DETAILED ACTION
Applicant’s response, filed 02 March 2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 02 March 2026 has been entered.
Status of Claims
Claims 1-67, 69, 74-75, 78-83, and 85 are cancelled.
Claims 86 is newly added.
Claims 68, 70-73, 76-77, 84, and 86 are pending.
Claims 68, 70-73, 76-77, 84, and 86 are rejected.
Claim 68 is objected to.
Priority
Applicant’s claim for the benefit of a prior-filed application, U.S. Non-Provisional App. No. 17/842,893 filed 17 March 2021, U.S. Non-Provisional App. No. 16/730,938 filed 30 Dec. 2019, U.S. Provisional App. No. 62/795,900 filed 23 Jan. 2019, and U.S. Provisional App. No. 62/673,516 filed 18 May 2018 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Accordingly, the effective filing date of the claimed invention is 18 May 2018.
Information Disclosure Statement
The information disclosure statement (IDS) filed 20 March 2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Objections
The previous objection to claim 68 in the Office action mailed 31 Oct. 2025 has been withdrawn in view of claim amendments received 02 March 2026.
Claim 68 is objected to because of the following informalities. This objection is newly recited and necessitated by claim amendment.
Claim 68 recites “…h) comparing…, wherein the determination of cancer status…of cancer; wherein position….thereby determining the cancer status”, which is grammatically incorrect and should include and “and” rather than a “;” between the two wherein clauses, and furthermore, a comma should be placed before “thereby”. The claim should recite “…h) comparing…, wherein the determination of cancer status…of cancer and wherein position…., thereby determining the cancer status”
Appropriate correction is required.
Response to Arguments
Applicant's arguments filed 02 March 2026 regarding the claim objections have been fully considered but they do not pertain to the newly recited objection set forth above.
Claim Interpretation
Claim 84 recites “The method of claim 70 wherein the reference profile is obtained from the subject prior to a cancer treatment”. This limitation only serves to define the process in which the reference profile was previously determined. However, the claims do not require a step of obtaining the reference profile. "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985) (citations omitted). See MPEP 2113 I.
Claim Rejections - 35 USC § 112(a)
The rejection of claims 84-85 under 35 U.S.C. 112(a) in the Office action mailed 31 Oct. 2025 has been withdrawn in view of claim amendments cancellations received 02 March 2026.
Claim Rejections - 35 USC § 112(b)
The previous rejection of claims 70-72, 76, and 84-85 under 35 U.S.C. 112(b) in the Office action mailed 31 Oct. 2025 has been withdrawn in view of claim amendments cancellations received 02 March 2026.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 68, 70-73, 76-77, 84, and 86 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. This rejection is newly recited and necessitated by claim amendment.
Claim 68, is indefinite for recitation of “f)…a ratio of small cfDNA fragments to large cfDNA fragments”. The terms “small” and “large” are relative terms which render the claim indefinite. The terms are not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. As a result it is not clear what size fragments would be considered “small… fragments” and/or “large…fragments”. Clarification is requested via claim amendment. For purpose of examination, the claim will be interpreted to mean the ratio is of smaller cfDNA fragments to larger cfDNA fragments, such that the ratio is of any size small to any size large fragments so long as the numerator size is smaller than the denominator size.
Dependent claims 70-73, 76-77, and 84 are rejected based on their dependency to claim 68, and because they do not serve to resolve the indefiniteness. It is noted that dependent claim 86 does resolve the indefiniteness and is not rejected under 112(b).
Claim 86 is indefinite for recitation of “about 151 bp to 220 bp in length”. The term “about” is a relative terms which render the claim indefinite. The term is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. As a result, it is unclear what range of sizes is encompassed by “about 151 bp to 220 bp”. Clarification is requested.
Claim Rejections - 35 USC § 112(d)
The rejection of claim 78 under 35 U.S.C. 112(d) in the Office action mailed 31 Oct. 2025 has been withdrawn in view of the cancellation of this claim received 02 March 2026.
Claim Rejections - 35 USC § 101
The rejection of claims 78 and 85 under 35 U.S.C. 101 in the Office action mailed 31 Oct. 2025 has been withdrawn in view of the cancellation of these claims received 02 March 2026.
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 68, 70-73, 76-77, 84, and 86 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception(s) without significantly more. Any newly recited portion herein is necessitated by claim amendment.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claim 68 being representative) is directed a method of determining a fragmentation profile. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claim 68 recites the following steps which fall under the mental processes and/or mathematical concepts groupings of abstract ideas:
e) mapping the sequenced fragments to a reference genome to generate positional and size-based data;
f) producing a cfDNA fragmentation profile from the mapped sequencing data wherein the fragmentation profile comprises a ratio of small cfDNA fragments to large cfDNA fragments, a fragment size distribution, a fragment coverage, and positional fragmentation metrics across the whole genome or subgenomic intervals;
g) determining a change in chromosomal arm DNA copy number from the sequenced fragments of cfDNA from the subject;
h) comparing the cfDNA fragmentation profile to a reference cfDNA fragmentation profile to determine the cancer status of the subject, wherein the determination of the cancer status is based on fragmentation patterns indicative of cancer; wherein position dependent differences in fragmentation patterns are used to distinguish cancer-derived cfDNA from reference cfDNA, thereby determining the cancer status of the subject.
The identified claim limitations falls into the mental processes grouping of abstract ideas for the following reasons. Mapping sequenced fragments to a reference genome to generate the recited data can be practically performed in the mind by performing one to one comparisons of each sequence read and locations in a reference genome to identify a matching sequence in the reference genome and then identify the length of the matching region to determine the length of the respective read. Producing the cfDNA fragmentation profile as claimed involves counting numbers of cfDNA fragments of each length to produce ratios, a distribution, counts of each cfDNA fragments corresponding to a particular region or regions in a genome to obtain a coverage, and simply analyzing the fragment position to identify “metrics”, which amounts to a mere analysis of data that can be practically performed in the mind. Determining the existence of a change in chromosomal DNA copy number arm from a cfDNA sample encompasses comparing read counts at particular bins in the sample to reference read bins of a reference profile to determine if there is a difference (i.e. a copy number change exists). Last, comparing the cfDNA fragmentation profile to a reference to determine a cancer status involves performing data comparisons to determine if the cfDNA fragmentation profile has characteristics similar to a cancer reference or different than a healthy reference, including comparing fragmentation patterns between the profile and reference profile, which can be practically performed in the human mind. Therefore, these limitations recite a mental process. See MPEP 2106.04(a)(2) III.
The limitations of producing a cfDNA fragmentation profile comprising a ratio of small cfDNA fragments to large cfDNA fragments, a fragment size distribution, a fragment coverage, and positional fragmentation metrics further recites a mathematical concept. For example, determining a ratio is a mathematical relationship and similarly determining a fragment size distribution represents a mathematical relationship of sizes of cell-free DNA. Determining fragment coverages involves determining proportions of a region covered by fragments, which is a textual equivalent to performing mathematical calculations. Last, determining fragmentation “metrics” encompasses statistical metrics in light if Applicant’s specification ([0020]) which discloses metrics relating to ratios of small to large fragments. Therefore, these limitations further recite a mathematical concept. See MPEP 2106.04(a)(2) I.
