DETAILED ACTION
Applicant’s response filed 12/19/2025 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 Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn.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.
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 .
Status of the Claims
Claims 1-8, 10-20, and 26 are pending and under consideration in this action. Claims 8 and 21-25 were previously canceled.
Priority
The instant application is 371 of PCT/US2020/039279, filed 06/24/2020, which claims priority to U.S. Provisional Application number 62/868,460, filed 06/28/2019, as reflected in the filing receipt mailed 03/29/2024. The claim for domestic benefit for claims 1-8, 10-20, and 26 is acknowledged. As such, the effective filing date of claims 1-8, 10-20, and 26 is 06/28/2019.
Specification
The objections to the Specification are withdrawn in view of Applicant’s amendments to the Specification filed 12/19/2025 (Applicant’s Remarks, Pg. 13).
Claim Objections
The objection to claims 4, 6, and 20 is withdrawn in view of Applicant’s amendments to the claims filed 12/19/2025 (Applicant’s Remarks, Pg. 13-14).
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1-8, 13, 15-20, and 26 under 35 U.S.C. 112(b) as being indefinite is withdrawn in view of Applicant’s amendments to the claims filed 12/19/2025 (Applicant’s Remarks, Pg. 16).
Claim Rejections - 35 USC § 101
Maintained Rejections
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 1-8, 10-20, and 26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite both (1) mathematical concepts (mathematical relationships, formulas or equations, or mathematical calculations) and (2) mental processes, i.e., concepts performed in the human mind (including observations, evaluations, judgements or opinions) (see MPEP § 2106.04(a)).
Any newly recited portion is necessitated by claim amendment.
Step 1:
In the instant application, claims 1-8, 15-20, and 26 are directed towards a method, claims 10-14 are directed towards a system, which falls into one of the categories of statutory subject matter (Step 1: YES).
Step 2A, Prong One:
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong One). The following instant claims recite limitations that equate to one or more categories of judicial exceptions:
Claim 1 recites a mental process (i.e., an evaluation of bases to include) in “generating first data indicating one or more sequences of nucleotides”, a mental process (i.e., an evaluation of bases to include) and a mathematical concept (i.e., using random number generator) in “generating second data indicating a second sequence of nucleotides for a synthetic molecule, the synthetic molecule including first regions that include nucleotide sequences of a biological organism and second regions that include additional nucleotide sequences selected from the one or more sequences of nucleotides included in the first data, wherein the one or more sequences of nucleotides are machine-generated nucleotide sequences produced using one or more pseudo-random number generators”, a mathematical concept (i.e., using a formula to calculate the initial number of genetic molecules in a sample) in “determining the initial number of the genetic molecule included in the sample based at least partly on a number of the synthetic molecule included in the sample, a volume of the sample, and the first number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data”.
Claim 2 recites a mental process (i.e., an observation of sample volume) in “individual samples of the plurality of samples have a volume from 10 microliters to 500 microliters”, a mental process (i.e., a judgement of which amplification process to use) in “the amplification process includes a polymerase chain reaction (PCR) or multiple displacement amplification (MDA) technique”, a mental process (i.e., an evaluation of the nucleotide sequences to determine if they correspond to primers) in “the nucleotide sequences of the biological organism correspond to primers included in the one or more amplification reagents”, and a mental process (i.e., a judgment in choosing the conserved region of the rRNA gene) in “the nucleotide sequences of the biological organism are selected from conserved regions of a ribosomal ribonucleic acid gene (rRNA gene)”.
Claim 3 recites a mental process (i.e., a judgement of which genetic molecules to include) in “wherein the genetic molecule includes deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) shared with additional biological organisms”, a mathematical concept (i.e., using an algorithm to generate data) in “implementing the one or more pseudo-random number generators to generate the first data indicating the one or more sequences of nucleotides”, and a mathematical concept (i.e., dividing the data into sections) in “dividing a nucleotide sequence generated using the one or more pseudo-random number generators into a plurality of segments to generate a plurality of sequences of nucleotides included in the first data”.
Claim 4 recites a mental process (i.e., a comparison of the two initial numbers) in “determining a difference between the initial number of the genetic molecule included in the first sample and the initial number of the genetic molecule included in the second sample”, and a mathematical concept (i.e., determining a probability) in “performing an analysis based on the difference to determine a probability that a factor of a plurality of factors is causing the difference”.
Claim 5 recites a mental process (i.e., an observation of the mixture contents) in “wherein the volume of the mixture includes a third portion that includes an amount of an additional molecule”, and a mathematical concept (i.e., using a formula to calculate the initial number of additional molecules in a sample) in “determining an initial number of the additional molecule included in the sample based at least partly on the number of the synthetic molecule included in the sample, the volume of the sample, and the third number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data”.
Claim 6 recites a mathematical concept (i.e., calculating a correlation) in “determining a correlation between the number of synthetic molecule included in the sample and the initial number of an additional molecule included in the sample”, a mental process (i.e., an evaluation of how the correlation compares to a threshold) in “determining that the correlation satisfies one or more threshold criteria”, and a mental process (i.e., an evaluation of the molecule to determine contamination) in “determining that the additional molecule is a contaminant included in the one or more amplification reagents”.
Claim 7 recites a mental process (i.e., an evaluation of whether or not a value is greater than a threshold) in “determining that the third number of the additional molecule is greater than a threshold number”, and a mental process (i.e., an evaluation of the composition of the additional molecule) in “determining that the additional molecule is another genetic molecule included in the sample”.
Claim 8 recites a mathematical concept (i.e., using a formula to calculate the number of synthetic molecules) in “determining the number of the synthetic molecule included in the sample based on a number of samples derived from the volume of the mixture and the amount of the synthetic molecule included in the volume of the mixture”.
Claim 10 recites a mental process (i.e., an evaluation/analysis of the sequences) and a mathematical concept (i.e., using a random number generator) in “determining, based on the sequence data, a first number of nucleotide sequences included in the sequence data that correspond to a first genetic molecule included in the sample and a second number of nucleotide sequences included in the sequence data that correspond to a synthetic molecule included in the sample, the synthetic molecule including first regions that include first nucleotide sequences of a biological organism and second regions that include second nucleotide sequences selected from one or more machine-generated sequences of nucleotides, wherein the one or more machine-generated sequences of nucleotides are produced using one or more pseudo-random number generators”; and a mathematical concept (i.e., using a formula to calculate the initial number of genetic molecules in a sample) in “determining, an initial number of the first genetic molecule included in the sample based at least partly on an initial number of the synthetic molecule included in the sample, a volume of the sample, and the first number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data”.
Claim 11 recites a mental process (i.e., an evaluation of the sequences) in “performing a comparison of a nucleotide sequence of the genetic molecule to one or more nucleotide sequences included in a library of nucleotide sequences, the library of nucleotide sequences including a plurality of nucleotide sequences that correspond to a plurality of additional biological organisms”, and a mental process (i.e., an evaluation of the comparison to determine additional organisms) in “determining, based on the comparison, an additional biological organism of the plurality of additional biological organisms that corresponds to a genetic molecule”.
Claim 12 recites a mental process (i.e., an evaluation of the nucleotide sequences) in “performing a comparison of an additional nucleotide sequence of the additional genetic molecule to the one or more nucleotide sequences included in the library of nucleotide sequences”, a mental process (i.e., an evaluation to determine correlation between a genetic molecule and an organism) in “determining, based on the comparison, a second additional biological organism of the plurality of additional biological organisms that corresponds to the additional genetic molecule”, and a mental process (i.e., an observation of where the organisms are located) in “determining that the additional biological organism and the second additional biological organism are present in environments where at least one of crude oil, natural gas, and formation water are located”.
Claim 13 recites a mathematical concept (i.e., determining a correlation) in “determining a correlation between the third number of nucleotide sequences and the second number of nucleotide sequences”, a mental process (i.e., an evaluation of a value meets a threshold) in “determining that the correlation satisfies one or more threshold criteria”, and a mental process (i.e., an evaluation of whether the additional molecule is a contaminant) in “determining that the additional molecule is a contaminant included in the one or more amplification reagents”.
Claim 14 recites a mental process (i.e., an evaluation of the precision and lower limit of detection) in “wherein the initial number of the genetic molecule is determined with a precision of at least 95% and with a lower limit of detection between 1 and 10 of the genetic molecule included in the sample”.
