CA3193183A1 - Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease - Google Patents
Compositions and methods for analyzing dna using partitioning and a methylation-dependent nucleaseInfo
- Publication number
- CA3193183A1 CA3193183A1 CA3193183A CA3193183A CA3193183A1 CA 3193183 A1 CA3193183 A1 CA 3193183A1 CA 3193183 A CA3193183 A CA 3193183A CA 3193183 A CA3193183 A CA 3193183A CA 3193183 A1 CA3193183 A1 CA 3193183A1
- Authority
- CA
- Canada
- Prior art keywords
- subsample
- dna
- methylation
- target region
- region set
- 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
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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
- C12Q1/6804—Nucleic acid analysis using immunogens
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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
- C12Q1/6876—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
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- 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
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- 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
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
- C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
-
- 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
- C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
-
- 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
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
- C12Q1/683—Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
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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
- C12Q1/6869—Methods for sequencing
-
- 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
- C12N2800/00—Nucleic acids vectors
- C12N2800/80—Vectors containing sites for inducing double-stranded breaks, e.g. meganuclease restriction 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
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/112—Disease subtyping, staging or classification
-
- 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
-
- 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
- C12Q2600/156—Polymorphic or mutational markers
-
- 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
- C12Q2600/166—Oligonucleotides used as internal standards, controls or normalisation probes
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Organic Chemistry (AREA)
- Engineering & Computer Science (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Genetics & Genomics (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- Biotechnology (AREA)
- Molecular Biology (AREA)
- Analytical Chemistry (AREA)
- Microbiology (AREA)
- General Health & Medical Sciences (AREA)
- Biochemistry (AREA)
- Immunology (AREA)
- Biophysics (AREA)
- Physics & Mathematics (AREA)
- Biomedical Technology (AREA)
- Pathology (AREA)
- Hospice & Palliative Care (AREA)
- Oncology (AREA)
- Medicinal Chemistry (AREA)
- Bioinformatics & Computational Biology (AREA)
- Crystallography & Structural Chemistry (AREA)
- Plant Pathology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Applications Claiming Priority (5)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US202063086000P | 2020-09-30 | 2020-09-30 | |
| US63/086,000 | 2020-09-30 | ||
| US202063105183P | 2020-10-23 | 2020-10-23 | |
| US63/105,183 | 2020-10-23 | ||
| PCT/US2021/071649 WO2022073012A1 (en) | 2020-09-30 | 2021-09-29 | Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA3193183A1 true CA3193183A1 (en) | 2022-04-07 |
Family
ID=78333328
Family Applications (2)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA3193183A Pending CA3193183A1 (en) | 2020-09-30 | 2021-09-29 | Compositions and methods for analyzing dna using partitioning and a methylation-dependent nuclease |
| CA3193090A Pending CA3193090A1 (en) | 2020-09-30 | 2021-09-29 | Methods and systems to improve the signal to noise ratio of dna methylation partitioning assays |
