DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-6 and 13-26 are pending and currently under examination.
Priority
The instant application 18/016,957 filed on 1/19/23 is a 371 US national phase of PCT/US2021/042360 filed on 7/20/21 and claims domestic priority to provisional application 63/054,671 filed 7/21/20. The priority date is determined to be 7/21/20.
Claim Rejections - 35 USC § 112 – Indefiniteness
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.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 6 and 13-15 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 6 recites the limitations “transcriptome profile” in line 2 and “expression levels of one or more genes” in line 4. These limitations would be unclear to the skilled artisan because transcriptomic profiles and expression levels typically involve measuring RNA. How does one measure these in ctDNA? For purposes of compact prosecution, this limitation is interpreted as measuring expression levels in ctDNA via indirect measurements (promoter methylation, nucleosome-associated fragmentation patterns, etc.) capable of measurement in ctDNA.
Claims 13-15 directly depend on claim 6 and are similarly indefinite.
Claim Rejections - 35 USC § 101
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 1-6 and 13-26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims have been evaluated using the 2019 Revised Patent Subject Matter Eligibility Guidance (see Federal Register Vol. 84, No. 4 Monday, January 7, 2019).
Step 1: The claim is directed to the statutory category of a process.
Step 2A, prong one: The claim recites a judicial exception.
Claim 1 recites “determining at least some of the sequencing reads”. This limitation is an abstract mental process (see MPEP 2106.04(a)(2)(III)).
Step 2A, prong two: The judicial exception is not integrated into a practical application.
Claims 1-6 and 13-26 recite extra-solution, data-gathering limitations at high levels of generality. The claims end with the judicial exception.
Step 2B: The claim does not provide an inventive concept.
MPEP 2106.05(d)):
The courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity:
• i. Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
• ii. Using polymerase chain reaction to amplify and detect DNA, Genetic Techs. Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115 USPQ2d 1152, 1157 (Fed. Cir. 2015);
• iii. Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017);
• iv. Immunizing a patient against a disease, Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
• v. Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377, 118 USPQ2d at 1546;
• vi. Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119 USPQ2d at 1375;
• vii. Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014); and
• viii. Hybridizing a gene probe, Ambry Genetics, 774 F.3d at 764, 113 USPQ2d at 1247.
The claims are directed to well-understood, routine, and conventional activities in the life science arts recited at a high-level of generality. Circulating tumor DNA and cell-free DNA analyses are not inventive (see Maguire et al. (2017; US 2017/0275689 A1); Snyder et al. (2016; "Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin"; Cell. 2016 Jan 14;164(1-2):57-68. doi: 10.1016/j.cell.2015.11.050); or Ivanov et al. (2015; "Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation"; BMC Genomics. 2015;16 Suppl 13(Suppl 13):S1. doi: 10.1186/1471-2164-16-S13-S1)).
For the reasons set forth above, claims 1-6 and 13-26 are not directed to patent eligible subject matter.
Claim Rejections - 35 USC § 102
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.
Claims 1-3 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wan et al. (2019; NPL citation 7 in IDS filed 5/12/23; “High-sensitivity monitoring of ctDNA by patient-specific sequencing panels and integration of variant reads”; bioRxiv 759399; doi: https://doi.org/10.1101/759399).
Relevant to claim 1, Wan et al. pages 14-15 Materials and Methods sections “Sample collection and processing” and “Tissue and plasma extraction and quantification” teach claim 1 obtaining a sample from a subject, wherein the plasma samples contain quantifiable cell-free DNA (see page 15, lines 413-419), further reading on claim 1 the sample comprising DNA comprising circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA).
Further relevant to claim 1, Wan et al. One Sentence Summary teaches “Integrating tumor-derived sequences across large panels of patient-specific mutations offers enhanced sensitivity for ctDNA detection and monitoring from both high-depth and low-depth plasma sequencing data.”
This teaching reads on claim 1 sequencing the DNA to generate sequencing reads; detecting at least one ctDNA property of (i) a patient-specific ctDNA property.
