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 .
Priority
This application is a CON of 17/054,293 file 11/10/2020 which is a 371 of PCT/US2019/032227 05/14/2019 which claims benefit of 62/671,389 filed 05/14/2018.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 1/16/2025 and 9/27/2023 is acknowledged and has been considered. However, citation 21 on page 9 of the IDS filed 1/16/2025 (14 pages document) has been lined through because no translation is provided for the document and the citation on the IDS does not include a publication date.
Drawings
The drawings were received on 9/18/2023. These drawings are found acceptable to the examiner.
Specification
The disclosure is objected to because of the following informalities:
(a) The use of the term ”MagPix” at para. [0078] which is a trade name or a mark used in commerce, has been noted in this application. The term 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.
Appropriate 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.
Claim 2 is 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.
(a) Claim 2 is indefinite at the recitation of “preferably” because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
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 1-3 are rejected under 35 U.S.C. 101 because they are not directed to patent eligible subject matter. Based upon an analysis with respect to the claims as a whole, claims 1-3 do not recited something significantly different than a judicial exception (nature-based products, specifically naturally occurring nucleic acids). The rationale for this determination is explained below: The claims are directed to an oligonucleotide probe set comprising a capture probe and a detector probe, the capture probe and detector probe each being adapted to selectively hybridize to a first target sequence of rRNA molecules released from the first target microbe (claim 1). The claim 2 recites that the probe set is adapted to selectively bind to rRNA molecules released from a pre-determined microorganism. The claim 3 recites wherein the oligonucleotide probe set is adapted to hybridize with rRNA molecules released from substantially all eubacteria (EU) or similar microbes. The probes of claims 1-3 encompass oligonucleotide sequences that are not markedly different from its naturally occurring counterparts (microbial sequences). Likewise, none of the claims recited above comprise of additional elements that are sufficient to amount to significantly more than the judicial exception. See, e.g., University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 760, 113 USPQ2d 1241, 1241 (Fed. Cir. 2014) (comparing single-stranded nucleic acid to the same strand found in nature, even though "single-stranded DNA cannot be found in the human body"). See also, e.g., Funk Bros., 333 U.S. at 130, 76 USPQ at 281 (comparing claimed mixture of bacterial species to each species as it occurs in nature); Ambry Genetics, 774 F.3d at 760, 113 USPQ2d at 1244 (although claimed as a pair, individual primer molecules were compared to corresponding segments of naturally occurring gene sequence). Accordingly, these claims lack subject matter eligibility under 35 USC 101.
Claim Rejections - 35 USC § 102
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 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-18 is/are rejected under 35 U.S.C. 102(a)(1) and/or alternatively 35 U.S.C. 102(a)(2) as being anticipated by Haake et al {Haake, used interchangeably} (US 200801998963, August 21, 2008, effective filing date May 2007).
Regarding claim 1, Haake teaches an oligonucleotide probe set for use in identifying a first target microbe in a specimen, wherein the oligonucleotide probe set comprises a capture probe and a detector probe, the capture probe and detector probe each being adapted to selectively hybridize to a first target sequence of rRNA molecules released from the first target microbe (para. [0010]-[0011], [0014], [0018], -[0020], [0023], [0063]-[0064], [0101], [0102], see also Tables and figures).
Regarding claim 2, Haake et al teach the oligonucleotide probe set wherein the probe set is adapted to selectively bind to rRNA molecules released from a pre- determined microorganism (para. [0010]-[0011], [0014], [0018], -[0020], [0023], [0063]-[0064], [0101], [0102], see also Tables and figures).
Regarding claim 3, the specification notes at e.g., paragraphs [0041] and [0043], that the probes sets is designed to hybridize to 16S rRNA sequences. 16S rRNA sequences are well-known to be present in bacterial species. Haake discloses an oligonucleotide probe set wherein the oligonucleotide probe set is adapted to hybridize with rRNA molecules released from substantially all eubacteria (EU) or similar microbes, i.e., 16S rRNA ([0018], [0040], [0073] (see also Tables and figures).
