DETAILED ACTION
The amendment filed on 08/13/2025 has been entered.
Claims 1, 6, 7, 13, and 31 were amended in the claim set filed on 08/13/2025.
Claims 1-4, 6-8, 11-14, 16-20, 22, 24-27, and 30-31 in the claim set filed on 8/13/2025 are currently under examination.
Response to the Arguments
Objections to the Drawings in the previously mailed non-final are withdrawn in light of applicants replacement Drawings. Note, a higher quality image for Figure 1 may be required by printing if the claims of the instant application become allowable.
Applicant’s arguments, see Pg. 6-7, regarding previous rejection(s) of claims 1-4, 6-8, 11-14, 16-20, 22, 24-27, and 30-31 under 35 U.S.C. 112 have been fully considered and are persuasive. The 35 U.S.C. 112 rejections documented in the previously mailed non-final have been withdrawn.
Applicant’s arguments, see Pg. 7-10, regarding previous rejection(s) of claims 1-4, 6-8, 11-14, 16-20, 22, 24-27, and 30-31 under 35 U.S.C. 101 have been fully considered and are persuasive. The 35 U.S.C. 101 rejections documented in the previously mailed non-final have been withdrawn.
Applicant’s arguments, see Pg. 10-11, regarding previous rejection(s) of claim(s) 1, 6, 13-14, 20, 22, 26-27, and 30-31 under 35 U.S.C. 102 have been fully considered and are persuasive. Applicant’s argument on Pg. 10, states that “Applicant has amended claim 1 to recite, after step (a), "(b) preparing a single stranded DNA library from said plurality of nucleic acid molecules or derivatives thereof." For anticipation under 35 U.S.C. § 102, the reference must teach every aspect of the claimed invention, either explicitly or inherently. See VerdegaalBros. v. Union Oil Co. of California, 814 F.2d 628, 631 (Fed. Cir.1987) (A claim is anticipated "only if each and every -10-Atty. Docke element as set forth in the claim is found, either expressly or inherently described, in a single prior art reference."). Applicant submits that claim 1 is novel over Chan because Chan does not teach or disclose all of the elements of this claim. For example, Chan does not disclose a method using a single stranded DNA library prepared from a plurality of nucleic acid molecules derived from a cfDNA sample of the subject, as recited in claim 1. Accordingly, Applicant respectfully requests that claim 1 is novel over Chan be withdrawn. Claims 6, 13-14, 20, 22, 26-27, and 30-31 are also novel over Chan at least because they depend from claim 1 and recite additional elements of particular advantage and utility.” The 35 U.S.C. 102 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim amendments and arguments on Pg. 10-11. However, upon further consideration and search, new grounds of rejection are made as documented below in the 35 U.S.C. 103 rejection of this office action on Pg. 4-7.
Applicant’s arguments, see Pg. 11-13, regarding previous rejection(s) of claim(s) 1-2, 4, 7-8, 11, 12, 16-19, 24-25 under 35 U.S.C. 103 have been fully considered and are persuasive. Applicant’s argument on Pg. 11-13, states that “Applicant has amended claim 1 to recite, after step (a), "(b) preparing a single stranded DNA library from said plurality of nucleic acid molecules or derivatives thereof." Applicant respectfully submits that Chan does not teach, disclose, or even suggest a method using a single stranded DNA library prepared from a plurality of nucleic acid molecules derived from a cfDNA sample of the subject, as recited in claim 1. The problem solved by the claims herein is obtaining a more representative sequence analysis of nucleic acid molecules from the cell-free nucleic acid sample, which naturally has single and double stranded nucleic acid molecules. Claim 1 solves this problem by preparing a single stranded DNA library from the nucleic acid molecules so that single stranded and double stranded nucleic acid molecules are represented in the library. The 35 U.S.C. 103 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim amendments. However, upon further consideration and search, new grounds of rejection are made as documented below in the 35 U.S.C. 103 rejection of this office action on Pg. 8-15.
