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 2/6/2026.
Claims 1, 6, 9, 11, 15, 18, 24-26 have been amended.
Claims 33 has been added by amendment.
Applicant's election with traverse of A method that is not computer-implemented; A limited volume sample of less than 500 uL; A blood, serum or plasma sample of less than 500u1; A dried blood spot sample; Adjusting the total volume of the extracted DNA solution to between 20u1 and 200u1; A sample that has not been subject to a processing step to remove cells or cellular material prior to the size selection step;
A size-selection step that comprises removing genomic DNA (gDNA) fragments of >1000bp; Analysis that interrogates at least 50 loci; DNA sequencing the size-selected sample or a library generated from the size- selected sample to generate a plurality of sequence reads and analyzing the sequence reads to detect the presence of ctDNA;
A subject that is a human or a non-human animal; A method that is used to guide treatment decisions; A patient that is a human child having or suspected of having paediatric cancer; Variant cell-free DNA that comprises: cfDNA from different cell types, tissues, or organs; A method that is for detection of a disease; Analyzing a signal by performing a method that summarizes the signal across multiple loci, wherein a signal is obtained and/or analyzed for at least 50 loci; Analyzing a signal from cell free DNA comprises determining and comparing the amounts of different variants cfDNA, wherein different variants originate from different biological sources; Amounts of first and second variants are determined for each of multiple loci as a combined amount that represents multiple loci. in the reply filed on 7/24/2024is acknowledged. The traversal is on the ground(s) that the response asserts the species election does not provide adequate support why there is a search. This is not found persuasive because The response argues search burden, however the instant application is filed under lack of unity.(MPEP 801) Further searching computer implemented method will not inherently provide art on a method that is not computer implemented. Furthers search a sample which is 500 µl will not inherently provide art on 75µl or less. ; and/or wherein the sample comprises at most 200, 150, 100 or 80 human haploid genome equivalents of cell-free DNA; preferably wherein the sample is a sample of bodily fluid from claim 2. Further searching a blood sample will not inherently provide art on serum or plasma sample of less than 500pl, less than 400, less than 200, less than 1001, less than 75pl (e.g. a blood or plasma sample of about 50pl)or less than 50p1; a fine needle aspirate (FNA); a lymph node biopsy; a urine, cerebrospinal fluid, sputum, bronchial lavage, cervical smear or a cytological sample; (v) a sample that has been stored for more than 1 year, 2 years, 3 years, 5 years or 10 years from the time of collection from the patient; and (vi) a sample that has been previously processed and failed quality metrics for DNA or sequencing quality, or a sample that belongs to a set of samples from which other samples have been previously processed and failed quality metrics for DNA or sequencing quality; (vii) a sample that has been stored for more than 1 day, more than 2 days, more than 3 days, more than 5 days, more than 10 days prior to processing to remove, deplete, filter out or neutralize cellular material and/or prior to any DNA size selection step to remove, deplete or filter out DNA other than cell-free DNA in the sample; (viii) a sample that has been dried up after collection, such as e.g. a dried blood spot or a pin-prick blood sample; optionally wherein the sample has been dried up on filter paper or in a tube or capillary; and (ix)a sample that contains genomic DNA or other contaminating (non cell-free DNA)in an amount such that the cell-free DNA represents less than 5%, less than 3%, less than 2% or less than 1% of the DNA in the sample consistent with the election from claim 2. Further searching a dried blood spot sample will not provide art on a pin-prick blood sample; an archival blood, serum or plasma sample that has been of less than 500pl that has been stored for greater than 1 day (e.g. at least 2 days, at least 3 days, at least a week, or at least one month), at least 1 year or at least 10 years after collection from the subject. Further searching sample has not been subject to a processing step to remove, deplete will not inherently provide art on filter cells or cellular material prior to the size selection step. Further searching filtering-out, depleting or removing genomic DNA (gDNA) fragments of > 2000 bp prior to analysis will not inherently provide art on > 200 bp, > 300 bp, > 500 bp, > 700 bp, > 1000 bp, > 1200 bp, > 1500 bp, or, e.g. prior to DNA sequencing or other molecular biology techniques to detect signal from cell-free DNA consistent with claim 3. Further searching analysis interrogates at least 5000 loci, or a whole genome will not provide art on 50, 100, 500, 1000, 2500.. Further searching analyzing DNA modifications, such as methylation will not inherently provide art on ; (iii) analysis using polymerase enzymes, such as e.g. PCR, qPCR, digital PCR; (iv) analysis using nucleic acid reagents, such as e.g. primers or probes or other sequences that can interact with DNA in the sample by hybridization; (v)analysis using binding or affinity reagents, such as e.g. antibodies .Further searching a healthy subject will not provide art on a subject with a disease (e.g. a cancer). Further searching human will not inherently provide art on non-human animal (e.g. a rodent) and/or wherein the animal model is a rodent having xenografted or Xeno transplanted human tumour tissue. Further searching early detection of cancer will not inherently provide art on monitoring of cancer treatment, detection of residual disease, is used to guide treatment decisions, to assess the status of a cancer in the subject or cancer progression or cancer response to treatment, or the need for or the type of further treatment for the subject optionally wherein the subject is a human or an animal model of a cancer (e.g. a rodent). Searching of detection or monitoring of Xeno transplanted cells in a host organism will not inherently provide art on , or wherein the patient is a human child having or suspected of having a paediatric cancer, which is consistent with previous elections. Searching cfDNA from a donor tissue or organ that has been transplanted into the patient will not inherently provide art on cfDNA from different cell types, tissues or organs; DNA from a pathogen such as a virus; foetal cfDNA from a foetus in gestation in the patient; or abnormally methylated cfDNA consistent with a prior elections. Searching to provide information to guide medical treatment will not inherently provide art on changes in diet, or physical training, is for detection of a disease, pathology or physiological state detectable by analysis of cell-free DNA, or is used for forensic analysis or to identify individuals whose biological material is present in the sample or to identify organisms whose biological material is present in the sample, the election must be consistent with prior elections. Further searching analyzing the size-selected sample or a library generated from the size-selected sample to obtain a signal from cell free DNA, such as e.g. by sequencing to generate sequence reads, and further comprises analysis of the signal, such as e.g. the sequence reads, by performing a method that summarizes or combines the signal across multiple loci, optionally wherein a signal is obtained and/or analyzed 50 loci will not inherently provide art on 100, 500, 1000, 2500 or 5000 loci, or a whole genome. Searching copy number analysis will not inherently provide art on processing the signal, such as e.g. the sequence reads to determine a trimmed Median Absolute Deviation from copy number neutrality (t-MAD) score or an ichorCNA score; determining and comparing the amounts of different variants cfDNA, wherein different variants originate from different biological sources, optionally wherein different biological sources are selected from different cell types or tissues, different physiological states such as disease/pathological sources and healthy sources, different organisms such as a host organism and a foreign or transplanted biological source; and/or aligning the sequence reads to at least two different reference genomes, e.g. a human reference genome and a rodent reference genome, and optionally deriving a summary metric associated with the amount or proportion of reads that map to one of the reference genomes, this must be consistent with prior elections.
Claims 28-29 withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 7/24/2024.
Claims 1-2, 5-6, 9, 11, 13, 15-16, 18, 20, 22, 24-27, 31-33 are being examined.
The previous objection to the claims has been withdrawn.
Priority
The instant application was filed 05/19/2021 is a National Stage entry of PCT/EP2019/082268 , International Filing Date: 11/22/2019 and claims foreign priority to EP1819134.6, filed 11/23/2018.
Specification
The specification is objected to as failing to provide proper antecedent basis for the claimed subject matter. See 37 CFR 1.75(d)(1) and MPEP § 608.01(o). Correction of the following is required: Claim 1 has been amended to recite, “analyzing the size-selected sample to detect signal from circulating tumour DNA.” Review and searching of the specification did not reveal antecedent basis for these limitations in the specification.
Response to Arguments
The objection with respect to analyzing a sample has been withdrawn in view of arguments.
The response traverses the objection with respect to, “analyzing the size-selected sample to detect signal from circulating tumour DNA” in view of initially filed claim 24. This argument has been thoroughly reviewed but is not considered persuasive as originally filed claim 24 (filed 5/19/2021) merely provides for detecting cell free DNA. Thus it does not provide antecedent basis for the species required of the claims.
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 1-2, 5-6, 9, 11, 13, 15-16, 18, 20, 22, 24-27, 31-33 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.