Relevant to claims 1-3, Wan et al. Abstract teaches “We describe the INtegration of VAriant Reads (INVAR) analysis pipeline, which combines patient-specific mutation lists with both custom error-suppression methods and signal enrichment based on biological features of ctDNA.”
This teaching reads on claim 1 determining at least some of the sequencing reads as ctDNA sequencing reads based on the at least one ctDNA property; claim 2 wherein the at least one ctDNA property comprises a mutation; and claim 3 wherein the mutation is a tumor somatic mutation.
These Wan et al. teachings read on claims 1-3 limitations.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-3 are rejected under 35 U.S.C. 103 as being unpatentable over Maguire et al. (2017; US 2017/0275689 A1).
Relevant to claims 1-3, Maguire et al. teaches "The method provided utilizes cell free DNA (cfDNA) including circulating tumor DNA (ctDNA) as the source of the target sequences that are to be captured" (paragraph 0214).
Further relevant to claims 1-3, Maguire et al. teaches "In some embodiments, the identifying said first set of segregating markers and said subset of segregating markers comprises whole genome sequencing or targeted sequencing... In some embodiments, the segregating marker is either an inherited mutation or a somatic mutation" (paragraph 0011).
Further relevant to claims 1-3, Maguire et al. teaches "Additionally, provided herein is a personalized method for determining tumor fraction in a patient comprising: screening genomic DNA from tumor tissue from a patient to identify a set of somatic mutations; identifying a subset of somatic mutations specific to said patient's tumor from said set of mutations to create a signature panel of mutations, said panel being specific for said patient; and screening said signature panel to ascertain the proportion of circulating tumor DNA in said cell free DNA from said patient thereby determining the tumor fraction in said patient" (paragraph 0008).
Further relevant to claims 1-3, Maguire et al. teaches “FIG. 3 illustrates the relationship between number of tumor reads observed and the nucleic acid sample's tumor fraction. Reference is made to Example 1” (paragraph 0018) and “FIGS. 5A-C shows in (A) the graph provided in FIG. 4, and the number of reads normal reads (B) and cancer reads (C) obtained for the conditions described for the previous plot. Reference is made to Example 2” (paragraph 0020).
The Maguire et al. “identifying a subset of somatic mutations specific to said patient” reads on patient-specific ctDNA property, and the “set of mutations” reads on a general ctDNA property. The Maguire et al. ascertaining/determining of tumor fraction, taken with the teaching that Maguire et al. analyzes whole genome sequencing or targeted sequencing data for the method, reads on determining at least some of the sequencing reads as ctDNA sequencing reads based on the at least one ctDNA property.
Thus, these teachings read on claim 1 A method, comprising: obtaining a sample from a subject, the sample comprising DNA comprising circulating tumor DNA (ctDNA) and cell-free DNA (cfDNA); sequencing the DNA to generate sequencing reads; detecting at least one ctDNA property of (i) a patient-specific ctDNA property and (ii) a general ctDNA property; and determining at least some of the sequencing reads as ctDNA sequencing reads based on the at least one ctDNA property; claim 2 wherein the at least one ctDNA property comprises a mutation; and claim 3 wherein the mutation is a tumor somatic mutation.
Maguire et al. does not teach a specific embodiment having all the claimed elements. That being said, however, it must be remembered that "[w]hen a patent simply arranges old elements with each performing the same function it had been known to perform and yields no more than one would expect from such an arrangement, the combination is obvious." KSR v. Teleflex, 127 S.Ct. 1727, 1740 (2007) (quoting Sakraida v. AG. Pro, 425 U.S. 273, 282 (1976)). "[W]hen the question is whether a patent claiming the combination of elements of prior art is obvious," the relevant question is "whether the improvement is more than the predictable use of prior art elements according to their established functions." (Id.). Addressing the issue of obviousness, the Supreme Court noted that the analysis under 35 USC 103 "need not seek out precise teachings directed to the specific subject matter of the challenged claim, for a court can take account of the inferences and creative steps that a person of ordinary skill in the art would employ." KSR at 1741. The Court emphasized that "[a] person of ordinary skill is... a person of ordinary creativity, not an automaton." Id. At 1742.
