DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status and Formal Matters
This action is in response to papers filed 12/5/2025.
Claims 1-3 have been amended,
Applicant’s election without traverse of presence of cancer loss or duplication, presence of quantity of cell surface receptor and treatment based on one or more mutations in the reply filed on 12/27/2023 is acknowledged.
Claims 1-3, 5-6 are pending.
Claims 1-3, 5-6 are being examined..
The previous objection to the claims has been withdrawn.
Priority
The instant application was filed 04/14/2022 and is a divisional of 17482816 , filed 09/23/2021.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-3, 5-6 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Written Description
Claim 1 has been amended to recite, “A method of administering treatment based on analyzing nucleic acid data of a human subject, comprising: sequencing a first target-enriched complementary DNA (cDNA) library and a second target-enriched cDNA library to thereby obtain respective first and second sequence data sets; wherein the first target-enriched cDNA library is prepared by isolating a cell-free RNA (cfRNA) fraction from cell-free total nucleic acid (cfTNA) of a biological fluid of the subject, excluding a cell-free DNA (cfDNA) fraction; wherein the second target-enriched cDNA library is prepared by collecting from said biological fluid, including the cfDNA fraction; wherein the first and second target-enriched cDNA libraries are prepared by:(i) digesting a first portion of cfTNA from the biological fluid of the subject with DNase isolate the cfRNA fraction;(ii) converting the first cfRNA fraction and a second portion of undigested cfTNA into respective first and second cDNA libraries by a) reverse transcribing the nucleic acids to produce cDNA, b) ligating adapters to the cDNA, and c) amplifying the cDNA toenriching each of the first and second cDNA libraries for a plurality of target cDNAs by hybridizing each target cDNA with a plurality of tiled hybridization probes that bind to the target cDNA at respective different positions to produce the first and second target-enriched cDNA libraries; identifying, for each gene in the first and second sequence data sets, one or more mutations, and quantifying expression in at least the first sequence data set; and administering a treatment to a patient suspected of or diagnosed with a disease or condition associated with the identified one or more mutations and/or quantified expression.. “ Specifically 1 claim 1 has been amended to recite, “administering a treatment to a patient suspected of or diagnosed with a disease or condition associated with the identified one or more mutations and/or quantified expression.”
As set forth in In re Alonso 88 USPQ2d 1849 (Fed. Cir. 2008), at 1851:
The written description requirement of 35 U.S.C. § 112, ¶ 1, is straightforward: “The specification shall contain a written description of the invention ….” To satisfy this requirement, the specification must describe the invention in sufficient detail so “that one skilled in the art can clearly conclude that the inventor invented the claimed invention as of the filing date sought.” Lockwood v. Am. Airlines, Inc., 107 F.3d 1565, 1572 [41 USPQ2d 1961] (Fed. Cir. 1997); see also LizardTech, Inc. v. Earth Res. Mapping, Inc., 424 F.3d 1336, 1345 [76 USPQ2d 1724] (Fed. Cir. 2005); Eiselstein v. Frank, 52 F.3d 1035, 1039 [34 USPQ2d 1467] (Fed. Cir. 1995).
Alonso at 1852:
A genus can be described by disclosing: (1) a representative number of species in that genus; or (2) its “relevant identifying characteristics,” such as “complete or partial structure, other physical and/or chemical properties, functional characteristics when coupled with a known or disclosed correlation between function and structure, or some combination of such characteristics.” Enzo, 323 F.3d at 964.
In applying the test as set forth in Alonso, it is noted that applicant is claiming administering any treatment based on any of one or more identified mutations and/or quantified expression. This is an enormous genus of treatments, mutations and quantified gene expression. Further the claim has been limited to human, but does not require the patient is sick, diseased or has cancer.
Further the claim encompasses administering a treatment based on any mutation or quantitated expression this encompasses any increased or decreased expression relative to any control. Further the claim thus encompasses and SNP, insertion , deletion, translocation, rearrangement, etc. This is an enormous genus.
Dependent claim 2 requires, “further comprising a step of using the first and second sequence data sets in a machine learning algorithm to identify (a) one or more genes associated with a disease parameter, wherein the disease parameter is presence of a cancer, type of cancer, recurrence of cancer, and/or residual cancer,(b) one or more genes associated with a cytogenetic parameter, wherein the cytogenetic parameter is a translocation and/or loss or duplication of at least a portion of a chromosome, and/or (c) one or more genes associated with an immunohistochemical parameter, wherein the immunohistochemical parameter is a presence or quantity of a cell surface receptor and/or presence or quantity of a cell surface enzyme, wherein the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter is identified..” Thus claim 2 depends from claim 1 and appears to require treatment based on something different than claim 1. Further claim 2 requires the use of any machine learning algorithm. This is an enormous genus. The claim does not require algorithm is trained or provide how the machine learning algorithm is trained or used.
Claim 3 depends from claim 1 and draws the invention to further comprising a step of using at least some of the first and second sequence data sets in a model to thereby identify a disease parameter, a cytogenetic parameter, an immunophenotype, a biomarker for diagnosis prognosis, selection of therapy, biomarker for detection of minimal residual disease, and/or an immunohistochemical parameter, wherein the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, the immunophenotype, the biomarker for diagnosis prognosis, the selection of therapy, the biomarker for detection of minimal residual disease, and or the immunohistochemical parameter is identified.. This does not depend from claim 2 and thus encompasses any disease parameter, any cytogenetic parameter, any immunophenotype, any biomarker for diagnosis prognosis, selection of therapy, biomarker for detection of minimal residual disease, and/or an immunohistochemical parameter. Further the claim encompasses treatment based on wherein the treatment is administered based on any disease parameter, any cytogenetic parameter, any immunophenotype, any biomarker for diagnosis prognosis, the selection of therapy, the biomarker for detection of minimal residual disease, and or the immunohistochemical parameter. This is different from what the treatment of claim 1 is based on. Further it is different than what claim 2 is limited to. Further this is an enormous genus. The specification provides no specific guidance on how to perform the treatment of claim 1 and dependent claims 2 or claim 3.
Modrek (Nucleic Acid Research (2001) volume 29, pages 2850-2859) teaches they assayed more than 2.1 million mRNA and EST transcripts. Thus the gene expression encompasses an enormous genus.
Medline plus What are single nucleotide polymorphisms (SNPs) (https://medlineplus.gov/genetics/understanding/genomicresearch/snp/) Updated 3/22/2022) states, “SNPs occur normally throughout a person’s DNA. They occur almost once in every 1,000 nucleotides on average, which means there are roughly 4 to 5 million SNPs in a person's genome. These variations occur in many individuals; to be classified as a SNP, a variant is found in at least 1 percent of the population. Scientists have found more than 600 million SNPs in populations around the world.” This is an enormous genus and a large portion of the 600 SNPs are not know to be associated with disease.
Fedorova ( Genes 2022, 13, 1472. https://doi.org/10.3390/genes13081472) teaches, “The 1000 Genomes Project revealed 81 million SNPs in humans [1]. Most of these SNPs present rare alleles with worldwide population frequencies less than 1% (68.4 million SNPs in 1000 genomes). Of the remaining SNPs, 2.7 million have alternative allele frequencies between 1 and 2%; 1.2 million between 2 and 3%; 0.76 million between 3 and 4%, and so on with fewer SNPs as allele frequencies increase.”
The specification does not define what is required by sequencing. The specification states, “especially where the sequencing is not paired end sequencing (e.g., nanopore sequencing, single molecule real time sequencing, ion torrent sequencing, SOLiD sequencing, etc.)” (0068). Thus the claims encompass Sanger sequencing which does not inherently provide for quantified expression.
The specification provides no specific examples in which mutations or quantified expression is used to select and administer treatment.
