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 .
Claim Interpretation
Attention is directed to MPEP 904.01 [R-08.2012].
The breadth of the claims in the application should always be carefully noted; that is, the examiner should be fully aware of what the claims do not call for, as well as what they do require. During patent examination, the claims are given the broadest reasonable interpretation consistent with the specification. See In re Morris, 127 F.3d 1048, 44 USPQ2d 1023 (Fed. Cir. 1997). See MPEP § 2111 - § 2116.01 for case law pertinent to claim analysis.
It is noted with particularity that narrowing limitations found in the specification cannot be inferred in the claims where the elements not set forth in the claims are linchpin of patentability. In re Philips Industries v. State Stove & Mfg. Co, Inc., 186 USPQ 458 (CA6 1975). While the claims are to be interpreted in light of the specification, it does not follow that limitations from the specification may be read into the claims. On the contrary, claims must be interpreted as broadly as their terms reasonably allow. See Ex parte Oetiker, 23 USPQ2d 1641 (BPAI, 1992). In added support of this position, attention is directed to MPEP 2111 [R-11.2013], where, citing In re Prater, 415 F.2d 1393, 1404-05, 162 USPQ 541, 550-51 (CCPA 1969), is stated:
The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.
Additionally, attention is directed to MPEP 2111.01 [R-01.2024], wherein is stated:
II. IT IS IMPROPER TO IMPORT CLAIM LIMITATIONS FROM THE SPECIFICATION
“Though understanding the claim language may be aided by explanations contained in the written description, it is important not to import into a claim limitations that are not part of the claim. For example, a particular embodiment appearing in the written description may not be read into a claim when the claim language is broader than the embodiment.” Superguide Corp. v. DirecTV Enterprises, Inc., 358 F.3d 870, 875, 69 USPQ2d 1865, 1868 (Fed. Cir. 2004).
Attention is also directed to MPEP 2111.02 II [R-07.2022]. As stated herein:
II. PREAMBLE STATEMENTS RECITING PURPOSE OR INTENDED USE
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The claim preamble must be read in the context of the entire claim. The determination of whether preamble recitations are structural limitations or mere statements of purpose or use "can be resolved only on review of the entirety of the [record] to gain an understanding of what the inventors actually invented and intended to encompass by the claim" as drafted without importing "'extraneous' limitations from the specification." Corning Glass Works, 868 F.2d at 1257, 9 USPQ2d at 1966. If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction. Shoes by Firebug LLC v. Stride Rite Children’s Grp., LLC, 962 F.3d 1362, 2020 USPQ2d 10701 (Fed. Cir. 2020) (The court found that the preamble in one patent’s claim is limiting but is not in a related patent); Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305, 51 USPQ2d 1161, 1165 (Fed. Cir. 1999). See also Rowe v. Dror, 112 F.3d 473, 478, 42 USPQ2d 1550, 1553 (Fed. Cir. 1997) ("where a patentee defines a structurally complete invention in the claim body and uses the preamble only to state a purpose or intended use for the invention, the preamble is not a claim limitation")… (Emphasis added)
Attention is directed to MPEP 2111 [R-10.2019]. As stated therein:
During patent examination, the pending claims must be "given their broadest reasonable interpretation consistent with the specification." The Federal Circuit’s en banc decision in Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) expressly recognized that the USPTO employs the "broadest reasonable interpretation" standard:
The Patent and Trademark Office ("PTO") determines the scope of claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction "in light of the specification as it would be interpreted by one of ordinary skill in the art." In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364[, 70 USPQ2d 1827, 1830] (Fed. Cir. 2004). Indeed, the rules of the PTO require that application claims must "conform to the invention as set forth in the remainder of the specification and the terms and phrases used in the claims must find clear support or antecedent basis in the description so that the meaning of the terms in the claims may be ascertainable by reference to the description." 37 CFR 1.75(d)(1). (Emphasis added).
Attention is directed to MPEP 2173.04 [R-10.2019]. As stated therein:
Breadth of a claim is not to be equated with indefiniteness. In re Miller, 441 F.2d 689, 169 USPQ 597 (CCPA 1971); In re Gardner, 427 F.2d 786, 788, 166 USPQ 138, 140 (CCPA 1970) ("Breadth is not indefiniteness."). A broad claim is not indefinite merely because it encompasses a wide scope of subject matter provided the scope is clearly defined. But a claim is indefinite when the boundaries of the protected subject matter are not clearly delineated and the scope is unclear. For example, a genus claim that covers multiple species is broad, but is not indefinite because of its breadth, which is otherwise clear. But a genus claim that could be interpreted in such a way that it is not clear which species are covered would be indefinite (e.g., because there is more than one reasonable interpretation of what species are included in the claim). (Emphasis added)
Claim Rejections - 35 USC § 112, Second Paragraph / (b)
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.
Standard for Definiteness.
Attention is directed to MPEP 2171 [R-11.2013]:
Two separate requirements are set forth in 35 U.S.C. 112(b) and pre-AIA 35 U.S.C. 112, second paragraph, namely that:
(A) the claims must set forth the subject matter that the inventor or a joint inventor regards as the invention; and
(B) the claims must particularly point out and distinctly define the metes and bounds of the subject matter to be protected by the patent grant.
The first requirement is a subjective one because it is dependent on what the inventor or a joint inventor for a patent regards as his or her invention. Note that although pre-AIA 35 U.S.C. 112, second paragraph, uses the phrase "which applicant regards as his invention," pre-AIA 37 CFR 1.41(a) provides that a patent is applied for in the name or names of the actual inventor or inventors.
The second requirement is an objective one because it is not dependent on the views of the inventor or any particular individual, but is evaluated in the context of whether the claim is definite — i.e., whether the scope of the claim is clear to a hypothetical person possessing the ordinary level of skill in the pertinent art.
Attention is directed to MPEP 2173.02 I [R-01.2024]:
During prosecution, applicant has an opportunity and a duty to amend ambiguous claims to clearly and precisely define the metes and bounds of the claimed invention. The claim places the public on notice of the scope of the patentee’s right to exclude. See, e.g., Johnson & Johnston Assoc. Inc. v. R.E. Serv. Co., 285 F.3d 1046, 1052, 62 USPQ2d 1225, 1228 (Fed. Cir. 2002) (en banc). As the Federal Circuit stated in Halliburton Energy Servs., Inc. v. M-I LLC, 514 F.3d 1244, 1255, 85 USPQ2d 1654, 1663 (Fed. Cir. 2008):
“We note that the patent drafter is in the best position to resolve the ambiguity in the patent claims, and it is highly desirable that patent examiners demand that applicants do so in appropriate circumstances so that the patent can be amended during prosecution rather than attempting to resolve the ambiguity in litigation.”
