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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 2/6/2026 has been entered.
Applicant’s arguments and amendments have been thoroughly reviewed and considered. Claims 23 and 45 have been canceled. Claims 59-61 have been added. Claims 48-49 and 51-57 remain withdrawn. and Claims 16-17, 42, 44, 46-47 and 58-61 are pending and are examined on the merits herein.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 7/21/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner, except where noted.
The information disclosure statement filed 7/21/2026 fails to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. A copy of the non-patent literature document number 3, Xiaoyan et al., has not been provided, and so this reference has not been considered.
The information disclosure statement filed 2/6/2026 contains no citations to any references, and so there are no references to consider. The information disclosure statement has been placed in the application file for the sake of clarity and completeness of the record.
In Applicant’s Remarks submitted 2/6/2026, a size fee assertion for the IDS submitted 5/27/2026 was provided. This IDS has now been considered in its entirety, and a copy has been provided herein.
Response to Applicant’s Amendments and Arguments
Claims 16-17, 23, 42, 44-47, and 58 were rejected under 35 U.S.C. 103 as being unpatentable over Garcia-Murillas et al. (Sci. Transl. Med., 2015), in view of Tan et al. (Isolation and Molecular Characterization of Circulating Tumor Cells, 2017), and in view of Kennedy et al. (US 2018/0305738 A1).
Applicant’s arguments and amendments have been thoroughly reviewed and considered. These rejections have been withdrawn for all currently pending claims. Claims 23 and 45 have been canceled, and so these rejections have been rendered moot. See also new grounds of rejection below.
Applicant has provided arguments against the 35 USC 103 Rejections presented in the Final Rejection mailed 11/6/2025.
After further search and consideration of the amended claims of record, prior art has been found that is considered more relevant to Applicant’s currently claimed invention than Garcia-Murillas and Tan, and thus new grounds of rejection are provided below. Applicant’s arguments concerning these references are thus considered moot.
It is noted that Applicant states that Kennedy, which is used in the rejections below, “does not teach or suggest anything about CTCs,” (Remarks, page 10). Though Kennedy does not use the term “circulating tumor cells,” the reference teaches that tumor cells can be used as an alternative to analyzing cell-free DNA (para. 156), and teaches that samples can be a blood bodily fluid sample (para. 133). Therefore, analyzing tumor cells within a blood sample is considered to be encompassed by the reference. Kennedy is also generally considered analogous art to the claimed invention as it is in the same field of endeavor, and so can be used in obviousness rejections. See MPEP 2141.01(a) I.
Claim Interpretation
It is noted that the term “multiplex amplification” is not specifically defined in the instant specification, and so is not limited to any particular type of amplification. Prior art will be considered to read on this term if it generally teaches amplification of multiple genes.
The term “cellular sample” is also not specifically defined in the instant specification. In the instant claims, these samples must be obtained from the blood sample, must contain at least two potential CTCs, and cellular DNA must be capable of being isolated from them. However, the cellular sample is not limited to only containing the CTCs, as noted by the use of the term “comprising” in step (c). Therefore, the blood sample itself, or a treated version thereof, could be considered a cellular sample, so long as it contains cells suspected of being CTCs. It is also noted that the cellular DNA isolated from the cellular samples does not have to be directed isolated from the cellular samples, and other steps may be performed to obtain said DNA, such as aliquoting, cell lysing, centrifuging, etc.
The term “patient-specific mutation” is also not specifically defined in the instant specification, and is taken to refer to any mutation identified in a cancer patient.
Regarding claim 58, a “hetrate plot” will be considered any plot that utilizes the allele ratios as claimed to determine the presence of cancer cells, regardless of the format of said plot. Thus, the plots do not need to look precisely like those in instant Figures 3-4, for example.
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 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.
Claims 16-17, 42, 44, 46 and 58-61 are rejected under 35 U.S.C. 103 as being unpatentable over Dago et al. (PLoS ONE, 2014) in view of Kennedy et al. (US 2018/0305738 A1).
