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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 3/5/2026 has been entered.
Election/Restrictions
Applicant’s election without traverse of Group I (claims 125-129 and 131-144) and species (A) bisulfite sequencing, (B) CpG islands, and (C) lung cancer in the reply filed on 5/6/2025 is acknowledged.
Claim Status
Claims 125-129, 131-144, and 170-173 are pending and being examined on the merits.
Claim Rejections - 35 USC § 112b - Indefiniteness
Withdrawn 112b Claim Rejections
The rejection of claim 132 under 35 U.S.C. 112(b) as described in the Office Action of 11/10/2025 is withdrawn in light of Applicant’s amendment of the claim.
New 112b Claim Rejections
Claims 125-129, 131-144, and 170-173 are 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 125 is directed to a method for assessing tumor status of a subject with cancer. In lines 10-13 and 14, claim 125 recites “obtaining first sequencing data of a first plurality of cfDNA molecules, wherein the first plurality of cfDNA molecules is obtained or derived from a bodily fluid sample of the subject at the first time point”. However, in lines 3-5, claim 125 recites “obtaining first methylation sequencing (MS) data of a first plurality of cell-free DNA (cfDNA molecules) across a region of a genome, wherein the first plurality of cfDNA molecules across the region of the genome is obtained or derived from a first bodily fluid sample of the subject at a first time point”. Given the additional recitation of “a first plurality of cfDNA molecules” and “a bodily fluid sample” in the same claim, it is unclear if these are the same first plurality of cfDNA molecules from the same bodily fluid sample or not. The same repetition occurs for “a second plurality of cfDNA molecules” from “a second bodily fluid sample” in lines 19-22 and lines 26-31. Clarification is required.
Claim 125 also recited the limitation “determining a first tumor fraction of the subject at the first timepoint and a second tumor fraction of the subject at the second timepoint, based at least in part on the CNA profile change, the fragment length profile change, and the respective methylation profiles”. However, it is unclear how a change in CNA profile and fragment length profile can be used to determine a first tumor fraction at the first time point. The instant specification states in paragraph [0250] that:
“Assessing changes in ctDNA over time via a direct comparison of the CNA-derived estimate of TF between a patient's time points may not always be reliable because there may be ambiguity in which read depth levels correspond to which structural events. For example, two regions may be called as either a neutral region and a duplicated region, or a heterozygous deletion and a neutral region, in a highly mutated tumor where there is an ambiguous neutral level. To circumvent this challenge, CNAs detected at multiple time points were compared longitudinally with a linear model to quantify TFR.”
So, change in CNA or fragment length profile can be used for determination of the tumor fraction ratio (to determine tumor status), but cannot be used at individual time points to determine a first tumor fraction or second tumor fraction, as currently claimed. Clarification is required. For the purposes of examination, CNA profile and fragment length profile can be used at individual time points to calculate the first or second tumor fractions, while change in the profiles is used for calculation tumor status/tumor fraction ratio.
Claims 126-129, 131-144, and 170-173 depend from claim 125, inherit these deficiencies, and are rejected on the same basis.
Claim 170 is directed to the method of claim 125 “wherein the first and second pluralities of fragment lengths are determined by processing first and second whole genome sequencing (WGS) data obtained from the first and second pluralities of cfDNA molecules, respectively”. However, it is unclear which first and second pluralities of cfDNA molecules are being subjected to whole genome sequencing to yield said data, as there are two sets of first and second pluralities of cfDNA molecules, one set for methylation sequencing and one set for an unspecified form of sequencing. Clarification is required.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 125-129, 131-132, 137-140, 142-144, and 170-173 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Davis (Davis et al., MedRxiv November 25, 2019; cited on IDS of 5/6/2025).
Regarding claim 125: Davis teaches a method for assessing a tumor status of a subject with cancer by, at a first time point preceding administration of a therapeutic configure to treat the cancer to the subject and a second time point subsequent to administration of the therapeutic, obtaining first methylation sequencing (MS) data and second MS data of a first plurality and second plurality of cell-free DNA molecules across a region of a genome from a first bodily fluid sample and a second bodily fluid sample (pg 9-10, Longitudinal changes in methylation levels may complement tumor fraction changes). Davis teaches that the MS data is used to construct a methylation profile at each time point (Fig. 5). Davis additionally teaches at said first and second time points, obtaining sequencing data from the plurality of cfDNA molecules from a bodily fluid sample and determining CNAs and fragment lengths to construct CNA and fragment length profiles and used the difference in said profiles to determine tumor status (tumor fraction ratio, TFR; pg 7, Serial measurements of ctDNA show rapid changes early on treatment). Davis teaches detecting a tumor status, at least in part, based on the CNA profile change, fragment length profile change, and methylation profiles (pg 9-10, Longitudinal changes in methylation levels may complement tumor fraction changes).
