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 .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on March 25, 2026 was filed after the mailing date of the Non-final Rejection on September 26, 2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of claims / Response to Amendment
This office action is in response to an amendment filed on March 25, 2026.
Claims 1-20 were previously pending. Applicant amended claims 1 and 10; cancelled claims 8-9 and 11.
Claims 1-7, 10 and 12-20 are currently pending and under consideration.
All of the amendment and arguments have been thoroughly reviewed and considered. All of the previously presented rejections have been withdrawn as being obviated by the amendment of the claims, which added new limitations to the claims, that were not considered in the previous rejections.
The previously set forth prior art rejections have been withdrawn in view of the recent claim amendment filed on March 25, 2026, which added new limitations to the claims (i.e., the newly amended method in claim 1 now recites "wherein the sequencing panel comprises a plurality of subpanels, including a subpanel for identifying tissue of origin which targets markers for a tissue of origin which are tissue-specific epigenetic markers").
Thus, the scope of the claims has been changed in a manner that were not considered in the previous rejections.
Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
This office action contains new grounds for rejection necessitated by amendment.
Priority -- Updated
For the instant claims 1-7, 10 and 12-20 in this U.S. Application, the applicant claims priority of US provisional Application NOs. 62/322,783; 62/322,786; 62/322,773; 62/322,784 ; and 62/322,775, all of which have a filling date on 04/14/2016.
Claim Interpretation
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 5 recites "wherein the determining the consensus sequence is performed on a base by base basis." The application's disclosure does not expressly define the phrase "base by base basis."
Therefore, under BRI, this phrase is interpreted to encompass any approach with single-nucleotide base resolution.
For the purpose of applying prior art, claim 16 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 1, such as number of reads allocated in a sequencing run, sequencing coverage, and sequencing depth.
For the purpose of applying prior art, claim 16 recites "wherein the plurality of cfDNA molecules comprises no more than a pre-determined amount of DNA." The specification does not expressly define the term "pre-determined amount of DNA."
Therefore, under BRI, an amount that is "no more than a pre-determined amount of DNA" is interpreted to encompass any amount, as a pre-determined amount can be any arbitrarily chosen value for any reason, and there will always be an amount less than any specified value.
New Grounds of 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.
Claims 1-7, 10 and 12-20 are rejected under 35 U.S.C. 103 as being unpatentable over Diehn (WO2014151117A1 - Identification and use of circulating nucleic acid tumor markers; Published on 2014-09-25; cited as Foreign Patent Document #10 in IDS filed on 05/23/2024), in view of
Berlin (Berlin et al., US20050221314A1 - Method and device for determination of tissue specificity of free floating dna in bodily fluids; published 2005-10-06) , as evidenced by
Bennett (Bennett et al. Library construction for ancient genomics: single strand or double strand? Biotechniques. 2014 Jun 1;56(6):289-90, 292-6, 298, passim. doi: 10.2144/000114176. PMID: 24924389).
A) Diehn teaches methods for analyzing cell-free DNA (cf-DNA) using Cancer Personalized Profiling by deep Sequencing (CAPP-Seq), for monitoring residual disease (e.g., Abstract; [0016]; [0029]).
Regarding claim 1, Diehn teaches a method comprising:
(a) obtaining a plurality of polynucleotides which are or 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”; [00590]; [00428]; [00485]; [00590]; [00437-00441]; [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 five thousand sequence reads per base to generate sequence reads ([00851] lines 11-14; [00430]; [00454] references Figure 12, which shows sequencing depth higher than 5000 reads per base; [00771] mean sequencing depth of ~5000X);
(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; [00437-00441]; [00655]; [00659]), thereby determining the molecular residual disease in the subject.
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]). While Diehn does not explicitly teach a subpanel of selectors for identifying tissue of origin which targets tissue-specific epigenetic markers, this feature is obvious in view of Berlin.
Berlin teaches methods for determining cell-free DNA tissue of origin based on the DNA’s methylation pattern (Abstract).
Berlin teaches the usefulness of cell free DNA as a cancer biomarker is limited because “detecting the level of free floating DNA does not on its own serve as a useful diagnostic method as the information gained is too unspecific to be of any use.” ([0090]).