Dependent claims 70-73, 76, 84, and 86 further recite an abstract idea and/or are part of the judicial exception of claim 68. Dependent claim 70 further recites the mental process of identifying the subject as having cancer when the cfDNA fragmentation profile obtained from the subject is different from the reference cfDNA fragmentation profile. Dependent claims 71-72 further limit the reference cfDNA fragmentation profile to be of at least one mammal without cancer and to have been generated from a sample obtained from the at least one mammal without cancer, and thus are part of the judicial exception(s) of comparing the cfDNA fragmentation profile to a reference cfDNA fragmentation profile and identifying cancer of claim 70, from which claims 71-72 depend. Dependent claim 73 fails to further limit claim 68 and thus is part of the judicial exception of claim 68. Dependent claim 76 further recites the mental process of the cfDNA fragmentation profile of the subject comprising a sequence coverage of cfDNA fragments in chromosome arms, which encompasses counting reads aligned to the chromosome arms to determine a depth of coverage. Dependent claim 84 further limits the reference profile used in the mental process of claim 70 and thus is part of the abstract idea. Dependent claim 86 further limits the mental process and mathematical concept of determining ratios to be a ratio of particular cfDNA sizes for the small and large fragments.
Dependent claims 70-72 further recite the law of nature of a natural correlation between cell-free DNA fragment sizes in a subject and the presence of cancer in the subject, similar to a correlation between the presence of myeloperoxidase in a bodily sample (such as blood or plasma) and cardiovascular disease risk, Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1361, 123 USPQ2d 1081, 1087 (Fed. Cir. 2017). Therefore, claims 68, 70-73, 76-77, 84, and 86 recite an abstract idea and law of nature. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Claims 70-73, 76, 85, and 86 do not recite any elements in addition to the judicial exception and thus are part of the judicial exception.
The additional elements of claim 68 include:
a) processing a sample obtained from the subject to obtain a plasma fraction;
b) extracting cfDNA fragments from the plasma fraction, wherein the cfDNA fragments from the plasma fraction comprise nucleosome protected cfDNA fragments;
c) processing the cfDNA fragments into sequencing libraries;
d) subjecting the sequencing libraries to whole genome sequencing to obtain sequenced fragments, wherein genome coverage is 9x to 0.1x; and
i) administering to the subject a cancer treatment, wherein the cancer treatment comprises an immune checkpoint inhibitor, adoptive T cell therapy or chemotherapeutic agent.
The additional element of claim 77 includes:
wherein the genome coverage is 2x, 1x, 0.5x, 0.2x, or 0.1x.
The additional elements of claim 68 of processing a sample to obtain a plasma fraction, extracting cfDNA fragments from the plasma fraction, including nucleosome protected cfDNA fragments, processing the cfDNA fragments of the sample to obtain sequencing libraries, and sequencing the sequencing libraries at the recited depth only serves to collect sequencing data for use by the abstract idea (i.e. for generation of the cfDNA fragmentation profile and cancer classification), which amounts to insignificant extra-solution activity that does not integrate the recited judicial exception into a practical application. See MPEP 2106.05(g).
The step of administering to the subject a cancer treatment is not sufficient to integrate the recited judicial exception into a practical application for the following reasons. MPEP 2106.04(d)(2) states the treatment or prophylaxis limitation must have more than a nominal or insignificant relationship to the exception(s). In the instant case, claim 68 compares the cfDNA fragmentation profile to a reference profile to determine a cancer status of the subject, and then administers the subject a cancer treatment regardless of whether the cancer status of the subject indicates no cancer or indicates cancer. As a result, the administering step does not have a significant relationship with the judicial exception, as it does not apply the judicial exception in any meaningful way. Instead, the limitation amounts to mere instructions to apply the exception (e.g. administer a cancer treatment), regardless of the cancer status identified by the judicial exception. See MPEP 2106.04(d)(2) and MPEP 2106.05(f).
Therefore, the additionally recited elements amount to insignificant extra-solution activity and, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 68, 70-73, 76-77, 84, and 86 are directed to an abstract idea and/or law of nature. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
Claims 70-73, 76, 77, 84, and 86 do not recite any elements in addition to the judicial exception and thus are part of the judicial exception. The additional elements of claims 68 and 77 are set forth above.
The additional elements of processing a sample to obtain a plasma fraction, extracting cfDNA fragments from the plasma fraction, including nucleosome protected cfDNA fragments, processing cfDNA fragments obtained from the sample of the subject into sequencing libraries and performing whole genome sequencing at a coverage of 9x to 0.1x, including 2x, 1x, 0.5x, 0.2x, or 0.1x, to obtain sequence fragments are well-understood, routine, and conventional. This position is supported by Cai et al. (Accessing Genetic Information with Liquid Biopsies, 2015, Trends in Genetics, 31(10), pg. 564-575; previously cited), Ma et al. (Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns, 2017, PLOS ONE, pg. 1-18; previously cited), and Heitzer et al. (Circulation Tumor DNA as a Liquid Biopsy for Cancer, 2015, Clinical Chemistry, 61:1, pg. 112-123; previously cited). Cai reviews circulating tumor cells in cell-free DNA (Abstract), and discloses that whole genome next generation sequencing is a major approach for analyzing cell-free DNA (pg. 571, para. 1), and that sequencing involves preforming library preparation on a cfDNA sample prior to sequencing (pg. 567, para. 3). Cai further discloses sequencing cell-free DNA involves analyzing cfDNA from plasma samples (i.e. plasma fractions obtained from blood sample of subject) (pg. 571, para. 1; pg. 572, para. 1). Furthermore, Ma analyzes methods for performing sequencing on cfDNA (Abstract), and discloses that next-generation sequencing techniques have been deployed at low coverage depths from 0.1X-10X to successfully identify copy number variation in cfDNA, citing multiple studies (pg. 2, para. 2; pg. 7, para. 3). Heitzer reviews the use of circulating tumor DNA as a liquid biopsy for cancer, and discloses that since 1994, numerous studies have analyzed DNA in plasma (i.e. cfDNA), including by performing library preparation and whole-genome sequencing (pg. 118, col. 3, para. 4 to pg. 119, col. 1, para. 1). Heitzer discloses such liquid biopsies include blood collection, processing, and DNA extraction from plasma fractions (pg. 120, col. 2, para. 3), and that that methods based on low-coverage sequencing of cell-free DNA have been shown to provide clinically relevant information in a cost-effective manner (pg. 120, col. 1, para. 3). Last, Heitzer discloses that it is known that cell-free DNA fragments being analyzed in plasma correspond to nucleosome-protected fragments, such that the limitation of extracting and purifying nucleosome protected fragments is inherent in extraction and purification of cell-free DNA from plasma (Fig. 4; pg. 114, col. 2, para. 1). Last, Applicant’s specification at pg. 27 lines 5-26, discloses using various commercially available kits known in the art for purifying and preparing cfDNA fragments for sequencing, such that the written description describes the additional elements as known in the art. See MPEP 2106.05(d) I. In addition, Applicant’s remarks filed 06 Feb. 2025, at pg. 12, para. 2, states it is common to make use of these commercial kits and reagents. Accordingly, the combination of additional elements of obtaining a blood/plasma sample of the subject, processing the sample to obtain a plasma fraction, extract/purify nucleosome protected cfDNA, generating sequencing libraries, and then performing whole-genome sequencing on the sequencing libraries at a coverage of 0.1X is well-understood, routine, and conventional.
The step of administering to the subject a cancer treatment including an immune checkpoint inhibitor, adoptive T cell therapy, or chemotherapeutic agent is well-understood, routine, and conventional. This position is supported by Applicant’s specification at para. [0054]-[0056] which discloses a plurality of commercially available immune checkpoint inhibitors, adoptive T cell therapies, and chemotherapeutic agents available for cancer treatment.