Regarding claim 126: Davis teaches using bisulfite conversion for methylation sequencing, and thus comprises 5-methylcytosine status (pg 5, Sample preparation).
Regarding claim 127: Davis teaches that the first or second bodily fluid sample is blood (pg 5, Sample preparation).
Regarding claim 128: Davis teaches obtaining first MS data by performing methylation sequencing on a first plurality of cDNA molecules to generate a first plurality of sequencing reads (pg 5, Sample preparation).
Regarding claim 129 and 131: Davis teaches using whole genome bisulfite sequencing (pg 5, Sample preparation).
Regarding claim 132: Davis teaches aligning the first plurality of sequencing reads to a reference genome, thereby producing a plurality of aligned sequencing reads (pg 5, Bioinformatics methods).
Regarding claim 137: Davis teaches detecting tumor progression of the subject when a tumor fraction ratio (TFR) is greater than 1 (pg 10, Longitudinal changes in methylation levels may complement tumor fraction changes; Fig. 2D).
Regarding claim 138: Davis teaches detecting a major molecular response of the subject when a TFR is less than 0.4 (Fig. 2E).
Regarding claim 139: Davis teaches determining non-progression if progression is not detected (Fig. 2D).
Regarding claim 140: Davis teaches that based on the determined tumor status, patients could be administered a different, potentially effective therapy to treat the cancer (pg 12).
Regarding claim 142: Davis teaches that the detected tumor status is indicateive of tumor-progression or non-progression (Fig 2D).
Regarding claim 143: Davis teaches that the fist and second MS data are obtained by a sequencing device (Illumina HiSeq X, pg 5 Sample preparation).
Regarding claim 144: Davis teaches that the subject has lung cancer (Table 1).
Regarding claim 170-171: Davis teaches that the plurality of fragment lengths are determined by processing WGS data of the cfDNA and Davis teaches that the first and second sequencing data are WGS data (pg 7, Serial measurements of ctDNA show rapid changes early on treatment).
Regarding claim 172: Davis teaches that WGS and WGBS could be performed on the same samples data (pg 7, Serial measurements of ctDNA show rapid changes early on treatment).
Regarding claim 173: Davis teaches obtaining first and second WGS data by sequencing the first and second pluralities of cfDNA molecules to generate a first and second plurality of sequencing reads (pg 7, Serial measurements of ctDNA show rapid changes early on treatment and pg5, Sample preparation).
Claim Rejections - 35 USC § 103
Withdrawn:
The rejection of claims 125-129 and 131-140, 142-144, and 170 under 35 U.S.C. 103 as being unpatentable over Valouev et al. (US2021/0065842A1; published Mar 4, 2021, filed July 23, 2020, with an effectively filed date of July 23, 2019; cited on PTO-892 of 5/30/2025) in view of Velculescu et al. (US 2020/0131571 A1, EFD of May 18, 2018) is withdrawn in light of Applicant’s amendments to the claims.
The rejection of claim 141 under 35 U.S.C. 103 as being unpatentable over Valouev et al. (US2021/0065842A1; published Mar 4, 2021, filed July 23, 2020, with an effectively filed date of July 23, 2019; cited on PTO-892 of 5/30/2025) in view of Velculescu et al. (US 2020/0131571 A1, EFD of May 18, 2018) as applied to claims 125-129 and 131-140, 142-144, and 170 above, and further in view of Sun et al. (PNAS, 2015; cited on PTO-892 of 5/30/2025) is withdrawn in light of Applicant’s amendments to the claims.
New:
Claims 133-136 are rejected under 35 U.S.C. 103 as being unpatentable over Davis (Davis et al., MedRxiv November 25, 2019; cited on IDS of 5/6/2025) in view of Valouev et al. (US2021/0065842A1; published Mar 4, 2021, filed July 23, 2020, with an effectively filed date of July 23, 2019; cited on PTO-892 of 5/30/2025).
