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 .
Notice of New Examiner
The Examiner would like to note for the Applicant that this case has been
transferred to a new examiner for examination. Any further communications on this case may be directed to the contact information included in the conclusion of this office action.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on April 14th, 2023, May 23rd, 2024, and March 19th, 2025 are acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-10, in the reply filed on February 23rd, 2026 is acknowledged. The Applicant has further cancelled claims 6 and 11-20.
The Applicant has further provided species elections as previously required. After further consideration, all species elections are hereby withdrawn. All species will be examined.
Claim Summary
Claims 1 and 7 have been amended. Claims 6 and 11-20 have been canceled. Claims 1-5 and 7-10 are pending. Claims 1-5 and 7-10 are under examination and discussed in this Office action.
Specification
The abstract of the disclosure is objected to because of undue length and not being a single paragraph. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The use of terms such as BIOTAQ, Ampdirect, TaqMan, Cy dyes, TAMRA, and others, which are trade names or marks used in commerce, has been noted in this application. All terms should be accompanied by the generic terminology; furthermore all terms should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 1 and 8 are objected to because of the following informalities:
Claim 1 recites the limitation “2. a step of adding the followings to the specimen”. The “s” at the end of “followings” should be deleted.
Claim 8 recites the limitation “wherein the PCR primer pair is a pair of base sequences represented by the followings”. The “s” at the end of “followings” should be deleted.
Claim Interpretation
Claim 8 recites specific primer pairs and their corresponding SEQ ID NOs. Based on the language of the claim, it is interpreted that the sequences of the primers match the provided SEQ ID NOs exactly, with no differences or additional bases. In addition, based on the description provided in the specification (see Pages 10-11, paragraphs [0035] and [0036] of the specification), it is interpreted that primer pairs SEQ ID NO:1/SEQ ID NO:2 and SEQ ID NO:3/SEQ ID NO:4 are meant for amplifying the sequence containing the 112th amino acid, and primer pairs SEQ ID NO:5/SEQ ID NO:6 and SEQ ID NO:7/SEQ ID NO:8 are meant for amplifying the sequence containing the 158th amino acid.
Claim 9 recites specific probes and their corresponding SEQ ID NOs. As above for the primers and based on the language of the claim, it is interpreted that the sequences of the probes match the provided SEQ ID NOs exactly, with no differences or additional bases.
Claim Rejections - 35 USC § 112(a)
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.
Scope of Enablement
Claims 1-5 and 7-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph. The specification, while being enabling for a human subject, does not reasonably provide enablement for any subject as embraced by the claims. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
There are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “undue.” See MPEP § 2164. These factors include, but are not limited to: the breadth of the claims, the nature of the invention, the state of the prior art, the level of one of ordinary skill, the level of predictability in the art, the amount of direction provided by the inventor, the existence of working examples, the quantity of experimentation needed to make or use the invention based on the content of the disclosure.
The office has analyzed the specification in direct accordance to the factors outlines in In re Wands. MPEP 2164.04 states: “[W]hile the analysis and conclusion of a lack of enablement are based on factors discussed in MPEP 2164.01(a) and the evidence as whole, it is not necessary to discuss each factor in written enablement rejection.” These factors will be analyzed, in turn, to demonstrate that one of ordinary skill in the art would have had to perform “undue experimentation” to make and/or use the invention and therefore, applicant’s claims are not enabled.
(A) With respect to the breadth of the claims: Claim 1 as currently drafted encompasses a method for detecting a genetic polymorphism of apolipoprotein E present in genomic DNA collected from a subject. Claim 10 as currently drafted encompasses a method for determining a genetic polymorphism of apolipoprotein E present in genomic DNA collected from a subject.
“A subject” does not limit the subject to a human subject and the analysis of human samples as described in the specification. Consequently, the breadth of the claim is expansive since they encompass any kind of subject. Claims 2-5 and 7-9 encompass the same breadth as claim 1 since they do not limit the subject to a human subject.
(B) The nature of the invention: The invention is in the field of genetic polymorphism detection methods related to polymorphisms in apolipoprotein E.