***
During examination, after applying the broadest reasonable interpretation to the claim, if the metes and bounds of the claimed invention are not clear, the claim is indefinite and should be rejected. Packard, 751 F.3d at 1310 (“[W]hen the USPTO has initially issued a well-grounded rejection that identifies ways in which language in a claim is ambiguous, vague, incoherent, opaque, or otherwise unclear in describing and defining the claimed invention, and thereafter the applicant fails to provide a satisfactory response, the USPTO can properly reject the claim as failing to meet the statutory requirements of § 112(b).”); Zletz, 893 F.2d at 322, 13 USPQ2d at 1322.
Attention is also directed to MPEP 2173.02 III B [R-01-2024], which states in part:
To comply with 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph, applicants are required to make the terms that are used to define the invention clear and precise, so that the metes and bounds of the subject matter that will be protected by the patent grant can be ascertained. See MPEP § 2173.05(a), subsection I. It is important that a person of ordinary skill in the art be able to interpret the metes and bounds of the claims so as to understand how to avoid infringement of the patent that ultimately issues from the application being examined. See MPEP § 2173.02, subsection II (citing Morton Int ’l, Inc. v. Cardinal Chem. Co., 5 F.3d 1464, 1470 (Fed. Cir. 1993)); see also Halliburton Energy Servs., 514 F.3d at 1249, 85 USPQ2d at 1658 (“Otherwise, competitors cannot avoid infringement, defeating the public notice function of patent claims.”). Examiners should bear in mind that “[a]n essential purpose of patent examination is to fashion claims that are precise, clear, correct, and unambiguous. Only in this way can uncertainties of claim scope be removed, as much as possible, during the administrative process.” Zletz, 893 F.2d at 322, 13 USPQ2d at 1322 [Fed. Cir. 1989]. (Emphasis added)
Attention is also directed to MPEP 2173.04 [R-10-2019], which states in part:
A broad claim is not indefinite merely because it encompasses a wide scope of subject matter provided the scope is clearly defined. But a claim is indefinite when the boundaries of the protected subject matter are not clearly delineated and the scope is unclear. For example, a genus claim that covers multiple species is broad, but is not indefinite because of its breadth, which is otherwise clear. But a genus claim that could be interpreted in such a way that it is not clear which species are covered would be indefinite (e.g., because there is more than one reasonable interpretation of what species are included in the claim).
Holding and Rationale
Claims 1-16 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.
Claims 1 and 8 are indefinite with respect to what constitutes the metes and bounds of “specific hybridization”. In support of this position attention is directed to paragraph [0058] of the disclosure. As stated therein: "Specific hybridization" is an indication that two nucleic acid sequences share a high degree of complementarity. (Emphasis added) While it is understood that there needs to be “a high degree of complementarity”, it is less than clear as to just what constitutes the metes and bounds of “a high degree of complementarity”.
Claims 2-7, which depend from claim 1; and claims 9-16, which depend from claim 8, fail to overcome these issues and are similarly rejected.
Response to argument
At pages 7-9 of the response of 30 December 2025, hereinafter the response, applicant’s representative traverses the rejection of claims under 35 USC 112(b). At page 8 of the response said representative asserts:
Applicants note that a person of ordinary skill in the art would be able to interpret what constitutes a high degree of complementarity, because they would be able to easily ascertain the required degree of complementarity to enable specific hybridization and/or amplification of the target nucleic acids, as required in the claim's language.
This argument has been fully considered and has not been found persuasive. Attention is directed to MPEP 2145 I [R-01.2024].
An argument by the applicant is not evidence unless it is an admission, in which case, an examiner may use the admission in making a rejection. See MPEP § 2129 and § 2144.03 for a discussion of admissions as prior art.
Arguments presented by applicant cannot take the place of evidence in the record. See In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984); In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965); In re Geisler, 116 F.3d 1465, 43 USPQ2d 1362 (Fed. Cir. 1997) ("An assertion of what seems to follow from common experience is just attorney argument and not the kind of factual evidence that is required to rebut a prima facie case of obviousness."). See MPEP § 716.01(c) for examples of applicant statements which are not evidence and which must be supported by an appropriate affidavit or declaration
In view of the above analysis and in the absence of convincing evidence to the contrary, the rejection is maintained.
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.
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.
Standard for Obviousness.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) 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.
Attention is directed to In re Jung, 98 USPQ2d 1174, 1178 (Fed. Cir. 2011) wherein is stated:
There has never been a requirement for an examiner to make an on-the-record claim construction of every term in every rejected claim and to explain every possible difference between the prior art and the claimed invention in order to make out a prima facie rejection. This court declines to create such a burdensome and unnecessary requirement. “[Section 132] does not mandate that in order to establish prima facie anticipation, the PTO must explicitly preempt every possible response to a section 102 rejection. Section 132 merely ensures that an applicant at least be informed of the broad statutory basis for the rejection of his claims, so that he may determine what the issues are on which he can or should produce evidence.” Chester, 906 F.2d at 1578 (internal citation omitted). As discussed above, all that is required of the office to meet its prima facie burden of production is to set forth the statutory basis of the rejection and the reference or references relied upon in a sufficiently articulate and informative manner as to meet the notice requirement of § 132. As the statute itself instructs, the examiner must “notify the applicant,” “stating the reasons for such rejection,” “together with such information and references as may be useful in judging the propriety of continuing prosecution of his application.” 35 U.S.C. § 132.
Attention is directed to the decision in KSR International Co. v. Teleflex Inc., 82 USPQ2d 1385 (U.S. 2007):
When there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill in the art has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely the product not of innovation but of ordinary skill and common sense.
It is further noted that prior art is not limited to the four corners of the documentary prior art being applied. Prior art includes both the specialized understanding of one of ordinary skill in the art, and the common understanding of the layman. It includes “background knowledge possessed by a person having ordinary skill in the art. . . [A] court can take account of the inferences and creative steps that a person of ordinary skill in the art would employ.” KSR at 1396.
Suggestion, teaching or motivation does not have to be explicit and “may be found in any number of sources, including common knowledge, the prior art as a whole or the nature of the problem itself’” Pfizer, Inc. v. Apotex, Inc. 480 F.3d 1348, 82 USPQ2d 1321 (Fed. Cir. 2007) citing Dystar Textilfarben GMBH v. C. H. Patrick Co., 464 F.3d 1356 (Fed. Cir. 2006).
