DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restriction
2. Applicant’s election without traverse of “HCV” as the pathogen for examination in the reply filed on April 27, 2026 is acknowledged.
All of the pending claims (i.e., claims 1-15) read on the elected species and are examined on the merits herein.
Information Disclosure Statement
3. Applicant’s submission of an Information Disclosure Statement on January 10, 2025 is acknowledged. All of the cited references have been considered.
Drawings
4. 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).
In this case, in the drawings filed on December 22, 2023, Figures 3, 7, 11, and 12 contain color (see the document with the document code “DRW.SUPP”), but the requirements for color drawings set forth above have not been satisfied.
Accordingly, the drawings filed on December 22, 2023 are objected to.
Specification
5. The specification is objected to because it fails to provide support for the subject matter of all of the original claims. In particular, the specification fails to provide support for the subject matter of original claim 14, which requires the DNA extracted from the urine sample to be intracellular DNA or extracellular DNA. The specification only provides support for extracting DNA from cells or pathogens in a urine sample (see, e.g., para. 75), but extracting cell-free DNA from the urine sample, as also encompassed by original claim 14, is not described.
It is noted that this is not a new matter issue since the original claims are part of the original disclosure. See, e.g., MPEP 2163.06 III. And, as also discussed in MPEP 2163.06 III, the specification may be amended to provide support for the subject matter of original claims without introducing new matter.
Claim Objections
6. Claim 3 is objected to because of the following minor informality. Amending the claim to replace the capitalization at the beginning of each step (i.e., “Providing,” “Extracting,” “Subjecting,” and “Testing”) with lower-case letters is suggested to maintain consistency with claim 1.
Claim 10 is objected to because “the system” in line 1 should be replaced with “the automated system” to maintain consistency with claim 9.
Claim 13 is objected to because it contains a typographical error in line 1 where “where in” is recited for “wherein.”
Claim Rejections - 35 USC § 112
7. 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 1-15 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 enablement requirement. The claims contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). These factors include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative
skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims. Each of these factors is discussed below.
Nature of the Invention
The instant claims are drawn to a method for detecting the presence of a pathogen in a urine specimen from a patient. The method comprises extracting DNA in the urine specimen, amplifying the extracted DNA, and testing the amplified DNA for the presence or absence of the pathogen.
Applicant has elected “HCV” as the species of pathogen for examination.
The claimed invention is classified in the unpredictable arts of molecular biology and biochemistry.
Relative Skill of the Ordinary Artisan
The ordinary artisan typically holds a graduate degree and has at least several years of post-graduate laboratory and/or clinical experience.
Breadth of the Claims
Several aspects of the claims are very broad. In particular, the patient is not limited and encompasses human and animal subjects. As well, the extraction and testing steps are broadly written, encompassing any method of extracting DNA from a urine specimen and testing DNA amplified from the extracted DNA for the presence or absence of the pathogen. The amplification step is similarly broad, except for dependent claim 6, which requires PCR amplification. The pathogen is limited by the species election to HCV.
State of the Prior Art
The prior art teaches that HCV has an RNA genome and is directly translated. See, e.g., Holland and Pribyl at page 263, col. 1.1 In other words, a patient sample containing HCV particles/nucleic acids will have HCV RNA, but not HCV DNA. All of the claims, though, require extracting DNA from the patient sample and then amplifying the extracted DNA to test for the presence or absence of HCV in the patient sample.
The prior art also discloses amplification methods for detecting the presence of HCV, including in urine samples. See, e.g., Attallah et al. (Clinica Chimica Acta 2004; 346: 171-179) at sections 2.3-2.4. See also Lu et al. (Journal of Medical Virology 2018; 91: 115-123) at sections 2.3-2.4. See also Holland and Pribyl at pages 266-268 and also Villar et al. (World Journal of Virology 2015; 4: 323-342) at Table 4 on page 330 for a general review of methods for detecting HCV by nucleic acid amplification. All of these methods begin with HCV RNA rather than HCV DNA as required by the claims in view of the species election.
Thus, the prior art fails to describe extracting HCV DNA from a urine sample and amplifying said extracted HCV DNA as required by the claims in view of the species election.
Guidance Presented in the Application & Working Examples
The specification contains guidance relevant to the claimed methods. For example, in paras. 88-106, the specification provides guidance as to urine sample collection and the use of a commercially available system to amplify and detect HCV as well as guidance as to useful reaction conditions for amplification reactions.
Working Example 1, which appears on pages 19-25, is relevant to the claims in view of the species election since it describes using amplification to detect the presence of HCV in a urine sample. The example does not remedy the deficiency in the prior art, though, because it fails to describe amplifying and detecting HCV DNA extracted from a urine sample and instead states that the Cobas® system used in the method reports “HCV RNA detected” (page 20, para. 125; see also pages 22-23, para. 134 and page 24, para. 140). The example also reports detecting the presence or absence of HCV by performing RT-PCR (i.e., beginning the amplification step with an RNA template), rather than via PCR using a DNA template (pages 21-22, para. 128).
Thus, although the specification provides some guidance as to the claimed methods, it does not remedy the deficiency in the prior art concerning amplifying and detecting HCV DNA extracted from a urine sample.