Claim 15 recites a mathematical concept (i.e., generating a function/algorithm) in “generating a function to determine a number of the genetic molecule included in the sample”, a mental process (i.e., an evaluation/analysis of the sequences) and a mathematical concept (i.e., using a random number generator) in “determining, by at least one computing device of the one or more computing devices and based on the sequence data, a first number of nucleotide sequences included in the sequence data that correspond to a genetic molecule included in the amplification product and a second number of nucleotide sequences included in the sequence data that correspond to a synthetic molecule included in the amplification product, the synthetic molecule including first regions that include nucleotide sequences of a biological organism and second regions that include nucleotide sequences selected from one or more machine-generated sequences of nucleotides, wherein the one or more machine-generated sequences of nucleotides are produced using one or more pseudo-random number generators”, and a mathematical concept (i.e., using the function/algorithm to determine the number of genetic molecules in the sample) in “determining the number of the genetic molecule included in the sample based on the number of the synthetic molecule included in the sample and the first number of nucleotide sequences included in the sequence data”.
Claim 16 recites a mental process (i.e., an evaluation of the possible biochemical reactions that took place) in “determining, based on a presence of the genetic molecule in the sample, that one or more biochemical reactions have taken place in an environment from which the sample was obtained, wherein the one or more biochemical reactions include at least one of a nitrate reducing reaction, a sulfate reducing reaction, methanogenesis, a hydrocarbon conversion reaction, or a biosurfactant generating reaction”.
Claim 18 recites a mental process (i.e., an evaluation of nucleotide sequences) in “performing comparisons between a nucleotide sequence of the genetic molecule with respect to a plurality of additional nucleotide sequences that are associated with a plurality of individuals”, a mental process (i.e., an evaluation of the comparison to determine a threshold) in “determining, based on the comparisons, a threshold amount of identity between the nucleotide sequence of the genetic molecule and an additional nucleotide sequence of the plurality of additional nucleotide sequences”, and a mental process (i.e., an evaluation to determine a matching sequence) in “identifying an individual of the plurality of individuals that corresponds to the additional nucleotide sequence”.
Claim 19 recites a mental process (i.e., an evaluation of the nucleotide sequences) in “performing comparisons between a nucleotide sequence of the genetic molecule with respect to a plurality of additional nucleotide sequences that are associated with contaminants”, a mental process (i.e., an evaluation of the comparison to determine a threshold) in “determining, based on the comparisons, a threshold amount of identity between the nucleotide sequence of the genetic molecule and an additional nucleotide sequence of the plurality of additional nucleotide sequences”, and a mental process (i.e., an evaluation to determine a corresponding sequence) in “identifying a contaminant of the environment, wherein the contaminant corresponds to the additional nucleotide sequence”.
Claim 20 recites a mental process (i.e., an observation of a sequence) in “identifying a first barcode sequence included in a first nucleotide sequence” and “identifying a second barcode sequence included in a second nucleotide sequence”, a mental process (i.e., a comparison of sequences) in “determining, based on the first barcode sequence, that the first nucleotide sequence corresponds to a first molecule” and “determining, based on the second barcode sequence, that the second nucleotide sequence corresponds to a second molecule”, and a mathematical concept (i.e., a calculation of the number of nucleotide sequences) in “determining a number of the first nucleotide sequences based on a number of nucleotide sequences included in the first group” and “determining the number of the second nucleotide sequences based on a number of nucleotide sequences included in the second group”.
Claim 26 recites a mathematical concept (i.e., calculation of a difference) in “a difference between a first amount of biomass included in the first sample and a second amount of biomass included in the second sample” and a mental process (i.e., an evaluation of how conditions differ between sources and a judgment of conditions to include) in “a difference between one or more first conditions related to the first source and one or more second conditions related to the second source, the one or more first conditions and the one or more second conditions include at least one of temperature, humidity, or amount of exposure to a range of wavelengths of electromagnetic radiation”.
These recitations are similar to the concepts of collecting information, and displaying certain results of the collection and analysis is Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)), and organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships.
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification, and are determined to be directed to mental processes that in the simplest embodiments are not too complex to practically perform in the human mind. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind. The instant claims must therefore be examined further to determine whether they integrate the abstract idea into a practical application (Step 2A, Prong One: YES).
Step 2A, Prong Two:
In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP § 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP § 2106.04(d)(I)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP § 2106.04(d)(III)). The following claims recite limitations that equate to additional elements:
Claim 1 recites “obtaining an amount of a material from a source”, “extracting a genetic molecule from the amount of the material, the genetic molecule having a first sequence of nucleotides”, “by at least one computing device of the one or more computing devices”, “producing a volume of a mixture that includes a first portion having an amount of the synthetic molecule and a second portion that includes one or more amplification reagents”, “producing a plurality of samples from the mixture, individual samples of the plurality of samples including a portion of the volume of the mixture, and an additional portion that includes an amount of the genetic molecule”, “performing an amplification process to produce an amplification product for a sample of the plurality of samples, wherein the amplification product includes an amplified number of the genetic molecule and an amplified number of the synthetic molecule that is greater than an initial number and an initial number of the synthetic molecule included in the sample”, “performing a sequencing process to determine nucleotide sequences of molecules included in the amplification product”, “obtaining, based on the sequencing process, sequence data indicating the nucleotide sequences of the molecules included in the amplification product”, and “determining, based on the sequence data, a first number of nucleotide sequences included in the sequence data that correspond to the genetic molecule and a second number of nucleotide sequences included in the sequence data that correspond to the synthetic molecule”.
Claim 4 further recites “obtaining a second amount of a second material from a second source included in the environment, the second material including the genetic molecule”, “producing a second sample that includes at least a portion of the second amount of the second material, the one or more amplification reagents, and an amount of the synthetic molecule”, “performing an additional amplification process with the one or more amplification reagents to produce an additional amplification product for the second sample, the additional amplification product including an additional amplified number of the genetic molecule that is greater than an initial number of the genetic molecule included in the second sample and an additional amplified number of the synthetic molecule that is greater than an additional initial number of the synthetic molecule included in the second sample”, “performing an additional sequencing process to produce additional sequence data, the additional sequence data indicating nucleotides sequences of molecules included in the additional amplification product”, and “determining the initial number of the genetic molecule included in the second sample based on the second sequence data and the initial number of the synthetic molecule included in the second sample”.
Claim 5 further recites “by at least one computing device of the one or more computing devices”, and “determining, based on the sequence data, a third number of nucleotide sequences included in the sequence data that correspond to the additional molecule”.
Claims 6 and 7 further recites “by at least one computing device of the one or more computing devices”.
Claim 10 recites “at least one hardware processor”, “a computer-readable medium storing instructions, that when executed by the at least one hardware processor, cause the at least one hardware processor to perform operations”, and “obtaining sequence data indicating nucleotide sequences of molecules included in an amplification product, the amplification product corresponding to a sample that has undergone an amplification process to increase an initial number of molecules included in the sample, wherein a first genetic molecule in the sample is extracted from material”.
Claim 12 further recites “determining, based on the sequence data, a third number of nucleotide sequences included in the sequence data that correspond to an additional genetic molecule included in the sample”.
Claim 13 further recites “determining, based on the sequence data, a third number of nucleotide sequences included in the sequence data that correspond to an additional molecule”.
Claim 15 recites “extracting a genetic molecule from a sample”, and “obtaining, by one or more computing devices, sequence data indicating nucleotide sequences of molecules included in an amplification product, the amplification product corresponding to a sample that has undergone an amplification process to increase an initial number of molecules included in the sample”
Claim 17 further recites “extracting the genetic molecule from a cell included in an amount of a fluid obtained from a subterranean environment that stores at least one of a fossil fuel-based petroleum substance or natural gas”.
Claim 19 further recites “obtaining an amount of a material from an environment”, and “extracting a cell from the material that includes the genetic molecule”.
Claim 20 further recites “producing a first group of nucleotide sequences that include the first barcode sequence” and “producing a second group of nucleotide sequences that include the second barcode sequence”.