Regarding claim 4, Haake et al teach a probe panel disposed on a substrate, the probe panel comprising a plurality of detection regions, each detection region comprising an oligonucleotide probe set configured to selectively bind to RNA molecules released from a pre-determined microorganism, each detection region comprising a different oligonucleotide probe set ([0010]-[0011], [0014], [0018], -[0020], [0023], [0063]-[0064], [0101], [0102], see also Tables and figures).
Regarding claim 5, Haake teaches probe panel wherein each oligonucleotide probe set comprises a first capture probe having an oligonucleotide adapted to hybridize with a first target sequence of the rRNA molecules of the pre-determined microorganism, and a first detector probe having a detectably labeled oligonucleotide adapted to hybridize with a second sequence of the rRNA molecules of the pre-determined microorganism ([0162] and [0168]).
Regarding claim 6, Haake et al teach the probe panel wherein the pre-determined microorganism is selected from the group consisting of: E. coli, P. mirabilis, P. aeruginosa, Enterococcus spp., Acinetobacter baumannii, Serratia marcescens, Stenotrophomonas maltophilia, the Klebsiella-Enterobacter group, and the Enterobacteriaceae group and other Gran-positive bacteria [0063] – [0064] and Tables 1, 3-70.
Regarding claim 7, Haake et al teach the probe panel wherein the substrate comprises at least one of a plastic (para. [0023], [0089], [0090]).
Regarding claim 8, Haake et al teach the oligonucleotide probe set wherein the oligonucleotide probe set further comprises a helper probe adapted to hybridize with a helper sequence of the capture probe to help immobilize the capture probe ([0213]).
Regarding claims 9-10, Haake et al the oligonucleotide probe set wherein the oligonucleotide probe set is adapted to hybridize 16S rRNA sequences or 23S rRNA sequences ([0018] and [0073]).
Regarding claims 11-13, Haake et al teach the probe panel wherein the number of detection regions is at least 16 (see figure 1, [0172], [0200]).
Regarding claim 14, Haake et al teach a system for identifying at least two microbes in a specimen, the system comprising:(a) the probe panel of claim 4; and (b) a detection apparatus configured to detect hybridized complexes present in any detection regions of the probe panel (Figure 1, [102] – [0106], [0162], [0173], [0183], [0209]).
Regarding claim 15, Haake et al teach system wherein the detection apparatus comprises a plurality of sensors, each sensor associated with a single detection region and configured to detect a signal from a hybridized complex when present in the single detection region ([0023], [0035], [0045], [0084], [0099]).
Regarding claim 16, Haake et al teach the system wherein the plurality of sensors is operable simultaneously (Figure 1, [0073], [0165], [0199]).
Regarding claim 17, Haake et al teach the system wherein the detection apparatus comprises a single sensor, movable to be associated with each detection region and configured to detect a single from a hybridize complex when present in a detection region proximal to the single sensor (Figure 1, [0023], [0030], [0089]).
Regarding claim 18, Haake et al teach the system wherein the specimen is selected from the group consisting of urine, blood, saliva, sputum, semen, cerebrospinal fluid, prostatic secretion ( [021]). Thus, Haake meets the limitation of the claims recited above.
Claim(s) 1-4, 6-7, 9-16 and 18 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Li et al {Li, used interchangeably herein} (SLAS Technology, vol. 22(6): 585-608, 2017).
Regarding claim 1, Li teaches an oligonucleotide probe set for use in identifying a first target microbe in a specimen, wherein the oligonucleotide probe set comprises a capture probe and a detector probe, the capture probe and detector probe each being adapted to selectively hybridize to a first target sequence of rRNA molecules released from the first target microbe (page 594-595, especially Figure 3 and Legend).
Regarding claim 2, Li et al teach the oligonucleotide probe set wherein the probe set is adapted to selectively bind to rRNA molecules released from a pre- determined microorganism (page 594-595, especially Figure 3 and Legend).
Regarding claim 3, the specification notes at paragraphs [0041] and [0043], that the probes sets is designed to hybridize to 16S rRNA sequences. 16S rRNA sequences are well-known to be present in bacterial species. Li discloses an oligonucleotide probe set wherein the oligonucleotide probe set is adapted to hybridize with rRNA molecules released from substantially all eubacteria (EU) or similar microbes, i.e., 16S rRNA (page 594-595, especially Figure 3 and Legend).).
