Patent Application 17529876 - Compositions and Methods for Detecting or - Rejection
Appearance
Patent Application 17529876 - Compositions and Methods for Detecting or
Title: Compositions and Methods for Detecting or Quantifying Hepatitis B Virus
Application Information
- Invention Title: Compositions and Methods for Detecting or Quantifying Hepatitis B Virus
- Application Number: 17529876
- Submission Date: 2025-05-20T00:00:00.000Z
- Effective Filing Date: 2021-11-18T00:00:00.000Z
- Filing Date: 2021-11-18T00:00:00.000Z
- National Class: 536
- National Sub-Class: 024330
- Examiner Employee Number: 88675
- Art Unit: 1681
- Tech Center: 1600
Rejection Summary
- 102 Rejections: 0
- 103 Rejections: 1
Cited Patents
The following patents were cited in the rejection:
- US 0081645đ
- US 0050470đ
Office Action Text
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 DIV of U.S. Patent Application No. 16/672,224, filed November 1, 2019, which is a DIV of Application No. 15/816,036, filed November 17, 2017, which claims the benefit of priority of U.S. Provisional Application No. 62/424,956, filed November 21, 2016. Election/Restrictions Applicantâs election without traverse of the following species in the reply filed on 12/20/2024 is acknowledged. For species group A, concerning Amplicon type, Applicant elects (a): one or both of the first and second amplicons comprise sequence from the S ORF of HBV. For species group B, concerning First amplicon, Applicant elects (e): at least 10 contiguous nucleotides of one of SEQ ID NOs: 20, 21, or 22. For species group C, concerning Second amplicon, Applicant elects (g): at least 10 contiguous nucleotides of one of SEQ ID NOs: 34 or 35. For species group D, concerning Predetermined threshold value, Applicant elects (h): value where expected random error is greater than or about equal to expected error due to a point mutation. Claims 141-143, 145 and 148 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention(s), there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/20/2024. Status of the claims Claims 135-153 are pending. Claims 1-134 and 154-164 are canceled. Claims 135-140, 144, 146-147 and 149-153 are currently under review. Claim Interpretation Prior to analysis of the art, the claims must be construed. As noted in MPEP 2111, citing Phillips v. AWH Corp., 415 F.3d l303, 75 USPQ2d l321 (Fed. Cir. 2005), "During patent examination, the pending claims must be 'given their broadest reasonable interpretation consistent with the specification.' ". Claim 135 is drawn to a method of determining a level of Hepatitis B virus in a sample comprising first and second Hepatitis B amplicons associated with first and second labels, respectively, the method comprising: detecting a first signal emitted from the first label; detecting a second signal emitted from the second label; determining whether the first signal or the second signal is above a predetermined threshold; and calculating a level of Hepatitis B virus in the sample, wherein if the first signal or the second signal is above a predetermined threshold, the level is calculated from the greater of the first and second signals; and wherein if the first signal and the second signal are below a predetermined threshold, the level is calculated from an average of the first and second signals. Claim 135 lacks clarity since the claim does not disclose or provide a definition or structure for first and second Hepatitis B amplicons, does not disclose or provide a definition or structure for an âassociatedâ first and second labels, does not disclose or provide a definition or structure for a predetermined threshold and how to derive such âpredetermined thresholdâ and does not disclose or provide a definition or structure for âa level of Hepatitis B virus in a sampleâ. To expedite prosecution, the claimed first and second Hepatitis B amplicons of claim 135 are construed as referring to an identical first and second Hepatitis B target sequence (in different viral nucleic acid strands). Claim 135 does not make clear the type of association of the claimed first and second labels, so to expedite prosecution, the labels are construed as being covalently attached to the HBV target sequence(s) (i.e. a nucleotide-based mass tag). To expedite prosecution, the claimed predetermined thresholdâ is construed as referring to any signal selected by a user to provide to compare to a measured signal of the first and/or second associated detectable label, and the claimed âa level of Hepatitis B virus in a sampleâ is construed as referring to a quantity or concentration of the HBV target sequence(s) in the sample. Claim Rejections - 35 USC § 112 The following is a quotation of 35 U.S.C. 112(b): (b) CONCLUSION.