Regarding the above cited limitations in claims 1, 5-7, 10, and 15 of (i) by one or more computing devices, (ii) at least one hardware processor, (iii) a computer-readable medium storing instructions, that when executed by the at least one hardware processor, cause the at least one hardware processor to perform operations, and (vi) by at least one computing device of the one or more computing devices. These limitations require only a generic computer component, which does not improve computer technology. Therefore, these limitations equate to mere instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983.
Regarding the above cited limitations in claims 1, 4-5, 10, 12-13, 15, 17, and 19-20 of (v) obtaining an (second) amount of a material from a (second) source/environment, (vi) extracting a genetic molecule from the amount of the material, the genetic molecule having a first sequence of nucleotides, (vii) producing a volume of a mixture that includes a first portion having an amount of the synthetic molecule and a second portion that includes one or more amplification reagents, (viii) producing a plurality of samples from the mixture, individual samples of the plurality of samples including a portion of the volume of the mixture, and an additional portion that includes an amount of the genetic molecule, (ix) performing an amplification process to produce an amplification product for a sample of the plurality of samples, wherein the amplification product includes an amplified number of the genetic molecule and an amplified number of the synthetic molecule that is greater than an initial number and an initial number of the synthetic molecule included in the sample, (x) performing a sequencing process to determine nucleotide sequences of molecules included in the amplification product, (xi) obtaining sequence data indicating the nucleotide sequences of the molecules included in the amplification product, (xii) determining a first number of nucleotide sequences included in the sequence data that correspond to the genetic molecule and a second number of nucleotide sequences included in the sequence data that correspond to the synthetic molecule, (xiii) producing a second sample that includes at least a portion of the second amount of the second material, the one or more amplification reagents, and an amount of the synthetic molecule, (xiv) performing an additional amplification process with the one or more amplification reagents to produce an additional amplification product for the second sample, the additional amplification product including an additional amplified number of the genetic molecule that is greater than an initial number of the genetic molecule included in the second sample and an additional amplified number of the synthetic molecule that is greater than an additional initial number of the synthetic molecule included in the second sample, (xv) performing an additional sequencing process to produce additional sequence data, the additional sequence data indicating nucleotides sequences of molecules included in the additional amplification product, (xvi) determining the initial number of the genetic molecule included in the second sample based on the second sequence data and the initial number of the synthetic molecule included in the second sample, (xvii) a third number of nucleotide sequences included in the sequence data that correspond to the additional molecule, (xviii) obtaining sequence data indicating nucleotide sequences of molecules included in an amplification product, the amplification product corresponding to a sample that has undergone an amplification process to increase an initial number of molecules included in the sample, (xix) determining, based on the sequence data, a third number of nucleotide sequences included in the sequence data that correspond to an additional genetic molecule included in the sample, (xx) extracting the genetic molecule from a cell included in an amount of a fluid obtained from a subterranean environment that stores at least one of a fossil fuel-based petroleum substance or natural gas, (xxi) extracting a cell from the material that includes the genetic molecule, and (xxii) producing a first/second group of nucleotide sequences that include the first/second barcode sequence. These limitations equate to insignificant, extra-solution activity of mere data gathering because these limitations gather data before or after the recited judicial exceptions of determining the initial number of the genetic molecule included in the sample based at least partly on a number of the synthetic molecule included in the sample, a volume of the sample, and the first number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data (see MPEP § 2106.04(d)). As such, claims 1-8, 10-20, and 26 are directed to an abstract idea (Step 2A, Prong Two: NO).
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 claims recite additional elements that equate to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The instant claims recite same additional elements described in Step 2A, Prong Two above. Limitations are numbered the same as in Step 2A, Prong Two above.
Regarding the above cited limitations in claims 1, 5-7, 10, and 15 of (i) by one or more computing devices, (ii) at least one hardware processor, (iii) a computer-readable medium storing instructions, that when executed by the at least one hardware processor, cause the at least one hardware processor to perform operations, and (vi) by at least one computing device of the one or more computing devices. These limitations equate to instructions to implement an abstract idea on a generic computing environment, which the courts have established does not provide an inventive concept (see MPEP § 2106.05(d) and MPEP § 2106.05(f)).
Regarding the above cited limitations in claims 1, 4-5, 10, 12-13, 15, 17, and 19-20 of (vi) extracting a genetic molecule from the amount of the material…, (vii) producing a volume of a mixture that includes …the synthetic molecule…and…one or more amplification reagents, (viii) producing a plurality of samples from the mixture…including…an additional portion that includes an amount of the genetic molecule, (ix) performing an amplification process to produce an amplification product for a sample of the plurality of samples…, (x) performing a sequencing process to determine nucleotide sequences of molecules included in the amplification product, (xi) obtaining sequence data indicating the nucleotide sequences of the molecules included in the amplification product, (xii) determining a first number of nucleotide sequences included in the sequence data that correspond to the genetic molecule and a second number of nucleotide sequences included in the sequence data that correspond to the synthetic molecule, (xiii) producing a second sample that includes at least a portion of the second amount of the second material, the one or more amplification reagents, and an amount of the synthetic molecule, (xiv) performing an additional amplification process with the one or more amplification reagents to produce an additional amplification product for the second sample…, (xv) performing an additional sequencing process to produce additional sequence data…, (xvi) determining the initial number of the genetic molecule included in the second sample based on the second sequence data and the initial number of the synthetic molecule included in the second sample, (xvii) a third number of nucleotide sequences included in the sequence data that correspond to the additional molecule, (xviii) obtaining sequence data indicating nucleotide sequences of molecules included in an amplification product…, (xix) determining, based on the sequence data, a third number of nucleotide sequences included in the sequence data that correspond to an additional genetic molecule included in the sample, (xx) extracting the genetic molecule from a cell included in an amount of a fluid…, (xxi) extracting a cell from the material that includes the genetic molecule, and (xxii) producing a first/second group of nucleotide sequences that include the first/second barcode sequence. These limitations equate to laboratory techniques that are WURC limitations in the life science arts (see MPEP 2106.05(d)). Detecting DNA or enzymes in a sample is a WURC limitation in Sequenom, 788 F.3d at 1377-78, 115 USPQ2d at 1157, and Cleveland Clinic Foundation 859 F.3d at 1362, 123 USPQ2d at 1088 (Fed. Cir. 2017). Analyzing DNA to provide sequence information or detect allelic variants is a WURC limitation in Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546. Amplifying and sequencing nucleic acid sequences is a WURC limitation in University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014).
Regarding the above cited limitations in claims 1, 4, and 19 of (v) obtaining an (second) amount of a material from a (second) source/environment. These limitations when viewed individually and in combination, are WURC limitations as taught by Knight et al. (US Patent Application Publication, US 2017/0139078 A1). Knight et al. discloses a method for obtaining first/second microbiome information from hydrocarbons produced in a first/second well in an oil field at various times (limitation (v)) (Para. [0045]).
These additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the instant claims do not amount to significantly more than the judicial exception itself (Step 2B: NO). As such, claims 1-8, 10-20, and 26 are not patent eligible.
Response to Arguments under 35 U.S.C. 101
Applicant’s arguments filed 12/19/2025 have been fully considered but they are not persuasive.
1. Applicant argues that amended independent claim 1 recites extracting a genetic molecule from the amount of the material, performing an amplification process to produce an amplification product, and performing a sequencing process to determine nucleotide sequences of molecules included in the amplification product. As such, these claims recite processes that requiring extraction of biological materials and, thus, cannot practically be performed in the human mind and, as such, do not fall within the mental process grouping of abstract ideas. (Applicant’s Remarks, Pg. 14-15). Applicant’s arguments are not persuasive for the following reasons:
The limitations indicated by Applicant of “extracting a genetic molecule from the amount of the material”, “performing an amplification process to produce an amplification product”, and “performing a sequencing process to determine nucleotide sequences of molecules included in the amplification product” were identified as additional elements in Step 2A, Prong Two above. These three limitations were not identified as judicial exceptions, and thus do not need to be practically performed in the human mind. Claim 1 also recites judicial exceptions in the limitations of “generating first data indicating one or more sequences of nucleotides”, “generating second data indicating a second sequence of nucleotides for a synthetic molecule…”, and “determining the initial number of the genetic molecule included in the sample…”, as described in Step 2A, Prong One above. As such, amended claim 1 is directed to an abstract idea, and this argument is thus not persuasive.