Therefore, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception. Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea and/or law of nature without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Arguments
Applicant's arguments filed 02 March 2026 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks that claim 68 is amended to require that the treatment step is mandatory rather than condition, and therefore the amended claims integrate the recited judicial exception into a practical application of effecting a particular treatment for a disease or medical condition (Applicant’s remarks at pg. 6, para. 5 to pg. 9, para. 1).
This argument is not persuasive. As discussed in the above rejection, while the treatment step is no longer a contingent limitation and is instead required by the claims, the claimed administering step has a nominal relationship to the judicial exception. MPEP 2106.04(d)(2) states the treatment or prophylaxis limitation must have more than a nominal or insignificant relationship to the exception(s). In the instant case, claim 68 compares the cfDNA fragmentation profile to a reference profile to determine a cancer status of the subject, and then administers the subject a cancer treatment regardless of whether the cancer status of the subject indicates no cancer or indicates cancer. As a result, the administering step does not have a significant relationship with the judicial exception, as it does not apply the judicial exception in any meaningful way. Instead, the limitation amounts to mere instructions to apply the exception (e.g. administer a cancer treatment), regardless of the cancer status identified by the judicial exception. See MPEP 2106.04(d)(2) and MPEP 2106.05(f).
Claim Rejections - 35 USC § 103
The rejection of claims 78 and 85 under 35 U.S.C. 103 in the Office action mailed 31 Oct. 2025 has been withdrawn in view of the cancellation of these claims received 02 March 2026.
The rejection of claims 68, 70-73, 76-77, and 84 under 35 U.S.C. 103 as being unpatentable over Lo (2017) in view of Ma (2017), as evidenced by Heitzer (2015) in the Office action mailed 31 Oct. 2025 has been withdrawn in view of claim amendments received 02 March 2026. However, after further consideration, a new grounds of rejection is set forth below in view of the claim amendments.
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.
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 68, 70-73, 76-77, 84, and 86 are rejected under 35 U.S.C. 103 as being unpatentable over Lo (2017) in view of Ma (2017) and Chiu (2013), as evidenced by Heitzer (2015). This rejection is newly recited and necessitated by claim amendment.
Cited reference:
Lo et al., US 2019/0130065 A1; effectively filed 02 Nov. 2017 based on priority to Provisional App. No. 62/580,906 (previously cited);
Ma et al., Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns, 2017, PLOS ONE, pg. 1-18 (previously cited);
Lo et al. (referred to as Chiu) US 2013/0237431 A1 (newly cited); and
Heitzer et al., Circulation Tumor DNA as a Liquid Biopsy for Cancer, 2015, Clinical Chemistry, 61:1, pg. 112-123 (previously cited).
Regarding claim 68 Lo discloses a method for detecting cancer in a subject (Abstract; [0007]; [0028]), comprising the following steps:
Lo discloses a) processing a blood sample to obtain plasma ([0028]; [0050]; [0185]).
Lo discloses b) extracting and purifying cfDNA fragments from the plasma ([0185]-[0186]).
Lo discloses c) performing sequencing library preparation on the cfDNA fragments to obtain sequence libraries ([0147], e.g. fragments from entire genome; [0186]; [0190]).
Lo discloses d) subjecting the sequencing libraries to whole genome sequencing to obtain sequenced fragments ([0032]; [0191], e.g. random sequencing is performed on all nucleic acid fragments in sample).
Lo discloses e) after sequencing, mapping the sequence reads to a reference genome to provide a length of the fragment and to determine the location of each read (i.e. positional and size-based data) ([0029]; [0192]).
Lo discloses f) producing a fragment size distribution of the sequence reads in the sample ([0031]; [0062]; FIG. 1), a ratio of a first amount of cell-free DNA molecules in a first size range to a second amount of cell-free DNA molecules in a second size range, ([0101]-[0102]; [0160]; FIG. 12; claims 1 and 11), sequence coverages for each size ratio of cfDNA fragments in chromosome arms (FIG. 10, #1040, e.g. Genomic Representation for sample for chromosome arms 1-N; [0147], e.g. genomic representation of a sequence coverage on a particular region), and cfDNA fragment size ratios of cfDNA fragments in each of multiple regions (i.e. positional fragmentation metrics across subgenomic intervals) (FIG. 6 #602, 604 and 610; [0097]-[0100]), thus producing the cfDNA fragmentation profile as claimed.
Lo discloses (g) determining the presence of a DNA copy number (CN) change of a chromosomal arm in the sequenced fragments ([0071]; [0097], e.g. cell-free DNA sample; [0098], e.g. copy number determined for chromosomal arm; [0099]; [0109], e.g. the machine learning outputs probability of a copy number aberration based on comparison to a reference size pattern; Fig. 6).
Lo discloses h) comparing the cfDNA fragmentation profile to a reference cfDNA fragmentation profile (FIG. 12 #1202-1208, e.g. size ratio pattern of sample and reference are compared; [0158]-[0161] and [0164]), and classifying (i.e. determining) the subject as having cancer based on differences between the fragment size ranges (i.e. fragmentation profile) of the subject and the reference size ranges exceeding a threshold, wherein the size ranges are determined for a specific genomic region (i.e. i.e. based on position dependent differences in fragmentation patterns indicative of cancer, thereby determining the cancer status) (FIG. 10, e.g. ratios for different chromosomal arms; [0102]; [0164]-[0165], e.g. subject classified as having cancer based on a similarity of the measurement sizes to the reference sizes exceeding a cutoff; FIG. 12).
Lo discloses i) treating the disease in the patient after determining the level of the disease or the condition of the patient, wherein the treatment may include any suitable therapy described herein ([0184]; [0110]),
Regarding claims 68 and dependent claim 77, Lo does not disclose the following:
Regarding claim 68, Lo does not explicitly disclose the cfDNA fragments are nucleosome protected cfDNA fragments. However, this limitation is inherent in Lo, as evidenced by Heizer.
Specifically, Heitzer reviews the use of circulating tumor DNA as a liquid biopsy for cancer, and discloses that since 1994, numerous studies have analyzed DNA in plasma (i.e. cfDNA), including by performing library preparation and whole-genome sequencing (pg. 118, col. 3, para. 4 to pg. 119, col. 1, para. 1). Heitzer discloses such liquid biopsies include blood collection, processing, and DNA extraction from plasma fractions (pg. 120, col. 2, para. 3), and that it is known that cell-free DNA fragments being analyzed in plasma correspond to nucleosome-protected fragments, such that the limitation of extracting and purifying nucleosome protected fragments is inherent in extraction and purification of cell-free DNA from plasma (Fig. 4; pg. 114, col. 2, para. 1). Therefore, given Lo discloses extracting and purifying cfDNA fragments, as discussed above, this inherently discloses that nucleosome-protected cfDNA fragments are extracted and purified.
Further regarding claim 68 and dependent claims 77 and 86, Lo does not disclose the following limitations:
Regarding claims 68 and 77, Lo further does not disclose the whole genome sequencing is performed at a coverage of 9x to 0.1x, as recited in claim 68, or at a coverage of 2x, 1x, 0.5x, 0.2x or 0.1x, as recited in claim 77.
