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 .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 1/15/2025 is in compliance with the provisions of 37 CFR 1.97 and is being considered by the examiner. The Foreign Patent document by Univ. Korea Res. and Bus Found is not filed in English and therefore not being considered by the examiner.
Drawings
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2). Color drawings werefiled in the application in the graph of FIG. 9 without an accompanying petition, proper correction is required.
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.
Claims 3 and 7 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 3 recites the limitation "said Ras gene". There is insufficient antecedent basis for this limitation in the claim. Claim 1 in which claim 3 depends upon does not mention a Ras gene.
Claim 7 recites the limitation "said fluid sample". There is insufficient antecedent basis for this limitation in the claim. Claim 1 in which claim 7 depends upon does not mention a fluid sample. Furthermore, the use of the term “selectively” in claim 7 is unclear as to what conditions are considered sufficient to form a blocking probe-mutated gene duplex and a single stranded mutated gene.
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, 6-12, and 14-19 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 recites “a method for directly diagnosing a gene mutation in a subject…”. The specification of the instant application describes examples of specific genes and mutations that are indicative of cancer. When turning to the specifications, paragraph [0017] recites” In some embodiments, said probe oligonucleotide comprises a complementary oligonucleotide of a wild-type gene selected from the group consisting of Ras, EGFR, and PIK3CA. In some instances, said Ras gene is selected from the group consisting of KRas, HRas, NRas, R-Ras, M-Ras, E-ras, Di-Rasl, Di-Ras2, NKIRasl, NKIRas2, TC21, Rap1, Rap2, Ritl, Rit2, Reml, Rem2, Rad, Gem, Rhebl, Rheb2, Noey2, R-Ras, Rerg, RalA, RalB, RasDl, RasD2, RRP22, RasL10B, RasL11A, RasL11B, Ris/RasL12, and FLJ22655. In one particular embodiment, said method detects a mutation in codon 12 or 13 of KRas gene. Still in another embodiment, said method detects a mutation in codon 12 of KRas gene.” The instant claim language is broadly written to encompass any gene mutation that may or may not be associated with a cancer. Claims 2-3 fail to further clarify the diagnosing of a gene mutation in a subject of claim 1.
Independent claims 10 and 18 recite the limitations “diagnosing for a presence of cancer in a subject” and “screening a subject for cancer” respectively. The specification of the instant application describes examples of detecting genes and mutations indicative of cancer; however, it fails to define what indicates a diagnosis for cancer in a subject, and how a subject is being screened for the presence of cancer.
Regarding claim 10, the specification does not clearly describe or define what indicates a diagnosis for a presence of cancer in a subject. When turning to the specification, there are numerous examples of detecting different mutations in clinical cfDNA samples to include paragraph [0116] which describes detection of KRAS G12D mutated DNA in a cfDNA reference standard set, paragraph [0118] which describes detection of EGFR L858R mutated DNA in a cfDNA reference standard set, and paragraph [0119] which describes detection of KRAS mutation at codon 12 in clinical cfDNA samples. Paragraph [0124] recites “… methods of the invention can be used to detect other common KRAS-mutated DNAs related to cancers in cfDNA samples via the use of suitable blocker(s) (FIG. 8A). Methods and apparatuses of the invention can be used to detect any types of the mutation (codons 12 and 13) if a mixture of the blockers corresponding to G12D, G12V, G12C, G12A, G12S, G12R, and G13D are used. Apart from KRAS mutation, methods and apparatuses of the invention has also been validated for the detection of other mutations (e.g., EGFR mutation) in cfDNA samples. Accordingly, methods and apparatuses of the invention can be used for the detection of point mutation of various other gene and their mutation types.” These cited descriptions indicate some amount of ambiguity regarding the detection of genetic mutations in cfDNA clinical samples as it pertains to diagnosing a subject for the presence of cancer. However, KRas mutations are present in various cancers as evidenced by Yang (Yang et. al., 2023, KRAS Mutations in Solid Tumors: Characteristics, Current Therapeutic Strategy, and Potential Treatment Exploration. J. Clin. Med., 12, 709); rendering the diagnosing for the presence of cancer as recited by claim 10 to possess a broader scope than that of the specifications. Yang teaches that Kirsten rat sarcoma (KRAS) gene is one of the most common mutated oncogenes in numerous cancer types, such as non-small cell lung cancer (NSCLC), colorectal cancer (CRC), and pancreatic ductal adenocarcinoma (PDAC) (Yang et. al., pg.1, par. 1). Yang further teaches that According to The Cancer Genome Atlas (TCGA) database, KRAS mutations are present in approximately 11.6% of all carcinomas, the mutation rates and subtypes of which vary widely between tumors (Yang et. al. pg.2, par. 2). Claims 6, 11-12, and 17 suffer from the same issue of determining the presence of a mutation in various genes, but ultimately do not further clarify the diagnosing for a presence of cancer. The scope of the claims is broad and do not have support based on the specification that the applicant has possession of the method as claimed.