2. Applicant argues that amended independent claim 10 includes determining ... a first number of nucleotide sequences ... and a second number of nucleotide sequences ... and determining an initial number of the first genetic molecule ... based at least partly on an initial number of the synthetic molecule ... and the first number of nucleotide sequences ... relative to the second number of nucleotide sequences.... Likewise, amended independent claim 15 similarly recites determining ... a first number of nucleotide sequences ... and a second number of nucleotide sequences ... and determining ... the number of the genetic molecule included in the sample based on the number of the synthetic molecule included in the sample and the first number of nucleotide sequences… However, neither independent claim 10 nor independent claim 15 sets forth or describes any specific mathematical formulas, equations, calculations, or relationships. While the determinations may involve mathematical operations such as comparing sequence counts or calculating ratios, the claims does not specify how these determinations are performed or what mathematical relationships are used. As such, under the USPTO's guidance in Example 48, claims 10 and 15 are merely based on or involve a mathematical concept but does not recite a mathematical concept. Accordingly, claims 10 and 15 does not fall within the mathematical concepts grouping of abstract ideas and are patent-eligible under 35 U.S.C. § 101. (Applicant’s Remarks, Pg. 15-16). Applicant’s arguments are not persuasive for the following reasons:
Regarding claim 10, the limitations identified as judicial exceptions are (i) determining, based on the sequence data, a first number of nucleotide sequences included in the sequence data that correspond to a first genetic molecule included in the sample and a second number of nucleotide sequences included in the sequence data that correspond to a synthetic molecule included in the sample…wherein the one or more machine-generated sequences of nucleotides are produced using one or more pseudo-random number generators and (ii) determining, an initial number of the first genetic molecule included in the sample based at least partly on an initial number of the synthetic molecule included in the sample, a volume of the sample, and the first number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data. Regarding limitation (i), the broadest reasonable interpretation (BRI) of the limitation is an analysis of the sequences to compare sequence data, and the generation of sequences using a random number generator. Limitation (i) therefore recites both a mental process (i.e., the sequence analysis) and a mathematical concept (i.e., using the random number generator). Regarding limitation (ii), the BRI is a determination of a value of the first genetic molecule based on data (i.e., sequence and volume data). While Examiner agrees that the limitation does not explicitly recite a mathematical formula, it does indicate a mathematical relationship at least in relative to the second number of nucleotide sequences, as this indicates that a ratio is being calculated. As such, claim 10 recites abstract ideas in both limitations (i) and (ii).
Regarding claim 15, the limitations identified as judicial exceptions are (i) generating a function to determine a number of the genetic molecule included in the sample, (ii) determining a first number of nucleotide sequences included in the sequence data that correspond to a genetic molecule included in the amplification product and a second number of nucleotide sequences included in the sequence data that correspond to a synthetic molecule included in the amplification product…wherein the one or more machine-generated sequences of nucleotides are produced using one or more pseudo-random number generators, and (iii) determining the number of the genetic molecule included in the sample based on the number of the synthetic molecule included in the sample and the first number of nucleotide sequences included in the sequence data. Regarding limitation (i), the BRI of the limitation is generating a function to perform a calculation, which equates to a mathematical concept. Regarding limitation (ii), this limitation recites both mental processes and mathematical concepts, as described in the arguments directly above for claim 10. Regarding limitation (iii), the BRI of the limitation is a determination of a value of the first genetic molecule based on data (i.e., number of molecules and number of sequences). Examiner agrees that this limitation does not explicitly recite mathematical formulas; however, this limitation could also be interpreted as an evaluation or analysis of the number of the synthetic molecules and the first number of nucleotide sequences to determine the number of genetic molecules. Since there are no recited details about how this step is performed, an evaluation of data can reasonably be performed in the human mind or using a generic computer as a tool. As such, limitation (iii) could also be interpreted as reciting a mental process. Therefore, claim 15 recites abstract ideas in limitations (i), (ii), and (iii), and this argument is thus not persuasive.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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.
1. Claims 1, 3-8, 10-11, 13-15, and 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Christians et al. (US Patent Application Publication, US 2017/0275691 A1; published 9/28/2017; provided in the IDS dated 12/28/2021; previously cited) in view of Willey et al. (US Patent Application Publication, US 2018/0216163 A1; published 8/2/2018; provided in the IDS dated 12/28/2021; previously cited) and Ling et al. (RANDOMSEQ: Python command-line random sequence generator. MOJ Proteomics Bioinform. 7(4): 206-208 (2018); published 7/13/2018; newly cited).
This rejection is newly recited and necessitated by claim amendment.
Regarding claim 1, Christians et al. teaches a method for improved identification and quantification of nucleic acids in next generation sequence assays using spike-in synthetic nucleic acids (Para. [0092]). Christians et al. further teaches that the methods including obtaining a sample from a subject, such as a human patient. The sample may be a blood or plasma sample, or any other type of biological sample (i.e., obtaining an amount of a material from a source) (Para. [0096]). Christians et al. further teaches that nucleic acids (e.g., cell-free nucleic acids) from the sample may be extracted and used in an assay, such as a next generation sequencing assay (Para. [0097]). Christians et al. further teaches that determining the relative abundance of the first pathogen nucleic acid comprises generating one or more genome copies (i.e., extracting a genetic molecule from the amount of the material, the genetic molecule having a first sequence of nucleotides) (Para. [0040]). Christians et al. further teaches that the methods further comprise obtaining sequence information of at least one of the target nucleic acids using a computer (Para. [0058]). Christians et al. further teaches that the sample may be a nucleic acid sample, wherein nucleic acids may include DNA, RNA, etc. (i.e., generating, by one or more computing devices, first data indicating one or more sequences of nucleotides) (Para. [0119]). Christians et al. further teaches a computer control system that is programed or otherwise configured to implement the methods provided herein (i.e., by the at least one computing device of the one or more computing devices) (Para. [0069]). Christians et al. further teaches that one or more types of synthetic nucleic acids may be added (or spiked-in). The synthetic nucleic acids may have lengths designed to approximate the lengths of the set of target nucleic acids to be analyzed (Para. [0097]). Christians et al. further teaches that the synthetic nucleic acids may include any types of nucleic acids disclosed herein, including DNA, RNA, etc. (i.e., second data including a second sequence of nucleotides for a synthetic molecule) (Para. [0119]). Christians et al. further teaches that synthetic nucleic acids or spike-ins can contain adapters, common sequences, random sequences, poly-(A) tails, blunt ends, or ragged ends, or any combination thereof. In some cases, synthetic nucleic acids or spike-ins are designed to mimic nucleic acids in a sample (e.g., a biological sample) (i.e., the synthetic molecule including fist regions that include a nucleotide sequence of a biological organism) (Para. [0143]). Christians et al. further teaches that the lengths of the species of synthetic nucleic acids within a collection may exactly match the lengths of particular target nucleic acids (e.g., the observable range of pathogen or disease-specific nucleic acids in a sample) (Para. [0135]). Christians et al. further teaches that synthetic nucleic acids may contain one or more domains or regions of interest (i.e., second regions that include additional nucleotide sequences selected from the one or more sequences of nucleotides included in the first data) (Para. [0136]). Christians et al. further teaches that the method involves adding a starting quantity of at least 1000 synthetic nucleic acids to a sample (i.e., based on the sequence data) (Para. [0004]). Christians et al. further teaches that the method includes a sequencing assay, which is performed on a portion of the target nucleic acids and on a portion of the unique synthetic nucleic acids in the sample, thereby obtaining target and synthetic nucleic acid reads. (i.e., determining a first number of nucleotide sequences included in the sequence data that correspond to the genetic molecule and a second number of nucleotide sequences included in the sequence data that correspond to the synthetic molecule) (Claim 1). Christians et al. further teaches that the diversity loss of the unique synthetic nucleic acids is used to calculate the abundance of the target nucleic acids in the initial sample (i.e., an initial number of the genetic molecule included in the sample based at least partly on number of the synthetic molecule included in the sample) (Claim 1). Christians et al. further teaches that determining the relative abundance of the first pathogen nucleic acid comprises generating one or more genome copies which can be expressed as genome copies per volume (i.e., based on a volume of the sample) (Para. [0040]). Christians et al. further teaches the method of calculating abundance that depends on the sequence reads of the target and synthetic nucleic acids (i.e., based on the first number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data) (Claim 1).
