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 .
Election/Restrictions
Restriction to one of the following inventions is required under 35 U.S.C. 121:
I. Claims 1-13, drawn to a method for detecting and/or identifying bacterial vaginosis (BV), Candida spp., Trichomonas vagina/is, or a combination thereof in a biological sample obtained from a subject, classified in C12Q 2600/16.
II. Claims 14-26, drawn to a cartridge for performing a multiplex vaginal panel (MVP) for identifying bacterial vaginosis, Candida spp., Trichomonas vagina/is, or a combination thereof in a subject, classified in C12Q 2565/629.
lll. Claims 27-28, drawn to a system for performing a multiplex vaginal panel (MVP) for identifying bacterial vaginosis, Candida spp., Trichomonas vaginalis, or a combination thereof in a subject, classified in C12Q 2565/101.
The inventions are independent or distinct, each from the other because:
Inventions Group l and Group ll are related as process and apparatus for its practice. The inventions are distinct if it can be shown that either: (1) the process as claimed can be practiced by another and materially different apparatus or by hand, or (2) the apparatus as claimed can be used to practice another and materially different process. (MPEP § 806.05(e)). In this case the cartridge can be used to perform a method of detecting
Inventions Group ll and Group lll are related as product and process of use. The inventions can be shown to be distinct if either or both of the following can be shown: (1) the process for using the product as claimed can be practiced with another materially different product or (2) the product as claimed can be used in a materially different process of using that product. See MPEP § 806.05(h). In the instant case , the system can be programmed to perform a different protocol for DNA sequencing detection.
Inventions Group l and Group lll are directed to related processes. The related inventions are distinct if: (1) the inventions as claimed are either not capable of use together or can have a materially different design, mode of operation, function, or effect; (2) the inventions do not overlap in scope, i.e., are mutually exclusive; and (3) the inventions as claimed are not obvious variants. See MPEP § 806.05(j). In the instant case, the inventions as claimed have different functions (method of detection versus system for analysis). Furthermore, the inventions as claimed do not encompass overlapping subject matter and there is nothing of record to show them to be obvious variants.
Restriction for examination purposes as indicated is proper because all the inventions listed in this action are independent or distinct for the reasons given above and there would be a serious search and/or examination burden if restriction were not required because one or more of the following reasons apply:
a) the inventions have acquired a separate status in the art in view of their different
classification;
(b) the inventions have acquired a separate status in the art due to their recognized
divergent subject matter; and/or
(c) the inventions require a different field of search (e.g., searching different
classes/subclasses or electronic resources, or employing different search strategies or
search queries).
Applicant is advised that the reply to this requirement to be complete must include (i) an election of an invention to be examined even though the requirement may be traversed (37 CFR 1.143) and (ii) identification of the claims encompassing the elected invention.
The examiner has required restriction between product or apparatus claims and process claims. Where applicant elects claims directed to the product/apparatus, and all product/apparatus claims are subsequently found allowable, withdrawn process claims that include all the limitations of the allowable product/apparatus claims should be considered for rejoinder. All claims directed to a nonelected process invention must include all the limitations of an allowable product/apparatus claim for that process invention to be rejoined.
In the event of rejoinder, the requirement for restriction between the product/apparatus claims and the rejoined process claims will be withdrawn, and the rejoined process claims will be fully examined for patentability in accordance with 37 CFR 1.104. Thus, to be allowable, the rejoined claims must meet all criteria for patentability including the requirements of 35 U.S.C. 101, 102, 103 and 112. Until all claims to the elected product/apparatus are found allowable, an otherwise proper restriction requirement between product/apparatus claims and process claims may be maintained. Withdrawn process claims that are not commensurate in scope with an allowable product/apparatus claim will not be rejoined. See MPEP § 821.04. Additionally, in order for rejoinder to occur, applicant is advised that the process claims should be amended during prosecution to require the limitations of the product/apparatus claims. Failure to do so may result in no rejoinder. Further, note that the prohibition against double patenting rejections of 35 U.S.C. 121 does not apply where the restriction requirement is withdrawn by the examiner before the patent issues. See MPEP § 804.01.
