CA3077798A1 - Method of isolating eukaryotic nucleic acid from a stool sample - Google Patents

Method of isolating eukaryotic nucleic acid from a stool sample Download PDF

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Publication number
CA3077798A1
CA3077798A1 CA3077798A CA3077798A CA3077798A1 CA 3077798 A1 CA3077798 A1 CA 3077798A1 CA 3077798 A CA3077798 A CA 3077798A CA 3077798 A CA3077798 A CA 3077798A CA 3077798 A1 CA3077798 A1 CA 3077798A1
Authority
CA
Canada
Prior art keywords
genes
nucleic acid
rna
eukaryotic
panel
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
CA3077798A
Other languages
English (en)
French (fr)
Inventor
Erica BARNELL
Andrew BARNELL
Yiming KANG
Elizabeth WURTZLER
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.)
Geneoscopy Inc
Original Assignee
Geneoscopy 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 Geneoscopy LLC filed Critical Geneoscopy LLC
Publication of CA3077798A1 publication Critical patent/CA3077798A1/en
Pending 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
    • C12Q1/6883—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
    • 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
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • 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
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
    • C12N15/1013—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers by using magnetic beads
    • 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
    • C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1017—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by filtration, e.g. using filters, frits, membranes
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5044—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving specific cell types
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57419—Specifically defined cancers of colon
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57446—Specifically defined cancers of stomach or intestine
    • 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
    • C12Q2600/136—Screening for pharmacological compounds
    • 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
    • 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
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/06—Gastro-intestinal diseases
    • G01N2800/065—Bowel diseases, e.g. Crohn, ulcerative colitis, IBS

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  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Biotechnology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Analytical Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • Pathology (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Cell Biology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Toxicology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
CA3077798A 2016-10-27 2017-10-27 Method of isolating eukaryotic nucleic acid from a stool sample Pending CA3077798A1 (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201662413708P 2016-10-27 2016-10-27
US62/413,708 2016-10-27
US201762523511P 2017-06-22 2017-06-22
US62/523,511 2017-06-22
US201762547046P 2017-08-17 2017-08-17
US62/547,046 2017-08-17
PCT/US2017/058789 WO2018081580A1 (en) 2016-10-27 2017-10-27 Detection method

Publications (1)

Publication Number Publication Date
CA3077798A1 true CA3077798A1 (en) 2018-05-03

Family

ID=62024023

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3077798A Pending CA3077798A1 (en) 2016-10-27 2017-10-27 Method of isolating eukaryotic nucleic acid from a stool sample

Country Status (8)

Country Link
US (2) US11479820B2 (enExample)
EP (1) EP3532637B1 (enExample)
JP (1) JP7109462B2 (enExample)
CN (1) CN110291197B (enExample)
AU (1) AU2017348369B2 (enExample)
CA (1) CA3077798A1 (enExample)
ES (1) ES2986412T3 (enExample)
WO (1) WO2018081580A1 (enExample)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2018081580A1 (en) 2016-10-27 2018-05-03 Geneoscopy, Llc Detection method
CA3136405A1 (en) 2018-06-01 2019-12-05 Geneoscopy, Inc. Detection method for cancer using rna biomarkers
KR102775904B1 (ko) * 2018-12-06 2025-03-05 주식회사 씨젠 핵산이 결합된 입자로부터 핵산을 용출하는 방법
AU2023386217A1 (en) * 2022-11-25 2025-06-05 Yaarob KHAMAS Colorectal cancer risk assessment

Family Cites Families (21)

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ES2287134T3 (es) 2000-06-02 2007-12-16 Bayer Corporation Procedimiento para la deteccion y localizacion de genes in situ usando hibridacion de adn ramificado.
JP4033820B2 (ja) * 2003-07-29 2008-01-16 株式会社日立製作所 細胞回収方法
JP2007175021A (ja) 2005-12-28 2007-07-12 Sysmex Corp 大腸がんのリンパ節転移マーカー
EP1862803A1 (en) 2006-06-02 2007-12-05 Atlas Antibodies AB Use of protein SATB2 as a marker for colorectal cancer
US20120196827A1 (en) 2006-06-12 2012-08-02 Oncomethylome Sciences S.A. Methylation markers for early detection and prognosis of colon cancers
US20100196889A1 (en) 2006-11-13 2010-08-05 Bankaitis-Davis Danute M Gene Expression Profiling for Identification, Monitoring and Treatment of Colorectal Cancer
JPWO2008093530A1 (ja) * 2007-01-30 2010-05-20 国立大学法人浜松医科大学 大腸癌病期検出方法
WO2009042676A1 (en) 2007-09-24 2009-04-02 University Of South Florida Method for early detection of cancers
JP5616786B2 (ja) 2008-05-12 2014-10-29 オリンパス株式会社 糞便処理容器
CN102105583A (zh) * 2008-07-23 2011-06-22 奥林巴斯株式会社 从粪便试样中回收核酸的方法、核酸分析方法以及粪便试样处理装置
EP2347256A4 (en) * 2008-10-09 2012-02-08 Alfagene Bioscience Inc USE AND IDENTIFICATION OF BIOMARKERS FOR GASTROINTESTINAL DISEASES
US20100112713A1 (en) 2008-11-05 2010-05-06 The Texas A&M University System Methods For Detecting Colorectal Diseases And Disorders
WO2010134246A1 (ja) 2009-05-20 2010-11-25 オリンパス株式会社 核酸含有試料の調製方法
WO2010134245A1 (ja) 2009-05-20 2010-11-25 オリンパス株式会社 哺乳細胞由来核酸の回収方法、核酸解析方法、及び採便用キット
US10036070B2 (en) 2010-12-23 2018-07-31 Agendia N.V. Methods and means for molecular classification of colorectal cancers
KR20140057354A (ko) 2011-08-31 2014-05-12 온코사이트 코포레이션 결장직장암의 치료 및 진단을 위한 방법 및 조성물
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WO2016176446A2 (en) 2015-04-29 2016-11-03 Geneoscopy, Llc Colorectal cancer screening method and device
WO2018081580A1 (en) 2016-10-27 2018-05-03 Geneoscopy, Llc Detection method
CA3136405A1 (en) 2018-06-01 2019-12-05 Geneoscopy, Inc. Detection method for cancer using rna biomarkers

Also Published As

Publication number Publication date
AU2017348369B2 (en) 2023-09-28
WO2018081580A1 (en) 2018-05-03
JP7109462B2 (ja) 2022-07-29
US20230203591A1 (en) 2023-06-29
EP3532637A4 (en) 2020-10-14
JP2020500551A (ja) 2020-01-16
US20190271046A1 (en) 2019-09-05
CN110291197B (zh) 2024-01-12
EP3532637B1 (en) 2024-07-10
ES2986412T3 (es) 2024-11-11
AU2017348369A1 (en) 2019-06-13
CN110291197A (zh) 2019-09-27
US11479820B2 (en) 2022-10-25
EP3532637A1 (en) 2019-09-04

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