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 .
Please note: The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 2/26/2026 has been entered.
Claim Status
Claims 1-4, 7-11, 14-15, 17-19, and 33-36 are pending and being examined on the merits.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. For example, see the references listed on page 23-27 of the Specification. These references are not all present on the provided IDS. 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.
Claim Objections
The objection to claim 1 is withdrawn in light of Applicant’s amendment to the claims.
Claim Rejections - 35 USC § 112b – Indefiniteness
Claim 17 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 17 depends from a cancelled claim, and therefore the scope of the claim is indefinite. For the purposes of examination, claim 17 is being interpreted as depending from claim 1. However, clarification is required.
Claim Rejections - 35 USC § 112d – Failure to Further Limit
The rejection of claim 16 under 35 U.S.C. 112(d) is withdrawn in light of Applicant’s cancellation of the claim.
Claim Rejections - 35 USC § 103
Withdrawn 103 Rejections
The rejections of claims under 35 U.S.C. 103 as presented in the Office Action of 8/26/2025 are withdrawn after further consideration of the claims and Applicant’s amendments and arguments presented in the response of 2/26/2026.
New 103 Rejections
Claims 1, 3-4, 7-8, 14-15, 17-19, and 33-35 are rejected under 35 U.S.C. 103 as being unpatentable over Lo (Lo et al., WO 2018/137685 A1; cited on IDS of 6/6/2024) in view of Shi (Shi et al., EP 3480310 A1; cited on IDS of 6/6/2024).
Regarding claim 1: Lo teaches a method of hybrid capture target enrichment for capturing ctDNA of interest from a human patient sample comprising cell free DNA and wherein the ctDNA corresponds to an oncogenic virus (EBV, HBV, or HPV; paragraphs [0360-0363]). Lo teaches adding a library of nucleic acid hybrid capture probes that are complementary to the ctDNA of interest across the entire oncogenic virus genome and are biotinylated (tagged for capture), allowing the probes to hybridize to the ctDNA, and capturing the hybridized ctDNA using a tag on the probes (paragraph [0360-0361]).
Lo does not teach that the library of probes is complementary to both strands of the double stranded ctDNA of interest, or that the probes complementary to the sense strand of the ctDNA are offset by 40-60% from the probes complementary to the antisense strand. However, using probes that are complementary to both strands of the double stranded DNA of interest that are offset by 40-60% is known in the art, as taught by Shi.
Shi teaches a method of nucleic acid enrichment and capture using sense and antisense probes without an overlapping design that are offset by 50% (Abstract and paragraphs [0005 and 0009]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, to have modified the method of Lo to include antisense probes that are offset by 50% for the antisense strand, as taught by Shi, in addition to the probes tiled along the entire oncogenic virus genome length for the sense strand. One would be motivated to do so given the assertion by Shi that targeting of both the sense and antisense strands “can improve the capture specificity and increase the number of original copies of the nucleic acid capture from the sample” (paragraphs [0004 and 0015]). One would be motivated to stagger/offset the probes by 40-50% given the assertion by Shi that this “minimizes the interaction between the sense strand probes and the antisense strand probes” (paragraph [0009]). One would have a reasonable expectation of success given that Shi demonstrates that a two-probe design (sense and antisense) demonstrates greater capture yield/efficiency than a one-probe design on DNA in plasma samples (paragraphs [0024-0027]).
Lo in view of Shi does not explicitly teach that the combined methodology captures and detects <1 genome equivalent of the oncogenic virus in the human patient sample. However, capturing and detecting <1 genome equivalent of the oncogenic virus is not a positive process step. Given that that the combined references teach all the limitations of the proposed method of claim 1, it is therefore obvious that the method is capable of the intended use of the claimed methodology.
Regarding claims 3 and 4: Lo teaches sequencing the captured ctDNA with next-generation sequencing (paragraph [0363]).