Claim 1 has been amended to recite, method for detecting circulating tumor DNA (ctDNA) in a sample that has been obtained from a subject, the method comprising: analyzing the sample by performing a size-selection step to separate out different fragment sizes of DNA to obtain a size-selected sample, wherein the sample is a dried blood sample from a limited volume sample of blood of less than 100µl that comprises at least 2 human haploid genome equivalents of cell-free DNA, wherein the size-selection step is a right-sided size selection employing bead-based capture of genomic DNA fragments, and wherein the size-selection step comprises two separate bead-based capture steps; and analyzing the size-selected sample to detect a signal from circulating tumour DNA, wherein detecting the signal from circulating tumour DNA comprises: (i) DNA sequencing the size-selected sample or a library generated from the size-selected sample to generate a plurality of sequence reads and analyzing the sequence reads; or (ii) analysing the size-selected sample using PCR, qPCR or digital PCR: or (iii) analysing the size-selected sample using a hybridization based technique; or (iv) analysing the size-selected sample using binding or affinity reagents.”
The claim as amended in view of the claims encompasses all size selected DNA is cell free tumor DNA. However, the response asserts the support for the preamble can be found in the preamble of originally filed 1 and originally filed claim 17. This argument has been thoroughly reviewed but is not considered persuasive as both claims are to detect the detection of cell free variant DNA, which is of different scope than requiring detecting cell free tumor DNA in a sample.
The response continues noting the where clause of originally filed claim 1 provides basis for analysing the sample by performing a size-selection step to separate out different fragment sizes of DNA to obtain a size-selected sample. This is accepted.
The response continues by asserting the amendment with respect to dried blood sample of 100microliters or less is supported by originally filed claim 2, 4 and page 23, lines 23-24. This argument has been thoroughly reviewed but is not considered persuasive as while claims 2 and 4 provide the 100 microliters or less. Claim 4 provides the 100 microliters or less as an alternative to a dried blood spot and thus does not provide for the claimed combination. Further page 23 lines 23-24 provides for at least approximately 2 human haploid genome equivalents, it does not provide support for the dried blood or the volume of the claim. Further at least approximately 2 human haploid genome equivalents is of different scope than at least 2 human genome equivalents.
The response asserts the support for the amendment with respect to “wherein the size-selection step is a right-sided size selection employing bead-based capture of genomic DNA fragments” is supported by originally filed claim 14 and page 22 line 33. This argument has been thoroughly reviewed but is not considered persuasive as claim 14 recites, “A method according to any one of the preceding claims, wherein the size selection step is a right-sided size selection employing bead-based capture of gDNA fragments, optionally wherein the amount of bead solution used is determined relative to the volume of DNA containing sample according to the manufacturer's instructions.” Thus the amendment is of different scope as it is not limited to “according to manufactures instructions.” Further the claims paragraph of page 22 states:
In some embodiments the sample obtained from the patient is subjected to a size-selection step in which genomic DNA (gDNA) fragments of > 200 bp, > 300 bp, > 500 bp, > 700 bp, > 1000 bp, > 1200 bp, > 1500 bp or > 2000 bp are filtered-out, depleted or removed from the sample prior to analysis, e.g. prior to DNA sequencing, to generate a size-selected sample.
This is of different scope than from a dried blood sample or detecting circulating tumor DNA.
The response asserts the amendment of “wherein the size-selection step comprises two separate bead-based capture steps” is supported by previous claim 15. This is accepted.
The response asserts the analyzing step is supported by originally filed claim 24 and page 1 lines 3-4. This argument has been thoroughly reviewed but is not considered persuasive as claim 24 recites:
A method according to any one of the preceding claims, wherein said analysis comprises analysing the size-selected sample or a library generated from the size-selected sample to obtain a signal from cell free DNA, such as e.g. by sequencing to generate sequence reads, and further comprises analysis of the signal, such as e.g. the sequence reads, by performing a method that summarizes or combines the signal across multiple loci, optionally wherein a signal is obtained and/or analyzed for at least 50, 100, 500, 1000, 2500 or 5000 loci, or a whole genome.
Thus claim 24 is of different scope as it is to the detection of cell free DNA, not cell free tumor DNA. Further the cited portion of page 1 states:
The present invention relates in part to methods for detecting the presence of variant DNA, such as circulating tumour DNA (ctDNA) from, e.g., a cell-free DNA (cfDNA) source.
This does not support the context of the claims that all cell free DNA is cell free tumor DNA.
