JP7874822B2 - 細胞状態を測定するための方法及びシステム - Google Patents

細胞状態を測定するための方法及びシステム

Info

Publication number
JP7874822B2
JP7874822B2 JP2022523301A JP2022523301A JP7874822B2 JP 7874822 B2 JP7874822 B2 JP 7874822B2 JP 2022523301 A JP2022523301 A JP 2022523301A JP 2022523301 A JP2022523301 A JP 2022523301A JP 7874822 B2 JP7874822 B2 JP 7874822B2
Authority
JP
Japan
Prior art keywords
cell
dna
tumor
methylation
inventors
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Active
Application number
JP2022523301A
Other languages
English (en)
Japanese (ja)
Other versions
JP2022552723A (ja
JP2022552723A5 (enExample
Inventor
チャウドゥリ，アーデル
ニューマン，アーロン
エラヒ，イルファン
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
Leland Stanford Junior University
Original Assignee
Washington University in St. Louis
Leland Stanford Junior University
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Washington University in St. Louis, Leland Stanford Junior University filed Critical Washington University in St. Louis
Publication of JP2022552723A publication Critical patent/JP2022552723A/ja
Publication of JP2022552723A5 publication Critical patent/JP2022552723A5/ja
Priority to JP2026000406A priority Critical patent/JP2026064241A/ja
Application granted granted Critical
Publication of JP7874822B2 publication Critical patent/JP7874822B2/ja
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • 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
    • C12Q1/6881—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
    • C12Q1/6876—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)
JP2022523301A 2019-10-18 2020-10-18 細胞状態を測定するための方法及びシステム Active JP7874822B2 (ja)

Priority Applications (1)

Application Number Priority Date Filing Date Title
JP2026000406A JP2026064241A (ja) 2019-10-18 2026-01-05 細胞状態を測定するための方法及びシステム

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

Related Child Applications (1)

Application Number Title Priority Date Filing Date
JP2026000406A Division JP2026064241A (ja) 2019-10-18 2026-01-05 細胞状態を測定するための方法及びシステム

Publications (3)

Publication Number Publication Date
JP2022552723A JP2022552723A (ja) 2022-12-19
JP2022552723A5 JP2022552723A5 (enExample) 2023-10-25
JP7874822B2 true JP7874822B2 (ja) 2026-06-17

Family

ID=75538680

Family Applications (2)

Application Number Title Priority Date Filing Date
JP2022523301A Active JP7874822B2 (ja) 2019-10-18 2020-10-18 細胞状態を測定するための方法及びシステム
JP2026000406A Pending JP2026064241A (ja) 2019-10-18 2026-01-05 細胞状態を測定するための方法及びシステム

Family Applications After (1)

Application Number Title Priority Date Filing Date
JP2026000406A Pending JP2026064241A (ja) 2019-10-18 2026-01-05 細胞状態を測定するための方法及びシステム

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

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015169857A1 (en) 2014-05-07 2015-11-12 Université Libre de Bruxelles Breast cancer epigenetic markers useful in anthracycline treatment prognosis
WO2018119216A1 (en) 2016-12-21 2018-06-28 The Regents Of The University Of California Deconvolution and detection of rare dna in plasma
WO2019200410A1 (en) 2018-04-13 2019-10-17 Freenome Holdings, Inc. Machine learning implementation for multi-analyte assay of biological samples

Family Cites Families (7)

* 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
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
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

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015169857A1 (en) 2014-05-07 2015-11-12 Université Libre de Bruxelles Breast cancer epigenetic markers useful in anthracycline treatment prognosis
WO2018119216A1 (en) 2016-12-21 2018-06-28 The Regents Of The University Of California Deconvolution and detection of rare dna in plasma
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
CA3155073A1 (en) 2021-04-22
US20240401134A1 (en) 2024-12-05
AU2020365150A1 (en) 2022-05-26
EP4045685A4 (en) 2023-11-15
CN114746559A (zh) 2022-07-12
JP2026064241A (ja) 2026-04-13

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20231017

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20231017

A977 Report on retrieval

Free format text: JAPANESE INTERMEDIATE CODE: A971007

Effective date: 20241030

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20241105

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20250131

A601 Written request for extension of time

Free format text: JAPANESE INTERMEDIATE CODE: A601

Effective date: 20250403

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20250507

A02 Decision of refusal

Free format text: JAPANESE INTERMEDIATE CODE: A02

Effective date: 20250902

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20260105

TRDD Decision of grant or rejection written
A01 Written decision to grant a patent or to grant a registration (utility model)

Free format text: JAPANESE INTERMEDIATE CODE: A01

Effective date: 20260414

A61 First payment of annual fees (during grant procedure)

Free format text: JAPANESE INTERMEDIATE CODE: A61

Effective date: 20260511

R150 Certificate of patent or registration of utility model

Ref document number: 7874822

Country of ref document: JP

Free format text: JAPANESE INTERMEDIATE CODE: R150