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 12/17/2025.
Claims 1-12, 14-21 are pending.
Claim 21 has been amended.
Applicant’s election without traverse of Group I, claims 1-16l, With respect to the species election for claim 10, the applicant elects without traverse the combination of adapters that comprise a p5 sequence portion, a p7 sequence portion, a first index sequence portion, a second index sequence portion, a first sequencing primer binding site sequence portion, and a second sequencing primer binding site sequence portion, regarding claim 12, the applicant elects without traverse wherein the plurality of hybridization probes bind to the target cDNA in a tiled fashion, and wherein the plurality of hybridization probes provide a tiling density of at least 2x, regarding claim 13, the applicant elects without traverse a combination of ABCC3, ABIl, ABL1, ABL2, ABLIMI, ACACA, ACE, and ACER1 in the reply filed on 4/13/2022 is acknowledged.
Claims 17-20 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 4/13/2022.
Priority
The instant application was filed on 09/23/2021.
Claim Rejections - 35 USC § 112
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.
Claim 21 is 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 21 has been amended to recite, “wherein generating the first and the second target-enriched cDNA libraries provides improved sensitivity of mutation detection as the first cDNA library is enriched in RNA relative to DNA and the second cDNA library is rich in DNA relative to RNA to thereby provide two distinct but complementary views of the target cDNA...” It is unclear how improved sensitivity of mutation detection occurs. Further it is unclear what “rich in DNA” requires, “rich in DNA appears to be a relative term and suggests there can be non-rich or less than rich in DNA. Further the claim does not require a mutation is present or exists or how it improves the detection. Further the assertion is confusing as reverse transcriptase reverse transcribes RNA to cDNA and thus “the cfRNA fraction” and “cfTNA “ appear to be from RNA.
Response to arguments
The response begins traversing the previous rejection by asserting the claims must be read in light of the specification. This is noted.
The response continues by asserting, “or example, as discussed in the specification at para [0074], improved sensitivity of mutation detection occurs because RNA converted to cDNA is more abundant than DNA generated from the same cell. However, the co-sequencing of DNA in the TNA sequencing will compensate for detecting mutations in cases where the RNA may be degraded, for example, due to change in its stability on account of a mutation. Viewed from another perspective, "as the first and second cDNA libraries [are] prepared from the same biological fluid (and most typically from the same cfTNA isolation) these two cDNA libraries represent two distinct but complementary views of the same sample: one enriched in RNA (relative to DNA) and another rich in DNA (relative to RNA)" (bold italics added for emphasis); See para [0067].” This argument has been thoroughly reviewed but is not considered persuasive as the claims are not limited to RNA from cells, but any cel-free fluid. Further the second assertion from paragraph 0067 is unclear as identified in the rejection in view of the recitation of “rich DNA.”
The response continues by providing arguments with respect to paragraph 0082. The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.). See also In re Morris, 127 F.3d 1048, 1054-55, 44 USPQ2d 1023, 1027-28 (Fed. Cir. 1997)
The response continues by asserting, “in terms of whether a mutation is required to be present, the Applicant specifies at para [0060] that the human or other mammal, from which the biological fluid is derived, "may be healthy or diagnosed with or suspected to have a condition or disease, particularly where such disease can be linked or attributed to a mutation in and/or (over- or under-) expression pattern of one or more genes. Therefore, the subject may be treatment naive or undergoing treatment when the cfRNA and cfTNA is obtained from the subject." (emphasis added). In other words, claim 21 does not require that a mutation is present or exists because the use of cfRNA and cfTNA may be applied to detection of a disease, monitoring the progression of a disease, monitoring the treatment effect of a treatment given to treat the disease, as well as for detection of residual or recurring disease, i.e., instances in which a mutation may or may not be present. Id.” This argument has been thoroughly reviewed but is not considered persuasive as the response concedes the claim does not require a mutation. Thus apparently the claim would not appear to further limit the claim in the absence of a mutation.
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 1-7, 9-10, 16, 21 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( Volume 78, Issue 2, August 2020, Pages 173-180).
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 ofDNase I reaction buffer (final concentration lOmM Tris-HCl, 2.5mM MgCl2, 0.5mM CaCl2 pH 7.6) and 2 units ofDNase 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 DNA 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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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)
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.).
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 and sequencing. The artisan would be motivated to use DNase in one portion to degrade DNA including cfDNA and allow 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 TNA without DNAse treatment as Reis specifically teaches it. 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.
With regards to claims 2-3, 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). Ma in supplemental figure 1 teaches most cell free DNA is 400 base pairs or less.
With regards toc claims 4-5, cfRNA and cfDNA would logically be over 40% of cfTNA.
With regards to claim 6, Arnesdorf, Feng, Reis teach isolating cfTNA including cfRNA and cfDNA from a sample.
With regards to claim 7, Arnesdorf teaches, “[0171] In one such method, random primers are used to synthesize cDNA from cfRNA, preferably from rRNA-depleted RNA,”
With regards to claim 9, Arnesdorf teaches the use of primers with T overhang (0107).