Regarding claim 7: Shi teaches that the probes complementary to the sense strand of the ctDNA are offset by 50% from the probes complementary to the antisense strand (“each sense strand and the corresponding antisense strand probes have a complementary part of half length of probes”, paragraph [0009]).
Regarding claim 8: Shi teaches that the probes are 30-89 bp in length (which significantly overlaps with the claimed range of 50-160 bp in length; paragraph [0010]).
Regarding claim 14 and 15: Lo teaches that the oncogenic virus is HPV (paragraph [0363]).
Regarding claim 17: Lo teaches mapping the location of the ctDNA to the genome (paragraphs [0358 and 0363]).
Regarding claims 18 and 19: Lo teaches that the patient sample is peripheral blood plasma (paragraph [0355]).
Regarding claims 33-35: As discussed in the rejection of claim 1 above, Lo in view of Shi does not explicitly teach that the combined methodology captures and detects ctDNA at levels less than 1%, less than 0.1%, or less than 0.001% in the human patient sample. However, capturing and detecting ctDNA at levels less than 1%, 0.1%, and 0.001% is not a positive process step. Given that that the combined references teach all the limitations of the proposed method of claim 1, from which claims 33-35 depend, it is therefore obvious that the method is capable of the intended use of the claimed methodology.
Claim 2 is rejected under 35 U.S.C. 103 as being unpatentable over Lo (Lo et al., WO 2018/137685 A1; cited on IDS of 6/6/2024) in view of Shi (Shi et al., EP 3480310 A1; cited on IDS of 6/6/2024) as applied to claims 1, 3-4, 7-8, 14-15, 17-19, and 33-35 above, and further in view of Czar (Czar et al., Trends in Biotechnology 2008; cited on PTO-892 of 1/31/2025).
The teachings of Lo in view of Shi as it applies to claim 1, from which claim 2 depends, are described above. Relevant to the instantly rejected claim, Lo in view of Shi teach enrichment of target ctDNA corresponding to an oncogenic virus from a human patient sample using capture probes targeting both strands of the double-stranded ctDNA of interest, capturing the ctDNA using the probes, and amplifying the captured ctDNA with PCR.
Lo in view of Shi do not teach assembling the captured fragments via polymerase chain reaction (PCR) assembly. However, assembling overlapping reads via PCR assembly to examine a sequence of interest was known in the art, as taught by Czar.
Czar review methods of gene synthesis by methods of assembly of overlapping oligomers (“Assembling oligomers into genes”). This includes the method of PCR assembly, which utilizes the design of oligos with partial overlap against both strands of a target sequence. Hybridization of this partial overlap and subsequent extensions of those products leads to assembly of a target sequence spanning all of the designed overlapping oligos ("Polymerase chain assembly").
It would have been prima facie obvious to one having ordinary skill in the art, as of the effective filing date of the instant application, to have modified the method of Lo in view of Shi to perform a polymerase chain assembly on the captured DNA as described by Czar. One would be motivated to do so given the assertion by Czar that PCR assembly of a target region using sense and antisense overlapping probes tiled across the region would allow for greater depth of coverage for subsequent sequencing reactions of the full target region.
Claims 9-11 are rejected under 35 U.S.C. 103 as being unpatentable over Lo (Lo et al., WO 2018/137685 A1; cited on IDS of 6/6/2024) in view of Shi (Shi et al., EP 3480310 A1; cited on IDS of 6/6/2024) as applied to claims 1, 3-4, 7-8, 14-15, 17-19, and 33-35 above, and further in view of Clark (Clark et al., The Journal of Molecular Diagnostics 2018).
The teachings of Lo in view of Shi as it applies to claim 8, from which claims 9-11 depend, are described above. Relevant to the instantly rejected claim, Lo in view of Shi teach enrichment of target ctDNA corresponding to an oncogenic virus from a human patient sample using capture probes targeting both strands of the double-stranded ctDNA of interest. Lo in view of Shi teach that the probes are 30-89 base pairs in length.