(C), (D), (E) With respect to the state of the prior art, the level of one of ordinary skill and predictability of the art:
Juppner (Functional properties of the PTH/PTHrP receptor, Bone, August 1995, S39-S42) teaches that despite significant structural conservation, rat, opossum, and human PTH/PTHrP receptor homologs display distinct functional characteristics (Abstract; Pages 39S-40S). This art indicates that there is known functional differences between homologs in different organisms, and therefore inter-species extrapolation would be unpredictable.
The art supports use of specific subjects. However, methods comprising any subject are highly unpredictable.
The invention is drawn to biological molecules, and is therefore in a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001). The level of skill in the art is therefore deemed to be high.
(F), (G) With respect to the amount of direction and working examples provided by the applicant: The Applicant has not provided a general description directed towards subjects. However, the Applicant has provided working examples that are directed only to human subjects. As noted at Page 18, paragraph [0074], the samples used in the working examples are samples from humans. The Applicant has not provided working examples directed towards any other type of subject.
(H) Undue experimentation would be required to practice the invention as claimed due to the amount of experimentation necessary because of the expansive breadth of the claims, the state of the prior art and its high predictability, and the limited amount of guidance in the form of varied working examples in the specification. A skilled artisan recognizes that a subject very broadly refers to any number of different species and thus applicability of the claimed method to a subject as embraced by the claims remains unpredictable, requiring undue experimentation. For example, an artisan would need to test the method on an expansive number of different organisms to determine if it is applicable to detecting a genetic polymorphism of apolipoprotein E in these other organisms. This reasonably represents undue experimentation.
MPEP §2164.01(a), 4th paragraph, provides that, “A conclusion of lack of enablement means that, based on the evidence regarding each of the above factors, the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention without undue experimentation. In re Wright, 999 F.2d 1157, 1562; 27 USPQ2d 1510, 1513 (Fed. Cir. 1993).
Genentech Inc. v. Novo Nordisk A/S, 42 USPQ2d 1001, 1005 (CA FC), states that, “[p]atent protection is granted in return for an enabling disclosure of an invention, not for vague intimations of general ideas that may or may not be workable,” citing Brenner v. Manson, 383 U.S. 519, 536 (1966) (stating, in the context of the utility requirement, that “a patent is not a hunting license. It is not a reward for search, but compensation for its successful conclusion”). The Genentech decision continued, “tossing out the mere germ of an idea does not constitute enabling disclosure. While every aspect of a generic claim certainly need not have been carried out by an inventor, or exemplified in the specification, reasonable detail must be provided in order to enable members of the public to understand and carry out the invention.” Id. at p. 1005.
After applying the Wands factors and analysis to claims 1-5 and 7-10, in view of the applicant’s entire disclosure, and considering the In re Wright, In re Fisher and Genentech decisions discussed above, it is concluded that the practice of the full scope of the invention as claimed would not be enabled by the written disclosure. Therefore, claims 1-5 and 7-10 are rejected under 35 U.S.C. §112(a) for failing to disclose sufficient information to enable a person of skill in the art to practice the claimed invention to it the full scope embraced by the claims.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Koch (TaqMan Systems for Genotyping of Disease-Related Polymorphisms Present in the Gene Encoding Apolipoprotein E, Clinical Chemistry and Laboratory Medicine, June 2005, 40, 1123-1131; cited on the IDS filed April 14th, 2023), in view of Haisong (CN108504731A; cited on the IDS filed May 23rd, 2024, citations made using English translation provided in the file wrapper dated May 23rd, 2024).