The response asserts support to provide the wherein clause, “wherein detecting the signal from circulating tumour DNA comprises: (i) DNA sequencing the size-selected sample or a library generated from the size-selected sample to generate a plurality of sequence reads and analysing the sequence reads; or (ii) analysing the size-selected sample using PCR, qPCR or digital PCR: or (iii) analysing the size-selected sample using a hybridization based technique; or (iv) analysing the size-selected sample using binding or affinity reagents.” While the cited portion of pages 26-27 provide support for the (i), (ii), (iii), (iv) it does not specifically envision the recited assays inherently require detection of cel free tumor DNA to the exclusion of cell free DNA from other sources. Thus the amendment has introduced new matter.
MPEP 2163 IB New or amended claims section II
With respect to newly added or amended claims, applicant should show support in the original disclosure for the new or amended claims. See, e.g., Hyatt v. Dudas, 492 F.3d 1365, 1370, n.4 (Fed. Cir. 2007) (citing MPEP § 2163.04 which provides that a "simple statement such as ‘applicant has not pointed out where the new (or amended) claim is supported, nor does there appear to be a written description of the claim limitation ‘___’ in the application as filed’ may be sufficient where the claim is a new or amended claim, the support for the limitation is not apparent, and applicant has not pointed out where the limitation is supported."); see also MPEP §§ 714.02 and 2163.06 ("Applicant should ... specifically point out the support for any amendments made to the disclosure."); and MPEP § 2163.04
Claim 11 has been amended to recite, “analysing the sample by performing a size-selection step to separate out different fragment sizes of DNA to obtain a size-selected sample comprises preparing a sequencing library and performing the size-selection step on the sequencing library thereby obtaining the size-selected sample.” The response provides no indication of where support can be found. Review and searching of the specification did not reveal support of size selection of a library after it had been already been size selected wherein the size-selection step comprises two separate bead-based capture steps. Thus the amendment appears to introduce new matter.
Response to Arguments
The rejection is maintained for the reasons of record as the arguments are addressed in the rejection.
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 1-2, 5-6, 9, 11, 13, 15-16, 18, 20, 22, 24-27, 31-33 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 has been amended to recite, “:wherein the size-selection step is a right-sided size selection employing bead-based capture of genomic DNA fragments, and wherein the size-selection step comprises two separate bead-based capture steps.” The limitation is vague, unclear, and incomplete what two separate bead-based capture steps require. While the specification states:
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The metes and bounds are unclear and this appears to be an attempt to incorporate by reference to a publication which is not a US patent or US patent application.
Claim 1 has been amended to recite, “comprises at least 2 human haploid genome equivalents of cell-free DNA.” However claim 9 requires, “wherein the subject is has a disease and/or wherein the subject is human or a non-human animal and/or wherein the subject is an animal model and the animal model is a rodent having xenografted or Xeno transplanted human tumour tissue.” Thus the metes and bounds are unclear what is required of human genome equivalents when dependent claims encompass non-human animals. Further the dependent claims encompass diseases which include asthma, athletes foot, dandruff, etc., but do not require the subset has a tumor, thus the claim is confusing and unclear.
Further it is unclear the method is done as blood of less than 100µl encompasses 0.00000000000000000000000000000000000000000000001 µl. The specification provides no guidance on how to measure or assay such a sample.
Claim 1 has been amended to recite, “analysing the size-selected sample to detect a signal from circulating tumour DNA, wherein detecting the signal from circulating tumour DNA comprises: (i) DNA sequencing the size-selected sample or a library generated from the size-selected sample to generate a plurality of sequence reads and analysing the sequence reads; or (ii) analysing the size-selected sample using PCR, qPCR or digital PCR: or (iii) analysing the size-selected sample using a hybridization based technique; or (iv) analysing the size-selected sample using binding or affinity reagent.” Thus the metes and bounds are unclear how size selection provides for all size selected DNA being cell free tumor DNA. Thus the metes and bounds are unclear.