Holding and Rationale
Claims 1, 4-6, 8 and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over US 2016/0040219 (Johnson et al.; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
As an initial matter, it is noted that the applicant of the instant application is the same as that of Johnson et al. – Luminex Corporation. It is also noted that there is a common inventor, Doug Whitman. It is also noted that Johnson et al., was published 11 February 2016, which is greater than one year prior to the effective filing date of the instant application (22 January 2018), and thusly qualifies as available prior art.
Johnson et al., in paragraphs [0009] and [0149], teach:
[0009] In a first embodiment, a method is provided for detecting the presence of a target nucleic acid comprising: (a) contacting a sample with a cleavable probe, said probe comprising, from 5' to 3', (i) a first sequence region comprising a label; (ii) a second sequence region; (iii) a sequence that is the reverse complement of the second sequence region; and (iv) a sequence comprising one or more ribonucleotide base that is complimentary to a first region on a first strand of the target nucleic acid; (b) contacting the cleavable probe with an endoribonuclease, thereby cleaving probe that is hybridized with target nucleic acid to form a truncated cleavable probe; (c) allowing the truncated cleavable probe to hybridize to itself to form a hairpin probe; ( d) extending the hairpin probe; and (e) detecting the target nucleic acid by detecting a change in signal from the label. In certain aspects, the label in first sequence region (i) is: a reporter-quencher pair and extension of the hairpin probe on the first sequence region changes the distance between the reporter and quencher; or at least one non-natural nucleotide labeled with a first member of a reporter-quencher pair and extension of the hairpin probe on the first sequence region results in the incorporation of a complementary non-natural nucleotide labeled with a second member of the reporter-quencher pair. In certain aspects, all of, a portion of, or none of the sequence that is the reverse complement of the second sequence region (iii) may be complimentary to a first region on a first strand of the target nucleic acid. In some embodiments, the method further comprises performing a melt analysis on the hairpin probe.
[0149] As discussed above, the polymerase chain reaction (PCR) is an example of a reaction that may be performed within a droplet. In particular, droplets are useful in digital PCR (dPCR) techniques. dPCR involves partitioning the sample such that individual nucleic acid molecules contained in the sample are localized in many separate regions, such as in individual wells in microwell plates, in the dispersed phase of an emulsion, or arrays of nucleic acid binding surfaces. Each partition (e.g., droplet) will contain 0 or greater than zero molecules, providing a negative or positive reaction, respectively. Unlike conventional PCR, dPCR is not dependent on the number of amplification cycles to determine the initial amount of the target nucleic acid in the sample. Accordingly, dPCR eliminates the reliance on exponential data to quantify target nucleic acids and provides absolute quantification. Bead emulsion PCR, which clonally amplifies nucleic acids on beads in an emulsion, is one example of a dPCR technique in which the reactions are portioned into droplets. See, e.g., U.S. Pat. Nos. 8,048,627 and 7,842,457, which are hereby incorporated by reference. When dPCR is performed in an emulsion as discussed in more detail below, the emulsion should be heat stable to allow it to withstand thermal cycling conditions. (Emphasis added)
Johnson et al., at paragraph [0081], teach:
[0081] The methods disclosed herein may be performed in droplets. Likewise, the compositions disclosed herein may be disposed within droplets. For example, the cleavable probes disclosed herein may be divided into many separate reactions for PCR or isothermal amplification using droplets. Thus, in certain embodiments the methods disclosed herein are compartmentalized in droplets to perform quantitative digital PCR reactions, or other quantitative digital amplification reactions. As described in Vogelstein et al., 1999, at pgs. 9236-9241, digital PCR methods may be helpful for distributing the target nucleic acid such that the vast majority of reactions contain either one or zero target nucleic acid molecules. At certain dilutions the number of amplification positive reactions is equal to the number of template molecules originally present.
Johnson et al., in paragraph [0072], teach:
Typically, the amplification cycle is repeated between about 10 to 40 times. For real-time PCR, detection of the amplification products will typically be done after each amplification cycle. Although in certain aspects of the invention, detection of the amplification products may be done after every second, third, fourth, or fifth amplification cycle. Detection may also be done such that as few as 2 or more amplification cycles are analyzed or detected.
The aspect of detecting the amplification products (fluorescent intensity values) after any of a variety of amplification cycles (thermocycles) speaks to how the limitations of “acquiring a first, second and third set of fluorescent intensity values”, as well as a “ninth intensity value” are obvious design choices.
Johnson et al., at paragraph [0122], teach:
Specific hybridization complexes form under permissive annealing conditions and remain hybridized after any subsequent washing steps. Permissive conditions for annealing of nucleic acid sequences are routinely determinable by one of ordinary skill in the art and may occur, for example, at 65° C. in the presence of about 6×SSC. Stringency of hybridization may be expressed, in part, with reference to the temperature under which the wash steps are carried out. Such temperatures are typically selected to be about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Equations for calculating Tm for example, nearest-neighbor parameters, and conditions for nucleic acid hybridization are known in the art.
Johnson et al., in paragraph [0148], teach:
The droplets, as well as labeled analytes or reaction products (e.g., hairpin probes) within the droplets, may be detected using an imaging system. For example, detection may comprise imaging fluorescent wavelengths and/or fluorescent intensities emitted from the labeled hairpin probes. (Emphasis added)
Johnson et al., in paragraph [0089] teach:
The probes can be designed to have unique melt temperatures (T.sub.m), such as by adjusting the sequence and length of the sequence regions. Thus, a melt analysis can be performed to differentiation probes having different melt temperatures (and thus unquenching at different temperatures). (Emphasis added)
Johnson et al., in paragraph [0100] teach:
The probes can be designed to have unique melt temperatures (T.sub.m), such as by adjusting the sequence and length of the first sequence region. Thus, a melt analysis can be performed to differentiation probes having different melt temperatures (and thus unquenching at different temperatures). (Emphasis added)
Johnson et al., in paragraph [0137], teach:
The fluorescent dye may function as a fluorescence donor for fluorescence resonance energy transfer (FRET). The detectable signal may be quenched when the oligonucleotide is used to amplify a target nucleic acid. For example, the amplification mixture may include nucleotides that are labeled with a quencher for the detectable signal emitted by the fluorophore. Optionally, the oligonucleotides may be labeled with a second fluorescent dye or a quencher dye that may function as a fluorescence acceptor (e.g., for FRET). Where the oligonucleotide is labeled with a first fluorescent dye and a second fluorescent dye, a signal may be detected from the first fluorescent dye, the second fluorescent dye, or both. Signals may be detected at a gradient of temperatures (e.g., in order to determine a melting temperature for an amplicon, a complex that includes a probe hybridized to a target nucleic acid, a hairpin, or a T probe complex). (Emphasis added)
Johnson et al., in paragraph [0109], teach:
[0109] The hydrogen bonding of these non-standard or non-natural nucleotide pairs is similar to those of the natural bases where two or three hydrogen bonds are formed between hydrogen bond acceptors and hydrogen bond donors of the pairing non-standard or non-natural nucleotides. One of the differences between the natural bases and these non-standard or non-natural nucleotides is the number and position of hydrogen bond acceptors and hydrogen bond donors. For example, cytosine can be considered a donor/acceptor/acceptor base with guanine being the complementary acceptor/donor/donor base. Iso-C is an acceptor/acceptor/donor base and iso-G is the complementary donor/donor/acceptor base, as illustrated in U.S. Pat. No. 6,037,120, incorporated herein by reference. (Emphasis added)
The above presentation is deemed to fairly suggest limitations of claims 4, 5, 14 and 15.