Family Applications After (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA3193090A Pending CA3193090A1 (en) | 2020-09-30 | 2021-09-29 | Methods and systems to improve the signal to noise ratio of dna methylation partitioning assays |
Country Status (5)
| Country | Link |
|---|---|
| US (3) | US20220154285A1 (https=) |
| EP (2) | EP4222278A1 (https=) |
| JP (2) | JP2023544721A (https=) |
| CA (2) | CA3193183A1 (https=) |
| WO (2) | WO2022073011A1 (https=) |
Families Citing this family (13)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| JP2023547620A (ja) | 2020-10-23 | 2023-11-13 | ガーダント ヘルス, インコーポレイテッド | 分配および塩基変換を使用してdnaを解析するための組成物および方法 |
| WO2022204730A1 (en) * | 2021-03-25 | 2022-09-29 | Guardant Health, Inc. | Methods and compositions for quantifying immune cell dna |
| IL293202A (en) * | 2022-05-22 | 2023-12-01 | Nucleix Ltd | Useful combinations of restriction enzymes |
| EP4536845A1 (en) * | 2022-06-13 | 2025-04-16 | Freenome Holdings, Inc. | Sequence process validation methods and compositions |
| JP2025522763A (ja) * | 2022-06-30 | 2025-07-17 | ガーダント ヘルス, インコーポレイテッド | 異常にメチル化されたdnaの富化 |
| NL2033070B1 (en) * | 2022-09-19 | 2024-03-25 | Univ Twente | Method for detecting CpG methylation in a DNA target sequence |
| EP4646493A1 (en) * | 2023-01-04 | 2025-11-12 | Natera, Inc. | Methods and compositions for amplifying methylated target dna molecules |
| EP4655070A1 (en) * | 2023-01-27 | 2025-12-03 | The Regents of the University of California | Methods of hyper- and hypo-methylation analysis for disease detection |
| WO2024211551A1 (en) | 2023-04-06 | 2024-10-10 | Glaxosmithkline Intellectual Property (No.4) Limited | Methods for treating and monitoring cancer |
| IL324647A (en) * | 2023-05-19 | 2026-01-01 | Nucleix Ltd | Detection of methylation changes in DNA samples using restriction enzymes and high-throughput sequencing |
| CN116926194A (zh) * | 2023-06-29 | 2023-10-24 | 纳昂达(南京)生物科技有限公司 | 一种检测dna样本甲基化状态的方法 |
| WO2025106807A1 (en) * | 2023-11-16 | 2025-05-22 | The Board Of Trustees Of The Leland Stanford Junior University | Classification of samples using methylation enrichment |
| WO2025165106A1 (ko) * | 2024-01-29 | 2025-08-07 | 주식회사 지씨지놈 | 핵산의 메틸화 마커 검출 방법 |
Family Cites Families (35)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US6582908B2 (en) | 1990-12-06 | 2003-06-24 | Affymetrix, Inc. | Oligonucleotides |
| US20030017081A1 (en) | 1994-02-10 | 2003-01-23 | Affymetrix, Inc. | Method and apparatus for imaging a sample on a device |
| DE69528706T2 (de) | 1994-08-19 | 2003-06-12 | Pe Corp. (Ny), Foster City | Gekoppeltes ampflikation- und ligationverfahren |
| GB9620209D0 (en) | 1996-09-27 | 1996-11-13 | Cemu Bioteknik Ab | Method of sequencing DNA |
| GB9626815D0 (en) | 1996-12-23 | 1997-02-12 | Cemu Bioteknik Ab | Method of sequencing DNA |
| US6969488B2 (en) | 1998-05-22 | 2005-11-29 | Solexa, Inc. | System and apparatus for sequential processing of analytes |
| AR021833A1 (es) | 1998-09-30 | 2002-08-07 | Applied Research Systems | Metodos de amplificacion y secuenciacion de acido nucleico |
| US6818395B1 (en) | 1999-06-28 | 2004-11-16 | California Institute Of Technology | Methods and apparatus for analyzing polynucleotide sequences |
| US7501245B2 (en) | 1999-06-28 | 2009-03-10 | Helicos Biosciences Corp. | Methods and apparatuses for analyzing polynucleotide sequences |
| AU7537200A (en) | 1999-09-29 | 2001-04-30 | Solexa Ltd. | Polynucleotide sequencing |
| ATE377093T1 (de) | 2000-07-07 | 2007-11-15 | Visigen Biotechnologies Inc | Sequenzbestimmung in echtzeit |
| WO2003046146A2 (en) | 2001-11-28 | 2003-06-05 | Applera Corporation | Compositions and methods of selective nucleic acid isolation |
| ATE443765T1 (de) | 2003-03-21 | 2009-10-15 | Santaris Pharma As | Analoga kurzer interferierender rna (sirna) |
| WO2005040399A2 (en) * | 2003-10-21 | 2005-05-06 | Orion Genomics Llc | Methods for quantitative determination of methylation density in a dna locus |
| US7169560B2 (en) | 2003-11-12 | 2007-01-30 | Helicos Biosciences Corporation | Short cycle methods for sequencing polynucleotides |
| US7170050B2 (en) | 2004-09-17 | 2007-01-30 | Pacific Biosciences Of California, Inc. | Apparatus and methods for optical analysis of molecules |