Further the claim 25 recite, “wherein analysing the signal from circulating tumor DNA comprises performing a method selected from: performing copy number analysis; determining and comparing amounts of different variants cfDNA, wherein the different variants cfDNA originate from different biological sources, optionally wherein different biological sources are selected from different cell types or tissues, different physiological states such as disease/pathological sources and healthy sources, different organisms such as a host organism and a foreign or transplanted biological source; and/or aligning sequence reads to at least two different reference genomes, and optionally deriving a summary metric associated with the amount or proportion of reads that map to one of the reference genome.” The metes and bounds are unclear how the method is done as the independent claim requires detecting a signal from circulating tumor DNA however the instant claim requires from cell free DNA. Thus the claim is confusing and unclear. Further it is unclear what is required of variant as it is a relative term. It is unclear how analyzing cells and tissues provide information on cell free DNA, or if the claims encompass any isolated DNA.
Response to Arguments
The response traverses the previous rejections in view of the amendment.. It is noted the amendments have introduced new issues.
The response further asserts the amendment to claim 25 has overcome previous issues. This argument has been thoroughly reviewed but is not considered persuasive as the amendment has introduced new issues.
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 (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1-2, 5-6, 9, 11, 13, 16, 18, 22, 24-27, 31-32is/are rejected under 35 U.S.C. 103 as being unpatentable over Yeh (WO2017027835), Bischoff (Vol 6. No 3. 349–351 Reproductive BioMedicine Online; www.rbmonline.com/Article/796 on web 5 February 2003), Karadjian (Proceedings National Academy of Sciences USA (2016) volume 113, pages 9834-9839), Bronner (Curr Protoc Hum Genet. 2009 July ; 0 18: . doi:10.1002/0471142905.hg1802s62), QIAamp® DNA Mini and Blood Mini Handbook (2010)
Attention is directed to MPEP 2129 [R-6], Admissions as Prior Art, which states in part:
I. ADMISSIONS BY APPLICANT CONSTITUTE PRIOR ART
A statement by an applicant >in the specification or made< during prosecution identifying the work of another as “prior art” is an admission **>which can be relied upon for both anticipation and obviousness determinations, regardless of whether the admitted prior art would otherwise qualify as prior art under the statutory categories of 35 U.S.C. 102. Riverwood Int’l Corp. v. R.A. Jones & Co., 324 F.3d 1346, 1354, 66 USPQ2d 1331, 1337 (Fed. Cir. 2003); Constant v. Advanced Micro-Devices Inc., 848 F.2d 1560, 1570, 7 USPQ2d 1057, 1063 (Fed. Cir.1988).
Further, the courts have held information that an applicant admits is in the prior art "may be considered 'prior art' for any purpose, including use as evidence of obviousness under § 103." In re Nomiya, 509 F.2d 566, 570-71 (CCPA 1975).
The specification teaches, “without wishing to be bound by theory, it is believed that a blood drop sample of 50 μl from a patient with advanced cancer is expected to comprise about 80 copies of the genome as cfDNA (based on an estimated 16000 amplifiable copies per mL of blood)” (0091)
With regards to claim 1, Yeh teaches “The disclosed methods enable multiple analyses with microliter volumes (blood-drop volumes) of sample on a broad range of genomic platforms, including, but not limited to, next-generation sequencing (NGS) and qPCR. The methods of the present disclosure enable clinicians to work with a sample volume as small as 10 microliters (via a finger-prick, for example). “ (page 2-3)
Yeh teaches, “Most of the nucleic acids (DNA and RNA) in the body are located within cells, but a significant amount of extracellular nucleic acids can also be found circulating in the bloodstream. Since the first discovery of cfDNA in the blood in 1948 by Mandel and Metais, researchers have found that cfDNA discriminates patients with a disease or condition (for example cancer) and healthy individuals in two ways: first by the elevated concentration cfDNA in the blood in patients with a disease or condition; and second, by the presence of tumor-specific alterations in cfDNA in patients with a disease or condition.” (page 25, last paragraph)
Yeh does not specifically teach dried blood or 2 right sided size selection using two separate capture steps.
