CA3155073A1 - Methods and systems for measuring cell states - Google Patents

Methods and systems for measuring cell states Download PDF

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Publication number
CA3155073A1
CA3155073A1 CA3155073A CA3155073A CA3155073A1 CA 3155073 A1 CA3155073 A1 CA 3155073A1 CA 3155073 A CA3155073 A CA 3155073A CA 3155073 A CA3155073 A CA 3155073A CA 3155073 A1 CA3155073 A1 CA 3155073A1
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Prior art keywords
cell
dna
abundance
read
identity
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Pending
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CA3155073A
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English (en)
French (fr)
Inventor
Aadel Chaudhuri
Aaron NEWMAN
Irfan ALAHI
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Washington University in St Louis WUSTL
Leland Stanford Junior University
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Individual
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Publication of CA3155073A1 publication Critical patent/CA3155073A1/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
    • C12Q1/68—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
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • 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
    • C12Q1/6869—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
    • C12Q1/6883—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
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • 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
    • C12Q2600/154—Methylation markers

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Oncology (AREA)
  • Hospice & Palliative Care (AREA)
  • Cell Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Medicinal Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Medical Treatment And Welfare Office Work (AREA)
CA3155073A 2019-10-18 2020-10-18 Methods and systems for measuring cell states Pending CA3155073A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201962916961P 2019-10-18 2019-10-18
US62/916,961 2019-10-18
PCT/US2020/056218 WO2021077063A1 (en) 2019-10-18 2020-10-18 Methods and systems for measuring cell states

Publications (1)

Publication Number Publication Date
CA3155073A1 true CA3155073A1 (en) 2021-04-22

Family

ID=75538680

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3155073A Pending CA3155073A1 (en) 2019-10-18 2020-10-18 Methods and systems for measuring cell states

Country Status (7)

Country Link
US (1) US20240401134A1 (https=)
EP (1) EP4045685A4 (https=)
JP (2) JP2022552723A (https=)
CN (1) CN114746559A (https=)
AU (1) AU2020365150A1 (https=)
CA (1) CA3155073A1 (https=)
WO (1) WO2021077063A1 (https=)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP4373972A4 (en) * 2021-07-23 2025-06-18 Georgetown University USE OF METHYLATED CIRCULATING FREE DNA TO DETECT TISSUE INJURY
WO2023129969A1 (en) * 2021-12-30 2023-07-06 Yissum Research Development Company Of The Hebrew University Of Jerusalem Ltd. Compositions and methods for identifying cell types
WO2023178319A2 (en) * 2022-03-17 2023-09-21 Washington University Methods and systems for measuring multiple cell states
EP4573217A1 (en) * 2022-08-18 2025-06-25 Yissum Research Development Company of the Hebrew University of Jerusalem Ltd. A method for determining the tissue or cell of origin of dna
CA3268032A1 (en) * 2022-09-23 2024-03-28 Flagship Pioneering Innovations Vi, Llc NUCLEIC ACID AMPLIFICATION PROCESSES
WO2024081689A1 (en) * 2022-10-11 2024-04-18 LiquidCell Dx Inc. Tumor microenvironment by liquid biopsy
WO2024124207A2 (en) * 2022-12-08 2024-06-13 The Board Of Trustees Of The Leland Stanford Junior University Systems and methods for cell-free nucleic acids methylation assessment

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012045888A1 (en) * 2010-10-08 2012-04-12 Epiontis Gmbh Method for determining cancer patient survival based on analyzing tumor-infiltrating overall t-lymphocytes
WO2015159292A2 (en) * 2014-04-14 2015-10-22 Yissum Research Development Company Of The Hebrew University Of Jerusalem Ltd. A method and kit for determining the tissue or cell origin of dna
EP3140420B1 (en) * 2014-05-07 2019-09-11 Universite Libre De Bruxelles Breast cancer epigenetic markers useful in anthracycline treatment prognosis
CA2971129A1 (en) * 2015-01-22 2016-07-28 The Board Of Trustees Of The Leland Stanford Junior University Methods and systems for determining proportions of distinct cell subsets
US10689706B2 (en) * 2015-07-20 2020-06-23 The Chinese University Of Hong Kong Methylation pattern analysis of haplotypes in tissues in a DNA mixture
WO2017201400A1 (en) * 2016-05-19 2017-11-23 The Regents Of The University Of California Determination of cell types in mixtures using targeted bisulfite sequencing
ES3022457T3 (en) * 2016-12-21 2025-05-28 Univ California Deconvolution and detection of rare dna in plasma
EP3382033B1 (en) * 2017-03-30 2020-08-05 Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen Method for determining blood counts based on dna methylation
EP3655955B1 (en) * 2017-07-21 2025-04-09 The Board of Trustees of the Leland Stanford Junior University Systems and methods for analyzing mixed cell populations
JP7455757B2 (ja) * 2018-04-13 2024-03-26 フリーノーム・ホールディングス・インコーポレイテッド 生体試料の多検体アッセイのための機械学習実装

Also Published As

Publication number Publication date
JP2026064241A (ja) 2026-04-13
WO2021077063A1 (en) 2021-04-22
AU2020365150A1 (en) 2022-05-26
CN114746559A (zh) 2022-07-12
EP4045685A1 (en) 2022-08-24
JP2022552723A (ja) 2022-12-19
EP4045685A4 (en) 2023-11-15
US20240401134A1 (en) 2024-12-05

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