightmost endpoint at said position), 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., identifying a probability of the presence or absence of cancer in the subject based on the correlation of the first value to the corresponding value in the reference dataset and/or the correlation of the second value to the corresponding value in the reference dataset) 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 1-4 and 7-10 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 2, 3, and 7-10 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:
isolating a plurality of cell free DNA (cfDNA) fragments from a biological sample from the subject;
sequencing at least a portion of the plurality of cfDNA fragments; and
a computer.
The additional elements in dependent claim 4 include:
treating cancer in the subject.
The additional element of a computer (claim 1) invokes a computer and/or computer-related components merely as tools 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 element of isolating a plurality of cell free DNA (cfDNA) fragments from a biological sample from the subject (claim 1) is merely a pre-solution activity of gathering data for use in the claimed process – a nominal or tangential addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional element of sequencing at least a portion of the plurality of cfDNA fragments (claim 1) is merely a pre-solution activity of gathering data for use in the claimed process – a nominal or tangential addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional element of treating cancer in the subject (claim 4) does not recite an action that effects a particular treatment or prophylaxis for a disease or medical condition, and therefore, does not integrate the judicial exception into a practical application (MPEP 2106.04(d)). When determining whether a claim applies or uses a recited judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, the following factors are relevant: (a.) The particularity or generality of the treatment or prophylaxis; (b.) Whether the limitation(s) have more than a nominal or insignificant relationship to the exception(s); and (c.) Whether the limitation(s) are merely extra-solution activity or a field of use. The additional element of “treating a cancer in the subject” does not satisfy factors a., b. or c., because with respect to factor a., the claim does not recite a particular, i.e., specifically identified treatment; with respect to factor b., the recited judicial exceptions are related to the step of classifying the subject as either having or not having cancer, however the additional element of treating cancer in the subject does not apply or use the judicial exceptions in any meaningful way; and with respect to factor c., the additional element of treating cancer in the subject does not amount to more than generally linking the use of a judicial exception to a particular field of use (i.e., cancer treatment).
Thus, the additionally recited elements merely invoke a computer as a tool, and/or amount to insignificant extra-solution data gathering activity, and/or do not affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition, and as such, when all limitations in claims 1-4 and 7-10 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-4 and 7-10 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 2, 3, and 7-10 do not recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claim 1 and dependent claim 4 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 (claim 1), 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 treating cancer in the subject (claim 4), is conventional. Evidence of conventionality is shown by:
Hui (Obstetric Medicine, 2016, vol. 9(4), pp. 148-152, as cited in the Office action mailed 16 March 2023).
Hui reviews maternal malignancy (page 151, column 1, para. 2) and a case with serial blood samples where the plasma DNA aberrations seen on NIPT cleared after cancer treatment, confirming the relationship between ctDNA, tumor load, and NIPT result.
The additional elements of isolating a plurality of cell free DNA (cfDNA) fragments from a biological sample from the subject (claim 1), and sequencing at least a portion of the plurality of cfDNA fragments (claim 1), are conventional. Evidence of conventionality is shown by:
Chan et al. (Clinical Biochemistry, 2015, vol. 48, pp. 962-975, as cited in the Office action mailed 16 March 2023).
Chan et al. reviews the discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis and that cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases (Abstract); the advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cfDNA molecules in plasma in a genome-wide fashion and at single-base resolution (Abstract); a whole-genome approach for cfDNA analysis showing mapping each sequence read to the human genome (page 966, column 2, Section 5.2.1); and clinical situations in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved (Abstract).
Therefore, when taken alone, all additional elements in claims 1-4 and 7-10 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 1-4 and 7-10 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 20 January 2026 have been fully considered, but are not persuasive.
Regarding Step 2A Prong One, the Applicant states on page 6 (para. 1) of the Remarks that independent claim 1 is not directed to a mental process or law of nature, and further states that the claim recites a multi-step method that operates on physical cfDNA fragments, requires DNA sequencing, and uses computer-implemented mapping and endpoint-specific tallying operations that cannot be practically performed in the human mind or by pen and paper, and therefore the claim does not fall within the mental processes category of abstract ideas.
These arguments are not persuasive, because first, claim 1 is identified as reciting a law of nature because the claim correlates genomic data (i.e., cell-free DNA fragment endpoints) with a phenotype (i.e., a subject either having or not having cancer), which is a genotype-phenotype association. Second, claim 1 is identified as reciting mental processes because the claim recites steps (e.g., assigning to each of a plurality of genomic positions, a first value corresponding to the number of cfDNA fragments having their leftmost endpoint at said position and a second value corresponding to the number of cfDNA fragments having their rightmost endpoint at said position, wherein the first value and the second value are determined by separately tallying the leftmost endpoints and the rightmost endpoints of cfDNA fragments at each of the plurality of genomic positions) that can practically be performed in the human mind, with or without the use of a physical aid such as pen and paper, and therefore, at least this limitation falls within the mental processes grouping, and thus the claim recites an abstract idea. Third, claims can recite a mental process even if they are claimed as being performed on a computer. Fourth, the claim limitations reciting steps of “isolating a plurality of cell free DNA (cfDNA) fragments from a biological sample from the subject” and “sequencing at least a portion of the plurality of cfDNA fragments” are identified as additional elements at Step 2A Prong Two that are conventional at Step 2B.
