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 .
Office Action: Notice
Any objection or rejection of record in the previous Office Action, mailed 4/23/2025,
which is not addressed in this action has been withdrawn in light of Applicants' amendments
and/or arguments. This action is FINAL.
Election/Restriction
Applicant’s election without traverse of Group 1 claims or claims 2-7 in the reply filed on 3/25/2025 is acknowledged. Claims 8-14, 22, 35-36, and 41-42 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected Groups 2 and 3, there being no allowable generic or linking claim.
Claim Status
Applicant amended claims 2-3, 5-7, 43-45, 47, 49-52, 57-58 (10/22/2025). Claims 1, 4, 8-42, 48, 53, 55, and 59 are canceled (10/22/2025). No new matter was added. Thus, claims 2-3, 5-7, 43-47, 49-52, 54, 56-58 and 60-61 are under examination.
Priority
Claims 2-3, 5-7, 43-47, 49-52, 54, 56-58 and 60-61 receive a priority date of 11/21/2018, the filing date of US Provisional No. 62/770, 181.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
The Information Disclosure Statements from 4/21/2025, 10/23/2025 and 10/30/2025 are considered.
Objections Withdrawn
Specification:
The objections to the specification due to the use of a trademark or tradenames are withdrawn in view of Applicant’s amendments.
Rejections Withdrawn
Claim Rejections - 35 USC § 112(b)
The rejections of claims 2-7 and 43-61 under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, 2nd paragraph, are withdrawn in view of Applicant’s amendments of claims 2, 3, and 47, as well as cancellation of claims 4, 48, 53, 55 and 59.
Claim Rejections – 35 USC § 101
The rejection of claims 2-7 and 43-61 under 35 USC 101, is withdrawn in view of Applicant’s amendments of independent claim 2, as well as clarification of invention in Applicant’s amendments. Specifically, amended independent claim 2 is not directed to a judicial exception, but to a specific, practical laboratory method for preparing and analyzing microbial cell-free nucleic acids. The instant claim recites concrete sample-preparation and sequencing steps, such as adapter ligation to non-extracted nucleic acids, primer extension, and sequencing, that are physical, technical operations and cannot be performed in the human mind. Any analysis of fragment length characteristics is tied to these upstream laboratory manipulations and reflects a particular technological implementation, not an abstract idea or mere observation of a natural phenomenon. Consistent with Illumina v. Ariosa, the claimed steps create an improved, human-engineered end product that mitigates biases introduced by conventional extraction workflows. Accordingly, the claims are eligible under Step 2A, Prong One, and do not require further analysis under Step 2B.
Claim Rejections – 35 USC § 102
The rejections of claims 2-7, 43-51 and 53-59 under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Venn (WO 2018/085862 A2; published 5/11/2018) are withdrawn in view of Applicant’s amendments of claims 2-3, 5-7, 43-45, 47, 49-52, 57-58 and cancellation of claims 1, 4, 8-42, 48, 53, 55, and 59.
Claim Rejections – 35 USC § 103
The rejections of claims 52 and 60-61 under 35 U.S.C. 103 as being unpatentable over Venn (WO 2018/085862 A2; published 5/11/2018), as applied to claims 2-7, 43-51 and 53-59, in view of Ricci et al. (“Diagnosis of Helicobacter pylori: Invasive and non-invasive tests”, Best Practice & Research Clinical Gastroenterology, published 4/2007) are withdrawn in view of Applicant’s amendments of claims 2-3, 5-7, 43-45, 47, 49-52, 57-58 and cancellation of claims 1, 4, 8-42, 48, 53, 55, and 59.
New Rejections
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
Claim(s) 2-3, 5-7, 43-47, 49-52, 54, 56-58 and 60-61 are rejected under 35 U.S.C. 103 as being unpatentable over Venn (WO 2018/085862 A2; published 5/11/2018), in view of Ricci et al. (“Diagnosis of Helicobacter pylori: Invasive and non-invasive tests”, Best Practice & Research Clinical Gastroenterology, published 4/2007) and in further view of Refseth et al. (“Hybridization capture of microsatellites directly from genomic DNA”, Electrophoresis, published 1997).
Regarding claim 2, Venn teaches preparing a sequencing or nucleic acid library (Paragraph 111, lines 1-5) preparation method via the addition of unique molecular identifiers (UMI) to the nucleic acid molecules (i.e., DNA molecules) through adapter ligation (Paragraph 111, lines 1-10). Further, Venn teaches that the adapters are ligated to the 5' and 3' ends of the fragments and DNA fragments that are attached to the surface of flow cell channels are extended and bridge amplified for sequencing (Paragraph 129, lines 1-5) of cell free nucleic acid (i.e., cfDNA) extracted from a sample contained in several bodily fluids (i.e., plasma, stool, urine) (Paragraph 138, lines 1-5).