Johnson et al., paragraphs [060] and [0061], teach:
[0060] The cleavage and extension of the cleavable probes as disclosed herein may be performed under isothermal conditions in which the cleavable probes are cleaved and extended while reaction conditions are maintained at a substantially constant temperature. Isothermal amplification of signal may be achieved because both fragments of a cleaved probe possess a lower melting temperature than the probe to target before cleavage. This causes the two fragments to disassociate from the target, allowing another probe to hybridize and cleave. This process repeats itself allowing multiple probes to cleave and extend from a single target at a constant temperature. This feature is unique compared to other methods related to closed tube multiplexed detection by melt analysis, which rely on 5′-nuclease activity to obtain unique melt signatures, which cannot amplify the signal of targets or amplicons isothermally. Alternatively, the cleavage and extension of the cleavable probes as disclosed herein may be performed under non-isothermal conditions, such as under the cycling temperature conditions of PCR. (Emphasis added)
[0061] In some aspects, a method of the embodiments may further comprise performing an amplification step to amplify a target sequence. The cleavage and extension of the cleavable probes may be performed during or subsequent to the amplification process. For example, the amplification can be isothermal amplification or one or more polymerase chain reaction cycles. Isothermal amplification techniques include, for example, strand displacement amplification (SDA), loop-mediated amplification (LAMP), rolling circle amplification (RCA), and helicase-dependent amplification (HAD) (see, e.g., Yan et al., 2014). In some aspects, detecting the change in signal from the label comprises detecting the signal before, during, or after performing the isothermal amplification or the multiple polymerase chain reaction cycles. In another aspect, detecting the change in signal from the label comprises detecting the signal only after performing the isothermal amplification or the multiple polymerase chain reaction cycles. In this aspect, the method may further comprise comparing the detected signal from the label to a predetermined ratio of the signal of the label to a reference signal from a label on a non-hybridizing probe. (Emphasis added)
The above presentation is deemed to fairly suggest limitations of claims 6 and 16.
In view of the detailed teachings of Johnson et al., it would have been obvious to one of ordinary skill in the art at the time of the claimed invention to have applied the teachings of Johnson et al., so as to enable the amplification method where multiple target nucleic acids are detected at different temperatures.
In view of the above analysis and in the absence of convincing evidence to the contrary, claims 1, 4-6, 8 and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over US 2016/0040219 (Johnson et al.; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
Response to traversal
Applicant’s representative, at pages 9-11 of the response, traverses the rejection of claims under 35 USC 103(a). At page 10 of the response said representative asserts:
Furthermore, Johnson does not disclose that probes with varying Tms could be distinguished by only taking measurements at two temperatures (one below and one above the Tm of the probe). Example 4 of Johnson teaches multiplexing using a single dye, and states that "melt analysis includes ramping from 60 to 95°C and reading at every 0.5°C to generate a melt profile (see paragraph [0184] of Johnson). As such, Johnson only teaches that probes with varying Tms can be distinguished by full melt profiles, not by measurements of one temperature above and one temperature below the Tm of the probe. Johnson fails to teach each element of the claimed invention. As such, no prima facie case of obviousness has been put forth. Reconsideration and withdrawal of the rejections is respectfully requested.
The above cited argument has been considered and has not been found persuasive. Contrary to assertions by said representative, Johnson does in fact teach performing melt analysis. As noted above in the body of the rejection, Johnson et al., in paragraph [0089] teach:
The probes can be designed to have unique melt temperatures (T.sub.m), such as by adjusting the sequence and length of the sequence regions. Thus, a melt analysis can be performed to differentiation probes having different melt temperatures (and thus unquenching at different temperatures). (Emphasis added)
Johnson et al., in paragraph [0100] teach:
The probes can be designed to have unique melt temperatures (T.sub.m), such as by adjusting the sequence and length of the first sequence region. Thus, a melt analysis can be performed to differentiation probes having different melt temperatures (and thus unquenching at different temperatures). (Emphasis added)
Johnson et al., in paragraph [0137], teach:
The fluorescent dye may function as a fluorescence donor for fluorescence resonance energy transfer (FRET). The detectable signal may be quenched when the oligonucleotide is used to amplify a target nucleic acid. For example, the amplification mixture may include nucleotides that are labeled with a quencher for the detectable signal emitted by the fluorophore. Optionally, the oligonucleotides may be labeled with a second fluorescent dye or a quencher dye that may function as a fluorescence acceptor (e.g., for FRET). Where the oligonucleotide is labeled with a first fluorescent dye and a second fluorescent dye, a signal may be detected from the first fluorescent dye, the second fluorescent dye, or both. Signals may be detected at a gradient of temperatures (e.g., in order to determine a melting temperature for an amplicon, a complex that includes a probe hybridized to a target nucleic acid, a hairpin, or a T probe complex). (Emphasis added)
As evidenced above, Johnson et al., clearly do teach designing probes such that they have a plurality of “unique melting temperatures”. The selection of just how many probes one uses, and the number of unique melting temperatures one uses, is deemed to be a matter of obvious design choices.
In view of the above analysis and in the absence of convincing evidence to the contrary, claims 1, 4-6, 8 and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over US 2016/0040219 (Johnson et al.; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
Claim(s) 2-3, 7, and 9-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Johnson et al., (US 2016/0040219; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016) as applied to claims 1, 4-6, 8 and 14-16 above, and further in view of Johnson et al. (WO 2016/025452 A1).