Applicant’s arguments regarding previous rejection(s) of claim(s) 1-4, 6-8, 11-14, 16-20, 22, 24-27, and 30-31 under Double patenting have been fully considered and are persuasive. However, upon further consideration and search, new grounds of rejection are made as documented below in the Double Patenting rejections of this office action on Pg. 15-21.
The rejections for claims 1-4, 6-8, 11-14, 16-20, 22, 24-27, and 30-31 are documented below in this Final Office Action are necessitated by claim amendments filed on 08/13/2025.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 08/12/2025 was filed after the mailing date of the non-final office action on 05/21/2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 103
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, 6, 13-14, 20, 22, 26-27, and 30-31 are rejected under 35 U.S.C. 103 as being unpatentable over Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.)
Regarding claim 1 step a, Chan teaches a method comprising “differentiating between cancer patients and individuals without cancer” (determining if a subject has a disease) (pg. 222 Para. 1 lines 9-11) and “through obtaining a cell-free biological sample of a subject by extracting the cell-free DNA from the subject’s peripheral blood sample” (pg. 212 col. 1 para. 4 lines 1-6).
Regarding claim 1 step b-c, Chan teaches “Sequencing libraries of the genomic DNA samples were constructed” and “sequencing on a HiSeq 2000 system (Illumina)”) (pg. 212 column 2, DNA SEQUENCING Para.1 and Para. 3).
Regarding claim 1 step d-e, Chan teaches method comprising “The paired-end sequencing data were analyzed by means of the Short Oligonucleotide Alignment Program 2 (SOAP2) in the paired-end mode … each end was aligned to the non–repeat-masked reference human genome (Hg18) … mapping to a single location in the reference human genome” (Pg. 212, Col. 2, SEQUENCE ALIGNMENT AND FILTERING, Para. 1) and “We sequenced the paired tumor and constitutional DNA samples to identify the tumor-associated single nucleotide variants” (SNVs) (pg. 214 col. 2 DETECTION OF TUMOR-ASSOCIATED, Para 1). Chan also teaches a method wherein “These results indicate ... differentiating between cancer patients and individuals without cancer (pg. 222 Col. 1, Para. 1).
Regarding claim 6, Chan teaches a method comprising “15-cycle PCR when constructing the DNA libraries from the plasma samples” (Pg. 212, Col. 2, DNA SEQUENCING, Para. 1).
Regarding claim 13-14, Chan teaches a method wherein “The adapter-ligated DNA was enriched with a 12-cycle PCR” (Pg. 212, Col. 2, DNA SEQUENCING, Para. 1).
Regarding claim 20, Chan teaches a method comprising obtaining tumor tissue samples from patients (pg. 212 col. 1 para. 3 ln 14-16).
Regarding claim 22, Chan teaches a method wherein “cell-free biological sample is from blood and plasma” (pg. 212 col. 1 para. 4 ln 1-6).
Regarding claim 26, Chan teaches a method comprising sequencing and comparing the genomic DNA from the subjects buffy coat sample (reference) and plasma DNA (cell-free DNA molecules) can be applied to cancer patients (disease is cancer) and specifically demonstrate this method in patients with hepatocellular carcinoma (HCC), liver cancer, breast cancer, and ovarian cancer (pg. 211 column 1 paragraph 1 lines 1-5; pg. 211 column 1 paragraph 2 lines 1-2; pg. 211 column 2 paragraph 1 lines 1-3 & pg. 212 column 1 paragraph 2 lines 1-4; pg. 212 column 1 paragraph 3 lines 1,7,& 10-11).
Regarding claim 27, Chan teaches a method wherein “the fractional concentrations of tumor-derived DNA in plasma were determined by the fractional counts of the mutant with respect to the total (i.e., mutant plus wild type) sequences (Table 2) (Pg. 218 last Para., Pg. 219 first para.); Table 2 shown below). Increase or decrease is interpreted as variance in fractional concentrations.
