# US 11,079,320 B2 · Methods of characterizing a urine sample > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 11,079,320 B2 - Document ID: US11079320B2 - Status: Granted - Kind: B2 - Application number: 16/564,170 - Filed: 2019-09-09 - Published: 2020-04-16 - Granted: 2021-08-03 - Earliest claimed: 2016-10-11 - Assignees: Genotox Laboratories - Applicants: Genotox Laboratories - Inventors: Nicholas D. Laude; William S. Edgemond; Keqin Gregg - Web page: https://patentgrep.com/patent/US11079320B2 ## CPC - G01N 21/3103: {Atomic absorption analysis} - G01N 21/31: Investigating relative effect of material at wavelengths characteristic of specific elements or molecules, e.g. atomic absorption spectrometry {(G01N21/72 takes precedence)} - G01N 21/314: {with comparison of measurements at specific and non-specific wavelengths (dual wavelength spectrometry G01J3/427)} - G01N 21/3151: {using two sources of radiation of different wavelengths (G01N21/33 - G01N21/39 take precedence)} - G01N 21/6486: {Measuring fluorescence of biological material, e.g. DNA, RNA, cells (G01N21/6428 takes precedence)} - G01N 21/76: Chemiluminescence; Bioluminescence - G01N 33/493: urine - G16H 50/20: for computer-aided diagnosis, e.g. based on medical expert systems - C12Q 2537/165: Mathematical modelling, e.g. logarithm, ratio - G01N 21/33: using ultraviolet light (G01N21/39 takes precedence) - G01N 21/3577: for analysing liquids, e.g. polluted water - G01N 21/359: using near infrared light - G01N 21/763: {Bioluminescence} - G01N 2021/3595: {using FTIR} - G01N 2201/1293: resolving multicomponent spectra - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - G16H: HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract This disclosure relates to methods of characterizing a urine sample from a subject. ## Claims ### Claim 1 A method of characterizing a urine sample from a subject, the method comprising: (a) providing a urine sample from a subject; (b) determining one or more of the light absorption, luminescence, phosphorescence, fluorescence, and chemiluminescence of the urine sample at two or more wavelengths of light; (c) applying one or more eigenvectors derived from a principle component algorithm to a standardized dataset derived from the determined light absorption, luminescence, phosphorescence, fluorescence, and chemiluminescence of the urine sample to generate a Urine Characterization Index (UCI) comprising one or more values for corresponding principle component(s); and (d) characterizing a urine sample as a natural urine sample, based on the UCI; (e) enriching the characterized urine sample for mammalian cells, if present; (f) isolating any genomic DNA from the enriched sample of step (e) to form an isolated genomic DNA test sample; (g) adding to the isolated genomic DNA test sample of step (f) a control DNA to form a control sample or adding the control DNA to the enriched sample of step (e) and then isolating the DNA to form a control sample; (h) performing an assay to determine the genotype of at least 6 single nucleotide polymorphisms (SNPs) in the isolated genomic DNA test sample of (f) or the control sample of step (g); (i) comparing the genotype of the at least 6 SNPs in the isolated genomic DNA test sample of step (f) or the control sample of step (g) with the genotype of the at least 6 SNPs in a control cell sample from the subject; and (j) further identifying a characterized urine sample having a detectable level of the control DNA and having the same genotype of the at least 6 SNPs in the isolated genomic DNA test sample of step (f) or the control sample of step (g) as the genotype of the at least 6 SNPs in the control cell sample as originating from the subject, or identifying a characterized urine sample having a detectable level of the control DNA and not having the same genotype of the at least 6 SNPs in the isolated genomic DNA test sample of step (f) or the control sample of step (g) as the genotype of the at least 6 SNPs in the control cell sample as not originating from the subject. ### Claim 2 (depends on 1) The method of claim 1, wherein step (b) comprises determining the light absorption of the urine sample. ### Claim 3 (depends on 2) The method of claim 2, wherein step (b) comprises determining the light absorption of one or more of ultraviolet light wavelength(s), visible light wavelength(s), near-infrared light wavelength(s), and infrared absorption light wavelengths. ### Claim 4 (depends on 2) The method of claim 2, wherein step (b) comprises determining the light absorption of the urine sample at wavelengths of about 200 nm to about 1000 nm. ### Claim 5 (depends on 2) The method of claim 2, wherein step (b) comprises determining the light absorption of the urine sample at wavelengths of about 200 nm to about 340 nm. ### Claim 6 (depends on 2) The method of claim 2, wherein step (c) comprises applying an eigenvector derived from the principle component algorithm to a dataset derived from the determined light absorption to generate a value for one principle component. ### Claim 7 (depends on 1) The method of claim 1, wherein step (c) comprises applying two eigenvectors derived from the principle component algorithm to a dataset derived from the determined light absorption, luminescence, phosphorescence, fluorescence, chemiluminescence, or bioluminescence to generate values in two-dimensional principal component space. ### Claim 8 (depends on 7) The method of claim 7, wherein step (c) comprises applying two eigenvectors derived from the principle component algorithm to a dataset derived from the determined light absorption to generate values in two-dimensional principle component space. ### Claim 9 (depends on 1) The method of claim 1, wherein step (c) comprising applying three eigenvectors derived from the principle component algorithm to a dataset derived from the determined light absorption, luminescence, phosphorescence, fluorescence, chemiluminescence, or bioluminescence to generate values in three-dimensional principle component space. ### Claim 10 (depends on 9) The method of claim 9, wherein step (c) comprises applying three eigenvectors derived from the principle component algorithm to a dataset derived from the