The teachings of Davis in regards to claims 125 and 128, from which these claims depend, are detailed above. Relevant to the instantly rejected claims, Davis teaches a method of using methylation profiles, CNA profiles, and fragmentation profiles of pluralities of cfDNA at first and second time points for determining tumor fraction ratios and thus a tumor status of a subject with cancer.
Davis does not teach enriching the pluralities of cfDNA for regions of the genome (claim 133), that the region of the genome comprises CpG islands (claim 134), that the regions of the genome comprise a plurality of non-overlapping regions of the genome (claim 135), or that determining the first or second tumor fraction comprises comparing the first or second methylation profile with a reference methylation profile (claim 136). However, each of these steps in regards to building molecular profiles for determination of tumor status in a patient is known in the art, as taught by Valouev et al.
Regarding claim 133: Valouev et al. teach a method of obtaining first and second pluralities of cfDNA from a subject and analyzing the methylation status of genomic regions (“bins”) to determine tumor fraction and subsequently tumor status of the patient. Valouev et al. teach enriching the cfDNA molecules for specific regions of the genome (paragraph [0235 and 0357]).
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 Davis with that of Valouev et al. One would be motivated to do so given the assertion by Valouev et al. that performing targeted sequencing “obtains significant information about regions of interest in the reference genome of the subject while being more efficient” (paragraph [0235]). One would have a reasonable expectation of success given that Valouev et al. performs enrichment on biological samples that contain cfDNA.
Regarding claim 134: Valouev et al. teach that the region of the genome analyzed comprises CpG islands (paragraph [0189]).
Regrading claim 135: Valouev et al. teach that each region of the genome (or “bin”) analyzed in a plurality of regions is non-overlapping (paragraph [0044]).
Regarding claim 136: Valouev et al. teach determining abnormal methylation by comparing methylation states to a reference dataset of methylation states such as those observed in a cohort of healthy reference subjects (paragraph [0194]). Additionally, Valouev et al. teach that abnormal methylation can be determined by comparison to a control sample from the subject themselves (which reads on subjects with cancer; paragraph [0118]).
Claim 141 is rejected under 35 U.S.C. 103 as being unpatentable over Davis (Davis et al., MedRxiv November 25, 2019; cited on IDS of 5/6/2025) in view of Landau et al. (WO 2019/169044 A1; published 9/6/2019).
The teachings of Davis in regards to claims 125 and 128, from which these claims depend, are detailed above. Relevant to the instantly rejected claims, Davis teaches a method of using methylation profiles, CNA profiles, and fragmentation profiles of pluralities of cfDNA at first and second time points for determining tumor fraction ratios and thus a tumor status of a subject with cancer.
Davis does not teach that a source of cfDNA in the biological sample is from immune cells of the subject. However, cfDNA originating from immune cells in the biological samples from subjects with cancer is known in the art, as taught by Landau et al.
Landau et al. teach a method for detecting minimal residual tumor disease in a human cancer patient (Abstract). Landau et al. teaches constructing an integrative mathematical model that uses information on CNVs to estimate tumor fraction in a patient plasma or blood sample through sequencing of cfDNA (paragraph [0008]). Landau et al. teaches that immune cells are a source of cfDNA in patient samples (paragraph [00295]).
It would have been prima facie obvious to one having ordinary skill in the art, before the effective filing date of the instant application, that the method of Davis (collection of blood samples from patients to analyze cfDNA) would have contained cfDNA molecules from immune cells of the subject, as taught by Landau et al. Landau et al. teaches that normal DNA degradation during blood circulation involves generation of DNA fragments “that originate mainly from apoptosis of hematopoietic cells (immune cells)” (paragraph [0295]).
Claims 125-129, 131-140, 142-144, 170-171, and 173 are rejected under 35 U.S.C. 103 as being unpatentable over Valouev et al. (US2021/0065842A1; published Mar 4, 2021, filed July 23, 2020, with an effectively filed date of July 23, 2019; cited on PTO-892 of 5/30/2025) in view of Landau et al. (WO 2019/169044 A1; published 9/6/2019).