Regarding instant claim 1, Koch teaches a method for detecting a genetic polymorphism of apolipoprotein E present in genomic DNA collected from a subject, comprising the following steps 1 to 3: 1. a step of releasing a DNA from blood collected from a subject and preparing a specimen containing the DNA (Page 1124, column 1, paragraph 5); 2. a step of adding the followings to the specimen containing the DNA and then mixing: (1) a PCR enzyme (Page 1125, column 1, paragraph 2), (2) a PCR primer pair for amplifying a nucleic acid fragment of the apolipoprotein E gene containing a codon encoding the 112th or 158th amino acid residue (Cys or Arg) of apolipoprotein E (Page 1125, column 1, paragraph 2; Table 1B: primer pairs 6 and 7), and (3) a set consisting of a fluorescent labeled probe which has an oligonucleotide that binds to a nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding wild-type Cys which is the 112th amino acid residue of apolipoprotein E, and a fluorescent labeled probe which has an oligonucleotide that binds to a nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding mutant Arg which is the 112th amino acid residue of apolipoprotein E, wherein the fluorescent dyes used for labeling are different from each other (Page 1125, column 1, paragraph 2; Table 1C: probe pair 3), or a set consisting of a fluorescent labeled probe which has an oligonucleotide that binds to a nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding wild-type Arg which is the 158th amino acid residue of apolipoprotein E, and a fluorescent labeled probe which has an oligonucleotide that binds to a nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding mutant Cys which is the 158th amino acid residue of apolipoprotein E, wherein the fluorescent dyes used for labeling are different from each other (Page 1125, column 1, paragraph 2; Table 1C: probe pair 4); and 3. a step of performing PCR on the said mixture and measuring the fluorescence intensity from the PCR product corresponding to the 112th or 158th amino acid residue of apolipoprotein E of the said subject (Page 1125, column 1, paragraph 2; Figure 2, bottom row).
Koch does not teach performing this assay using saliva containing epithelial cells collected from a subject.
Haisong, in the same field of endeavor, teaches performing apolipoprotein E genotyping using saliva containing epithelial cells collected from a subject (Page 3, paragraph [0008]: saliva sample contains oral epithelial cells; Page 4, paragraph [0022]).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Koch with the saliva sample of Haisong. Since both Koch and Haisong are in the same field of endeavor (e.g. detecting apolipoprotein E), one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because saliva sampling is simple and painless (Page 3, paragraph [0008]). Although Haisong describes difficulties with using saliva samples, it is noted that the courts have found, “A known or obvious composition does not become patentable simply because it has been described as somewhat inferior to some other product for the same use." In re Gurley, 27 F.3d 551, 553, 31 USPQ2d 1130, 1132 (Fed. Cir. 1994) (see MPEP 2123(II)). Thus, an option that may be described as inferior is still considered to be known in the art. In addition, Haisong goes on to describe use of saliva for apolipoprotein E genotyping, which supports use of saliva as a sample type given the nature of the teaching. Furthermore, the use of a saliva sample instead of a blood sample amounts to simple substitution of one known element for another to obtain predictable results (see MPEP 2141(III)).
Regarding instant claim 7, Koch, in view of Haisong, teaches the method for detecting a genetic polymorphism according to claim 1. Haisong further teaches wherein the saliva is collected by a cotton swab (Page 4, paragraph [0018]).
Claims 2 and 3 are rejected under 35 U.S.C. 103 as being unpatentable over Koch (TaqMan Systems for Genotyping of Disease-Related Polymorphisms Present in the Gene Encoding Apolipoprotein E, Clinical Chemistry and Laboratory Medicine, June 2005, 40, 1123-1131; cited on the IDS filed April 14th, 2023) and Haisong (CN108504731A; cited on the IDS filed May 23rd, 2024, citations made using English translation provided in the file wrapper dated May 23rd, 2024), as applied to claims 1 and 7, and further in view of Goldenberger (A simple "universal" DNA extraction procedure using SDS and proteinase K is compatible with direct PCR amplification, Genome Research, 1995, 4, 368-370).
Regarding instant claim 2, Koch, in view of Haisong, teaches the method for detecting a genetic polymorphism according to Claim 1. Haisong further teaches using proteinase K to process samples (Page 13, paragraph [0083]).
Neither reference teaches wherein DNA is released by using a surfactant and protease K in the step 1.
Goldenberger, in a reasonably pertinent field, teaches on DNA extraction using SDS and proteinase K that is compatible with direct PCR amplification (Page 368, column 2, paragraph 2).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Koch, in view of Haisong, with the surfactant and proteinase K of Goldenberger. Since Goldenberger teaches on use of SDS and proteinase K in PCR, which is reasonably pertinent to Koch, in view of Haisong, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because SDS and proteinase K extraction is easy to use and almost universally applicable, including to body fluid samples (Page 370, column 2, paragraph 1).