The specification provides no limiting definition of a first index sequence portion, a second index sequence portion, a first sequencing primer binding site sequence portion, and a second sequencing primer binding site sequence portion. Thus the broadest reasonable interpretation is this encompasses any nucleic acid sequence.
With regards to claim 10, Arnesdorf teaches, “The custom oligonucleotides in Table 1 (obtained from IDT, Integrated DNA Technologies, Coralville, Iowa) included three subsets: (1) truncated adapter oligonucleotides for hybridization and generation of adapter constructs; (2) indexing PCR oligonucleotides for amplification of adapter ligated products and incorporation of sample indexing; and (3) universal PCR oligonucleotides for re-amplification of libraries containing any index motif.” Table 1 teaches P5 truncated, P7 truncated, index primer1, universal primer, index x primer and additional indexing primers.
Arnesdorf does not specifically teach a p5 sequence portion, a p7 sequence portion, a first index sequence portion, a second index sequence portion, a first sequencing primer binding site sequence portion, and a second sequencing primer binding site sequence portion.
However, in view of the lack of a definition of first index sequence portion, a second index sequence portion, a first sequencing primer binding site sequence portion, and a second sequencing primer binding site sequence portion.
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 the teachings of table 1 encompass the recitation of the claims. The artisan would be motivated to have multiple primer and indexing sites in the adapters to use during sequencing and analysis. The artisan would have a reasonable expectation of success as the artisan is merely using elements suggested by the art.
With regards to claim 16, Feng teaches P53 and APC were sequenced (figure 2A).
With regards to claim 21, 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”
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 artisan would be motivated to use DNase in one portion to degrade DNA including cfDNA and allow 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 TNA without DNAse treatment as Reis specifically teaches it. 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..” 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.
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 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.
Claim 8 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 (2018126278) , 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).
The teachings of Yeh, Suliman, Tzimagiorgis , Arensdorf, Feng, Reis, Yang, Ma, Fettke are set forth above.
Yeh, Suliman, Tzimagiorgis , Arensdorf, Feng, Reis, Yang, Ma, Fettke do not specifically teach the use of dUTP on second strand synthesis.
However, Parkhomchuk teaches second strand synthesis using dUTP (second strand synthesis (page 2, 2nd column). Parkhomchuk teaches, “we describe a simple modification of RNA-Seq method that addresses this problem. Incorporation of deoxy-UTP during the second strand cDNA synthesis and subsequent destruction of the uridine-containing strand in the sequencing library allowed us to identify the orientation of transcripts.”
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 substitute second strand synthesis using dUTP in the method of Yeh, Suliman, Tzimagiorgis , Arensdorf, Feng, Reis, Yang, Ma, Fettke. The artisan would be motivated to substitute second strand synthesis using dUTP be able to determine orientation of the transcript. The artisan would have a reasonable expectation of success as the artisan is merely substituting one method of substitute second strand synthesis for another.
Response to Arguments
The response traverses the rejection in view of the arguments with respect to the independent claims. These arguments are not persuasive for the reasons of record.
Claim 11-12, 14-15 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 (2018126278) , 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) as applied to claim1-7, 9-10, 13, 16 above, and further in view of Summerer (Genome Research (2009) 19:1616–1621).
The teachings Yeh, Suliman, Tzimagiorgis , Arensdorf, Feng, Reis, Yang, Ma, Fettkeare set forth above.
Yeh, Suliman, Tzimagiorgis , Arensdorf, Feng, Reis, Yang, Ma, Fettke do not specifically teach 6-15amplification cycles, and reamplification of libraries, 2x coverage on a tiling array or hybridization probes of 50-100 bases.
However, Summerer teaches 10 cycles of PCR (page 1621, 1st column NGS using Illumina technology) of gDNA library.
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 amplify libraries (gDNA or cDNA) using 10 cycles prior to sequencing. The artisan would be motivated as Summerer teaches reamplification of libraries was done as part of NGS to increase amount of DNA. The artisan would have a reasonable expectation of success as the artisan would have a reasonable expectation of success as the artisan is merely using known methods to amplify nucleic acids for NGS.
Summerer further teaches, “We designed an array of 50mer DNA oligonucleotide probes with a tiling density of 8 bp.”(page 1617. 1st column, bottom). Summerer teaches, “We achieved overall enrichment factors of up to 1062-fold and average coverage depths of 470-fold.”
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 use the 50mer probes with a tiling density of 8bp in the method of Arensdorf, Feng, Reis, Yang, Ma. The artisan would be motivated as Summerer teaches, “We achieved overall enrichment factors of up to 1062-fold and average coverage depths of 470-fold.” The artisan would have a reasonable expectation of success as the artisan would merely be using known methods to increase coverage of specific genes.
Response to Arguments
The response traverses the rejection in view of the arguments with respect to the independent claims. These arguments are not persuasive for the reasons of record.
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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