DETAILED ACTION
Applicant' s response, filed 04 December 2025, has been fully considered. 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 .
Claim Status
Claims 1, 2, 4-14, 16-21, 47, 212, and 213 are pending and examined herein.
Claims 1, 2, 4-14, 16-21, 47, 212, and 213 are rejected.
Priority
Claims 1, 2, 4-14, 16-18, 20, 21, 47, 212, and 213 are given benefit of U.S. provisional application 62/934,323 filed 12 November 2019. Claim 19 is given benefit of U.S. provisional application 62/993,567 filed 23 March 2020. Claim 19 is not given benefit to 62/934,323 because there is no discussion of the pathogen being SARS-CoV-2. Thus, the effective filling date of claims 1, 2, 4-14, 16-18, 20, 21, 47, 212, and 213 is 12 November 2019 and the effective filling date of claim 19 is 23 March 2020.
Information Disclosure Statement
The information disclosure statement (IDS) received on 29 September 2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Claim Interpretation
Claim 1 recites “aligning, by the processor, the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios, classifying each of a plurality of portions of the aligned amino acid sequences…, selecting portions of the amino acid sequences classified as conserved, comparing the selected conserved sequences to human protein sequences, classifying the selected conserved sequences as identical or not identical to a human protein sequence, categorizing a selected conserved sequence not identical to a human protein sequence as a candidate antigen in the development of the personalized therapy against the pathogen, wherein the method further comprises producing an antibody or fragment thereof that specifically binds to an epitope on the candidate antigen” are contingent limitations because these steps are contingent on the condition that the polypeptides from the same one or more biological samples are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios and the preceding step is limited to making a determination whether the polypeptides in these samples are or include amino acid sequences that have matching mass-to-charge ratios to the determined mass to charge ratios. The MPEP states at 2111.04(II) “The broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met.” Thus, BRI of the method claims do not require these contingent steps to be performed.
Claim 47 recites “aligning, by the processor, the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios, classifying each of a plurality of portions of the aligned amino acid sequences…, selecting a conserved portion of the aligned amino acid sequences, and administering the therapeutic agent to the subject with the pathogen, wherein the therapeutic agent selectively binds the conserved portion of the amino acid sequence” are contingent limitations because these steps are contingent on the condition that the polypeptides from the same one or more biological samples are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios and the preceding step is limited to making a determination whether the polypeptides in these samples are or include amino acid sequences that have matching mass-to-charge ratios to the determined mass to charge ratios. The MPEP states at 2111.04(II) “The broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met.” The BRI of the method claims do not require these contingent steps to be performed. Further, claim 212 recites “wherein the method comprises administering to the subject infected with the pathogen, an antibody or fragment thereof, that selectively binds the conserved portion of the amino acid sequence” which relies on the contingent limitation of selecting a conserved portion of the aligned amino acid sequences which is not required to be performed by method. Therefore, the administration step in claim 212 is not required to be performed under the BRI of the method because there exists an embodiment where a conserved portion is not selected and further the administration of an antibody based on the conserved portion is not performed.
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.
The rejection has been modified necessitated by claim amendment.
Claims 1, 2, 4-14, 16-21, 47, 212, and 213 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
(Step 1)
Claims 1, 2, 4-14, 16-21, 47, 212, and 213 fall under the statutory category of a process.
(Step 2A Prong 1)
Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. The instant claims further recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations.
Independent claims 1 recite mental processes of “constructing a plurality of complete or partial genomic sequences…”, “extracting coding sequences…”, “categorizing the coding sequences according to a measure of identity and a measure of coverage…”, “selecting coding sequences…”, “converting the selecting coding sequences into corresponding amino acid sequences”, “determining whether the polypeptides from the same one or more biological samples are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to- charge ratios”, “aligning the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios”, “classifying each of a plurality of portions of the aligned amino acid sequences…”, “selecting portions of the amino acid…”, “comparing the selected conserved sequences…”, “classifying the selected conserved sequences…”, and “categorizing a selected conserved sequence…”.
Independent claim 47 recite mental processes of “extracting coding sequences…”, “categorizing the coding sequences according to a measure of identity and a measure of coverage…”, “selecting coding sequences…”, “converting the selecting coding sequences into corresponding amino acid sequences”, “determining whether the polypeptides from the same one or more biological samples are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to- charge ratios”, “aligning the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios”, “classifying each of a plurality of portions of the aligned amino acid sequences…” and “selecting a conserved portion…”.