Regarding instant claim 3, Koch, in view of Haisong and Goldenberger, teaches the method for detecting a genetic polymorphism according to Claim 2. Goldenberger further teaches wherein the surfactant is sodium dodecyl sulfate (Page 368, column 2, paragraph 2).
Claims 4 and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Koch (TaqMan Systems for Genotyping of Disease-Related Polymorphisms Present in the Gene Encoding Apolipoprotein E, Clinical Chemistry and Laboratory Medicine, June 2005, 40, 1123-1131; cited on the IDS filed April 14th, 2023) and Haisong (CN108504731A; cited on the IDS filed May 23rd, 2024, citations made using English translation provided in the file wrapper dated May 23rd, 2024), as applied to claims 1 and 7, and further in view of Nacalai (Ampdirect Plus Procedure [online]. Nacalai, [2007] [retrieved on August 6th, 2026]. Retrieved from: https://www.nacalai.com/global/reagent/img/amp_emn.pdf), as evidenced by the MSDS for Ampdirect Plus (Material Data Safety Sheet for Ampdirect Plus [online]. Nacalai, [2006] [retrieved on August 6th, 2026]. Retrieved from: https://www.nacalai.com/global/reagent/img/ampmsdse.pdf).
Regarding instant claim 4, Koch, in view of Haisong, teaches the method for detecting a genetic polymorphism according to Claim 1. Koch teaches using TaqMan Universal PCR Master Mix for amplification reactions (Page 1125, column 1, paragraph 2).
Neither reference teaches wherein Tris hydrochloric acid buffer solution containing potassium chloride, magnesium chloride, and dNTP mix is further added and mixed with the above specimen.
Nacalai, in a reasonably pertinent field, teaches a PCR buffer called Ampdirect Plus from the series Ampdirect, which contains Tris hydrochloric acid buffer solution containing potassium chloride, magnesium chloride, and dNTP mix, for addition to PCR reactions (whole document). While not explicitly stated in Nacalai, as evidenced by the MSDS for Ampdirect Plus, the Ampdirect Plus reagent contains potassium chloride (whole document).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Koch, in view of Haisong, with the Ampdirect buffer of Nacalai. Since Nacalai teaches on a PCR buffer, which is reasonably pertinent to the method of Koch, in view of Haisong, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because the Ampdirect buffer can neutralize inhibitory substances in biological samples for direct PCR from human samples (Nacalai, Page 1, paragraph 2).
Regarding instant claim 5, Koch, in view of Haisong, teaches the method for detecting a genetic polymorphism according to Claim 1.
Neither reference teaches the method further comprising a step of adding and mixing with the above specimen a substance which binds to substances that inhibit PCR, which are a biologically derived negatively charged substance that adsorbs to PCR enzymes and a biologically derived positively charged substance that adsorbs to DNA, thereby neutralizing the PCR inhibitory action of the negatively charged substance and the positively charged substance.
Nacalai, in a reasonably pertinent field, teaches a PCR buffer called Ampdirect Plus from the series Ampdirect that is capable of neutralizing inhibitory substances in biological samples for direct PCR (Page 1, paragraph 2). As indicated in the specification, Ampdirect and Ampdirect Plus are reagents capable of the above claimed aspects related to positively and negatively charged substances (see Page 13, paragraph [0047]). Thus, the claim has been given the broadest reasonable interpretation consistent with the teachings of the specification regarding “Ampdirect” (In re Hyatt, 211 F.3d1367, 1372, 54 USPQ2d 1664, 1667 (Fed. Cir. 2000) (see MPEP 2111).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Koch, in view of Haisong, with the substance of Nacalai. Since Nacalai teaches on a PCR buffer, which is reasonably pertinent to the method of Koch, in view of Haisong, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because the Ampdirect buffer can neutralize inhibitory substances in biological samples for direct PCR from human samples (Nacalai, Page 1, paragraph 2).