Lo in view of Shi do not teach that the probes are 120 bp in length. However, use of 120 bp long probes for hybrid capture-based NGS of target ctDNA in blood samples in known in the art, as taught by Clark.
Clark teaches a method of hybrid capture-based NGS for profiling of ctDNA from blood (Abstract). Clark teaches using 120-bp 5’-biotinlated ssDNA oligonucleotide baits for target capture (reads on between 80 bp to 160 bp in length, 100 bp and 140 bp in length, and 120 bp in claims 9, 10, and 11, respectively; Materials and Methods - Panel Design, Hybrid Capture, and Sequencing).
It would have been prima facie obvious to one having ordinary skill in the art, as of the effective filing date of the instant application, to have modified the method of Lo in view of Shi to have used the 120-bp probes as taught by Clark. One would be motivated to do so given the sensitivity of detection that Clark demonstrates in blood samples from patients when sequencing ctDNA captured by the 120 bp probes (Figure 5). One would have a reasonable expectation of success given that Clark successfully captures target ctDNA from blood samples and performs next generation sequencing.
Claim 36 is rejected under 35 U.S.C. 103 as being unpatentable over Lo (Lo et al., WO 2018/137685 A1; cited on IDS of 6/6/2024) in view of Shi (Shi et al., EP 3480310 A1; cited on IDS of 6/6/2024) as applied to claims 1, 3-4, 7-8, 14-15, 17-19, and 33-35 above, and further in view of Damerla (Damerla et al., JCO Precision Oncology 2019; cited on IDS of 6/6/2024).
The teachings of Lo in view of Shi as it applies to claim 1, from which claim 36 depends, are described above. Relevant to the instantly rejected claim, Lo in view of Shi teach enrichment of target ctDNA corresponding to an oncogenic virus from a human patient sample using capture probes targeting both strands of the double-stranded ctDNA of interest, capturing the ctDNA using the probes, and amplifying the captured ctDNA with PCR.
Lo in view of Shi do not specifically teach that the patient sample contains less than 1 genome equiavalent of the oncogenic virus. However, patient samples with less than 1 genome equivalent of oncogenic virus are known in the art, as taught by Damerla.
Damerla teaches a method of ddPCR for sensitive detection of an oncogenic virus (HPV) in patient samples. Damerla teaches that HPV genomic copies per tumor genome can be widely variable in pathologic samples, ranging from 0.8 to 57 copies per tumor genome (pg 5, col 3, paragraph 3) and specifically they show data from patients that have less than 1 genome equivalent of the oncogenic virus (Figure 2).
It would have been prima facie obvious to one having ordinary skill in the art, as of the effective filing date of the instant application, to have employed the method of Lo in view of Shi on patient samples with less than 1 genome equivalent of the oncogenic virus as described by Damerla. One would be motivated to do so given the assertion by Damerla that HPV levels vary greatly in patients, and employing more sensitive detection methods can aid in early detection or determination of response to treatment (Abstract, Conclusion). One would have a reasonable expectation of success given that Damerla specifically teaches the variability of the HPV virus in samples as ranging from less than 1 genome equivalent (0.8) to 57 copies, and Lo teaches employing their methodology on the HPV oncogenic viral genome.
Response to Remarks
Applicant’s arguments regarding the new limitation added in the most recent amendment (“capable of capturing and detecting <1 genome equivalent of the oncogenic virus in the human patient sample”) are moot given that this limitation was newly added. This new limitation, as well as the new claims (claims 33-36) have been addressed in the new 103 rejections presented above.
Applicant’s arguments, see Remarks (pages 5-6), filed 2/26/2026, with respect to the rejection of claim 1 under Eattock in view of Frampton and Lo, have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground of rejection is made in view of Lo in view of Shi (as presented in the 103 rejections above).
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAILEY E CASH whose telephone number is (571)272-0971. The examiner can normally be reached Monday-Friday 8:30am-6pm ET.
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, Anne Gussow can be reached at (571)272-6047. 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.
/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683