Dependent claim 4 recites a mental process and mathematical concept of “computing, for each of a set of query coding sequences against a set of subject sequences, measures of similarity…”. Dependent claim 5 recites a mental process and mathematical concept of “creating a matrix of said measures of similarity…” and “rendering a graphical representation of said matrix”. Dependent claim 10 recites a mental process of “determining the presence or absence…”. Dependent claim 11 recites a mental process of “determining whether the candidate antigen corresponds to a protein…”. Dependent claim 12 recites a mental process of “determining the presence of a transmembrane domain…”. Dependent claim 13 recites a mental process of “non-clinically evaluating the candidate antigen…”.
The claims require a process of considering genomic data, extracting coding sequences from the data, categorizing the coding sequences based on criteria, selecting coding sequences from the categorized sequences, converting the coding sequences to amino acids, determining the mass to charge ratio of the one or more amino acids, determining a match between a sample and determined mass to charge ratios, aligning the amino acid sequences, classifying amino acids according to a level of conservation, selecting sequences classified as conserved, comparing selected conserved sequences to human protein sequences, classifying the conserved sequences based on criteria, categorizing a selected conserved sequence based on criteria. The BRI of the claim limitations encompass steps that are evaluating/analyzing data and organizing data. The human mind is capable of evaluating, analyzing, and organizing data. The claims require a process of calculations and mathematical relationships of computing measures of similarities and generating a matrix with these similarity measures. The instant disclosure provides that the measure of similarity is computed and is a function of percent identity a percent coverage (instant disclosure [0218]) this function intakes these numerical values to produce a numerical value of similarity which is a mathematical calculation. Further, generating a matrix with numerical values is a mathematical process which of generating a mathematical object (i.e. the matrix) with numerical similarity measures. Dependent claims 2, 6-9, and 16-21 further limit the mental process/mathematical concept recited in the independent claim but do not change their nature as a mental process/mathematical concept.
(Step 2A Prong 2)
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). Integration into a practical application is evaluated by identifying whether there are any additional elements recited in the claim and evaluating those additional elements to determine whether they integrate the exception into a practical application.
The additional element in claims 1 and 47 of using a generic computer to perform judicial exceptions does not integrate the judicial exception into a practical application because this is simply applying the judicial exception to a generic computer without an improvement to computer technology. The generic computer and the judicial exceptions only interact by utilizing the generic computer as a tool to perform judicial exceptions.
The additional element in claims 1 and 47 of performing mass spectrometry of one or more polypeptides from a sample comprising one or more strains of the pathogen and the additional elements in claims 16-21 of limiting the pathogen in the sample being used in the step of performing mass spectrometry of does not integrate the judicial exception into a practical application because this is adding insignificant extra solution activity of data gathering. These additional elements only interact with the judicial exceptions by gathering data to be analyzed.
The additional element in claim 1 of wherein the method further comprises producing an antibody or fragment thereof that specifically binds to an epitope on the candidate antigen does not integrate the judicial exception because this step is a contingent limitation and is not required under the BRI of the method.
The additional element in claim 14 of administering a polypeptide comprising the candidate antigen to an animal does not integrate the judicial exceptions into a practical application because this step is not a particular treatment. This step is not a particular treatment because this step is a contingent limitation which is not required under the BRI of the method.
The additional element in claim 47 of administering the therapeutic agent to the subject infected with the pathogen and the additional element in claim 212 of administering to the subject infected with a pathogen an antibody or fragment thereof does not integrate the judicial exceptions into a practical application because this step is not a particular treatment. This administering step is not a particular treatment because it is not required to be performed. The additional element in claim 213 of administering to the subjected infected with the pathogen a vaccine does not integrate the judicial exception into a practical application because this step is not a particular treatment. This administering step is not a particular treatment because it does not interact with or rely on the judicial exceptions recited in the claim.
It is noted if required the administration step in claim 47 and claim 213 would not integrate the judicial exceptions into a practical application because these steps would be mere instructions to apply the exception. The administration step in claim 47 would be mere instructions to apply the exception because of the generality of the therapeutic agent which is being administered and the administration step in claim 213 would be mere instructions to apply the exception due to the generality of the application of the judicial exception due to the general link between the judicial exceptions for determining a candidate antigen and administering a generic vaccine. It is further noted that if required the limitation of administering an antibody in claim 212 would be a particular treatment.
The additional elements in claim 47 of receiving data (i.e. data pertaining to complete or partial genomics sequences) does not integrate the judicial exceptions into a practical application because this is adding insignificant extra solution activity of data gathering. It is noted that the contents of the data does not change the active step of receiving data and the content falls under the abstract idea.