determined light absorption to generate values in three-dimensional principle component space. ### Claim 11 (depends on 1) The method of claim 1, wherein step (c) comprising applying four eigenvectors derived from the principle component algorithm to a dataset derived from the determined light absorption, luminescence, phosphorescence, fluorescence, chemiluminescence, or bioluminescence to generate values in four-dimensional principle component space. ### Claim 12 (depends on 11) The method of claim 11, wherein step (c) comprises applying four eigenvectors derived from the principle component algorithm to a dataset derived from the determined light absorption to generate values in four-dimensional principle component space. ### Claim 13 (depends on 1) The method of claim 1, wherein step (d) comprises characterizing a urine sample through the use of a clustering algorithm. ### Claim 14 (depends on 13) The method of claim 13, wherein the clustering algorithm is a hierarchical clustering algorithm, a k-means clustering algorithm, or a statistical distribution model. ### Claim 15 (depends on 1) The method of claim 1, wherein step (d) comprises characterizing a urine sample by performing regression analysis on the values of principle components. ### Claim 16 (depends on 1) The method of claim 1, wherein step (d) comprises comparing the UCI of the sample to a UCI of a natural urine sample. ### Claim 17 A method of characterizing a urine sample from a subject, the method comprising: (a) providing a urine sample collected from a subject; (b) determining the absorbance at a first wavelength (A1) and the absorbance at a second wavelength (A2) of the urine sample, wherein the first wavelength is from about 230 nm to 250 nm, and the second wavelength is from about 260 nm to 340 nm; (c) applying an algorithm to the determined A1 and the determined A2 to generate a Urine Characterization Score (UCS), wherein the algorithm includes a ratio of the determined A1 to the determined A2; and (d) characterizing a urine sample as a natural urine sample, based on the UCS; (e) enriching the characterized urine sample for mammalian cells, if present; (f) isolating any genomic DNA from the enriched sample of step (e) to form an isolated genomic DNA test sample; (g) adding to the isolated genomic DNA test sample of step (f) a control DNA to form a control sample or adding the control DNA to the enriched sample of step (e) and then isolating the DNA to form a control sample; (h) performing an assay to determine the genotype of at least 6 single nucleotide polymorphisms (SNPs) in the isolated genomic DNA test sample of (f) or the control sample of step (g); (i) comparing the genotype of the at least 6 SNPs in the isolated genomic DNA test sample of step (f) or the control sample of step (g) with the genotype of the at least 6 SNPs in a control cell sample from the subject; and (j) further identifying a characterized urine sample having a detectable level of the control DNA and having the same genotype of the at least 6 SNPs in the isolated genomic DNA test sample of step (f) or the control sample of step (g) as the genotype of the at least 6 SNPs in the control cell sample as originating from the subject, or identifying a characterized urine sample having a detectable level of the control DNA and not having the same genotype of the at least 6 SNPs in the isolated genomic DNA test sample of step (f) or the control sample of step (g) as the genotype of the at least 6 SNPs in the control cell sample as not originating from the subject. ### Claim 18 (depends on 17) The method of claim 17, wherein the UCS is generated using the Formula (XI): UCS=A1/A2. ### Claim 19 (depends on 17) The method of claim 17, wherein the UCS is generated using the Formula (XII): UCS=10×log (A1/A2). ### Claim 20 (depends on 17) The method of claim 17, wherein the first wavelength is 240 nm and the second wavelength is 280 nm. ### Claim 21 (depends on 18) The method of claim 18, wherein step (d) comprises charactering the urine sample as a synthetic urine sample if UCS is greater than 0.8. ### Claim 22 (depends on 19) The method of claim 19, wherein step (d) comprises charactering the urine sample as a synthetic urine sample if the UCS is less than 0.25. ### Claim 23 (depends on 1) The method of claim 1, wherein the characterized urine sample is identified as originaling from the subject and the method further comprises: (k) performing an assay to determine the level of one or more drug metabolites in the characterized urine sample. ### Claim 24 (depends on 23) The method of claim 23, further comprising: (l) identifying a subject having an elevated level of one or more drug metabolites in the characterized urine sample as compared to a reference level of the one or more drug metabolites, where the drug metabolites are metabolites of an illegal or controlled substance; and (m) admitting the subject into a drug dependency program, ceasing administration of the controlled substance to the subject, or reducing the dose and/or frequency of administration of the controlled substance to the subject. ### Claim 25 (depends on 1) The method of claim 1, wherein the control cell sample is a buccal cell sample obtained from the subject. ### Claim 26 (depends on 17) The method of claim 17, wherein the characterized urine sample is identified as originating from the subject and the method further comprises: (k) performing an assay to determine the level of one or more drug metabolites in the characterized urine sample. ### Claim 27 (depends on 26) The method of claim 26, further comprising: (l) identifying a subject having an elevated level of one or more drug metabolites in the characterized urine sample as compared to a reference level of the one or more drug metabolites, where the drug metabolites are metabolites of an illegal or controlled substance; and (m) admitting the subject into a drug dependency program, ceasing administration of the controlled substance to the subject, or reducing the dose and/or frequency of administration of the controlled substance to the subject. ### Claim 28 (depends on 17) The method of claim 17, wherein the control cell sample is a buccal cell sample obtained from the subject.