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Koch (TaqMan Systems for Genotyping of Disease-Related Polymorphisms Present in the Gene Encoding Apolipoprotein E, Clinical Chemistry and Laboratory Medicine, June 2005, 40, 1123-1131; cited on the IDS filed April 14th, 2023) and Haisong (CN108504731A; cited on the IDS filed May 23rd, 2024, citations made using English translation provided in the file wrapper dated May 23rd, 2024), as applied to claims 1 and 7, and further in view of GenBank (GenBank accession number AF261279.1 [online]. GenBank, [2008] [retrieved on August 6th, 2026]. Retrieved from: https://www.ncbi.nlm.nih.gov/nucleotide/AF261279.1), Dieffenbach (General concepts for PCR primer design, Genome Research, 1993, 3, S30-S37), and Roux (Optimization and troubleshooting in PCR, Genome Research, 1995, 4, S185-S194).
Regarding instant claim 8, Koch, in view of Haisong, teaches the method for detecting a genetic polymorphism according to Claim 1. Koch further teaches specific primers related to amplification of the 112th and 158th codon of apolipoprotein E (Table 1B: primer pairs 6 and 7). Koch also teaches on the known alterations associated with these codons (Page 1123, column 2, paragraph 2).
Neither reference teaches wherein the PCR primer pair is a pair of base sequences represented by the followings: SEQ ID NO: 1 and SEQ ID NO: 2, or SEQ ID NO: 3 and SEQ ID NO: 4, or SEQ ID NO: 5 and SEQ ID NO: 6, or SEQ ID NO: 7 and SEQ ID NO: 8.
GenBank, in a reasonably pertinent field, teaches on the known sequences of apolipoprotein E (whole document). Dieffenbach, in a reasonably pertinent field, teach parameters and principles of primer design include primer length, terminal nucleotide, GC content, melting temperature, PCR product length, and placement of target sequence (Pages S30-S34). Dieffenbach also teaches PCR software was known (Page S35). In addition, Roux, in a reasonably pertinent field, teaches optimization of PCR by the presence of enhancing agents, Mg2+, annealing temperature, primer design, cycle number, and hot start PCR (Pages S185-S194). Thus, designing oligonucleotides to hybridize to specific targets, which are equivalents to those taught in the art (see Koch and GenBank), is routine experimentation and is a known prior art technique. The prior art teaches the parameters and objectives involved in the selection of oligonucleotides that function as primers (see Dieffenbach and Roux). The prior art is replete with guidance and information necessary to permit the ordinary artisan in the field of nucleic acid detection to design primers.
It would therefore have been obvious one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Koch, in view of Haisong, to further comprise a pair of primers in accordance with the teachings of Koch, GenBank, Dieffenbach, and Roux to arrive at the instantly claimed primers with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because said modification would have resulted in the design and testing of new primers to obtain additional oligonucleotides that function to detect the claimed amino acid residues and identify oligonucleotides with improved properties for such detection. In addition, it would have been obvious to the ordinary artisan that the known techniques of Dieffenbach and Roux could have been applied to the method of Koch, in view of Haisong, with predictable results because the known techniques of Dieffenbach and Roux predictably result in molecules useful for obtaining more sample nucleic acid.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Koch (TaqMan Systems for Genotyping of Disease-Related Polymorphisms Present in the Gene Encoding Apolipoprotein E, Clinical Chemistry and Laboratory Medicine, June 2005, 40, 1123-1131; cited on the IDS filed April 14th, 2023) and Haisong (CN108504731A; cited on the IDS filed May 23rd, 2024, citations made using English translation provided in the file wrapper dated May 23rd, 2024), as applied to claims 1 and 7, and further in view of GenBank (GenBank accession number AF261279.1 [online]. GenBank, [2008] [retrieved on August 6th, 2026]. Retrieved from: https://www.ncbi.nlm.nih.gov/nucleotide/AF261279.1) and Johnson (Application of TaqMan® Chemistry for Allelic Discrimination, DNA Press, 2005, Chapter 11, 237-254).
Regarding instant claim 9, Koch, in view of Haisong, teaches the method for detecting a genetic polymorphism according to Claim 1. Koch further teaches specific probes related to the detection of the known alleles of the 112th and 158th codon of apolipoprotein E (Table 1C: probe pairs 3 and 4). Koch also teaches on the known alterations associated with these codons (Page 1123, column 2, paragraph 2).