PNG
media_image1.png
281
590
media_image1.png
Greyscale
Regarding claim 30, Chan teaches a method wherein “spanning an insert size_600 bp, and mapping to a single location in the reference human genome” (Pg. 212, col. 2, SEQUENCE ALIGNMENT AND FILTERING, Para. 1). Chan teaches a method wherein “For each paired-end read, 50 bp or 75 bp from each end was aligned to the non–repeat-masked reference human genome (Hg18)” (Pg. 212, col. 2, SEQUENCE ALIGNMENT AND FILTERING, Para. 1).
Regarding claim 31, Chan teaches method comprising “mapping to a single location” (Pg. 212, col. 2, SEQUENCE ALIGNMENT AND FILTERING, Para. 1).
Therefore, the invention as recited in claims 1, 6,13-14, 20, 22, 26-27, and 30-31 are prima facie obvious over the prior art Chan et al. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to identify whether a subject has a disease according to the limitations of the instant application claims 1, 6, 13-14, 20, 22, 26-27, and 30-31 based on Chan et al.
Response to Arguments
Applicant' s arguments filed 08/13/2025 (Pg.10-11) with respect to claim 1, 6, 13-14, 20, 22, 26-27, and 30-31 have been considered but do not apply to the new grounds of rejections. To clarify some instances argued in the response filed 08/13/2025 see responses to each argument made by Applicant below:
Applicants’ argument: “Applicant has amended claim 1 to recite, after step (a), "(b) preparing a single stranded DNA library from said plurality of nucleic acid molecules or derivatives thereof.” (Pg. 11)
Response: In response to applicant's arguments, it would be obvious to one skilled in the art to prepare single stranded DNA library according to the limitations of claim 1. Further, Chan does not explicitly specify single or double stranded DNA, thus it would be obvious to prepare a library based off of the contents of the cfDNA which generally comprises single stranded DNA according to the teachings by Chan.
Claims 1 and 2-4 are rejected under 35 U.S.C. 103 as being unpatentable over Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.) in view of Ulz et al. (“Ulz”, (2019). Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection. Nature communications, 10(1), 4666.
The teachings of Chan with respect to claim 1 are documented above in the rejection under 35 U.S.C. 103. Chan does not teach claims 2-4.
Regarding claim 2-4, Ulz teaches “TF accessibilities as established from ATAC-seq data can be inferred from the cfDNA nucleosome occupancy patterns. However, currently no means of assessing TF accessibility and changes thereof in cfDNA exist. To implement such an approach, we first investigated TF-specific nucleosome coverage profiles, which led us to conduct calculations separately for TFBSs within and outside of TSSs (, Para. X).
Therefore, it would have been prima facie obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified Chan to incorporate the teachings of Ulz including a locus that is a chromatin accessible site comprises transcription factor binding site because Ulz teaches that doing so would provide evaluation of the important part of noncoding genome and that cell-free DNA TF profiling is capable of detecting early-stage disease.
Response to Arguments
Applicant's arguments filed 08/13/2025 do not apply to the new grounds of rejections. Please see response to arguments documented above in the rejection of claims 1, 6, 13-14, 20, 22, 26-27, and 30-31 under 35 U.S.C. 103.
Claims 1 and 7-8 are rejected under 35 U.S.C. 103 as being unpatentable over Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.) in view of Rabinowitz et al. (“Rabinowitz”, U.S. Patent App. Pub. US 2019/0309358 A1).
The teachings of Chan with respect to claim 1 are documented above in the rejection under 35 U.S.C. 103. Chan does not teach claims 7-8.
Regarding claim 7, Rabinowitz teaches a method comprising “ligation of the 3’ end and 5’ end of a target DNA to create a circular DNA molecule where the target DNA is obtained from extracting cell-free DNA from a biological sample of a subject” (pg. 68 column 1 lines 2-6). Rabinowitz also teaches a method wherein “circularizing DNA molecules followed by high throughput sequencing provides better genotypic data and more accurate results” (para. 240, ln 8-13).
Regarding claim 8, Rabinowitz teaches a method wherein “the unamplified genetic material of the target individual may be circularized, amplified, and then sequenced” (para. 238 ln 12-15 & ln 19-24). Amplification of the circularized nucleic acid is interpreted as RCA.