Regarding Step 2A Prong Two, the Applicant states on page 6 (para. 2) of the Remarks that even if an abstract idea were implicated, claim 1 integrates any such exception into a practical application by reciting a specific technical improvement in the processing of cfDNA sequencing data, and that specifically, claim 1 computationally transforms raw sequencing data into mapped cfDNA fragment endpoints and further into an endpoint-resolved positional data structure – a “two value” data structure, and that this “two-value” data structure comprises two distinct values per genomic position, namely a first value corresponding to the number of fragments having a leftmost endpoint at the position and a second value corresponding to the number of fragments having a rightmost endpoint at the position. The Applicant further states that these values are generated using a tallying operation that separately quantifies left and right endpoints for each genomic position across a plurality of genomic positions, and that the “two-value” data structure is the basis for ultimately determining whether the subject has a presence or absence of cancer. The Applicant further states (para. 3) that as disclosed in paragraph [00025], separately tallying left and right endpoints reveals positional limits of protected DNA regions that are otherwise obscured when fragment endpoints are aggregated into only a single value per position – a “single-value” data structure. The Applicant further states that Figures 2 and 3 visually illustrate this distinction, and further states on page 7 (bottom) of the Remarks that Figure 2 depicts the “two-value” data structure – there are two values per genomic position corresponding to the number of “left” endpoints (light gray line) and the number of “right” endpoints (dark gray line) while Figure 3 shows only the “single value” data structure – a count of all fragment end points at a particular position. The Applicant further states that paragraph [00050] explains that the “two-value” endpoint separation shown in Figure 2 provides finer resolution of nucleosome positioning information that is lost when using a single-value endpoint count as in Figure 3, and further states on page 8 (para. 1) that accordingly, the claimed method uses a “two-value” fragment endpoint data structure and tallying operation that improves how cfDNA sequencing data are represented and analyzed, enabling extraction of biologically relevant signal that is not detectable using conventional fragment endpoint analysis, and that this constitutes a technical improvement to data processing.
These arguments are not persuasive, because first, regarding the Applicant’s argument that “claim 1 integrates any such exception into a practical application by reciting a specific technical improvement in the processing of cfDNA sequencing data, and that specifically, claim 1 computationally transforms raw sequencing data into mapped cfDNA fragment endpoints and further into an endpoint-resolved positional data structure,” it is noted that the purported improved step of processing cfDNA sequencing data comprises the judicial exceptions, and the judicial exceptions alone cannot provide the practical application, and alone are also not eligible subject matter, and further noted that 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, however, as noted in the above rejection, the claim does not recite any additional elements that either apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, and therefore the recited judicial exceptions are not integrated into a practical application. Second, regarding Figures 2 and 3, and the Applicant’s argument that raw sequencing data is transformed “into mapped cfDNA fragment endpoints and further into an endpoint-resolved positional data structure – a “two value” data structure, and that this “two-value” data structure comprises two distinct values per genomic position,” it is noted that the data points on a graph are technically “structured data” and the graph itself is the “data structure” or defined structure, e.g., a table or coordinate system. Nonetheless, the step of “separately tallying left and right endpoints” comprises the judicial exceptions, as noted in the above rejection, and furthermore, a step of plotting the endpoint data on a graph would also be part of the judicial exceptions. Third, regarding the Applicant’s argument that the tallying operation “improves how cfDNA sequencing data are represented and analyzed, enabling extraction of biologically relevant signal that is not detectable using conventional fragment endpoint analysis, and that this constitutes a technical improvement to data processing,” it is noted that each of the elements of the Applicant’s argument comprise the judicial exceptions, and as noted above, the claim does not recite any additional elements that either apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, and therefore the recited judicial exceptions are not integrated into a practical application.
Regarding Step 2B, the Applicant states on page 8 (para. 2) that claim 1 further recites an inventive concept, and that the claimed combination of steps – particularly the generation and use of the “two-value” data structure reflecting the endpoint-specific positional tallies for both left and right cfDNA fragment endpoints – was not routine or conventional at the time of filing, and that there are no references that disclose such an ordered combination. The Applicant further states (para. 3) that when considered as a whole, the claim recites more than generic sequencing and data comparison, it defines a non-conventional data structure and processing workflow that improves signal resolution in cfDNA analysis and enables cancer classification without reliance on current endpoint fragment analysis or on more traditional somatic base calling methods that use genotypic information rather than epigenomic or fragmentomic information, and therefore, this ordered combination amounts to significantly more than any alleged judicial exception.
These arguments are not persuasive, because first, regarding the Applicant’s argument that “the claimed combination of steps – particularly the generation and use of the ‘two-value’ data structure reflecting the endpoint-specific positional tallies for both left and right cfDNA fragment endpoints – was not routine or conventional at the time of filing, and that there are no references that disclose such an ordered combination” it is noted that these steps comprise the judicial exceptions identified at Step 2A Prong One, and therefore, these limitations are not evaluated at Step 2B, because Step 2B asks: Does the claim recite additional elements that amount to significantly more than the judicial exception? Examiners answer this question by first identifying whether there are any additional elements (features/limitations/steps) recited in the claim beyond the judicial exception(s), and then evaluating those additional elements individually and in combination to determine whether they contribute an inventive concept (i.e., amount to significantly more than the judicial exception(s)). Thus, only the additional elements identified at Step 2A Prong Two are carried over to Step 2B for further evaluation, and it is these additional elements that may or may not require evidentiary references supporting conventionality, as noted in the above rejection.
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
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