Dago teaches an analysis of circulating tumor cells (CTCs) in prostate cancer patients to determine treatment efficacy and detect resistance to treatment (Abstract). For the patient, a baseline blood draw was taken before treatment, then chemotherapy in combination with various other treatments was performed. Blood was then taken at three times after the initiation of treatment (page 2, “Patient Clinical History and Blood Draws Collected During Treatment”). For each sample, CTC were identified and extracted, and each cell underwent whole genome amplification and next generation sequencing and bioinformatics analysis (page 3, “Extraction of Single Cells” and “Single Cell Next Generation Sequencing and Bioinformatic Analysis”; instant claim 61). Note that as whole genome amplification would include multiple genes, this falls under the interpretation of “multiplex amplification” described in the “Claim Interpretation” section above. Additionally, the treated blood samples that were then used to isolate CTCs can be considered analogous to the claimed cellular samples in accordance with the claim interpretation described above (see “Blood Sample Collection and Processing for CTC Detection” and “Extraction of Single Cells”). It is noted that each blood draw contained more than one CTC, as shown in Figure 1A. For the single cell analysis, CNVs were analyzed (page 3, “Treatment Response Monitored by Longitudinal CTC Molecular Analysis”; instant claim 17). A bone metastasis sample was also taken before treatment and the initial blood draw began, and was sequenced to obtain a CNV profile for comparison (page 4, column 1, para. 1). Genomic profiling/analysis occurred based on the CTCs taken at each time point (see Figures 2-3), showing areas of amplification/deletion specific to the patient at each time point.
As the entire genome was analyzed, CNVs detected in the baseline draw and bone metastasis data could be analyzed for changes over time in the later blood draws. Similarities between the CNVs in the baseline data and the during treatment blood draws indicated disease progression/treatment response. Page 4, column 2, para. 2 details using genomic evidence to confirm that isolated cells were CTCs (“To the level of resolution available, each of the shared events showed identical genomic breakpoints…From this evidence, we infer that these cells are bona fide CTCs derived from the patient’s metastatic lineage.”). Page 4, column 2, para. 3 describes that response to treatment, “coincided with an abrupt change in CTC phenotypes and genotypes,” that were similar to a normal profile (compare the Draw 3 data to the WBC data in Figure 2). Draw 4 represented disease progression, where CNVs were now more similar to bone metastasis data, though contained its own distinct differences (page 5).
In their conclusions, Dago states, “The bulk metastatic biopsy taken prior to initiation of therapy provides the root CNV profile to from which the subsequent time course CTC profiles have evolved. It exhibits a backbone of CNV elements that defines a lineage, based on CNV breakpoints, that is carried forward in the circulating cells from blood draws taken during later treatment,” (page 6, column 2, para. 1), and “In an era of clinical oncology that is progressively moving towards targeted cancer therapy, approaches that allow for non invasive monitoring of therapeutic response at both phenotypic and genetic levels are essential,” (page 7, column 2, para. 2).
Thus, Dago overall teaches that their CTC genotyping data can be used to monitor treatment response, and it would be prima facie obvious that if CTC data is showing mutations similar to baseline data, that treatment is ineffective and disease progression is worsening, which would be indicative of relapse or metastasis in a patient that has previously been responsive to treatment, as occurred in the patient examined in Dago. As all of the CNVs in the patient are examined in Dago, each of these is considered a “patient-specific mutation” as described in the “Claim Interpretation” section above.
However, Dago does not specify the depth of their next-generation sequencing.
Regarding claim 16, Kennedy teaches methods related to amplification and sequencing (Abstract). These methods involve sequencing to detect variants associated with cancer, where the sequencing is at a depth of at least 100,000 reads per base (para. 34). Kennedy notes that read depth allows detection of low frequency markers in a sample (para. 14). Though in many of these embodiments Kennedy teaches this sequencing depth with cell-free DNA, in para. 156, the reference teaches that cellular DNA can be used as an alternative to cell-free DNA, and specifically notes the use of tumor cells. These cellular DNA can be sequenced at a read depth that is the same or greater than that of the cell-free DNA. Para. 211 states how read depth can be calculated, and how amplification cycles can be used with the starting molecules to generate specific read depths. The reference states that sequencing depths up to 2,000,000 reads per base can be achieved with their methods (para. 213). In considering particular sequencing methods, the reference teaches the use of next generation sequence and high-throughput sequencing methods (para. 165).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the teachings of Kennedy to create a high sequencing read depth in the method of Dago. Kennedy teaches that such a read depth per base is possible to achieve with cellular tumor DNA, and specifically teaches read depths per base that are the same or higher than those claimed. Kennedy also notes that such read depths can improve detection of rare variants, which would be particularly useful when detecting tumor cells in blood samples, as is done in the method of Dago, and would be particularly useful in light of the genotypic comparisons made in this latter reference. Because this read depth can be achieved by sequencing means already taught by Dago (i.e. next generation sequencing), there would also be a reasonable expectation of success. Additionally, MPEP 2144.05 I states, “In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990).” It is noted that Applicant has provided no evidence of unexpected or critical results with respect to the claimed read depth, and thus said claimed depth is considered prima facie obvious.
