AU2020365150A1 - Methods and systems for measuring cell states - Google Patents

Methods and systems for measuring cell states Download PDF

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Publication number
AU2020365150A1
AU2020365150A1 AU2020365150A AU2020365150A AU2020365150A1 AU 2020365150 A1 AU2020365150 A1 AU 2020365150A1 AU 2020365150 A AU2020365150 A AU 2020365150A AU 2020365150 A AU2020365150 A AU 2020365150A AU 2020365150 A1 AU2020365150 A1 AU 2020365150A1
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AU
Australia
Prior art keywords
cell
dna
abundance
read
identity
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Pending
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AU2020365150A
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English (en)
Inventor
Irfan ALAHI
Aadel Chaudhuri
Aaron NEWMAN
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.)
Washington University in St Louis WUSTL
Leland Stanford Junior University
Original Assignee
Washington University in St Louis WUSTL
Leland Stanford Junior University
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Application filed by Washington University in St Louis WUSTL, Leland Stanford Junior University filed Critical Washington University in St Louis WUSTL
Publication of AU2020365150A1 publication Critical patent/AU2020365150A1/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
    • C12Q1/6881—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)
AU2020365150A 2019-10-18 2020-10-18 Methods and systems for measuring cell states Pending AU2020365150A1 (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
AU2020365150A1 true AU2020365150A1 (en) 2022-05-26

Family

ID=75538680

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2020365150A Pending AU2020365150A1 (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
CN114746559A (zh) 2022-07-12
EP4045685A1 (en) 2022-08-24
CA3155073A1 (en) 2021-04-22
JP2022552723A (ja) 2022-12-19
EP4045685A4 (en) 2023-11-15
US20240401134A1 (en) 2024-12-05

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