Quantity of Experimentation & Unpredictability
In view of the limitations in the specification and prior art, the ordinary artisan would have to conduct a very large quantity of highly unpredictable experimentation to enable practice of the claimed methods. In particular, the ordinary artisan would have to determine that, contrary to the teachings in the prior art, HCV DNA can be extracted from a urine sample and amplified. The required experimentation would be highly unpredictable and inventive in nature since there is nothing in the prior art or the specification to indicate that HCV DNA exists in nature at all, let alone in a urine sample. Thus, the required experimentation would have to be conducted in the absence of any guidance from the specification and prior art and in spite of contrary teachings in the prior art and specification. Thus, it is clear that undue experimentation would be required to practice the claimed methods, and claims 1-15 are rejected as lacking enablement.
Claim Rejections - 35 USC § 112
8. 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 1-15 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1
Claim 1 is indefinite because it is unclear as to how “providing a urine specimen from a patient” can be performed without manual manipulation as required by the last line of the claim. Instead, it seems that at least some sort of manual step(s) would be required to provide the required specimen. Therefore, it is not clear whether (i) claim 1 contains a typographical error in the last line with “steps a-d” recited for “steps b-d”, or (ii) if Applicant intends to somehow provide a urine specimen from a patient without any sort of manual steps. And, if the latter is the correct interpretation, it is unclear as to how this step could be accomplished.
Claim 1 is also indefinite because its requirements are not entirely clear in view of claim 15, which depends from claim 1 or claim 3. Claim 1 is drawn to a method for testing for the presence of a pathogen in a patient sample and recites the following steps: (i) providing a urine specimen from a patient, (ii) extracting DNA from the urine specimen, (iii) amplifying the extracted DNA, and (iv) testing the amplified DNA for the presence or absence of the pathogen.
These steps strongly suggest that the DNA extracted from the urine specimen and subjected to amplification and testing includes DNA from the pathogen if the pathogen is present in the urine specimen. In other words, claim 1 would be reasonably interpreted as determining the presence of the pathogen when the amplified DNA includes DNA from the pathogen.
Claim 15, though, casts doubt on this interpretation of claim 1 by reciting “wherein the DNA is from the pathogen.” It is unclear whether (i) claim 15 is simply not further limiting and reciting something already required by claim 1, or (ii) if claim 1 encompasses indirect detection of the pathogen (e.g., by detecting a nucleic acid that is not from the pathogen but indicates its presence in the urine specimen). Therefore, claim 1 is indefinite for this additional reason.
Claim 3
Claim 3 is indefinite because of the recitation “wherein the pathogen is HIV, HCV, HSV, and/or syphilis,” which appears in the last line of the claim. More specifically, it is not clear how “the pathogen” recited in this line can be, e.g., HIV and syphilis, as encompassed by the “and/or” language. This also creates uncertainty as to whether the method of claim 3 must be capable of testing for multiple different pathogens because all of the claim language other than the last line indicates that the method only needs to be capable of testing for the presence of a pathogen.
Claim 3 is also indefinite because its requirements are not entirely clear in view of claim 15, which depends from claim 1 or claim 3. Claim 3 is drawn to a method for testing for the presence of a pathogen in a patient sample and recites the following steps: (i) providing a urine specimen from a patient, (ii) extracting DNA from the urine specimen, (iii) amplifying the extracted DNA, and (iv) testing the amplified DNA for the presence or absence of the pathogen.
These steps strongly suggest that the DNA extracted from the urine specimen and subjected to amplification and testing includes DNA from the pathogen if the pathogen is present in the urine specimen. In other words, claim 3 would be reasonably interpreted as determining the presence of the pathogen when the amplified DNA includes DNA from the pathogen.
Claim 15, though, casts doubt on this interpretation of claim 3 by reciting “wherein the DNA is from the pathogen.” It is unclear whether (i) claim 15 is simply not further limiting and reciting something already required by claim 3, or (ii) if claim 3 encompasses indirect detection of the pathogen (e.g., by detecting a nucleic acid that is not from the pathogen but indicates its presence in the urine specimen). Therefore, claim 3 is indefinite because its requirements are not entirely clear.
Claims 2 and 4-15
Claims 2 and 4-15 are also indefinite since they depend from claim 1 or claim 3 and do not correct all of their indefiniteness issues.
Claim 10
Claim 10 is also indefinite for an additional reason. More specifically, claim 10 contains the trademark/trade name COBAS. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a particular type of automated system, and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 112
9. The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 14 and 15 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 14 depends from claim 1 or claim 3 and requires the DNA extracted from the urine specimen to be extracellular DNA or intracellular DNA. This is not further limiting because it encompasses all possible options for the DNA in the urine specimen. In other words, the DNA in the urine specimen is necessarily either contained in a cell or not contained in a cell. Therefore, claim 14 adds nothing relative to claim 1 or claim 3. One way to address the issue would be to present the two options in separate dependent claims.
Claim 15 depends from claim 14 and recites “wherein the DNA is from the pathogen.” As discussed above, claims 1 and 3, from which claim 15 ultimately depends, are indefinite, but one possible interpretation is that claims 1 and 3 require extracting, amplifying, and testing DNA from a pathogen. If this interpretation is correct, claim 15 is not further limiting because its requirements are already present in claims 1 and 3.
Applicant may cancel the claims, amend the claims to be in proper dependent form, or present a sufficient showing that the dependent claims comply with the statutory requirements.
Conclusion
10. No claims are currently allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Angela Bertagna whose telephone number is (571)272-8291. The examiner can normally be reached 8-5, M-F.
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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1681
1 Holland, C.A. and Pribyl, T.M. “Molecular Diagnostics for the Hepatitis C Virus” in: Grody, W.M., Nakamura, R.M., Kiechle, F.L, & Strom, C, Molecular Diagnostics: Techniques and Applications for the Clinical Laboratory 1 ed (Academic Press, 2010), pp. 263- 275.
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