Specifically, Venn teaches that cfDNA fragment length data across all SNVs obtained from subjects a high rate of exposure showcased that the lower-most distribution or first peak was obtained from a subject with breast cancer, and shows that the fragment length distribution is shifted to the left, away from the vertical dashed line (which indicates the location where the peak of the fragment length distribution is anticipated to occur in healthy control samples) while the upper-most distribution or second peak was obtained from a subject who self-reported as healthy, but whose analysis revealed a high level of exposure causing the fragment length distribution for this subject to shift to the left, which indicates shorter cfDNA fragment lengths, and possible presence of cancer (Figure 31; Paragraph 200, lines 1-10).
Regarding claims 3 and 5, Venn teaches that examples of relevant features incorporated into the previously described method includes; a deletion, a somatic copy number alteration (SCNA), a translocation, a genomic methylation status, a chromatin state, a sequencing depth of coverage, an early versus late replicating region, a sense versus antisense strand, an inter mutation distance, a variant allele frequency, a fragment start/stop, a fragment length, and a gene expression status (Figure 3; Paragraph 91, lines 5-10). Further, Venn teaches that the specified fragment length characteristics or associated features include, absolute SNV or fragment count ratio (Figure 34; Paragraph 206, lines 1-5), differences in the fragment length distribution profiles (Figure 32; Paragraph 201, lines 1-5), peak of the fragment length distribution (i.e., shape) (Figure 31; Paragraph 200, lines 1-5), and height or shape of each base motif relation amongst mutations (Figure 13; Paragraph 178, lines 1-5).
Venn also teaches that upon investigating liver cancer in biological samples, each sample showed a length shift to shorter fragments, increasing the confidence that the observed SNVs were due to a mutational process, and not derived from a sequencing artifact, explaining that fragment length profiling of cfDNA samples is known in the art (Paragraph 199, lines 1-5).
Venn further teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile includes in vitro amplification of specific DNA sequences by the simultaneous primer extension of complementary strands of DNA via targeted nucleic acids flanked by primer or adapter binding sites, comprising one or more repetitions of the following steps: (i) denaturing the target nucleic acid, (ii) annealing primers or adapters to binding sites, and (iii) extending the adapters by a nucleic acid polymerase in the presence of nucleoside triphosphate (Paragraph 56, lines 15-20).
Regarding claims 6-7, Venn teaches that via fragment length profiling, as previously described, individual subsets or mutational types (i.e., T>C mutations only) can be analyzed separately or distinguished from all of the SNVs through differences in the fragment length distribution profiles showcasing a more pronounced response and a shift toward shorter fragment lengths from other samples (Figure 32). Venn further teaches that these data demonstrate that fragment length profiling can be used in conjunction with the subject methods to provide further confidence in the detection of active mutational processes (Paragraph 201, lines 1-5).
Specifically, Venn teaches that generating length profiles or mutational profiles considers various mutational signatures, including up to 30 underlying mutational or length signatures (Figures 10-11; Paragraph 172, lines 1-5).
Regarding claim 43, Venn teaches that examples of relevant features incorporated into the previously described method includes; a deletion, a somatic copy number alteration (SCNA), a translocation, a genomic methylation status, a chromatin state, a sequencing depth of coverage, an early versus late replicating region, a sense versus antisense strand, an inter mutation distance, a variant allele frequency, a fragment start/stop, a fragment length, and a gene expression status (Figure 3; Paragraph 91, lines 5-10). Further, Venn teaches that the specified fragment length characteristics or associated features include, absolute SNV or fragment count ratio (Figure 34; Paragraph 206, lines 1-5), differences in the fragment length distribution profiles (Figure 32; Paragraph 201, lines 1-5), peak of the fragment length distribution (i.e., shape) (Figure 31; Paragraph 200, lines 1-5), and height or shape of each base motif relation amongst mutations (Figure 13; Paragraph 178, lines 1-5).
Regarding claims 44-45, Venn teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile includes acquiring sequencing data from the enriched DNA sequences, including next generation sequencing (NGS) techniques (i.e., high-throughput sequencing assay) and synthesis technology (Paragraph 113, lines 1-5).
Regarding claim 46, Venn teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile can be used to analyze mucous, blood, plasma, serum, serum derivatives, synovial fluid, lymphatic fluid, bile, phlegm, saliva, sweat, tears, sputum, amniotic fluid, menstrual fluid, vaginal fluid, semen, urine, cerebrospinal fluid (CSF), such as lumbar or ventricular CSF, gastric fluid, a liquid sample comprising one or more material(s) derived from a nasal, throat, or buccal swab, a liquid sample comprising one or more materials derived from a lavage procedure, such as a peritoneal, gastric, thoracic, or ductal lavage procedure samples (Paragraph 133, lines 5-10).
