CA3223500A1 - Methods and compositions for combinatorial indexing of bead-based nucleic acids - Google Patents
Methods and compositions for combinatorial indexing of bead-based nucleic acids Download PDFInfo
- Publication number
- CA3223500A1 CA3223500A1 CA3223500A CA3223500A CA3223500A1 CA 3223500 A1 CA3223500 A1 CA 3223500A1 CA 3223500 A CA3223500 A CA 3223500A CA 3223500 A CA3223500 A CA 3223500A CA 3223500 A1 CA3223500 A1 CA 3223500A1
- Authority
- CA
- Canada
- Prior art keywords
- polynucleotide
- linker
- beads
- indexed
- index
- 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
Links
Classifications
-
- 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
- C12N15/1034—Isolating an individual clone by screening libraries
- C12N15/1065—Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
-
- 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
- C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
-
- 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
- C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
-
- 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
- C12Q2521/00—Reaction characterised by the enzymatic activity
- C12Q2521/10—Nucleotidyl transfering
- C12Q2521/101—DNA polymerase
-
- 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
- C12Q2521/00—Reaction characterised by the enzymatic activity
- C12Q2521/50—Other enzymatic activities
- C12Q2521/501—Ligase
-
- 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
- C12Q2525/191—Modifications characterised by incorporating an adaptor
-
- 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
- C12Q2537/149—Sequential reactions
-
- 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
- C12Q2563/149—Particles, e.g. beads
-
- 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
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Wood Science & Technology (AREA)
- Zoology (AREA)
- Genetics & Genomics (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- General Engineering & Computer Science (AREA)
- Biotechnology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Biochemistry (AREA)
- Molecular Biology (AREA)
- Microbiology (AREA)
- Physics & Mathematics (AREA)
- General Health & Medical Sciences (AREA)
- Biophysics (AREA)
- Analytical Chemistry (AREA)
- Immunology (AREA)
- Biomedical Technology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Crystallography & Structural Chemistry (AREA)
- Plant Pathology (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Preparation Of Compounds By Using Micro-Organisms (AREA)
- Medicinal Preparation (AREA)
- Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US202163214693P | 2021-06-24 | 2021-06-24 | |
| US63/214,693 | 2021-06-24 | ||
| PCT/US2022/034734 WO2022271954A1 (en) | 2021-06-24 | 2022-06-23 | Methods and compositions for combinatorial indexing of bead-based nucleic acids |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA3223500A1 true CA3223500A1 (en) | 2022-12-29 |
Family
ID=84544839
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA3223500A Pending CA3223500A1 (en) | 2021-06-24 | 2022-06-23 | Methods and compositions for combinatorial indexing of bead-based nucleic acids |
Country Status (11)
| Country | Link |
|---|---|
| US (1) | US20240287505A1 (https=) |
| EP (1) | EP4359557A4 (https=) |
| JP (1) | JP2024523570A (https=) |
| KR (1) | KR20240024835A (https=) |
| CN (1) | CN117580959A (https=) |
| AU (1) | AU2022297521A1 (https=) |
| BR (1) | BR112023026984A2 (https=) |
| CA (1) | CA3223500A1 (https=) |
| IL (1) | IL309566A (https=) |
| MX (1) | MX2023014950A (https=) |
| WO (1) | WO2022271954A1 (https=) |
Families Citing this family (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2024006797A1 (en) * | 2022-06-29 | 2024-01-04 | 10X Genomics, Inc. | Methods and compositions for refining feature boundaries in molecular arrays |
| CN116287124A (zh) * | 2023-05-24 | 2023-06-23 | 中国农业科学院农业基因组研究所 | 单链接头预连接方法、高通量测序文库的建库方法及试剂盒 |
Family Cites Families (32)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| JP2002503954A (ja) | 1997-04-01 | 2002-02-05 | グラクソ、グループ、リミテッド | 核酸増幅法 |
| AR021833A1 (es) | 1998-09-30 | 2002-08-07 | Applied Research Systems | Metodos de amplificacion y secuenciacion de acido nucleico |
| US20060275782A1 (en) | 1999-04-20 | 2006-12-07 | Illumina, Inc. | Detection of nucleic acid reactions on bead arrays |
| ATE377093T1 (de) | 2000-07-07 | 2007-11-15 | Visigen Biotechnologies Inc | Sequenzbestimmung in echtzeit |
| AU2002227156A1 (en) | 2000-12-01 | 2002-06-11 | Visigen Biotechnologies, Inc. | Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity |
| US7057026B2 (en) | 2001-12-04 | 2006-06-06 | Solexa Limited | Labelled nucleotides |
| WO2004018497A2 (en) | 2002-08-23 | 2004-03-04 | Solexa Limited | Modified nucleotides for polynucleotide sequencing |
| WO2005003304A2 (en) | 2003-06-20 | 2005-01-13 | Illumina, Inc. | Methods and compositions for whole genome amplification and genotyping |