âThe 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 135-153 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claim 135 lacks clarity since the claim does not disclose or provide a definition or structure for first and second Hepatitis B amplicons, does not disclose or provide a definition or structure for an âassociatedâ first and second labels, does not disclose or provide a definition or structure for a predetermined threshold and how to derive such âpredetermined thresholdâ and does not disclose or provide a definition or structure for what constitute the limitation of âa level of Hepatitis B virus in a sampleâ. Claims 136-150 are further rejected as they depend from claim 135. Claim 138 and 139 recites the limitation, âwherein the level of Hepatitis B virus is a concentration.â And wherein the level of Hepatitis B virus is an amountâ, respectively. These limitations are found to be indefinite and lacking in clarity and clarity of scope. The scope of âan amountâ or âa concentrationâ is not readily discernible. It is unclear e.g. whether the limitation refers to an amount or concentration in the number of atoms, or an amount by weight or concentration (e.g. pg to mg). Claim 151 is indefinite since this claim fails to indicate whether or not the claim depends from claim 135, or from itself. Claims 152-153 are further rejected as they depend from claim 151. 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 135-153 are rejected under 35 U.S.C. §101 because these claims are not directed to patent eligible subject matter. Based upon an analysis with respect to the claims as a whole, claim(s) 135-150 and152-153 do not recite something significantly more than a judicial exception. The rationale for this determination is explained below: According to the 2019 Revised Patent Subject Matter Eligibility Guidance, Docket No. PTO-P-2018-0053 (January 7, 2019), an initial two step analysis is required for determining statutory eligibility. According to the Manual of Patent Examination Procedure (MPEP) sections 2103 through 2106.07(c), which now incorporates the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG), October 2019 Patent Eligibility Guidance Update (October 2019 Update), and the Berkheimer Memo, an initial two step analysis is required for determining statutory eligibility. Step 1 Step 1 requires a determination of whether the claims are directed to a process, machine, manufacture, or a composition of matter. In the instant case, the Step 1 requirement is satisfied as the claims are directed towards a process. Step 2 The Step 2 analysis is a two-part analysis, Step 2A and Step 2B. Step 2A, prong 1 Step 2A, prong 1 requires a determination of whether the claims are directed towards a judicial exception, i.e. a law of nature, natural phenomenon, or an abstract idea, while step 2A, prong 2 requires an analysis of whether the judicial exception integrated into a practical application if the claim recites a judicial exception under Prong 1. Step 2A, prong 2 Step 2A, prong 2 requires an analysis of whether the judicial exception integrated into a practical application if the claim recites a judicial exception under Prong 1. Step 2B The second part, Step 2B of the two-step analysis is drawn to determining whether any element or combination of elements, in the instant claims is/are sufficient to ensure that the claims as a whole amount to significantly more than the judicial exception. Following the analysis below the claims are not patent eligible under 35 U.S.C. 101. Concerning Step 1: YES. Claims 135-153 are directed to methods, therefore the claims are directed to a process, which is a statutory category. Concerning Step 2A: YES. Claims 135-153 recite methods of determining a level of Hepatitis B virus in a sample comprising detecting signals associated with first and second labels of a first and second Hepatitis B amplicons, respectively. Claims 135-153 rely on a naturally-occurring correlation between signals associated with each labeled HBV target sequence in a sample and the naturally occurring amounts/ level/quantity/concentration of Hepatitis B viral sequence. In other words, claims 135-153 rely on a judicially excluded natural principle i.e. a quantity reflecting/associated with/constituting a quantity/concentration of HBV sequence(s) within a test sample, without significantly more. Concerning Step 2A, prong 1, claims 135-153 are directed towards a judicial exception, i.e. a law of nature, as noted above. Claims 135-153 recite abstract ideas of comparing and parsing data, as these claims recite step(s) of calculating a level/quantity/concentration of Hepatitis B virus in a sample based on a first signal from a first HBV target sequence and a second signal from a second HBV target sequence and based on a signal designated as a predetermined threshold. The step of calculating a level of Hepatitis B virus in a sample, falls within the grouping of abstract ideas and as they merely instruct a user to analyze changes of signals from various HBV target sequence(s) relative to a signal