Therefore, it would have been prima facie obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified Chan to incorporate the teachings of Rabinowitz to comprise circularization of DNA molecules and amplification of circularized nucleic acids because Rabinowitz teaches that doing so would provide better genotypic data and more accurate results.
Response to Arguments
Applicant's arguments filed 08/13/2025 do not apply to the new grounds of rejections. Please see response to arguments documented above in the rejection of claims 1, 6, 13-14, 20, 22, 26-27, and 30-31 under 35 U.S.C. 103.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.) in view of Rabinowitz et al. (“Rabinowitz”, U.S. Patent App. Pub. US 2019/0309358 A1), as applied to claim 1 and 7-8 above, and further in view of Dean et al. (“Dean”, (2001). Rapid amplification of plasmid and phage DNA using phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome research, 11(6), 1095-1099.).
The teachings of Chan and Rabinowitz are documented above in the rejection of claims 1 and 7-8 under 35 U.S.C. 103. Chan and Rabinowitz do not teach claim 11.
Regarding claim 11, Rabinowitz teaches that the circular DNA molecules may be amplified by methods including rolling circle amplification (RCA), multiple displacement amplification (MDA), or other amplification protocols (Para. 238, ln 12-19).
Rabinowitz does not teach that the circular DNA molecule in the rolling circle amplification step amplified in a reaction comprising random primers (claim 11).
Dean teaches a method wherein “rolling circle amplification using phi-29 DNA polymerase and random primers has an increased rate of synthesis and yield” (pg. 1095 Abstract para. 1 ln 2-5; pg. 1095 col. 1 para. 3; pg. 1097 col. 2 para. 1-2).
Therefore, it would have been prima facie obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified Chan and Rabinowitz to incorporate the teachings of Dean to amplify circular DNA molecules with random primers because Dean teaches this would allow for the amplification of the circular DNA molecules to generate a plurality of sequences reads with faster processing and less error with the goal of amplifying the signal of the sequence used to determine if a subject has or is at risk of having a disease.
Response to Arguments
Applicant's arguments filed 08/13/2025 do not apply to the new grounds of rejections. Please see response to arguments documented above in the rejection of claims 1, 6, 13-14, 20, 22, 26-27, and 30-31 under 35 U.S.C. 103.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.) in view of Rabinowitz et al. ("Rabinowitz", U.S. Patent App. Pub. US 2019/0309358 A1), as applied to claim 1 and 7-8 above, and further in view of Gong et al. (“Gong”, (2018). Multiplex real-time PCR assay combined with rolling circle amplification (MPRP) using universal primers for non-invasive detection of tumor-related mutations. RSC advances, 8(48), 27375-27381.).
The teachings of Chan and Rabinowitz are documented above in the rejection of claims 1 and 7-8 under 35 U.S.C. 103. Chan and Rabinowitz do not teach claim 12.
Regarding claim 12, Chen and Rabinowitz fail to teach contacting the circular nucleic acid molecules to an amplification reaction mixture comprising one or more primers where each specifically hybridizes to a different target sequence via sequence complementary.
Gong teaches a multiplex method with rolling circle amplification with cell-free DNA in which padlock probes (primers) can only ligate with target DNA that is completely complementary to it allowing for the ligation of different probes (primers) with different target sequences with sequence complementary (pg. 27376 paragraph that bridges col. 1 and 2 lines 1-23; pg. 27376 col. 2 1st full para. lines 5-10). In addition, Gong teaches that method increases the sensitivity over other advanced PCR methods (pg. 27375 abstract para. 1 lines 6-7).
Therefore, it would have been prima facie obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified Chan and Rabinowitz to incorporate the teachings of Gong because Gong teaches the use an amplification mixture of one or more primers in which each specifically hybridizes to a different target sequences would allow for the detection of cancer-related mutations and risk for disease in a method that provides better sensitivity.
Response to Arguments
Applicant's arguments filed 08/13/2025 do not apply to the new grounds of rejections. Please see response to arguments documented above in the rejection of claims 1, 6, 13-14, 20, 22, 26-27, and 30-31 under 35 U.S.C. 103.