See above for the basis of the rejection as it pertains to the disclosure of Johnson et al., (US 2016/0040219; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
Regarding claims 2 and 12, Johnson et al. (WO 2016/025452 A1) teaches that “In another aspect, the first and second probes may comprise the same reporters.” (See [0019] on page 7, lines 2-3)
Regarding claims 3, 9 and 14, Johnson et al. (WO 2016/025452 A1) teaches that “a first member of a reporter-quencher pair and extension of the hairpin probe on the first sequence region results in the incorporation of a complementary non-natural nucleotide labeled with a second member of the reporter-quencher pair.” (See [0007] on page 6, lines 1-4).
Regarding intensity value recited in claims 7 and 9-11, Johnson et al. (WO 2016/025452 A1) teaches :
[00157] “The melt profile of the hairpin probes of FIG. 2 were generated to determine the folding temperature of various constructs. This was measured by monitoring drop in fluorescence intensity over a temperature gradient of 95 ° C to 41 ° C (FIG. 4). Graphs showing the quenching profile for three exemplary constructs RTx-5, RTx-10 and RTx-11 are shown in FIGs 5-7, respectively. The results of all studies are shown in Table 2, below. It was found that hairpin constructs RTx-1, 2, 3, 5, 6, 7, and 8 are completely quenched by 71 ° C temperature step corresponding to calculated Tm of the extended hairpin ~71 ° C (IDT). Hairpin constructs RTx-4, 9 and 10 are quenched by the 62 °C and hairpin RTx-11 at 41 ° C.
[0158] Table 2: Summary of folding temperature for various hairpin probes.
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[0159] When the Tm of stem loop, delta G values, loop size and stem size are compared the data suggests that the main factor influencing the formation of the hairpin is the number of bases in the stem. The secondary factor may be the Gibbs Free energy associated with the folding of the hairpin as the delta G of the constructs with the correct folding Tm are lower than the constructs with Tm's of 62° C and 41 ° C.
In view of the above presentation, it would have been obvious to one of ordinary skill in the art to have applied the teachings of Johnson et al. (WO 2016/025452 A1) to the guidance of Johnson et al., (US 2016/0040219; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016) for to do so would allow for the application of known procedures and reagents in the detection of first and second target nucleic acids in a sample.
In view of the well-developed state of the art, said ordinary artisan would have been amply motivated and would have had a most reasonable expectation of success.
In view of the above presentation and in the absence of convincing evidence to the contrary, claims 2-3, 7, and 9-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Johnson et al., (US 2016/0040219; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016) as applied to claims 1, 4-6, 8 and 14-16 above, and further in view of Johnson et al. (WO 2016/025452 A1).
Response to traversal
Applicant’s representative, at pages 10-11 of the response traverse the rejection of claims 2-3, 7, and 9-13 under 35 USC 103(a). As is asserted to therein:
The Action rejected claims 2, 3, 7, and 9-13 as allegedly obvious over US 2016/0040219 ("Johnson"), in view of WO 2016/025452 A1. Applicants traverse. WO 2016/025452 A1 does not cure the deficiencies of Johnson as discussed above. As such, reconsideration and withdrawal of the rejections is respectfully requested.
The above argument has been considered and has not been found persuasive for as presented above, Johnson et al., clearly do teach performing melt analysis, the alleged deficiency. Given such, and in the absence of convincing evidence to the contrary, claims 2-3, 7, and 9-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Johnson et al., (US 2016/0040219; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016) as applied to claims 1, 4-6, 8 and 14-16 above, and further in view of Johnson et al. (WO 2016/025452 A1).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 4, 5, 6, 8, 14, 15, and 16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of U.S. Patent No. 10,752, 939 (Johnson et al.; Johnson I) in view of US 2016/0040219 (Johnson et al.; Johnson II; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
Johnson I, claims:
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Johnson II, in paragraphs [0009] and [0149], teach:
[0009] In a first embodiment, a method is provided for detecting the presence of a target nucleic acid comprising: (a) contacting a sample with a cleavable probe, said probe comprising, from 5' to 3', (i) a first sequence region comprising a label; (ii) a second sequence region; (iii) a sequence that is the reverse complement of the second sequence region; and (iv) a sequence comprising one or more ribonucleotide base that is complimentary to a first region on a first strand of the target nucleic acid; (b) contacting the cleavable probe with an endoribonuclease, thereby cleaving probe that is hybridized with target nucleic acid to form a truncated cleavable probe; (c) allowing the truncated cleavable probe to hybridize to itself to form a hairpin probe; ( d) extending the hairpin probe; and (e) detecting the target nucleic acid by detecting a change in signal from the label. In certain aspects, the label in first sequence region (i) is: a reporter-quencher pair and extension of the hairpin probe on the first sequence region changes the distance between the reporter and quencher; or at least one non-natural nucleotide labeled with a first member of a reporter-quencher pair and extension of the hairpin probe on the first sequence region results in the incorporation of a complementary non-natural nucleotide labeled with a second member of the reporter-quencher pair. In certain aspects, all of, a portion of, or none of the sequence that is the reverse complement of the second sequence region (iii) may be complimentary to a first region on a first strand of the target nucleic acid. In some embodiments, the method further comprises performing a melt analysis on the hairpin probe.
[0149] As discussed above, the polymerase chain reaction (PCR) is an example of a reaction that may be performed within a droplet. In particular, droplets are useful in digital PCR (dPCR) techniques. dPCR involves partitioning the sample such that individual nucleic acid molecules contained in the sample are localized in many separate regions, such as in individual wells in microwell plates, in the dispersed phase of an emulsion, or arrays of nucleic acid binding surfaces. Each partition (e.g., droplet) will contain 0 or greater than zero molecules, providing a negative or positive reaction, respectively. Unlike conventional PCR, dPCR is not dependent on the number of amplification cycles to determine the initial amount of the target nucleic acid in the sample. Accordingly, dPCR eliminates the reliance on exponential data to quantify target nucleic acids and provides absolute quantification. Bead emulsion PCR, which clonally amplifies nucleic acids on beads in an emulsion, is one example of a dPCR technique in which the reactions are portioned into droplets. See, e.g., U.S. Pat. Nos. 8,048,627 and 7,842,457, which are hereby incorporated by reference. When dPCR is performed in an emulsion as discussed in more detail below, the emulsion should be heat stable to allow it to withstand thermal cycling conditions. (Emphasis added)
Johnson II, at paragraph [0081], teach:
[0081] The methods disclosed herein may be performed in droplets. Likewise, the compositions disclosed herein may be disposed within droplets. For example, the cleavable probes disclosed herein may be divided into many separate reactions for PCR or isothermal amplification using droplets. Thus, in certain embodiments the methods disclosed herein are compartmentalized in droplets to perform quantitative digital PCR reactions, or other quantitative digital amplification reactions. As described in Vogelstein et al., 1999, at pgs. 9236-9241, digital PCR methods may be helpful for distributing the target nucleic acid such that the vast majority of reactions contain either one or zero target nucleic acid molecules. At certain dilutions the number of amplification positive reactions is equal to the number of template molecules originally present.