However, Bischoff teaches, “Both intact fetal cells and cell-free fetal DNA are present in the maternal circulation and have been used for non-invasive prenatal genetic diagnosis. However, broad clinical application awaits development of robust methods for collecting, transporting and enriching maternal blood samples to recover rare fetal cells. To circumvent this impediment, we have devised a reliable method of fetal DNA detection using dried maternal blood spots and real-time polymerase chain reaction. Fetal Y-specific (DYS1) sequences were detected in all 19 (100%) maternal blood specimens from women carrying male fetuses, in genome equivalents of 4.20–24.68 per ml of blood; the ubiquitous glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene, reflecting both maternal and fetal DNA, concurrently showed 43,684 to 680,357 genome equivalents per ml of blood. The results demonstrate that fetal DNA detection using dried maternal blood spots is highly feasible and easily adaptable for population screening.” Bischoff teaches, “in each of 26 pregnant women, 6—7 drops of blood from a finger stick were obtained prior to an ultrasound screening and/or invasive prenatal procedure. Blood drops were placed onto spots pre-outlined on the specimen collection filter paper ….. From each blood spot sample, six 3 mm punched-out circles were placed together in a 1.5 ml microcentrifuge tube with DNA extracted using the QIAamp DNA blood kit for dried blood spots.”(materials and methods).
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.).
Yeh teaches isolation of cfDNA from 20 µl of urine, amplification and size selected by Ampurebeads (pages 58-59 and 61). The use of Ampurebeads is size separating.
Karadjian teaches extraction of DNA from a dried blood sample (DNA extraction (9838)) and sizing by Ampure beads (whole genome sequencing of Nycteria Parasites).
Bronner teaches, “Binding to solid-phase reversible immobilization (SPRI) beads (DeAngelis et al., 1995) can be controlled by altering the PEG/NaCl concentration (Borgstrom et al., 2011; Lundin et al., 2010). A single AMPure XP treatment can be used to remove DNA fragments below a certain size (typically 150-200bp). A double (upper and lower) size selection can be performed by two consecutive AMPure XP steps. “(page 4 size selection)
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 dried blood samples in the method of Yeh including detection of cfDNA that is elevated in cancer subjects. The artisan would be motivated as Bischoff teaches the use of QIAamp Mini spin to isolate cfDNA from dried blood, while Yeh teaches isolation of cell free DNA including tumor DNA from blood and correlations of cfDNA with cancer. The artisan would have reasonable expectation of success as Bischoff teaches detection of cfDNA from dried blood was known.
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 100 µl or less of a dried blood sample which comprises 2 or more human haploid genome equivalents and size select using 2 consecutive AMPure XP bead treatments. The artisan would be motivated to minimize the amount of filter and/or blood to be used. The artisan would be motivated to use two consecutive AMPUre XP bead treatments as Bronner teaches it allows for upper and lower size selection. The artisan would have a reasonable expectation of success as it allows for double selection Yeh suggests the use of 10 microliters. (claim 1 and 15)
With regards to claim 2, , Qiagen teaches the use of 3 punched out circles of dried blood which is less than 100µl based on the teachings of Bischoff. .
With regards to claim 5, 32 Bronner teaches, “A single AMPure XP treatment can be used to remove DNA fragments below a certain size (typically 150-200bp).”( page 4 size selection). Yeh teaches, “after the fragmenting step, the cfNA has a fragment size distribution from 50 bp to 600 bp, 100 bp to 500 bp, 100 bp to 400 bp, 100 bp to 300 bp, 100 bp to 200 bp, 200 bp to 300 bp, 300 bp to 400 bp, 400 bp to 500 bp or 500 bp to 600 bp.” (page 35, top)
With regards to claim 6,11, 24- 27 Yeh teaches, “ the targeted sequencing libraries were generated using the Ion AmpliSeq Library kit 2.0 and Cancer Hotspot Panel v2 according to the manufacturer's instructions (Life Technologies, Carlsbad, CA). This test panel is designed to target 2,855 mutations in the following 50 key cancer genes.” (page 61).
With regards to claim 9 Yeh teaches, “ In certain embodiments, the liquid sample is from a subject, including a human subject, suspected of having a disease or condition, such as cancer, a bacterial infection or a viral infection.”(page 33)
With regards to claims 13, Yeh teaches volumes of isolated nucleic acids of less than 20 microliters (table 14).
With regards to claim 18, 22 Yeh teaches, “Circulating cfDNA-based testing offers clinicians the ability to ensure treatment efficacy, monitor drug resistance, metastasis and recurrence, and tailor individualized therapeutic interventions for patients in real time. The use of tumor genome sequencing of circulating cfDNA to guide treatment decisions would greatly improve clinical outcomes. As such the clinical utility of cfDNA in the personalized management of cancer diagnosis and therapy has the ability to significantly alter current treatment models, increase overall cancer survival rates and become the standard-of-care for a new-generation of cancer management.” (page 2, 2nd full paragraph )
With regards to claim 31, Bischoff teaches dried blood samples in a filter paper.