Berlin then suggests in determining the origin of the cell-free DNA, “the diagnostic value of such an assay increases dramatically.” ([0091]) And explains that:
“This is because such an assay elucidates the location of said DNA and the possible cause. That way an early screen that does reveal the organ, tissue or cell type affected by a cell proliferative disease is highly advantageous. The information gained will aid the further diagnostic procedure. It tells the practitioner quite precisely what the next steps towards a more differentiated diagnosis would need to be and gives guidance as to which clinical specialist to refer the patient to.” ([0091])
Berlin discloses its solution to determine the tissue origin of cell-free DNA is based on the characteristic methylation patterns of certain genes that can be positively correlated with specific organs, tissues and cell types:
“The present invention provides a method for the analysis of circulating, free floating nucleic acids in bodily fluids. It discloses a means on how to predict which organ, tissue or cell type has developed a medical condition, by employing means of distinguishing between DNA originating from different healthy or different diseased tissues, organs or cell types of the human body. Characteristic methylation patterns of certain genes can be positively correlated with specific organs, tissues and cell types. Preferably the identification of the free floating DNA's origin, or in other words the determination of the organic source of a significant part of those circulating nucleic acids in said bodily fluid is done by an assay that detects methylation at specific CpG sites. It is especially preferred, to detect methylation by nucleic acid based methods, such as hybridization, sequencing and PCR, or even more preferably, by employing real-time PCR methods. The result of said analysis give further guidance to a practitioner on how to tailor a more differentiated diagnostic strategy. “([0093])
Berlin teaches probes designed to specifically only hybridize with the amplified version of bisulfite treated nucleic acid that has a methylation pattern characteristic for a specific organ ([0228] lines 9-12), for identification of the organ from which the cell-free DNA is from ([0229])).
In view of the above, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the CAPP-Seq methods of Diehn, to further include a subpanel of selectors comprising oligonucleotide probes that target tissue-specific, differentially methylated regions (i.e., epigenetic markers) for identifying tissue of origin, as taught by Berlin.
Both references teach analyzing cell free DNA for disease diagnosis, with Berlin providing a specific improvement by identifying the DNA tissue of origin through the detection of DNA methylation. Specifically, while Diehn’s sequencing of tumor-specific mutations can detect tumor-specific cfDNA, it does not allow for the determination of tissue of origin of the tumor-specific cfDNA or whether the tumor has metastasized. Berlin addresses this limitation by offering a solution to determine cfDNA tissue of origin.
Berlin’s tumor origin determination can be achieved by probe hybridization, which is the same technique Diehn employs for target enrichment in its sequencing methods. Thus, a skilled artisan would recognize a reasonable expectation of success, as both references operate within the same field of analyzing cell-free DNA and disclose technically compatible teachings.
A skilled artisan would have been motivation to apply this modification to link the general observation of increased DNA levels in bodily fluids, such as in serum, to the risk of a cell proliferative disease (e.g., cancer) in a specific tissue or organ, thereby enhancing the diagnostic value of a cell-free DNA assay, as suggested by Berlin.
B) Regarding claim 2, Diehn teaches the cfDNA molecules are uniquely tagged with respect to one another ([00851] lines 6-9; [00121]).
Regarding claim 3, Diehn teaches amplifying the cfDNA prior to sequencing (entire document; Fig 22; [00862] for examples), and determining a consensus sequence from sequence reads obtained from the sequencing to reduce errors from amplification or sequencing ( [00278]; [00402]).
Regarding claim 4, Diehn teaches determining the consensus sequence is performed on a molecule-by-molecule basis ([00278] Determining the consensus sequence based on the molecular barcode).
Regarding claim 5, Diehn teaches determining the consensus sequence is performed on a base by base basis ([00278] determining a consensus sequence for the genomic region comprising the one or more mutations, wherein a consensus nucleotide is determined for a base at a given position).
Regarding claim 6, Diehn teaches determining the consensus sequence is performed using molecular barcodes that tag individual cfDNA molecules derived from the subject ([00278] Determining the consensus sequence based on the molecular barcode).