Neither reference teaches wherein, in the fluorescent labeled probe, the base sequence of the oligonucleotide that binds to the nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding wild- type Cys which is the 112th amino acid residue of apolipoprotein E, and the base sequence of the oligonucleotide that binds to the nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding mutant Arg which is the 112th amino acid residue of apolipoprotein E, are the base sequences represented by the following SEQ ID NO: 9 and SEQ ID NO: 10, respectively; and the base sequence of the oligonucleotide that binds to the nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding wild-type Arg which is the 158th amino acid residue of apolipoprotein E, and the base sequence of the oligonucleotide that binds to the nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding mutant Cys which is the 158th amino acid residue of apolipoprotein E, are the base sequences represented by the following SEQ ID NO: 11 and SEQ ID NO: 12, respectively.
GenBank, in a reasonably pertinent field, teaches on the known sequences of apolipoprotein E (whole document). Johnson, in a reasonably pertinent field, teaches parameters and principles of TaqMan probe design for allelic discrimination, including terminal nucleotide, nucleotide runs, melting temperature, SNP site, and strand specificity (Page 241 and Page 242, bulleted list). Johnson also teaches TaqMan design software was known (Page 242, paragraph 1). Thus, designing probes to hybridize to specific SNPs, which are equivalents to those taught in the art (see Koch and GenBank), is routine experimentation and is a known prior art technique. The prior art teaches the parameters and objectives involved in the selection of oligonucleotides that function as probes (see Dieffenbach and Roux). The prior art is replete with guidance and information necessary to permit the ordinary artisan in the field of nucleic acid detection to design probes.
It would therefore have been obvious one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Koch, in view of Haisong, to further comprise probes in accordance with the teachings of Koch, GenBank, and Johnson to arrive at the instantly claimed probes with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because said modification would have resulted in the design and testing of new probes to obtain additional oligonucleotides that function to detect the claimed amino acid residues and identify oligonucleotides with improved properties for such detection. In addition, it would have been obvious to the ordinary artisan that the known techniques of Johnson could have been applied to the method of Koch, in view of Haisong, with predictable results because the known techniques of Johnson predictably result in molecules useful for detecting allelic variation (Johnson, Page 241, paragraph 1).
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Koch (TaqMan Systems for Genotyping of Disease-Related Polymorphisms Present in the Gene Encoding Apolipoprotein E, Clinical Chemistry and Laboratory Medicine, June 2005, 40, 1123-1131; cited on the IDS filed April 14th, 2023) and Haisong (CN108504731A; cited on the IDS filed May 23rd, 2024, citations made using English translation provided in the file wrapper dated May 23rd, 2024), as applied to claims 1 and 7, and as further evidenced by/obvious over Johnson (Application of TaqMan® Chemistry for Allelic Discrimination, DNA Press, 2005, Chapter 11, 237-254).
Regarding instant claim 10, Koch, in view of Haisong, teaches the method for detecting a genetic polymorphism of according to Claim 1. Koch further teaches a method for determining a genetic polymorphism of apolipoprotein E present in genomic DNA collected from a subject, comprising a step of obtaining amplification curves based on the 112th amino acid residue and the 158th amino acid residue (Page 1124, column 2, paragraph 4 to Page 1125, column 1, paragraph 2; Figure 2, bottom row).
While Koch does not provide examples of these amplification curves, as evidenced by, and alternatively as obvious over, Johnson, TaqMan probes like those used by Koch produce amplification curves as amplification progresses (Page 239, paragraph 2 to Page 240; Figure 1B, 1C, and 1D and captions). Johnson also teaches that amplification curves can discriminate alleles and be used to determine genotype (Page 240; Figures 1B, 1C, and 1D and captions). Therefore, Johnson both provides evidence for and makes obvious that the method of Koch produces amplification curves that can be used for genotyping apolipoprotein E. This information is processed by the ABI PRISM 7700 Sequence Detection System, which automatically calls genotypes, as taught by Koch (Page 1125, column 1, paragraph 2).