Thus, claims 16-17 and 61 are prima facie obvious over Dago in view of Kennedy.
Regarding claim 42, in Dago, CNVs were analyzed over the entire genome, and so include more than 16 patient-specific mutations, as shown in Figures 2-3.
Regarding claim 44, even though Dago initially uses visual methods to identify CTCs (see page 2, column 2, “Immunofluorescence Staining and CTC Enumeration”), as noted above in the rejection of claim 16, the reference also uses the genotype data to draw conclusions confirming that suspected CTCs are indeed CTCs (“To the level of resolution available, each of the shared events showed identical genomic breakpoints…From this evidence, we infer that these cells are bona fide CTCs derived from the patient’s metastatic lineage,” page 4, column 2, para. 2). Additionally, even in the Draw 3 CTCs, which are closest in genotype to WBC data, more than 5 patient-specific mutations were seen (Figures 2-3).
Regarding claim 46, the claimed “additional patient-specific mutations” are considered to be mutations in addition to the 8 patient-specific mutations described in instant claim 16. As noted above, Dago teaches many more than 8 patient-specific mutations, and analyzed these mutations via a genotype analysis with next-generation sequencing data (page 3, “Single Cell Next Generation Sequencing and Bioinformatic Analysis” and Figures 2-3).
Regarding claim 58, though Dago does not specifically use the term “allele frequency,” the reference does teach a frequency analysis of CNV genomic alterations (page 3, “Frequency Analysis to Define Genomic Alterations”). Figure 3A shows a comparison of various CNV amplifications and deletions across the genome for both the bone metastasis sample (in green) and each of the blood draws (the colors for each are described in the figure caption). These comparisons resulted in the forming of three hierarchical clusters. Figure 3B shows the frequencies of deletion/amplification for the CNVs across the genome for each cluster.
Kennedy teaches the examination of mutant allele frequency (e.g. para. 68) and also minor allele frequency, which is the frequency at which minor alleles occur in a given population of nucleic acids, which can be tumor markers (para. 187). In their working examples, Kennedy shows that minor allele frequencies can be detected in blood draws and compared to tissue values for reference, and also before, during, and after cancer related operations (paras. 325-328, and see Figure 5). Figures 9A-9D also show time courses for mutations in cancer patients, where filled circles indicate concordance with sequencing results from a tumor, while open points show a discordance. The plots show minor allele frequency over time either before and during surgical intervention or before and after surgical intervention. Thus, the interpretation of these results is similar to that of the genotypic CTC analyses of Dago, where similarity between tumor sample and pre- and post-treatment allele frequency can indicate that a treatment was not effective, whereas a difference between tumor sample/pre-treatment data and post-treatment data cam indicate treatment efficacy. Kennedy also teaches that CNVs can be analyzed as the genetic variants associated with cancer in their methods (paras. 36, 112, 164 and 289), particularly in frequency analyses at different time points over the course of a treatment (paras. 307-308).
Taken together, these teachings would render it prima facie obvious to conduct the method described by instant claim 58 in the method of Dago in view of Kennedy. Specifically, Dago and Kennedy both teach measuring mutant allele frequencies before and after cancer treatment. In Dago, baseline measurements at least partially come from a tumor biopsy (the bone metastasis sample), and thus this would also be true in the method of Dago in view of Kennedy. Additionally, in the method of Dago in view of Kenedy, post-treatment measurements are of CTCs. Thus, utilizing the sequencing methods of this combination of references, along with the mutant allele frequency measurements of Dago and Kennedy, the ordinary artisan would arrive at allele frequency comparison measurements before and after treatment, where these allele frequencies could be compared to initial tumor values to determine if there is a match, which would indicate that a particular cell is a CTC and that treatment is/was not effective in mitigating disease (the opposite would also apply, where differences in allele frequencies of CTCs to initial tumor values would indicate potential treatment efficacy). This analysis is analogous to the bone metastasis/blood draw comparisons of Dago and the tumor/blood sample DNA comparisons of Kennedy, and thus the ordinary artisan would have a reasonable expectation of success. Additionally, there would be no further manipulation of the samples required, as this would only involve downstream analysis with data already accessible utilizing the method of Dago in view of Kennedy, further adding to this reasonable expectation.