Thus while the claims encompass the use of enriched cell free nucleic acids (cFTNA) and cfRNA to be sequenced by any means to allow for quantification of expression and/or mutation detection for any treatment of any disease or any condition, the specification provides no working examples. The specification provides no teachings with respect to how to select and administer treatment based on any of the more than 81 million SNPs, numerous insertions, deletions, translocations, etc. or any quantified expression.
Thus the claims lack adequate written description on how to administer treatment based on mutations and or quantified expression. The specification provide no specific guidance on how treatment is based on disease parameter, the cytogenetic parameter, the immunophenotype, the biomarker for diagnosis prognosis, the selection of therapy, the biomarker for detection of minimal residual disease, and or the immunohistochemical parameter as encompassed by claim 3.
Claim 2 has been amended depends from claim 1 and recites, “ further comprising a step of using the first and second sequence data sets in a machine learning algorithm to identify (a) one or more genes associated with a disease parameter, wherein the disease parameter is presence of a cancer, type of cancer, recurrence of cancer, and/or residual cancer,(b) one or more genes associated with a cytogenetic parameter, wherein the cytogenetic parameter is a translocation and/or loss or duplication of at least a portion of a chromosome, and/or (c) one or more genes associated with an immunohistochemical parameter, wherein the immunohistochemical parameter is a presence or quantity of a cell surface receptor and/or presence or quantity of a cell surface enzyme, wherein the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter is identified..”
Thus the claims require any means of identifying of any mutation and prescribing treatment on the mutation or gene expression levels. Claim 2 encompasses the analysis of the first and second data set using a machine learning algorithm or model and treatment is administered based on the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter. The specification generically discusses the use of data to train machine learning algorithms or models. However the specification does not provide how two different datasets are used to identify mutations, or are used to provide the intended outcomes of the claims without prior training of the algorithm and the specific data used for such training of the algorithm or models. It provides no data or guidance on how to train the machine learning algorithm. Further The specification does not teach how the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter is identified
The claims recite, “further comprising a step of using at least some of the first and second sequence data sets in a model to thereby identify a disease parameter, a cytogenetic parameter, an immunophenotype, a biomarker for diagnosis prognosis, selection of therapy, biomarker for detection of minimal residual disease, and/or an immunohistochemical parameter” or “the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter is identified.” Thus the claims lack adequate written description.
Response to Arguments
The response begins traversing the rejection asserting the claim does not require literal support. Thus argument has been thoroughly reviewed is not considered persuasive as the rejection is a written description rejection and not new matter.
The response continues by alleging the claims are not unlimited but tethered to the cTNA and cfRNA. This argument has been thoroughly reviewed but is not considered persuasive as this encompasses sequencing any cTNA and/or cfRNA from any human subject and administering treatment on conditions or diseases based on the quantified expression and/or mutation. Thus the claims encompass over 81 million SNPs and the specification has not provided how to administer treatment based on any of the SNPs, gene expression, cytogenetic parameters, immunohistochemical parameter, etc.
The response on page 8 asserts the specification in 0019 defines mutations encompassed. The response specifically cites, “[i]n contemplated methods, the step of detecting mutations detects at least one of a single nucleotide change, an insertion of one or more nucleotides, a deletion of one or more nucleotides, an inversion, a translocation, and copy number variation." This is not an open-ended genus, but a representative list of mutation types commonly associated with disease states, particularly cancer, as further detailed in paras [0073], [0074], [0082], [0083]. “ This argument has been thoroughly reviewed but is not considered persuasive as the cited portion of paragraph 0019 provides a preferred embodiment. Further the claims are not limited to any specific genes, but encompass any single nucleotide change, any insertion of one or more nucleotides, any deletion of one or more nucleotides, any inversion, any translocation, and any copy number variation. This is an enormous genus of any single nucleotide change, any insertion of one or more nucleotides, any deletion of one or more nucleotides, any inversion, any translocation, and any copy number variation. Paragraph 0073-0074 provides a description of sequencing which does not limit the genus encompassed. Paragraphs 0082-0083 describe further analysis, but do not limit the any of the SNPs, any gene expression, any cytogenetic parameters, any immunohistochemical parameter, any mutations, etc. The response asserts, “These paragraphs correlate mutations and expression levels to be particularly beneficial in cases where "the sole identification of a mutated gene may be clinically irrelevant as a pharmaceutical target where that mutated gene is only weakly or not at all expressed" “ This demonstrates the issue as the specification provides no specific guidance on how to identify and/or treat based on clinically irrelevant mutations which is encompassed by the claims. The response continues by asserting, “para [0069]) and demonstrate higher mutation detection sensitivity using cfRNA fractions (para [0081]; FIG.1). Quantified expression is similarly described as being derived from sequencing data, with examples showing how expression profiles inform disease detection (see paras [0093]-[0094]). “ This argument has been thoroughly reviewed but is not considered persuasive a detection of a higher mutation rate appears to further confound the issue of how to detect and treat based on clinically irrelevant mutations, immunohistochemistry, cytogenetics, etc. Further Fedorova ( Genes 2022, 13, 1472. https://doi.org/10.3390/genes13081472) teaches, “The 1000 Genomes Project revealed 81 million SNPs in humans [1]. Most of these SNPs present rare alleles with worldwide population frequencies less than 1% (68.4 million SNPs in 1000 genomes). Of the remaining SNPs, 2.7 million have alternative allele frequencies between 1 and 2%; 1.2 million between 2 and 3%; 0.76 million between 3 and 4%, and so on with fewer SNPs as allele frequencies increase.”
The response continues by asserting, “According to MPEP §2163(II)(A)(3), this disclosure of representative species (e.g., SNVS, indels, translocations) and functional correlations (e.g., mutation/expression linkage to treatment targets) suffices to show possession, without needing to enumerate "every possible mutation" as the Examiner suggests.” This argument has been thoroughly reviewed but is not considered persuasive as the response has merely identified genus encompassed of mutations, immunohistochemistry, cytogenetic abnormalities, etc., but does not provide any specific species of mutations and how to treat based on the mutations. Further the specification provides no specific teachings on how to treat a human subject based on the data required or encompassed by the claims.
The response continues by arguing treatment based on identified mutations and/or quantified expression. (bottom of page 8). The response continues by asserting, “Para [0031] elaborates that "[t]he treatment may comprise administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, and/or a cancer vaccine...based on a model (e.g., Bayesian classifier-trained model) that uses the identified mutation and quantified expression level." Additional guidance appears in paras [0056]-[0059] (sample preparation and sequencing for mutation/expression analysis), para [0070] (targeting expressed mutations), and paras [0076]-[0094] (working examples of mutation detection and expression quantification leading to treatment decisions). These descriptions convey possession by linking the analytical outputs to specific treatment, satisfying MPEP §2163(II)(A)(3)(a)(ii)'s requirement for a "correlation between function and structure.” This argument has been thoroughly reviewed but is not considered persuasive as the cited portion of paragraph 0031 provides potential treatments for cancer, however the claims encompass any disease or condition. Thus it is not commensurate in scope with the claims. Further paragraph 0031 provides no specific guidance how mutations or quantified gene expression are used to determine and identify treatments to be administered.
The response continues by alleging, “The claims do not require treating "healthy humans" as alleged by the Examiner; the context (e.g., cancer-associated genes as in para [0032]) implies diseased subjects, but even if broader, the specification (e.g., detecting residual cancer in para [0068]) provides guidance.” This argument has been thoroughly reviewed but is not considered persuasive as the claims are not limited to cancer. The claims recite, “a patient suspected of or diagnosed of a disease or condition associated with the identified one or more mutations and/or quantified expression.” Thus the claims encompass any subject suspected of any condition or disease. Further the response on the bottom of page 9 states, “The claims are limited to human subjects but do not require a pre-existing disease diagnosis, consistent with preventive or diagnostic treatments.” Thus the response is providing contradictory arguments.