Claims 1 and 16-19 are rejected under 35 U.S.C. 103 as being unpatentable over Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.) in view of Blauwkamp (Blauwkamp et al., U.S. Patent App. Pub. US 2018/0371538 A1, Dec. 27, 2018).
The teachings of Chan with respect to claim 1 are documented above in the rejection under 35 U.S.C. 103. Chan does not teach claims 16-19.
Regarding claims 16-18, Blauwkamp teaches a method comprising “any type of nucleic acid including but not limited to: double-stranded (ds) nucleic acids, single stranded (ss) nucleic acids, DNA, RNA, cDNA… cell-free DNA…” (Pg. 8 Para. 81)
Regarding claim 19, Blauwkamp teaches a method comprising” reverse transcription products were collected in the supernatant, purified, amplified by PCR, and sequenced.
Therefore, it would have been prima facie obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified Chan to incorporate the teachings of Blauwkamp to comprise nucleic acid molecules that are ss, ds, and/or cfDNA because Blauwkamp teaches that doing so would allow for detection of nucleic acids of many forms.
Response to Arguments
Applicant's arguments filed 08/13/2025 do not apply to the new grounds of rejections. Please see response to arguments documented above in the rejection of claims 1, 6, 13-14, 20, 22, 26-27, and 30-31 under 35 U.S.C. 103.
Claims 1 and 24-25 are rejected under 35 U.S.C. 103 as being unpatentable over Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.) in view of Shen et al. (“Shen”, (2018). Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature, 563(7732), 579-583.).
The teachings of Chan with respect to claim 1 are documented above in the rejection under 35 U.S.C. 103. Chan does not teach claims 24-25.
Regarding claims 24-25, Chan fails to teach computer processing a sequence to identify an epigenetic modification in said plurality of sequences (Claim 24) and wherein said epigenetic modification is selected from methylation, phosphorylation, ubiquitination, sumoylation, acetylation, ribosylation, citrullination, and fragmentation (Claim 25).
Shen teaches a machine learning (computer processing) method for detecting DNA methylation in cell-free DNA samples with the goal of detecting, intercepting, or classifying early-stage cancers (pg. 579 abstract paragraph 1 lines 1-19; pg. 585 column 2 paragraph 3 lines 1-5). Shen also teaches that this method is robust and sensitive (pg. 583 column 1 1st full paragraph lines 1-3).
Therefore, it would have been prima facie obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified Chan to incorporate the teachings of Shen to computer process sequences to identify methylation because Yi Shen teaches that doing so would allow for detection of DNA methylation in cell-free nucleic acid molecules with high sensitivity.
Response to Arguments
Applicant's arguments filed 08/13/2025 do not apply to the new grounds of rejections. Please see response to arguments documented above in the rejection of claims 1, 6, 13-14, 20, 22, 26-27, and 30-31 under 35 U.S.C. 103.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, , In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (, PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-4, 6-8, 11-14, 16-20, 22, 24-28, and 30-31 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-26 of U.S. Patent No. US 11,859,246 B2 (US Patent No. ‘246) in view of Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.). Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over the claims of US Patent No. ‘246.
