DETAILED ACTION
Applicant’s response, filed Nov 18 2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claim Status
Claims 1-20 are pending.
Claim 13 is objected to.
Claims 1-20 are rejected.
Priority
Applicant's claim for the benefit of a prior-filed application, PCT/EP2020/070715, filed Jul 22 2020, is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) to App. No. FR1908363, filed Jul 23 2019. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Accordingly, each of claims 1-20 are afforded the effective filing date of Jul 23 2019.
Information Disclosure Statement
The information disclosure statement filed Jul 24 2025 fails to comply with the provisions of 37 CFR 1.98(a)(4) because it lacks the appropriate size fee assertion. It has been placed in the application file, but the information referred to therein has not been considered as to the merits. It is noted that the IDS filed on Nov 18 2025 refers to the same references as the IDS filed Jul 24 2025, but does contain an appropriate size fee assertion.
The information disclosure statements (IDS) filed on Nov 18 2025 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action.
Claim Objections
The outstanding objections to the claims are withdrawn in view of the amendments submitted herein.
The claims are objected to because of the following informalities. The instant objection is newly stated and is necessitated by claim amendment.
Claim 13 recites, in the final two limitations, a plurality of steps: “determining… and confirming…”. As set forth in 37 CFR 1.75, where a claim sets forth a plurality of steps, each step of the claim should be separated by a line indentation (see MPEP 608.01(i)).
Claim Interpretation
The interpretation of contingent limitations recited in claims 6, 11, and 13-14 is withdrawn in view of the amendments and Applicant’s remarks on p. 3, section II, submitted herein.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portions are necessitated by claim amendment.
MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to a method, i.e., a process, machine, or manufacture within the above 101 categories [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) and mathematical concepts (in particular mathematical relationships and formulas) are as follows:
Independent claim 1: c) on the basis of the result of the sequencing, performing:
(i) assigning the sequences resulting from b) the sequencing, based on a reference database of sequences;
(ii) determining a quantity of sequences assigned to the biological species of interest;
(iii) taking into account a detection threshold associated with the biological species of interest;
(iv) comparing the quantity resulting from (ii) the determining of the quantity of sequences assigned to the biological species of interest to the detection threshold associated with the biological species of interest, resulting from (iii) the taking into account of the detection threshold associated with the biological species of interest;
wherein (c) the performing on the basis of the result of the sequencing comprises: (v) determining a quantity of sequences assigned to the control species;
(vi) taking into account a detection threshold associated with the control species;
(vii) comparing the quantity resulting from (v) the determining of the quantity of sequences assigned to the control species with the detection threshold associated with the control species, resulting from (vi) the taking into account of the detection threshold associated with the control species;
d) depending on the comparisons made in (iv) the comparing of the quantity resulting from the determining of the quantity of sequences assigned to the biological species of interest to the detection threshold associated with the biological species of interest and (vii) the comparing of the quantity resulting from the determining of the quantity of sequences assigned to the control species with the detection threshold associated with the control species, taking into account a concentration of the control species, so as to determine a presence of the biological species of interest in the sample.
Dependent claim 3: taking into account a decision threshold.
Dependent claim 15: a prior phase of determining the detection threshold associated with the biological species of interest, using a plurality of first training samples, which are considered to not comprise the biological species of interest, the method comprising, for each first training sample of the first training samples:
- determining a quantity of sequences of interest assigned to the biological species of interest;
- optionally normalizing the quantities of sequences of interest assigned to the biological species of interest;
the method then comprising: - computing a dispersion indicator for the quantities, or for the normalized quantities, of sequences of interest determined for each first training sample;
- determining the detection threshold associated with the biological species of interest depending on the dispersion indicator thus computed.
Dependent claim 16: a prior phase of determining the detection threshold associated with the control species, using a plurality of second training samples, which are considered to not comprise the control species, the method comprising, for each second training sample of the second training samples:
- determining a quantity of sequences assigned to the control species;
- optionally normalizing the quantities of sequences assigned to the control species;
the method then comprising:
- computing a dispersion indicator for the quantities, or for the normalized quantities, of sequences assigned to the control species and determined for each second training sample;
- determining the detection threshold associated with the control species depending on the dispersion indicator thus computed.
Dependent claims 2-9, 11-14, and 17-19 recite further steps that limit the judicial exceptions in independent claim 1 and, as such, also are directed to those abstract ideas. For example, claims 2 and 4 further limits the determining in (ii) and (v) to include normalizing by a reference quantity; claims 3, 5-9, 11-14 further limit d); claim 17 further limits at least one second training sample of claim 16; claim 18 further limits c) and d); and claim 19 further limits c), d), (v), (vi), and (vii).
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually determine whether a biological species of interest is present in a sample based on a comparison to the detection of a control species added into the sample. Without further detail as to the methodology involved in “performing”, “assigning”, “determining”, “taking into account”, “comparing”, “normalizing”, “computing”, and “estimating” under the BRI, one may simply, for example, use pen and paper to assign sequences to a biological species of interest or a control species, determine the quantity of those sequences, normalize the sequences, compute a dispersion indicator, determining a detection threshold based on the dispersion indicator, compare the quantity to the threshold, determine a presence of the biological species of interest based on those comparisons, and estimate a concentration of the biological species of interest based on the concentration of the control species. Some of these steps, such as normalizing the quantities of the sequences, computing a dispersion indicator, and estimating a concentration, require mathematical techniques as the only supported embodiments, as is disclosed in the specification as published at: [0116-0123: normalizing by dividing and multiplying; 0125, 0173-0176, and 0219-0220: computing a dispersion indicator and determining a detection threshold; 0131-0148 and 0154-0160: estimating a concentration].
Therefore, claim 1 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d).III).
Additional elements, Step 2A, Prong Two
With respect to the instant recitations, the claims recite the following additional elements:
Independent claim 1: a) extracting nucleic acids from the analysis sample;
b) sequencing = nucleotide sequences of the nucleic acids extracted in a) the extracting;
wherein the method further comprises, prior to a) the extracting, adding a control species, the control species being added, in a known concentration, to the analysis sample, the control species having a known genome.
Dependent claim 8: adding a calibrator, in a known concentration, to the sample, the calibrator having a known genome.
Dependent claim 15: - extracting nucleotide sequences;
- sequencing the nucleotide sequences thus extracted.
Dependent claim 16: - extracting nucleotide sequences;
- sequencing the nucleotide sequences thus extracted.
Dependent claim 19: prior to a) the extracting, adding a plurality of control species.