The response traverses the rejection with respect to claims 2 and 3 asserting, “Claims 2's use of a machine learning algorithm to identify genes associated with disease, cytogenetic, or immunohistochemical parameters is supported by para [0094] ("[u]sing expression profile of cfRNA or cfTNA along with a machine learning approach, enabled prediction of patients with active cancer that shows mutation in peripheral blood circulation") and para [0086] (k-fold cross-validation for gene selection of genes relevant to cancer). In addition, training of a "naive Bayesian classifier" is also discussed at para [0086] as well as the specific data used for training.” This argument has been thoroughly reviewed but is not considered persuasive as paragraph 0094 states, “More specifically, using expression profile of cfRNA or cfTNA along with a machine learning approach, enabled prediction of patients with active cancer that shows mutations in peripheral blood circulation.” However, this provides no specific guidance on how to do this in the absence of training data. It does not provide how the machine learning is trained. Further the teachings are limited to cancer. However the claims encompass any subject suspected of any condition or disease. Further paragraph 0086 states:
[0086] Similarly for solid tumors, expression levels of CA15-3 (MUC1) in cfRNA samples can be used to distinguish samples with active breast cancer from other conditions as can be seen from patient #2 and #7 of FIG.7. Also these patients with breast cancer and high ERBB2 (HER2) could be distinguished by evaluating ERBB2 mRNA in peripheral blood cfRNA as is clearly shown in FIG.8.
Thus paragraph 0086 does not support this assertion.
The response traverses claim 3 asserting, “Claims 3's model-based identification of parameters is described in paras [0029], [0059], and [0088], with treatment based thereon. Claims 2 and 3 are not "different" from claim 1 as alleged by the Examiner, but rather build upon claim 1 and the specification integrates them functionally. " Scope and Human Subjects: The claims are limited to human subjects but do not require a pre-existing disease diagnosis, consistent with preventive or diagnostic treatments (e.g., paras [0055] and [0093] for minimal residual disease). The Examiner's cited art (see Non-Final Office Action dated 2025-05-15, pgs. 8-9) highlights genomic variability but does not undermine the sufficiency of the written description.” This argument has been thoroughly reviewed but is not considered persuasive as the cited paragraphs state:
[0029] Consequently, the inventors also contemplate a method of classifying a cancer in a subject that includes a step of sequencing (e.g., using paired-end sequencing sequencing) a first target-enriched cDNA library and a second target-enriched cDNA library to thereby obtain respective first and second sequence data sets. Preferably, the first target-enriched cDNA library does not comprise a cfDNA fraction of cfTNA of a biological fluid of the subject, whereas the second target-enriched cDNA library comprises a cfDNA fraction of cfTNA of the same biological fluid. In a further step of such method, one or more mutations are identified for each gene in the first and second sequence data sets, and an expression level is quantified for one or more genes in at least the first sequence data set. The so identified mutation and quantified expression level can then be used in a trained model to thereby classify the cancer in the subject.
[0059] The so amplified first and second cDNA libraries are then subjected to target gene enrichment using multiple tiled hybridization probes for each target gene. Most typically, the entire target gene or transcript is targeted by hybridization probes having a step length of between 1 and 10 (i.e., first and second hybridization probes bind to the target sequence at a linear distance of between 1-10 nt). It is further preferred that the hybridization probes will have a length of between 100-150 nt. In the present example, the target genes are genes encoding one or more cancer associated genes, cell signaling associated genes, immunophenotype associated genes, and/or receptor associated genes, and an exemplary collection of 1458 target genes is shown in Table 1 below. Hybridization is performed in liquid phase over at least 8 hours and captured cDNA will be removed using magnetic beads.
[0088] Predicting the presence of any cancer: Using the measured expression levels with the machine learning approached described above, analysis of the 160 patients described above showed that one can indeed distinguish patients with cancer with an area under the curve (AUC) of 0.786 using the 1450 genes of Table 1 as is shown in FIG.9. This prediction is expected to improve by adding mutation profiling to this system.
Paragraphs 0029 and 0059 merely provide, “identified mutation and quantified expression level can then be used in a trained model to thereby classify the cancer in the subject” and “In the present example, the target genes are genes encoding one or more cancer associated genes, cell signaling associated genes, immunophenotype associated genes, and/or receptor associated genes, and an exemplary collection of 1458 target genes.” It provides support for the ideas of machine learning. However claim 3 merely requires a model and does not require machine learning. Further the cited paragraphs are limited to cancer, have the claims encompass any subject suspected of any condition or disease and administering treatment based on quantified expression or mutations.
The response on the bottom of page 9 traverses the scope and human subjects. The response specifically asserts, “The claims are limited to human subjects but do not
require a pre-existing disease diagnosis, consistent with preventive or diagnostic
treatments (e.g., paras [0055] and [0093] for minimal residual disease). The Examiner's
cited art (see Non-Final Office Action dated 2025-05-15, pgs. 8-9) highlights genomic
variability but does not undermine the sufficiency of the written description.” This argument has been thoroughly reviewed but is not considered persuasive as the response provides no indication where or how the specification provides any specific mutations or quantified gene expression is used to determine a specific treatment for any disease. Further the response is merely asserting the 2.1 million EST and mRNA, 500 million SNPs or 81 million SNPs in humans does not undermine written description. This is confusing as the cited prior art demonstrates the enormous genus encompassed by the claims. Thus this argument is not persuasive.
The response traverses the rejection with respect to sequencing by asserting, “The Applicant notes that the specification explicitly provides what kind of sequencing may be used and Sanger sequencing is not mentioned once.” This argument has been thoroughly reviewed but is not considered persuasive as the claims and specification provide no definition which excludes Sang sequencings. Thus this argument is not persuasive.
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 1-3, 5-6 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 1 recites, “and administering a treatment to a patient suspected of or diagnosed with a disease or condition associated with the identified one or more mutations and/or quantified expression.” “Associated with” is not art accepted term. Further “associated with” is a relative term and suggest some mutations are not associated with. The specification and claims provide no specific guidance on how to differentiate disease or condition associated with the identified one or more mutations and/or quantified expression from disease or condition not associated with the identified one or more mutations and/or quantified expression. Thus it is unclear what “Associated with” encompasses, requires or excludes. Modrek (Nucleic Acid Research (2001) volume 29, pages 2850-2859) teaches they assayed more than 2.1 million mRNA and EST transcripts. Thus the gene expression encompasses an enormous genus. Fedorova ( Genes 2022, 13, 1472. https://doi.org/10.3390/genes13081472) teaches, “The 1000 Genomes Project revealed 81 million SNPs in humans [1]. Most of these SNPs present rare alleles with worldwide population frequencies less than 1% (68.4 million SNPs in 1000 genomes). Of the remaining SNPs, 2.7 million have alternative allele frequencies between 1 and 2%; 1.2 million between 2 and 3%; 0.76 million between 3 and 4%, and so on with fewer SNPs as allele frequencies increase.” Further it is unclear what is administered based on any of the 81 million SNPs or the 2.1 million mRNA and EST. Thus the metes and bounds are vague and unclear.
Claim 1 recites, “ii) converting the first cfRNA fraction of the, and a second portion of undigested cfTNA into respective first and second cDNA libraries by a) reverse transcribing the nucleic acids to produce cDNA, b) ligating adapters to the cDNA, and c) amplifying the cDNA to generate respective first and second cDNA libraries.” However, Campbell (https://www.bio.davidson.edu/genomics/method/cDNAproduction.html, 2002) teaches, “By definition, cDNA is double-stranded DNA that was derived from mRNA which can be obtained from prokaryotes or eukaryotes.” Thus it is unclear how cfTNA is different than cfRNA fraction.
