WO2019046347A3 - Method and system for characterization for female reproductive system-related conditions associated with microorganisms - Google Patents

Method and system for characterization for female reproductive system-related conditions associated with microorganisms Download PDF

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Publication number
WO2019046347A3
WO2019046347A3 PCT/US2018/048412 US2018048412W WO2019046347A3 WO 2019046347 A3 WO2019046347 A3 WO 2019046347A3 US 2018048412 W US2018048412 W US 2018048412W WO 2019046347 A3 WO2019046347 A3 WO 2019046347A3
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WO
WIPO (PCT)
Prior art keywords
female reproductive
related conditions
characterization
reproductive system
microorganisms
Prior art date
Application number
PCT/US2018/048412
Other languages
French (fr)
Other versions
WO2019046347A2 (en
WO2019046347A9 (en
Inventor
Zachary APTE
Elisabeth BIK
Sara W. BIRD
Luis Leon
Pamela A. NIETO
Victor ALGERIA-MERA
Christian BRAVO
Juan P. CARDENAS
Paulo Covarrubias
Sarah L. GUPTA
Kira HARMAN
Juan Jimenez
Felipe MELIS-ARCOS
Camila F. NAVAS
Harold NUNEZ
Eduardo Olivares
Nicolas ORDENES-AENISHANSLINS
Francisco J. OSSANDON
Ignacio VARAS
Patricia Vera-Wolf
Donna Marie B. HONGO
Laurens KRAAL
Nathaniel A. WALTON
Amanda MORTON
Juan P. BUSTAMANTE
Kwasi ADDAE
Graham GASS
Katia SOTO-LIEBE
Juan A. UGALDE
Eduardo H. MORALES
Daniel Almonacid
Jessica RICHMAN
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
Application filed by uBiome, Inc. filed Critical uBiome, Inc.
Priority to EP18826836.1A priority Critical patent/EP3676405A2/en
Priority to JP2020512725A priority patent/JP2020532979A/en
Priority to CN201880070585.0A priority patent/CN111278995A/en
Priority to KR1020207008963A priority patent/KR20200047626A/en
Priority to AU2018323509A priority patent/AU2018323509A1/en
Priority to SG11202001676PA priority patent/SG11202001676PA/en
Publication of WO2019046347A2 publication Critical patent/WO2019046347A2/en
Publication of WO2019046347A3 publication Critical patent/WO2019046347A3/en
Publication of WO2019046347A9 publication Critical patent/WO2019046347A9/en

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    • 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
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/708—Specific hybridization probes for papilloma
    • 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
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • 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
    • G16B40/30—Unsupervised 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
    • C12Q2600/16—Primer sets for multiplex assays

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Genetics & Genomics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Medical Informatics (AREA)
  • Pathology (AREA)
  • Data Mining & Analysis (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Virology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Medicines Containing Material From Animals Or Micro-Organisms (AREA)

Abstract

Embodiments of a method and/or system for characterizing one or more female reproductive system-related conditions can include determining a microorganism dataset associated with a set of subjects; and/or performing a characterization process associated with the one or more female reproductive system-related conditions, based on the microorganism dataset, where performing the characterization process can additionally or alternatively include performing a female reproductive system-related characterization process for the one or more female reproductive system-related conditions, and/or determining one or more therapies.
PCT/US2018/048412 2017-08-28 2018-08-28 Method and system for characterization for female reproductive system-related conditions associated with microorganisms WO2019046347A2 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
EP18826836.1A EP3676405A2 (en) 2017-08-28 2018-08-28 Method and system for characterization for female reproductive system-related conditions associated with microorganisms
JP2020512725A JP2020532979A (en) 2017-08-28 2018-08-28 Methods and systems for characterization of female reproductive system-related conditions associated with microorganisms
CN201880070585.0A CN111278995A (en) 2017-08-28 2018-08-28 Method and system for characterizing conditions related to the female reproductive system associated with a microbial organism
KR1020207008963A KR20200047626A (en) 2017-08-28 2018-08-28 Methods and systems for characterization of female reproductive system-related conditions related to microorganisms
AU2018323509A AU2018323509A1 (en) 2017-08-28 2018-08-28 Method and system for characterization for female reproductive system-related conditions associated with microorganisms
SG11202001676PA SG11202001676PA (en) 2017-08-28 2018-08-28 Method and system for characterization for female reproductive system-related conditions associated with microorganisms

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US201762551155P 2017-08-28 2017-08-28
US62/551,155 2017-08-28
US201762585131P 2017-11-13 2017-11-13
US62/585,131 2017-11-13
US201862653402P 2018-04-05 2018-04-05
US62/653,402 2018-04-05

Publications (3)

Publication Number Publication Date
WO2019046347A2 WO2019046347A2 (en) 2019-03-07
WO2019046347A3 true WO2019046347A3 (en) 2019-03-28
WO2019046347A9 WO2019046347A9 (en) 2019-07-25

