CA3249276A1 - ITERATIVE SHORT PLAY SEQUENCING WITHIN A CELL SAMPLE - Google Patents

ITERATIVE SHORT PLAY SEQUENCING WITHIN A CELL SAMPLE

Info

Publication number
CA3249276A1
CA3249276A1 CA3249276A CA3249276A CA3249276A1 CA 3249276 A1 CA3249276 A1 CA 3249276A1 CA 3249276 A CA3249276 A CA 3249276A CA 3249276 A CA3249276 A CA 3249276A CA 3249276 A1 CA3249276 A1 CA 3249276A1
Authority
CA
Canada
Prior art keywords
nucleic acid
nucleotide
sequence
concatemer
group
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
CA3249276A
Other languages
English (en)
French (fr)
Inventor
Tsung-Li Liu
Sinan ARSLAN
Michael Previte
Tuval Ben-Yehezkel
Connor THOMPSON
Matthew Kellinger
Hui Zhen MAH
Molly He
Andrew Price
Original Assignee
Element Biosciences Inc
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 Element Biosciences Inc filed Critical Element Biosciences Inc
Publication of CA3249276A1 publication Critical patent/CA3249276A1/en
Pending legal-status Critical Current

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
    • 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
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
    • 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
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • 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
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • 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
    • 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
    • C12Q2537/143—Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
    • 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
    • C12Q2563/107—Nucleic acid detection characterized by the use of physical, structural and functional properties fluorescence

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Biotechnology (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Pathology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Cell Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Physics & Mathematics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
CA3249276A 2022-04-20 2023-04-19 ITERATIVE SHORT PLAY SEQUENCING WITHIN A CELL SAMPLE Pending CA3249276A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202263332690P 2022-04-20 2022-04-20
US63/332,690 2022-04-20
US202263334023P 2022-04-22 2022-04-22
US63/334,023 2022-04-22
PCT/US2023/065972 WO2023205707A2 (en) 2022-04-20 2023-04-19 Reiterative short read sequencing inside a cellular sample

Publications (1)

Publication Number Publication Date
CA3249276A1 true CA3249276A1 (en) 2023-10-26

Family

ID=88420782

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3249276A Pending CA3249276A1 (en) 2022-04-20 2023-04-19 ITERATIVE SHORT PLAY SEQUENCING WITHIN A CELL SAMPLE

Country Status (8)

Country Link
US (1) US20250146068A1 (https=)
EP (1) EP4511515A4 (https=)
JP (1) JP2025514791A (https=)
KR (1) KR20250011725A (https=)
CN (1) CN119487210A (https=)
AU (1) AU2023258027A1 (https=)
CA (1) CA3249276A1 (https=)
WO (1) WO2023205707A2 (https=)

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
GB2589496B (en) 2018-06-12 2023-01-25 Element Biosciences Inc Improved reverse transcriptase for nucleic acid sequencing
US10768173B1 (en) 2019-09-06 2020-09-08 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
US10704094B1 (en) 2018-11-14 2020-07-07 Element Biosciences, Inc. Multipart reagents having increased avidity for polymerase binding
GB2613480B (en) 2018-11-15 2023-11-22 Element Biosciences Inc Methods for generating circular nucleic acid molecules
US12313627B2 (en) 2019-05-01 2025-05-27 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
US12391929B2 (en) 2019-05-24 2025-08-19 Element Biosciences, Inc. Polymerase-nucleotide conjugates for sequencing by trapping
US11287422B2 (en) 2019-09-23 2022-03-29 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
KR20240063107A (ko) 2021-07-21 2024-05-10 엘리먼트 바이오사이언스, 인크. 핵산 시퀀싱을 위한 광학 시스템 및 이의 방법
AU2023325064A1 (en) 2022-08-15 2025-03-06 Element Biosciences, Inc. Spatially resolved surface capture of nucleic acids
WO2025147667A1 (en) * 2024-01-05 2025-07-10 Element Biosciences, Inc. Target probe complexes and analyte detection complexes for in situ detecting and identifying target analytes
WO2025235016A1 (en) 2024-05-07 2025-11-13 Element Biosciences, Inc. Sequencing method with spatial flexibility
WO2026080904A2 (en) 2024-10-11 2026-04-16 Element Biosciences, Inc. Systems and methods for performing dna sequencing