Claim 2 has been amended to recite,” further comprising a step of using the first and second sequence data sets in a machine learning algorithm to identify (a) one or more genes associated with a disease parameter, wherein the disease parameter is presence of a cancer, type of cancer, recurrence of cancer, and/or residual cancer,(b) one or more genes associated with a cytogenetic parameter, wherein the cytogenetic parameter is a translocation and/or loss or duplication of at least a portion of a chromosome, and/or (c) one or more genes associated with an immunohistochemical parameter, wherein the immunohistochemical parameter is a presence or quantity of a cell surface receptor and/or presence or quantity of a cell surface enzyme, wherein the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter is identified.” “It is further confusing as claim 1 requires administering based on “the one or more identified mutations and/or quantified expression.” It is unclear how treatment is selected the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter or limitations from the independent claims. Modrek (Nucleic Acid Research (2001) volume 29, pages 2850-2859) teaches they assayed more than 2.1 million mRNA and EST transcripts. Thus the gene expression encompasses an enormous genus. Fedorova ( Genes 2022, 13, 1472. https://doi.org/10.3390/genes13081472) teaches, “The 1000 Genomes Project revealed 81 million SNPs in humans [1]. Most of these SNPs present rare alleles with worldwide population frequencies less than 1% (68.4 million SNPs in 1000 genomes). Of the remaining SNPs, 2.7 million have alternative allele frequencies between 1 and 2%; 1.2 million between 2 and 3%; 0.76 million between 3 and 4%, and so on with fewer SNPs as allele frequencies increase.” Further it is unclear what is administered based on the 81 million SNPs or the 2.1 million mRNA and EST. Further in response to written description the response has asserted, “The claims are limited to human subjects but do not require a pre-existing disease diagnosis, consistent with preventive or diagnostic treatments.” Thus it is confusing and unclear why one of skill in the art would treat asthma, psoriasis, edema, etc. with chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter is identified.
Claim 3 has been amended to recite,” further comprising a step of using at least some of the first and second sequence data sets in a model to thereby identify a disease parameter, a cytogenetic parameter, an immunophenotype, a biomarker for diagnosis prognosis, selection of therapy, biomarker for detection of minimal residual disease, and/or an immunohistochemical parameter, wherein the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, the immunophenotype, the biomarker for diagnosis prognosis, the selection of therapy, the biomarker for detection of minimal residual disease, and or the immunohistochemical parameter is identified. The metes and bounds are unclear what model is used and how treatment is determined. Further in response to written description the response has asserted, “The claims are limited to human subjects but do not require a pre-existing disease diagnosis, consistent with preventive or diagnostic treatments.” Thus it is confusing and unclear why one of skill in the art would treat asthma, psoriasis, edema, etc. with a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, the immunophenotype, the biomarker for diagnosis prognosis, the selection of therapy, the biomarker for detection of minimal residual disease, and or the immunohistochemical parameter is identified. It is further confusing as claim 1 requires administering based on “the one or more mutations and/or quantified expression.” It is unclear how treatment is selected based on the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter or limitations from the independent claims. Modrek (Nucleic Acid Research (2001) volume 29, pages 2850-2859) teaches they assayed more than 2.1 million mRNA and EST transcripts. Thus the gene expression encompasses an enormous genus. Fedorova ( Genes 2022, 13, 1472. https://doi.org/10.3390/genes13081472) teaches, “The 1000 Genomes Project revealed 81 million SNPs in humans [1]. Most of these SNPs present rare alleles with worldwide population frequencies less than 1% (68.4 million SNPs in 1000 genomes). Of the remaining SNPs, 2.7 million have alternative allele frequencies between 1 and 2%; 1.2 million between 2 and 3%; 0.76 million between 3 and 4%, and so on with fewer SNPs as allele frequencies increase.” Further it is unclear what is administered based on the 81 million SNPs or the 2.1 million mRNA and EST.
Response to Arguments
The response begins traversing the 112(b) by asserting, “The understanding of "based on" as provided throughout the specification is not ambiguous; it delineates the causal or relational link without requiring exhaustive enumeration of every possible mutation or expression level as suggested by the Examiner.” This argument has been thoroughly reviewed but is inconsistent with the plain reading of the claims. The claims encompass any mutations, any quantified expression, etc. and thus encompasses treatment for all known and unknown mutations.
The response traverses the rejection with respect to cDNA by asserting, “claim 1 distinguishes that the first library is from cfRNA (after DNase digestion removes cfDNA, generating a cfRNA fraction); the second is from cfTNA (undigested, including cfDNA and cfRNA). Both fractions are subjected to reverse transcription (converting RNA to cDNA), adapter ligation, and amplification, resulting in cDNA libraries. A skilled artisan would understand that for the cfTNA portion, reverse transcription acts on the RNA component, while the DNA component (cfDNA) is directly amendable to adapter ligation and amplification as double-stranded DNA. The resulting "cDNA library" for cfTNA thus includes sequences from both original RNA (now cDNA) and DNA sources, whereas the cfRNA library is RNA-derived only. This is also supported in the specification at paras [0056]-[0059] (detailing the process, including DNase digestion to isolate cfRNA) and para [0065]. However, Campbell's RNA-only definition (cDNA from mRNA) as quoted by the Examiner (see Non-Final Office Action dated 2025-05-15, pg. 17), fails to consider that claim 1 differentiates the two cDNA libraries via DNase, where the cfRNA library is pure RNA-derived cDNA and the cfTNA library is a combination of RNA-cDNA + DNA.” This argument has been thoroughly reviewed but is not considered persuasive as the art of Campbell demonstrates what the art accepts as a definition. Applicant is attempting to be its own lexicographer. However, MPEP 2173.01 states:
A fundamental principle contained in 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph is that applicants are their own lexicographers. They can define in the claims what the inventor or a joint inventor regards as the invention essentially in whatever terms they choose so long as any special meaning assigned to a term is clearly set forth in the specification
In the instant case, the response has failed to provide where the specification explicitly provides a definition consistent with the argument. Thus the rejection is maintained.
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 1-3, 4-5 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural correlation and mental step without significantly more. The claim(s) recite(s) the abstract idea or mental step of identifying mutations and quantifying expression. The claim attempts to integrate a law of nature by applying a generic treatment based on the quantified expression or mutation detection. Dependent claims require the natural correlations of (a) one or more genes associated with a disease parameter, wherein the disease parameter is presence of a cancer, type of cancer, recurrence of cancer, and/or or residual cancer, (b) one or more genes associated with a cytogenetic parameter, wherein the cytogenetic parameter is a translocation and/or loss or duplication of at least a portion of a chromosome, and/or (c) one or more genes associated with an immunohistochemical parameter, wherein the immunohistochemical parameter is a presence or quantity of a cell surface receptor and/or presence or quantity of a cell surface enzyme or identify a disease parameter, a cytogenetic parameter, an immunophenotype, a biomarker for diagnosis prognosis, selection of therapy, biomarker for detection of minimal residual disease, and/or an immunohistochemical parameter. This judicial exception is not integrated into a practical application because the claims have been amended provide treatment with a high degree of generality and/or merely applying the judicial exception . The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims require no specific reagents..
Claim analysis
The instant claim 1 is directed towards A method of administering treatment based on analyzing nucleic acid data of a human subject, comprising: sequencing a first target-enriched complementary DNA (cDNA) library and a second target-enriched cDNA library to thereby obtain respective first and second sequence data sets; wherein the first target-enriched cDNA library is prepared by isolating a cell-free RNA (cfRNA) fraction from cell-free total nucleic acid (cfTNA) of a biological fluid of the subject, excluding a cell-free DNA (cfDNA) fraction; wherein the second target-enriched cDNA library is prepared by collecting cfTNA from said biological fluid, including the cfDNA fraction; wherein the first and second target-enriched cDNA libraries are prepared by:(i) digesting a first portion of cfTNA from the biological fluid of the subject with DNase isolate the cfRNA fraction;(ii) converting the first cfRNA fraction of the, and a second portion of undigested cfTNA into respective first and second cDNA libraries by a) reverse transcribing the nucleic acids to produce cDNA, b) ligating adapters to the cDNA, and c) amplifying the cDNA to generate respective first and second cDNA libraries; and (iii) enriching each of the first and second cDNA libraries for a plurality of target cDNAs by hybridizing each target cDNA with a plurality of tiled hybridization probes that bind to the target cDNA at respective different positions to produce the first and second target-enriched cDNA libraries; identifying, for each gene in the first and second sequence data sets, one or more mutations, and quantifying expression in at least the first sequence data set; and administering a treatment to a patient suspected of or diagnosed with a disease or condition associated with the identified one or more mutations and/or quantified expression.