Consistent with this reasoning, it would have been prima facie obvious to have selected various combinations of various disclosed elements — including sequencing, tumor somatic mutations, and determining sequencing reads — for a method, to arrive at compositions "yielding no more than one would expect from such an arrangement."
Claims 4-5, 16-18, and 23-26 are rejected under 35 U.S.C. 103 as being unpatentable over Maguire et al. (2017; US 2017/0275689 A1), as applied to claims 1-3 above, and further in view of Snyder et al. (2016; "Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin"; Cell. 2016 Jan 14;164(1-2):57-68. doi: 10.1016/j.cell.2015.11.050).
The teachings of Maguire et al. are applied to instantly rejected claims 4-5, 16-18, and 23-26 as they were previously applied to claims 1-3 as rendering obvious a method.
Maguire et al. is silent to specifics regarding genomic DNA accessibility, nucleic acid fragment native ends, depth coverage, and fragment overhangs (relevant to claims 4-5, 16-18, and 23-26). However, these limitations were known in the prior art and taught by Snyder et al.
Relevant to claims 4-5, Snyder et al. Figure 2 and associated caption teach “(A) Schematic of inference of nucleosome positioning. A per-base WPS [windowed protection score] is calculated by subtracting the number of fragment endpoints within a 120 bp window from the number of fragments completely spanning the window. High WPS values indicate increased protection of DNA from digestion; low values indicate that DNA is unprotected. Peak calls identify contiguous regions of elevated WPS.”
Snyder et al. teaching of nucleosome positioning, and quantification of WPS, reads on genomic accessibility, because nucleosome positioning correlated with increased protection/inaccessibility for degradation. As such, this teaching reads on claim 4 wherein the at least one ctDNA property comprises genomic DNA accessibility; and claim 5 wherein the genomic DNA accessibility is a differential genomic DNA accessibility compared to an expectation set of genomic DNA accessibility.
Relevant to claim 16, Snyder et al. Figure S1C-S1D and associated captions teach "(C) and (D) Cleavage biases of cfDNA fragments. (C) Mononucleotide frequencies at the 5′ (top panels) and 3′ (bottom panels) ends of fragments, calculated on the basis of aligned sequencing reads and flanking genomic coordinates, are shown for libraries prepared with the conventional double-stranded protocol (left panels) and the single-stranded protocol (right panels)."
The Snyder et al. figure depicts the base composition of nucleic acid fragment native ends, and thus reads on claim 16 wherein the at least one ctDNA property comprises base composition of nucleic acid fragment native ends.
Relevant to claim 17, Snyder et al. Figure S3 and associated caption teach "Aggregate, adjusted long fragment WPS [windowed protection score] (120-180 bp fragments, 120 bp window) are shown around 22,626 transcription start sites (TSS, row 1), 22,626 transcription end sites (TSE, row 2), 22,070 start codon sites (row 3), 22,131 stop codon sites (row 4), 224,910 splice acceptor sites of exons (row 5), and 224,910 splice donor sites of exons (row 6) in the combined healthy sample CH01."
Further relevant to claim 17, Snyder et al. teaches "We next asked whether the predominant local positions of nucleosomes in tissue(s) contributing to cfDNA could be inferred from the distribution of aligned fragment endpoints. Specifically, we expect that cfDNA fragment endpoints should cluster adjacent to NCP boundaries, while also being depleted on the NCP itself. To quantify this, we developed a windowed protection score (WPS), which is the number of DNA fragments completely spanning a 120 bp window centered at a given genomic coordinate minus the number of fragments with an endpoint within that same window" (page 58, first three sentences of "A Genome-wide Map of In Vivo Nucleosome Protection Based on Deep cfDNA Sequencing" Results section).