Dependent claims 10 and 20 recite steps that further limit the recited additional elements in the claims. For example, claims 10 and 20 further limit the control species to being the calibrator.
Considerations under Step 2A, Prong Two
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “adding” a control species and/or a calibrator, “extracting nucleic acids”, and “sequencing ”, perform functions of collecting the data needed to carry out the judicial exceptions. Data gathering does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
The specification as published discloses using a control species allowed a significant improvement to the specificity of the metagenomic test and a better detection of infections, without loss of sensitivity at [0242], but does not provide a clear explanation for how the additional elements provide these improvements because improved specificity and better detection are improvements afforded by the judicial exceptions which use the data provided by the sequenced control species, as is supported by the specification as published at [0082], which states that “Bioinformatical means then allow sequences of interest, associated with the biological species of interest, to be identified and a quantity thereof”. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exceptions [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B (MPEP 2106.05.A i-vi)
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the prior art reviews to Gu et al. (Annual Review of Pathology: Mechanisms of Disease, 2019, 14(1):319-338; newly cited) and Chiu et al. (Nature Reviews Genetics, 2019, 20(6):341-355; newly cited) disclose that spiking in internal controls of microorganisms to samples isolated from patients which contain unknown communities of microorganisms, and then extracting and sequencing nucleic acids from those samples, are data gathering elements that is routine, well-understood and conventional in the art. Said portions of the prior art are, for example, p. 327 in Gu and p. 350 in Chiu. The specification as published also notes that high-throughput sequencing is a commercially available method which is relatively common [0006], and that the technique used to sequence nucleic acid is well-known [0110]. Further, the courts have found that analyzing DNA to provide sequence information or detect allelic variants when claimed in a merely generic manner or as insignificant extra-solution activity is a well-understood, routine, conventional activity in the life science arts (Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546; University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014); see MPEP 2106.05(d)(II)). As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exceptions without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106.
Response to Applicant Arguments
At p. 4, section IV., Applicant submits that that the limitation of “wherein the method further comprises, prior to a) the extracting, adding a control species, the control species being added, in a known concentration, to the analysis sample, the control species having a known genome” provides a practical application of the control species.
It is respectfully submitted that this is not persuasive. When considering the claims as a whole, the additional element of adding the control species before extraction is considered to provide a data gathering function to the judicial exceptions recited in c) and d), where the nucleotide sequences derived from the sample and the added control species are examined. It is considered that the addition of the control species to the sample prior to extraction and sequencing does not provide an integration of the judicial exceptions, or of the control species as submitted by Applicant, because the control species was added to the sample for the purpose of using the data derived therefrom by the judicial exceptions. At Step 2A, Prong 2, data gathering does not impose any meaningful limitation on the judicial exceptions, or on how the judicial exceptions are performed. Data gathering steps are not sufficient to integrate judicial exceptions into a practical application (MPEP 2106.05(g)).
At p. 4-7, section IV., Applicant submits that the present claims are analogous to Rapid Litig. Mgmt. Ltd v. CellzDirect, Inc., 827 F.3d 1042 (Fed. Cir. 2016) because the claims define an “ordered combination” of modifying a sample which makes it possible to apply the processing as recited in order to improve accuracy of the detection of the biological species of interest. Applicant submits that the present claims define a technological process and device that improve on previously known techniques, in particular by using specific, non-conventional mathematical methods applied to a specific, non-conventional modified sample, i.e., by adding the control species to the analysis sample, and they result in an identification decision whose accuracy and reliability has been demonstrably improved. Applicant points to examples of improvements in false positive rates in the specification.
It is respectfully submitted that this is not persuasive. The instant claims are not considered to be analogous to Rapid for the following reasons. As submitted by Applicant, Rapid was found to be patent eligible because the claims applied the discovery that hepatocytes can be twice frozen to achieve a new and useful preservation process. In other words, the additional element of the preservation process was improved by freezing the cells twice, which recited a judicial exception of a natural process. Therefore, the recited judicial exception of the claim improved an additional element within the claim. However, as discussed in the above rejection, the instant claims do not recite the improvement in an additional element. The accuracy of the detection of the biological species of interest is directed to an improvement in the judicial exception of the claims, as set forth in the above rejection. The only additional elements in the claims recite steps for processing the sample to provide the sequencing data which is analyzed by the judicial exceptions of the claims. At Step 2A, Prong 2, such additional elements are found, as described above, to serve in the claim as a whole (i.e., in combination with the judicial exceptions), a data gathering function. At Step 2B, the data gathering elements are found, as described in the above rejection, to perform well-understood, routine, and conventional activities in the field.
Regarding Applicant’s remarks about a device in the claims, it is noted that Applicant’s argument is not commensurate with the scope of the claims because there is no claimed device.
Claim Rejections - 35 USC § 102
The outstanding rejection to claim 13 is withdrawn in view of the amendments submitted herein. Specifically, claim 13 no longer recites a contingent limitation, and the active steps recited therein are not completely taught by Chiu.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-7, 11, 14-15, and 18-20 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Chiu et al. (US20180203976; cited on the Jan 21 2022 IDS). Any newly cited portions are necessitated by claim amendment.
The prior art to Chiu discloses methods for pathogen detection using next-generation sequencing (NGS) analysis of a sample (abstract), where the sample includes DNA molecules from a plurality of organisms and the sequence reads are aligned to a plurality of classified reference genomes in a database (claim 1). Chiu teaches the instant features as follows.
Claim 1 discloses a method for detecting a biological species of interest (SOI) potentially present in an analysis sample, the biological species of interest having a known or partially known genome, the analysis sample comprising a mixture of various biological species, the method comprising:
a) extracting nucleic acids from the analysis sample;
b) sequencing nucleotide sequences of the nucleic acids extracted in a) the extracting;
c) on the basis of the result of the sequencing, performing: (i) assigning the sequences resulting from b) the sequencing, based on a reference database of sequences;
(ii) determining a quantity of sequences assigned to the biological species of interest;
(iii) taking into account a detection threshold associated with the biological species of interest;
(iv) comparing the quantity resulting from (ii) the determining of the quantity of sequences assigned to the biological species of interest to the detection associated with the biological species of interest, resulting from (iii) the taking into account of the detection threshold associated with the biological species of interest;
wherein the method further comprises, prior to a) the extracting, adding a control species, the control species being added, in a known concentration to the analysis sample, the control species having a known genome;
wherein (c) the performing on the basis of the result of the sequencing comprises:(v) determining a quantity of sequences assigned to the control species;
(vi) taking into account a detection threshold associated with the control species;
(vii) comparing the quantity resulting from (v) the determining of the quantity of sequences assigned to the control species with the detection threshold associated with the control species, resulting from (vi) the taking into account of the detection threshold associated with the control species;
d) depending on the comparisons made in (iv) the comparing of the quantity resulting from the determining of the quantity of sequences assigned to the biological species of interest to the detection threshold associated with the biological species of interest and (vii) the comparing of the quantity resulting from the determining of the quantity of sequences assigned to the control species with the detection threshold associated with the control species, taking into account a concentration of the control species, so as to determine a presence of the biological species of interest in the sample.