The claims of US Patent No. ‘246 are drawn to:
1. A method for processing or analyzing a biological sample of a subject, comprising: (a) obtaining said biological sample of said subject; (b) using a nucleic acid molecule derived from said biological sample to generate a circular nucleic acid molecule; and (c) subjecting said circular nucleic acid molecule or derivative thereof to amplification in a reaction mixture comprising a first primer, a second primer, a third primer, and said circular polynucleotide, said amplification comprising: (i) hybridizing said first primer to a first sequence of said circular polynucleotide, the first primer comprising a first 3′ end that specifically hybridizes to the target polynucleotide via sequence complementarity and a first 5′ end comprising a first common sequence that does not specifically hybridize to the target polynucleotide via sequence complementarity; (ii) extending said first primer to generate a first concatemer comprising a first single-stranded polynucleotide hybridized to said circular polynucleotide, wherein said first single-stranded polynucleotide comprises a second sequence that is complementary to said first sequence of said circular polynucleotide; (iii) separating said first single-stranded polynucleotide from said circular polynucleotide (iv) hybridizing said second primer to a portion of said second sequence of said first single-stranded polynucleotide of (iii) and said third primer to a third sequence of said circular polynucleotide, the third primer comprising a second 3′ end that specifically hybridizes to the circular polynucleotide via sequence complementarity and a second 5′ end comprising a second common sequence that does not specifically hybridize to the circular polynucleotide via sequence complementarity, the second primer comprises a sequence that specifically hybridizes to the first common sequence and/or the second common sequence via sequence complementarity; (v) extending said second primer to generate a nucleic acid molecule comprising said first single-stranded polynucleotide and a complement of said first single-stranded polynucleotide, and extending said third primer to generate a second concatemer comprising a second single-stranded polynucleotide hybridized to said circular polynucleotide; and (vi) amplifying said nucleic acid molecule of (v) to generate a plurality of amplicons, and (d) subjecting said plurality of amplicons or derivative thereof to sequencing to identify a sequence of said nucleic acid molecule derived from said biological sample.
2. The method of claim 1, further comprising processing said sequence to identify a cancer in said subject.
3. The method of claim 2, wherein said sequence is computer processed against a reference to identify one or more genetic variants, and wherein said one or more genetic variants identify said cancer.
4. The method of claim 1, wherein said sequence of said circular nucleic acid molecule or derivative thereof comprises a junction sequence in which a 5′ end and a 3′ end of said nucleic acid molecule are joined.
5. The method of claim 4, wherein said sequence of said nucleic acid molecule identifies said 5′ end or said 3′ end of said nucleic acid molecule.
6. The method of claim 1, wherein (a) comprises ligating ends of said nucleic acid molecule to one another.
7. The method of claim 1, wherein (a) comprises coupling an adapter to a 3′ end, a 5′ end, or both a 5′ end and a 3′ end of said nucleic acid molecule.
8. The method of claim 1, further comprising, subsequent to (a), subjecting said circular nucleic acid molecule to nucleic acid amplification to generate an amplification product of said circular nucleic acid molecule, wherein (bd) comprises subjecting said amplification product or derivative thereof to sequencing to identify a sequence of said amplification product or derivative thereof, which sequence corresponds to said sequence of said nucleic acid molecule derived from said cell-free biological sample.
9. The method of claim 8, wherein said nucleic acid amplification is effected by a polymerase having strand-displacement activity.
10. The method of claim 8, wherein subjecting said circular nucleic acid molecule to said amplification comprises contacting said circular nucleic acid molecule with an amplification reaction mixture comprising random primers.
11. The method of claim 8, wherein subjecting said circular nucleic acid molecule to said nucleic acid amplification comprises contacting said circular nucleic acid molecule with an amplification reaction mixture comprising a primer which hybridizes to a target sequence of said circular nucleic acid molecule.
12. The method of claim 1, further comprising processing said sequence of said nucleic acid molecule against a reference.
13. The method of claim 1, wherein said-nucleic acid molecule is single stranded.
14. The method of claim 1, wherein said nucleic acid molecule is a cell-free deoxyribonucleic (DNA) molecule or a cell-free ribonucleic acid (RNA) molecule.
15. The method of claim 14, wherein said cell-free DNA molecule or said cell-free RNA molecule is from a tumor.
16. The method of claim 1, further comprising processing said sequence to monitor a progression of a disease in said subject in response to treatment.
17. The method of claim 16, wherein said disease is cancer.
18. The method of claim 1, wherein said sequencing comprises (i) bringing said plurality of amplicons or derivative thereof in contact with a plurality of nucleotides in presence of a polymerase to incorporate one or more nucleotides of said plurality of nucleotides into a growing strand complementary to a strand of said circular nucleic acid molecule or derivative thereof, and (ii) detecting one or more signals indicative of incorporation of said one or more nucleotides into said growing strand.