Regarding claim 47, Venn teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile includes short base nuclear-derived DNA fragments present in several bodily fluids (i.e., plasma, stool, urine) (Paragraph 138, lines 1-5). Further, Venn teaches that fragment lengths can include regions preferably from about 2 to about 40 bp (Paragraph 4, lines 5-10), although inter-mutational or longer read distances <100 bp (i.e., >64 bp) in certain sequence contexts (Figure 12C; Paragraph 25, lines 1-3).
Regarding claims 49-50, Venn teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile is comprised of approximately 1,000 copies of single-stranded DNA molecules via denaturation of the double-stranded fragments (Paragraph 129, lines 1-10). Venn further teaches that the DNA molecules can be derived from human or non-human mammals (Paragraph 133, lines 1-5) and can include viral DNA/RNA (Paragraph 136, lines 1-2).
Regarding claim 51, Venn teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile can further be used as an assessment of the patient’s cancer status, including to monitor the effectiveness of a therapeutic regimen or other cancer treatment (Paragraph 108, lines 1-5).
Regarding claims 52 and 60-61, Venn teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile can further be used as an assessment of the patient’s cancer status, including to monitor the effectiveness of a therapeutic regimen or other cancer treatment (Paragraph 108, lines 1-5). Venn further teaches that the DNA molecules can be derived from human or non-human mammals (Paragraph 133, lines 1-5) and can include viral DNA/RNA (Paragraph 136, lines 1-2).
Regarding claim 54, Venn teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile is comprised of approximately 1,000 copies of single-stranded DNA molecules via denaturation of the double-stranded fragments (Paragraph 129, lines 1-10).
Regarding claims 56-58, Venn teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile comprises 10,000 or more mutational profiles or molecules from cancer patients (Figure 3; Paragraph 90, lines 5-10). Specifically, Venn teaches that the previously mentioned mutational profiles are generated from strength and duration of exposure to each mutational process (i.e., environmental factors and DNA repair processes) results in a unique profile of somatic mutations in a subject (i.e., a cancer patient) (Paragraph 11, lines 1-5) and that each can then be identified and assigned unique signatures that can be used to distinguish between the contribution from true somatic variants and artifactual variants arising from the technical processes in the assay (Paragraph 8, lines 1-5). Further, Venn teaches that based on these unique contributions, bon-negative linear regressions can be used to determine, or infer, cancer status or a diversity loss value from the patient's unique mutational profile (Paragraph 86, lines 1-5).
Venn also teaches that the previously described nucleic acid or cfDNA library for generating a fragment length profile incorporates sequence reads from a test sample and aligning it with a reference genome or reference fragment length for identification of somatic mutations (Figure 1; Paragraph 80, lines 1-5).
Venn does not teach or suggest that the fragment length profile library generation is comprised of microbial cell-free nucleic acid fragments from Heliobacter pylori generated via adapter attachment to a non-extracted nucleic acid or that later assessments of the methodology can be used to assess treatment via antibiotics.
Ricci teaches that Helicobacter pylori infection includes non-invasive tests, such as the urea breath test and the stool antigen test, that detect active infection: these are called ‘active tests; however, serology, urine, near-patient tests are markers of exposure to H. pylori, but do not indicate if active infection is ongoing; these are ‘passive tests’ (Abstract). Further, Ricci teaches that choice of test should therefore be based on: (1) the prevalence of the infection in the population; (2) the symptoms, such as the presence of alarm symptoms; (3) the likelihood ratio for a positive and negative test; (4) the costs; and (5) the availability of the tests in the different settings (Introduction: Paragraphs 6-7). Ricci also teaches that two molecular tests or invasive tests are available include in-situ hybridization and PCR to detect specific virulence markers (Molecular Tests: Paragraph 1). Additionally, Ricci teaches that when testing for antibiotic sensitivity on a routine basis, the two most used invasive tests are disc diffusion and the E-test, with the agar dilution test as the reference (Culture: Paragraphs 2-3).
Refseth teaches a rapid approach for isolation of microsatellites and other tandem repeated sequences in described where the method is based on hybridization capture of repetitive elements from digested genomic DNA using biotinylated oligonucleotide probes in solution and subsequent attachment to magnetic beads coated with streptavidin, and captured fragments are amplified by adapter polymerase chain reaction (PCR) and the PCR products enriched for microsatellites cloned directly into a T-vector for sequencing (Abstract). Further, Refseth teaches that the microsatellites are captured directly from genomic DNA by hybridization to probes in solution, subsequent ex-traction with magnetic beads coated with streptavidin, and amplification by PCR followed by cloning (Introduction: Paragraph 3). Refseth also teaches that target sequences are captured by incubating the DNA mixture with streptavidin-coated magnetic beads and fragments not attached to the beads are subsequently removed by repealed washing of the beads (Figure 1).