However, Ma analyzes methods for performing sequencing on cfDNA (Abstract), and discloses that next-generation sequencing techniques have been deployed at low coverage depths from 0.1X-10X to successfully identify copy number variation in cfDNA (pg. 2, para. 2; pg. 7, para. 3), and specifically discloses performing whole-genome sequencing a depth of coverage of 1X (Fig. 1B; pg. 5, para. 2).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Lo to have performed whole-genome sequencing at depth of 1X on the cfDNA fragments, as shown by Ma (pg. 2, para 2; pg. 5, para. 2; pg. 7, para. 3; Fig. 1B). One of ordinary skill in the art would have been motivated to combine the methods of Lo and Ma to utilize coverage that allows for successful identification of copy number variation, as shown by Ma (pg. 2, para. 2; pg. 7, para. 3), given Lo involves detecting copy numbers from sequencing cell-free DNA, as discussed above. This modification would have had a reasonable expectation of success because both Lo and Ma discloses performing whole-genome sequencing on cell-free DNA, such that the low-coverage sequencing method of Ma is applicable to the method of Lo.
Further regarding claims 68 and 86, Lo does not disclose the size ratio is a ratio of small cfDNA fragments of 100 to 150 base pairs in length to large cfDNA fragments 151 to 220 base pairs in length.
However, Chiu similarly discloses a method for determining a cell-free DNA fragmentation profile for a subject (Abstract), which comprises determining a size profile including size parameters ([0051]; [0099]), wherein the size parameters include a ratio of the amount of cfDNA fragment of 100 to 150 base pairs in length to the amount of cfDNA fragments 163-169 base pairs in length (i.e. a ratio of smaller 100-150 base pair fragments to larger 151-220 base pair fragments) ([0019]; [0099]; FIG. 5; FIG. 20). Regarding the claimed range of large fragments of 151 bp to 220 bp in length, the range of 163-169 bp in length is within the claimed range of 151-220 and therefore anticipates the range. See MPEP 2131.03. Chiu further discloses the ratio of small to large fragments is compared to a reference ratio to classify a likelihood cancer exists in the subject ([0174]; FIG. 16A, e.g. higher size ratio corresponds to higher tumor %). Chiu discloses this ratio of small to large fragments is positively correlated with tumor percentage in the subject (FIG. 15A-B; FIG. 16A-B; FIG. 17).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the size ratio of Lo to have utilized a size ratio of 100 to 150 bp to 163-169 bp in the classification of cancer, as shown by Chiu, discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Lo and Chiu given Chiu discloses that the size ratio of 100 to 150 bp to 163-169 bp is positively correlated with a tumor percentage in the subject (FIG. 15-17), thus providing a predictive biomarker for cancer classification as performed in Lo. This modification would have had a reasonable expectation of success given both Lo and Chiu use a size ratio of cfDNA fragments to predict cancer in a subject, such that the ratio of Chiu is applicable to the method of Lo.
Further regarding claim 68, Lo does not explicitly disclose the cancer treatment comprises an immune checkpoint inhibitor, adoptive T cell therapy, or chemotherapeutic agent.
However, Ma further discloses chemotherapy is a treatment for patients with cancer (pg. 120, col. 2, para. 2).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the administering a treatment step of Lo to have used a chemotherapy treatment as shown by Ma (pg. 120, col. 2, para. 2). One of ordinary skill in the art would have been motivated to further combine the methods of Lo and Ma based on the simple substitution of the cancer therapy shown by Lo with the prior art element of a chemotherapy cancer treatment shown by Ma. One of ordinary skill in the art would have recognized that the results of the substitution would have been predictable given Lo discloses the treatment may include any suitable therapy ([0184]; [0110]), and Ma provides a suitable chemotherapy therapy for cancer (pg. 120, col. 2, para. 2).
Regarding claim 70, the step of identifying the subject as having cancer when the cfDNA fragmentation profile obtained from the subject is different from the reference cfDNA fragmentation profile, the broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met. See MPEP 2111.04. Because the claim does not require that the cfDNA fragmentation profile of the subject is different from the reference cfDNA fragmentation profile, identifying the subject as having cancer is not required under the broadest reasonable interpretation of the claim.
Regardless, Lo further discloses classifying the subject as having cancer based on differences between the fragment size ranges (i.e. fragmentation profile) of the subject and the reference size ranges exceeding a threshold (i.e. when the cfDNA fragmentation profile of the subject is determined different than the reference profile) ([0164]-[0165], e.g. subject classified as having cancer based on a similarity of the measurement sizes to the reference sizes exceeding a cutoff; FIG. 12).
Regarding claim 71, Lo further discloses the reference cfDNA fragmentation profile is determined from subjects without cancer ([0161]), and the subjects can be human (i.e. a mammal without cancer) ([0191]), such that the reference cfDNA fragmentation profile is of at least one mammal without cancer.
Regarding claim 72, Lo further discloses the reference cfDNA fragmentation profile is generated from reference samples from subjects without cancer ([0135]; [0161]), and the subjects can be human (i.e. a mammal without cancer) ([0191]).
Regarding claim 73, Lo discloses the cancer can be lung cancer, colon cancer, or ovarian cancer ([0165]).
Regarding claim 76, Lo discloses the cfDNA fragmentation profile of the subject comprises sequence coverages for each size ratio of cfDNA fragments in chromosome arms (FIG. 10, #1040, e.g. Genomic Representation for sample for chromosome arms 1-N; [0147], e.g. genomic representation if a sequence coverage on a particular region).
Regarding claim 84, the claims recites a product by process limitation as explained in the claim interpretation section. As discussed above, Lo discloses the reference cfDNA fragmentation profile is determined from subjects without cancer ([0161]), and the subjects can be human (i.e. a mammal without cancer) ([0191]), such that the reference cfDNA fragmentation profile is of at least one mammal without cancer. A reference profile generated from a human without cancer, as disclosed in Lo, is the same product as a reference profile generated from the subject prior to cancer treatment, since the latter encompasses a reference profile taken while the subject is healthy (i.e. a reference profile from a human without cancer, as described in Lo). Therefore, Lo discloses the limitations of claim 84 See MPEP 2113. I.
Therefore, the invention is prima facie obvious.
Response to Arguments
Applicant's arguments filed 02 March 2026 regarding 35 U.S.C. 103 have been fully considered but they are not persuasive.
Applicant’s remarks that Lo does not disclose or suggest the claimed ratio of small to large fragments, and while Lo discloses using numerous overlapping size bands as sliding windows for analysis, Lo does not disclose define small as 100-150 bp and large as 151-220 base pairs or calculating a ratio between small and large fragments (Applicant’s remarks at pg. 10, para. 3-4), Applicant remarks that Lo discloses using sliding windows centered at sizes 100-150, but does not define two discrete non-overlapping populations with a cutoff at 150/151, and further remarks that the 150/151 boundary disclosed in the current application is specifically chosen because it corresponds to the nucleosomal DNA length which has biological significance for distinguishing cancer derived cfDNA from healthy cfDNA (Applicant’s remarks at pg. 10, para. 3 to pg. 11, para. 1).
This argument is not persuasive. First, this argument is not commensurate with the scope of independent claim 68. Claim 68 only requires the fragmentation profile comprises “a ratio of small cfDNA fragments to large cfDNA fragments”, but does not define small to be 100-150 bp and large to be 151-220 bp.
Furthermore, the argument is not persuasive because it does not take into account the newly cited reference, Chiu, which discloses the use of a size ratio of 100-150 bp to 163-169 bp fragments (i.e. 151-220 bp fragments) to predict cancer in a subject, as discussed in the above rejection.