19. The method of claim 1, wherein said sequencing comprises sequencing by ligation.
20. The method of claim 1, wherein said cell-free biological sample comprises less than 75 nanograms of nucleic acids.
21. The method of claim 1, wherein said cell-free biological sample comprises a bodily fluid.
22. The method of claim 21, wherein said bodily fluid is urine, saliva, blood, serum, or plasma.
23. The method of claim 1, wherein said nucleic acid molecule has a length from about 10 to about 300 nucleotides.
24. The method of claim 1, further comprising computer processing said sequence to identify an epigenetic modification in said sequence.
25. The method of claim 24, wherein said epigenetic modification includes methylation.
26. The method of claim 1, wherein said sequence is computer processed against a reference to identify (i) one or more copy number variants, (ii) one or more single nucleotide variants, (iii) a fusion, (iv) one or more mitochondrial deoxyribonucleic acid (DNA) copy number variants, (v) one or more mitochondrial DNA single nucleotide variants, (vi) one or more mitochondrial DNA insertions, (vii) one or more mitochondrial DNA deletions, or (viii) an allele frequency for a variant.
27. The method of claim 1, wherein said sequence is computer processed against a reference to identify a microbial nucleic acid.
28. The method of claim 1, wherein said separating of (iii) comprises denaturing at a denaturation temperature.
The teachings of Chan with respect to claim 1 are documented above in the rejection under 35 U.S.C. 103. Claims of U.S. Patent No. ‘246 are made obvious over the instantly claimed invention. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to identify a subject with a disease, comprising: providing cell free nucleic acids of a subject, sequencing nucleic acid sample, process sequences using a computer to compare against a reference, identify an epigenetic modification variation in a sequence, and relate to identification of disease according to the limitations of the instant application based on US Patent No. ‘246. Thus, the invention as a whole is made obvious by US Patent No. ‘246.
Claims 1-4, 6-8, 11-14, 16-20, 22, 24-28, and 30-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-5, 7-14, 17, 19, 21, 23, 25, and 31 of copending Application No. 17/557972 in view of Chan et al. (“Chan”, (2013). Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clinical chemistry, 59(1), 211-224.). Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over the claims of copending Application No. 17/557972.
The claims of copending Application No. 17/557972 are drawn to:
1. A method for determining that a subject has or is at risk of having a disease, comprising:(a) obtaining a cell-free biological sample of said subject;(b) using a plurality of nucleic acid molecules derived from said cell-free biological sample to generate a plurality of circular nucleic acid molecules;(c) subjecting each of said plurality of circular nucleic acid molecules to nucleic acid amplification to generate a plurality of amplification products of said plurality of circular nucleic acid molecules; (d) subjecting said plurality of amplification products or derivatives thereof to sequencing to generate a plurality of sequence reads; and (e) processing said plurality of sequence reads against a plurality of reference sequence reads to identify at least a subset of said plurality sequence reads as corresponding to at least a subset of said plurality of reference sequence reads, thereby determining that said subject has or is at risk of having said disease.
2. A method for determining that a subject has or is at risk of having a disease, comprising:(a) obtaining a cell-free biological sample of said subject; (b) using a plurality of nucleic acid molecules derived from said cell-free biological sample to generate a plurality of circular nucleic acid molecules; (c) subjecting each of said plurality of circular nucleic acid molecules to nucleic acid amplification to generate a plurality of amplification products of said plurality of circular nucleic acid molecules; (d) subjecting said plurality of amplification products or derivatives thereof to sequencing to identify a plurality of breakpoint sequences; and (e) processing said plurality of breakpoint sequences against a plurality of reference breakpoint sequences to identify at least a subset of said plurality breakpoint sequences as corresponding to at least a subset of said plurality of reference breakpoint sequences, thereby determining that said subject has or is at risk of having said disease.
3. The method of claim 2, wherein each of said plurality of breakpoint sequences comprises a 5' end and a 3' end of a nucleic acid molecule derived from said cell-free biological sample.
4. The method of claim 1, wherein (b) comprises ligating ends of each of said plurality of nucleic acid molecules to one another.
