CA3219339A1 - Co-mapping transcriptional states and protein histology - Google Patents

Co-mapping transcriptional states and protein histology Download PDF

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Publication number
CA3219339A1
CA3219339A1 CA3219339A CA3219339A CA3219339A1 CA 3219339 A1 CA3219339 A1 CA 3219339A1 CA 3219339 A CA3219339 A CA 3219339A CA 3219339 A CA3219339 A CA 3219339A CA 3219339 A1 CA3219339 A1 CA 3219339A1
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cells
cell
oligonucleotide probe
disease
interest
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CA3219339A
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English (en)
French (fr)
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Xiao Wang
Hu ZENG
Jingyi Ren
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Massachusetts Institute of Technology
Broad Institute Inc
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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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6841—In situ hybridisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/58—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
    • G01N33/582—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances with fluorescent label
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6854—Immunoglobulins
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6893—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids related to diseases not provided for elsewhere
    • G01N33/6896—Neurological disorders, e.g. Alzheimer's disease
    • 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/161—Modifications characterised by incorporating target specific and non-target specific sites
    • 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
    • C12Q2531/00—Reactions of nucleic acids characterised by
    • C12Q2531/10—Reactions of nucleic acids characterised by the purpose being amplify/increase the copy number of target nucleic acid
    • C12Q2531/125—Rolling circle
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/162—Helper probe
    • 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/179—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being a nucleic acid
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/28—Neurological disorders
    • G01N2800/2814—Dementia; Cognitive disorders
    • G01N2800/2821—Alzheimer

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Biomedical Technology (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Cell Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Neurosurgery (AREA)
  • Neurology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Peptides Or Proteins (AREA)
  • Medical Treatment And Welfare Office Work (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
CA3219339A 2021-05-28 2022-05-27 Co-mapping transcriptional states and protein histology Pending CA3219339A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202163194536P 2021-05-28 2021-05-28
US63/194,536 2021-05-28
PCT/US2022/031275 WO2022251586A1 (en) 2021-05-28 2022-05-27 Co-mapping transcriptional states and protein histology

Publications (1)

Publication Number Publication Date
CA3219339A1 true CA3219339A1 (en) 2022-12-01

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CA3219339A Pending CA3219339A1 (en) 2021-05-28 2022-05-27 Co-mapping transcriptional states and protein histology

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US (1) US20240376530A1 (enExample)
EP (2) EP4347878B1 (enExample)
JP (1) JP2024522350A (enExample)
KR (1) KR20240014486A (enExample)
CN (1) CN117813395A (enExample)
AU (1) AU2022281407A1 (enExample)
CA (1) CA3219339A1 (enExample)
IL (1) IL308570A (enExample)
WO (1) WO2022251586A1 (enExample)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN116189880A (zh) * 2023-01-21 2023-05-30 中国医学科学院北京协和医院 一种肺腺癌脑转移的预测指标及预测方法和应用

Families Citing this family (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12359253B2 (en) 2018-04-09 2025-07-15 The Board Of Trustees Of The Leland Stanford Junior University Method of in situ gene sequencing
US12497651B2 (en) 2020-11-23 2025-12-16 Pleno, Inc. Encoded dual-probe endonuclease assays
DE102022131444A1 (de) * 2022-11-28 2024-05-29 Carl Zeiss Microscopy Gmbh Verfahren zum Identifizieren von Analyten in einer Bildfolge
WO2025136916A1 (en) 2023-12-18 2025-06-26 The Board Institute, Inc. Thick tissue transcriptomics and translatomics
WO2025189030A1 (en) 2024-03-07 2025-09-12 Stellaromics, Inc. Methods and systems for volumetric imaging
CN119068988B (zh) * 2024-08-13 2025-04-15 北京国浩宇医疗科技有限公司 一种针对单细胞表达谱的智能化异常检测系统

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GB201107863D0 (en) * 2011-05-11 2011-06-22 Olink Ab Method and product
WO2014163886A1 (en) * 2013-03-12 2014-10-09 President And Fellows Of Harvard College Method of generating a three-dimensional nucleic acid containing matrix
WO2017079406A1 (en) * 2015-11-03 2017-05-11 President And Fellows Of Harvard College Method and apparatus for volumetric imaging of a three-dimensional nucleic acid containing matrix
CA3007292A1 (en) * 2015-12-02 2017-06-08 Clearlight Diagnostics Llc Methods for preparing and analyzing tumor tissue samples for detection and monitoring of cancers
WO2018035055A1 (en) * 2016-08-19 2018-02-22 Arizona Board Of Regents On Behalf Of Arizona State University High throughput oil-emulsion synthesis of bowtie barcodes for paired mrna capture and sequencing from individual cells
US20180208975A1 (en) * 2017-01-20 2018-07-26 Merck Sharp & Dohme Corp. Assay for simultaneous genomic and proteomic analysis
US12359253B2 (en) 2018-04-09 2025-07-15 The Board Of Trustees Of The Leland Stanford Junior University Method of in situ gene sequencing
US20230109070A1 (en) * 2019-10-18 2023-04-06 The Board of Trustees og the Leland Standford Junior University Clinical- and industrial-scale intact-tissue sequencing
EP4484571A3 (en) * 2020-02-21 2025-03-19 10X Genomics, Inc. Methods and compositions for integrated in situ spatial assay
US12060603B2 (en) * 2021-01-19 2024-08-13 10X Genomics, Inc. Methods for internally controlled in situ assays using padlock probes
CN114854838A (zh) * 2021-02-04 2022-08-05 美天施生物科技有限两合公司 结合靶向RNA或cDNA体外测序与原位测序的方法

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN116189880A (zh) * 2023-01-21 2023-05-30 中国医学科学院北京协和医院 一种肺腺癌脑转移的预测指标及预测方法和应用

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CN117813395A (zh) 2024-04-02
EP4644569A2 (en) 2025-11-05
JP2024522350A (ja) 2024-06-18
IL308570A (en) 2024-01-01
WO2022251586A1 (en) 2022-12-01
EP4644569A3 (en) 2026-01-07
US20240376530A1 (en) 2024-11-14
EP4347878A1 (en) 2024-04-10
KR20240014486A (ko) 2024-02-01
AU2022281407A1 (en) 2023-11-30
EP4347878B1 (en) 2025-07-16

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