Thus, the Snyder et al. fragment end WPS analyses and genomic contexts of transcription start/end sites, start/stop codon sites, etc. read on claim 17 wherein the at least one ctDNA property comprises genomic context of nucleic acid fragment native ends.
Relevant to claim 18, Snyder et al. Figures 2B-2C plot the read coverage depth at several loci along chromosomes 12 and 9, reading on claim 18 wherein the at least one ctDNA property comprises read depth coverage at one or more loci.
Relevant to claim 23, Snyder et al. Figure S1B and associated caption teach "(B) Gel images of example cfDNA sequencing libraries. (left) Conventional libraries were prepared with ThruPLEX DNA-seq 48D (Rubicon Genomics). (right) Single-stranded libraries were prepared as described in Supplemental Experimental Procedures." The gel images include a 25bp DNA ladder for fragment length evaluations, reading on claim 23 wherein the at least one ctDNA property comprises fragment length.
Relevant to claims 24-25, Snyder et al. Figure S1C-S1D and associated captions teach "(C) and (D) Cleavage biases of cfDNA fragments. (C) Mononucleotide frequencies at the 5′ (top panels) and 3′ (bottom panels) ends of fragments, calculated on the basis of aligned sequencing reads and flanking genomic coordinates, are shown for libraries prepared with the conventional double-stranded protocol (left panels) and the single-stranded protocol (right panels). Colored bands represent one SD for the respective samples. Double-stranded library fragments evidence symmetric 5′ and 3′ profiles, likely representing a combination of cleavage and adaptor ligation biases. Single-stranded library fragments have an asymmetric profile due to nucleotide preferences of single-stranded adaptor ligation (5′ end of fragments). (D) Dinucleotide frequencies at the 5′ and 3′ ends of fragments, calculated as in (C). Panels are grouped by 5′ or 3′ cleavage, library preparation protocol, and first nucleotide of the dinucleotide pair. "
The C-D panels depict the mono-/di- nucleotide frequencies flanking the fragment endpoints, reading on claim 24 fragment overhang sequence. The "Position relative to fragment endpoint" axes on the C-D panels indicates that Snyder et al. had to consider the claim 25 fragment overhang length in order to plot the nucleotide frequencies.
Relevant to claim 26, Snyder et al. Figure S1A and associated caption teach "(A) Schematic of single-stranded library preparation protocol. Input molecules, consisting of approximately 1-10 ng of cfDNA fragments, may have single stranded nicks and/or 5′ or 3′ overhangs (top, yellow, and blue bars)."
These teachings read on claim 26 wherein the at least one ctDNA property comprises fragment overhang directionality.
Although Maguire et al. does not explicitly teach the Snyder et al. genomic DNA accessibility, nucleic acid fragment native ends, depth coverage, and fragment overhangs, they would have been prima facie obvious to the skilled artisan. It is noted that Maguire et al. and Snyder et al. are analogous disclosures to the instant nucleic acid detection field.
The skilled artisan would be motivated to combine the analogous art. Snyder et al. teaches “Deep sequencing of circulating cell-free DNA yields a dense, genome-wide map of nucleosome occupancy that enables identification of its cell-types of origin, potentially enabling the noninvasive monitoring of a much broader set of clinical conditions than currently possible” (“In Brief”). The Snyder et al. genomic DNA accessibility, nucleic acid fragment native ends, depth coverage, and fragment overhangs enables noninvasive monitoring and cell-type origination determination. Thus, the skilled artisan would have been motivated to include the Snyder et al. parameters within the methodology rendered obvious by Maguire et al. in order to provide noninvasive monitoring and determination of cell-type origins. The skilled artisan would have a reasonable expectation of success based on the disclosures of Maguire et al., and further in view of Snyder et al.
Claims 6, 13-15, and 19-22 are rejected under 35 U.S.C. 103 as being unpatentable over Maguire et al. (2017; US 2017/0275689 A1), as applied to claims 1-3 above, and further in view of Ivanov et al. (2015; "Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation"; BMC Genomics. 2015;16 Suppl 13(Suppl 13):S1. doi: 10.1186/1471-2164-16-S13-S1).