During a telephone conversation with Joseph Murphy on 10/21/2025 a provisional election was made without traverse to prosecute the invention of Group ll drawn to the cartridge, claims 14-26. Affirmation of this election must be made by applicant in replying to this Office action. Claims 1-13 and 27-28 are withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to a non-elected invention.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on December 8th, 2023 has been considered by the examiner. The Non-Patent Literature document “BD Max System Benutzerhandbuch” is not filed in English and therefore has not been 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 were filed in the application without an accompanying petition, proper correction is required.
Specification
The use of the terms Armored RNA®, GENEXPERT®, TAQMAN®, SCORPION®, MOLECULAR BEACON®, TRITON®, PLURONIC®, TWEEN®, which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore, the term 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 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 16-18, 23, 24 and 26 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.
Regarding Claim 16, the use of the term” the chambers” is indefinite in that it is not clear which chambers are to be connected, in reference to independent claim 14 which states “a plurality of chambers”. Claims 17 and 18 are rejected in view of their dependency on 16 as they do not further rectify the indefiniteness issue.
Regarding Claims 23 and 26, the use of the term “preferably” is indefinite as it is unclear if the limitations further limit the scope of the independent claim.
Regarding Claim 24, the use of the term “hypothetical protein” is indefinite in that one skilled in the art would not know what hypothetical proteins are relevant to identifying Candida krusei to target for detection.
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.
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.
Claim(s) 14-16,21-23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Klapperich (US 20100203521 A1) in view of Paquette (WO 2016172204 A1; cited on IDS filed December 8th, 2023).
Regarding Claims 14 and 15, Klapperich teaches a cartridge body having a plurality of chambers defined therein, wherein the plurality of chambers are in fluidic communication through a fluidic path of the cartridge ([0029]), a reaction vessel configured for amplification of the nucleic acid by thermal cycling ([0037]; [0112]) and comprising a reaction chamber, wherein the reaction vessel comprises at least one amplification region and is attached to the cartridge body and fluidically coupled to the fluidic path of the cartridge [0115]); and a filter disposed in the fluidic path between the plurality of chambers and the reaction vessel ([0055]); wherein the plurality of chambers and/or the reaction chamber independently comprise lysis reagents for releasing nucleic acid from a sample ([0029]). The plurality of chambers include: a sample chamber having at least a fluid outlet in fluid communication with another chamber of the plurality ([0068]; [0313]); and a lysis chamber in fluidic communication with the sample chamber, the lysis chamber comprising lysis reagents for releasing nucleic acid, optionally wherein the sample chamber and lysis chamber are the same ([0029]).
Klapperich fails to teach performing a multiplex vaginal panel (MVP) for identifying bacterial vaginosis, Candida spp., Trichomonas vaginalis, or a combination thereof in a subject, and at least one amplification region comprises primers and probes for amplification and detection of DNA sequences characteristic of BVAB2, Megasphaera-1, Atopobium spp., Candida spp., and Trichomonas vaginalis.
However, Paquette teaches primers and probes that can bind to specific genes for detection of VVC-associated Candida species, Trichomonas vaginalis (T. vaginalis) and a plurality of BV-related bacteria in biological examples, such as vaginal swab samples from women with clinical symptoms of vaginitis and/or vaginosis, by nucleic acid-based test methods. ([0030])
PNG
media_image1.png
524
638
media_image1.png
Greyscale
In regard to Claim 16, Klapperich teaches a valve assembly configured to rotate and having at least two ports to fluidically connect the chambers ([FIG. 1]). An area of inlet and outlet is acknowledged by the arrows in Figure 1 for connection between channels ([0054], [0055]).
Regarding Claims 21 and 22, Klapperich teaches on the cartridge of claim 14 wherein the reaction vessel comprises one amplification region for analyzing a nucleic acid and at least 2 independent amplification regions. The embodiment of Klapperich as shown in FIG.1, contains a plurality of amplification PCR regions for analyzing nucleic acids ([0037]).
