CA3220740A1 - Next-generation volumetric in situ sequencing - Google Patents

Next-generation volumetric in situ sequencing Download PDF

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Publication number
CA3220740A1
CA3220740A1 CA3220740A CA3220740A CA3220740A1 CA 3220740 A1 CA3220740 A1 CA 3220740A1 CA 3220740 A CA3220740 A CA 3220740A CA 3220740 A CA3220740 A CA 3220740A CA 3220740 A1 CA3220740 A1 CA 3220740A1
Authority
CA
Canada
Prior art keywords
oligonucleotide
sequence
nucleic acid
probe
hydrogel
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.)
Pending
Application number
CA3220740A
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English (en)
French (fr)
Inventor
Karl A. DEISSEROTH
Ethan B. RICHMAN
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.)
Leland Stanford Junior University
Original Assignee
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 Leland Stanford Junior University filed Critical Leland Stanford Junior University
Publication of CA3220740A1 publication Critical patent/CA3220740A1/en
Pending legal-status Critical Current

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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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • 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
    • 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
    • G01N33/52—Use of compounds or compositions for colorimetric, spectrophotometric or fluorometric investigation, e.g. use of reagent paper and including single- and multilayer analytical elements
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/10—Screening for compounds of potential therapeutic value involving cells

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Biomedical Technology (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Photoreceptors In Electrophotography (AREA)
  • Particle Accelerators (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA3220740A 2021-05-21 2022-05-20 Next-generation volumetric in situ sequencing Pending CA3220740A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202163191455P 2021-05-21 2021-05-21
US63/191,455 2021-05-21
PCT/US2022/030370 WO2022246275A1 (en) 2021-05-21 2022-05-20 Next-generation volumetric in situ sequencing

Publications (1)

Publication Number Publication Date
CA3220740A1 true CA3220740A1 (en) 2022-11-24

Family

ID=84141872

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3220740A Pending CA3220740A1 (en) 2021-05-21 2022-05-20 Next-generation volumetric in situ sequencing

Country Status (6)

Country Link
US (1) US20240263228A1 (https=)
EP (1) EP4352254A4 (https=)
JP (1) JP2024521142A (https=)
AU (1) AU2022276537A1 (https=)
CA (1) CA3220740A1 (https=)
WO (1) WO2022246275A1 (https=)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP7502787B2 (ja) 2018-04-09 2024-06-19 ザ ボード オブ トラスティーズ オブ ザ レランド スタンフォード ジュニア ユニバーシティー インサイチュ遺伝子配列決定の方法
WO2023158821A2 (en) * 2022-02-17 2023-08-24 Vizgen, Inc. Methods of anchoring fragmented nucleic acid targets in a polymer matrix for imaging
CN117343993A (zh) * 2023-12-01 2024-01-05 中国科学院遗传与发育生物学研究所 原位检测样品中的靶核酸序列的方法
WO2025189030A1 (en) 2024-03-07 2025-09-12 Stellaromics, Inc. Methods and systems for volumetric imaging

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2012005595A2 (en) * 2010-07-09 2012-01-12 Wouter Leonard De Laat V3-d genomic region of interest sequencing strategies
US10982271B2 (en) * 2011-01-31 2021-04-20 Roche Sequencing Solutions, Inc. Methods of identifying multiple epitopes in cells
WO2014030066A2 (en) * 2012-08-22 2014-02-27 Bernitz Mats Nilsson Methods for identifying nucleic acid sequences
EP4339956A3 (en) * 2016-11-08 2024-06-19 President and Fellows of Harvard College Multiplexed imaging using merfish, expansion microscopy, and related technologies
WO2018136856A1 (en) * 2017-01-23 2018-07-26 Massachusetts Institute Of Technology Multiplexed signal amplified fish via splinted ligation amplification and sequencing
WO2019222284A1 (en) * 2018-05-14 2019-11-21 The Broad Institute, Inc. In situ cell screening methods and systems

Also Published As

Publication number Publication date
JP2024521142A (ja) 2024-05-28
AU2022276537A1 (en) 2023-12-07
EP4352254A1 (en) 2024-04-17
EP4352254A4 (en) 2025-04-16
WO2022246275A1 (en) 2022-11-24
US20240263228A1 (en) 2024-08-08

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