With regards to claim 32, Yeh teaches running on a gel which is size selection which removes or depletes genomic DNA from sample.
Response to Arguments
The response traverses the rejection in view of the amendments to the claims. This argument has been thoroughly reviewed but is not considered persuasive as the teachings of Karadjian (Proceedings National Academy of Sciences USA (2016) volume 113, pages 9834-9839), Bronner (Curr Protoc Hum Genet. 2009 July ; 0 18: . doi:10.1002/0471142905.hg1802s62) render these limitations obvious.
The response continues by providing arguments with respect to Beckman Coulter which are no longer relied upon. Thus this argument is not persuasive.
The response provides arguments with respect to the use of AMPure beads twice. This argument has been thoroughly reviewed but is not considered persuasive as Bronner specifically suggest the use of two rounds of AMPure size selection.
The response continues by asserting Maggi which is not relied upon teaches away from the use of two rounds of SPRI purification. This argument has been thoroughly reviewed but is not considered persuasive as the art of Bronner specifically suggest two rounds of AMPure beads. Further the response does not provide where in Maggi the teachings occurs. However, Maggi teaches on page 5m 2nd column first full paragraph, “Since the SPRI AMPure bead purification resulted in higher DNA recovery yield we proceeded to test the efficiency of high molecular weight DNA removal using the bead purification protocol on one additional human cfDNA sample that we spiked with 10% genomic DNA. To ensure that the protocol would work equally well using murine samples, which contained far less starting material and a small cfDNA peak at ∼150–200 bp, we also carried on the same SPRI AMPure beads based purification protocol using the murine cfDNA samples. In this case we omitted the genomic DNA spike since we specifically selected murine samples that showed visible contaminating high molecular weight DNA in the bioanalyzer profile (Figures 2D,G). The results from the AMPure bead protocols with two size selections (beads concentration 0.5X followed 1.6X) are summarized in Table 4. This purification method allows for a sensitive estimation of large versus small cfDNA fractions. For example, from the human sample that was isolated from a control individual (C1) we recovered 100% of starting material.” Thus the argument of counsel appears to be inconsistent with the art of record.
Claim(s) 9, 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Yeh (WO2017027835), Bischoff (Vol 6. No 3. 349–351 Reproductive BioMedicine Online; www.rbmonline.com/Article/796 on web 5 February 2003), Karadjian (Proceedings National Academy of Sciences USA (2016) volume 113, pages 9834-9839), Bronner (Curr Protoc Hum Genet. 2009 July ; 0 18: . doi:10.1002/0471142905.hg1802s62) QIAamp® DNA Mini and Blood Mini Handbook (2010) as applied to claims 1-2, 5-6, 9, 11, 13, 16, 18, 22, 24-27, 31-32above, and further in view of Kurihara (Journal of Pediatric Surgery (2015) volume 50, pages 2004-2007).
Yeh, Bischoff, Karadjian, Bronner and Qiagen do not specifically teach subjects with pediatric cancer..
However, Kurihara teaches, “: These data demonstrate the feasibility and potential utility of mutation/deletion/amplification screening in cfDNA using NGS and dPCR for the detection of tumor biomarkers in children with solid tumors. These markers also have the potential utility to evaluate complete resection after surgery.”
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 blood from subject thought to have pediatric cancer in the method of Yeh, Bischoff, Karadjian, Bronner and Qiagen. The artisan would be motivated to screen pediatric cancer with a blood sample instead of biopsy. The artisan would have reasonable expectation of success as Kurihara teaches detection of cfDNA from childhood tumors..
Response to Arguments
This is a new ground of rejection necessitated by amendment.
Claim(s) 14-15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Yeh (WO2017027835), Bischoff (Vol 6. No 3. 349–351 Reproductive BioMedicine Online; www.rbmonline.com/Article/796 on web 5 February 2003), QIAamp® DNA Mini and Blood Mini Handbook (2010) as applied to claims 1-3, 5-7, 9, 11, 13-14, 16-18, 21-22, 24, 31-32 and in further view of Beckman Coulter (SPRIselect User Guide SPRI Based Size Selection (2012).
The teachings of Yeh, Bischoff, and Qiagen are set forth above.
Yeh, Bischoff, and Qiagen do not teach two separate bead-based capture step.