Valouev et al. teach a method of obtaining first and second pluralities of cfDNA from a subject and analyzing the methylation status of genomic regions (“bins”) to determine tumor fraction and subsequently tumor status of the patient.
Regarding claim 125: Valouev et al. teach obtaining methylation sequencing data from a first plurality of cfDNA molecules (paragraph [0046]) across a region of a genome (“bin”, paragraph [0012]) from a first bodily fluid sample of a subject (paragraph [0012]). Valouev et al. teach that sampling of cfDNA from bodily fluid and determining the tumor fraction can occur at one or more time points, such as before or after treatment (paragraph [0288 and 0291]). Valouev et al. teach that based on the methylation sequencing data, a methylation profile can be determined for a specific region which in turn can be used to determine tumor fraction (paragraphs [0129 and 0264]). Valouev et al. additionally teaches that the tumor fraction can be estimated by copy number values given the known association between copy number variations and ctDNA (paragraphs [0005, 0015, 0097]). Valouev et al. teaches determining copy number values from a plurality of cfDNA molecules using sequencing data (paragraphs [0012, 0013, 0250, 0252]). Valouev et al. teaches that copy number can be used alone or in combination with methylation data to determine tumor fraction (paragraph [0277]). Using the methylation sequencing data and the copy number data at the various timepoints (before and after treatment), the tumor fractions at the respective time points are determined (Figure 9 and paragraphs [0059, 0102, and 0277]). Valouev et al. teach that methylation sequencing alone or in combination with other values (copy number) can be used to determine tumor fraction at various time points (paragraph [0102 and 0277]). Valouev et al. teach that the tumor status can be determined in part by the first tumor fraction and/or the second tumor fraction (paragraph [0288]). Valouev et al. teach comparing the tumor fraction between first and second time points, which also reads on comparing the first and second methylation profiles and the first and second CNA profiles, given that the methylation profiles and CNA profiles are used to determine the tumor fraction. Valouev et al. teach that the tumor status is assessed in a subject with cancer (monitoring disease progression before and after treatment indicates that the subject is known to have cancer; paragraph [0291]).
Valouev et al. do not teach obtaining a first or second plurality of fragment lengths associated with the first and second plurality of cfDNA molecules and determining a first and second fragment length profile which is then used in conjunction with the methylation profiles and CNA profiles, in part, to determine the first and second tumor fractions at the first and second time points to assess tumor status. However, use of fragment length profiles in conjunction with CNAs to determine tumor fraction is known in the art, as taught by Landau et al.
Landau et al. teach a method for detecting minimal residual tumor disease in a human cancer patient (Abstract). Landau et al. teaches constructing an integrative mathematical model that uses information on CNVs to estimate tumor fraction in a patient plasma or blood sample (paragraph [0008]). Landau et al. teach receiving a first compendium of reads (sequencing reads, such as from whole genome sequencing, paragraph [0198]) from a biological sample as a baseline sample and then comparing said CNV profile to a second compendium of reads from a second biological sample to calculate CNVs to obtain a change in CNV profile to determine true CNVs and calculate a first estimated tumor fraction and a second estimated tumor fraction to perform comparisons such as to be used for monitoring effectiveness of therapy (paragraph [0014, 0026, 0030]). Landau et al. additionally teaches that fragment size profiles can be orthogonally integrated with CNVs to calculate tumor fraction (paragraph [0050, 00159, 00213, 00295, 00298-00302]).
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 Valouev et al. with that of Landau et al. One would be motivated to do so given the assertion by Landau et al. integration of orthogonal measures such as change in fragment size profile increases “sensitivity, specificity and/or reliability of detection” (paragraph [00159]). One would have a reasonable expectation of success given that Landau et al. successfully performs whole genome sequencing and fragment length analysis at multiple time points throughout treatment and orthogonally combines said measurements with CNV analysis (reads on CNAs) to determine tumor fraction (Figure 11).
Regarding claim 126: Valouev et al. teach that the methylation profile contains information on 5-methylcytosine status (paragraph [0129]).
Regarding claim 127: Valouev et al. teach that the bodily fluid sample is blood (paragraph [0038]).
Regarding claim 128: Valouev et al. teach performing methylation sequencing to generate a plurality of sequencing reads for the first time point (paragraph [0395]).
Regarding claim 129: Valouev et al. teach that the methylation sequencing comprises whole genome bisulfite sequencing (paragraphs [0260-0261]).