Claims 7-9 and 14-16 recite the addition of a chimeric Locked nucleic acid blocking probe to a sample for diagnosing a gene mutation (claims 7-9) and presence of cancer in a subject (claims 14-16). When turning to the specification, paragraph [0029] recites “…said step of contacting said sample with said solid substrate further comprises the step of contacting said sample with a blocking probe under conditions sufficient to selectively form a blocking probe-mutated gene duplex and a single stranded mutated gene, when said mutated gene is present in said fluid sample. In some instances, said blocking probe comprises locked-nucleic acid/DNA ("LNA/DNA") chimeric blocking probe.” The limitations of the instant claims fail to further clarify the diagnosing of a gene mutation and presence of cancer in a subject.
Claim 18 is noted for further issues and recites “a method for directly screening a subject for cancer…”. The claim as written appears to embrace a method wherein the presence of a DNA mismatched target-probe oligonucleotide duplex is used to screen the subject for a presence of cancer. The screening of a subject for a presence of cancer is broad and not supported by the specification.
Regarding claim 18, the specification does not clearly describe or define directly screening a subject for the presence of cancer. When turning to the specification, paragraphs [0084], [0085], and [0086] discusses the detection of BRAF V600E mutation, RET mutation. Paragraph [0085] recites “Mutations in the RET gene have been implicated in various types of cancers including, but not limited to, medullary thyroid carcinoma (MTC), multiple endocrine neoplasias type 2A and 2B, pheochromocytoma, and parathyroid hyperplasia. Genetic testing for RET mutations is often used to help diagnose and determine the prognosis of certain cancers, particularly medullary thyroid carcinoma.” Paragraph [0086] recites “RET mutations screening is a well-established test that allows for prophylactic surgery in asymptomatic gene carriers.” These paragraphs describe using the claimed method to determine the presence of BRAF V600E and RET mutations. Claim 19 fails to further clarify the direct screening of a subject for cancer. The scope of the instant independent claim is broadly drawn to screening a subject for any type of cancer and does not have support based on the specification that the applicant has possession of the method as claimed.
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 10-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural correlation without significantly more.
Subject Matter Eligibility Test (see MPEP § 2106):
Step 1: Are the claims to a process, machine, manufacture, or composition of matter?
Yes, the claims are directed to a process (method of diagnosing for a presence of cancer in a subject).
Step 2A: Are the claims directed to a judicial exception?
Prong 1: Do the claims recite an abstract idea, law of nature, or natural phenomenon?
As discussed in MPEP 2106.04(II)(A)(1), the meaning of “recites” is “set
forth” or “describes”. That is, a claim recites a judicial exception when the judicial
exception is “set forth” or “described” in the claim. In the instant case, the claims
describe a natural phenomenon (the natural correlation between a genetic mutation and cancer) and an abstract idea (the mental process of diagnosing and screening for the presence of cancer).
Independent claims 10 and 18 recite methods for diagnosing and screening for the presence of cancer, respectively, where a natural correlation/law of nature between the presence of a DNA mismatched target-probe oligonucleotide duplex indicates the presence of cancer. Furthermore, both claims recite the probe oligonucleotide comprises a portion of a BRAF or RAS wild- type gene. These genes are commonly known within the art as biomarkers for cancer detection as evidenced by Oikonomou (Oikonomou et. al., 2014, BRAF vs RAS oncogenes: Are mutations of the same pathway equal Differential signalling and therapeutic implications, Oncotarget).