Regarding claim 3, Christians et al. teaches that nucleic acids within a sample may include double-stranded nucleic acids, single stranded nucleic acids, DNA, RNA, etc. (i.e., wherein the genetic molecule includes deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) shared with additional biological organisms) (Para. [0119]).
Regarding claim 4, Christians et al. teaches that in some cases, target nucleic acids comprise pathogen nucleic acids from at least two different pathogens (i.e., a second amount, second material, second source, second sample) (Para. [0005]). Christians et al. further teaches the limitation of obtaining an amount of a material from a source and extracting a genetic molecule from the amount of the material as described for claim 1 above (i.e., obtaining a second amount of a second material from a second source included in the environment, the second material including the genetic molecule). Christians et al. further teaches the limitation of determining the initial number of the genetic molecule included in the sample based at least partly on a number of the synthetic molecule included in the sample as described for claim 1 above (i.e., determining the initial number of the genetic molecule included in the second sample based on the second sequence data and the initial number of the synthetic molecule included in the second sample). Christians et al. further teaches that the method enables improved identification or quantification of target nucleic acids when multiple samples or multiple target nucleic acids are compared or tracked (i.e., determining a difference between the initial number of the genetic molecule included in the first sample and the initial number of the genetic molecule included in the second sample) (Para. [0101]).
Regarding claim 5, Christians et al. teaches that the methods provided herein may be used to assist with certain calculations, including determining genome copies per volume of a microbe or pathogen in a sample from the next generation sequencing results. In general, copies per volume refers to an absolute measure of the amount of target nucleic acid (e.g., target nucleic acid derived from a specific pathogen) per 1 ml of fluid, and may be used to indicate abundance of individual pathogens (i.e., the volume of the mixture) (Para. [0174]). Christians et al. further teaches that in some cases, the method described herein comprises detecting 3 or more, 5 or more, 10 or more, etc. pathogen nucleic acids in the sequencing assay (i.e., includes a third portion that includes an amount of an additional molecule and determining a third number of nucleotide sequences included in the sequence data that correspond to the additional molecule) (Para. [0040]). Christians et al. further teaches the limitation of by at least one computing device of the one or more computing devices and based on the sequence data as described for claim 1 above. Christians et al. further teaches the limitation of determining the initial number of the genetic molecule included in the sample based at least partly on a number of the synthetic molecule included in the sample, a volume of the sample, and the first number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data as described for claim 1 above (i.e., since methods can detect three or more pathogens, determining an initial number of the additional molecule included in the sample based at least partly on the number of the synthetic molecule included in the sample, the volume of the sample, and the third number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data).
Regarding claim 6, Christians et al. teaches the limitation of by at least one computing device of the one or more computing devices as described for claim 1 above. Christians et al. further teaches that the abundance of the target nucleic acids in the initial sample is calculated using the diversity loss of the unique synthetic nucleic acids (i.e., determining a correlation between the number of the synthetic molecule in the sample and the initial number of an additional molecule in the sample) (Claim 1). Christians et al. further teaches that the synthetic nucleic acids provided herein may also be used to track samples, to monitor cross-contamination between samples, etc. (Para. [0132]). Christians et al. further teaches that the ratio of pathogen sequence count (or other class of sequences) to cross-contaminating or carry-over spike-in molecule counts can be used to identify any pathogen sequences that could be a result of sample-to-sample cross contamination or carry-over. In some cases, the absence of a cross-contaminating or carry-over spike-in molecule, or its presence at a level below a threshold level, is used to indicate that the sample has not been contaminated (i.e., determining that the correlation satisfies one or more threshold criteria and determining that the additional molecule is a contaminant included in the one or more amplification reagents) (Para. [0184]).
Regarding claim 7, Christians et al. teaches the limitation of by at least one computing device of the one or more computing devices as described for claim 1 above. Christians et al. further teaches that the methods and synthetic nucleic acids provided herein may be used to assist with certain calculations, including determining genome copies per volume of a microbe or pathogen in a sample from next generation sequencing results. In general, genome copies per volume may refer to an absolute measure of the amount of target nucleic acid (e.g., target nucleic acids derived from a specific pathogen) per 1 ml of fluid and may often be used as an expression to indicate the abundances of individual pathogens. The total number of reads and/or the magnitudes of the pathogen abundances may vary from sample to sample. It can be desirable to report a value that corresponds to the biological level of the infection and that can be useful for sample-to-sample comparisons (i.e., determining that the third number of the additional molecule is greater than a threshold number and determining that the additional molecule is another genetic molecule in the sample) (Para. [0174]).
Regarding claim 8, Christians et al. teaches the limitations of producing a volume of a mixture that includes a first portion having an amount of the synthetic molecule and producing a plurality of samples from the mixture, individual samples of the plurality of samples including a portion of the volume of the mixture as described for claim 1 above (i.e., based on a number of samples derived from the volume of the mixture and the amount of the synthetic molecule included in the volume of the mixture).
Regarding claim 10, Christians et al. teaches the computer control systems to implement methods of the present disclosure (Para. [0315]). Christians et al. further teaches that the computer system includes a central processing unit (CPU, also "processor" and "computer processor"), which can be a single core or multi core processor, or a plurality of processors for parallel processing (i.e., at least one hardware processor) (Para. [0316]). Christians et al. further teaches that common-forms of computer-readable media include: a floppy disk, hard disk, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying one or more sequences of one or more instructions to a processor for execution (i.e., a computer-readable medium storing instructions that, when executed by at least one hardware processor, cause the at least one hardware processor to perform operations) (Para. [0324]). Christians et al. further teaches the limitations of wherein a first genetic molecule in the sample is extracted from material; determining, based on the sequence data, a first number of nucleotide sequences included in the sequence data that correspond to the genetic molecule and a second number of nucleotide sequences included in the sequence data that correspond to the synthetic molecule; the synthetic molecule including first regions that include nucleotide sequences of a biological organism and second regions that include additional nucleotide sequences selected from one or more machine-generated sequences of nucleotides; and determining an initial number of the first genetic molecule included in the sample based at least partly on a number of the synthetic molecule included in the sample, a volume of the sample, and the first number of nucleotide sequences included in the sequence data relative to the second number of nucleotide sequences included in the sequence data as described for claim 1 above. Christians et al. further teaches that the synthetic nucleic acids can have a randomized section (Para. [0049]) and that methods described herein can be implemented by way of machine executable code (i.e., one or more machine-generated sequences of nucleotides) (Para. [0321]).
Regarding claim 11, Christians et al. teaches that the method further comprises generating a sequencing library from the sample, wherein the synthetic nucleic acids are added to the sample before generating the sequencing library (Para. [0007]). Christians et al. further teaches that in some cases, the target nucleic acids comprise pathogen nucleic acids from at least ten different pathogens (Para. [0005]). Christians et al. further teaches that the method described herein further comprises identifying co-incidence of 2 or more; 3 or more; etc. pathogens within the sample. (i.e., performing a comparison of a nucleotide sequence of the genetic molecule to one or more nucleotide sequences included in a library of nucleotide sequences, the library of nucleotide sequences including a plurality of nucleotide sequences that correspond to a plurality of additional biological organism and determining, based on the comparison, an additional biological organism of the plurality of biological organisms that corresponds to the genetic molecule) (Para. [0040]).
Regarding claim 13, Christians et al. teaches the limitation of determining, based on the sequence data, a third number of nucleotide sequences included in the sequence data that correspond to the additional molecule as described for claim 5 above. Christians et al. teaches that method described herein comprises identifying co-incidence of 2 or more, 3 or more, etc. pathogens within the sample (i.e., determining a correlation between the third number of nucleotide sequences and the second number of nucleotide sequences) (Para. [0040]). Christians et al. further teaches the limitations of determining that the correlation satisfies one or more threshold criteria and determining that the additional molecule is a contaminant included in the one or more amplification reagents as described for claim 6 above.
