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 . Applicants’ amendment filed 9/8/2026 is acknowledged. Claims 1, 3, 15 have been amended. Claims 1-20 are pending. All of the amendments and arguments have been thoroughly reviewed and considered.
Any rejection not reiterated in this action has been withdrawn as being obviated by the amendment of the claims.
Applicant's submission of an information disclosure statement under 37 CFR 1.97(c) with the timing fee set forth in 37 CFR 1.17(p) on 9/8/2026 prompted the new ground(s) of rejection presented in this Office action.
Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 609.04(b).
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Previous Rejections
The double patenting rejection is withdrawn in view of Applicant’s submission of a proper terminal disclaimer in compliance with 37 CFR 1.32 1.321(b).
3. The prior art rejection under 35 USC 103 as being unpatentable over Diehn in view of Sims et al directed to claims 1-20 is withdrawn in view of the new grounds of rejections.
Information Disclosure Statement
4. The information disclosure statements (IDS) submitted on 9/8/2026 are acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
New Ground(s) of Rejection
The new ground of rejections were necessitated by Applicant’s submission of IDS under 37 CFR 1.97(c).
Claim Interpretation
5. In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, claim 12 recites the term “read budget," which is not expressly defined in the application's disclosure.
The specification provides the following relevant description regarding "read budget" in para. [0241]:
"The amount of sequencing data that can be obtained from a sample is finite, and constrained by such factors as the quality of nucleic acid templates, number of target sequences, scarcity of specific sequences, limitations in sequencing techniques, and practical considerations such as time and expense. Thus, a “read budget” is a way to conceptualize the amount of genetic information that can be extracted from a sample. A per-sample read budget can be selected that identifies the total number of base reads to be allocated to a test sample comprising a predetermined amount of DNA in a sequencing experiment. The read budget can be based on total reads produced, e.g., including redundant reads produced through amplification. Alternatively, it can be based on number of unique molecules detected in the sample. In certain embodiments read budget can reflect the amount of double-stranded support for a call at a locus. That is, the percentage of loci for which reads from both strands of a DNA molecule are detected." [emphasis added]
Thus, in light of the specification and under BRI, the term "read budget" is interpreted to encompass any amount of information related to sequencing such as number of reads allocated in a sequencing run, sequencing coverage, and/or sequencing depth.
Claim Rejections - 35 USC § 103
6. 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.
7. 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.
8. 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.
9. Claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Diehn (WO2014151117A1) in view of Stamatoyannopoulos (WO 2014039729, March 2014, citation #10 made of record on IDS filed 9/8/2026) and further in view of Sims et al (Nature Reviews, 15:121-132, 02-2014).
Regarding claims 1-20, Diehn teaches methods for analyzing cell-free DNA (cf-DNA) using Cancer Personalized Profiling by deep Sequencing (CAPP-Seq), for detecting the presence or absence of genetic variants associated with cancer, wherein said genetic variants comprise SNV, copy number variations, insertions-deletions (e.g., Abstract; entire documents especially e.g., [0024], [0057], [00115], [00241] – [00242], [00409]).
Diehn teaches a method comprising:
(a) obtaining a plurality of polynucleotides which are derived from cell-free deoxyribonucleic acid (cfDNA) molecules of the subject (Figure 1; Figure 6; [0720] “hybrid selection of cfDNA corresponding to regions of recurrent mutation for diagnosis and monitoring of cancer in an individual patient”; Figure 22);
(b) enriching a plurality of the polynucleotides for a sequencing panel of genomic regions to generate an enriched set of polynucleotides (Figure 1; [00851] enriching for tumor-specific markers in a patient using a custom, personalized selector library comprising a set of biotinylated oligonucleotides for “selective hybrid affinity capture of corresponding circulating tumor DNA (ctDNA) molecules,” thereby “allowing the tracking and quantitation of those mutations originally discovered in the primary tumor within the corresponding cfDNA.”),
wherein the enriching comprises
selecting the sequencing panel of genomic regions using information derived from cancer tumor biopsies (Figure 1; [00851] “tumor(s) from a patient known to have cancer are genotyped by profiling the tumor genome, exome, or targeted region expected to be enriched for somatic aberrations…The resulting lesions are then catalogued and used to build a custom, personalized selector comprising a set of biotinylated oligonucleotides for selective hybrid affinity capture of corresponding circulating tumor DNA (ctDNA) molecules” for lung adenocarcinoma; [00590]; [00428]; [00485]; [00590]; [00437-00443]; [00767]), and
