AU2022398491A1 - Sample contamination detection of contaminated fragments for cancer classification - Google Patents

Sample contamination detection of contaminated fragments for cancer classification Download PDF

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Publication number
AU2022398491A1
AU2022398491A1 AU2022398491A AU2022398491A AU2022398491A1 AU 2022398491 A1 AU2022398491 A1 AU 2022398491A1 AU 2022398491 A AU2022398491 A AU 2022398491A AU 2022398491 A AU2022398491 A AU 2022398491A AU 2022398491 A1 AU2022398491 A1 AU 2022398491A1
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Australia
Prior art keywords
contamination
cancer
sites
fragments
markers
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Pending
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AU2022398491A
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English (en)
Inventor
Siddhartha BAGARIA
Samuel S. GROSS
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Grail Inc
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Grail Inc
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Publication date
Application filed by Grail Inc filed Critical Grail Inc
Publication of AU2022398491A1 publication Critical patent/AU2022398491A1/en
Pending legal-status Critical Current

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6827Hybridisation assays for detection of mutation or polymorphism
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20Supervised data analysis
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16HHEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20ICT 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
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2523/00Reactions characterised by treatment of reaction samples
    • C12Q2523/10Characterised by chemical treatment
    • C12Q2523/125Bisulfite(s)
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2537/00Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/164Methylation detection other then bisulfite or methylation sensitive restriction endonucleases
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00Detection or diagnosis of diseases
    • G01N2800/70Mechanisms involved in disease identification
    • G01N2800/7023(Hyper)proliferation
    • G01N2800/7028Cancer

Landscapes

  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Public Health (AREA)
  • Pathology (AREA)
  • Data Mining & Analysis (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Biomedical Technology (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Primary Health Care (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Theoretical Computer Science (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Evolutionary Biology (AREA)
  • Bioethics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Artificial Intelligence (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
AU2022398491A 2021-11-23 2022-11-23 Sample contamination detection of contaminated fragments for cancer classification Pending AU2022398491A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202163282509P 2021-11-23 2021-11-23
US63/282,509 2021-11-23
PCT/US2022/080431 WO2023097278A1 (en) 2021-11-23 2022-11-23 Sample contamination detection of contaminated fragments for cancer classification

Publications (1)

Publication Number Publication Date
AU2022398491A1 true AU2022398491A1 (en) 2024-06-06

Family

ID=84830091

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2022398491A Pending AU2022398491A1 (en) 2021-11-23 2022-11-23 Sample contamination detection of contaminated fragments for cancer classification

Country Status (10)

Country Link
US (1) US20230272477A1 (https=)
EP (1) EP4437130A1 (https=)
JP (1) JP2024544597A (https=)
KR (1) KR20240103061A (https=)
CN (1) CN118591638A (https=)
AU (1) AU2022398491A1 (https=)
CA (1) CA3237953A1 (https=)
IL (1) IL312808A (https=)
TW (1) TW202330933A (https=)
WO (1) WO2023097278A1 (https=)

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2019234843B2 (en) * 2018-03-13 2025-12-04 Grail, Inc. Anomalous fragment detection and classification
EP4177356B1 (en) * 2018-08-08 2024-05-08 PML Screening, LLC Methods for assessing risk of developing a viral disease using a genetic test
US12234514B2 (en) * 2018-12-21 2025-02-25 Grail, Inc. Source of origin deconvolution based on methylation fragments in cell-free DNA samples
WO2020232109A1 (en) * 2019-05-13 2020-11-19 Grail, Inc. Model-based featurization and classification
US20210310075A1 (en) * 2020-03-30 2021-10-07 Grail, Inc. Cancer Classification with Synthetic Training Samples
AU2021248552A1 (en) * 2020-03-31 2022-11-03 Grail, Llc Cancer classification with genomic region modeling
JP2024538725A (ja) * 2021-10-08 2024-10-23 ファウンデーション・メディシン・インコーポレイテッド コピー数変化呼び出しに対する汚染を検出及び除去するための方法及びシステム

Also Published As

Publication number Publication date
TW202330933A (zh) 2023-08-01
CN118591638A (zh) 2024-09-03
KR20240103061A (ko) 2024-07-03
WO2023097278A1 (en) 2023-06-01
US20230272477A1 (en) 2023-08-31
JP2024544597A (ja) 2024-12-03
CA3237953A1 (en) 2023-06-01
EP4437130A1 (en) 2024-10-02
IL312808A (en) 2024-07-01

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Legal Events

Date Code Title Description
DA3 Amendments made section 104

Free format text: THE NATURE OF THE AMENDMENT IS: TO AMEND THE APPLICANT NAME TO GRAIL, INC.