Thus, the additional elements do not integrate the judicial exceptions into a practical application and claims 1, 2, 4-14, 16-21, 47, 212, and 213 are directed to the abstract idea.
(Step 2B)
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because:
The additional element in claim 1 and 47 of using a generic computer to perform judicial exceptions as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II).
The additional elements in claim 47 of receiving data is conventional see MPEP 2106.05(b) and 2106.05(d)(II).
The additional element in claim 1 and 47 of performing mass spectrometry of one or more polypeptides from a sample comprising one or more strains of the pathogen and the additional elements in 16-21 which limits the pathogen in the sample are conventional as shown on page 2712 left column of Karlsson et al. (J Proteome Res. 2012 May 4;11(5):2710-20; previously cited) and page 967 right column and page 968 left column of Seyfarth et al. (Experimental Dermatology, 17: 965-971; previously cited), Zheng et al. (Anal Chim Acta. 2011 Sep 30;702(2):149-59; previously cited) which is a review that shows it was conventional to perform mass spectrometry on peptides from various viruses including influenza virus and SARS-CoV, and Lay (Mass Spectrom Rev. 2001 Jul-Aug;20(4):172-94; previously cited) which is a review that shows it was conventional to perform mass spectrometry on bacteria such as a Staphylococcus species and Pseudomonas species.
The combination of additional elements in claims 1 and 47 of using a generic computer and performing mass spectrometry on a sample containing one or more strains of pathogen is conventional as shown by Zheng et al. reviews different mass spectrometry approaches that use software to analyze the data and discusses different viruses that mass spectrometry methods have been applied.
The combination of additional elements in claims 1 and 16-21 of using a generic computer and performing mass spectrometry on a sample containing one or more strains of pathogen wherein the pathogen is limited in claims 16-21 is conventional as shown by Zheng et al. (Anal Chim Acta. 2011 Sep 30;702(2):149-59) and Lay (Mass Spectrom Rev. 2001 Jul-Aug;20(4):172-94; previously cited). Zheng et al. and Lay et al. reviews different mass spectrometry approaches that use software to analyze the data and discusses different viruses and bacteria that mass spectrometry methods have been applied.
Thus, the additional elements are not sufficient to amount to significantly more than the judicial exception because they are conventional.
Response to Arguments
Applicant's arguments filed 04 December 2025 have been fully considered but they are not persuasive.
Applicant argues the claims recites methods that represent non-conventional and non-generic mass spectrometry protocols that allow for improved identification of new candidate antigens from biological samples for development and production of antibodies or fragments thereof against a pathogen (Reply p. 8-10).
This argument has been fully considered but found to be not persuasive. MPEP 2106.05(d) states “Another consideration when determining whether a claim recites significantly more than a judicial exception is whether the additional element(s) are well-understood, routine, conventional activities previously known to the industry” which shows that the analysis of conventionality is reserved for the additional elements. As shown above, performing mass spectrometry on polypeptides of a sample is conventional. It is noted that the judicial exceptions of processing sequencing data to determine mass spectra and determining whether there is a match between the mass spectra data from performing spectroscopy and the determined mass spectra data are not analyzed for conventionality because this analysis is reserved for the additional elements of the claim.
Applicant argues that amended claim 47 is amended to require administering the treatment (Reply p. 10-11).
This argument has been fully considered but found to be not persuasive. The BRI of claim 47 does not require the limitation of administering the treatment because there exists an embodiment where the condition of the polypeptides from the same one or more biological samples infected with the pathogen obtained from the patient are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios is not met and the subsequent steps depending on the aligned amino acid sequences are not performed.
Claim Rejections - 35 USC § 103
The rejection on the ground of 103 of claims 1, 2, 4-9, 13, 14, 16-21, 47, 180, 212, and 213 as being unpatentable over Heunis et al. (J Proteome Res. 2017 Oct 6;16(10):3841-3851; previously cited) in view of Chiu et al. (US 20180203976 A1; previously cited) in view of Moise et al. (Hum Vaccin Immunother. 2015;11(9):2312-21; previously cited) in view of Fischman et al. (Current opinion in structural biology 51 (2018): 156-162; previously cited) in Office action mailed 01 October 2025 is withdrawn in view of the amendment of “aligning, by the processor, the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios” received 04 December 2025.
