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 .
Claim Status
Claims 1-4 and 6-20 are pending and under examination.
Claims 1-4 and 6-20 are rejected.
Claim 5 is canceled.
Claim 1 is independent.
Claims 3 and 8 are amended.
No claims are allowed, new, or withdrawn.
Office Action Overview
Rejections applied
Abbreviations
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
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
X
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed in the 06/10/2025 filing receipt, this application is a continuation application of U.S. Patent Application No. 16/678,060, filed 11/08/2019, which is a continuation of application PCT/US2018/033038, filed 05/16/2018, which claims the benefit of priority to Provisional Application No. 62/507,127, filed 05/16/2017. The pending claims are each afforded the benefit of priority to Provisional Application No. 62/507,127, filed 05/16/2017.
Withdrawal/Revision of Objections and/or Rejections
In view of the amendment and remarks received 06/15/2026:
• The 112(b) rejections are withdrawn.
• The 101 rejection is maintained with revision.
• The Non-Statutory Double Patenting rejection is maintained with revision.
Rejections and/or objections not maintained from previous office actions are withdrawn. The following rejections and/or objections are either maintained or newly applied. They constitute the complete set applied to the instant application.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4 and 6-20 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)).
• 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:
Claims 1-4 and 6-20 are directed to a 101 process, here a method, which falls under a category of statutory subject matter. (See MPEP § 2106.03).
Step 2A, Prong One:
The claims recite judicial exceptions in the form of abstract ideas as follows:
Claim 1 recites mental processes and mathematical concepts of:
• allocating a read budget
• determining allele frequency
• determining a measure of variability of the allele frequency
• determining an allele frequency threshold for classification of the variant of interest
• classifying the selected genomic region as being unaffected by copy number variation
• classifying the variant of interest as germline origin or as somatic origin based respectively on the allele frequency of the variant being greater or being less than the allele frequency threshold.
Claim 2 further limits the selected genomic region and abstract ideas of claim 1. Claim 3 further limits the measure of variability and abstract ideas of claim 1. Claim 4 further limits the allele frequency threshold and abstract ideas of any of claim 1-3. Claim 6 further limits the measure of variability, allele frequency variability threshold, and abstract ideas of claim 1 by: considering the measure of variability is standard deviation and the variability threshold is a standard deviation threshold. Claim 7 further limits the classification of the selected genomic region and abstract ideas of claim 6. Claim 8 further limits the selected genomic region and abstract ideas of any preceding claim. Claim 11 further limits any preceding claim and recites abstract ideas of detecting and quantifying genetic variants. Claim 14 further limits the allele frequency threshold and abstract ideas of claim 1 by reciting the abstract idea of comparing allele frequency distributions. Claim 15 further limits the classification of the variant of interest and abstract ideas of claim 1 by reciting the abstract idea of designating the variant of interest as ambiguous when the measure of variability exceeds the allele frequency variability threshold. Claim 16 further limits the abstract ideas of claim 1 by: generating a report. Claim 17 further limits the determining the allele frequency threshold and abstract ideas of claim 1 by: applying statistical and/or probabilistic models to allele-frequency distributions of allele frequencies of the plurality of genetic variants of the plurality of genomic regions to generate a classification boundary for separating germline and somatic allele-frequency values. Claim 18 further limits the empirically derived allele frequency distributions and allele frequency threshold and abstract ideas of claim 1. Claim 19 further limits the abstract idea of allocating the read budget of claim 1. Claim 20 further limits the abstract idea of allocating of claim 20.
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., allocating a read budget, determining allele frequency, determining a measure of variability, determining allele frequency threshold, classifying the selected genomic region as being unaffected by copy number variation, classifying the variant of interest as having germline or somatic origin, etc.) can be performed mentally because no limitations are recited which would prevent performance in the human mind or with pen and paper.