Oikonomou recites “KRAS gene mutations have been reported in approximately 15–30% of human solid tumours, where the MAP kinase (MAPK) pathway is found hyperactivated (Figures 2–3). This mutation is the most common abnormality of dominant oncogenes in human tumours and is a common event in the development and progression of adenocarcinomas of the pancreas (90%), colon (50%), thyroid (50%), bladder (50%), and lung (30%).” Oikonomou Further recites “Mutations in BRAF, the downstream effector of KRAS are reported in up to 70% of melanoma cancer cell lines and they are highly prevalent in most common cancers with poor prognosis such as malignant melanoma (Figures 4–5).” ([pg.11754, right col. Par. 3]; [pg. 11755, left col. Par. 2])
Prong 2: Do the claims recite additional elements that integrate the judicial exception into a practical application?
As discussed in MPEP 2106.04(II)(A)(2), “Because a judicial exception is
not eligible subject matter, Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06
(quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)), if there are no
additional claim elements besides the judicial exception, or if the additional claim
elements merely recite another judicial exception, that is insufficient to integrate the
judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract
idea (math) to another abstract idea (encoding and decoding) does not render the claim
non-abstract"); Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541,
1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature
(or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, the additional elements (if any) in the claim must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice
Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B.” The
considerations to be used are set forth at MPEP 2106.05(a) through (c) and (e) through
(h).
Claims 10 and 18 recite “analyzing said target-probe oligonucleotide duplex for the presence of a mismatched target-probe oligonucleotide duplex with an atomic force microscope (AFM) comprising a DNA mismatch repair protein attached to the cantilever. The addition of analysis by using an AFM is considered insignificant extra-solution activity because there is no change to the nature of the claim. The term "extra-solution activity" can be understood as activities incidental to the primary process or product that are merely a nominal or tangential addition to the claim. As explained by the Supreme Court, the addition of insignificant extra-solution activity does not amount to an inventive concept, particularly when the activity is well-understood or conventional. Parker v. Flook, 437 U.S. 584, 588-89, 198 USPQ 193, 196 (1978). See MPEP §2106.05(g).
There are no additional elements in claims 10 and 18; therefore, the judicial
exception is not integrated into a practical application.
Step 2B: Do the claims recite additional elements that amount to significantly more than the judicial exception?
Claims 11-17, 19, and 20 are drawn to determining a genetic mutation (claims 11-13, 19 and 20), and contacting a sample with a blocking probe (claims 14-17). These claims do not provide additional elements that amount to significantly more than the judicial exception; therefore, the judicial exception is not integrated into a practical application, meaning these claims do not contain eligible subject matter.
For these reasons, the claims are rejected under U.S.C. 35 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1-5, 7-8, 10-15, and 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Maney et. al. (WO 2014193999 A2, Filed: 5/28/2014) in view of Tessmer (Tessmer et. al., The Journal of Biological Chemistry, 2008, Vol.283, No.52) as evidenced by Koçum (Koçum et. al., 2006, NPL).
Maney teaches a method of detecting a biomarker in a sample by contacting the sample with at least one binding agent, which can be a probe comprising an oligonucleotide. A method of determining a KRAS nucleotide sequence in a biological sample is also provided and modifications or binding of molecules in solution or immobilized on an array can be detected using detection techniques known in the art. Examples of such techniques include scanning probe microscopies, such as atomic force microscopy (AFM). Maney teaches detecting a biomarker that forms a complex with at least one binding agent to thereby detect the biomarker and characterization by determining whether the circulating biomarkers in the sample are altered as compared to a reference. The analysis of circulating biomarkers associated with diseases, including vesicles and/or microRNA, can aid in detection of disease or severity thereof, determining predisposition to a disease, as well as making treatment decisions. Maney further teaches an alteration can include any measurable difference between the sample and the reference such as a mutation (Instant claim 1, [0007], [0011], [00187], [00261], [00510], [00716]).
Maney teaches a method determining a KRAS nucleotide sequence in a biological sample (instant claim 2, [00716]).