Applicant remarks there is no motivation to combine Lo with Ma as evidenced by Heitzer to arrive at the claimed invention because there is no teaching or suggestion in Lo, Ma, or Heitzer to substitute Lo’s multi-dimensional sliding window approach with exactly two non-overlapping fragment populations and calculate a ratio between these specific populations, and Lo in view of Ma as evidenced by Heitzer do not arrive at the instant claims (Applicant’s remarks at pg. 11, para. 2 and pg. 12, para. 2). Applicant further remarks Ma and Heitzer do not disclose the suggested ratio of small cfDNA fragments to large cfDNA fragments (Applicant’s remarks at pg. 11, para. 3 to pg. 12, para. 1).
This argument is not persuasive because it does not take into account the newly cited reference, Chiu, which discloses the use of a size ratio of 100-150 bp to 163-169 bp fragments (i.e. 151-220 bp fragments) to predict cancer in a subject, as discussed in the above rejection.
Further regarding Applicant’s statement that it would not have been obvious to substitute Lo’s sliding window approach with a ratio of exactly two non-overlapping fragment populations, Lo does disclose that the size ranges may be non-overlapping rather than using sliding (overlapping) size ranges ([0099]). Lo additionally discloses a size ratio may be determined for each genomic region and used for cancer classification ([0160]; FIG. 12). One of ordinary skill in the art would be able to calculate the size ratio of Chiu for each genomic region in Lo in order to classify cancer according to the method of Lo (FIG. 12).
Double Patenting
The various nonstatutory double patenting rejections of claims 78 and 85 in the Office action mailed 31 Oct. 2025 have been withdrawn in view of the cancellation of these claims received 02 March 2026.
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, e.g., 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 (e.g., 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 68, 70-73, 76-77, and 84 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. US 10,982,279 B2 in view of Lo (2017), as evidenced by Heitzer (2015). Any newly recited portion is necessitated by claim amendment.
Cited reference:
Lo et al., US 2019/0130065 A1; effectively filed 02 Nov. 2017 based on priority to Provisional App. No. 62/580,906; and
Heitzer et al. (Circulation Tumor DNA as a Liquid Biopsy for Cancer, 2015, Clinical Chemistry, 61:1, pg. 112-123 previously cited)
Regarding instant claim 68¸ reference claim 1 discloses a method comprising processing cfDNA fragments obtained from a sample into sequencing libraries, which would involve obtaining a sample and extracting and purifying cfDNA from the sample.
Reference claim 1 discloses subjecting the sequencing libraries to whole genome sequencing to obtain sequenced fragments, wherein genome coverage is about 9× to 0.1x.
Reference claim 1 discloses analyzing, from the cell free DNA (cfDNA) sample of a mammal, genomic intervals of mapped sequences to determine cfDNA fragment lengths and determining the cfDNA fragmentation profile using the lengths (i.e. a cfDNA fragmentation profile in a sample obtained from the subject).
Reference claims 6-11 discloses the various elements of the fragmentation profile as claimed.
Reference claim 1 further discloses determining the subject has cancer by detecting the cfDNA fragmentation profile is more variable than a reference profile (i.e. based on positional fragmentation characteristic differences).
Reference claim 1 discloses the administering step.
Further regarding instant claim 68, the reference claims do not disclose determining the existence of a change in chromosomal arm DNA copy number from a sample of cfDNA from the subject or that the sample is a plasma sample.
However, Lo discloses a method for detecting cancer in a subject (Abstract; [0007]; [0028]), comprising determining the presence of a DNA copy number (CN) change of a chromosomal arm in a plasma sample comprising cell-free DNA (cfDNA) from a subject relative to a reference ([0071]; [0097], e.g. cell-free DNA sample; [0098], e.g. copy number determined for chromosomal arm; [0099]; [0109], e.g. the machine learning outputs probability of a copy number aberration based on comparison to a reference size pattern; Fig. 6). Lo further discloses that the determined copy number change of the chromosomal arm relative to the reference indicates cancer and using the determined copy number change to determine a level of cancer in the subject (i.e. classifying the subject as having cancer when there is a change in the copy number relative to the reference) ([0110]; [0120]). Lo discloses determining the change in chromosomal arm copy number from a profile of cfDNA fragment size ratios (i.e. a cfDNA fragmentation profile) determined from a sample of the subject (FIG. 6 #602, 604 and 610; [0097]-[0100]). Lo further discloses the detected change in copy number can be used to indicate cancer in the subject ([0110]; [0120]).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims to have used a cfDNA fragmentation profile of the subject, to determine the existence of a change in chromosomal arm DNA copy number from a sample of cfDNA from the subject, as shown by Lo ([0071] ;[0097]; [0099]; [0109]-[0110]; [0112]; FIG. 6). One of ordinary skill in the art would have been motivated to combine the method of the reference claims and Lo to indicate cancer in the subject, as shown by Lo ([0110]; [0120]), given the reference claims also pertain to identifying cancer in a subject.
Further regarding instant claim 68, the reference claims do not explicitly disclose purifying nucleosome protected cfDNA fragments from the plasma fraction. However, this limitation is inherent in the reference claims, as evidenced by Heizer.
Specifically, Heitzer reviews the use of circulating tumor DNA as a liquid biopsy for cancer, and discloses that since 1994, numerous studies have analyzed DNA in plasma (i.e. cfDNA), including by performing library preparation and whole-genome sequencing (pg. 118, col. 3, para. 4 to pg. 119, col. 1, para. 1). Heitzer discloses such liquid biopsies include blood collection, processing, and DNA extraction from plasma fractions (pg. 120, col. 2, para. 3), and that it is known that cell-free DNA fragments being analyzed in plasma correspond to nucleosome-protected fragments, such that the limitation of extracting and purifying nucleosome protected fragments is inherent in extraction and purification of cell-free DNA from plasma (Fig. 4; pg. 114, col. 2, para. 1). Therefore, given the reference claims disclose extracting and purifying cfDNA fragments, as discussed above, this inherently discloses that nucleosome-protected cfDNA fragments are extracted and purified.
Regarding instant claim 70, Reference claim 1 further discloses detecting that the cfDNA fragmentation profile that is more variable than a reference cfDNA fragmentation profile from a healthy subject (i.e. comparing the cfDNA fragmentation profile to a reference cfDNA fragmentation profile).
Reference claim 1 further discloses the increased variability of the fragmentation profile obtained from the mammal compared to the reference profile (i.e. the cfDNA fragmentation profile is different from the reference fragmentation profile) is indicative of the mammal as having cancer and that the mammal was identified as having cancer.
Regarding instant claims 71 and 84¸ reference claim 1 discloses the reference cfDNA fragmentation profile is from a healthy mammal (i.e. a mammal without cancer).
Regarding instant claim 72, reference claim 1 discloses the reference cfDNA fragmentation profile was generated from cfDNA of a healthy mammal (i.e. a mammal without cancer).
Regarding instant claim 73, instant claim 73 fails to further limit instant claim 68 and thus is rejected for the same reasons as instant claim 68 discussed above.
Regarding instant claim 76, reference claim 9 discloses the cfDNA fragmentation profile comprises the sequence coverage of small cfDNA fragments in genomic intervals across the genome, such that the cfDNA fragmentation profile necessarily comprises the sequence coverage of chromosome arms within the genome.
Regarding instant claim 77, reference claim 15 discloses the genome coverage is from about 2x, 1x, 0.5x, 0.2x or 0.1x.