Regarding Claim 23, Klapperich fails to teach lyophilized reagents, however, Paquette teaches at least one of the plurality of chambers comprises lyophilized reagents, preferably wherein the lyophilized reagents is in the form of one or more beads ([0052]).
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 Klapperich to incorporate the teachings of Paquette, resulting in an efficient method of detection in which the vaginal disorders of Paquette (VVC-associated Candida species, Trichomonas vaginalis (T. vaginalis) and a plurality of BV-related bacteria) are combined with the cartridge of Klapperich to generate a product for biological testing in a singular assay.
Claim(s) 17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Klapperich (US 20100203521 A1) and Paquette (WO 2016172204 A1;cited on IDS filed December 8th,2023) as applied to claims 14-16 and 21-23 above and further in view of Acquah (Acquah, et. al, Journal of Chromatography B, 2016).
Claims 14-16 and 21-23 have been discussed above.
Regarding Claim 17, the cartridge of claim 16, wherein the valve assembly is resistant to alkali corrosion. Klapperich teaches a device with porous monolithic columns embedded with carbon particles (carbon nanotubes) used for cell lysis [0032].
The Lysis and filtration region of the embodiment lyses the cells and outputs nucleic acids suspended in a complex mixture. The filtration module filters the complex mixture, leaving only small molecules such as proteins and nucleic acids to move on to the extraction and isolation module [0068]. Klapperich further recites an outlet of the filter membrane is connected to the inlet of the channel comprising the monolith embedded with carbon particles, and wherein a sample can be passed through the filter membrane prior to the channel comprising the carbon embedded monolith [0055]. As indicated by Klapperich, preferred substrates for forming channel or tube surfaces, are selected from the group consisting of poly(methyl methacrylate), poly(butyl methacrylate), poly(dimethylsiloxane), poly(ethylene terephthalate), poly(butylene terephthalate), hydrogenated polystyrene, polyolefins such as, cyclic olefin copolymer, polyethylene, polypropylene, and polyimide [0197].
Acquah recites amongst organic monoliths, polymethacrylate and polystyrene monoliths demonstrate unique physicochemical properties, such as good resistance to pH and resistant to some alkaline solvents [sec.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 Klapperich and Paquette to incorporate the teachings of Acquah to produce a valve assembly that is resistant to alkali corrosion resulting from continuous exposure to alkaline lysis reagents within the cartridge.
Claim(s) 18 is/ are rejected under 35 U.S.C. 103 as being unpatentable over Klapperich (US 20100203521 A1) and Paquette (WO 2016172204 A1; cited on IDS filed December 8th,2023) as applied to claims 14-16 and 21-23 above and further in view of Sepe (Michael Sepe, Materials: Annealing Tips for Amorphous Polymers, Part 2 , 2020).
Claims 14-16 and 21-23 have been discussed above.
Regarding Claim 18, the cartridge of claim 16, wherein the valve assembly is derived from a polycarbonate material annealed at a temperature of at least 100° C for at least 1 hour. Sepe teaches an appropriate annealing temperature for polycarbonate between 121° C and 135° C at minimum 30 min (par. 6)
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 Klapperich and Paquette to incorporate the teachings of Sepe to produce a polycarbonate valve assembly that aims to reduce high levels of internal stress and ductility by slowly cooling the material over a longer period of time.
Claim(s) 19 is/ are rejected under 35 U.S.C. 103 as being unpatentable over Klapperich (US 20100203521 A1) and Paquette (WO 2016172204 A1; cited on IDS filed December 8th,2023) as applied to claims 14-16 and 21-23 above and further in view of Selden (US 20150259672) and Ausubel (Ausubel et al., Current Protocols in Molecular Biology, 2003)
Claims 14-16 and 21-23 have been discussed above.
Regarding Claim 19, Selden teaches a cartridge using lysis reagents comprising a guanidinium compound, EDTA, a buffer, and a detergent ([0149]).
