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EP3484348A4 - METHOD AND SYSTEM FOR MICROBIAL PHARMACOGENOMICS - Google Patents

METHOD AND SYSTEM FOR MICROBIAL PHARMACOGENOMICS Download PDF

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Publication number
EP3484348A4
EP3484348A4 EP17828501.1A EP17828501A EP3484348A4 EP 3484348 A4 EP3484348 A4 EP 3484348A4 EP 17828501 A EP17828501 A EP 17828501A EP 3484348 A4 EP3484348 A4 EP 3484348A4
Authority
EP
European Patent Office
Prior art keywords
pharmacogenomics
microbial
microbial pharmacogenomics
Prior art date
Legal status (The legal status 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 status listed.)
Pending
Application number
EP17828501.1A
Other languages
German (de)
French (fr)
Other versions
EP3484348A1 (en
Inventor
Zachary APTE
Jessica RICHMAN
Daniel Almonacid
Inti Pedroso
Juan Ugalde
Rodrigo Ortiz
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Macrogen Inc
Original Assignee
Psomagen 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 Psomagen Inc filed Critical Psomagen Inc
Publication of EP3484348A1 publication Critical patent/EP3484348A1/en
Publication of EP3484348A4 publication Critical patent/EP3484348A4/en
Pending legal-status Critical Current

Links

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
    • 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
    • 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
    • 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

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Medical Informatics (AREA)
  • Public Health (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Veterinary Medicine (AREA)
  • Animal Behavior & Ethology (AREA)
  • Surgery (AREA)
  • Heart & Thoracic Surgery (AREA)
  • Pathology (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Medicinal Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Nursing (AREA)
  • Physiology (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
EP17828501.1A 2016-07-13 2017-07-13 METHOD AND SYSTEM FOR MICROBIAL PHARMACOGENOMICS Pending EP3484348A4 (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 (2)

Publication Number Publication Date
EP3484348A1 EP3484348A1 (en) 2019-05-22
EP3484348A4 true EP3484348A4 (en) 2021-11-24

Family

ID=60953350

Family Applications (1)

Application Number Title Priority Date Filing Date
EP17828501.1A Pending EP3484348A4 (en) 2016-07-13 2017-07-13 METHOD AND SYSTEM FOR MICROBIAL PHARMACOGENOMICS

Country Status (12)

Country Link
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)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2021505194A (en) * 2017-12-04 2021-02-18 サイベル マイクロバイオーム インコーポレイテッド Methods and compositions for the identification and regulation of microbial biochemical pathways for phenotypic changes
AU2019233926A1 (en) * 2018-03-16 2020-06-18 Psomagen, Inc. Method and system for characterization of metabolism-associated conditions, including diagnostics and therapies, based on bioinformatics approach
US11681953B2 (en) * 2018-04-13 2023-06-20 Freenome Holdings, Inc. Machine learning implementation for multi-analyte assay development and testing
EP3803901A1 (en) * 2018-06-07 2021-04-14 4D Pharma Plc Method for stratifying ibs patients
KR102346398B1 (en) 2020-09-01 2022-01-03 주식회사 에이아이바이오틱스 System For Analyzing and Evaluating Gut Microbiome And Evaluation Method For The Same
JP7634701B2 (en) 2021-02-03 2025-02-21 タタ コンサルタンシー サービシズ リミテッド Methods and systems for designing personalized treatments and diets based on microbiome function
US20220367050A1 (en) * 2021-05-12 2022-11-17 Zoe Limited Predicting gut microbiome diversity
KR20240099759A (en) 2022-12-22 2024-07-01 주식회사 오디엔 System for managing pharmacotherapy and operating method thereof

Citations (3)

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WO2015066625A1 (en) * 2013-11-01 2015-05-07 Washington University Methods to establish and restore normal gut microbiota function of subject in need thereof
US20160110515A1 (en) * 2014-10-21 2016-04-21 Zachary Apte Method and system for microbiome-derived diagnostics and therapeutics
WO2016086305A1 (en) * 2014-12-05 2016-06-09 University Of Saskatchewan Methods and reagents for detecting neisseria gonorrhoeae and its antimicrobial resistance determinants

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US9107831B2 (en) * 2003-06-02 2015-08-18 Novartis Vaccines And Diagonstics, Inc. Immunogenic compositions containing microparticles comprising adsorbed toxoid and polysaccharide-containing antigens
CA2627360C (en) * 2005-10-29 2014-06-10 Bayer Technology Services Gmbh Process for determining one or more analytes in samples of biological origin having complex composition, and use thereof
CN104031984A (en) * 2008-02-28 2014-09-10 俄亥俄州立大学研究基金会 Microrna-based methods and compositions for the diagnosis, prognosis and treatment of prostate related disorders
KR20110101143A (en) * 2008-11-04 2011-09-15 블러드 셀 스토리지 인코퍼레이티드 Nucleic Acid Extraction on Curved Glass Surfaces
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CN101833613A (en) * 2010-06-04 2010-09-15 中国科学院青岛生物能源与过程研究所 A kind of oral microbial community database and its application
US20130121968A1 (en) * 2011-10-03 2013-05-16 Atossa Genetics, Inc. Methods of combining metagenome and the metatranscriptome in multiplex profiles
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US9466024B2 (en) * 2013-03-15 2016-10-11 Northrop Grumman Systems Corporation Learning health systems and methods
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WO2015013214A2 (en) * 2013-07-21 2015-01-29 Whole Biome, Inc. Methods and systems for microbiome characterization, monitoring and treatment
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Patent Citations (3)

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Publication number Priority date Publication date Assignee Title
WO2015066625A1 (en) * 2013-11-01 2015-05-07 Washington University Methods to establish and restore normal gut microbiota function of subject in need thereof
US20160110515A1 (en) * 2014-10-21 2016-04-21 Zachary Apte Method and system for microbiome-derived diagnostics and therapeutics
WO2016086305A1 (en) * 2014-12-05 2016-06-09 University Of Saskatchewan Methods and reagents for detecting neisseria gonorrhoeae and its antimicrobial resistance determinants

Also Published As

Publication number Publication date
KR20190033561A (en) 2019-03-29
EP3484348A1 (en) 2019-05-22
CN109475305B (en) 2022-01-25
AU2017295861A1 (en) 2019-01-24
KR102397683B1 (en) 2022-05-13
JP2019521706A (en) 2019-08-08
CO2019001319A2 (en) 2019-02-19
JP2022079646A (en) 2022-05-26
SG11201900253TA (en) 2019-02-27
EA201990294A1 (en) 2019-08-30
ZA201900473B (en) 2019-09-25
WO2018013865A1 (en) 2018-01-18
BR112019000709A8 (en) 2023-03-21
BR112019000709A2 (en) 2019-05-14
CN109475305A (en) 2019-03-15
CA3030792A1 (en) 2018-01-18

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