Family Cites Families (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10059990B2 (en) * 2015-04-14 2018-08-28 Massachusetts Institute Of Technology In situ nucleic acid sequencing of expanded biological samples
US11287422B2 (en) * 2019-09-23 2022-03-29 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis

Also Published As

Publication number Publication date
EP4511515A2 (en) 2025-02-26
EP4511515A4 (en) 2026-04-29
WO2023205707A3 (en) 2023-11-30
KR20250011725A (ko) 2025-01-21
CN119487210A (zh) 2025-02-18
WO2023205707A2 (en) 2023-10-26
AU2023258027A1 (en) 2024-12-05
US20250146068A1 (en) 2025-05-08
JP2025514791A (ja) 2025-05-09

Similar Documents

Publication Publication Date Title
US20250146068A1 (en) Reiterative short read sequencing inside a cellular sample
JP7846146B2 (ja) 連結型ライゲーション
US20250002996A1 (en) Bi-directional in situ analysis
US20220403445A1 (en) Compositions and methods for pairwise sequencing
JP7026248B2 (ja) 二本鎖ｄｎａを増幅するための方法およびキット
CN103781918B (zh) 用于组织样本中核酸的局部或空间检测的方法和产品
CN110312800A (zh) 处理核酸样本的方法
KR20250086817A (ko) 범용 긴 스플린트 가닥을 갖는 이중가닥 스플린트 어댑터 및 사용 방법
JP2025528821A (ja) 核酸の空間的に分解された表面キャプチャ
US20240384337A1 (en) Linked target capture and ligation
KR20250028294A (ko) 차세대 시퀀싱에서 염기 호출의 페이징 및 사전 페이징 교정
CN119630954A (zh) 初步分析中的图像配准
WO2025147667A1 (en) Target probe complexes and analyte detection complexes for in situ detecting and identifying target analytes
US20240002921A1 (en) Rna and dna analysis using engineered surfaces
HK40124113A (zh) 细胞样品内的反复短读测序
US20240287502A1 (en) Oligonucleotide-tethered nucleotides
WO2025170937A1 (en) Direct in situ sequencing
HK40120147A (zh) 双链夹板衔接子和使用方法

Legal Events

Date Code Title Description
A00 Application filed

Free format text: ST27 STATUS EVENT CODE: A-0-1-A10-A00-A101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: APPLICATION RECEIVED - PCT

Effective date: 20241016

A15 Pct application entered into the national or regional phase

Free format text: ST27 STATUS EVENT CODE: A-1-1-A10-A15-X000 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: NATIONAL ENTRY REQUIREMENTS DETERMINED COMPLIANT

Effective date: 20241122

P18 Priority claim added or amended

Free format text: ST27 STATUS EVENT CODE: A-1-1-P10-P18-P105 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: PRIORITY CLAIM REQUIREMENTS DETERMINED COMPLIANT

Effective date: 20241122

W00 Other event occurred

Free format text: ST27 STATUS EVENT CODE: A-1-1-W10-W00-W100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: LETTER SENT

Effective date: 20241122

A00 Application filed

Free format text: ST27 STATUS EVENT CODE: A-1-1-A10-A00-A102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: COMPLIANCE REQUIREMENTS DETERMINED MET

Effective date: 20241127

P13 Application amended

Free format text: ST27 STATUS EVENT CODE: A-1-1-P10-P13-P146 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: BSL VERIFIED - NO DEFECTS

Effective date: 20241127

MFA Maintenance fee for application paid

Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 2ND ANNIV.) - STANDARD

Year of fee payment: 2

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-1-1-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20250410

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-1-1-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20250410

MFA Maintenance fee for application paid

Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 3RD ANNIV.) - STANDARD

Year of fee payment: 3

U00 Fee paid

Free format text: ST27 STATUS EVENT CODE: A-1-1-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED

Effective date: 20260408

U11 Full renewal or maintenance fee paid

Free format text: ST27 STATUS EVENT CODE: A-1-1-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL

Effective date: 20260408