Regarding claim 14, Christians et al. teaches that the methods provided herein may provide a specificity (or negative percent agreement) and/or sensitivity (or positive percent agreement) that is at least 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%,or more (i.e., wherein the initial number of the genetic molecule is determined with a precision of at least 95%) (Para. [0293]).
Regarding claim 15, Christians et al. teaches the limitations of extracting a genetic molecule from a sample and by at least one computing device of the one or more computing devices as described for claim 1 above. Christians et al. further teaches the limitation of determining a first number of nucleotide sequences included in the sequence data that correspond to the genetic molecule and a second number of nucleotide sequences included in the sequence data that correspond to the synthetic molecule as described for claim 1 above (i.e., determining a first number of nucleotide sequences included in the sequence data that correspond to a genetic molecule included in the amplification product and a second number of nucleotide sequences included in the sequence data that correspond to a synthetic molecule included in the amplification product). Christians et al. further teaches the limitation of the synthetic molecule including first regions that include first nucleotide sequences of a biological organism and second regions that include second nucleotide sequences selected from one or more machine-generated sequences of nucleotides as described for claim 10 above. Christians et al. further teaches a method for determining abundance of nucleic acids in a sample, including steps of (a) adding a starting quantity of unique synthetic nucleic acids to the sample, (b) performing a sequencing assay on a portion of the target nucleic acids and on a portion of the unique synthetic nucleic acids in the sample, thereby obtaining target and synthetic nucleic acid sequence reads, (c) detecting diversity loss of the unique synthetic nucleic acids, and (d) using the diversity loss of the unique synthetic nucleic acids to calculate abundance of the target nucleic acids in the initial sample (Claim 1). Christians et al. further teaches a computer control system that is programed to implement the methods provided herein (i.e., generating a function to determine a number of the genetic molecule included in a sample) (Para. [0069]). Christians et al. further teaches the limitation of determining the number of the genetic molecule included in the sample based on the number of the synthetic molecule included in the sample and the first number of nucleotide sequences included in the sequence data as described for claim 1 above.
Regarding claim 18, Christians et al. teaches that the method described herein comprises identifying co-incidence of 2 or more; 3 or more; 5 or more; 10 or more; 50 or more; or 100 or more pathogens within the sample (Para. [0040]). Christians et al. further teaches a method for computational analysis, wherein the reads for an individual sample were identified based on the corresponding adapter barcode sequence ("demuxing"). Following removal of adapter dimer sequences and quality-based read trimming, the likely origin of the read sequences was determined by alignment to human genome, spike-in and pathogen genome reference sequences (i.e., performing comparisons between a nucleotide sequence of the genetic molecule with respect to the plurality of additional nucleotide sequences that are associated with a plurality of individuals) (Para. [0412]). Christians et al. further teaches that sequencing data may be used to determine genetic sequence information, ploidy states, the identity of one or more genetic variants, as well as a quantitative measure of the variants, including relative and absolute relative measures (i.e., determining, based on the comparisons, a threshold amount of identify between the nucleotide sequence of the genetic molecule and an additional nucleotide sequence of the plurality of additional nucleotide sequences and identifying an individual of the plurality of individuals that corresponds to the additional nucleotide sequence) (Para. [0279]).
Regarding claim 19, Christians et al. teaches the limitation of obtaining an amount of material from a source (i.e., an environment) as described for claim 1 above. Christians et al. further teaches the limitation of extracting the genetic molecule from a cell included in an amount of fluid (i.e., extracting a cell from the material that includes the genetic molecule) as described for claim 17 above. Christians et al. further teaches that the method described herein comprises identifying co-incidence of 2 or more; 3 or more; 5 or more; 10 or more; 50 or more; or 100 or more pathogens within the sample (Para. [0040]). Christians et al. further teaches that the synthetic nucleic acids provided herein may also be used to track samples, to monitor cross-contamination between samples, to track reagents, to track reagent lots, and numerous other applications (i.e., performing comparisons between a nucleotide sequence of the genetic molecule with respect to a plurality of additional nucleotide sequences that are associated with contaminants) (Para. [0132]). Christians et al. further teaches that the ratio of pathogen sequence count (or other class of sequences) to cross-contaminating or carry-over spike-in molecule counts can be used to identify any pathogen sequences that could be a result of sample-to-sample cross contamination or carry-over. In some cases, the absence of a cross-contaminating or carry-over spike-in molecule, or its presence at a level below a threshold level, is used to indicate that the sample has not been contaminated (i.e., determining, based on the comparisons, a threshold amount of identify between the nucleotide sequence of the genetic molecule and an additional nucleotide sequence of the plurality of nucleotide sequences and identifying a contaminant of the environment, wherein the contaminant corresponds to the additional nucleotide sequence) (Para. [0184]).
Regarding claim 20, Christians et al. teaches a computational analysis wherein the reads for an individual sample were identified based on the corresponding adapter barcode sequence ("demuxing") (i.e., identifying a first barcode sequence included in a first nucleotide sequence and identifying a second barcode sequence included in a second nucleotide sequence) (Para [0412]). Following removal of adapter dimer sequences and quality-based read trimming, the likely origin of the read sequences was determined by alignment to human genome, spike-in and pathogen genome reference sequences (i.e., determining, based on the first barcode sequence, that the first nucleotide sequence corresponds to a first molecule; determining, based on the second barcode sequence, that the second nucleotide sequence corresponds to a second molecule; producing a first group of nucleotide sequences that include the first barcode sequence; and producing a second group of nucleotide sequences that include the second barcode sequence) (Para. [0412]).
Christians et al. does not teach wherein the one or more sequences of nucleotides are machine-generated nucleotide sequences produced using one or more pseudo-random number generators; producing a volume of a mixture that includes a first portion having an amount of the synthetic molecule and a second portion that includes one or more amplification reagents; producing a plurality of samples from the mixture, individual samples of the plurality of samples including a portion of the volume of the mixture, and an additional portion that includes an amount of the genetic molecule; performing an amplification process to produce an amplification product for a sample of the plurality of samples, wherein the amplification product includes an amplified number of the genetic molecule and an amplified number of the synthetic molecule that is greater than an initial number and an initial number of the synthetic molecule included in the sample; performing a sequencing process to determine nucleotide sequences of molecules included in the amplification product; obtaining, based on the sequencing process, sequence data indicating the nucleotide sequences of the molecules included in the amplification product; implementing the one or more pseudo-random number generators to generate the first data indicating one or more sequences of nucleotides; dividing a nucleotide sequence generated using the one or more pseudo-random number generators into a plurality of segments to generate a plurality of sequences of nucleotides in the first data; producing a second sample that includes at least a portion of the second amount of the second material, the one or more amplification reagents, and an amount of the synthetic molecule; performing an additional amplification process with the one or more amplification reagents to produce an additional amplification product for the second sample, the additional amplification product including an additional amplified number of the genetic molecule that is greater than an initial number of the genetic molecule included in the second sample and an additional amplified number of the synthetic molecule that is greater than an additional initial number of the synthetic molecule included in the second sample; performing an additional sequencing process to produce additional sequence data, the additional sequence data indicating nucleotides sequences of molecules included in the additional amplification product; performing an analysis based on the difference to determine a probability that a factor of a plurality of factors is causing the difference; determining the number of the synthetic molecule included in the sample; obtaining sequence data indicating nucleotide sequences of molecules included in an amplification product, the amplification product corresponding to a sample that has undergone an amplification process to increase an initial number of molecules included in the sample; with a lower limit of detection between 1 and 10 of the genetic molecule included in the sample; obtaining sequence data indicating nucleotide sequences of molecules included in an amplification product, the amplification product corresponding to a sample that has undergone an amplification process to increase an initial number of molecules included in the sample;
Regarding claim 1, Ling et al. teaches a python-based method for generating random sequences for fixed or variable length nucleotide or amino acid sequences using a pseudo-random number generator (Abstract and Pg. 206, Col. 2, Para. 2). The random sequences can be applied to many applications in molecular biology, including as barcodes, experimental controls or experimental tools, and null hypotheses. The random sequences significant implications in the origins and functional evolution of biological properties (i.e., wherein the one or more sequences of nucleotides are machine-generated nucleotide sequences produced using one or more pseudo-random number generators) (Pg. 208, Col. 1, Para. 2).