Selden fails to specifically teach the use of sodium hydroxide in the lysis buffer. However, Ausubel, teaches alkaline lysis procedure for bacterial lysing with a solution containing sodium hydroxide for the denaturation of chromosomal and plasmid DNA, as commonly known within the art (pg.80/Unit 1.6).
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 Klapperich and Paquette, to have incorporated the materials of Selden and Ausubel for the lysis solution as a component of the sample preparation method prior to testing.
Claim(s) 20 is/ are rejected under 35 U.S.C. 103 as being unpatentable over Klapperich (US 20100203521 A1) and Paquette (WO 2016172204 A1; cited on IDS filed December 8th,2023) as applied to claims 14-16 and 21-23 above and further in view of DeJohn (US20200276582A1).
Claims 14-16 and 21-23 have been discussed above.
Regarding Claim 20, wherein the sodium hydroxide is isolated from the lysis reagents in one of the plurality of chambers prior to lysing the sample. DeJohn recites “An example of a lysis buffer is sodium hydroxide (NaOH).” ([0081]) and that filling the sample chamber with a buffer (e.g., a lysis buffer) prior to adding the sample may prevent loss of target nucleic acids within the sample (e.g., due to adhesion along the wall of the sample chamber) ([0062]).
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 Klapperich and Paquette to incorporate the teaching of DeJohn by isolating the NaOH buffer in a separate chamber prior to lysing to preserve nucleic acids within a biological sample.
Claim(s) 25 is/ are rejected under 35 U.S.C. 103 as being unpatentable over Klapperich (US 20100203521 A1) and Paquette (WO 2016172204 A1; cited on IDS filed December 8th,2023) as applied to claims 14-16 and 21-23 above and further in view of Jainlabdin (Jainlabdin et. al, Scientific Reports, 2019).
Claims 14-16 and 21-23 have been discussed above.
Regarding Claim 25, the cartridge of claim 14, wherein the cartridge further comprises primers and probes to amplify and detect nucleic acid sequences characteristic of antifungal resistant Candida spp. comprising Candida glabrata and Candida krusei in a subject. Jainlabdin teaches a Multiplex Probe Amplification (MPA) based assay for the identification of invasive Candida strains, including three species-specific biomarker probes for individual identification of multidrug-resistant C. auris, C. glabrata and C. krusei (pg.2/par.3). Figure 1 (pg.2) illustrates the relative position of amplification primers and probes along the fungal ribosomal genes.
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 Klapperich and Paquette to incorporate the teaching of Jainlabdin to result in a singular cartridge for biological testing capable of accurate identification and detection of anti-fungal resistant Candida spp. to administer effective treatment and improve patient outcome.
Claim(s) 26 is/ are rejected under 35 U.S.C. 103 as being unpatentable over Klapperich (US 20100203521 A1) and Paquette (WO 2016172204 A1; cited on IDS filed December 8th,2023) as applied to claims 14-16 and 21-23 above and further in view of IDEXX (IDEXX Laboratories Inc., 2021).
Claims 14-16 and 21-23 have been discussed above.
Regarding Claim 26, the cartridge of claim 14, wherein each component of the cartridge is stable from 2-30°C for at least 5 months, preferably each component of the cartridge is stable at ambient temperature (about 25°C) for at least 9 months, more preferably each component of the cartridge is stable at ambient temperature (about 25°C) for at least 12 months. IDEXX Laboratories teaches a testing device for screening six vector-borne disease-causing pathogens in dogs, with a cartridge comprising stabilized components that can be stored from 2-25°C for 6 months (pg.5).
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 Klapperich and Paquette to incorporate the teaching of IDEXX to enhance the stability of the cartridge components for improved storage.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Avanda Harvey-Butler whose telephone number is (571)272-6511. The examiner can normally be reached M-F, 9-5 ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571) 272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/AVANDA E. HARVEY-BUTLER/ Examiner, Art Unit 1683
/ANNE M. GUSSOW/ Supervisory Patent Examiner, Art Unit 1683