Regarding claim 7, Diehn teaches comparing sequence information obtained from the plurality of polynucleotides to sequence information obtained from a cohort of healthy individuals ([00772]; [00445]; [00808]).
Regarding claim 10, Diehn teaches a plasma sample ([0046]; [00444]).
Regarding claim 12, Diehn teaches subject has previously received a treatment for a cancer ([00446]; [00739]; [00763]).
Regarding claim 13, Diehn teaches colorectal cancer, ovarian cancer, lung cancer, pancreatic cancer, and liver cancer ([00753], [0063]).
Regarding claim 14, Diehn teaches chemotherapy ([00774]).
Regarding claim 15, Diehn teaches subject does not detectably exhibit any symptoms of the cancer ([00776] lines 11-17).
Regarding claim 16, Diehn teaches sequencing is performed within a read budget that allocates a pre-determined total number of base reads ([00795] 250 million 100bp reads per lane; FIG. 5b, Gbs sequenced), wherein a given amount of cfDNA is used ([00454]; Figure 12).
Regarding claim 17, Diehn teaches multiple cfDNA samples are collected from the subject over a plurality of time points and analyzed ([0016]; [0029] for examples).
Regarding claim 18, Diehn teaches sequencing panel is selected to achieve a sensitivity of at least 85% ([0060] lines 5-6; [0063]) for lung cancer ([0088-0089]).
Regarding claims 19-20, Diehn teaches Y-shaped adaptors comprising barcodes that are between 2 and 32 nucleotides in length ([00401] lines 5-6; [00402] lines 9-10). Y-shaped adaptors are duplex tags which differentially label the complementary strands of the DNA, as evidenced by Bennett (Fig 1).
Prior Art
Below are relevant prior art not used in rejection but pertinent to the claims or disclosure.
The prior art has disclosed a large number of methods for detecting tumor-specific genomic variants in cell-free DNA using sequencing:
Chan et al. Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin. Chem. 59, 211–224 (2013); cited as NPL on IDS filed 01/27/2025, page 50;
Crowley, E. et al."Liquid biopsy: monitoring cancer-genetics " Nat. Rev. Clin. Oncol. advance online publication 9 July 2013; doi:10.1038/nrclinonc.2013.110;
Dawson et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013 Mar 28;368(13):1199-209. doi: 10.1056/NEJMoa1213261. Epub 2013 Mar 13. PMID: 23484797;
Leary et al. Development of personalized tumor biomarkers using massively parallel sequencing. Sci Transl Med. 2010 Feb 24;2(20):20ra14. doi: 10.1126/scitranslmed.3000702. PMID: 20371490; PMCID: PMC2858564;
Diaz et al. Liquid biopsies: genotyping circulating tumor DNA. J Clin Oncol. 2014 Feb 20;32(6):579-86. doi: 10.1200/JCO.2012.45.2011. Epub 2014 Jan 21. PMID: 24449238; PMCID: PMC4820760;
WO2014039556A1 - Systems and methods to detect rare mutations and copy number variation.
Methods for enriching cfDNA using tissue-of-origin specific epigenetic markers are known in the art:
Mann (WO2017083366A1 - Methods for determining the origin of dna molecules; Effective date: Nov 9, 2015) teaches using transcription factor that differentially binds to DNA molecules to determine an origin of a sample;
Chiu (WO2014043763A1- Non-invasive determination of methylome of fetus or tumor from plasma; published 2014-03-27) teaches using methylation changes detected in the plasma for inferring the origin or type of the cancer;
DOR (WO2015159292A2 - A method and kit for determining the tissue or cell origin of dna; Published 2015-10-22) teaches DNA of each cell type in the body carries unique epigenetic marks correlating with its gene expression profile, and that tissue-specific DNA methylation pattern of cfDNA can be used to determine its tissue of origin and hence to infer cell death in the source organ.
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.
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/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
1 See Illumina's Estimating Sequencing Coverage; published 2014; www.illumina.com/documents/products/technotes/technote_coverage_calculation.pdf
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