Chiu teaches including an internal spiked control of an organism added to every sample in specific concentrations [0173-0177; 0225-0231]. As Chiu teaches that the internal spiked controls can be detected through sequencing [0177], it is considered that the internal spiked controls have a known genome as instantly claimed. Chiu teaches performing nucleic acid extraction of the samples (i.e., step a)) [0038; 0040; 0238; 0245], sequencing DNA molecules (i.e., step b)) (claims 11 and 14; [0042; 0239]), aligning individual sequence reads from a sample in a next-generation sequencing (NGS) dataset against reference genome entries in a classified reference genome database (i.e., step (i)) (abstract; claims 1 and 9; [0009-0012; 0030-0033; 0044-0048]), and determining an amount of sequence reads that align to the matching reference genomes and the internally spiked control sequences (i.e., steps (ii and v)) (claim 13; [0184; 0198; 0201]). Chiu teaches comparing the read ratio of pathogens with a threshold to determine whether the pathogen is in the sample or just background (i.e., steps (iii-iv)) (claim 13; [0181; 0204]). Chiu teaches determining whether the samples passed quality control metrics of internally spiked read levels compared to an acceptable, pre-established threshold (i.e., steps (vi-vii)) [0184; 0229]. As Chiu teaches determining whether samples pass quality control before determining the presence of specific pathogens [0184], where the quality control depends on an internally spiked control added at a specific concentration, it is considered that Chiu fairly teaches step d).
Regarding claim 2, Chiu teaches the method of claim 1 as described above. Claim 2 further adds that in (ii) and (v) of claim 1, the sequence quantities respectively assigned to the biological species of interest and to the control species are normalized by a reference quantity. Chiu teaches normalizing the aligned reads [0178-0181].
Regarding claim 3, Chiu teaches the method of claim 1 as described above. Claim 3 further adds that in d) of claim 1, the presence of the biological species of interest above or below the decision threshold is confirmed or not confirmed. Chiu teaches comparing the read ratio of pathogens with a threshold to determine whether the pathogen is in the sample or just background (claim 13; [0181; 0204]). Chiu teaches determining whether the samples passed quality control metrics of internally spiked read levels compared to an acceptable, pre-established threshold [0184; 0229]. As Chiu teaches determining whether samples pass quality control before determining the presence of specific pathogens [0184], where the quality control depends on an internally spiked control added at a specific concentration, it is considered that Chiu fairly teaches step d).
Regarding claim 4, Chiu teaches the method of claims 1-2 as described above. Claim 4 further adds that the reference quantity is the total number of sequences produced during the sequencing. Chiu teaches normalizing by the total number of reads to determine the reads per million [0179].
Regarding claim 5, Chiu teaches the method of claim 1 as described above. Claim 5 further adds that d) comprises estimating a concentration of the biological species of interest; or estimating a minimum concentration of the biological species of interest; or taking into account a decision threshold and estimating a concentration of the biological species of interest relative to the decision threshold. Chiu teaches comparing the read ratio of pathogens with a threshold (i.e., decision threshold) to determine whether the pathogen is in the sample or just background (claim 13; [0181; 0204]), which is considered to read on “estimating a minimum concentration of the biological species of interest” because, under the broadest reasonable interpretation, estimating encompasses an approximation of an amount but does not require calculating a specific value. Chiu teaches that the sequencing data can yield additional information besides whether or not a given microorganism or microorganism type is present or absent including quantitative information based on the identified reads aligned to a control [0039], which is considered to fairly read on “estimating a concentration of the biological species” as instantly claimed, where a concentration, under the broadest reasonable interpretation, reads on an amount of reads sequenced.
Regarding claim 6, Chiu teaches the method of claim 1 as described above. Claim 6 further adds that d) comprises determining the quantity of sequences assigned to the control species and to the biological species of interest are higher than their associated detection thresholds, and confirming the presence of the biological species of interest in the analysis sample. As Chiu teaches determining whether samples pass quality control by comparing internal spiked control reads to a pre-established threshold (i.e., a detection threshold) before determining the presence of specific pathogens based on comparison to a threshold [0184], where the quality control depends on an internally spiked control added at a specific concentration, it is considered that Chiu fairly teaches the limitation of claim 6.
Regarding claim 7, Chiu teaches the method of claims 1 and 6 as described above. Claim 7 further adds that d) further comprises estimating a concentration of the biological species of interest. Chiu teaches that the sequencing data can yield additional information besides whether or not a given microorganism or microorganism type is present or absent including quantitative information based on the identified reads aligned to a control [0039], which is considered to fairly read on “estimating a concentration of the biological species” as instantly claimed, because, under the broadest reasonable interpretation, estimating encompasses an approximation of an amount but does not require calculating a specific value, and a concentration, under the broadest reasonable interpretation, reads on an amount of reads sequenced.
Regarding claim 11, Chiu teaches the method of claims 1 and 3 as described above. Claim 11 further adds that d) comprises determining that the quantity of sequences assigned to the control species is higher than the detection threshold associated with the control species, and that the quantity of sequences assigned to the biological species of interest is lower than the detection threshold associated with the biological species of interest; estimating a minimum detectable concentration of the biological species of interest and comparing the minimum detectable concentration of the biological species of interest with the decision threshold; determining that the minimum concentration of the biological species of interest is lower than the decision threshold, and estimating that the biological species of interest is not present in the analysis sample in a concentration higher than the decision threshold. Chiu teaches determining whether samples pass quality control by comparing internal spiked control reads to a pre-established threshold (i.e., a detection threshold) before determining the presence of specific pathogens based on comparison to a threshold [0184], where samples with more reads than detection thresholds based on background reads in a no template control sample are determined to have the pathogen present [0172-0176], which is considered to read on “estimating a minimum detectable concentration” as instantly claimed, because, under the broadest reasonable interpretation, estimating encompasses an approximation of an amount but does not require calculating a specific value, and a concentration, under the broadest reasonable interpretation, reads on an amount of reads sequenced.