Given the evidence and teaching of Johnson, as well as Koch’s exemplified ability to determine genotype of apolipoprotein E in unknown genotypes (Figure 2 and caption; Table 5B), Koch teaches step 2. of claim 10, comprising:
2. (a) a step of determining the genetic polymorphism to be apolipoprotein E3/E3, when a substantial increase is observed only in the fluorescence intensity derived from a fluorescent labeled probe which has an oligonucleotide that binds to a nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding wild-type Cys (112th Cys probe), but not in the fluorescence intensity derived from a fluorescent labeled probe which has an oligonucleotide that binds to a nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding mutant Arg (112th Arg probe), in the amplification curve based on the 112th amino acid residue obtained in the step 1, and in addition, a substantial increase is observed only in the fluorescence intensity derived from a fluorescent labeled probe which has an oligonucleotide that binds to a nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding wild-type Arg (158th Arg probe), but not in the fluorescence intensity derived from a fluorescent labeled probe which has an oligonucleotide that binds to a nucleic acid fragment of the apolipoprotein E gene, containing a codon encoding mutant Cys (158th Cys probe), in the amplification curve based on the 158th amino acid residue obtained in the step 1 (Figure 2 and caption; Table 5B);
(b) a step of determining the genetic polymorphism to be apolipoprotein E2/E2, when a substantial increase is observed only in the fluorescence intensity derived from the 112th Cys probe, but not in the fluorescence intensity derived from the 112th Arg probe, in the amplification curve based on the 112th amino acid residue obtained in the step 1, and in addition, a substantial increase is not observed in the fluorescence intensity derived from the 158th Arg probe, but observed only in the fluorescence intensity derived from the 158th Cys probe, in the amplification curve based on the 158th amino acid residue obtained in the step 1 (Figure 2 and caption; Table 5B);
(c) a step of determining the genetic polymorphism to be apolipoprotein E2/E3, when a substantial increase is observed only in the fluorescence intensity derived from the 112th Cys probe, but not in the fluorescence intensity derived from the 112th Arg probe, in the amplification curve based on the 112th amino acid residue obtained in the step mentioned 1, and in addition, a substantial increase is observed in the fluorescence intensity derived from the 158th Arg probe as well as in the fluorescence intensity derived from the 158th Cys probe, in the amplification curve based on the 158th amino acid residue obtained in the step 1 (Figure 2 and caption; Table 5B);
(d) a step of determining the genetic polymorphism to be apolipoprotein E4/E4, when a substantial increase is not observed in the fluorescence intensity derived from the 112th Cys probe, but a significant increase is observed only in the fluorescence intensity derived from the 112th Arg probe, in the amplification curve based on the 112th amino acid residue obtained in the step 1, and in addition, a substantial increase is observed only in the fluorescence intensity derived from the 158th Arg probe, but not in the fluorescence intensity derived from the 158th Cys probe, in the amplification curve based on the 158th amino acid residue obtained in the step 1 (Figure 2 and caption; Table 5B);
(e) a step of determining the genetic polymorphism to be apolipoprotein E3/E4, when a substantial increase is observed both in the fluorescence intensity derived from the 112th Cys probe and in the fluorescence intensity derived from the 112th Arg probe, in the amplification curve based on the 112th amino acid residue obtained in the step 1, and in addition, a substantial increase is observed only in the fluorescence intensity derived from the 158th Arg probe, but not in the fluorescence intensity derived from the 158th Cys probe, in the amplification curve based on the 158th amino acid residue obtained in the step 1 (Figure 2 and caption; Table 5B);
(f) a step of determining the genetic polymorphism to be apolipoprotein E2/E4, when a substantial increase is observed both in the fluorescence intensity derived from the 112th Cys probe and in the fluorescence intensity derived from 112th Arg probe, in the amplification curve based on the 112th amino acid residue obtained in the step 1, and in addition, a substantial increase is observed both in the fluorescence intensity derived from the 158th Arg probe and in the fluorescence intensity derived from the 158th Cys probe, in the amplification curve based on the 158th amino acid residue obtained in the step 1 (Figure 2 and caption; Table 5B).
Conclusion
All claims stand rejected.
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/ALLISON E SCHLOOP/Examiner, Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683
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