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
Leland Stanford Junior University
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Individual
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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)
  • Zoology (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (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 (enExample)
EP (1) EP4045685A4 (enExample)
JP (2) JP7874822B2 (enExample)
CN (1) CN114746559A (enExample)
AU (1) AU2020365150A1 (enExample)
CA (1) CA3155073A1 (enExample)
WO (1) WO2021077063A1 (enExample)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20240279720A1 (en) * 2021-07-23 2024-08-22 Georgetown University Use of genetic and epigenetic markers to detect cell death
CN120129757A (zh) * 2021-12-30 2025-06-10 耶路撒冷希伯来大学伊森姆研究发展有限公司 用于鉴定细胞类型的组合物和方法
JP2025509614A (ja) * 2022-03-17 2025-04-11 ワシントン・ユニバーシティ 多数の細胞状態を測定するための方法およびシステム
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
EP4630585A2 (en) * 2022-12-08 2025-10-15 The Board of Trustees of the Leland Stanford Junior University Systems and methods for cell-free nucleic acids methylation assessment
CN118016166B (zh) * 2024-02-04 2026-07-17 清华大学 扰动单细胞转录组测序数据的肿瘤药物响应类型鉴定方法

Family Cites Families (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP2625288B1 (en) * 2010-10-08 2016-05-25 Epiontis GmbH Method for determining cancer patient survival based on analyzing tumor-infiltrating overall t-lymphocytes
SI4026917T1 (sl) * 2014-04-14 2024-05-31 Yissum Research And Development Company Of The Hebrew University Of Jerusalem Ltd. Metoda in komplet za določanje smrti celic ali tkiva oz. izvora DNK tkiva ali celice z analizo metilacije DNK
EP3140420B1 (en) * 2014-05-07 2019-09-11 Universite Libre De Bruxelles Breast cancer epigenetic markers useful in anthracycline treatment prognosis
WO2016118860A1 (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
WO2017012544A1 (en) * 2015-07-20 2017-01-26 The Chinese University Of Hong Kong Methylation pattern analysis of haplotypes in tissues in 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
EP3559259B1 (en) * 2016-12-21 2025-02-05 The Regents of the University of 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
EP4546353A3 (en) * 2017-07-21 2025-07-23 The Board of Trustees of the Leland Stanford Junior University Systems and methods for analyzing mixed cell populations
WO2019200410A1 (en) * 2018-04-13 2019-10-17 Freenome Holdings, Inc. Machine learning implementation for multi-analyte assay of biological samples

Also Published As

Publication number Publication date
EP4045685A1 (en) 2022-08-24
JP2022552723A (ja) 2022-12-19
WO2021077063A1 (en) 2021-04-22
US20240401134A1 (en) 2024-12-05
JP7874822B2 (ja) 2026-06-17
AU2020365150A1 (en) 2022-05-26
EP4045685A4 (en) 2023-11-15
CN114746559A (zh) 2022-07-12
JP2026064241A (ja) 2026-04-13

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