• "Allocating a/the read budget" of amended claim 1 and new claims 19 and 20 is characterized as a mental process of assigning (i.e., dividing) the number of to-be-obtained reads in a sample in order to provide greatest sensitivity and specificity for the regions (e.g., hotspot and genomic) in the sample, as discussed in Specification paragraphs [232-234]. Note, the actual sequencing of claim 11 is characterized as an additional process of data gathering at Step 2A Prong Two below, while the aspect of sequencing based on a "read budget" is shown as conventional below at Step 2B by the Illumina reference.
• Additionally, the limitations for determining allele frequency, determining a measure of variability (i.e., standard deviations, and standard deviation thresholds), determining allele frequency threshold, classifying the selected genomic region as being unaffected by copy number variation, classifying the variant of interest as having germline or somatic origin, etc. recite mathematical concepts such as discussed in Specification [76, 220, 260, 293]. 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:
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 claims recite additional elements as follows:
Additional elements of data gathering and outputting data (including samples and sequencing): Claim 1 recites additional elements of providing sequence reads based on the read budget. Claim 9 recites an additional element of isolating cfDNA molecules from a body fluid. Claim 10 recites an additional element of circulating tumor DNA. Claim 11-13 recite additional elements for: sequencing cfDNA; preparing a nucleic acid library, and the cfDNA molecule is barcoded. Data gathering steps are additional elements which perform functions of inputting, collecting, and outputting the 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, and as such do not integrate the recited judicial exception into a practical application. [see MPEP § 2106.04(d)(I)].
Additional elements of a computer and a computer system: The preamble of claim 1 recites an additional element of a computer. Claim 16 recites “a computer system”. The claims require only a generic computer, which does not improve computer technology, and does not integrate the recited judicial exception into a practical application (see MPEP § 2106.04(d)(1) and MPEP § 2106.05(f)).
Further concerning the additional elements of a computer/ computer system of claims 1 and 16, the MPEP 2106.05(f) discusses limitations identified by the courts that do not integrate a judicial exception into a practical application. These limitations include: merely including instructions to implement an abstract idea on a computer or merely using a computer as a tool to perform an abstract idea, (as in a “computer-implemented method” of claim 1). See MPEP 2106.05(f).
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:
Because the additional claim elements do not integrate the judicial exceptions (i.e., 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 exception because the claims recite additional elements that are well-understood, routine, and conventional. Those additional elements are as follows:
Additional elements of data gathering: The additional elements of providing sequence reads based on the read budget in claim 1; isolating cfDNA from a body fluid, and ctDNA of claims 9 and 10; and sequencing cfDNA, preparing a nucleic acid library, and barcoded cfDNA molecules, of claims 11-13, 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; determining the level of a biomarker in blood by any means; using polymerase chain reaction to amplify and detect DNA; detecting DNA or enzymes in a sample; analyzing DNA to provide sequence information or detect allelic variants; and amplifying and sequencing nucleic acid sequences, [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 extra-solution activity. Additionally, the following reference shows isolating cfDNA from a body fluid, ctDNA, sequencing, barcoded samples, and preparation of libraries to be well understood, routine, and conventional:
Kamps, (International journal of molecular sciences, vol. 18(2):308, 57 pages (Jan.2017); cited on the Form PTO-892 mailed 07/01/2025) present a review on next generation sequencing (NGS) in oncology, and shows analysis of cell-free tumor DNA from patient plasma (p.30-31); sequencing (p.2-4, and entire document), library prep (p.3-5), and barcoding (p.3).
Illumina, ((2014) Considerations for Designing a Successful TruSeq® Targeted RNA Expression Experiment [Online]; 2 pages; accessed: 02/27/2026. Available at www.illumina.com/documents/products/technotes/technote_truseq_targ_rna_design.pdf ), shows sequencing with a read budget and discusses read budget with regard to read depth (p.1-2).
Therefore the additional elements of data gathering are shown to be routine, well-understood, and conventional in the art, and do not provide an inventive concept needed to amount to significantly more than the judicial exception.