Claim 86 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. US 10,982,279 B2 in view of Lo (2017), as evidenced by Heitzer (2015), as applied to claim 68 above, and further in view of Chiu (2013). This rejection is newly recited and necessitated by claim amendemtn.
Cited reference: Lo et al. (referred to as Chiu) US 2013/0237431 A1 (newly cited).
Regarding claim 86, the reference claims in view of Lo do not disclose a small fragment is 100-150 base pairs and a large fragment is 151 to 220 base pairs in length.
However, Chiu similarly discloses a method for determining a cell-free DNA fragmentation profile for a subject (Abstract), which comprises determining a size profile including size parameters ([0051]; [0099]), wherein the size parameters include a ratio of the amount of cfDNA fragment of 100 to 150 base pairs in length to the amount of cfDNA fragments 163-169 base pairs in length (i.e. a ratio of smaller 100-150 base pair fragments to larger 151-220 base pair fragments) ([0019]; [0099]; FIG. 5; FIG. 20). Regarding the claimed range of large fragments of 151 bp to 220 bp in length, the range of 163-169 bp in length is within the claimed range of 151-220 and therefore anticipates the range. See MPEP 2131.03. Chiu further discloses the ratio of small to large fragments is compared to a reference ratio to classify a likelihood cancer exists in the subject ([0174]; FIG. 16A, e.g. higher size ratio corresponds to higher tumor %). Chiu discloses this ratio of small to large fragments is positively correlated with tumor percentage in the subject (FIG. 15A-B; FIG. 16A-B; FIG. 17).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the size ratio of the reference claims to have utilized a size ratio of 100 to 150 bp to 163-169 bp in the classification of cancer, as shown by Chiu, discussed above. One of ordinary skill in the art would have been motivated to combine the methods of the reference claims and Chiu given Chiu discloses that the size ratio of 100 to 150 bp to 163-169 bp is positively correlated with a tumor percentage in the subject (FIG. 15-17), thus providing a predictive biomarker for cancer classification as performed in the reference claims This modification would have had a reasonable expectation of success given both the reference claims and Chiu use a size ratio of cfDNA fragments to predict cancer in a subject, such that the ratio of Chiu is applicable to the method of the reference claims.
Claims 68, 70-73, 76-77, 84, and 86 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. US 10,975,431 B2 in view of Lo (2017), as evidenced by Heitzer (2015). Any newly recited portion herein is necessitated by claim amendment.
Cited reference:
Lo et al., US 2019/0130065 A1; effectively filed 02 Nov. 2017 based on priority to Provisional App. No. 62/580,906 (previously cited); and
Heitzer et al. (Circulation Tumor DNA as a Liquid Biopsy for Cancer, 2015, Clinical Chemistry, 61:1, pg. 112-123’ previously cited)
Regarding instant claim 68¸ reference claim 1 discloses a cfDNA fragmentation profile of sequenced fragments obtained through whole genome sequencing of a sample obtained from the subject, and reference claim 13 discloses the genome coverage is 1X genome coverage. Reference claim 16 discloses the sample is a plasma sample.
Reference claim 1 discloses analyzing, from a cell free DNA (cfDNA) sample of a mammal, genomic intervals of mapped sequences to determine a cfDNA fragmentation profile(i.e. a cfDNA fragmentation profile in a sample obtained from the subject).
Reference claims 1 and 7-11 discloses the fragmentation profile comprises small to large fragments, a fragment size distribution, fragment coverage metrics, and positional metrics across the genome.
Reference claim 1 further discloses determining the subject has cancer by detecting the cfDNA fragmentation profile is more variable than a reference profile (i.e. based on fragmentation characteristics).
Reference claim 1 disclose administering an immunotherapeutic treatment to the subject.
Regarding instant claim 68¸ the reference claims do not disclose the following limitations:
Regarding instant claim 68¸ while the reference claims utilize sequenced fragments from whole-genome sequencing data, the claims do not explicitly require a step of processing the cfDNA fragments into sequencing libraries and performing whole genome sequencing on the sequencing library.
However, Lo further discloses processing cfDNA fragments from the subject into sequencing libraries ([0186]; [0190]), and discloses subjecting the sequencing libraries to whole genome sequencing to obtain sequenced fragments ([0032]; [0191], e.g. random sequencing is performed on all nucleic acid fragments in sample).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention to have modified the method of the reference claims to have performed the steps of library preparation and whole genome sequencing on the sequencing library, as shown by Lo ([0032]; [0186]; [0190]-[0191]). One of ordinary skill in the art would have been motivated to combine the method of the reference claims with the method of Lo in order to generate the sequenced fragments that are required for the method of the reference claims, thus facilitating the generation of cfDNA fragmentation profiles and the detection of cancer according to the reference claims. This modification would have had a reasonable expectation of success given the reference claims analyze sequenced fragments across a genome, such that the sequencing data of Lo is applicable to the reference claims.
Further regarding instant claim 68, the reference claims do not explicitly disclose purifying nucleosome protected cfDNA fragments from the plasma fraction. However, this limitation is inherent in the reference claims, as evidenced by Heizer.
Specifically, Heitzer reviews the use of circulating tumor DNA as a liquid biopsy for cancer, and discloses that since 1994, numerous studies have analyzed DNA in plasma (i.e. cfDNA), including by performing library preparation and whole-genome sequencing (pg. 118, col. 3, para. 4 to pg. 119, col. 1, para. 1). Heitzer discloses such liquid biopsies include blood collection, processing, and DNA extraction from plasma fractions (pg. 120, col. 2, para. 3), and that it is known that cell-free DNA fragments being analyzed in plasma correspond to nucleosome-protected fragments, such that the limitation of extracting and purifying nucleosome protected fragments is inherent in extraction and purification of cell-free DNA from plasma (Fig. 4; pg. 114, col. 2, para. 1). Therefore, given the reference claims disclose extracting and purifying cfDNA fragments, as discussed above, this inherently discloses that nucleosome-protected cfDNA fragments are extracted and purified.
Further regarding instant claim 68, the reference claims do not disclose determining the existence of a change in chromosomal arm DNA copy number from a sample of cfDNA from the subject.
However, Lo discloses a method for detecting cancer in a subject (Abstract; [0007]; [0028]), comprising determining the presence of a DNA copy number (CN) change of a chromosomal arm in a biological sample comprising cell-free DNA (cfDNA) from a subject relative to a reference ([0071]; [0097], e.g. cell-free DNA sample; [0098], e.g. copy number determined for chromosomal arm; [0099]; [0109], e.g. the machine learning outputs probability of a copy number aberration based on comparison to a reference size pattern; Fig. 6). Lo further discloses that the determined copy number change of the chromosomal arm relative to the reference indicates cancer and using the determined copy number change to determine a level of cancer in the subject (i.e. classifying the subject as having cancer when there is a change in the copy number relative to the reference) ([0110]; [0120]). Lo discloses determining the change in chromosomal arm copy number from a profile of cfDNA fragment size ratios (i.e. a cfDNA fragmentation profile) determined from a sample of the subject (FIG. 6 #602, 604 and 610; [0097]-[0100]). Lo further discloses the detected change in copy number can be used to indicate cancer in the subject ([0110]; [0120]).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims to have determined the existence of a change in chromosomal arm DNA copy number from a sample of cfDNA from the subject, as shown by Lo ([0071] ;[0097]; [0099]; [0109]-[0110]; [0112]; FIG. 6). One of ordinary skill in the art would have been motivated to combine the method of the reference claims and Lo to indicate cancer in the subject, as shown by Lo ([0110]; [0120]), given the reference claims also pertain to identifying cancer in a subject.
