SG11201900253TA - Method and system for microbial pharmacogenomics - Google Patents

Method and system for microbial pharmacogenomics

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Publication number
SG11201900253TA
SG11201900253TA SG11201900253TA SG11201900253TA SG11201900253TA SG 11201900253T A SG11201900253T A SG 11201900253TA SG 11201900253T A SG11201900253T A SG 11201900253TA SG 11201900253T A SG11201900253T A SG 11201900253TA SG 11201900253T A SG11201900253T A SG 11201900253TA
Authority
SG
Singapore
Prior art keywords
microbiome
dataset
street
pharmacogenomics
antibiotics
Prior art date
Application number
SG11201900253TA
Inventor
Zachary Apte
Jessica Richman
Daniel Almonacid
Inti Pedroso
Juan Ugalde
Rodrigo Ortiz
Original Assignee
Ubiome Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority claimed from US15/606,743 external-priority patent/US10803991B2/en
Application filed by Ubiome Inc filed Critical Ubiome Inc
Publication of SG11201900253TA publication Critical patent/SG11201900253TA/en

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Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61B—DIAGNOSIS; SURGERY; IDENTIFICATION
    • A61B5/00—Measuring for diagnostic purposes; Identification of persons
    • A61B5/48—Other medical applications
    • A61B5/4848—Monitoring or testing the effects of treatment, e.g. of medication
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61B—DIAGNOSIS; SURGERY; IDENTIFICATION
    • A61B5/00—Measuring for diagnostic purposes; Identification of persons
    • A61B5/48—Other medical applications
    • A61B5/4836—Diagnosis combined with treatment in closed-loop systems or methods
    • A61B5/4839—Diagnosis combined with treatment in closed-loop systems or methods combined with drug delivery
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61B—DIAGNOSIS; SURGERY; IDENTIFICATION
    • A61B5/00—Measuring for diagnostic purposes; Identification of persons
    • A61B5/74—Details of notification to user or communication with user or patient ; user input means
    • A61B5/746—Alarms related to a physiological condition, e.g. details of setting alarm thresholds or avoiding false alarms
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61B—DIAGNOSIS; SURGERY; IDENTIFICATION
    • A61B5/00—Measuring for diagnostic purposes; Identification of persons
    • A61B5/74—Details of notification to user or communication with user or patient ; user input means
    • A61B5/7465—Arrangements for interactive communication between patient and care services, e.g. by using a telephone network
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
    • G16H20/10—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to drugs or medications, e.g. for ensuring correct administration to patients
    • G16H20/13—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to drugs or medications, e.g. for ensuring correct administration to patients delivered from dispensers
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H40/00—ICT specially adapted for the management or administration of healthcare resources or facilities; ICT specially adapted for the management or operation of medical equipment or devices
    • G16H40/60—ICT specially adapted for the management or administration of healthcare resources or facilities; ICT specially adapted for the management or operation of medical equipment or devices for the operation of medical equipment or devices
    • G16H40/63—ICT specially adapted for the management or administration of healthcare resources or facilities; ICT specially adapted for the management or operation of medical equipment or devices for the operation of medical equipment or devices for local operation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/50—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for simulation or modelling of medical disorders
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/70—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Medical Informatics (AREA)
  • Public Health (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Surgery (AREA)
  • Veterinary Medicine (AREA)
  • Pathology (AREA)
  • Animal Behavior & Ethology (AREA)
  • Heart & Thoracic Surgery (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Medicinal Chemistry (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Nursing (AREA)
  • Physiology (AREA)
  • Bioethics (AREA)
  • Evolutionary Computation (AREA)
  • Software Systems (AREA)