The identifying and quantifying are mental steps.. The administering step is a treatment with a high degree of generality and/or merely applying the judicial exception.
The wherein clause provides a description of how the data was obtained, but does not limit how the data is analyzed. There is no specific target, no specific enrichment, etc.
The sequencing is considered to be an active step requiring the analysis of a sample.
Claim 2 requires,” further comprising a step of using the first and second sequence data sets in a machine learning algorithm to identify (a) one or more genes associated with a disease parameter, wherein the disease parameter is presence of a cancer, type of cancer, recurrence of cancer, and/or residual cancer,(b) one or more genes associated with a cytogenetic parameter, wherein the cytogenetic parameter is a translocation and/or loss or duplication of at least a portion of a chromosome, and/or (c) one or more genes associated with an immunohistochemical parameter, wherein the immunohistochemical parameter is a presence or quantity of a cell surface receptor and/or presence or quantity of a cell surface enzyme, wherein the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter is identified.” This is a mental step or natural correlation. The administering step is interpretated as conditional as the claim recites, “when the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter is identified.” Thus in the absence of the disease parameter, the cytogenetic parameter, and/or the immunohistochemical parameter being identified no treatment is required and thus no integration.
Claim 3 requires, “further comprising a step of using at least some of the first and second sequence data sets in a model to thereby identify a disease parameter, a cytogenetic parameter, an immunophenotype, a biomarker for diagnosis prognosis, selection of therapy, biomarker for detection of minimal residual disease, and/or an immunohistochemical parameter, wherein the treatment comprises administering a chemotherapeutic agent, an immune stimulatory agent, a checkpoint inhibitor, or a cancer vaccine when the disease parameter, the cytogenetic parameter, the immunophenotype, the biomarker for diagnosis prognosis, the selection of therapy, the biomarker for detection of minimal residual disease, and or the immunohistochemical parameter is identified.” This is a mental step or natural correlation. The administering step is a treatment is only required when the disease parameter, the cytogenetic parameter, the immunophenotype, the biomarker for diagnosis prognosis, the selection of therapy, the biomarker for detection of minimal residual disease, and or the immunohistochemical parameter is identified. Thus treatment is conditional and does not integrate the judicial exception.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, the independent claim an abstract idea. Dependent claims abstract idea and/or natural correlation.
With regards to claim 1, the claim recites, “identifying, for each gene in the first and second sequence data sets, one or more mutations, and quantifying expression in at least the first sequence data set..” This is an abstract idea or mental step.
With regards to claim 2, the claim recites, “using the first and second sequence data sets in a machine learning algorithm to identify (a) one or more genes associated with a disease parameter, wherein the disease parameter is presence of a cancer, type of cancer, recurrence of cancer, and/or residual cancer,(b) one or more genes associated with a cytogenetic parameter, wherein the cytogenetic parameter is a translocation and/or loss or duplication of at least a portion of a chromosome, and/or (c) one or more genes associated with an immunohistochemical parameter, wherein the immunohistochemical parameter is a presence or quantity of a cell surface receptor and/or presence or quantity of a cell surface enzyme.” This is an abstract idea or mental step.
With regards to claim 3, the claim recites, “ step of using at least some of the first and second sequence data sets in a model to thereby identify a disease parameter, a cytogenetic parameter, an immunophenotype, a biomarker for diagnosis prognosis, selection of therapy, biomarker for detection of minimal residual disease, and/or an immunohistochemical parameter.” This is an abstract idea or mental step.
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as none of the claims provide a limitation which depends from and integrates the judicial exception as the administering step is not a particular treatment or prophylaxis for a disease or medical condition in the independent claim and conditional in the dependent claims. Further treating encompass watchful waiting, getting sunshine, etc.
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No, the claims set forth routine and conventional steps required to provide the data to correlate with disease or conditions.
Yeh (WO2017027835), Suliman ( Trends in Medicine (2019) volume 19, pages 1-4), Enderle (wo2018126278) , Tzimagiorgis (Cancer Epidemiology (2011) volume 35, pages 589-589), Feng (Advances in Liquid Biopsies. January 13 - 16 2020, abstract A22), Arensdorf (WO2020072829 (9 April 2020), , Reis ((2018) Gene rearrangements in lung cancer: towards the detection in cell free nucleic acids), Yang (bioRxiv (July, 2019) pages 1-23), Ma (PLos One (. (2017) Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns. PLoS ONE 12(1): e0169231), Fettke( Volume 78, Issue 2, August 2020, Pages 173-180)., Wang (WO2019182887) Mockeler (Genomics 85 (2005) 1 –15) demonstrate the active step of sequencing is routine and conventional as is the wherein clause.
Response to Arguments
The response traverses by reviewing the amendment to the claims this is noted.
The response continues by arguing the claims are to a method. This has been conceded in the rejection.
The response continues by providing arguments with respect to court and PTAB decisions. These are noted, but the fact pattern is different in the instant case. Further the PTAB decision is not precedential and thus is not binding on the Corp.
The response continues by asserting the rejection has provided only conclusory statements. This argument has been thoroughly reviewed but is not considered persuasive as the rejection has specifically identified the limitations which are mental steps, abstract ideas or natural correlations. Thus this argument is not persuasive.
The response further alleges the rejection provides conclusory statements about the claims not being significantly more. This argument has been thoroughly reviewed but is not considered persuasive as Yeh (WO2017027835), Suliman ( Trends in Medicine (2019) volume 19, pages 1-4), Enderle (wo2018126278) , Tzimagiorgis (Cancer Epidemiology (2011) volume 35, pages 589-589), Feng (Advances in Liquid Biopsies. January 13 - 16 2020, abstract A22), Arensdorf (WO2020072829 (9 April 2020), , Reis ((2018) Gene rearrangements in lung cancer: towards the detection in cell free nucleic acids), Yang (bioRxiv (July, 2019) pages 1-23), Ma (PLos One (. (2017) Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns. PLoS ONE 12(1): e0169231), Fettke( Volume 78, Issue 2, August 2020, Pages 173-180)., Wang (WO2019182887) Mockeler (Genomics 85 (2005) 1 –15) demonstrate the active step of sequencing is routine and conventional as is the wherein clause.
The response asserts the method cannot be performed in the human mind and thus is not a mental step. This argument has been thoroughly reviewed but is not considered persuasive as the rejection states the only explicit active step of sequencing was/is routine and conventional. Further the claims encompass sequencing, finding a mutation and referencing a table for the mutation, possible disease and treatment. Thus this argument is not persuasive.
The response continues arguing 2A by asserting, “However, as amended, claim 1 recites additional elements that as a whole amount to "significantly more" than the judicial exception itself. Specifically, claim 1, as amended, recites a specific, unconventional technological process for preparing and analyzing dual target-enriched cDNA libraries from cfTNA, which improves the sensitivity and accuracy of mutation detection and expression quantification to thereby allow for informed treatment administration to individuals with or suspected to have corresponding diseases and/or conditions.” This argument has been thoroughly reviewed but is not considered persuasive as the only active step is sequencing. The wherein clause provides how the data is obtained, but does not limit how it is analyzed.