| CA2579150C (en) | 2004-09-17 | 2014-11-25 | Pacific Biosciences Of California, Inc. | Apparatus and method for analysis of molecules |
| US7482120B2 (en) | 2005-01-28 | 2009-01-27 | Helicos Biosciences Corporation | Methods and compositions for improving fidelity in a nucleic acid synthesis reaction |
| US7282337B1 (en) | 2006-04-14 | 2007-10-16 | Helicos Biosciences Corporation | Methods for increasing accuracy of nucleic acid sequencing |
| US8486630B2 (en) | 2008-11-07 | 2013-07-16 | Industrial Technology Research Institute | Methods for accurate sequence data and modified base position determination |
| WO2010080617A2 (en) * | 2008-12-19 | 2010-07-15 | The Board Of Trustees Of The University Of Illinois | Detecting and sorting methylated dna using a synthetic nanopore |
| US20130157266A1 (en) | 2009-03-15 | 2013-06-20 | Ribomed Biotechnologies, Inc. | Abscription based molecular detection of dna methylation |
| US20110237444A1 (en) * | 2009-11-20 | 2011-09-29 | Life Technologies Corporation | Methods of mapping genomic methylation patterns |
| US8835358B2 (en) | 2009-12-15 | 2014-09-16 | Cellular Research, Inc. | Digital counting of individual molecules by stochastic attachment of diverse labels |
| CN104781421B (zh) | 2012-09-04 | 2020-06-05 | 夸登特健康公司 | 检测稀有突变和拷贝数变异的系统和方法 |
| US20160040229A1 (en) | 2013-08-16 | 2016-02-11 | Guardant Health, Inc. | Systems and methods to detect rare mutations and copy number variation |
| ES2660989T3 (es) | 2013-12-28 | 2018-03-27 | Guardant Health, Inc. | Métodos y sistemas para detectar variantes genéticas |
| EP4358097A1 (en) | 2014-07-25 | 2024-04-24 | University of Washington | Methods of determining tissues and/or cell types giving rise to cell-free dna, and methods of identifying a disease or disorder using same |
| US11384382B2 (en) * | 2016-04-14 | 2022-07-12 | Guardant Health, Inc. | Methods of attaching adapters to sample nucleic acids |
| KR102522067B1 (ko) * | 2016-05-03 | 2023-04-13 | 유니버시티 헬스 네트워크 | 무-세포 메틸화된 dna의 포획 방법 및 이의 이용 |
| WO2018009723A1 (en) | 2016-07-06 | 2018-01-11 | Guardant Health, Inc. | Methods for fragmentome profiling of cell-free nucleic acids |
| US9850523B1 (en) | 2016-09-30 | 2017-12-26 | Guardant Health, Inc. | Methods for multi-resolution analysis of cell-free nucleic acids |
| MX2019007444A (es) | 2016-12-22 | 2019-08-16 | Guardant Health Inc | Metodos y sistemas para analisis de moleculas de acido nucleico. |
| SG11202007686VA (en) * | 2018-02-12 | 2020-09-29 | 10X Genomics Inc | Methods characterizing multiple analytes from individual cells or cell populations |
| WO2020160414A1 (en) | 2019-01-31 | 2020-08-06 | Guardant Health, Inc. | Compositions and methods for isolating cell-free dna |
-
2021
- 2021-09-29 EP EP21798252.9A patent/EP4222278A1/en active Pending
- 2021-09-29 WO PCT/US2021/071648 patent/WO2022073011A1/en not_active Ceased
- 2021-09-29 JP JP2023519658A patent/JP2023544721A/ja active Pending
- 2021-09-29 CA CA3193183A patent/CA3193183A1/en active Pending
- 2021-09-29 EP EP21806592.8A patent/EP4222279A1/en active Pending
- 2021-09-29 CA CA3193090A patent/CA3193090A1/en active Pending
- 2021-09-29 US US17/489,687 patent/US20220154285A1/en active Pending
- 2021-09-29 JP JP2023519657A patent/JP2023544720A/ja active Pending
- 2021-09-29 WO PCT/US2021/071649 patent/WO2022073012A1/en not_active Ceased
- 2021-09-29 US US17/489,677 patent/US20220162670A1/en active Pending
-
2022
- 2022-12-22 US US18/087,724 patent/US11946106B2/en active Active
Also Published As
| Publication number | Publication date |
|---|---|
| JP2023544720A (ja) | 2023-10-25 |
| EP4222278A1 (en) | 2023-08-09 |
| JP2023544721A (ja) | 2023-10-25 |
| US20230130140A1 (en) | 2023-04-27 |
| US20220154285A1 (en) | 2022-05-19 |
| US11946106B2 (en) | 2024-04-02 |
| US20220162670A1 (en) | 2022-05-26 |
| WO2022073012A1 (en) | 2022-04-07 |
| EP4222279A1 (en) | 2023-08-09 |
| CA3193090A1 (en) | 2022-04-07 |
| WO2022073011A1 (en) | 2022-04-07 |
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