Maney teaches a Ras gene is selected from the group consisting of KRas, HRas, NRas, R-Ras, M-Ras, E-ras, Di-Rasl, Di-Ras2, NKIRasl, NKIRas2, TC21, Rap1, Rap2, Rit1, Rit2, Reml, Rem2, Rad, Gem, Rhebl, Rheb2, Noey2, R- Ras, Rerg, RalA, RalB, RasDl, RasD2, RRP22, RasLIOB, RasLiA, RasL11B, Ris/RasL12, and FLJ22655 (Instant claims 3 and 11, [00367]).
Maney teaches that mutational analysis may be carried out for mRNAs and DNA, including those that are identified from a vesicle. For example, once the total RNA has been obtained from isolated colon cancer-specific vesicles, cDNA can be synthesized and primers specific for exons 2 and 3 of the KRAS gene can be used to amplify these two exons containing codons 12, 13 and 61 of the KRAS gene (Instant claims 4 and 12 [00561]).
Maney teaches in Table 8, examples of biomarkers that can be detected and treatment agents that can be selected or possibly avoided to include BRAF V600E (Instant claims 5 and 20, [00660]).
Maney teaches the usages of various types of binding agents to include locked nucleic acids (LNA) and that a single binding agent may be employed to isolate or detect a vesicle from a biological sample. Maney teaches detecting a biomarker that forms a complex with at least one binding agent to thereby detect the biomarker, reading on the limitations of instant claims 7-8, and 14-15 ([0011],[0022], [00175]).
Maney teaches on the method of directly diagnosing for a presence of cancer in a subject, said method comprising: contacting a fluid sample obtained from subject with a solid substrate comprising a probe oligonucleotide under conditions sufficient to form a target-probe oligonucleotide duplex when a target oligonucleotide is present in said sample ([0025], [00187]), wherein said probe oligonucleotide comprises at least a portion of a wild-type Ras gene ([00716]) and analyzing said target-probe oligonucleotide duplex for the presence of a mismatched target-probe oligonucleotide duplex with an atomic force microscope (AFM) ([00510], instant claim 10).
Maney teaches the method used to determine the presence of G12D, G12A, G12R, G12C, G12S, G12V, G13D, or a combination thereof (Instant claim 13, [00718]).
Maney teaches the cancer characterized by the methods can be thyroid cancer (Instant claim 19, [0026]).
Maney does not teach a DNA mismatch repair protein attached to a cantilever of an atomic force microscope (limitations of instant claims 10 and 18) or the use of a cell free DNA (cfDNA) sample for screening a subject for the presence of cancer (limitation of instant claim 18). However, this technique of using DNA mismatch repair proteins and atomic force microscopy (AFM) is known within the art and taught by Tessmer and Koçum.
Tessmer teaches the usage of AFM to visualize directly MutS proteins bound to mismatches and to homoduplex DNA. This AFM method is particularly useful for proteins, such as MutS, that have high affinities for DNA ends, which can prevent accurate determination of the specificity for a mismatch using bulk methods. The images were captured in air with the microscope in tapping mode (pg.36647, col.1, par. 2). Immobilization of a molecule on a cantilever tip of an AFM is commonly known within the art as evidenced by Koçum, who teaches a method where a model single strand DNA (ssDNA) was covalently immobilized onto AFM tips (cantilevers) as specific ligand (Koçum et. al., abstract).
It would have been obvious to one of ordinary skill within the art before the effective filing date of the claimed invention to have combined the teachings of Maney with the teachings of Tessmer and Koçum to use an Atomic Force Microscope (AFM) with a DNA mismatch repair protein for the detection of a genetic mutation in a clinical sample. The AFM method for detection allows for enhanced sensitivity and specificity, and high reliability for distinguishing types of mutations while offering a faster result than other traditional methods such as PCR.
Claim(s) 6, 17, and 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Maney et. al. (WO 2014193999 A2, Filed: 5/28/2014) and Tessmer (Tessmer et. al., The Journal of Biological Chemistry, 2008, Vol.283, No.52) as applied to claims 1-5, 7-8, 10-15, and 19 above, and further in view of Zaher (Zaher et. al., Indian Journal of Cancer, 2013, 50(3)).