Regarding claim 1, Willey et al. teaches a schematic illustration of a PCR master mix with a mixture of Internal Amplification Controls (IAC) (i.e., synthetic molecules) (Para. [0046]). The mixture consists of a sequencer tag, barcode tag (to identify sample and standard), universal primer for multi-template PCR, and amplicon sequence (i.e., producing a volume of a mixture that includes a first portion having an amount of the synthetic molecule and a second portion that includes one or more amplification reagents) (Fig. 9). Willey et al. further teaches that 1 μL from each of the five reverse transcribed RNA Titration Pools of cDNA (Samples A-RT1, A-RT2, B, C, and D) was spiked into 1 of the 12 Multiplex-PCR reactions containing serially diluted mixture of competitive IAC mixture representing 150 targets (i.e., producing a plurality of samples from the mixture, individual samples of the plurality of samples including a portion of the volume of the mixture, and an additional portion that includes an amount of the genetic molecule) (Para. [0124]). Willey et al. further teaches that the method comprises co-amplifying said first nucleic acid and said competitive template for said first nucleic acid to produce amplified product thereof (i.e., performing an amplification process to produce an amplification product for a sample of the plurality of samples) (Para. [0022]). Willey et al. further teaches a comparison of said amplified product of said first nucleic acid to said amplified product of said competitive template for said first nucleic acid, wherein the ratio is about 1:10 (i.e., wherein the amplification product includes an amplified number of the genetic molecule and an amplified number of the synthetic molecule that is greater than an initial number and an initial number of the synthetic molecule included in the sample) (Para. [0023]). Willey et al. further teaches that the method uses a gene specific reverse transcription and/or PCR for library preparation for quantification by sequencing (i.e., performing a sequencing process to determine nucleotide sequences of the molecules included in the amplification product) (Para. [0098]). Willey et al. further teaches that at the end of sequencing, the proportion of sequencing events, (i.e., observations, counts, reads) between the native target and its respective internal standard is assessed, along with the original number of internal standard nucleic acid molecules input into the sample prior to library preparation, in order to quantifiably determine the original amount of each native target in the original sample prior to library preparation and sequencing (i.e., obtaining sequence data indicating the nucleotide sequences of the molecules included in the amplification product) (Para. [0089]).
Regarding claim 3, Ling et al. teaches a python-based method for generating random sequences for fixed or variable length nucleotide or amino acid sequences using a pseudo-random number generator (i.e., implementing the one or more pseudo-random number generators to generate the first data indicating the one or more sequences of nucleotides) (Abstract and Pg. 206, Col. 2, Para. 2). Ling et al. further teaches that a random sequence is generated by concatenating randomly chosen atomic sequences from a bag, up to the required length (Pg. 206, Col. 2, Para. 2). Ling et al. further teaches an example wherein the code will generate 10 random sequence of 100 nucleotides each where each sequence will have uniform nucleotide distribution, and without start and stop codons within the sequence but flanked with a randomly selected start and stop codons from the specified list of start and stop codons (i.e., dividing a nucleotide sequence generated using the one or more pseudo-random number generators into a plurality of segments to generate a plurality of sequences of nucleotides in the first data) (Pg. 207, Col. 2, Para. 1).
Regarding claim 4, Willey et al. teaches that two samples correspond to separate biological states (Para. [0219]). Willey et al. further teaches the limitation of producing a volume of a mixture that includes a first portion having an amount of the synthetic molecule and a second portion that includes one or more amplification reagents as described for claim 1 above (i.e., producing a second sample that includes at least a portion of the second amount of the second material, the one or more amplification reagents, and an amount of the synthetic molecule). Willey et al. further teaches the limitation of performing an amplification process to produce an amplification product for a sample of the plurality of samples, wherein the amplification product includes an amplified number of the genetic molecule and an amplified number of the synthetic molecule that is greater than an initial number and an initial number of the synthetic molecule included in the sample as described for claim 1 above (i.e., performing an additional amplification process with the one or more amplification reagents to produce an additional amplification product for the second sample, the additional amplification product including an additional amplified number of the genetic molecule that is greater than an initial number of the genetic molecule included in the second sample and an additional amplified number of the synthetic molecule that is greater than an additional initial number of the synthetic molecule included in the second sample). Willey et al. further teaches the limitation of performing a sequencing process to determine nucleotide sequences of molecules included in the amplification product as described for claim 1 above (i.e., performing an additional sequencing process to produce additional sequence data, the additional sequence data indicating nucleotides sequences of molecules included in the additional amplification product). Willey et al. further teaches that more than two biological states can be compared. Samples may provide a range of biological states, e.g., corresponding to different stages of disease progression, e.g., different stages of cancer (i.e., factors) (Para. [0229]). Willey et al. further teaches that a nucleic acid may be said to be "associated with" a particular biological state where the nucleic acid is either positively or negatively associated with the biological state. For example, a nucleic acid may be said to be "positively associated" with a first biological state where the nucleic acid occurs in higher amounts in a first biological state compared to a second biological state (i.e., performing an analysis based on the difference to determine a probability that a factor of a plurality of factors is causing the difference) (Para. [0224]).
Regarding claim 8, Willey et al. teaches that at the end of the sequencing, the proportion of sequencing events, (i.e., observations, counts, reads) between the native target and its respective internal standard is assessed, along with the original number of internal standard nucleic acid molecules input into the sample prior to library preparation, in order to quantifiably determine the original amount of each native target in the original sample prior to library preparation and sequencing (i.e., determining the amount of synthetic molecule included in the sample) (Para. [0089]).
Regarding claim 10, Willey et al. teaches the limitation of obtaining sequence data indicating the nucleotide sequences of the molecules in the amplification process as described for claim 1 above (i.e., obtaining sequence data including nucleotide sequences of molecules included in an amplification product). Christians et al. further teaches that amplification may refer to any method for increasing the number of copies of a nucleic acid sequence (i.e., the amplification product corresponding to a sample that has undergone an amplification process to increase an initial number of molecules included in the sample) (Para. [0391]).
Regarding claim 10, Ling et al. teaches the limitation of wherein the one or more machine-generated sequences of nucleotides are produced using one or more pseudo-random number generators as described for claim 1 above.
Regarding claim 14, Willey et al. teaches that the measurements represent true negative measurements and the lower limit of accurate quantification can be determined from these data (i.e., with a lower limit of detection between 1 and 10 of the genetic molecule included in the sample) (Para. [0196]).
Regarding claim 15, Willey et al. teaches the limitation of obtaining sequence data indicating nucleotide sequences of molecules included in an amplification product, the amplification product corresponding to a sample that has undergone an amplification process to increase an initial number of molecules included in the sample as described for claim 10 above.
Regarding claim 15, Ling et al. teaches the limitation of wherein the one or more machine-generated sequences of nucleotides are produced using one or more pseudo-random number generators as described for claim 1 above.
Therefore, regarding claims 1, 3-8, 10-11, 13-15, and 18-20, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of detecting and quantifying nucleic acids in low abundance samples of Christians et al. with the method of co-amplification of synthetic and target molecules of Willey et al. because the method enables low-abundance native targets to be preferentially amplified (i.e., enriched) relative to higher-abundance native targets during library preparation (Willey et al., Para [0090]). One of ordinary skill in the art would be able to combine the teachings of Christians et al. with Willey et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both are drawn towards a method for quantifying nucleic acids using next generation sequencing.
Additionally, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of detecting and quantifying nucleic acids in low abundance samples of Christians et al. with the method of generating random sequences of Ling et al. because Christians et al. discloses that the synthetic nucleic acids can have a randomized section (Christians et al., Para. [0049]) and Ling et al. discloses that the random sequences can be used as experimental controls (i.e., the synthetic nucleic acid sequences) (Ling et al. Pg. 208, Col. 1, Para. 2). One of ordinary skill in the art would be able to combine the teachings of Christians et al. with Ling et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both include a step of generating randomized sequences. Therefore, regarding claims 1, 3-8, 10-11, 13-15, and 18-20, the instant invention is prima facie obvious (MPEP § 2142).
2. Claims 2, 12, 16-17, and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Christians et al. in view of Willey et al. and Ling et al. as applied to claims 1, 3-8, 10-11, 13-15, and 18-20 above, and further in view of Knight et al. (US Patent Application Publication, US 2017/0139078 A1; published 5/18/2017; provided in the IDS dated 12/28/2021; previously cited).