Thus, claim 58 is prima facie obvious over Dago and in view of Kennedy.
Regarding claim 59, the samples of Dago are blood samples, and so included red blood cells in addition to the CTCs (see page 2, “Blood Sample Collection and Processing for CTC Detection”).
Regarding claim 60, Figure 1A shows the number of CTCs/mL for each sample at each time point, where each sample contained more than 10 CTCs.
Claim 47 is rejected under 35 U.S.C. 103 as being unpatentable over Dago et al. (PLoS ONE, 2014), in view of Kennedy et al. (US 2018/0305738 A1), and further in view of De Luca et al. (Oncotarget, 2016).
Dago in view of Kennedy teaches the methods of claims 16-17, 42, 44, 46 and 58-61, as described above. However, Dago teaches their methods in a patient with prostate cancer, and not one of the cancers described in instant claim 47. It is noted that Kennedy does teach examining lung, breast, bladder, and colorectal cancers (e.g., paras. 9 and 161), though this reference does not teach a CTC analysis method as specific as that of Dago.
De Luca teaches a method similar to that of Dago but in breast cancer patients. CTCs from blood samples of breast cancer patients were taken, and whole genome amplification was performed followed by next generation sequencing (Abstract). For patient 1, genes associated with CTCs were examined before and after treatment (page 26109, “Comparison between CTCs isolated before and after treatment”). The study concludes that, “One of the major advantages of the liquid biopsy is the possibility of repeating the blood sample at various time points during the disease course. Our findings on patient 1 seem to indicate that CTC characterization may be applied to monitor the response to therapy; in fact CTCs collected after treatment share only few variants with those of the first blood sample, while they present some variants undetectable in baseline conditions. Interestingly the mutation p.V777L in exon 20 of the ERBB2 gene was common to all the CTCs at baseline and in the post therapy condition, indicating that the clone bearing this variant was resistant to the administered therapy,” (pages 26114-26115, joining para.), and “We believe that this pilot study supports the applicability of the liquid biopsy approach in MBC patients. These results provide a rationale for further studies aiming to integrate the liquid biopsy in the context of a new generation of trials for MBC patients. Our next step will be the activation of clinical trials testing the activity of targeted therapies and correlating the response to treatment with biomarkers assessed at the CTC level,” (page 26115, columns 1-2 joining para.).
Prior to the effective filing date of the claimed invention, it would have been prima facie obvious for one of ordinary skill in the art to use the general method described by Dago in view of Kennedy, where blood draws are taken before and during treatment and CTC genotype is compared/examined, on a breast cancer population, particularly in view of the guidance of De Luca. De Luca performs a similar gene examination to that of Dago on CTCs in breast cancer patients, and concludes that examining CTCs in this manner to monitor treatment efficacy/response is a next goal of their work. As Dago teaches this CTC examination over the course of treatment in prostate cancer, and shows that said examination is indicative of treatment response and disease progression, this illustrates that the future goals of De Luca are possible, and thus would be motivating the ordinary artisan. There would be a reasonable expectation of success as the methods of Dago in view of Kennedy would not be changing, they would simply be performed on samples for a different starting population.
Thus, claim 47 is prima facie obvious over Dago, in view of Kennedy, and further in view of De Luca.
Relevant Prior Art
Prior art that is relevant to Applicant’s invention is cited below, though this art is not currently in the rejections of record:
Wang (US 2018/0252722 A1): This reference teaches PCR-based methods related to circulating tumor cells from blood or lymphatic fluid samples (Abstract). Para. 11 teaches that tumor-specific marker genes can be examined in CTCs, and para. 3 notes that these markers can serve as a marker for tumor progression.
Conclusion
No claims are currently allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCESCA F GIAMMONA whose telephone number is (571)270-0595. The examiner can normally be reached M-Th, 7-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at (571) 272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/FRANCESCA FILIPPA GIAMMONA/Examiner, Art Unit 1681
Prosecution Insights