The teachings of Maney and Tessmer are discussed above.
Maney teaches screening a subject for cancer a solid substrate comprising a probe oligonucleotide under conditions sufficient to form a target- probe oligonucleotide duplex when a target oligonucleotide is present in said cfDNA, wherein said probe oligonucleotide comprises at least a portion of a wild- type BRAF gene or a wild-type Ras gene ([00660],[00716]); and analyzing said target-probe oligonucleotide duplex for the presence of a mismatched target-probe oligonucleotide duplex with an atomic force microscope (AFM) ([00510]), wherein the presence of said DNA mismatched target-probe oligonucleotide duplex is used to screen the subject for presence of cancer([0007], instant claim 18).
Maney and Tessmer fail to teach the use of a cell free DNA (cfDNA) sample for screening a subject for the presence of cancer (limitations of instant claims 6, 17, and 18).
Zaher teaches a study for evaluating cell-free DNA (cfDNA) concentration and integrity in patients with malignant and nonmalignant diseases and in controls to investigate their value as a screening test for cancer, and to correlate them with clinicopathological parameters of cancer patients (abstract, instant claim 18).
Zaher teaches a method in which one random blood sample was collected in EDTA containing tubes, from patients before surgery or treatment and from controls. Blood was centrifuged at 6000 rpm for 10 min at 4°C. Plasma samples were kept frozen at -80°C until the time of assay to detect total cell free concentration and integrity ([pg. 176, col.2, par.6], instant claims 6 and 17).
It would have been obvious to one of ordinary skill within the art before the effective filing date of the claimed invention to have combined the teachings of Maney and Tessmer with the teaching of Zaher to use cfDNA samples for detection of genetic mutations in a subject by AFM for the purpose of screening a subject for cancer. Zaher teaches that cfDNA is present in both malignant and non-malignant diseases; however, in cancer patients it is most likely a result from tumor necrosis, which generates a spectrum of DNA fragment with various lengths. (Zaher et. al. pg.176, col. 1, par. 3). The usage of cfDNA clinical serum samples combined with AFM analysis for cancer screening would provide the benefit of a non-invasive method with higher sensitivity, mutation identification and specificity, and faster result readout.
Claim(s) 9 and 16 is/are rejected under 35 U.S.C. 103 as being unpatentable over Maney et. al. (WO 2014193999 A2, Filed: 5/28/2014) and Tessmer (Tessmer et. al., The Journal of Biological Chemistry, 2008, Vol.283, No.52) as applied to claims 1-5, 7-8, 10-15, and 19 above, and further in view of Mishra (Mishra et. al., Analytical Chemistry, 2018, 90).
The teachings of Maney and Tessmer are discussed above.
Mishra teaches usage of Lock Nucleic Acids (LNA/DNA chimera and fully modified LNA) as a capture probe for more sensitive and specific detection of BCR-ABL fusion gene in Chronic myeloid leukemia (CML) using an AFM- based single molecule force spectroscopy approach. Mishra recites” Melting temperatures for the specific and nonspecific probe-target complexes were calculated to find an optimal probe. A 21-mer LNA/DNA chimeric capture probe was found, and it has melting temperature of 84 °C to BCR-ABL gene (21-base pair, b2a2 junction), 67 °C (15-base pair), and 67 °C (12-base pair) toward normal BCR gene and normal ABL gene, respectively.” (pg.12826, right col. par. 2), teaching on the limitations of instant claims 9 and 16.
It would have been obvious to one of ordinary skill within the art before the effective filing date of the claimed invention to have combined the teachings of Maney and Tessmer with the teaching of Mishra to incorporate usage of a Locked Nucleic Acid chimeric blocker probe to facilitate accessibility of the desired target sequence to the capture probe to prevent the target strand rebinding to its counterpart rather than the capture probe. Due to the high affinity and thermal stability of Lock Nucleic Acids, one of skill in the art would be motivated to select a LNA as the blocking probe for genetic mutation detection by AFM method in cfDNA analysis.
Conclusion
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/A.H.B./Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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