5. The method of claim 1, wherein (b) comprises coupling an adapter to a 3' end, a 5' end, or both a 5' end and a 3' end of each of said plurality of nucleic acid molecules.
7. The method of claim 1, wherein said nucleic acid amplification is effected by a polymerase having strand-displacement activity.
8. The method of claim 1, wherein said nucleic acid amplification is effected by a polymerase that does not have strand-displacement activity.
9. The method of claim 1, wherein said nucleic acid amplification comprises contacting said circular nucleic acid molecule to an amplification reaction mixture comprising random primers.
10. The method of claim 1, wherein said nucleic acid amplification comprises contacting said circular nucleic acid molecule to an amplification reaction mixture comprising one or more primers, each of which specifically hybridizes to a different target sequence via sequence complementarity.
11. The method of claim 1, wherein said plurality of nucleic acid molecules are single stranded.
12. The method of claim 1, wherein said plurality of nucleic acid molecules comprises cell-free DNA or RNA.
13. The method of claim 1, wherein said plurality of nucleic acid molecules is from a tumor.
14. The method of claim 1, further comprising processing said sequence to monitor a progression or regression of said disease in said subject in response to treatment.
17. The method of claim 1, wherein said cell-free biological sample comprises a bodily fluid comprising urine, saliva, blood, serum, plasma, tears, sputum, cerebrospinal fluid, synovial fluid, mucus, bile, semen, lymph, amniotic fluid, menstrual fluid, or combinations thereof.
19. The method of claim 1, further comprising computer processing said plurality of sequence reads to identify an epigenetic modification in said sequence, wherein said epigenetic modification is selected from methylation, phosphorylation, ubiquitination, sumoylation, acetylation, ribosylation, citrullination, and fragmentation.
21. The method of claim 1, wherein said disease is cancer, wherein said cancer is selected from the group consisting of colon cancer, non-small cell lung cancer, small cell lung cancer, breast cancer, hepatocellular carcinoma, liver cancer, skin cancer, malignant melanoma, endometrial cancer, esophageal cancer, gastric cancer, ovarian cancer, pancreatic cancer, brain cancer, leukemia, lymphoma, and myeloma.
23. The method of claim 1, further comprising using at least said subset of said plurality sequence reads identified in (e) to output an electronic report indicating that said subject has or is at risk of having said disease.
25. The method of claim 1, further comprising using at least said subset of said plurality sequence reads identified in (e) to provide a therapeutic intervention to said subject for said disease.
31. The method of claim 1, further comprising using at least said subset of said plurality sequence reads identified in (e) to monitor said subject for a progression or regression of said disease.
The teachings of Chan with respect to claim 1 are documented above in the rejection under 35 U.S.C. 103. Claims of copending Application No. 17/557972 is made obvious over instantly claimed invention. One of ordinary skill in the art would have had a reasonable expectation of success given the lack of novelty. It would have been obvious to identify a subject with a disease, comprising: providing cell free nucleic acids of a subject, sequencing nucleic acid sample, process sequences using a computer to compare against a reference, identify an epigenetic modification variation in a sequence, relate variation to identification of disease, and output an electronic report according to the limitations of the instant application based on copending US Patent Application No. 17/557972. Thus, the invention as a whole is made obvious over US Patent Application No. 17/557972.
This is a provisional nonstatutory double patenting rejection.
Applicants’ argument: “Applicant has amended claim 1 to recite, after step (a), "(b) preparing a single stranded DNA library from said plurality of nucleic acid molecules or derivatives thereof.” (Pg. 11)
Response: In response to applicant's arguments, it would be obvious to one skilled in the art to prepare single stranded DNA library according to the limitations of claim 1. Further, Chan does not explicitly specify single or double stranded DNA, thus it would be obvious to prepare a library based off of the contents of the cfDNA which generally comprises single stranded DNA according to the teachings by Chan.
Conclusion of Response to Arguments
In view of the amendments, new grounds of rejections and above responses to arguments are documented in this Final Office Action. No claims are in condition for allowance.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
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, Winston Shen can be reached at (571)272-3157. 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.
/KENDRA R VANN-OJUEKAIYE/ Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682