Regarding claim 4, Li et al teach a probe panel disposed on a substrate, the probe panel comprising a plurality of detection regions, each detection region comprising an oligonucleotide probe set configured to selectively bind to RNA molecules released from a pre-determined microorganism, each detection region comprising a different oligonucleotide probe set (page 594-595, especially Figure 3 and Legend).
Regarding claim 6, Li et al teach the probe panel wherein the predetermined microorganism comprises Campylobacter coli, Campylobacter jejuni (page 12, first full paragraph), Escherichia coli (page 13, first full paragraph), Staphylococcus Aureus and Mycobacterium tuberculosis (page 13, last line in last paragraph at bottom).
Regarding claim 7, Li et al teach the probe panel wherein the substrate comprises at least one of a magnetic-bead based platform (see e.g., Figure 3).
Regarding claim 9-10, Li et al the oligonucleotide probe set wherein the oligonucleotide probe set is adapted to hybridize 16S rRNA sequences or 23S rRNA sequences (bottom of column 2 on page 586 to top of col. 1 on page 590).
Regarding claims 11-13, Li et al teach the probe panel of claim 33, wherein the number of detection regions is at least 16 (see figure 3).
Regarding claim 14, Li et al teach a system for identifying at least two microbes in a specimen, the system comprising:(a) the probe panel of claim 4; and (b) a detection apparatus configured to detect hybridized complexes present in any detection regions of the probe panel (figure 3, page 594).
Regarding claim 15, Li et al teach system wherein the detection apparatus comprises a plurality of sensors, each sensor associated with a single detection region and configured to detect a signal from a hybridized complex when present in the single detection region (Figure 3 and page 594).
Regarding claim 16, Li et al teach the system of claim 53, wherein the plurality of sensors are operable simultaneously (Figure 3 and page 594).
Regarding claim 18, Li et al teach the system of claim 52, wherein the specimen is selected from the group consisting of urine or blood (page 594). Thus, Li meets the limitation of the claims recited above.
Claim(s) 1-3, 8 and 9 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Barken et al {Barken, used interchangeably herein} (BioTechniques, 36: 124-132, January 2004).
Regarding claim 1, Barken teaches an oligonucleotide probe set for use in identifying a first target microbe in a specimen, wherein the oligonucleotide probe set comprises a capture probe and a detector probe, the capture probe and detector probe each being adapted to selectively hybridize to a first target sequence of rRNA molecules released from the first target microbe (see abstract, pages 125, 128, Figure 1 and Table 1 at page 126).
Regarding claim 2, Barken et al teach the oligonucleotide probe set owherein the probe set is adapted to selectively bind to rRNA molecules released from a pre- determined microorganism selected from the microorganism selected from the group consisting of Escherichia coli (EC) B. lichenformis (see Table 1).
Regarding claim 3, the specification notes at paragraphs [0041] and [0043], that the probes sets is designed to hybridize to 16S rRNA sequences. 16S rRNA sequences are well-known to be present in bacterial species. Barken discloses an oligonucleotide probe set wherein the oligonucleotide probe set is adapted to hybridize with rRNA molecules released from substantially all eubacteria (EU) or similar microbes, i.e., 16S rRNA (see Table 1).
Regarding claim 8, Barken teaches the oligonucleotide probe set wherein the oligonucleotide probe set further comprises a helper probe adapted to hybridize with a helper sequence of the capture probe to help immobilize the capture probe. (page 128 and Figure 1 and 2; see also Figure 5).
Regarding claim 9, Barken teaches the oligonucleotide probe set wherein the oligonucleotide probe set is adapted to hybridize 16S rRNA sequences (Table 1). Thus, Barken meets the limitations of the claims recited above.
Conclusion
No claims are allowed. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA B WILDER whose telephone number is (571)272-0791. The examiner can normally be reached Flexible.
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/CYNTHIA B WILDER/Primary Examiner, Art Unit 1681