designated as a predetermined threshold (analyze natural law/natural sequences) and to draw a conclusion (i.e. the level/quantity/concentration of Hepatitis B virus). Concerning Step 2A, prong 2, the judicial exception of claims 135-153 are not integrated into a practical application because of the following. A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception, such that the claim is more than a drafting effort designed to monopolize the judicial exception. When the exception is so integrated, then the claim is not directed to a judicial exception. Claims 135-153 do not recite steps beyond the recited steps of comparing signals from HBV target sequences and a signal designated as a predetermined threshold, and determining level/quantity/concentration of Hepatitis B virus based on the signals. Claims 135-153 do not recite steps/elements that are construed to be a practical application that apply, rely on, or use the judicial exceptions. The steps of detecting a first and second signals from a first and second HBV target sequences respectively is not a practical application as this step must be applied to realize the judicial exception(s). They are also recited with a high level of generality and therefore do not add any meaningful limitation to practicing the natural law and/or abstract idea. Concerning Step 2B, claims 135-153 do not recite any additional elements that ensure that the claims as a whole amount to significantly more than the judicial exception(s). The steps of analyzing amplification data so as to conclude nucleic acid quantities constitute well-understood, routine, conventional activity. There is no inventive concept in claims 135-153, and thus they are rejected as being ineligible under 35 U.S.C. 101. 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. Claims 135-140, 144, 146-147 and 149-153 are rejected under 35 U.S.C. 103 as being unpatentable over Linnen et al. (US2011/0081645: cited on the IDS) in view of Rouet et al. (2008, Expert review of molecular diagnostics, 8(5), pp.635-650: newly cited), Giachetti et al. (2002, Journal of clinical microbiology, 40(7), pp.2408-2419: newly cited), Genbank Accession no. GU078862 (Oct 2009: cited on the IDS), An et al. (US2003/0050470: cited on the IDS), SantaLucia et al. (2007, HumanaPress: pp 3-33). Claims 135-136, 138-139, 149-154 Regarding claim 135, Linnen et al. teach a method of determining a level of Hepatitis B virus (HBV) in a sample comprising first and second Hepatitis B amplicons associated with first and second labels, respectively (see pg 25, Table 9, paragraphs [0097]-[0099], [0100]-[0102], [0111]-[0113], [0117]-[0122] and pg 18, Table 6), comprising: detecting a first signal emitted from the first label (see para [0095], Table 5, para [0100]-[0101], [0107]); detecting a second signal emitted from the second label (see para [0095], Table 5, para [0100]-[0101], [0107]). Linnen et al. teach generating a first and/or second signal(s) utilizing labeled probe oligomer(s) (see para [0136]-[0141]: and pg 13, Tables 13-14, wherein Linnen et al.âs method comprises providing at least one molecular beacon probe oligomer comprising a detectable label). Linnen et al. particularly teach quantifying a first and second HBV amplicons (see column entitled âHBV genotype A (copies)â of Table 6 on pg 18-20 and see column entitled âTemplate copy noâ of Table 7 on pg 22-23 or para [0120]-[0122]: which disclose use of the AMPLICOR HBV monitor assay and/or acridinium-ester labeled probes to quantify one or more HBV genotypes of one or more sample(s) and pg 25, Table 9: see column entitled âCopies/reactionâ). Regarding claim 136, Linnen et al. teach in-vitro sample (para [0105], [0115]). Regarding claim 138, Linnen et al. teach the level of Hepatitis B virus is a concentration (para [0127], Table 11 and para [0130], Table 12). Regarding claim 139, Linnen et al. teach wherein the level of Hepatitis B virus is an amount (para [0127], Table 11 and para [0130], Table 12). Regarding claim 149, Linnen et al. teach wherein the predetermined threshold corresponds to a concentration in the range of about 10 IU/ml to about 200 IU/ml (para [0100], [0115], [0124], [0127], [0130], Table 12). Regarding claim 150, Linnen et al. teach wherein the predetermined threshold is in the range of about 20 IU/ml to about 40 IU/ml, about 40 IU/ml to about 60 IU/ml, about 60 IU/ml to about 80 IU/ml, or about 80 IU/ml to about 100 IU/ml (para [0100], [0115], [0124], [0127], [0130], Table 12). Regarding claim 151, Linnen et al. teach wherein the first label, the second label, or both are fluorescent (para [0084], [0100], [0113], [0137], [0140], [0142]). Regarding claim 152, Linnen et al. teach wherein at least one of the first and second labels is attached to a probe (para [0084], [0100], [0113], [0137], [0140], [0142]). Regarding claim 153, Linnen et al. teach wherein the probe comprises a quencher (para [0084],[0136]-[0137], [0140], [0142]). Omitted from Linnen et al. Claims 135, 137, 140, 144, 146-147 Regarding claim 135, Linnen et al. do not expressly teach: determining whether the first signal or the second signal is above a predetermined threshold; and calculating a level of Hepatitis B virus in the sample, wherein if the first signal or the second signal is above a predetermined threshold, the level is calculated from the greater of the first and second signals; and wherein if the first signal and the second signal are below a predetermined threshold, the level is calculated from an average of the first and second signals Regarding claim 137, Linnen et al. do not teach determining the average of the first and second signals by determining first and second levels corresponding to the first and second signals, and arithmetically averaging the first and second levels. Regarding claim 140, Linnen et al. do not teach wherein one or both of the first and second amplicons comprise sequence from the S ORF of HBV. Regarding claim 144, Linnen et al. do not teach wherein the first amplicon comprises at least 10 contiguous nucleotides of one of SEQ ID NOs: 20, 21, or 22. Regarding claim 146, Linnen et al. do not teach wherein the second amplicon comprises at least 10 contiguous nucleotides of one of SEQ ID NOs: 34 or 35. Regarding claim 147, Linnen et al. do not teach wherein the predetermined threshold is at a value where expected random error is greater than or about equal to expected error due to a point mutation. Claim 135 and 137 Rouet et al. (2008) Regarding claim 135, Rouet et al. teach a method for quantifying a first and a second amplicon(s) in a sample by monitoring a first and second signals indicative of primer extension/probe hybridization to these amplicons respectively, and further determining whether the first signal or the second signal is above a predetermined threshold; and calculating a level of the amplicon(s) in the sample (see pg 637, Figure 1: the detected first and second signals are compared to Ct value, the instant predetermined threshold i.e. cycle 19 of figure 1). Rouet et al. teach if the first signal or the second signal is above a predetermined threshold, the level/quantity of amplicon is calculated from the greater of the first and second signals. Rouet et al. teach if the first signal and the second signal are below a predetermined threshold, the level is calculated from an average of the first and second signals (pg 637, Figure 1: signals below the Ct/predetermined are in the linear ground phase of Figure 1 and are average to establish the baseline/background signal). Regarding claim 137, Rouet et al. teach determining the average of the first and second signals by determining first and second levels corresponding to the first and second signals, and arithmetically averaging the first and second levels (pg 637, Figure 1: normal/routine detection to establish fluorescence burst in the early exponential and log-liner phase of Figure 1). Claim 147 Giachetti et al. (2002) Regarding claim 147, Giachetti et al. teach it already a matter of routine practice to choose the predetermined threshold with a value where expected random error is greater than or about equal to expected error due to a point mutation (see pg 2416, left col., 1st para below Table 6). The random error (i.e. variance within runsâ) is supposed to introduce the most variability over other factors assessed. Claims 140, 144, 146 GenBank Regarding claim 140 and/or claim 144, GenBank teach an oligonucleotide having the Accession No. GU078862 that is 100% identical to and indistinguishable from the instant (30 nt) SEQ ID NO: 20 at nucleotides 247-276 of GenBank GU078862. Regarding claim 140 and/or claim 144, GenBank teach an oligonucleotide having the Accession No. GU078862 that is 100% identical to and indistinguishable from the instant (22 nt) SEQ ID NO: 21 at nucleotides 247-268 of GenBank GU078862. Regarding claim 140 and/or claim 144, GenBank teach an oligonucleotide having the Accession No. GU078862 that is 100% identical to and indistinguishable from the instant (27 nt) SEQ ID NO: 22 at nucleotides 247-273 of GenBank GU078862. Accordingly, the oligonucleotide with the GenBank Accession No. GU078862 comprises at least 10 contiguous nucleotides of SEQ ID NO: 20, 21 or 22. Regarding claim 140 and/or claim 146, GenBank teach an oligonucleotide having the Accession No. GU078862 that is 100% identical to and indistinguishable from the instant (21 nt) SEQ ID NO: 34 at nucleotides 517-537 of GenBank GU078862. Regarding claim 140 and/or claim 146, GenBank teach an oligonucleotide having the Accession No. GU078862 that is 100% identical to and indistinguishable from the instant (27 nt) SEQ ID NO: 35 at nucleotides 517-543 of GenBank GU078862. Accordingly, the oligonucleotide with the GenBank Accession No. GU078862 comprises at least 10 contiguous