Regarding claim 14, Chiu teaches the method of claim 1 as described above. Claim 14 further adds determining the quantities of sequences assigned to the control species and biological species of interest are lower than their detection thresholds, and giving no confirmation as to the presence of the biological species of interest. Chiu teaches determining whether samples pass quality control by comparing internal spiked control reads to a pre-established threshold (i.e., a detection threshold) before determining the presence of specific pathogens based on comparison to a threshold, and not using those samples which do not pass [0184]. Chiu teaches that only samples with more reads than a detection threshold based on background reads in a no template control sample are determined to have the pathogen present [0172-0176; 0181].
Regarding claims 15, Chiu teaches the method of claim 1 as described above. Claim 15 further adds a prior phase of determining the detection threshold associated with the biological species of interest, using a plurality of first training samples, which are considered to not comprise the biological species of interest, the method comprising, for each first training sample of the plurality of first training samples: extracting nucleotide sequences; sequencing the nucleotide sequences thus extracted; determining a quantity of sequences of interest assigned to the biological species of interest; optionally normalizing the quantities of sequences of interest assigned to the biological species of interest; the method then comprising: computing a dispersion indicator for the quantities, or for the normalized quantities, of sequences of interest determined for each first training sample; determining the detection threshold associated with the biological species of interest depending on the dispersion indicator thus computed. Chiu teaches using a no template control to determine how many reads are classified as aligning to a microorganism and assigning those as background reads in order to reduce the number of hits in the actual sample [0176] by identifying contaminants and removing background reds [0172]. As Chiu teaches analyzing sequences from the no template controls, it is considered that Chiu extracted and sequenced the nucleotide sequences in the no template controls. Chiu teaches storing the levels of background sequences from multiple samples [0049]. Chiu teaches normalizing the reads in the sample and the no template control [0180]. Chiu teaches making a contaminants database based on the pathogens identified in the no template control, where the threshold for detecting a pathogen in a sample is based on the maximum amount (i.e., a dispersion indicator) of reads observed in the contaminant database in the last 3 months [0192-0195].
Regarding claim 18, Chiu teaches the method of claim 1 as described above. Claim 18 further adds that c) and d) are carried out in parallel respectively for various biological species of interest, each biological species of interest of the various biological species of interest being considered to be potentially present in the sample. Chiu teaches a method for a broad, comprehensive pathogen diagnostic for infectious diseases by analyzing sequencing results against many reference genomes, as a metagenomics analysis in order to detect all pathogens in a single assay [0030].
Regarding claim 19, Chiu teaches the method of claim 1 as described above. Claim 19 further adds adding a plurality of control species so that c) and d) are carried out taking into account a plurality of control species and that (v-vii) are implemented in parallel for each control species. Chiu teaches using an internally spiked DNA control and RNA control [0184]. As Chiu teaches a method for a broad, comprehensive pathogen diagnostic for infectious diseases by analyzing sequencing results against many reference genomes, as a metagenomics analysis in order to detect all pathogens in a single assay [0030], it is considered that Chiu teaches adding the DNA and RNA control to each samples and analyzing the results for each control for each sample.
Regarding claim 20, Chiu teaches the method of claims 1 and 9 as described above. Claim 20 further adds the control species is the calibrator. Chiu teaches that the sequencing data can yield additional information besides whether or not a given microorganism or microorganism type is present or absent including quantitative information based on the identified reads aligned to a control [0039], which is considered to fairly read on the control species being the calibrator as instantly claimed.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
A. Claims 8-10 and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Chiu, as applied to claims 1 and 11 in the above 35 USC 102 rejection, and in further view of Harness et al. (US 2022/0002781; priority to Oct 4 2018; previously cited). Any newly cited portions are necessitated by claim amendment.
Regarding claims 8-9, Chiu teaches the method of claims 1 and 6-7 as described above. Claim 8 further adds adding a calibrator, in a known concentration, to the sample, the calibrator having a known genome, and wherein estimating the concentration of the biological species of interest comprises: determining a quantity of sequences assigned to the calibrator; determining a first ratio, between the quantities of sequences respectively assigned to the biological species of interest and to the calibrator; determining a second ratio, between the respective genome sizes of the calibrator and of the biological species of interest; taking into account the calibrator concentration added to the analysis sample. Claim 9 further adds computing a product of the first ratio multiplied by the second ratio and by the concentration of the calibrator added to the analysis sample. Chiu teaches spiking in an internal control (i.e., calibrator) at specific concentrations in the clinical samples [0177]. Chiu does not teach determining a first or second ratio as instantly claimed.
However, the prior art to Harness discloses compositions and methods for the quantification of a target nucleic acid sequence or sequences in a sample using next generation sequencing (abstract). Harness teaches that normalizing controls are used to determine the absolute amounts of different nucleic acids in a sample, including a pathogen in an infected host sample [1005]. Harness teaches that an abundance value for the pathogen is determined by dividing the number of NGS reads that map to the pathogen by the number of NGS reads that map to the NCs (i.e., a first ratio as recited in claim 8) and then correcting that value for pathogen genome size [1005]. At [1006], Harness teaches an example of the normalizing control comprising T4 phage nucleic acid sequences, and the pathogen comprises cytomegalovirus. Harness teaches that because the T4 phage and CMV genomes are both around 200 kb, the two are about the same size, and it is assumed that plaque forming units/mL (pfu/mL, T4) and copies/mL (cp/mL, CMV) are equivalent. Harness teaches that if, after next generation sequencing, there are 2 CMV reads for every 1 read of T4 phage NC, and the NC was added at a concentration of 100 pfu/ml (i.e., taking into account the calibrator concentration in claim 8), then the CMV must have been at a concentration of 200 cp/ml. If the CMV were ½ the genome size of T4 (i.e., a second ratio as recited in claim 8), then the CMV and T4 would be present at approximately the same concentration (100 pfu/ml or cp/ml) in the initial sample. This example is considered to read on computing a product as recited in claim 9.
Regarding claim 10, Chiu teaches the method of claims 1 and 6-7 and, in further view of Harness, claim 8 as described above. Claim 10 further adds that the control species is the calibrator. Chiu teaches that the sequencing data can yield additional information besides whether or not a given microorganism or microorganism type is present or absent including quantitative information based on the identified reads aligned to a control [0039], which is considered to fairly read on the control species being the calibrator as instantly claimed.