Regarding instant claim 70, Reference claim 1 further discloses detecting that the cfDNA fragmentation profile that is more variable than a reference cfDNA fragmentation profile (i.e. comparing the cfDNA fragmentation profile to a reference cfDNA fragmentation profile).
Reference claim 1 further discloses the increased variability of the fragmentation profile obtained from the mammal compared to the reference profile (i.e. the cfDNA fragmentation profile is different from the reference fragmentation profile) is indicative of the mammal as having cancer and that the mammal was identified as having cancer.
Regarding instant claim 71 and 84¸ reference claim 4 discloses the reference cfDNA fragmentation profile is from a healthy subject.
Regarding instant claim 72, reference claim 1 discloses the reference cfDNA fragmentation profile was generated from cfDNA of a healthy subject (i.e. a subject without cancer).
Regarding instant claims 71-72, the reference claims do not disclose that the healthy subject is a mammal.
However, Lo further discloses the reference cfDNA fragmentation profile is determined from subjects without cancer ([0161]), and the subjects can be human (i.e. a mammal without cancer) ([0191]), such that the reference cfDNA fragmentation profile is of at least one mammal without cancer. Lo further discloses the method can be used to administer cancer treatments to the mammal upon identification of cancer ([0033]).
It would have been prima facie obvious, to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims to have obtained the reference cfDNA fragmentation profile from a mammal without cancer, as shown by Lo ([0161]; [0191]). One of ordinary skill in the art would have been motivated to combine the method of the reference claims with the method of Lo to identify cancer in a mammal, specifically, facilitating the administration of cancer therapy to a mammal, as shown by Lo ([0033]). This modification would have had a reasonable expectation of success because the method of the reference claims analyze cfDNA from a subject, which could also be applied to a mammal subject.
Regarding instant claim 73, instant claim 73 fails to further limit instant claim 68 and thus is rejected for the same reasons as instant claim 68 discussed above.
Regarding instant claim 76, reference claims 8-10 disclose the cfDNA fragmentation profile comprises an amount of small and large cfDNA fragments in genomic intervals across the genome, such that the cfDNA fragmentation profile necessarily comprises the sequence coverage of chromosome arms within the genome.
Regarding instant claim 77, reference claim 13 discloses the genome coverage is from about 2x, 1x, 0.5x, 0.2x or 0.1x.
Regarding instant claim 86, reference claim 8 discloses the claimed small and large fragment ranges.
Claims 68, 70-73, 76-77, 84, and 86 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 68, 70, 73-76, 78-83, 85, 88-97, and 100 of copending Application No. 17/204,892 in view of Lo (2017) as evidenced by Heitzer (2015). Any newly recited portion is necessitated by claim amendment.
Cited reference:
Lo et al., US 2019/0130065 A1; effectively filed 02 Nov. 2017 based on priority to Provisional App. No. 62/580,906 (previously recited); and
Heitzer et al. (Circulation Tumor DNA as a Liquid Biopsy for Cancer, 2015, Clinical Chemistry, 61:1, pg. 112-123’ previously cited)
Regarding instant claim 68, reference claim 68 discloses the limitations of instant claim 68, except for determining the existence of a change in chromosomal arm DNA copy number from the sequenced fragments.
Further regarding instant claim 68, the reference claims do not explicitly disclose extracting nucleosome protected cfDNA fragments from the plasma fraction. However, this limitation is inherent in the reference claims, as evidenced by Heizer.
Specifically, Heitzer reviews the use of circulating tumor DNA as a liquid biopsy for cancer, and discloses that since 1994, numerous studies have analyzed DNA in plasma (i.e. cfDNA), including by performing library preparation and whole-genome sequencing (pg. 118, col. 3, para. 4 to pg. 119, col. 1, para. 1). Heitzer discloses such liquid biopsies include blood collection, processing, and DNA extraction from plasma fractions (pg. 120, col. 2, para. 3), and that it is known that cell-free DNA fragments being analyzed in plasma correspond to nucleosome-protected fragments, such that the limitation of extracting and purifying nucleosome protected fragments is inherent in extraction and purification of cell-free DNA from plasma (Fig. 4; pg. 114, col. 2, para. 1). Therefore, given the reference claims disclose extracting and purifying cfDNA fragments, as discussed above, this inherently discloses that nucleosome-protected cfDNA fragments are extracted and purified.
Further regarding instant claim 68, the reference claims do not disclose determining the existence of a change in chromosomal arm DNA copy number from a sample of cfDNA from the subject.
However, Lo discloses a method for detecting cancer in a subject (Abstract; [0007]; [0028]), comprising using a machine learning model to determine the presence of a DNA copy number (CN) change of a chromosomal arm in a biological sample comprising cell-free DNA (cfDNA) from a subject relative to a reference ([0071]; [0097], e.g. cell-free DNA sample; [0098], e.g. copy number determined for chromosomal arm; [0099]; [0109], e.g. the machine learning outputs probability of a copy number aberration based on comparison to a reference size pattern; Fig. 6). Lo further discloses that the determined copy number change of the chromosomal arm relative to the reference indicates cancer and using the determined copy number change to determine a level of cancer in the subject (i.e. classifying the subject as having cancer when there is a change in the copy number relative to the reference) ([0110]; [0120]). Lo discloses determining the change in chromosomal arm copy number from a profile of cfDNA fragment size ratios (i.e. a cfDNA fragmentation profile) determined from a sample of the subject (FIG. 6 #602, 604 and 610; [0097]-[0100]). Lo further discloses the detected change in copy number can be used to indicate cancer in the subject ([0110]; [0120]).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims to have used a cfDNA fragmentation profile of the subject and determined the existence of a change in chromosomal arm DNA copy number from a sample of cfDNA from the subject as shown by Lo ([0071] ;[0097]; [0099]; [0109]-[0110]; [0112]; FIG. 6). One of ordinary skill in the art would have been motivated to combine the method of the reference claims and Lo to indicate cancer in the subject, as shown by Lo ([0110]; [0120]), given the reference claims also pertain to identifying cancer in a subject.
Regarding instant claim 69¸reference claim 89 discloses the limitation of instant claim 69.
Regarding instant claim 70, reference claims 68 discloses determining a cfDNA fragmentation profile in a sample from the subject, comparing the cfDNA fragmentation profile of the subject to a reference cfDNA fragmentation profile, and identifying the subject as having cancer when the cfDNA fragmentation profile of the subject is more variable (i.e. different) than the reference cfDNA fragmentation profile.
Regarding instant claims 71-72 and 84, the reference claims do not disclose that the reference cfDNA fragmentation profile was determined from at least one mammal without cancer.
However, Lo further discloses the reference cfDNA fragmentation profile is determined from subjects without cancer ([0161]), and the subjects can be human (i.e. a mammal without cancer) ([0191]), such that the reference cfDNA fragmentation profile is of at least one mammal without cancer. Lo further discloses the method can be used to administer cancer treatments to the mammal upon identification of cancer ([0033]).
It would have been prima facie obvious, to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims to have obtained the reference cfDNA fragmentation profile from a mammal without cancer, as shown by Lo ([0161]; [0191]). One of ordinary skill in the art would have been motivated to combine the method of the reference claims with the method of Lo to identify cancer in a mammal, specifically, facilitating the administration of cancer therapy to a mammal, as shown by Lo ([0033]). This modification would have had a reasonable expectation of success because the method of the reference claims analyze cfDNA from a subject, which could also be applied to a mammal subject.