Additional elements of a computer and computer system: The additional elements of a computer and computer system of claims 1 and 16 do not cause the claims to rise to the level of significantly more than the judicial exception; these are conventional computers, generically claimed and discussed at Specification [264-274]. The computer and computer system do not cause the claims to rise to the level of significantly more than the judicial exception as they do not provide an inventive concept.
Further regarding the conventionality of additional elements, the MPEP at 2106.05(b) and 2106.05(d) presents several points relevant to conventional computers and data gathering steps in regard to Step 2A Prong 2 and Step 2B, including:
• A general purpose computer that applies a judicial exception, such as an abstract idea, by use of conventional computer functions, does not qualify as a particular machine (see 2106.05(b)(I)), as in the case of claim 1 and 16, which are interpreted to recite conventional computers.
• Integral use of a machine to achieve performance of a method may integrate the recited judicial exception into a practical application or provide significantly more, in contrast to where the machine is merely an object on which the method operates, which does not integrate the exception into a practical application or provide significantly more (see 2106.05(b)(II). In the instant claims, the recited computer and computer system act only as a tool to perform the steps of data analysis or generating data, and do not integrate the exception into a practical application or provide significantly more.
• Use of a machine that contributes only nominally or insignificantly to the execution of the claimed method (e.g., in a data gathering step or in a field-of-use limitation) would not integrate a judicial exception or provide significantly more (see 2106.05(b)(III). The computers in claim 1 and 16 do not impose meaningful limitations on the claims.
• The courts have recognized “receiving or transmitting data over a network”, “performing repetitive calculations”, and “storing and retrieving information in memory”, as well-understood, routine, and conventional functions when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)(II)). The providing of data in claim 1 is recited in a generic manner.
All limitations of claims 1-4 and 6-20 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, the claims, 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 06/15/2026 have been fully considered but they are not yet persuasive.
Regarding Step 2A Prong One arguments:
Applicant asserts, p. 8-14, that the claims do not recite a judicial exception, as follows:
Regarding abstract ideas of mental processes at Step 2A Prong One:
Applicant asserts the claims do not recite a mental process (p.9-11) as follows:
• "The question is not whether the analytical concept underlying an operation could theoretically be understood by a human, but whether the operation as recited can
practically be performed mentally. Allocating and distributing billions of sequencing reads across genomic regions to generate empirical distributions is plainly not a task a human can practically perform." (p.10, ¶ 1)
• "Empirically deriving probability distributions from tens of thousands of data points is not something a human can practically do mentally." (bridging p.10-11)
• "the claim recites processor-executed operations on massive sequencing datasets, empirical statistical modeling, and threshold-based classification logic that cannot practically be performed in the human mind." (p.11, ¶ 4)
The arguments regarding mental processes at Step 2A Prong One are not persuasive because the claims and the abstract idea within are recited at a level of complexity such that there are embodiments which include performance of the steps mentally or with pen and paper. While the claims do not specifically recite any limitation similar to millions of reads or billions of reads, even if the claims recited as such, the claims would most likely still recite a mental process. This is because considering that the performance of the sequence data analysis mentally, or with paper and pencil, may take considerable time and effort, and although a general-purpose computer can perform the analysis 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. A claim that requires a computer may still recite a mental process [see MPEP 2106.04(a)(2)(III)(C)]. Additionally, limitations for sequencing and data gathering are additional elements, and not considered JEs.
Regarding abstract ideas of mathematical concepts at Step 2A Prong One:
Applicant asserts the claims do not recite a mathematical concept (p.12-14) as follows:
• "...amended claim 1 does not recite any mathematical relationship, formula, or equation in the abstract. The claim does not include any equation, numerical formula, or mathematical expression... does not recite any equation for variability, any formula for standard deviation, or any mathematical relationship in the abstract. It merely requires determining a characteristic of the biological data." (p.13, ¶ 1)
• "(the claim)...describes the use of empirically derived biological data distributions to determine a threshold used in classification...The claim itself, however, does not recite the mathematical form of that distribution or any equation describing it" (p.13, ¶ 2).