However, Beckman Coulter teaches, “As a general rule, increasing the ratio of SPRIselect volume to sample volume will increase the efficiency of binding smaller fragments. Figure 1 illustrates this relationship.” (page 1-3) Beckman Coulter teaches “As a general rule, increasing the ratio of SPRIselect volume to sample volume will decrease the efficiency of binding larger fragments. Figure 3 illustrates this relationship.” (1-5)
Therefore for 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 do two bead-based separation steps with different bead volume to sample volumes. The artisan would be motivated as Beckman Coulter figures 1 and 3 suggest different ratios of beads to sample favor selection of different size fragments(double size consideration 1-8). The artisan would have a reasonable expectation of success as the artisan is merely using art accepted methods.
Response to Arguments
This is a new ground of rejection necessitated by amendment.
Claim(s) 24-27, 32 is/are rejected under 35 U.S.C. 103 as being unpatentable over Yeh (WO2017027835), Bischoff (Vol 6. No 3. 349–351 Reproductive BioMedicine Online; www.rbmonline.com/Article/796 on web 5 February 2003), Karadjian (Proceedings National Academy of Sciences USA (2016) volume 113, pages 9834-9839), Bronner (Curr Protoc Hum Genet. 2009 July ; 0 18: . doi:10.1002/0471142905.hg1802s62) QIAamp® DNA Mini and Blood Mini Handbook (2010) as applied to claims 1-2, 5-6, 9, 11, 13, 16, 18, 22, 24-27, 31-32 and in further view of Mouuliere ( (May 5, 2017)bioRxiv preprprint doi:https://.doi.10.1101/134437)
The teachings of Yeh, Bischoff, Karadjian, Bronner and Qiagen are set forth above.
Yeh, Bischoff, Karadjian, Bronner and Qiagen do not explicitly detecting multi variants separately.
However, Mouuliere teaches, “Non-invasive analysis of cancer genomes using cell-free circulating tumour DNA (ctDNA) is being widely implemented for clinical indications. The sensitivity for detecting the presence of ctDNA and genomic changes in ctDNA is limited by its low concentration compared to cell-free DNA of nontumour origin. We studied the feasibility for enrichment of ctDNA by size selection, in plasma samples collected before and during chemotherapy treatment in 13 patients with recurrent high-grade serous ovarian cancer. We evaluated the effects using targeted and whole genome sequencing. Selecting DNA fragments between 90-150 bp before analysis yielded enrichment of mutated DNA fraction of up to 11-fold. This allowed identification of adverse copy number alterations, including MYC amplification, otherwise not observed. Size selection allows detection of tumour alterations masked by non-tumour DNA in plasma and could help overcome sensitivity limitations of liquid biopsy for applications in early diagnosis, detection of minimal residual disease, and genomic profiling.” (intro) Mouuliere teaches, “ we converted the amplitude of the CNAs into a quantitative metric called t-MAD (trimmed Mean Absolute Deviation from copy-number neutrality, see Methods). Size selection of plasma DNA resulted in a median of 1.5 fold (n=26) increase in the t-MAD score (figure 3c and 3d). However, in the samples collected after the initiation of treatment, when ctDNA content was low, the genome wide enrichment was higher (Fig. 3d), with a median increase of the t-MAD score of 2.9 fold (range: 0.6 - 4.5 fold), except for two samples. For those two samples we observed a decrease in the t-MAD score, and an analysis of the size profile before selection for these samples revealed that the DNA had been heavily fragmented, which could explain why the size selection did not result in enrichment for these cases (Suppl. Fig. 1). In this dataset, we did not identify a differential effect of size selection on the recovery of specific alterations, suggesting that there is a global genome enrichment post size selection. Additionally, size selection notably led to an increased detection of deletions (Suppl. Fig. 2). Analysis with greater sequencing depth, integration of samples from other cancer types and different stages of the disease would help to extend our observations and expand further our understanding of ctDNA biology and fragmentation.”
Thus 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 examine variants separately or in more than one fraction. The artisan would be motivated to extend the observations of Mouuliere expand further our understanding of ctDNA biology and fragmentation. The artisan would have a reasonable expectation of success as the artisan is merely using known methods to analyze data.
Response to Arguments
This is a new ground of rejection necessitated by amendment.
Summary
No Claims are allowed.
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.
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/Steven Pohnert/Primary Examiner, Art Unit 1683