Regarding claim 131: Valouev et al. teach the methylation sequencing comprises bisulfite sequencing (paragraph [0260]).
Regarding claim 132: Valouev et al. teach aligning the sequencing reads to a reference genome (paragraph [0397]).
Regarding claim 133: Valouev et al. teach enriching the cfDNA molecules for specific regions of the genome (paragraph [0357]).
Regarding claim 134: Valouev et al. teach that the region of the genome analyzed comprises CpG islands (paragraph [0189]).
Regrading claim 135: Valouev et al. teach that each region of the genome (or “bin”) analyzed in a plurality of regions is non-overlapping (paragraph [0044]).
Regarding claim 136: Valouev et al. teach determining abnormal methylation by comparing methylation states to a reference dataset of methylation states such as those observed in a cohort of healthy reference subjects (paragraph [0194]). Additionally, Valouev et al. teach that abnormal methylation can be determined by comparison to a control sample from the subject themselves (which reads on subjects with cancer; paragraph [0118]).
Regarding claim 137: Valouev et al. teach that increase in tumor fraction between the first and second time points indicates tumor progression (paragraph [0288]). Therefore, if the second tumor fraction is greater than the first tumor fraction, then the tumor fraction ratio is greater than 1.
Regarding claim 138: Valouev et al. teach that a decrease in the tumor fraction over time can indicate successful treatment (TFR < 1). Valouev et al. teach that monitoring treatment effectiveness comprises determining a change in tumor fraction by a threshold amount to inform treatment changes, diagnosis changes, or prognosis changes (paragraph [0290]). Valouev et al. specifically say that this threshold indicating a significant response is a greater than 50 percent change between the first tumor fraction to the second tumor fraction (which reads on less than 0.5; paragraph [0290]).
Regarding claim 139: Valouev et al. teach determining progression, remission, or recurrence of the tumor/cancer. Remission or recurrence of cancer are tumor non-progression states (paragraph [0291]).
Regarding claim 140: Valouev et al. teach administering a second therapeutic to treat the cancer of the subject based on the determined tumor status (paragraph [0302]).
Regarding claim 141: Landau et al. teaches that immune cells are a source of cfDNA in patient samples (paragraph [00295]).
Regarding claim 142: Valouev et al. teach determining progression, remission, or recurrence of the tumor/cancer based on tumor status (paragraph [0291]).
Regarding claim 143: Valouev et al. teach that the method is performed at a computer system comprising at least one processor (paragraph [0012]).
In addition, it is noted that the courts have held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art (In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958)). See MPEP 2144.04 III.
Thus, performing any step of the claimed method with a computer is obvious.
Regarding claim 144: Valouev et al. teach that the subject has lung cancer (paragraph [0039]).
Regarding claim 170, 171, and 173: Landau et al. teach obtaining CNV and fragment length profiles from whole genome sequencing data by sequencing the plurality of cfDNA molecules at different time points (paragraph [00198, 00301]), while Valouev et al. teaches enriching for specific genomic regions (paragraph [0357]).
Regarding claim 172: Valouev et al. teaches that the whole genome sequencing and the methylation sequencing can be obtained from different samples (paragraph [0234, 0239, 0241]).
Response to Remarks
In the Remarks submitted on 3/5/2026, Applicant traversed the rejection of claims 125-129, 131-140, 139, 142-144, and 170 under 35 USC 103 as being obvious over Valouev et al. in view of Velculescu et al. (pages 9-12). Applicant’s arguments regarding the rejection of the above claims as obvious over Valouev et al. in view of Velculescu et al. are rendered moot by the amendment of the claims to include the assessment of CNA profiles in the determination of tumor fraction in claim 125. The previous rejection of claims 129, 131-140, 139, 142-144, and 170 under 35 USC 103 as being obvious over Valouev et al. in view of Velculescu et al. has been withdrawn and a new 103 rejection is presented above to address the further limitations.
Applicant argues on page 13 of Remarks that “assessing tumor fraction was found to provide an indication of ‘molecular progression’ preceded detection of progression by imaging by a median of 40 days” as a superior result of the claimed methodology. In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., earlier indication of responsiveness or non-responsiveness than detection by imaging) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
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.
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/KAILEY ELIZABETH CASH/Examiner, Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683
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