The rejection on the ground of 103 of claims 10-12 as being unpatentable over Heunis et al. in view of Chiu et al. in view of Moise et al. in view of Fischman et al. as applied to claim 1 in further in view of Hassan et al. (BMC Genomics 17, 732 (2016); previously cited) in Office action mailed 01 October 2025 is withdrawn in view of the amendment of “aligning, by the processor, the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios” received 04 December 2025.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The rejection is newly recited necessitated by claim amendment.
Claims 1, 2, 4-14, 16-21, 47, 212, and 213 are rejected under 35 U.S.C. 103 as being unpatentable over Heunis et al. (J Proteome Res. 2017 Oct 6;16(10):3841-3851; previously cited) in view of Chiu et al. (US 20180203976 A1; previously cited).
Claim 1 is directed to constructing a plurality of complete or partial genomic sequences of one or more strains of the pathogen, wherein the one or more strains of the pathogen are derived from one or more biological samples infected with the pathogen obtained from a patient
Heunis et al. shows sequencing DNA extracted from M. tuberculosis clinical isolates (Henuis et al. page 3842 left col. - right col.). Heunis et al. shows analyzing the DNA sequencing data to obtain aligned genomic sequences (Heunis et al. page 3842 right col.).
extracting, by a processor of a computing device, coding sequences from the constructed complete or partial genomic sequences,
Heunis et al. shows identifying SNVs in coding regions using alignment files (Heunis et al. page 3842 right col.).
categorizing, by the processor, the coding sequences according to a measure of identity and a measure of coverage for each of a plurality of pairs, each of said pairs comprising an extracted coding sequence and a reference sequence of the one or more strains of the pathogen, wherein the measure of identity comprises one or more of percent identity, percent identity over a predetermined coverage length, number of mutations, and percent mutation, and wherein the measure of coverage comprises one or more of percent coverage and coverage length selecting coding sequences from among the categorized coding sequences according to the measure of identity and the measure of coverage,
Heunis et al. shows performing a phylogenomic analysis using the genomic sequences obtained from clinical isolates. Heunis et al. shows concatenated sequences containing high-confidence variable sites (such as coding SNVs) with respect to the reference genome were used to infer the phylogenetic relationship among the various strains (Heunis et al. page 3842 right col.).
selecting coding sequences from among the categorized coding sequences according to the measure of identity and the measure of coverage, converting, by the processor, the selected coding sequences into corresponding amino acid sequences
Heunis et al. shows the consensus sequence for coding DNA sequences (CDSs) of each strain and the strain-specific versions of CDSs were translated and appended to the M. tuberculosis H37Rv reference proteome (Heunis et al. page 3843 right col.).
determining, by the processor, the mass-to-charge ratio of one or more of the amino acid sequences or portions thereof, performing mass spectrometry of one or more polypeptides from the same one or more biological samples infected with the pathogen obtained from the patient and determining whether the polypeptides from the same one or more biological samples infected with the pathogen are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios,
Heunis et al. shows performing mass spectroscopy on polypeptides from the clinical isolates (Heunis et al. page 3843 left col. – right col.). Heunis et al. shows performing peptide identification using customized strain specific proteome databases by searching all tandem mass spectra using MS-GF+ (Heunis et al. page 3843 right col.). This implicitly shows determining whether the mass-to-charge ratio of one or more amino acid sequences that were converted from the genomic sequences because database search algorithms determine theoretical value from peptide sequences in a database to match experimental data with database data.
Heunis et al. does not explicitly show the categorization of coding sequences by a measure of identity and a measure of coverage for each of a plurality of pairs, each of said pairs comprising an extracted coding sequence and a reference sequence of the one or more strains of the pathogen, wherein the measure of identity comprises one or more of percent identity, percent identity over a predetermined coverage length, number of mutations, and percent mutation, and wherein the measure of coverage comprises one or more of percent coverage and coverage length selecting coding sequences from among the categorized coding sequences according to the measure of identity and the measure of coverage
Like Heunis et al., Chiu et al. shows a method of analyzing pathogenic genome sequences. Chiu et al. shows a program that categorizes sequences of a particular species by way of coverage, identity, and percent identity (Chiu et al. [084]-[092]).
aligning, by the processor, the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios, classifying each of a plurality of portions of the aligned amino acid sequences according to a level of conservation of said portion among the one or more strains of the pathogen, selecting portions of the amino acid sequences classified as conserved, comparing the selected conserved sequences to human protein sequences, classifying the selected conserved sequences as identical or not identical to a human protein sequence, categorizing a selected conserved sequence not identical to a human protein sequence as a candidate antigen in the development of the personalized therapy against the pathogen; wherein the method further comprises producing an antibody or fragment thereof that specifically binds to an epitope on the candidate antigen, and wherein the personalized therapy comprises an antibody therapy.