wherein the enriching is performed using capture probes specific for the genomic regions (Figure 1; [00851]; [00590]; [00428]; [00485]; [00590]; [00437-00441]),
wherein the genomic regions comprise single-nucleotide variants (SNVs) ([00428]; [00437-00441]),
(c) sequencing a plurality of the enriched set of polynucleotides at a sequence read depth of at least 30,000 sequence reads per base to generate sequence reads ([00661])
(d) computer processing a plurality of the sequence reads at least in part by aligning a plurality of the sequence reads to a reference genome to generate aligned sequence reads ([00790] Mapping and Quality Control of NGS Data. Paired-end reads were mapped to the hgl9 reference genome with BWA 0.6.2; [00414]; [00426]; [00836]); and
(e) computer processing a plurality of the aligned sequence reads to detect a variant corresponding to at least one of the single-nucleotide variants ([00851] The personalized selector would then be applied for capture of the fragments of interest, sequenced and analyzed in the same manner as the 'off-the-shelf' CAPP-Seq workflow, allowing the tracking and quantitation of those mutations originally discovered in the primary tumor within the corresponding cfDNA; [00590] producing a selector set comprising one or more genomic regions comprising the one or more mutations specific to the sequencing information of the tumor sample, the one or more mutations comprise SNV; [0031], [0057], [00437-00441]; [00655]; [00659]), thereby determining the molecular residual disease in the subject wherein the determining further comprise assembling a database of cfDNA background allele frequencies by binominal distribution and further selecting those with an average background frequency of a predetermined threshold and distinguishing tumor -derived SNVs from remaining background noise by outlier analysis ([0035]).
Deihn et al teach determining quantities of ctDNA comprising performing molecular barcoding of the ctDNA, wherein an adaptor may comprise a plurality of oligonucleotides. The adaptor may comprise of the molecular barcode, primer sequence, linker or a combination thereof ([00119]. [0152] – [0154]). Deihn teaches that the two or more samples may be the same type of sample or two different types of samples and may be obtained at the same time point or obtained at two or more time points ([0139]).
Diehn et al further teach the CAPP-seq identifies a mutation in a clinically actionable target from a ctDNA sample, wherein the actionable targets may include, ALK, ROS1, RET, EGFR, KRAS [0017], p53, BRAF, PIK3CA, ([0072], [0086], [0115], [00509]) which may be associated cancer.
Diehn additional teach that is some embodiments the individual may not previously diagnosed with cancer or the individual may be undergoing treatment for cancer ([0028]). Diehn teaches comparison of the fractional abundance in a given cfDNA sample against its fractional abundance in a cohort [0032] (see also Figure 1; see also Figure 4). Diehn teaches that cancers embodied by the method of Diehn encompass lung cancer, breast cancer, colorectal cancer, prostate cancer, ovarian cancer, esophageal cancer, breast cancer, lymphoma or leukemia ([00801], [00753]). Diehn teaches wherein the pre and post treatment may encompass chemotherapeutic drugs, radiation therapy, surgical removal and/or cytoreductive therapy ([0735], [0742] – [0743], [00763]).
Diehn’s CAPP-Seq method involves using a panel of selectors comprising oligonucleotide probes for selective hybrid affinity capture that target regions of interest for enrichment ([0851]).
Deihn does not expressly mention during the polynucleotide enriching steps, wherein the hotspot regions are sequenced a deeper average read depth relative to the backbone region.
However, in a similar embodiment to that of Deihn, Stamatoyannopoulos teaches methods and compositions for analyzing polynucleotides for the intended purpose of diagnosing, detecting or predicting the risk of a disease, disorder or trait [0007] wherein the method comprises steps of enriching a plurality of polynucleotides for a sequencing. Stamatoyannopoulos teaches the following:
[00177] Enrichment of the samples may be ascertained by trial DNA sequencing. In this step, sample sequences are obtained and their enrichment may be calculated. The amount of sequence obtained is instrument dependent, but preferably, for the human genome, at least 1 or 5 million sequence reads that map uniquely to the genome may be used to calculate the sample enrichment. Smaller numbers can also be used, and correspondingly lower numbers may be required for smaller genomes. The enrichment can be calculated by identifying statistically significant sequence tag clusters, and then computing the proportion of all uniquely mapping tags that fall within clusters. In a preferred embodiment, identification of significant clusters may be performed using a scan statistic algorithm to delineate DNasel hotspot. The percent of tags in hotspots (PTIH) may be calculated.