Regarding claim 12, Chiu teaches the method of claims 1, 3, and 11 as described above. Claim 12 further adds that estimating the minimum detectable concentration comprises: determining a first ratio, between the detection threshold of the biological species of interest and that of the quantity of sequences assigned to the control species; determining a second ratio of sizes, between the respective genome sizes of the control species and of the biological species of interest; and taking into account the concentration of the control species added to the analysis sample, which Chiu does not teach.
However, the prior art to Harness discloses compositions and methods for the quantification of a target nucleic acid sequence or sequences in a sample using next generation sequencing (abstract). Harness teaches that normalizing controls are used to determine the absolute amounts of different nucleic acids in a sample, including a pathogen in an infected host sample [1005]. Harness teaches that an abundance value for the pathogen is determined by dividing the number of NGS reads that map to the pathogen by the number of NGS reads that map to the NCs (i.e., a first ratio) and then correcting that value for pathogen genome size [1005]. At [1006], Harness teaches an example of the normalizing control comprising T4 phage nucleic acid sequences, and the pathogen comprises cytomegalovirus. Harness teaches that because the T4 phage and CMV genomes are both around 200 kb, the two are about the same size, and it is assumed that plaque forming units/mL (pfu/mL, T4) and copies/mL (cp/mL, CMV) are equivalent. Harness teaches that if, after next generation sequencing, there are 2 CMV reads for every 1 read of T4 phage NC, and the NC was added at a concentration of 100 pfu/ml (i.e., taking into account the calibrator concentration), then the CMV must have been at a concentration of 200 cp/ml. If the CMV were ½ the genome size of T4 (i.e., a second ratio), then the CMV and T4 would be present at approximately the same concentration (100 pfu/ml or cp/ml) in the initial sample.
Regarding claims 8-10 and 12, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Chiu and Harness because both references disclose the use of internal controls to identify pathogens. The motivation to estimate a concentration of the pathogen as taught by Harness would have been to compensate for differing background host contents and to derive an absolute pathogen abundance in the starting material, as taught by Harness [1005].
B. Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Chiu, as applied to claims 1 and 3 in the above 35 USC 102 rejection, and in further view of Miller et al. (Genome Research, Apr 16 2019, 29:831-842; cited on the Jan 21 2022 IDS). The rejection is newly stated and is necessitated by claim amendment.
Regarding claim 13, Chiu teaches the method of claims 1 and 3 as described above. Claim 13 further adds determining the quantity of sequences assigned to the control species is lower than its detection threshold, and that the quantity of sequences assigned to the biological species of interest is higher than the detection threshold associated with the biological species of interest, comparing the concentration of the control species added to the analysis sample with the decision threshold, including determining the concentration of the control species added to the analysis sample is higher than the decision threshold and confirming the presence of the biological species of interest in the analysis sample in a concentration higher than the decision threshold; or determining that the concentration of the control species added to the analysis sample is lower than the decision threshold, and confirming the presence of the biological species of interest in the analysis sample. Chiu teaches only providing results when the sample passes quality control metrics including having greater than a threshold of internally spiked species [0184]. Chiu therefore does not teach confirming the presence of the biological species of interest in these samples.
However, the prior art to Miller discloses a clinical metagenomic next-generation sequencing (mNGS) assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) (abstract). Miller teaches determining the limits of detection based on the concentration of the samples (p. 832, col. 2, par. 4). Miller teaches determining the presence of the pathogen when it has greater than a certain threshold of reads (p. 832, col. 2, par. 2-3). Miller teaches using a spiked phage internal control (IC) (p. 832, col. 2, par. 5; Figure 1), where samples with fewer than 100 RPM IC phage reads (i.e., a threshold) indicated a high host background in the sample and explained decreased sensitivity in the mNGS assay, indicating that those samples with high background and negative mNGS findings may be less useful for excluding infection (p. 839, col. 2, par. 1). However, Miller teaches only excluding samples with a lower RPM IC phage reads when a negative result is obtained during discrepancy testing by comparing mNGS results to clinical results which indicated a presence of the organisms (p. 833, col., 1, par. 1 through p. 837, col. 2, par. 3), which indicates that those samples are not excluded when a positive result is obtained. Therefore, it is considered that Miller fairly teaches confirming the presence of a biological species of interest in a sample when the control species is not detected at a high enough level as instantly claimed.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Chiu and Miller because both references disclose the use of internal controls to identify pathogens. The motivation would have been to follow a developed and validated mNGS assay for the detection of pathogens in a clinical sample, as taught by Miller (p. 832, col. 1, par. 3). It would have been obvious one of ordinary skill in the art to modify the method of Chiu to exclude samples with lower than a threshold level of spiked internal control reads from further consideration only when those samples had a negative result, because, as taught by Miller, those samples cannot be reliably used to determine that no infection is present because of a high host background (p. 839, col. 2, par. 1). Conversely, however, one of ordinary skill in the art would recognize that samples with lower than a threshold level of spiked internal control reads and a positive result for a biological species of interest could still be trusted to indicate that the biological species of interest is present in the sample.
C. Claims 16-17 are rejected under 35 U.S.C. 103 as being unpatentable over the features of Chiu, as applied to claim 1 in the above 35 USC 102 rejection. Any newly cited portions are necessitated by claim amendment.
Regarding claim 16, Chiu teaches the method of claim 1 as described above. Claim 16 further adds a prior phase of determining the detection threshold associated with the control species, using a plurality of second training samples, which are considered to not comprise the control species, the method comprising, for each second training sample of the plurality of second training samples: extracting nucleotide sequences; sequencing the nucleotide sequences thus extracted; determining a quantity of sequences assigned to the control species; optionally normalizing the quantities of sequences assigned to the control species; the method then comprising: computing a dispersion indicator for the quantities, or for the normalized quantities, of sequences assigned to the control species and determined for each second training sample; determining the detection threshold associated with the control species depending on the dispersion indicator thus computed. Chiu teaches using a no template control to determine how many reads are classified as aligning to a microorganism and assigning those as background reads in order to reduce the number of hits in the actual sample [0176] by identifying contaminants and removing background reds [0172]. As Chiu teaches analyzing sequences from the no template controls, it is considered that Chiu extracted and sequenced the nucleotide sequences in the no template controls. Chiu teaches storing the levels of background sequences from multiple samples [0049]. Chiu teaches normalizing the reads in the sample and the no template control [0180]. Chiu teaches making a contaminants database based on the pathogens identified in the no template control, where the threshold for detecting a pathogen in a sample is based on the maximum amount (i.e., a dispersion indicator) of reads observed in the contaminant database in the last 3 months [0192-0195]. Chiu does not teach determining the reads for the spiked in control sequences in the no template controls.
However, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify, in the course of routine experimentation and with a reasonable expectation of success, the features of Chiu to determine the reads for the spiked in control sequences along with the reads for the pathogen species in the no template controls. Chiu teaches using the contaminant database to determine background or contaminated buffers [0176; 0192]. One of ordinary skill in the art would similarly be motivated to include the reads for the spiked in control sequences in the no template controls in the contaminant database to ensure that the buffers used in the sample preparation were not contaminated with the internal control sequences because of common sense and a desire to improve sample integrity.
Regarding claim 17, the features of Chiu teach the method of claims 1 and 16 as described above. Claim 17 further adds that at least one second training sample of the plurality of second training samples is an analysis sample, with no control species added. Chiu teaches determining read counts in the negative no-template control (i.e., no control added) [0176; 0180]. The negative no-template control reads on an analysis sample as instantly claimed because the sample is analyzed in the method of Chiu.
Response to Applicant Arguments Regarding 35 USC 102 and 103
At p. 7-9, section V., Applicant submits that Chiu does not teach an equivalent of a control species with their spiked control, because the control species is added to a neutral matrix and not the test sample to monitor a PCR step and not sequencing as is discussed in [0147-0148] of Chiu. Applicant submits that as Chiu does not teach the control species as claimed, Chiu additionally does not use a detection threshold for the control species. Applicant submits that the other cited reference to Harness fails to remedy the supposed deficiencies of Chiu for the independent and dependent claims..
It is respectfully submitted that this is not persuasive. Chiu clearly teaches at [0177] that “An internal spiked control can include organisms spiked into a patient sample. For example, a DNA phage and/or an RNA phage can be spiked in specific concentrations in a clinical sample. Embodiments can check to make sure that the phages can be detected in the DNA library, e.g., a sufficient number of sequences from the DNA phage. Similarly, a check can make sure that the phages are detected in the RNA library, e.g., a sufficient number of sequences from the RNA phage. This control can be an internal control on every sample, in addition to external control.”. Chiu therefore clearly teaches the addition of an internal spiked control to a patient, or test, sample which is detected in the resulting sequencing data, contrary to Applicant’s assertions.
Further, Chiu clearly teaches at [0184] that “For result-based testing, for each sample, performance is evaluated as it pertains to detection of all 5 organism types (bacteria, fungi, DNA virus, RNA virus and parasites). Only results for acceptable samples (passed quality control metrics of >5,000,000 reads per library and >10 RPM of either an internally spiked DNA control, T1 bacteriophage, for DNA libraries, or an internally spiked RNA control, M2 bacteriophage, for RNA libraries; sufficient sample volume) are provided in the tables below.” Chiu therefore clearly teaches using the sequencing results of the internal spiked control to determine whether the species of interest was detected, contrary to Applicant’s assertions.
The rejections are therefore maintained.
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.
A. Claims 1-3, 5, 7-10, and 20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-2 and 7 of copending Application No. 17/629,065, claims 4, 6, 11, and 14-19 are rejected in further view of Chiu et al. (US20180203976; cited on the Jan 21 2022 IDS), claim 12 is rejected in further view of Harness et al. (US 2022/0002781; priority to Oct 4 2018; previously cited), and claim 13 is rejected in further view of Chiu and Miller et al. (Genome Research, Apr 16 2019, 29:831-842; cited on the Jan 21 2022 IDS). Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons. Any newly recited portions are necessitated by claim amendment. The rejection for claims 6 and 11-14 are newly cited and necessitated by claim amendment.
This is a provisional nonstatutory double patenting rejection.
Regarding instant claim 1, reference claim 1 discloses the limitations of instant claim 1.
Regarding instant claim 2, reference claim 2 discloses the limitations of instant claim 2.
Regarding instant claim 3, reference claim 1 discloses the limitations of instant claim 3.
Regarding instant claim 4, the reference patent does not disclose the limitations of instant claim 4.
However, prior art to Chiu discloses methods for pathogen detection using next-generation sequencing (NGS) analysis of a sample (abstract), where the sample includes DNA molecules from a plurality of organisms and the sequence reads are aligned to a plurality of classified reference genomes in a database (claim 1). Chiu teaches normalizing by the total number of reads to determine the reads per million [0179].
Regarding instant claim 5, reference claim 1 discloses the limitations of instant claim 5.
Regarding instant claim 6, the reference patent does not disclose the limitations of instant 6.
However, Chiu teaches determining whether samples pass quality control by comparing internal spiked control reads to a pre-established threshold (i.e., a detection threshold) before determining the presence of specific pathogens based on comparison to a threshold [0184], where the quality control depends on an internally spiked control added at a specific concentration, it is considered that Chiu fairly teaches the limitation of claim 6.
Regarding instant claim 7, reference claim 1 discloses the limitations of instant claim 7.
Regarding instant claim 8, reference claim 7 discloses the limitations of instant claim 8.
Regarding instant claim 9, reference claim 1 discloses the limitations of instant claim 9.
Regarding instant claim 10, reference claim 1 discloses the limitations of instant claim 10.
Regarding instant claim 11, the reference patent does not disclose the limitations of instant claim 11.
However, as this limitation is contingent up on the conditions recited in the claims, it is not required to be performed. As the reference patent discloses the limitations of claims 1 and 3 above, it is therefore considered that the reference patent also discloses the limitations of claim 11 as interpreted under the BRI.
Regarding instant claim 12, the reference patent does not disclose the limitations of instant claim 12.
However, However, the prior art to Harness discloses compositions and methods for the quantification of a target nucleic acid sequence or sequences in a sample using next generation sequencing (abstract). Harness teaches that normalizing controls are used to determine the absolute amounts of different nucleic acids in a sample, including a pathogen in an infected host sample [1005]. Harness teaches that an abundance value for the pathogen is determined by dividing the number of NGS reads that map to the pathogen by the number of NGS reads that map to the NCs (i.e., a first ratio) and then correcting that value for pathogen genome size [1005]. At [1006], Harness teaches an example of the normalizing control comprising T4 phage nucleic acid sequences, and the pathogen comprises cytomegalovirus. Harness teaches that because the T4 phage and CMV genomes are both around 200 kb, the two are about the same size, and it is assumed that plaque forming units/mL (pfu/mL, T4) and copies/mL (cp/mL, CMV) are equivalent. Harness teaches that if, after next generation sequencing, there are 2 CMV reads for every 1 read of T4 phage NC, and the NC was added at a concentration of 100 pfu/ml (i.e., taking into account the calibrator concentration), then the CMV must have been at a concentration of 200 cp/ml. If the CMV were ½ the genome size of T4 (i.e., a second ratio), then the CMV and T4 would be present at approximately the same concentration (100 pfu/ml or cp/ml) in the initial sample.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of the reference application and Harness because each reference discloses the use of internal controls to identify pathogens. The motivation to estimate a concentration of the pathogen as taught by Harness would have been to compensate for differing background host contents and to derive an absolute pathogen abundance in the starting material, as taught by Harness [1005].