Johnson II, in paragraph [0072], teach:
Typically, the amplification cycle is repeated between about 10 to 40 times. For real-time PCR, detection of the amplification products will typically be done after each amplification cycle. Although in certain aspects of the invention, detection of the amplification products may be done after every second, third, fourth, or fifth amplification cycle. Detection may also be done such that as few as 2 or more amplification cycles are analyzed or detected.
The aspect of detecting the amplification products (fluorescent intensity values) after any of a variety of amplification cycles (thermocycles) speaks to how the limitations of “acquiring a first, second and third set of fluorescent intensity values”, as well as a “ninth intensity value” are obvious design choices.
Johnson II, at paragraph [0122], teach:
Specific hybridization complexes form under permissive annealing conditions and remain hybridized after any subsequent washing steps. Permissive conditions for annealing of nucleic acid sequences are routinely determinable by one of ordinary skill in the art and may occur, for example, at 65° C. in the presence of about 6×SSC. Stringency of hybridization may be expressed, in part, with reference to the temperature under which the wash steps are carried out. Such temperatures are typically selected to be about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Equations for calculating Tm for example, nearest-neighbor parameters, and conditions for nucleic acid hybridization are known in the art.
Johnson II, in paragraph [0148], teach:
The droplets, as well as labeled analytes or reaction products (e.g., hairpin probes) within the droplets, may be detected using an imaging system. For example, detection may comprise imaging fluorescent wavelengths and/or fluorescent intensities emitted from the labeled hairpin probes. (Emphasis added)
Johnson II, in paragraph [0109], teach:
[0109] The hydrogen bonding of these non-standard or non-natural nucleotide pairs is similar to those of the natural bases where two or three hydrogen bonds are formed between hydrogen bond acceptors and hydrogen bond donors of the pairing non-standard or non-natural nucleotides. One of the differences between the natural bases and these non-standard or non-natural nucleotides is the number and position of hydrogen bond acceptors and hydrogen bond donors. For example, cytosine can be considered a donor/acceptor/acceptor base with guanine being the complementary acceptor/donor/donor base. Iso-C is an acceptor/acceptor/donor base and iso-G is the complementary donor/donor/acceptor base, as illustrated in U.S. Pat. No. 6,037,120, incorporated herein by reference. (Emphasis added)
The above presentation is deemed to fairly suggest limitations of claims 4, 5, 14 and 15.
Johnson II, paragraphs [060] and [0061], teach:
[0060] The cleavage and extension of the cleavable probes as disclosed herein may be performed under isothermal conditions in which the cleavable probes are cleaved and extended while reaction conditions are maintained at a substantially constant temperature. Isothermal amplification of signal may be achieved because both fragments of a cleaved probe possess a lower melting temperature than the probe to target before cleavage. This causes the two fragments to disassociate from the target, allowing another probe to hybridize and cleave. This process repeats itself allowing multiple probes to cleave and extend from a single target at a constant temperature. This feature is unique compared to other methods related to closed tube multiplexed detection by melt analysis, which rely on 5′-nuclease activity to obtain unique melt signatures, which cannot amplify the signal of targets or amplicons isothermally. Alternatively, the cleavage and extension of the cleavable probes as disclosed herein may be performed under non-isothermal conditions, such as under the cycling temperature conditions of PCR. (Emphasis added)
[0061] In some aspects, a method of the embodiments may further comprise performing an amplification step to amplify a target sequence. The cleavage and extension of the cleavable probes may be performed during or subsequent to the amplification process. For example, the amplification can be isothermal amplification or one or more polymerase chain reaction cycles. Isothermal amplification techniques include, for example, strand displacement amplification (SDA), loop-mediated amplification (LAMP), rolling circle amplification (RCA), and helicase-dependent amplification (HAD) (see, e.g., Yan et al., 2014). In some aspects, detecting the change in signal from the label comprises detecting the signal before, during, or after performing the isothermal amplification or the multiple polymerase chain reaction cycles. In another aspect, detecting the change in signal from the label comprises detecting the signal only after performing the isothermal amplification or the multiple polymerase chain reaction cycles. In this aspect, the method may further comprise comparing the detected signal from the label to a predetermined ratio of the signal of the label to a reference signal from a label on a non-hybridizing probe. (Emphasis added)
The above presentation is deemed to fairly suggest limitations of claims 6 and 16.
In view of the above presentation, it would have been obvious to one of ordinary skill in the art at the time of the invention to have modified the method of Johnson I with that of Johnson II for to do so would enhance the method of detecting the presence of multiple target nucleic acids via fluorescent signal wherein the target nucleic acids had been subjected to amplification and fluorescent signal intensity is measured at different temperatures.
In view of the above presentation and in the absence of convincing evidence to the contrary, claims 1, 4, 5, 6, 8, 14, 15, and 16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of U.S. Patent No. 10,752, 939 (Johnson et al.; Johnson I) in view of US 2016/0040219 (Johnson et al.; Johnson II; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
Claims 1, 4, 5, 6, 8, 14, 15, and 16 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 10,975,419 B2 (Johnson et al.; Johnson III) of US 2016/0040219 (Johnson et al.; Johnson II; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
Claims of Johnson III:
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Acknowledgement is made of the claims of the instant application are to a method while the claims in Johnson III are to a kit.
Attention is directed to MPEP 804 II B1. As stated therein:
[T]he court explained that it is also proper to look at the disclosed utility in the reference disclosure to determine the overall question of obviousness in a nonstatutory double patenting context. See Sun Pharm. Indus., Ltd. v. Eli Lilly & Co., 611 F.3d 1381, 95 USPQ2d 1797 (Fed. Cir. 2010); Pfizer, Inc. v. Teva Pharm. USA, Inc., 518 F.3d 1353, 86 USPQ2d 1001 (Fed. Cir. 2008); Geneva Pharmaceuticals Inc. v. GlaxoSmithKline PLC, 349 F3d 1373, 1385-86, 68 USPQ2d 1865, 1875 (Fed. Cir. 2003).