[00178] Suitably enriched samples may be subjected to deep sequencing. The number of reads required varies by organism, and may berelated to the number of DNasel hypersensitive sites within the genome, or, in the case of organisms that lack DNasel hypersensitive sites such as bacteria, the total size of the genome. For the human genome, more than 200 million uniquely mapping reads are preferably required, and complete footprinting of all DHSs may not be obtained until many more hundreds of millions or even billions of reads are obtained.
[00333] Next-generation sequencing may be used to determine the sequence of a set of nucleotides within a polynucleotide. In some cases, next-generation sequencing may include, massively parallel sequencing, deep sequencing, ultra-deep sequencing, high throughput sequencing, ultra-high throughput sequencing, single-molecule real-time sequencing, ion semiconductor sequencing, pyrosequencing, sequencing by synthesis, sequencing by ligation and chain terminator sequencing. The polynucleotide may be subject to at least one the methods described herein before sequencing. In some cases, the polynucleotide may be nucleic acid (e.g., genomic DNA).
[00382] In some cases, nucleic acid (e.g., genomic regions (e.g., hundreds to thousands of base- pairs), whose clustered scores are statistically higher than expected can be labeled as hotspot regions. Hotspot regions can be used in further analysis. In some cases, a false discovery rate (FDR) can be applied to determine relevant hotspot. In some cases, the FDR can be at the 0.5% level. In some cases, the location of the hotspot at an FDR can be expanded (e.g., by 100 base- pairs) in the 3' direction of the forward strand and scanned for footprints along the nucleotide sequence.
[00539] Highly enriched DNasel cleavage libraries from 41 diverse cell types in which 53-81% of DNasel cleavage sites localized to DNasel-hypersensitive regions were selected representing nearly tenfold higher signal-to-noise ratio than pervious results from yeast, and two- to fivefold greater enrichment than achieved using end-capture of single DNasel cleavages. Deep sequencing of these libraries was performed, and 14.9 billion Illumina sequence reads obtained, 11.2 billion of which mapped to unique locations in the human genome. An average sequencing depth of -273 million DNasel cleavages per cell type that enabled extensive and accurate discrimination of DNasel footprints was achieved.
[00779] DNasel hypersensitivity mapping was performed on a total of 125 cell types (Table 5). Data sets were sequenced to an average depth of 30 million uniquely mapping sequence tags (27-35 bp) and (20 bp) per replicate. For uniformity of analysis, some cell-type data sets that exceeded 40M tag depth were randomly subsampled to a depth of 30 million tags. Sequence reads were mapped using the Bowtie aligner, allowing a maximum of two mismatches. Only reads mapping uniquely to the genome were used in the analyses. Mappings were to male or female versions of hgl9/GRCh37, depending on cell type, with random regions omitted. Data were analyzed jointly using a single algorithm to localize DNasel hypersensitive sites.
Thus, Stamatoyannopoulos provides sufficient evidence of analyzing and sequencing hotspot regions at a deeper average read depth relative to a backbone region.
Still further, the prior art recognizes the inadequacies of sequencing method and suitable solutions to the problem as suggested by Sims. Sims teaches that high quality assemblies are now often produced using hybrid approaches in which the advantages of high-depth, short read sequencing are complemented with those of lower-depth but longer-read sequencing. Sim teaches one approach to sequencing repeat -rich genomes is to barcode and sequence to an average of 20X depth all reads that are derived from each of many collections of hundreds or thousands of short DNA fragments (page 122, col. 2). Sims teaches that increasing sequence depth can both improve variant detection and reduce the false discovery rate for variant calling (page 123, section “SNV and Indel Detection”).
In view of the foregoing, it would have been obvious to one of ordinary skill in the art at the time of the effective filing date of the claimed invention to have been motivated to sequence hotspot regions at a deeper average read depth relative to the backbone region with a reasonable expectation of success using enriching techniques as taught by Deihn and Stamatoyannopoulos with a reasonable expectation of success as evidence by Stamatoyannopoulos. The ordinary artisan would have been motivated to do so for the advantage of improving variant detection and reduce false discovery rate for variant calling as suggested by Sims in order to more accuracy detect variants associated with cancers as taught by Deihn and Stamatoyannopoulos as suggested by Stamatoyannopoulos.
Conclusion
10. No claims are allowed. Applicant's submission of an information disclosure statement under 37 CFR 1.97(c) with the timing fee set forth in 37 CFR 1.17(p) on 9/8/2026 prompted the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 609.04(b). 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.
11. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681
