CA3140850A1 - Rapid aneuploidy detection - Google Patents

Rapid aneuploidy detection Download PDF

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Publication number
CA3140850A1
CA3140850A1 CA3140850A CA3140850A CA3140850A1 CA 3140850 A1 CA3140850 A1 CA 3140850A1 CA 3140850 A CA3140850 A CA 3140850A CA 3140850 A CA3140850 A CA 3140850A CA 3140850 A1 CA3140850 A1 CA 3140850A1
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CA
Canada
Prior art keywords
cancer
amplicons
sample
dna
negative negative
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Pending
Application number
CA3140850A
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English (en)
French (fr)
Inventor
Bert Vogelstein
Kenneth W. Kinzler
Christopher Douville
Nickolas Papadopoulos
Cristian TOMASETTI
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.)
Johns Hopkins University
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Johns Hopkins University
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Publication date
Application filed by Johns Hopkins University filed Critical Johns Hopkins University
Publication of CA3140850A1 publication Critical patent/CA3140850A1/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
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • 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
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/5758—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites
    • 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
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/16—Assays for determining copy number or wherein the copy number is of special importance
    • 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
    • C12Q2600/118—Prognosis of disease development
    • 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
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/50—Determining the risk of developing a disease

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Immunology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Pathology (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Cell Biology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • General Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Food Science & Technology (AREA)
  • Medical Informatics (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Artificial Intelligence (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Bioethics (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
CA3140850A 2019-05-17 2020-05-15 Rapid aneuploidy detection Pending CA3140850A1 (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201962849662P 2019-05-17 2019-05-17
US62/849,662 2019-05-17
US201962905327P 2019-09-24 2019-09-24
US62/905,327 2019-09-24
US202062971050P 2020-02-06 2020-02-06
US62/971,050 2020-02-06
PCT/US2020/033209 WO2020236625A2 (en) 2019-05-17 2020-05-15 Rapid aneuploidy detection

Publications (1)

Publication Number Publication Date
CA3140850A1 true CA3140850A1 (en) 2020-11-26

Family

ID=71741878

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3140850A Pending CA3140850A1 (en) 2019-05-17 2020-05-15 Rapid aneuploidy detection

Country Status (14)

Country Link
US (1) US20220259668A1 (https=)
EP (1) EP3969616A2 (https=)
JP (2) JP2022532761A (https=)
KR (1) KR20220021909A (https=)
CN (1) CN114207147A (https=)
AU (2) AU2020279106B2 (https=)
BR (1) BR112021023025A2 (https=)
CA (1) CA3140850A1 (https=)
CL (1) CL2021003030A1 (https=)
CO (1) CO2021017009A2 (https=)
IL (1) IL288081A (https=)
MX (1) MX2021013834A (https=)
SG (1) SG11202112680XA (https=)
WO (1) WO2020236625A2 (https=)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4278012A4 (en) * 2021-01-14 2025-01-08 Case Western Reserve University METHODS FOR DETECTION OF HIGH-RISK BARRETT'S ESOPHAGUS WITH DYSPLASIA AND ESOPHAGEAL ADENOCARCINOMA

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3969616A2 (en) * 2019-05-17 2022-03-23 The Johns Hopkins University Rapid aneuploidy detection
US20260071279A1 (en) * 2022-06-10 2026-03-12 The Johns Hopkins University Methods for identifying cns cancer in a subject
CN114990202B (zh) * 2022-07-29 2022-09-30 普瑞基准科技（北京）有限公司 Snp位点在评估基因组异常的应用及评估基因组异常的方法
WO2024155909A1 (en) * 2023-01-19 2024-07-25 The Johns Hopkins University Methods for identifying ovarian cancer in a subject
EP4662335A2 (en) * 2023-02-09 2025-12-17 The Translational Genomics Research Institute Amplicon-based approach for detecting differences in human dna fragmentation patterns between cancer and non-cancer samples
AU2024216779A1 (en) * 2023-02-09 2025-08-28 The Translational Genomics Research Institute Amplicon-based approach for detecting differences in non-human dna fragmentation patterns between cancer and non-cancer samples
KR102630597B1 (ko) * 2023-08-22 2024-01-29 주식회사 지놈인사이트테크놀로지 종양 정보를 활용한 미세 잔존 질환 탐지 방법 및 장치

Family Cites Families (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2006214800B2 (en) * 2005-02-16 2012-06-07 Cy O'connor Erade Village Foundation Methods of genetic analysis involving the amplification of complementary duplicons
EP1712639B1 (en) 2005-04-06 2008-08-27 Maurice Stroun Method for the diagnosis of cancer by detecting circulating DNA and RNA
JP2008173083A (ja) * 2007-01-22 2008-07-31 Nippon Software Management Kk Ｄｎａタグによる生物の同定方法
CA2868836C (en) * 2012-03-26 2019-08-06 The Johns Hopkins University Rapid aneuploidy detection
JP6474058B2 (ja) * 2012-09-13 2019-02-27 御木本製薬株式会社 エンドセリン−１産生抑制剤
DK3201361T3 (da) * 2014-10-01 2020-05-18 Chronix Biomedical Fremgangsmåder til kvantificering af cellefrit DNA
JP6929778B2 (ja) * 2015-01-15 2021-09-01 グッド スタート ジェネティクス， インコーポレイテッド 着床前遺伝子スクリーニングにおける一塩基多型を用いた品質管理方法
US20160275240A1 (en) * 2015-02-18 2016-09-22 Nugen Technologies, Inc. Methods and compositions for pooling amplification primers
US11319594B2 (en) * 2016-08-25 2022-05-03 Resolution Bioscience, Inc. Methods for the detection of genomic copy changes in DNA samples
CN111868260B (zh) * 2017-08-07 2025-02-21 约翰斯霍普金斯大学 用于评估和治疗癌症的方法和材料
EP3969616A2 (en) * 2019-05-17 2022-03-23 The Johns Hopkins University Rapid aneuploidy detection

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4278012A4 (en) * 2021-01-14 2025-01-08 Case Western Reserve University METHODS FOR DETECTION OF HIGH-RISK BARRETT'S ESOPHAGUS WITH DYSPLASIA AND ESOPHAGEAL ADENOCARCINOMA

Also Published As

Publication number Publication date
KR20220021909A (ko) 2022-02-22
EP3969616A2 (en) 2022-03-23
MX2021013834A (es) 2022-06-29
US20220259668A1 (en) 2022-08-18
CL2021003030A1 (es) 2022-10-07
WO2020236625A2 (en) 2020-11-26
JP2026012754A (ja) 2026-01-27
AU2020279106A1 (en) 2021-12-09
CN114207147A (zh) 2022-03-18
CO2021017009A2 (es) 2022-04-08
AU2026201955A1 (en) 2026-04-16
WO2020236625A3 (en) 2021-02-11
JP2022532761A (ja) 2022-07-19
BR112021023025A2 (pt) 2022-01-04
AU2020279106B2 (en) 2025-12-18
SG11202112680XA (en) 2021-12-30
IL288081A (en) 2022-01-01

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