This rejection is newly recited and necessitated by claim amendment.
Regarding claim 2, Willey et al. teaches that for each multiplex competitive chain reaction PCR, a 10 μL reaction volume was prepared (i.e., individual samples of the plurality of samples have a volume from 10 microliters to 500 microliters and the amplification process includes a polymerase chain reaction (PCR)) (Para. [0167]). Willey et al. further teaches that NGS libraries were prepared from the reverse transcribed reference material using Multiplex-PCR in the presence of primers and competitive Internal Amplification Controls (IAC) for 150 gene targets (i.e., the nucleotide sequences of the biological organism correspond to primers included in the one or more amplification reagents) (Para. [0114]).
Regarding claim 12, Christians et al. teaches the limitation of determining, based on the sequence data, a third number of nucleotide sequences included in the sequence data that correspond to the additional molecule as described for claim 5 above. Christians et al. further teaches the limitations of performing a comparison of a nucleotide sequence of a genetic molecule to one or more nucleotide sequences included in a library of nucleotide sequences and determining, based on the comparison, an additional biological organism of the plurality of additional biological organisms that correspond to the genetic molecule as described for claim 11 above.
Regarding claim 17, Christians et al. teaches the extraction of nucleic acids from a sample (Para. [0040]), and that the sample may be a blood sample or plasma sample, or any other type of biological sample, especially a biological sample containing a bodily fluid, tissue, and/or cells (i.e., extracting the genetic molecule from a cell included in an amount of a fluid) (Para. [0100]).
Christians et al. in view of Willey et al. and Ling et al., as applied to claims 1, 3-8, 10-11, 13-15, and 18-20 above, does not teach the nucleotide sequences of the biological organisms are selected from conserved regions of the ribosomal ribonucleic acid gene (rRNA gene); determining that the additional biological organism and the second additional biological organism are present in environments where at least one of crude oil, natural gas, and formation water are located; determining, based on a presence of the genetic molecule in the sample, that one or more biochemical reactions have taken place in an environment from which the sample was obtained, wherein the one or more biochemical reactions include at least one of a nitrate reducing reaction, a sulfate reducing reaction, methanogenesis, a hydrocarbon conversion reaction, or a biosurfactant generating reaction; obtained from a subterranean environment that stores at least one of a fossil fuel-based petroleum substance or natural gas; a difference between a first amount of biomass included in the first sample and a second amount of biomass included in the second sample; and a difference between one or more first conditions related to the first source and one or more second conditions related to the second source, the one or more first conditions and the one or more second conditions include at least one of temperature, humidity, or amount of exposure to a range of wavelengths of electromagnetic radiation.
Regarding claim 2, Knight et al. teaches that the gene encoding the 16S subunit is referred to as the 16S rRNA gene. The 16S rRNA gene is used for reconstructing phylogenies because it is highly conserved between different species of bacteria and archaea, meaning that is an essential part of the organisms who encode it in their genomes, and it can be easily identified in genomic sequences (Para. [0215]). Knight et al. further teaches that the analysis includes extracting material including genetic material selected from the group consisting of a SSU rRNA gene 16S, SSU rRNA gene 1 SS, LSU rRNA gene 23S, LSU rRNA 28S, ITS in the rRNA operon, and ITS in the rRNA cpn60 (i.e., the nucleotide sequences of the biological organism are selected from conserved regions of the ribosomal ribonucleic acid gene (rRNA gene)) (Para. [0050]).
Regarding claim 12, Knight et al. teaches that in view of the ubiquitous nature of genetic material and microorganisms, the present inventions provide, among other things, the ability to control, enhance, plan, monitor, and predict performance of hydrocarbon exploration and production activities (Para. [0005]). Knight et al. further teaches that in the production of natural resources from formations, reservoirs, deposits, or locations within the earth a well or borehole is drilled into the earth to the location where the natural resource is believed to be located. These natural resources may be a hydrocarbon reservoir, containing natural gas, crude oil and combinations of these or the natural resource may be fresh water (i.e., determining that the additional biological organisms and the second additional biological organisms are present in environments where at least one of crude oil, natural gas, and formation water are located) (Para. [0025]).
Regarding claim 16, Knight et al. teaches that the existence of hydrogen sulfide in a reservoir typically can be a key factor when determining the value and method of production of a well. Hydrogen sulfide (H2S) gas enters drilling mud from subsurface formations and can also be generated by sulfate-reducing bacteria resident in the subsurface. H2S production also reduces the value of the produced oil. Because H2S is often produced by bacteria in the reservoir, microbial analysis and predictive modeling provide a new avenue for early detection of H2S formation (i.e., determining, based on the presence of the genetic molecule in the sample, that one or more biochemical reactions have taken place in an environment from which the sample was obtained, wherein the one or more biochemical reactions includes a sulfate reducing reaction) (Para. [0484]).
Regarding claim 17, Knight et al. teaches that the present inventions provide apparatus, systems and methods for determining and characterizing the microbiome associated with hydrocarbon exploration and production (Para. [0005]). Knight et al. further teaches these natural resources may be a hydrocarbon reservoir, containing natural gas, crude oil and combinations of these (i.e., obtained from a subterranean environment that stores at least one of a fossil fuel-based petroleum substance or natural gas) (Para. [0025]).
Regarding claim 26, Knight et al. teaches that many microbial communities residing in oil and gas fields may be of low biomass (e.g., relatively few organisms are present per unit volume or unit of mass) (Para. [0179]). Knight et al. further teaches that predictive microbiome information includes a determination and comparison of real-time microbiome information (i.e., a difference between a first amount of biomass included in the sample and a second amount of biomass included in the second sample) (Para. [0010]). Knight et al. further teaches that the following features are provided in the present systems, operations, and methods: location data, system component identification, subsystem component identification, pump station true vertical depth of a well, pH, processing stage, geological parameter, formation permeability, viscosity, porosity, pressure, flow, and temperature (i.e., a difference between one or more first conditions related to the first source and one or more second conditions related to the second source, the one or more first conditions and the one or more second conditions include at least one of temperature) (Para. [0041]).
Therefore, regarding claims 2, 12, 16-17, and 26, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of detecting and quantifying nucleic acids in low abundance samples of Christians et al. in view of Willey et al. and Ling et al. with the teachings of Knight et al. because the use of the 16S rRNA gene sequence enables the characterization of the microbiome associated with hydrocarbon exploration and production, including oil or natural gas wells (Knight et al., Para. [0004]-[0005] and [0050]). One of ordinary skill in the art would be able to combine the teachings of Christians et al. in view of Willey et al. and Ling et al. with Knight et al. with reasonable expectation of success due to the same nature of the problem to be solved, since both are drawn towards a method for quantifying nucleic acids using next generation sequencing. Therefore, regarding claims 2, 12, 16-17, and 26, the instant invention is prima facie obvious (MPEP § 2142).
Response to Arguments under 35 U.S.C. 103
Applicant’s arguments filed 12/19/2025 have been fully considered but they are not persuasive.
1. Applicant argues that either Christians, Willey, Knight, nor Piva, nor any combination thereof, includes the element that the one or more sequences of nucleotides are machine-generated nucleotide sequences produced using one or more pseudo-random number generators, as included in amended independent claims 1, 10, and 15. For at least the reasons given above, Applicant respectfully submits amended independent claims 1, 10, and 15 are allowable under 35 U.S.C. § 103 over the cited references. Dependent claims 2-8, 11-14, 16-20, and 26 must a fortiori also be allowable under 35 U.S.C. § 103 over the cited references since each carries with it all the limitations of claims 1, 10, or 15, as well as added features not taught by the cited references (Applicant’s Remarks, Pg. 17-18). Applicant’s arguments are not persuasive for the following reasons:
Applicant’s arguments regarding the obviousness of the claims over Christians et al., Willey et al., Knight et al. or Piva et al., as failing to teach that the sequences are machine-generated nucleotide sequences produced using one or more pseudo-random number generators, as in amended claims 1, 10, and 15 have been considered but they are not persuasive in view of the new grounds of rejection that relies on a new combination of references as necessitated by claim amendment.
Conclusion
No claims 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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/D.P.S./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687