The response continues by asserting, “The steps provided by the claims are not generic data gathering or mere application of natural law. As provided in the specification, analyzing cfRNA and cfTNA in separate fractions (with DNase to isolate cfRNA) significantly increases mutation detection sensitivity - e.g., detecting substantially more mutations in cfRNA than cfDNA or cfTNA alone and enabling detection of low-expression or unstable RNA mutations that cfDNA misses. “ The wherein clause provides a description of how the data was obtained, but does not limit how the data is analyzed. There is no specific target, no specific enrichment, etc. This argument has been thoroughly reviewed but is not considered persuasive as the claims do not require the treatment is dependent on the increased sensitivity of the sequencing. Thus the arguments are not commensurate in scope the limitations of the claims.
The response continues by asserting, “The treatment step further integrates the exception by applying the improved detection results practically: "administering a treatment to a patient suspected of or diagnosed with a disease or condition associated with the identified one or more mutations and/or quantified expression"”. This argument has been thoroughly reviewed but is not considered persuasive as MPEP 231064(d)(2) states: “Examiners should keep in mind that in order to qualify as a “treatment” or “prophylaxis” limitation for purposes of this consideration, the claim limitation in question must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. An example of such a limitation is a step of “administering amazonic acid to a patient” or a step of “administering a course of plasmapheresis to a patient.” If the limitation does not actually provide a treatment or prophylaxis, e.g., it is merely an intended use of the claimed invention or a field of use limitation, then it cannot integrate a judicial exception under the “treatment or prophylaxis” consideration.” Thus this argument is not persuasive. Further the administering in dependent claim is conditional.
The response continues traversing the rejection asserting, “The steps provided by the claims are not generic data gathering or mere application of natural law. As provided in the specification, analyzing cfRNA and cfTNA in separate fractions (with DNase to isolate cfRNA) significantly increases mutation detection sensitivity - e.g., detecting substantially more mutations in cfRNA than cfDNA or cfTNA alone and enabling detection of low-expression or unstable RNA mutations that cfDNA misses. See paras [0073] and [0081]. The use of tiled hybridization probes for enrichment further enhances coverage and accuracy for targeted genes. This specific combination addresses technical challenges posed by cfRNA degradation, low-abundance, or small size. See paras [0070] and [0074].” This argument has been thoroughly reviewed but is not considered persuasive as the claims do not require the treatment is dependent on the increased sensitivity. Thus the arguments are not commensurate in scope the limitations of the claims.
Claim Rejections - 35 USC § 103
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 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.
Claim 1-3, 5-6 is/are rejected under 35 U.S.C. 103 as being unpatentable over Yeh (WO2017027835), Suliman ( Trends in Medicine (2019) volume 19, pages 1-4), Enderle (wo2018126278) , Tzimagiorgis (Cancer Epidemiology (2011) volume 35, pages 589-589), Feng (Advances in Liquid Biopsies. January 13 - 16 2020, abstract A22), Arensdorf (WO2020072829 (9 April 2020), , Reis ((2018) Gene rearrangements in lung cancer: towards the detection in cell free nucleic acids), Yang (bioRxiv (July, 2019) pages 1-23), Ma (PLos One (. (2017) Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns. PLoS ONE 12(1): e0169231), Fettke ( Eur Urol Volume 78, Issue 2, August 2020, Pages 173-180)., Wang (WO2019182887) Mockeler (Genomics 85 (2005) 1 –15).
The prior art as exemplified below demonstrates that examination of cell free nucleic acids including RNA and DNA were known. Further the exemplified art demonstrates the production of libraries by reverse transcription, adapter ligation and amplification prior to enrichment was also known. The art demonstrates the use of DNase to reduce DNA in background to allow more accurate determination of RNA sequences. Thus the art demonstrates the instant claims are no more than the combination of known techniques.
Yeh teaches methods of isolating cell free nucleic acids. (title abstract). Ye teaches, “In certain embodiments, the c:tNA is cfRNA, or DNA derived from and which is representative of such cfRNA.(page 47). Ye claims CfNA includes CfDNA or cfRNA (claims 1-3). Peterson teaches cfNA from 50 to 600 bp (page 34). Ye teaches using a portion of a cfNA to be modified by adapter ligation (claim 1). Ye teaches , “1. Take 10 μL diluted plasma (1 :5) heated at 95°C for 2 min to inactivate endogenous nucleases, dissociate DNA complexes, and fragment/denature cfDNA; 2. Add 1 μL of DNase I reaction buffer (final concentration 10mM Tris-HCl, 2.5mM MgCl2, 0.5mM CaCl pH 7.6) and 2 units of DNase I, mix thoroughly and incubate at 37°C for 30 minutes; 3. Add 1 μL of 0 .5 M EDTA (to a final concentration of 5 mM); 4. Heat inactivate at 85°C for 15 minutes; 5. Perform reverse transcription and cDNA synthesis (for example using Protoscript II kit from New England BioLabs, Ipswich, MA). To 11 μL of the above DNase I treated sample, add 3 μL 5X first strand synthesis reaction buff er and 1 μL random primers; Incubate the sample at 94°C for 15 min, transfer the tube to ice; Add 0.5 μL murine RNase inhibitor (20 U) and 1 μL Reverse Transcriptase, and water to make up final volume to 20 μL; and incubate the sample in a preheated thermal cycler as follows: 10 minutes at 25°C; 15 minutes at 42°C; 15 minutes at 70°C; and hold at 4°C; 6. Perform second strand synthesis (for example using NEBNext Second Strand Synthesis Module from New England BioLabs, Ipswich, MA). Add the following reagents to the to the reaction (20 μl): Nuclease-free water 48 μl; synthesis reaction buffer 8 μl; synthesis enzyme mix 4 μl (total volume 80 μl); mix thoroughly and incubate in a thermal cycler for 1 hour at 16°C, with heated lid set at :S 40°C. 7. Purify the double-stranded cDNA using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). 8. Proceed to step 5 of the ISA protocol for cfDNA (for example, protocol A or protocol B). Step 5 is adapter ligation (p 57 or 58).
Suliman teaches kits for isolation of total nucleic acids from cell free samples (title abstract)
Enderle teaches, “[00155] In particular, a suitable experimental setup is outlined that will use a RNAse or DNase or mock digestion of a mixture of exosomal RNA and cell-free DNA to demonstrate the specificity and efficiency of the RNA tagging process and the detection of the tag in an NGS dataset. Sample ix1 (control) will contain RNA and DNA but use only regular hexamers without a tag in the cDNA synthesis, 1x2 (inventive process) will contain RNA and DNA and use tagged hexamers during cDNA synthesis, 1x3 (control) will contain only RNA left intact by DNase digestion and use tagged hexamers during cDNA synthesis, and 1x4 (control) will contain DNA left intact by RNase digestion. To demonstrate successful enzymatic digestion in the NGS libraries, 5,000,000 copies of a synthetic RNA and DNA of a specific, unique sequence were spiked into the nucleic acid extraction.”
Feng teaches isolation of cfDNA and cfRNA isolation from a single plasma sample. (sample collection).
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Feng teaches, “circulating cell-free RNA (cfRNA) sequencing confirmed and enhanced detection sensitivity for variants with low allele frequency. “ (abstract) Feng teaches, “Our results demonstrated the potential clinical utility/feasibility of simultaneous multi-parametric profiling of ctDNA and cfRNA for comprehensive molecular insight/ characterization in advanced stage cancer. cfRNA-derived variant detection confirms the variants originally detected in ctDNA test and further validates the high specificity results for report interpretation. The ctDNA and cfRNA-based combined liquid biopsy solution provides holistic molecular overview for detecting driver mutations, monitoring efficacy / disease burden, and identifying sub-clonal alterations that may related to
drug resistance and tumor heterogeneity.” (conclusion)
Yang teaches, “ cfRNA in plasma is usually made up of degradative small fragments with size smaller than 200nt, very low concentration (may lower than 10 ng/mL.”(page 3, 2nd paragraph). Yang further teaches, “DNase I treatment could also prevent the possible contamination of cell-free DNA.” (page 4, 1st paragraph).
