WO2014138119A3 - Method and kit for characterizing microorganisms - Google Patents

Method and kit for characterizing microorganisms Download PDF

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Publication number
WO2014138119A3
WO2014138119A3 PCT/US2014/020408 US2014020408W WO2014138119A3 WO 2014138119 A3 WO2014138119 A3 WO 2014138119A3 US 2014020408 W US2014020408 W US 2014020408W WO 2014138119 A3 WO2014138119 A3 WO 2014138119A3
Authority
WO
WIPO (PCT)
Prior art keywords
characterizing
sequence
gene sequence
microorganisms
kit
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.)
Ceased
Application number
PCT/US2014/020408
Other languages
French (fr)
Other versions
WO2014138119A2 (en
Inventor
Stephen E. FRY
Jeremy Ellis
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.)
Fry Laboratories LLC
Original Assignee
Fry Laboratories LLC
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 Fry Laboratories LLC filed Critical Fry Laboratories LLC
Priority to EP14717240.7A priority Critical patent/EP2964785B8/en
Publication of WO2014138119A2 publication Critical patent/WO2014138119A2/en
Publication of WO2014138119A3 publication Critical patent/WO2014138119A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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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
    • C12Q1/68—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
    • 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
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • 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
    • C12Q1/6869—Methods for sequencing
    • 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
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Virology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Botany (AREA)
  • Mycology (AREA)

Abstract

The present disclosure provides methods of characterizing one or more microorganisms and kits for characterizing at least one microorganism. Exemplary methods include preparing an amplicon library, sequencing a characteristic gene sequence to obtain a gene sequence, and characterizing the one or more microorganisms based on the gene sequence using a computer-based genomic analysis of the gene sequence. Exemplary kits include at least one forward primer including an adapter sequence and a priming sequence, for a target sequence, and at least one reverse primer.
PCT/US2014/020408 2013-03-04 2014-03-04 Method and kit for characterizing microorganisms Ceased WO2014138119A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP14717240.7A EP2964785B8 (en) 2013-03-04 2014-03-04 Method and kit for characterizing microorganisms

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201361772425P 2013-03-04 2013-03-04
US61/772,425 2013-03-04

Publications (2)

Publication Number Publication Date
WO2014138119A2 WO2014138119A2 (en) 2014-09-12
WO2014138119A3 true WO2014138119A3 (en) 2014-10-30

Family

ID=50483475

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2014/020408 Ceased WO2014138119A2 (en) 2013-03-04 2014-03-04 Method and kit for characterizing microorganisms

Country Status (3)

Country Link
US (4) US9914979B2 (en)
EP (1) EP2964785B8 (en)
WO (1) WO2014138119A2 (en)

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US9580758B2 (en) 2013-11-12 2017-02-28 Luc Montagnier System and method for the detection and treatment of infection by a microbial agent associated with HIV infection
EP3034618A1 (en) * 2014-12-16 2016-06-22 Marcos Isamat Riviere A nucleic acid CMOS based chip for diagnosing periodontal infectious disease
WO2016162504A1 (en) * 2015-04-09 2016-10-13 Koninklijke Philips N.V. Method and apparatus for estimating the quantity of microorganisms within a taxonomic unit in a sample
DE102015206444B3 (en) * 2015-04-10 2016-05-19 Siemens Aktiengesellschaft Method for detecting microorganisms
WO2016191249A1 (en) * 2015-05-22 2016-12-01 University Of Maryland, Baltimore Next-generation sequencing-based genotyping assay for human papilloma virus (hpv)
WO2016191384A1 (en) * 2015-05-22 2016-12-01 Translational Genomics Research Institute Enhanced amplicon sequencing analysis
CN105567681B (en) * 2015-12-31 2018-08-31 广州赛哲生物科技股份有限公司 A kind of method and label connector based on the noninvasive biopsy virus of high-throughput gene sequencing
CN106775998A (en) * 2016-11-09 2017-05-31 上海派森诺生物科技股份有限公司 High flux 16S sequencing data automatic processing methods
WO2018160899A1 (en) * 2017-03-01 2018-09-07 Bluedot Llc Systems and methods for metagenomic analysis
US11053532B2 (en) 2017-04-19 2021-07-06 CAP Diagnostics, LLC Methods for treating polymicrobial infections
US10774377B1 (en) 2017-10-05 2020-09-15 Verily Life Sciences Llc Use of unique molecular identifiers for improved sequencing of taxonomically relevant genes
CN107904297B (en) * 2017-12-28 2020-09-04 苏州协云基因科技有限公司 Primer group, joint group and sequencing method for microbial diversity research
EP3781702A4 (en) * 2018-04-20 2022-01-19 Longhorn Vaccines and Diagnostics, LLC METHODS FOR DETECTION OF AUTOLOGOUS BLOOD DOPING
WO2020088596A1 (en) * 2018-10-31 2020-05-07 Coyote Diagnostics Lab (Beijing) Co., Ltd. Methods, systems and kits for predicting premature birth condition
CN109652512A (en) * 2019-01-28 2019-04-19 南京师范大学 The quantitative detecting method of drug resistant gene in Taihu Lake water body and deposit
CA3176586A1 (en) * 2020-04-14 2021-10-21 CAP Diagnostics, LLC, dba Pathnostics Methods for treating polymicrobial infections
CN112710523B (en) * 2020-12-28 2023-09-19 山西省农业科学院农作物品种资源研究所 A collection device suitable for molecular marker detection
CN112813196B (en) * 2020-12-31 2023-10-13 广州微远基因科技有限公司 Capture probe sets, methods, kits and applications for detecting pathogenic microorganisms

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Also Published As

Publication number Publication date
US20210388419A1 (en) 2021-12-16
US9914979B2 (en) 2018-03-13
EP2964785B1 (en) 2020-08-26
US20140249037A1 (en) 2014-09-04
US20140249036A1 (en) 2014-09-04
US20180237829A1 (en) 2018-08-23
EP2964785A2 (en) 2016-01-13
WO2014138119A2 (en) 2014-09-12
EP2964785B8 (en) 2020-10-21

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