Regarding instant claim 73, instant claim 73 fails to further limit the subject matter of instant claim 68, and thus is rejected for the same reasons as instant claim 68 discussed above.
Regarding instant claim 76, reference claim 68 discloses the cfDNA fragmentation profile comprises a sequence coverage across the human genome.
Regarding instant claim 77, reference claim 83 discloses the genomic coverage is 0.1x, 0.2x, 0.5x, 1x, or 2x.
Regarding instant claim 86, reference claim 68 discloses the claimed ranges of small to large fragments.
This is a provisional nonstatutory double patenting rejection.
Claims 68, 70-73, 76-77, 84, and 86 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4, 6, 9-11, 14, and 16-20 of copending Application No. 17/056,726 in view of Lo (2017), as evidenced by Heitzer (2015). Any newly recited portion herein is necessitated by claim amendment.
Cited reference:
Lo et al., US 2019/0130065 A1; effectively filed 02 Nov. 2017 based on priority to Provisional App. No. 62/580,906 (newly cited); and
Heitzer et al. (Circulation Tumor DNA as a Liquid Biopsy for Cancer, 2015, Clinical Chemistry, 61:1, pg. 112-123; previously cited)
Regarding instant claim 68¸ reference claim 1 discloses processing cfDNA fragments of a sample into sequencing libraries.
Reference claim 1 discloses subjecting the sequencing libraries to low-coverage whole genome sequencing to obtain sequencing fragments. Regarding the ow-coverage whole genome sequencing (i.e. 0.1x-10x). "[A] prior art reference that discloses a range encompassing a somewhat narrower claimed range is sufficient to establish a prima facie case of obviousness." In re Peterson, 315 F.3d 1325, 1330, 65 USPQ2d 1379, 1382-83 (Fed. Cir. 2003). See MPEP 2144.05.
Reference claim 1 discloses mapping the sequenced fragments to a genome to obtained mapped sequences (i.e. location data) used to generate size information.
Reference claim 1 discloses determining cfDNA fragment lengths according to the mapped windows (i.e. the cfDNA fragmentation profile). Reference claims 1 and 6-11 disclose the elements of the fragmentation profile as claimed.
Reference claim 1 discloses the administering step.
Further regarding instant claim 68, the reference claims do not explicitly disclose purifying nucleosome protected cfDNA fragments from the plasma fraction. However, this limitation is inherent in the reference claims, as evidenced by Heizer.
Specifically, Heitzer reviews the use of circulating tumor DNA as a liquid biopsy for cancer, and discloses that since 1994, numerous studies have analyzed DNA in plasma (i.e. cfDNA), including by performing library preparation and whole-genome sequencing (pg. 118, col. 3, para. 4 to pg. 119, col. 1, para. 1). Heitzer discloses such liquid biopsies include blood collection, processing, and DNA extraction from plasma fractions (pg. 120, col. 2, para. 3), and that it is known that cell-free DNA fragments being analyzed in plasma correspond to nucleosome-protected fragments, such that the limitation of extracting and purifying nucleosome protected fragments is inherent in extraction and purification of cell-free DNA from plasma (Fig. 4; pg. 114, col. 2, para. 1). Therefore, given the reference claims disclose extracting and purifying cfDNA fragments, as discussed above, this inherently discloses that nucleosome-protected cfDNA fragments are extracted and purified.
Further regarding instant claims 68, the reference claims do not disclose determining the existence of a change in chromosomal arm DNA copy number from a sample of cfDNA from the subject, as recited in claim 68.
However, Lo discloses a method for detecting cancer in a subject (Abstract; [0007]; [0028]), comprising using a machine learning model to determine the presence of a DNA copy number (CN) change of a chromosomal arm in a biological sample comprising cell-free DNA (cfDNA) from a subject relative to a reference ([0071]; [0097], e.g. cell-free DNA sample; [0098], e.g. copy number determined for chromosomal arm; [0099]; [0109], e.g. the machine learning outputs probability of a copy number aberration based on comparison to a reference size pattern; Fig. 6). Lo further discloses that the determined copy number change of the chromosomal arm relative to the reference indicates cancer and using the determined copy number change to determine a level of cancer in the subject (i.e. classifying the subject as having cancer when there is a change in the copy number relative to the reference) ([0110]; [0120]). Lo discloses determining the change in chromosomal arm copy number from a profile of cfDNA fragment size ratios (i.e. a cfDNA fragmentation profile) determined from a sample of the subject (FIG. 6 #602, 604 and 610; [0097]-[0100]). Lo further discloses the detected change in copy number can be used to indicate cancer in the subject ([0110]; [0120]).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of the reference claims to have used a cfDNA fragmentation profile of the subject, to determine the existence of a change in chromosomal arm DNA copy number from a sample of cfDNA from the subject, as shown by Lo ([0071] ;[0097]; [0099]; [0109]-[0110]; [0112]; FIG. 6). One of ordinary skill in the art would have been motivated to combine the method of the reference claims and Lo to indicate cancer in the subject, as shown by Lo ([0110]; [0120]), given the reference claims also pertain to identifying cancer in a subject.
Regarding instant claim 70, reference claim 14 discloses determining a cell free DNA (cfDNA) fragmentation profile in a sample from a mammal, comparing the cfDNA fragmentation profile to a reference cfDNA fragmentation profile, and identifying the mammal as having cancer when the cfDNA fragmentation profile obtained from the mammal is different from the reference cfDNA fragmentation profile.
Regarding instant claims 71-72 and 84, reference claims 15-16 disclose the reference cfDNA fragmentation profile was generated from a cfDNA fragmentation profile in a sample obtained from a healthy mammal (i.e. a mammal without cancer).
Regarding instant claim 73, instant claim 73 fails to further limit the subject matter of instant claim 68, and thus is rejected for the same reasons as instant claim 68 discussed above.
Regarding instant claim 76, reference claims 9-11 disclose the cfDNA fragmentation profile comprises sequence coverage across the genome.
Regarding instant claim 77, reference claim 1 discloses subjecting the sequencing libraries to low-coverage whole genome sequencing (i.e. 0.1x-10x), which encompasses the range of 2x to 0.1x. "[A] prior art reference that discloses a range encompassing a somewhat narrower claimed range is sufficient to establish a prima facie case of obviousness." In re Peterson, 315 F.3d 1325, 1330, 65 USPQ2d 1379, 1382-83 (Fed. Cir. 2003). See MPEP 2144.05.
Regarding instant claim 86, reference claim 1 discloses the size ranges of the small and large cfDNA fragments.
Response to Arguments
Applicant's arguments filed 17 Oct. 2025 regarding double patenting have been fully considered but they are not persuasive.
Applicant remarks that the cited claims do not expressly recite Applicant’s claim 68 and thus the rejections should be withdrawn (Applicant’s remarks at pg. 12, para. 3 to pg. 13, para. 1).
This argument is not persuasive. Applicant's arguments fail to comply with 37 CFR 1.111(b) because they amount to a general allegation that the claims define a patentable invention without specifically pointing out how the language of the claims patentably distinguishes them from the reference applications and patents.
Furthermore, the above rejections are obviousness type double patenting rejections. Therefore, while the reference claims may not “expressly recite” the instant claims, the instant claims are obvious over the reference claims in view of additional references for the reasons discussed in the above rejections.
Conclusion
No claims are allowed.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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