nucleotides of SEQ ID NO: 34 or 35. Claims 140, 144, 146 An et al. (2003) Regarding primer and probe design, An et al. teach at paragraphs [0065]-[0067]:"Various probes and primers can be designed around the disclosed nucleotide sequences. Primers may be of any length but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the second residue is 2, etc., an algorithm defining all primers can be proposed: n to n+y where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus one (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 . . . and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 . . . and so on. For a 20-mer, the probes correspond to bases 1 to 20, 2 to 21, 3 to 22 . . . and so on." Therefore, An et al. not only taught designing primers of any length based on a known sequence, but also taught an algorithm for defining all possible primers of a given length based on a known sequence. In this respect, An et al. taught that all possible subsequences of a known sequence could be considered as a primer for that sequence. While An et al. was discussing in particular sequences having to do with prostate, bladder and breast cancer (see Abstract), one of ordinary skill in the art would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study. Claims 140, 144, 146 SantaLucia et al. (2007) SantaLucia et al. teach on page 14, âover the last 10 years (1996â2006), I have informally polled scientists who are experts in PCR and asked: âWhat percentage of the time does a casually designed PCR reaction âworkâ without any experimental optimization?â In this context, âworkâ means that the desired amplification product is made in good yield with a minimum of artifact products such as primer dimers, wrong amplicons, or inefficient amplification. By âcasually designed,â I mean that typical software tools are used by an experienced molecular biologist. The consensus answer is 70â75%. If one allows for optimization of the annealing temperature in the thermocycling protocol (e.g., by using temperature gradient optimization), magnesium concentration optimization, and primer concentration optimization, then the consensus percentage increases to 90â95%." Thus, SantaLucia et al. teach primers casually designed to a target sequence have a reasonable expectation of success at hybridizing, amplifying and detecting a target sequence. It would have been obvious to a person of ordinary skill in the art before the effective filing date of the invention to apply the teachings of Rouet et al. to the amplification and HBV detection method of Linnen et al. so as to enable the determining of a level or an amount of a first HBV amplicon and a second HBV amplicon by utilizing a first and second signal of a first and second detectable label respectively. Rouet et al. teach the signal phases during real-time monitoring of amplicon production. The ordinarily skilled artisan is readily apprised of how to establish baseline or background signal where signal detected in under the threshold line, and further how to quantify amplicons using the higher signal value âRn between the signals from two amplicons. Further, based on the teachings of Linnen et al. and Rouet et al., it was already known to provide probes comprising of detectable labels to generate signals useful for quantifying HBV amplicons. The ordinary skilled artisan would have readily quantified HBV amplicons comprising SEQ ID NO: 20, 21, 22, 34 or 35, by hybridizing detectably labeled probes to an amplicon comprising a HBV nucleotide sequence of SEQ ID NO: 20, 21, 22, 34 or 35, derived from the HBV oligonucleotide having the Genbank Accession Nos. GU078862 or V00866 (disclosed in para [0060] of Linnen et al.). The ordinary skilled artisan would have recognized that the sequence(s) derived from GenBank oligonucleotides correspond to homologs that are beneficial to use determining the level or an amount of would have been further motivated to follow guidance provided by An et al. and SantaLucia et al. for making and optimizing the hybridization of the detectably labeled probes suitable for determining the level or an amount of HBV amplicons comprising one of SEQ ID NO: 20, 21, 22, 34 or 35, or any nucleotide sequence derived from Genbank Accession Nos. GU078862 or V00866. In view of the combined teachings and suggestions of all of the cited prior art references, the instant claims 135-140, 144, 146-147 and 149-153 are prima facie obvious. Conclusion No claims are currently allowed. Correspondence Any inquiry concerning this communication or earlier communications from the examiner should be directed to OLAYINKA A OYEYEMI whose telephone number is (571)270-5956. 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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. OLAYINKA A. OYEYEMI Examiner Art Unit 1681 /OLAYINKA A OYEYEMI/Examiner, Art Unit 1681 /GARY BENZION/Supervisory Patent Examiner, Art Unit 1681