To avoid improperly treating what is disclosed in a reference patent or copending application as if it were prior art in the context of a nonstatutory double patenting analysis, the examiner must first properly construe the scope of the reference claims. The portion of the specification of the reference that describes subject matter that falls within the scope of a reference claim may be relied upon to properly construe the scope of that claim. In particular, when ascertaining the scope of the reference’s claim(s) to a compound, the examiner should consider the reference’s specification, including all of the compound’s uses that are disclosed. See Sun Pharm. Indus., 611 F.3d at 1386-88, 95 USPQ2d at 1801-02. (Emphasis added)
Accordingly, the specification of Johnson III can be relied on for the method of using claimed composition and kit. For instance, Fig. 1A of US 10,975,419 is identical to Fig. 1A of US 2016/0040219.
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Johnson III, at column 3, second paragraph, teaches:
In some aspects, a method of the embodiments may further comprise quantifying the amount of the target nucleic acid in the sample. For example, quantifying the amount of the target nucleic acid in the sample may comprise: using a standard curve; determining a relative amount of the nucleic acid target; using end-point quantitation; or determining an amount of the nucleic acid target by relating the PCR cycle number at which the signal is detectable over background to the amount of target present.
Johnson III, at column 24, penultimate paragraph, teaches:
An oligonucleotide may be designed to function as a “primer.” A “primer” is a short nucleic acid, usually a ssDNA oligonucleotide, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA or RNA strand by a polymerase enzyme, such as a DNA polymerase enzyme. Primer pairs can be used for amplification (and identification) of a nucleic acid sequence (e.g., by the polymerase chain reaction (PCR)). An oligonucleotide may be designed to function as a “probe.” A “probe” refers to an oligonucleotide, its complements, or fragments thereof, which are used to detect identical, allelic, or related nucleic acid sequences. Probes may include oligonucleotides that have been attached to a detectable label or reporter molecule. Typical labels include fluorescent dyes, quenchers, radioactive isotopes, ligands, scintillation agents, chemiluminescent agents, and enzymes.
Johnson II, in paragraphs [0009] and [0149], teach:
[0009] In a first embodiment, a method is provided for detecting the presence of a target nucleic acid comprising: (a) contacting a sample with a cleavable probe, said probe comprising, from 5' to 3', (i) a first sequence region comprising a label; (ii) a second sequence region; (iii) a sequence that is the reverse complement of the second sequence region; and (iv) a sequence comprising one or more ribonucleotide base that is complimentary to a first region on a first strand of the target nucleic acid; (b) contacting the cleavable probe with an endoribonuclease, thereby cleaving probe that is hybridized with target nucleic acid to form a truncated cleavable probe; (c) allowing the truncated cleavable probe to hybridize to itself to form a hairpin probe; ( d) extending the hairpin probe; and (e) detecting the target nucleic acid by detecting a change in signal from the label. In certain aspects, the label in first sequence region (i) is: a reporter-quencher pair and extension of the hairpin probe on the first sequence region changes the distance between the reporter and quencher; or at least one non-natural nucleotide labeled with a first member of a reporter-quencher pair and extension of the hairpin probe on the first sequence region results in the incorporation of a complementary non-natural nucleotide labeled with a second member of the reporter-quencher pair. In certain aspects, all of, a portion of, or none of the sequence that is the reverse complement of the second sequence region (iii) may be complimentary to a first region on a first strand of the target nucleic acid. In some embodiments, the method further comprises performing a melt analysis on the hairpin probe.
[0149] As discussed above, the polymerase chain reaction (PCR) is an example of a reaction that may be performed within a droplet. In particular, droplets are useful in digital PCR (dPCR) techniques. dPCR involves partitioning the sample such that individual nucleic acid molecules contained in the sample are localized in many separate regions, such as in individual wells in microwell plates, in the dispersed phase of an emulsion, or arrays of nucleic acid binding surfaces. Each partition (e.g., droplet) will contain 0 or greater than zero molecules, providing a negative or positive reaction, respectively. Unlike conventional PCR, dPCR is not dependent on the number of amplification cycles to determine the initial amount of the target nucleic acid in the sample. Accordingly, dPCR eliminates the reliance on exponential data to quantify target nucleic acids and provides absolute quantification. Bead emulsion PCR, which clonally amplifies nucleic acids on beads in an emulsion, is one example of a dPCR technique in which the reactions are portioned into droplets. See, e.g., U.S. Pat. Nos. 8,048,627 and 7,842,457, which are hereby incorporated by reference. When dPCR is performed in an emulsion as discussed in more detail below, the emulsion should be heat stable to allow it to withstand thermal cycling conditions. (Emphasis added)
Johnson II, at paragraph [0081], teach:
[0081] The methods disclosed herein may be performed in droplets. Likewise, the compositions disclosed herein may be disposed within droplets. For example, the cleavable probes disclosed herein may be divided into many separate reactions for PCR or isothermal amplification using droplets. Thus, in certain embodiments the methods disclosed herein are compartmentalized in droplets to perform quantitative digital PCR reactions, or other quantitative digital amplification reactions. As described in Vogelstein et al., 1999, at pgs. 9236-9241, digital PCR methods may be helpful for distributing the target nucleic acid such that the vast majority of reactions contain either one or zero target nucleic acid molecules. At certain dilutions the number of amplification positive reactions is equal to the number of template molecules originally present.
Johnson II, in paragraph [0072], teach:
Typically, the amplification cycle is repeated between about 10 to 40 times. For real-time PCR, detection of the amplification products will typically be done after each amplification cycle. Although in certain aspects of the invention, detection of the amplification products may be done after every second, third, fourth, or fifth amplification cycle. Detection may also be done such that as few as 2 or more amplification cycles are analyzed or detected.
The aspect of detecting the amplification products (fluorescent intensity values) after any of a variety of amplification cycles (thermocycles) speaks to how the limitations of “acquiring a first, second and third set of fluorescent intensity values”, as well as a “ninth intensity value” are obvious design choices.
Johnson II, at paragraph [0122], teach:
Specific hybridization complexes form under permissive annealing conditions and remain hybridized after any subsequent washing steps. Permissive conditions for annealing of nucleic acid sequences are routinely determinable by one of ordinary skill in the art and may occur, for example, at 65° C. in the presence of about 6×SSC. Stringency of hybridization may be expressed, in part, with reference to the temperature under which the wash steps are carried out. Such temperatures are typically selected to be about 5° C. to 20° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Equations for calculating Tm for example, nearest-neighbor parameters, and conditions for nucleic acid hybridization are known in the art.