Regarding instant claim 13, the reference patent does not disclose the limitations of instant claim 13.
However, Chiu teaches only providing results when the sample passes quality control metrics including having greater than a threshold of internally spiked species [0184]. Chiu therefore does not teach confirming the presence of the biological species of interest in these samples.
However, the prior art to Miller discloses a clinical metagenomic next-generation sequencing (mNGS) assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) (abstract). Miller teaches determining the limits of detection based on the concentration of the samples (p. 832, col. 2, par. 4). Miller teaches determining the presence of the pathogen when it has greater than a certain threshold of reads (p. 832, col. 2, par. 2-3). Miller teaches using a spiked phage internal control (IC) (p. 832, col. 2, par. 5; Figure 1), where samples with fewer than 100 RPM IC phage reads (i.e., a threshold) indicated a high host background in the sample and explained decreased sensitivity in the mNGS assay, indicating that those samples with high background and negative mNGS findings may be less useful for excluding infection (p. 839, col. 2, par. 1). However, Miller teaches only excluding samples with a lower RPM IC phage reads when a negative result is obtained during discrepancy testing by comparing mNGS results to clinical results which indicated a presence of the organisms (p. 833, col., 1, par. 1 through p. 837, col. 2, par. 3), which indicates that those samples are not excluded when a positive result is obtained. Therefore, it is considered that Miller fairly teaches confirming the presence of a biological species of interest in a sample when the control species is not detected at a high enough level as instantly claimed.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of the reference application, Chiu, and Miller because each reference discloses the use of internal controls to identify pathogens. The motivation would have been to follow a developed and validated mNGS assay for the detection of pathogens in a clinical sample, as taught by Miller (p. 832, col. 1, par. 3). It would have been obvious one of ordinary skill in the art to modify the method of Chiu to exclude samples with lower than a threshold level of spiked internal control reads from further consideration only when those samples had a negative result, because, as taught by Miller, those samples cannot be reliably used to determine that no infection is present because of a high host background (p. 839, col. 2, par. 1). Conversely, however, one of ordinary skill in the art would recognize that samples with lower than a threshold level of spiked internal control reads and a positive result for a biological species of interest could still be trusted to indicate that the biological species of interest is present in the sample.
Regarding instant claim 14, the reference patent does not disclose the limitations of instant claim 14.
However, Chiu teaches determining whether samples pass quality control by comparing internal spiked control reads to a pre-established threshold (i.e., a detection threshold) before determining the presence of specific pathogens based on comparison to a threshold, and not using those samples which do not pass [0184]. Chiu teaches that only samples with more reads than a detection threshold based on background reads in a no template control sample are determined to have the pathogen present [0172-0176; 0181].
Regarding instant claim 15, the reference patent does not disclose the limitations of instant claim 15.
However, Chiu teaches using a no template control to determine how many reads are classified as aligning to a microorganism and assigning those as background reads in order to reduce the number of hits in the actual sample [0176] by identifying contaminants and removing background reds [0172]. As Chiu teaches analyzing sequences from the no template controls, it is considered that Chiu extracted and sequenced the nucleotide sequences in the no template controls. Chiu teaches storing the levels of background sequences from multiple samples [0049]. Chiu teaches normalizing the reads in the sample and the no template control [0180]. Chiu teaches making a contaminants database based on the pathogens identified in the no template control, where the threshold for detecting a pathogen in a sample is based on the maximum amount (i.e., a dispersion indicator) of reads observed in the contaminant database in the last 3 months [0192-0195].
Regarding instant claim 16, the reference patent does not disclose the limitations of instant claim 16.
However, Chiu teaches using a no template control to determine how many reads are classified as aligning to a microorganism and assigning those as background reads in order to reduce the number of hits in the actual sample [0176] by identifying contaminants and removing background reds [0172]. As Chiu teaches analyzing sequences from the no template controls, it is considered that Chiu extracted and sequenced the nucleotide sequences in the no template controls. Chiu teaches storing the levels of background sequences from multiple samples [0049]. Chiu teaches normalizing the reads in the sample and the no template control [0180]. Chiu teaches making a contaminants database based on the pathogens identified in the no template control, where the threshold for detecting a pathogen in a sample is based on the maximum amount (i.e., a dispersion indicator) of reads observed in the contaminant database in the last 3 months [0192-0195]. Chiu does not teach determining the reads for the spiked in control sequences in the no template controls.
However, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify, in the course of routine experimentation and with a reasonable expectation of success, the features of Chiu to determine the reads for the spiked in control sequences along with the reads for the pathogen species in the no template controls. Chiu teaches using the contaminant database to determine background or contaminated buffers [0176; 0192]. One of ordinary skill in the art would similarly be motivated to include the reads for the spiked in control sequences in the no template controls in the contaminant database to ensure that the buffers used in the sample preparation were not contaminated with the internal control sequences because of common sense and a desire to improve sample integrity.
Regarding instant claim 17, the reference patent does not disclose the limitations of instant claim 17.
However, Chiu teaches determining read counts in the negative no-template control (i.e., no control added) [0176; 0180]. The negative no-template control reads on an analysis sample as instantly claimed because the sample is analyzed in the method of Chiu.
Regarding instant claim 18, the reference patent does not disclose the limitations of instant claim 18.
Chiu teaches a method for a broad, comprehensive pathogen diagnostic for infectious diseases by analyzing sequencing results against many reference genomes, as a metagenomics analysis in order to detect all pathogens in a single assay [0030].
Regarding instant claim 19, the reference patent does not disclose the limitations of instant claim 19.
However, Chiu teaches using an internally spiked DNA control and RNA control [0184]. As Chiu teaches a method for a broad, comprehensive pathogen diagnostic for infectious diseases by analyzing sequencing results against many reference genomes, as a metagenomics analysis in order to detect all pathogens in a single assay [0030], it is considered that Chiu teaches adding the DNA and RNA control to each samples and analyzing the results for each control for each sample.