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) -., (19) World Intellectual Property MD HIM 01110101011111 3E1 0 10111110111 OM 11111H10111111011110111111 Organization . International Bureau (10) International Publication Number (43) International Publication Date ......'\"' WO 2018/013865 Al 18 January 2018 (18.01.2018) W I P0 I PC T (51) International Patent Classification: (74) Agent: SCHOX, Jeffrey; 500 3rd Street, Suite 215, San A61B 5/00 (2006.01) A61K 35/74 (2015.01) Francisco, CA 94107 (US). (21) International Application Number: (81) Designated States (unless otherwise indicated, for every PCT/US2017/042015 kind of national protection available): AE, AG, AL, AM, (22) International Filing Date: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, 13 July 2017 (13.07.2017) CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, (25) Filing Language: English HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, (26) Publication Language: English KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (30) Priority Data: OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, 62/361,943 13 July 2016 (13.07.2016) US SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 15/606,743 26 May 2017 (26.05.2017) US TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (71) Applicant: UBIOME, INC. [US/US]; 360 Langton Street, (84) Designated States (unless otherwise indicated, for every #301, San Francisco, CA 94103 (US). kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (72) Inventors: APTE, Zachary; 360 Langton Street, #301, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, San Francisco, CA 94103 (US). RICHMAN, Jessica; 360 TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, Langton Street, #301, San Francisco, CA 94103 (US). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, — ALMONACID, Daniel; 360 Langton Street, #301, San MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, Francisco, CA 94103 (US). PEDROSO, Inti; 360 Lang- TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, = ton Street, #301, San Francisco, California 94103 (US). KM, ML, MR, NE, SN, TD, TG). _ UGALDE, Juan; 360 Langton Street, #301, San Francis- = co, California 94103 (US). ORTIZ, Rodrigo; 360 Langton Published: — Street, #301, San Francisco, California 94103 (US). — with international search report (Art. 21(3)) = = = (54) Title: METHOD AND SYSTEM FOR MICROBIAL PHARMACOGENOMICS = 00 (57) : Embodiments of a method and system for microbial pharma- — 1 — \...\"-\ cogenomics can include: a sample handling system operable to collect contain- ers including biological samples from a set of users, the handling system includ- = = — ta set determining at least one of a microbiome pharmacogenomics da microbiome composition dataset, and a microbiome functional diversity dataset based on processing biological samples associated with a set of users S110 —de- ing a sequencing system operable to determine microorganism sequences from the biological samples; a microbiome characterization system operable to: terrine microbiome pharmacogenomics data based on the microorganism se- = — quences, collect supplementary data associated with the antibiotics- associated = processing a supplementary dataset informative of the antibiotics- associated condition for the set of users S120 condition for the set of users, and transform the supplementary data and features = i extracted from the microbiome pharmacogenomics data into a characterization = = _ — performing a characterization process associated with the antibiotics-associated condition based on the supplementary dataset and features extracted from the at least one of the microbiome 4.. pharmacogenomics dataset, the i m crobiome composition dataset. and the microbiome functional diversity . dataset Si 30 determining a treatment configured to modulate microorganism abundance, distributions, functional diversity and/ or pharmacogenomics diversity in subjects characterized according to the characterization model associated with the antibiotics-associated condition; and a treatment sys- tem operable to promote a treatment to the user for the antibiotics-associated condition based on characterizing user biological material with the characteriza- . F tion model in relation to the antibiotics-associated condition. It ir) GC M It © r.„.... GC li © N processing a biological sample from . , a subject S150 i identifying a characterization of the user in relation to the antibiotics-associated condition based upon processing at least one of a user microbiome pharmacogenomics dataset, a user morobioroe composition dataset, and a user microbiome functional diversity dataset derived from the biological sample from the user, with the characterization process 6160 — monitoring effectiveness of a treatment for points, based upon processing biological samples, a microbiome pharmacogenomics profile, microbiome composition, mIcroblome functional diversity FIGURE 1A 4 the P rocess S140 P promoting a the subject based upon 1 subject at different time to assess at least one of 5180 the characterization 5170 i treatment to X and r O
SG11201900253TA 2016-07-13 2017-07-13 Method and system for microbial pharmacogenomics SG11201900253TA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662361943P 2016-07-13 2016-07-13
US15/606,743 US10803991B2 (en) 2014-10-21 2017-05-26 Method and system for microbiome-derived diagnostics and therapeutics
PCT/US2017/042015 WO2018013865A1 (en) 2016-07-13 2017-07-13 Method and system for microbial pharmacogenomics

Publications (1)

Publication Number Publication Date
SG11201900253TA true SG11201900253TA (en) 2019-02-27

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SG11201900253TA SG11201900253TA (en) 2016-07-13 2017-07-13 Method and system for microbial pharmacogenomics

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EP (1) EP3484348A4 (en)
JP (2) JP2019521706A (en)
KR (1) KR102397683B1 (en)
CN (1) CN109475305B (en)
AU (1) AU2017295861A1 (en)
BR (1) BR112019000709A8 (en)
CA (1) CA3030792A1 (en)
CO (1) CO2019001319A2 (en)
EA (1) EA201990294A1 (en)
SG (1) SG11201900253TA (en)
WO (1) WO2018013865A1 (en)
ZA (1) ZA201900473B (en)

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KR20190033561A (en) 2019-03-29
BR112019000709A2 (en) 2019-05-14
KR102397683B1 (en) 2022-05-13
CO2019001319A2 (en) 2019-02-19
WO2018013865A1 (en) 2018-01-18
AU2017295861A1 (en) 2019-01-24
ZA201900473B (en) 2019-09-25
BR112019000709A8 (en) 2023-03-21
CA3030792A1 (en) 2018-01-18
EA201990294A1 (en) 2019-08-30
EP3484348A1 (en) 2019-05-22
CN109475305B (en) 2022-01-25
CN109475305A (en) 2019-03-15
JP2022079646A (en) 2022-05-26
JP2019521706A (en) 2019-08-08
EP3484348A4 (en) 2021-11-24

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