Johnson II, in paragraph [0148], teach:
The droplets, as well as labeled analytes or reaction products (e.g., hairpin probes) within the droplets, may be detected using an imaging system. For example, detection may comprise imaging fluorescent wavelengths and/or fluorescent intensities emitted from the labeled hairpin probes. (Emphasis added)
Johnson II, in paragraph [0109], teach:
[0109] The hydrogen bonding of these non-standard or non-natural nucleotide pairs is similar to those of the natural bases where two or three hydrogen bonds are formed between hydrogen bond acceptors and hydrogen bond donors of the pairing non-standard or non-natural nucleotides. One of the differences between the natural bases and these non-standard or non-natural nucleotides is the number and position of hydrogen bond acceptors and hydrogen bond donors. For example, cytosine can be considered a donor/acceptor/acceptor base with guanine being the complementary acceptor/donor/donor base. Iso-C is an acceptor/acceptor/donor base and iso-G is the complementary donor/donor/acceptor base, as illustrated in U.S. Pat. No. 6,037,120, incorporated herein by reference. (Emphasis added)
The above presentation is deemed to fairly suggest limitations of claims 4, 5, 14 and 15.
Johnson II, paragraphs [060] and [0061], teach:
[0060] The cleavage and extension of the cleavable probes as disclosed herein may be performed under isothermal conditions in which the cleavable probes are cleaved and extended while reaction conditions are maintained at a substantially constant temperature. Isothermal amplification of signal may be achieved because both fragments of a cleaved probe possess a lower melting temperature than the probe to target before cleavage. This causes the two fragments to disassociate from the target, allowing another probe to hybridize and cleave. This process repeats itself allowing multiple probes to cleave and extend from a single target at a constant temperature. This feature is unique compared to other methods related to closed tube multiplexed detection by melt analysis, which rely on 5′-nuclease activity to obtain unique melt signatures, which cannot amplify the signal of targets or amplicons isothermally. Alternatively, the cleavage and extension of the cleavable probes as disclosed herein may be performed under non-isothermal conditions, such as under the cycling temperature conditions of PCR. (Emphasis added)
[0061] In some aspects, a method of the embodiments may further comprise performing an amplification step to amplify a target sequence. The cleavage and extension of the cleavable probes may be performed during or subsequent to the amplification process. For example, the amplification can be isothermal amplification or one or more polymerase chain reaction cycles. Isothermal amplification techniques include, for example, strand displacement amplification (SDA), loop-mediated amplification (LAMP), rolling circle amplification (RCA), and helicase-dependent amplification (HAD) (see, e.g., Yan et al., 2014). In some aspects, detecting the change in signal from the label comprises detecting the signal before, during, or after performing the isothermal amplification or the multiple polymerase chain reaction cycles. In another aspect, detecting the change in signal from the label comprises detecting the signal only after performing the isothermal amplification or the multiple polymerase chain reaction cycles. In this aspect, the method may further comprise comparing the detected signal from the label to a predetermined ratio of the signal of the label to a reference signal from a label on a non-hybridizing probe. (Emphasis added)
The above presentation is deemed to fairly suggest limitations of claims 6 and 16.
In view of the above presentation, it would have been obvious to one of ordinary skill in the art at the time of the invention to have modified the method of Johnson III with that of Johnson II for to do so would enhance the method of detecting the presence of multiple target nucleic acids via fluorescent signal wherein the target nucleic acids had been subjected to amplification and fluorescent signal intensity is measured at different temperatures.
Response to traversal
Applicant’s representative, at page 11 of the response traverses the rejections. As noted therein, the traversal is based on the assertion that Johnson et al., does not teach performing melting analysis of hybridization products. This argument ahs been considered and, as noted above, has not been found persuasive. In support of this position it is noted that Johnson et al., in paragraph [0089] teach:
The probes can be designed to have unique melt temperatures (T.sub.m), such as by adjusting the sequence and length of the sequence regions. Thus, a melt analysis can be performed to differentiation probes having different melt temperatures (and thus unquenching at different temperatures). (Emphasis added)
Johnson et al., in paragraph [0100] teach:
The probes can be designed to have unique melt temperatures (T.sub.m), such as by adjusting the sequence and length of the first sequence region. Thus, a melt analysis can be performed to differentiation probes having different melt temperatures (and thus unquenching at different temperatures). (Emphasis added)
Johnson et al., in paragraph [0137], teach:
The fluorescent dye may function as a fluorescence donor for fluorescence resonance energy transfer (FRET). The detectable signal may be quenched when the oligonucleotide is used to amplify a target nucleic acid. For example, the amplification mixture may include nucleotides that are labeled with a quencher for the detectable signal emitted by the fluorophore. Optionally, the oligonucleotides may be labeled with a second fluorescent dye or a quencher dye that may function as a fluorescence acceptor (e.g., for FRET). Where the oligonucleotide is labeled with a first fluorescent dye and a second fluorescent dye, a signal may be detected from the first fluorescent dye, the second fluorescent dye, or both. Signals may be detected at a gradient of temperatures (e.g., in order to determine a melting temperature for an amplicon, a complex that includes a probe hybridized to a target nucleic acid, a hairpin, or a T probe complex). (Emphasis added)
In view of the above analysis and in the absence of convincing evidence to the contrary, claims In view of the above presentation and in the absence of convincing evidence to the contrary, claims 1, 4, 5, 6, 8, 14, 15, and 16 remain rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of U.S. Patent No. 10,752, 939 (Johnson et al.; Johnson I) in view of US 2016/0040219 (Johnson et al.; Johnson II; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
Claims 1, 4, 5, 6, 8, 14, 15, and 16 remain rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of U.S. Patent No. 10,975,419 B2 (Johnson et al.; Johnson III) of US 2016/0040219 (Johnson et al.; Johnson II; Application 14/823,288, filed on 04/15/2015, publication date 02/11/2016).
Conclusion
Objections and/or rejections which appeared in the prior Office action and which have not been repeated hereinabove have been withdrawn.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Bradley L. Sisson whose telephone number is (571)272-0751. The examiner can normally be reached Monday to Thursday, from 6:30 AM to 5 PM..
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, Wu-Cheng Shen can be reached at 571-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Bradley L. Sisson/Primary Examiner, Art Unit 1682
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