Ma in supplemental figure 1 teaches most cell free DNA is 400 base pairs or less.
Tzimagiorgis teaches, “ Extracellular or cell-free nucleic acids (DNA or mRNA) have been isolated from various bodily fluids and used as biological markers for various diseases among which is cancer . Several terms are used for these extracellular nucleic acids such as: (1) Circulating nucleic acids, mainly used for DNA and RNA, circulating in plasma or serum (2) Extracellular, or (3) Cell-free nucleic acids, when isolated from other body fluids such as: saliva, urine, cerebrospinal fluid (CSF), bronchoalveolar lavage fluid (BALF) amniotic fluid and other.” (section 2).
Tzimagiorgis teaches, “ Several different mechanisms have been implicated as a potential source for the circulating extracellular or cell-free nucleic acids. One possible mechanism is cell necrosis resulting in the presence of high amounts of DNA (and probably RNA) in the plasma of cancer patients with large or advanced tumors.” (section 2, 2nd paragraph).
Tzimagiorgis teaches, “The first reports on increased circulating nucleic acids – both DNA and RNA – in the serum of cancer patients were back in 1977.”
Tzimagiorgis teaches, “Due to the sensitivity of PCR reaction, the presence of genomic DNA contamination in an RNA preparation may lead to ambiguous or misleading results. This problem is exaggerated when the analysis is performed using extracellular RNA, due to the small amounts of RNA obtained. To avoid this problem, it is highly recommended that RNA preparations be treated with DNase I (RNase-free) prior to cDNA synthesis” (4.3)
Wang teaches, “Target nucleic acids can be selectively degraded in the sample by treating the sample with agents that deliver a nuclease, such as a DNase or an RNase to the target nucleic acid, but not to the viral nucleic acid. Examples of delivery agents include cationic polymers, such as transfection reagents. Non target nucleic acids can be used to prepare a library of nucleic acids. As shown in FIG. 6, cell-free nucleic acids 320 including double-stranded and single-stranded nucleic acids, and vesicles 330 containing single-stranded nucleic acids, double stranded nucleic acids, or protein capsids 340 containing viral nucleic acids can be contacted with DNase and RNase using delivery agents which can enter the vesicles.” (0042)
Reis teaches, “From part of that plasma sample, exosomes were isolated in order to evaluate if extracellular vesicles represented a better source for cfRNA. Also, during cfTNA extraction we increased the agitation during cfTNA binding to the dynabeads to the maximum..” (10.2.3 (page 28). Reis teaches use of DNase to remove DNA contamination (9.2.1.2) Reis teaches, “Briefly, a minimum of 10ng of cfTNA were used for cDNA synthesis, using SuperScript VILO Master Mix (Invitrogen). Then, the DNA/cDNA pool was amplified, purified with Agencourt beads and linked to tag barcodes, to allow sample multiplexing upon sequencing. Agencourt beads were once again used for sample purification and size selection of the amplified library. The Ion Library TaqMan® Quantitation Kit was used to quantify the samples, Ion Chef was used for template preparation and Ion S5XL sequencer was used to sequence the samples. Ion Reporter 5.6 was used to analyze the results. The variants detected by NGS were confirmed by dPCR.”
Arensdorf teaches methods of SIMULTANEOUS, SEQUENCING-BASED ANALYSIS OF PROTEINS, NUCLEOSOMES, AND CELL-FREE NUCLEIC ACIDS FROM A SINGLE BIOLOGICAL SAMPLE (title). Arensdorf teaches, “[0003] It would be extremely useful if far more information could be obtained from a single low volume biological sample, including, without limitation, information pertaining to DNA sequences, DNA epigenetic modifications, RNA sequences, nucleosome structure and positioning, histone modifications, and both nucleic acid- associated and free plasma proteins.”
Arensdorf continues, “[0004] The invention is directed to the aforementioned need in the art and, in one embodiment, provides a combined workflow method for the analysis of a biological sample to determine multiple types of information therefrom without need for many independent analytical steps, a plurality of data-generating modalities, or a large quantity of sample. The types of information that may be obtained from a patient's blood sample, for instance, include the presence and concentration of specific plasma proteins; the number, location, and types of histone modifications associated with cfDNA (e.g., DNA from the cell-free fraction of a blood sample); the sequence of cfRNA and cfDNA in that fraction; and epigenetic information pertaining to the cell-free DNA, such as hydroxymethylation and methylation profiles, i.e., the distribution of 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) residues, respectively.”
Arensdorf teaches examination of multiple fractions of a blood sample including cfDNA, cfRNA, etc. (0005) Arensdorf teaches analysis of cell free nucleic acid fraction of the blood (0061).
Aresndorf teaches, “00053] In another embodiment, the invention provides a method for preparing cell-free DNA and cell-free RNA in a single cell-free nucleic acid sample for simultaneous, sequencing-based analysis. The method involves (a) ligating DNA adapters comprising a first adapter sequence that includes at least one UFI sequence onto the ends of end-blunted DNA in the cell-free sample to provide adapter-ligated DNA, where the at least one UFI sequence includes a source identifier barcode; (b) purifying the adapter-ligated DNA and RNA to provide a cell-free admixture of adapter-ligated DNA and RNA; (c) synthesizing a first strand of cDNA from the RNA; (d) synthesizing a second strand of cDNA”
Arensdorf teaches, “[00097] A "sample fraction" refers to a subset of an original biological sample, and may be a compositionally identical portion of the biological sample, as when a blood sample is divided into identical fractions. Alternatively, the sample fraction may be compositionally different, as will be the case when, for example, certain components of the biological sample are removed, with extraction of cell-free nucleic acids being one such example.”
MPEP 2144.05 III states:
Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955) (Claimed process which was performed at a temperature between 40°C and 80°C and an acid concentration between 25% and 70% was held to be prima facie obvious over a reference process which differed from the claims only in that the reference process was performed at a temperature of 100°C and an acid concentration of 10%.); see also Peterson, 315 F.3d at 1330, 65 USPQ2d at 1382 (“The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set of percentage ranges is the optimum combination of percentages.”); In re Hoeschele, 406 F.2d 1403, 160 USPQ 809 (CCPA 1969) (Claimed elastomeric polyurethanes which fell within the broad scope of the references were held to be unpatentable thereover because, among other reasons, there was no evidence of the criticality of the claimed ranges of molecular weight or molar proportions.). For more recent cases applying this principle, see Merck & Co. Inc. v. Biocraft Laboratories Inc., 874 F.2d 804, 10 USPQ2d 1843 (Fed. Cir.), cert. denied, 493 U.S. 975 (1989); In re Kulling, 897 F.2d 1147, 14 USPQ2d 1056 (Fed. Cir. 1990); and In re Geisler, 116 F.3d 1465, 43 USPQ2d 1362 (Fed. Cir. 1997).
Similarly, a prima facie case of obviousness exists where the claimed ranges and prior art ranges do not overlap but are close enough that one skilled in the art would have expected them to have the same properties. Titanium Metals Corp. of America v. Banner, 778 F.2d 775, 227 USPQ 773 (Fed. Cir. 1985) (Court held as proper a rejection of a claim directed to an alloy of “having 0.8% nickel, 0.3% molybdenum, up to 0.1% iron, balance titanium” as obvious over a reference disclosing alloys of 0.75% nickel, 0.25% molybdenum, balance titanium and 0.94% nickel, 0.31% molybdenum, balance titanium.).
Mockler teaches a review article in tiling of probes.