• ",,,the claim operates on biological sequencing data and empirically derived thresholds but does not "set forth or describe any mathematical relationships, calculations, formulas, or equations," and therefore does not recite a mathematical concept" (p.14, ¶ 2).
The arguments regarding mathematical concepts at Step 2A Prong One are not persuasive because genetic sequence analysis inherently involves the use of mathematical concepts to represent and statistically process genetic sequence data. In the case of the instant claims, the limitations for determining allele frequency, determining a measure of variability (i.e., standard deviations, and standard deviation thresholds), determining allele frequency threshold, classifying the selected genomic region as being unaffected by copy number variation, classifying the variant of interest as having germline or somatic origin, etc. inherently recite mathematical concepts such as discussed in Specification [76, 220, 260, 293]. While there is no step specifically reciting “calculating’, these steps of "determining" (of allele frequency, a measure of variability, an allele frequency threshold, etc.) are considered mathematical calculations in that the broadest reasonable interpretation of the claim in light of the specification encompasses a mathematical calculation [see MPEP 2106.04(a)(2)(I)(C)]. Regardless, even if the limitations did not recite math, they still recite a mental process and so would recite an abstract idea.
Regarding Step 2A Prong Two arguments:
Applicant asserts, p.14-21, that the claims integrate the alleged judicial exception into a practical application as follows:
• " The technology field is cell-free DNA ("cfDNA")-based genetic diagnostics, and more particularly, next-generation sequencing ("NGS") methods used to classify detected genetic variants as germline or somatic in origin based on cfDNA sequencing data." (p.15, ¶ 4)
• "The particular improvement is the ability to automatically and reliably classify genetic
variants detected in cfDNA as germline or somatic in origin without relying on individual human expert judgment or a consortium of experts (i.e., a "Tumor Board").... no computer implemented process can differentiate germline variants from somatic mutations automatically and that conventional systems instead "rely on the expertise of an individual human expert or a consortium of experts." Published Spec., ¶ 5. The claimed method overcomes this limitation by implementing a stability-gated classification architecture in which copy number variation is first assessed using allele frequency variability, and variant classification is conditioned on the genomic region passing a stability threshold. This approach increas[es] the predictive power of
the method." (bridging p.15-16)
• "When CNV is present, the allele frequency distributions of germline and somatic variants can overlap, rendering simple AF-threshold classification unreliable... The
conventional approach either relied on human expert review through a Tumor Board, or applied indiscriminate statistical thresholds that did not account for the CNV status of the genomic region being analyzed...The claimed method addresses this problem through a stability-gated classification architecture that conditions variant classification on the copy number state of the genomic region." (bridging p.16-17)
• "...the claimed method reflects an improvement to the technology of cfDNA-based variant classification by introducing a stability-gating architecture that conditions classification on measured copy number status, thereby increasing predictive accuracy." (p.18, ¶ 1)
• "...by applying the stability-gating approach of the claims, germline and somatic variant
populations are cleanly separable, whereas without it, the populations overlap and classification becomes unreliable." (p.18, ¶ 3)
• "The specification further validates this approach through a blinded clinical study... cohort A included 11 cases in which the distribution of somatic vs. germline derived variants led to the prediction of a germline T790M mutation being present...All 11 predictions of germline T790M in Cohort A were confirmed by the independent laboratory." (bridging p.18-19)
• "Because the claim conditions variant classification on the prior assessment of copy
number stability, every embodiment employs the same stability-gating mechanism that produces the improvement." (p.19, ¶ 4)
• "The classification output of the claimed method is not an abstract analytical result. It is a determination of whether a detected genetic variant is of germline or somatic origin, a
classification that directly informs clinical decision-making... this classification can impact oncology treatment planning,... and can "benefit families via increased
surveillance/primary prevention." (p.20, ¶ 2)
• "...the claims integrate any alleged judicial exception into a practical
application that delivers a concrete, measurable improvement to the technology of cfDNA-based germline/somatic variant classification." (p.21, ¶ 2)
Applicant's Step 2A Prong Two arguments are acknowledged to be substantive but are not yet entirely persuasive. This is because the showing of improvement needs refinement in order to demonstrate that a practical application is comprised by the claims. Specifically, it would be helpful if claim 1 were amended to include a step of sequencing particular regions using the read budget which results in the provided reads; this might clearly link the real world step of sequencing particular regions to the abstract ideas of sequence data analysis. There is no active step of sequencing in claim 1, although it is implied in the claim 1 recitation of: "providing, based on the read budget, a set of sequence reads of cfDNA molecules, wherein the set of sequence reads are mapped to the selected genomic region of a reference genome" (bold emphasis added).