Regarding instant claim 20, reference claim 1 discloses the limitations of instant claim 20.
Regarding claims 4, 6, 11, and 14-19, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of the reference patent and Chiu because both references disclose the use of internal controls to identify pathogens. The motivation would have been to quickly analyze millions of reads that include millions of data points that come out of a DNA sequence system, as well as interpret the data so that it is clinically useful to laboratory scientists and/or a physician, as taught by Chiu [0007].
B. Claims 1, 3, 5-14, and 20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-8, 10, 12-13, and 20 of copending Application No. 18/716,107, and claims 2, 4, and 15-19 are rejected in further view of Chiu et al. (US20180203976; cited on the Jan 21 2022 IDS). Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons. Any newly recited portions are necessitated by claim amendment.
This is a provisional nonstatutory double patenting rejection.
Regarding instant claim 1, reference claim 1 discloses the limitations of instant claim 1.
Regarding instant claim 2, the reference patent does not disclose the limitations of instant claim 2.
However, the prior art to Chiu discloses methods for pathogen detection using next-generation sequencing (NGS) analysis of a sample (abstract), where the sample includes DNA molecules from a plurality of organisms and the sequence reads are aligned to a plurality of classified reference genomes in a database (claim 1). Chiu teaches normalizing the aligned reads [0178-0181].
Regarding instant claim 3, reference claim 1 discloses the limitations of instant claim 3.
Regarding instant claim 4, the reference patent does not disclose the limitations of instant claim 4.
However, Chiu teaches normalizing by the total number of reads to determine the reads per million [0179].
Regarding instant claim 5, reference claim 3 discloses the limitations of instant claim 5.
Regarding instant claim 6, reference claims 3 and 10 disclose the limitations of instant claim 6.
Regarding instant claim 7, reference claim 3 discloses the limitations of instant claim 7.
Regarding instant claim 8, reference claim 3 discloses the limitations of instant claim 8.
Regarding instant claim 9, reference claim 20 discloses the limitations of instant claim 9.
Regarding instant claim 10, reference claim 1 discloses the limitations of instant claim 10.
Regarding instant claim 11, reference claims 5-6 disclose the limitations of instant claim 11.
Regarding instant claim 12, reference claims 3, 7, 12-13, and 20 disclose the limitations of instant claim 12.
Regarding instant claim 13, reference claim 4 discloses the limitations of instant claim 13.
Regarding instant claim 14, reference claim 8 discloses the limitations of instant claim 14.
Regarding instant claim 15, reference claims 3-5 discloses the limitations of instant claim 15, except for the limitation regarding computing a dispersion indicator.
However, Chiu teaches using a no template control to determine how many reads are classified as aligning to a microorganism and assigning those as background reads in order to reduce the number of hits in the actual sample [0176] by identifying contaminants and removing background reds [0172]. As Chiu teaches analyzing sequences from the no template controls, it is considered that Chiu extracted and sequenced the nucleotide sequences in the no template controls. Chiu teaches storing the levels of background sequences from multiple samples [0049]. Chiu teaches normalizing the reads in the sample and the no template control [0180]. Chiu teaches making a contaminants database based on the pathogens identified in the no template control, where the threshold for detecting a pathogen in a sample is based on the maximum amount (i.e., a dispersion indicator) of reads observed in the contaminant database in the last 3 months [0192-0195].
Regarding instant claim 16, reference claim 3-5 discloses the limitations of instant claim 16, except for the limitation regarding computing a dispersion indicator.
However, Chiu teaches using a no template control to determine how many reads are classified as aligning to a microorganism and assigning those as background reads in order to reduce the number of hits in the actual sample [0176] by identifying contaminants and removing background reds [0172]. As Chiu teaches analyzing sequences from the no template controls, it is considered that Chiu extracted and sequenced the nucleotide sequences in the no template controls. Chiu teaches storing the levels of background sequences from multiple samples [0049]. Chiu teaches normalizing the reads in the sample and the no template control [0180]. Chiu teaches making a contaminants database based on the pathogens identified in the no template control, where the threshold for detecting a pathogen in a sample is based on the maximum amount (i.e., a dispersion indicator) of reads observed in the contaminant database in the last 3 months [0192-0195]. Chiu does not teach determining the reads for the spiked in control sequences in the no template controls.
However, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify, in the course of routine experimentation and with a reasonable expectation of success, the features of Chiu to determine the reads for the spiked in control sequences along with the reads for the pathogen species in the no template controls. Chiu teaches using the contaminant database to determine background or contaminated buffers [0176; 0192]. One of ordinary skill in the art would similarly be motivated to include the reads for the spiked in control sequences in the no template controls in the contaminant database to ensure that the buffers used in the sample preparation were not contaminated with the internal control sequences because of common sense and a desire to improve sample integrity.
Regarding instant claim 17, the reference patent does not disclose the limitations of instant claim 17.
However, Chiu teaches determining read counts in the negative no-template control (i.e., no control added) [0176; 0180]. The negative no-template control reads on an analysis sample as instantly claimed because the sample is analyzed in the method of Chiu.
Regarding instant claim 18, the reference patent does not disclose the limitations of instant claim 18.
However, Chiu teaches a method for a broad, comprehensive pathogen diagnostic for infectious diseases by analyzing sequencing results against many reference genomes, as a metagenomics analysis in order to detect all pathogens in a single assay [0030].
Regarding instant claim 19, the reference patent does not disclose the limitations of instant claim 19.
However, Chiu teaches using an internally spiked DNA control and RNA control [0184]. As Chiu teaches a method for a broad, comprehensive pathogen diagnostic for infectious diseases by analyzing sequencing results against many reference genomes, as a metagenomics analysis in order to detect all pathogens in a single assay [0030], it is considered that Chiu teaches adding the DNA and RNA control to each samples and analyzing the results for each control for each sample.
Regarding instant claim 20, reference claim 1 discloses the limitations of instant claim 20.
Regarding claims 2, 4, and 15-19, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of the reference application and Chiu because both references disclose the use of internal controls to identify pathogens. The motivation would have been to quickly analyze millions of reads that include millions of data points that come out of a DNA sequence system, as well as interpret the data so that it is clinically useful to laboratory scientists and/or a physician, as taught by Chiu [0007].
Response to Applicant Arguments
At p. 9, section VI., Applicant requests reconsideration and withdrawal of the rejections in view of the amendments.
It is respectfully submitted that the amended claims continue to be unpatentable over the above copending applications in view of the cited secondary references. The rejections are therefore maintained.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
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/J.N.S./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685