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2018/048412 WO2019046347A2 (en) 2017-08-28 2018-08-28 Method and system for characterization for female reproductive system-related conditions associated with microorganisms

Country Status (7)

Country Link
EP (1) EP3676405A2 (en)
JP (1) JP2020532979A (en)
KR (1) KR20200047626A (en)
CN (1) CN111278995A (en)
AU (1) AU2018323509A1 (en)
SG (1) SG11202001676PA (en)
WO (1) WO2019046347A2 (en)

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Publication number Priority date Publication date Assignee Title
US11149322B2 (en) * 2019-06-07 2021-10-19 Chapter Diagnostics, Inc. Methods and compositions for human papillomaviruses and sexually transmitted infections detection, identification and quantification
CN112126671B (en) * 2020-08-18 2021-08-31 中山大学附属第五医院 Application of streptococcus agalactiae streptococcus agalactiae in treating endometriosis
EP4211150A1 (en) * 2020-09-10 2023-07-19 Microgenesis Corporation Methods and compositions relating to assessment of inflammatory conditions relating to fertility
CN112121066B (en) * 2020-11-25 2021-02-19 北京大学第三医院（北京大学第三临床医学院） Application of ruminococcus in preparation of medicine for treating polycystic ovarian syndrome and culture method
US20220341955A1 (en) * 2021-04-23 2022-10-27 Poppy Health, Inc. System and method for characterizing, monitoring, & detecting bioaerosol presence & movement in an indoor environment
CN115372482A (en) * 2021-05-17 2022-11-22 上海交通大学医学院附属仁济医院 Application of intestinal flora spectrum and metabolic markers in preparation of polycystic ovarian syndrome diagnostic kit
CN113215321B (en) * 2021-05-26 2022-09-30 北京毅新博创生物科技有限公司 Detection product for detecting genital tract pathogen by MALDI-TOF MS and application
CN113355456B (en) * 2021-05-26 2022-09-30 北京毅新博创生物科技有限公司 Preparation method of nucleic acid fingerprint spectrum library for detecting genital tract pathogens by MALDI TOF-MS
US11597980B2 (en) 2021-07-08 2023-03-07 Poppy Health, Inc. System and method for detecting pathogens in an environment via an electrostatic air sampler
CN117897497A (en) * 2021-09-17 2024-04-16 国立大学法人东海国立大学机构 Method for detecting bacteria of genus Fusobacterium for diagnosis of endometriosis
KR20230105080A (en) * 2022-01-03 2023-07-11 연세대학교 산학협력단 Method for providing information for diagnosis of endometriosis
CN114420210B (en) * 2022-03-28 2022-09-20 山东大学 Rapid trimming method and system for biological sequencing sequence
CN114480694B (en) * 2022-04-18 2022-06-17 北京起源聚禾生物科技有限公司 Vaginal microecological detection primer probe combination and kit

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20130184164A1 (en) * 2010-06-17 2013-07-18 Goodgene, Inc. DNA Chip for Genotyping of Human Papilloma Virus, Kit Having Same, and Method for Genotyping
WO2015013214A2 (en) * 2013-07-21 2015-01-29 Whole Biome, Inc. Methods and systems for microbiome characterization, monitoring and treatment
WO2017004379A1 (en) * 2015-06-30 2017-01-05 uBiome, Inc. Method and system for diagnostic testing

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US20060246423A1 (en) * 2005-02-10 2006-11-02 Adelson Martin E Method and kit for the collection and maintenance of the detectability of a plurality of microbiological species in a single gynecological sample
WO2014165810A2 (en) * 2013-04-05 2014-10-09 Akins Robert A Systems and methods to assess microbiomes and treatments thereof
AU2015335907A1 (en) * 2014-10-21 2017-04-13 Psomagen, Inc. Method and system for microbiome-derived diagnostics and therapeutics

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20130184164A1 (en) * 2010-06-17 2013-07-18 Goodgene, Inc. DNA Chip for Genotyping of Human Papilloma Virus, Kit Having Same, and Method for Genotyping
WO2015013214A2 (en) * 2013-07-21 2015-01-29 Whole Biome, Inc. Methods and systems for microbiome characterization, monitoring and treatment
WO2017004379A1 (en) * 2015-06-30 2017-01-05 uBiome, Inc. Method and system for diagnostic testing

Also Published As

Publication number Publication date
JP2020532979A (en) 2020-11-19
AU2018323509A1 (en) 2020-04-09
SG11202001676PA (en) 2020-03-30
KR20200047626A (en) 2020-05-07
CN111278995A (en) 2020-06-12
WO2019046347A2 (en) 2019-03-07
EP3676405A2 (en) 2020-07-08
WO2019046347A9 (en) 2019-07-25

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