It would have been obvious to one skilled in the art before the effective filing date of the claimed invention to modify the method of Venn to include administering antibiotic treatment when the human subject is infected with microbes, specifically analyze microbial cell-free DNA, and particularly focus on Helicobacter pylori, as taught by Ricci. One would have been motivated to make these modifications because Venn already suggests monitoring treatment effectiveness and using various DNA sources from biological fluids where microbial DNA would be present, while Ricci explicitly establishes that antibiotic treatment is a standard therapeutic approach for H. pylori infections and that H. pylori is a clinically relevant pathogen requiring detection and treatment. Further, one would have a reasonable expectation of success in making these modifications because Venn already demonstrates successful adapter ligation to nucleic acids from biological fluids and generation of fragment length profiles, and microbial DNA, including that from H. pylori, is known to be present in biological fluids and detected via PCR-based methods, as taught by Ricci. Additionally, the combination merely applies known molecular techniques (adapter ligation and fragment profiling from Venn) to a specific microbial target (H. pylori from Ricci) using standard antibiotic treatments that were well-established in the field. The combination would yield the predictable result of applying Venn’s fragment length profile analysis to detect, monitor and treat H. pylori infection through cell-free DNA analysis.
Further, it would have been obvious to one of ordinary skill in the art at the time of the invention to modify the method of Venn to attach adapters to nucleic acids prior to a conventional extraction step by incorporating the direct capture and adapter ligation techniques taught by Refseth, which teaches isolating and ligating adapters to target nucleic acids directly from sample-derived material without first performing a standalone extraction or library extractions step. A skilled artisan would have been motivated to make this modification in order to reduce sample loss, simplify workflow, and improve recovery of short of low-abundance nucleic acid fragments, such as cell-free or microbial DNA, consistent with Venn’s goal of efficient sequencing-based analysis from biological fluids. Further, a reasonable expectation of success would have existed because Refseth demonstrates that adapter ligation and PCR amplification can be successfully performed on captured nucleic acids using routine, well-established molecular biology techniques, and Venn already teaches that once adapters are attached, fragment profiling and sequencing proceed predictably.
Accordingly, the combination of Venn, Ricci and Refseth represents a predictable use of known techniques to achieve an expected result.
Applicant’s Response: The Applicant argues that Venn, even when in view of Ricci, does not disclose or suggest key limitations of amended claim 2, namely attaching adapters to nucleic acids that are not extracted from the biological fluid sample and the use of microbial cell-free nucleic acid fragments, such that Venn does not anticipate the claims under 35 USC 102 or in combination with Ricci for 35 USC 103. Therefore, the Applicant argues that Ricci does not remedy these deficiencies to modify Venn to perform adapter ligation on non-extracted nucleic acids or to analyze microbial cell-free nucleic acids.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully and fully considered and are found to be partially persuasive, as discussed below.
Although the prior 35 USC 102 rejection anticipated by Venn was withdrawn, the new 35 USC 103 rejection of obviousness by Venn in view of Ricci and Refseth relies on broadest reasonable interpretation (BRI) of the amended instant claims (MPEP 2111).
Under BRI, the limitation that the nucleic acid is not extracted from the biological fluid sample before attaching the adapter, does not preclude all handling or enrichment of nucleic acids, but reasonably excludes only a discrete conventional extraction and purification step. As discussed above, Refseth teaches direct capture and adapter ligation of nucleic acids from sample-derived material without prior standalone extraction or library construction, thereby curing the deficiency identified by the Applicant with respect to Venn. Further, Venn teaches the sequencing, adapter ligation, and fragment analysis framework, while Ricci teaches the routine detection and monitoring of Helicobacter pylori from biological samples and the clinical motivation to analyze microbial nucleic acids in such samples.
One of ordinary skill in the art would have been motivated to combine these teachings to streamline workflows, reduce sample loss, and improve detection sensitivity, and would have had a reasonable expectation of success because the references employ well-established, predictable molecular biology techniques (MPEP 2143).
Accordingly, the Applicant’s arguments only partially overcome the rejection. The combination of Venn, Ricci and Refseth teaches each and every limitation of claims 2-3, 5-7, 43-47, 49-52, 54, 56-58 and 60-61.
Conclusions
No claim is 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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIZABETH ROSE LAFAVE whose telephone number is (703)756-4747. The examiner can normally be reached Compressed Bi-Week: M-F 7:30-4:30.
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/ELIZABETH ROSE LAFAVE/ Examiner, Art Unit 1684
/HEATHER CALAMITA/ Supervisory Patent Examiner, Art Unit 1684