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Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to obtain cfTNA, comprising cfRNA and cfDNA, divide the sample into portions treating one portion with DNase, prior to reverse transcribing, adapter ligation, amplification and enriching by tiling probes and sequencing. The artisan would be motivated as Yeh suggests analysis of cfNA (cfTNA of claims), cfRNA and cfDNA. The artisan would be motivated to use DNase in one portion to degrade DNA including cfDNA and allow enrichment and examination of the smaller amount of RNA by itself, while allowing examination of cfTNA in the other fraction. The artisan would be motivated to do reverse transcriptase of cfTNA without DNase treatment as Reis specifically teaches it. The artisan would be motivated to enrich and using tiling arrays to target specific genes and redundantly sequence cDNA. The artisan would be motivated to use cfTNA, comprising cfRNA of 200 nt and cfDNA of less than 400 nt, as the art demonstrates this is the most prominent size of cfDNA and cfRNA in blood. The artisan would have a reasonable expectation of success as the artisan is merely combining known techniques.
The artisan would further be motivated to treat a human subject based on mutations or gene expression as Tzimagiorgis teaches, “ The earliest possible diagnosis and treatment is still the best approach to improve survival rates to the disease . The National Cancer Institute estimates that premature deaths, which may have been avoided through screening, range from 3% to 35% . Screening for cancer is usually attempted whenever worrying symptoms arise, having as a result the diagnosis of cancer as a late stage disease . The current methods for diagnosis of the disease are usually invasive (e.g. PAP smear, colonoscopy, etc.) and expensive whereas the existing biological markers are not definitive and lack high sensitivity and specificity. Many researchers therefore work on developing new, sensitive and inexpensive methods for cancer diagnostics . Detection of extracellular or cell-free nucleic acids (DNA or RNA) in plasma, serum and other bodily fluids using the PCR or RT-PCR methods have been suggested as non-invasive and cost effective methods for cancer detection.” (introduction). Reis teaches treatment based on cfTNA (10.3). The artisan would have a reasonable expectation of success as the art suggests and enables it.
With regards to claim 2-3, 5-6, Fettke teaches DeapSA TM ( a machine learning algorithm or model) for detection TPM3-NTRK1 fusion (which is a cell surface receptor) in cfDNA and cfRNA in subjects with prostate cancer. Fetke teaches, “We observed that AR gain was an independent negative prognostic biomarker for OS and PFS. These findings are consistent with previous reports supporting an association between AR amplification and resistance to ARPI therapy [6-8]. However, we observed no association between AR point mutations and time-to-event outcomes, even with ligand promiscuity-conferring point mutations L702H, T878A, H875Y, and W742C [24]. We note data on whether these mutations confer resistance to novel ARPI therapies are conflicting [6,7,22,25]..”(page 7)
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to treat subjects with chemotherapy other than ARPI when AR amplification was detected. The artisan would be motivated to treat with chemotherapy as Fetke teaches androgen receptor mutations were associated with resistance to androgen receptor pathway inhibitors. The artisan would have a reasonable expectation of success as the artisan is merely substituting one known cancer therapy for a therapy that is not likely to work.
Response to Arguments
The response begins by providing the representatives interpretation of what is required of an obviousness rejection. This is noted.
The response begins by asserting there is a lack of reasoning to combine. This argument has been thoroughly reviewed but is not considered persuasive as the rejection states, “The prior art as exemplified below demonstrates that examination of cell free nucleic acids including RNA and DNA were known. Further the exemplified art demonstrates the production of libraries by reverse transcription, adapter ligation and amplification prior to enrichment was also known. The art demonstrates the use of DNase to reduce DNA in background to allow more accurate determination of RNA sequences. Thus the art demonstrates the instant claims are no more than the combination of known techniques.” Further the rejection specifically teaches cftTNA and cfRNA and the rejection states, “The artisan would be motivated to use DNase in one portion to degrade DNA including cfDNA and allow enrichment and examination of the smaller amount of RNA by itself, while allowing examination of cfTNA in the other fraction. “
The response continues by providing the representatives interpretation/summary of the cited prior art. This is noted.
The response traverses the rejection by asserting the prior art does not specifically teach sequencing both cfTNA and cfRNA. This argument has been thoroughly reviewed but is not considered persuasive as the art Yeh teaches sequencing cfTNA (or cfNA) , cfRNA, and cfDNA. Further the skilled artisan realizes cfTNA is predominantly cfDNA relative to cfRNA. The art teaches sequencing cfDNA, cfRNA, or cfTNA is known in the art.
The response continues providing arguments with respect to increases sensitivity. This argument has been thoroughly reviewed but is not considered persuasive as the administering steps are limited to the alleged increased sensitivity, but encompass administering based on any mutation.
The response continues by asserting, “Applicant enumerates that a problem with traditional kits and methods of isolating circulating nucleic acids from biological fluid is the requirement for further analysis, the lack of mutation-specific information, the lack of identification of whether or not a mutation in a DNA segment of a cell is transcribed, being limited to RNA information only, analyzing only cfDNA in a sample, being limited by low sensitivity assays (especially where the DNA and/or RNA is present at low copy numbers/transcripts), and/or being limited to the population of nucleic acids already isolated. “ This argument has been thoroughly reviewed but is not considered persuasive as the art Yeh teaches sequencing cfTNA (or cfNA) , cfRNA, and cfDNA. Further the skilled artisan realizes cfTNA is predominantly cfDNA relative to cfRNA. The art teaches sequencing cfDNA, cfRNA, or cfTNA is known in the art.
The response continues by asserting, “There is no explicit or implicit reasoning why one having ordinary skill in the art would have modified certain features of the cited twelve references in the manner necessary to achieve the claimed invention. The Examiner also fails to provide a clear line of reasoning as to why each reference renders the claimed invention obvious as a whole. Therefore, the Office's position is without support in the prior art and such a position is merely conclusory.” This argument has been thoroughly reviewed but is not considered persuasive in view of the teachings of Yeh with respect to cfNA, cfRNA, cfDNA. Further the response appears to merely be alleging the method can detect mutations due to cfTNA and cfRNA, but provides no specific evidence how this relates to the full scope of the claim and/or administering step. Thus this argument does not appear to be commensurate in scope with the breadth of the claim.
The response continues by providing arguments with respect to impermissible hindsight. In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
The response continues traversing the rejection by asserting, “The unexpected and surprising effect of the method recited in claim 1 is evidenced by the discovery of analyzing cfRNA and cfTNA in separate fractions to enrich a plurality of target cDNAs to thereby generate respective first and second target-enriched cDNA libraries.” This argument is confusing as Campbell (https://www.bio.davidson.edu/genomics/method/cDNAproduction.html, 2002) teaches, “By definition, cDNA is double-stranded DNA that was derived from mRNA which can be obtained from prokaryotes or eukaryotes.” Thus it is unclear how cfTNA is different than cfRNA fraction.
The response continues by arguing the mutations are significantly higher in cfRNA than in cfDNA. This argument has been thoroughly reviewed but is not considered persuasive as Feng teaches, “circulating cell-free RNA (cfRNA) sequencing confirmed and enhanced detection sensitivity for variants with low allele frequency. “ (abstract) Feng teaches, “Our results demonstrated the potential clinical utility/feasibility of simultaneous multi-parametric profiling of ctDNA and cfRNA for comprehensive molecular insight/ characterization in advanced stage cancer. cfRNA-derived variant detection confirms the variants originally detected in ctDNA test and further validates the high specificity results for report interpretation. The ctDNA and cfRNA-based combined liquid biopsy solution provides holistic molecular overview for detecting driver mutations, monitoring efficacy / disease burden, and identifying sub-clonal alterations that may related to drug resistance and tumor heterogeneity.” (conclusion) Finally this argument is not commensurate with the administering step.
Thus the rejection is maintained.
Summary
No claims are allowed.
The following art may be of interest in the instant case:
Jin (Adv. Sci. 2018, 5, 1800614)
Qi (Journal of Cancer (2018; 9(18): 3417-3426.)
Sorber (Lung Cancer Volume 107, May 2017, Pages 100-107)
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday off.
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/Steven Pohnert/Primary Examiner, Art Unit 1683
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