Applicant states (remarks, p.15, ¶ 4): "The technology field of the improvement is cell-free DNA ('cfDNA')-based genetic diagnostics, and more particularly, next-generation sequencing ('NGS') methods used to classify detected genetic variants as germline or somatic in origin based on cfDNA sequencing data." It is important that independent claim 1 recite a sequencing step, and preferably a next-generation sequencing step, if Applicant is to claim that as the technology field for improvement and show a nexus of integration of the judicial exceptions with a practical application.
Applicant is encouraged to request an interview if it would be helpful.
Regarding Step 2B arguments:
Applicant asserts, p.21-22, that the claim recites elements that amount to significantly more as follows:
• "independent claim 1 does not merely invoke generic computation or conventional sequencing analysis. Instead, the claim recites a specific, non-routine architecture that governs whether and when variant classification may occur. The claim recites allocating a read budget sufficient to generate empirical allele-frequency distributions and variability measures for classification, followed by providing a set of sequence reads of cfDNA molecules based on that budget." (bridging p.21-22)
• "This ordered combination goes beyond conventional thresholding or post hoc analysis... no computer implemented process can differentiate germline variants from somatic mutations automatically..." (p.22, ¶ 2)
• "The claim's inventive concept lies in this gating logic, which changes how classification is executed." (p.22, ¶ 3)
• "...under Step 2B, independent claim 1 recites significantly more than well-understood, routine, and conventional activity. The combination of allocating a read budget, determining variability, inferring copy number stability, and conditionally permitting or suppressing classification provides an inventive concept that improves cfDNA variant analysis and therefore renders the claim patent eligible." (p.23, ¶ 3)
The arguments (regarding significantly more at Step 2B) are not persuasive because the sequence data analysis steps represent abstract ideas, while the identified additional elements of data gathering, sequencing (including sequencing with respect to using read budgets), and a conventional computer are conventional and do not provide significantly more needed to result in an inventive concept, even when considering each claim as a whole.
Double Patenting
Applicant's remarks at p.7, paragraph 2, regarding the request to hold the double patient rejections in abeyance until determination of allowable subject matter, are acknowledged, however, the double patenting rejection is maintained and revised..
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Instant claims 1-4 and 6-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over one or more claims in reference applications: 16/678,060, 19/170,982, and 19/440,954 in view of Illumina, ((2014) Considerations for Designing a Successful TruSeq® Targeted RNA Expression Experiment [Online]; 2 pages; accessed: 02/27/2026. Available at: www.illumina.com/documents/products/technotes/technote_truseq_targ_rna_design.pdf ).
Although the reference claims are not identical to the instant claims, in a BRI they also are not patentably distinct from the instant claims because each reference application recites method and/or system claims for classifying or identifying a genetic variant or locus as somatic or germline in cell-free DNA. Although the instant application recites limitations using a read budget, this narrowing versus the reference claims is now interpreted as obvious, such that the instant invention would have been prima facie obvious in view of the cited art.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Meredith A Vassell whose telephone number is (571)272-1771. The examiner can normally be reached 8:30 - 4:30.
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/M.A.V./Examiner, Art Unit 1687
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
Prosecution Insights