The BRI of claim 1 does not require these limitations because there exists an embodiment where the condition of the polypeptides from the same one or more biological samples infected with the pathogen obtained from the patient are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios is not met.
Claim 47 is directed to obtaining a plurality of complete or partial genomic sequences of one or more strains of the pathogen, wherein the one or more strains of the pathogen are derived from one or more biological samples infected with the pathogen obtained from a patient,
Heunis et al. shows sequencing DNA extracted from M. tuberculosis clinical isolates (Henuis et al. page 3842 left col. - right col.). Heunis et al. shows analyzing the DNA sequencing data to obtain aligned genomic sequences (Heunis et al. page 3842 right col.).
extracting, by a processor of a computing device, coding sequences from the constructed complete or partial genomic sequences,
Heunis et al. shows identifying SNVs in coding regions using alignment files (Heunis et al. page 3842 right col.).
categorizing, by the processor, the coding sequences according to a measure of identity and a measure of coverage for each of a plurality of pairs, each of said pairs comprising an extracted coding sequence and a reference sequence of the one or more strains of the pathogen, wherein the measure of identity comprises one or more of percent identity, percent identity over a predetermined coverage length, number of mutations, and percent mutation, and wherein the measure of coverage comprises one or more of percent coverage and coverage length selecting coding sequences from among the categorized coding sequences according to the measure of identity and the measure of coverage,
Heunis et al. shows performing a phylogenomic analysis using the genomic sequences obtained from clinical isolates. Heunis et al. shows concatenated sequences containing high-confidence variable sites (such as coding SNVs) with respect to the reference genome were used to infer the phylogenetic relationship among the various strains (Heunis et al. page 3842 right col.).
selecting coding sequences from among the categorized coding sequences according to the measure of identity and the measure of coverage, converting, by the processor, the selected coding sequences into corresponding amino acid sequences
Heunis et al. shows the consensus sequence for coding DNA sequences (CDSs) of each strain and the strain-specific versions of CDSs were translated and appended to the M. tuberculosis H37Rv reference proteome (Heunis et al. page 3843 right col.).
determining, by the processor, the mass-to-charge ratio of one or more of the amino acid sequences or portions thereof, performing mass spectrometry of one or more polypeptides from the same one or more biological samples infected with the pathogen obtained from the patient and determining whether the polypeptides from the same one or more biological samples infected with the pathogen are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios,
Heunis et al. shows performing mass spectroscopy on polypeptides from the clinical isolates (Heunis et al. page 3843 left col. – right col.). Heunis et al. shows performing peptide identification using customized strain specific proteome databases by searching all tandem mass spectra using MS-GF+ (Heunis et al. page 3843 right col.). This implicitly shows determining whether the mass-to-charge ratio of one or more amino acid sequences that were converted from the genomic sequences because database search algorithms determine theoretical value from peptide sequences in a database to match experimental data with database data.
Heunis et al. does not explicitly show the categorization of coding sequences by a measure of identity and a measure of coverage for each of a plurality of pairs, each of said pairs comprising an extracted coding sequence and a reference sequence of the one or more strains of the pathogen, wherein the measure of identity comprises one or more of percent identity, percent identity over a predetermined coverage length, number of mutations, and percent mutation, and wherein the measure of coverage comprises one or more of percent coverage and coverage length selecting coding sequences from among the categorized coding sequences according to the measure of identity and the measure of coverage
Like Heunis et al., Chiu et al. shows a method of analyzing pathogenic genome sequences. Chiu et al. shows a program that categorizes sequences of a particular species by way of coverage, identity, and percent identity (Chiu et al. [084]-[092]).
aligning, by the processor, the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios, classifying each of a plurality of portions of the aligned amino acid sequences according to a level of conservation of said portion among the different strains of the pathogen, and selecting a conserved portion of the aligned amino acid sequences; and administering the therapeutic agent to the subject infected with the pathogen, wherein the therapeutic agent selectively binds the conserved portion of the amino acid sequence.
The BRI of claim 47 does not require these limitations because there exists an embodiment where the condition of the polypeptides from the same one or more biological samples infected with the pathogen obtained from the patient are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios is not met.
Claim 2 is directed to wherein the one or more biological samples comprise one or more clinical samples.
Heunis et al. shows the samples are M. tuberculosis clinical isolates (Henuis et al. page 3842 left col.).