| EP1701785A1 (en) | 2004-01-07 | 2006-09-20 | Solexa Ltd. | Modified molecular arrays |
| CA2579150C (en) | 2004-09-17 | 2014-11-25 | Pacific Biosciences Of California, Inc. | Apparatus and method for analysis of molecules |
| WO2006064199A1 (en) | 2004-12-13 | 2006-06-22 | Solexa Limited | Improved method of nucleotide detection |
| GB0514936D0 (en) | 2005-07-20 | 2005-08-24 | Solexa Ltd | Preparation of templates for nucleic acid sequencing |
| US7405281B2 (en) | 2005-09-29 | 2008-07-29 | Pacific Biosciences Of California, Inc. | Fluorescent nucleotide analogs and uses therefor |
| US11591637B2 (en) * | 2012-08-14 | 2023-02-28 | 10X Genomics, Inc. | Compositions and methods for sample processing |
| KR102758333B1 (ko) * | 2013-08-28 | 2025-01-23 | 벡톤 디킨슨 앤드 컴퍼니 | 대량의 동시 단일 세포 분석 |
| US9677132B2 (en) | 2014-01-16 | 2017-06-13 | Illumina, Inc. | Polynucleotide modification on solid support |
| AU2015250034B2 (en) * | 2014-04-21 | 2019-06-20 | President And Fellows Of Harvard College | Systems and methods for barcoding nucleic acids |
| WO2016138496A1 (en) * | 2015-02-27 | 2016-09-01 | Cellular Research, Inc. | Spatially addressable molecular barcoding |
| WO2016138500A1 (en) * | 2015-02-27 | 2016-09-01 | Cellular Research, Inc. | Methods and compositions for barcoding nucleic acids for sequencing |
| EP3904514A1 (en) | 2016-07-22 | 2021-11-03 | Oregon Health & Science University | Single cell whole genome libraries and combinatorial indexing methods of making thereof |
| EP3529380B1 (en) | 2016-10-19 | 2022-06-29 | Illumina, Inc. | Methods for chemical ligation of nucleic acids |
| DK3635136T3 (da) | 2017-06-07 | 2022-01-10 | Univ Oregon Health & Science | Enkeltcelle-helgenombiblioteker til methyleringssekvensering |
| US11084037B2 (en) | 2017-09-25 | 2021-08-10 | Plexium, Inc. | Oligonucleotide encoded chemical libraries |
| WO2019126466A1 (en) * | 2017-12-22 | 2019-06-27 | Rootpath Genomics, Inc. | Compositions and methods for barcoding |
| US12286621B2 (en) * | 2018-09-28 | 2025-04-29 | California Institute Of Technology | Efficient combinatorial bead barcoding |
| EP3870704A4 (en) | 2018-10-25 | 2023-01-11 | Illumina, Inc. | METHODS AND COMPOSITIONS FOR IDENTIFICATION OF LIGANDS ON ARRAYS WITH INDEXES AND BARCODES |
| US11965208B2 (en) * | 2019-04-19 | 2024-04-23 | Becton, Dickinson And Company | Methods of associating phenotypical data and single cell sequencing data |
| US20220403374A1 (en) * | 2019-09-03 | 2022-12-22 | Flexomics, Llc | Optically readable barcodes and systems and methods for characterizing molecular interactions |
| SG11202113372WA (en) | 2019-09-20 | 2021-12-30 | Illumina Inc | Methods and compositions for identifying ligands on arrays using indexes and barcodes |
| JP2023508792A (ja) * | 2019-12-19 | 2023-03-06 | イルミナ インコーポレイテッド | ハイスループット単一細胞ライブラリー、並びに製造方法及び使用方法 |
| US11027272B1 (en) * | 2020-01-28 | 2021-06-08 | Plexium, Inc. | Transfer dispensers for assay devices |
| EP4182477A4 (en) * | 2020-07-15 | 2024-09-11 | Fluent Biosciences Inc. | MULTI-LEVEL LIGATION OLIGOS |
-
2022
- 2022-06-23 US US18/567,697 patent/US20240287505A1/en active Pending
- 2022-06-23 IL IL309566A patent/IL309566A/en unknown
- 2022-06-23 CN CN202280044218.XA patent/CN117580959A/zh active Pending
- 2022-06-23 AU AU2022297521A patent/AU2022297521A1/en active Pending
- 2022-06-23 MX MX2023014950A patent/MX2023014950A/es unknown
- 2022-06-23 KR KR1020237043987A patent/KR20240024835A/ko active Pending
- 2022-06-23 CA CA3223500A patent/CA3223500A1/en active Pending
- 2022-06-23 WO PCT/US2022/034734 patent/WO2022271954A1/en not_active Ceased
- 2022-06-23 BR BR112023026984A patent/BR112023026984A2/pt not_active Application Discontinuation
- 2022-06-23 JP JP2023579590A patent/JP2024523570A/ja active Pending
- 2022-06-23 EP EP22829309.8A patent/EP4359557A4/en active Pending
Also Published As
| Publication number | Publication date |
|---|---|
| WO2022271954A1 (en) | 2022-12-29 |
| EP4359557A4 (en) | 2025-05-21 |
| EP4359557A1 (en) | 2024-05-01 |
| MX2023014950A (es) | 2024-03-14 |
| US20240287505A1 (en) | 2024-08-29 |
| KR20240024835A (ko) | 2024-02-26 |
| AU2022297521A1 (en) | 2024-01-04 |
| BR112023026984A2 (pt) | 2024-03-12 |
| IL309566A (en) | 2024-02-01 |
| JP2024523570A (ja) | 2024-06-28 |
| CN117580959A (zh) | 2024-02-20 |
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Legal Events
| Date | Code | Title | Description |
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| MFA | Maintenance fee for application paid |
Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 3RD ANNIV.) - STANDARD Year of fee payment: 3 |
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| 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: 20250616 |
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| 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: 20250616 |