The teachings of Maguire et al. are applied to instantly rejected claims 6, 13-15, and 19-22 as they were previously applied to claims 1-3 as rendering obvious a method.
Maguire et al. is silent to specifics regarding expression levels of one or more genes and epigenetic protein modifications (relevant to claims 6, 13-15, and 19-22). However, these limitations were known in the prior art and taught by Ivanov et al.
Relevant to claims 6 and 13-15, Ivanov et al. teaches "In healthy patients, cfDNA fractions are mostly derived from apoptosis of various normal cells that generate small fragments of cell-free DNA, whereas the cell-free circulating DNA of cancer patients represents a mix of apotosis, necrosis, autophagy, or mitotic catastrophe [citation]. Necrosis produces relatively long fragments of DNA, about 10,000 b.p. in length, while in apoptosis, the activation of endogenous endonucleases lead to the cleavage of chromatin DNA into internucleosomal fragments [citation]" (page 2, column 1, paragraph 2).
Ivanov et al. teaches that apoptosis, necrosis, and nuclease pathways are activated to produce fragments in cancerous cfDNA. Thus, these activations – serving as indirect, cfDNA-enabled measurements of expression – would read on expression levels of one or more genes (claim 6), wherein the genes encode a nuclease (claim 13), an apoptosis pathway member (claim 14), and a necrosis pathway member (claim 15).
Relevant to claims 19-21, Ivanov et al. Table 1 teaches "Association of epigenetic marks and DNA fragmentation patterns (statistical significance)", wherein several marks contain epigenetic protein modification (claim 19) of histone methylation (e.g., H3k36me3; claim 20) and histone acetylation (e.g., H3k9ac; claim 21).
Relevant to claim 22, although Ivanov et al. does not include epigenetic marks of histone phosphorylation, Ivanov et al. does teach "cfDNA fragmentation patterns correlate with known epigenetic marks: Chromatin remodelling is one of the major factors contributing epigenetic regulation [citation]. In the mean time nucleosome organization is closely related to epigenetic marks, such as histone modifications and DNA methylation. Hence, in order to further assess the biological interpretation of the coverage function peaks, the association of fragmentation pattern and epigenetic marks was studied…" (page 7, column 1, paragraph 2).
Thus, although Ivanov et al. does not explicitly teach histone phosphorylation, the skilled artisan would find this additional histone modification as obvious, as Ivanov et al. teaches that "cfDNA fragmentation patterns correlate with known epigenetic marks". Histone phosphorylation is a known epigenetic mark, and the skilled artisan would find it obvious to examine the different histone modification pathways given their correlation with cfDNA fragmentation.
Although Maguire et al. does not explicitly teach the Ivanov et al. expression levels of one or more genes and epigenetic protein modifications, they would have been prima facie obvious to the skilled artisan. It is noted that Maguire et al. and Ivanov et al. are analogous disclosures to the instant nucleic acid detection field.
The skilled artisan would be motivated to combine the analogous art. Ivanov et al. teaches “Interestingly, in a study of the spacing of dinucleosome fragments, two cfDNA fragment histograms were observed. This feature of cfDNA may be of high interest due to its potential value in various diagnostic applications. It seems that cfDNA patterning reflects a general picture of gene expression. Hence, mapping and mining cfDNA fragment ends may aid in the development of novel biomarkers reflecting pathological changes in chromatin marks. The association of fragment copy number with the expression levels in respective locus may aid in detection of various pathologies, including the presence of different types of neoplasms” (page 11, paragraph 2 of “Conclusion”).
Thus, the skilled artisan would have been motivated to include the Ivanov et al. parameters within the methodology rendered obvious by Maguire et al. in order to provide novel biomarkers and insights into detection of various pathologies. The skilled artisan would have a reasonable expectation of success based on the disclosures of Maguire et al., and further in view of Ivanov et al.
Conclusion
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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682