Claim 4 is directed to computing, for each of a set of query coding sequences against a set of subject sequences, measures of similarity between the query coding sequence and each subject sequence, each of said measures of similarity a function of a measure of identity between the query sequence and the subject sequence and a measure of coverage between the query sequence and the subject sequence. Claim 7 is directed to wherein the measure of identity comprises number of mutations. Claim 8 is directed to wherein the measure of coverage comprises percent coverage. Claim 9 is directed to wherein the measure of identity comprises calculating an E-value.
Chiu et al. shows the use of comparisons of sequence that are based on coverage, identity, and percent identity (Chiu et al. [084]-[092]). Chiu et al. shows the use of E-values for similarity measure (Chiu et al. [065]).
Claim 5 is directed to creating a matrix of said measures of similarity and rendering a graphical representation of said matrix, thereby displaying levels of conservation between the query sequences and subject sequences. Claim 6 is directed to wherein the graphical representation comprises one or more of a heatmap, a graph, and a phylogeny.
Chiu et al. shows in figure 6 a table in which it shows the similarity between sequences by way of matches (Chiu et al. figure 6). Chiu et al. further shows in figure 2 a phylogeny graph (Chiu et al. figure 2). Chiu et al. shows displaying results to a clinician (Chiu et al. abstract).
Claim 10 is directed to wherein categorizing the selected conserved sequence as a candidate antigen further comprises determining the presence or absence or more amino acid domains in the selected conserved sequence. Claim 11 is directed to wherein categorizing the selected conserved sequence as a candidate antigen further comprises determining whether the candidate antigen corresponds to a protein that is secreted or is exposed within a membrane and/or cell wall of the pathogen. Claim 12 is directed to wherein categorizing the selected conserved sequence as a candidate antigen further comprises determining the presence of a transmembrane domain in a selected conserved sequence. Claim 13 is directed to non-clinically evaluating the candidate antigen for immunogenicity, and wherein the therapy comprises a vaccine. Claim 14 is directed to evaluating step comprises administering a polypeptide comprising the candidate antigen to an animal.
The BRI of the method does not require these limitations because there exists an embodiment where the condition of the polypeptides from the same one or more biological samples infected with the pathogen obtained from the patient are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios is not met. Thus, Heunis et al. in view of Chiu et al. renders the claimed method obvious.
Claim 16 is direct to wherein the pathogen is a virus. Claims 17-19 is directed to particular viruses. Claim 20 is directed to wherein the pathogen is a bacterium. Claim 21 is directed to particular bacterium.
Henuis et al. shows the pathogen is M. tuberculosis (Henuis et al. page 3842 left col.). It would have been obvious to one of ordinary skill in the art that since this method intakes genomic information from a pathogen for analysis to find a target for the development of a therapy that this may be extended to any pathogen in which genomic data may be extracted and analyzed.
Claims 212 and 213 recite further limitations to the administration step in claim 47.
The BRI of the method does not require these limitations because there exists an embodiment where the condition of the polypeptides from the same one or more biological samples infected with the pathogen obtained from the patient are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios is not met. Thus, Heunis et al. in view of Chiu et al. renders the claimed method obvious.
It would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have substituted the step of phylogenomic analysis using the genomic sequences obtained from clinical isolates in Heunis et al. with the use of categorizing sequences of a particular species by way of coverage, identity, and percent identity of Chiu et al. because the use of coverage, identity, and percent identity is a method for clustering similar genomic sequences from pathogen strains.
Response to Arguments
Applicant's arguments filed 04 December 2025 have been fully considered but they are not persuasive.
Applicant argues that the cited references do not show at least the step of aligning, by the processor, the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios as claimed in claims 1 and 47 (Reply p. 13).
This argument has been fully considered but found to be not persuasive. The MPEP states at 2111.04(II) “The broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met.” The BRI of the method does not require the limitation of aligning, by the processor, the amino acid sequences having the mass-to-charge ratios matching the determined mass-to-charge ratios because there exists an embodiment where the condition of the polypeptides from the same one or more biological samples infected with the pathogen obtained from the patient are or include amino acid sequences that have mass-to-charge ratios matching the determined mass-to-charge ratios is not met. Thus, Heunis et al. in view of Chiu et al. renders the BRI of the claimed method obvious.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JONATHAN EDWARD HAYES whose telephone number is (571)272-6165. The examiner can normally be reached M-F 9am-5pm.
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/J.E.H./Examiner, Art Unit 1685
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685