CA3195797A1 - Compositions and methods for analyzing dna using partitioning and base conversion - Google Patents
Compositions and methods for analyzing dna using partitioning and base conversionInfo
- Publication number
- CA3195797A1 CA3195797A1 CA3195797A CA3195797A CA3195797A1 CA 3195797 A1 CA3195797 A1 CA 3195797A1 CA 3195797 A CA3195797 A CA 3195797A CA 3195797 A CA3195797 A CA 3195797A CA 3195797 A1 CA3195797 A1 CA 3195797A1
- Authority
- CA
- Canada
- Prior art keywords
- dna
- subsample
- nucleobase
- 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
-
- 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
-
- 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
- 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
- C12Q1/6806—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
- 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
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Organic Chemistry (AREA)
- Genetics & Genomics (AREA)
- Engineering & Computer Science (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Biotechnology (AREA)
- General Engineering & Computer Science (AREA)
- Molecular Biology (AREA)
- Analytical Chemistry (AREA)
- Microbiology (AREA)
- Biochemistry (AREA)
- General Health & Medical Sciences (AREA)
- Immunology (AREA)
- Pathology (AREA)
- Physics & Mathematics (AREA)
- Biophysics (AREA)
- Biomedical Technology (AREA)
- Hospice & Palliative Care (AREA)
- Oncology (AREA)
- Crystallography & Structural Chemistry (AREA)
- Plant Pathology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Medicinal Chemistry (AREA)
- Chemical Kinetics & Catalysis (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US202063105184P | 2020-10-23 | 2020-10-23 | |
| US63/105,184 | 2020-10-23 | ||
| PCT/US2021/056106 WO2022087309A1 (en) | 2020-10-23 | 2021-10-21 | Compositions and methods for analyzing dna using partitioning and base conversion |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA3195797A1 true CA3195797A1 (en) | 2022-04-28 |
Family
ID=78622081
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA3195797A Pending CA3195797A1 (en) | 2020-10-23 | 2021-10-21 | Compositions and methods for analyzing dna using partitioning and base conversion |
Country Status (5)
| Country | Link |
|---|---|
| US (2) | US12234518B2 (https=) |
| EP (1) | EP4232599A1 (https=) |
| JP (1) | JP2023547620A (https=) |
| CA (1) | CA3195797A1 (https=) |
| WO (1) | WO2022087309A1 (https=) |
Families Citing this family (4)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2022221853A1 (en) * | 2021-04-13 | 2022-10-20 | Elegen Corp. | Methods and compositions for cell-free cloning |
| AU2022318379A1 (en) * | 2021-07-27 | 2024-02-08 | Ludwig Institute For Cancer Research Ltd | Compositions and methods related to tet-assisted pyridine borane sequencing for cell-free dna |
| 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 |
| WO2025207924A1 (en) * | 2024-03-28 | 2025-10-02 | Guardant Health, Inc. | Methods for selective deamination using cpg-binding proteins |
Family Cites Families (60)
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| 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 |
| JP3102800B2 (ja) | 1994-08-19 | 2000-10-23 | パーキン−エルマー コーポレイション | 増幅及び連結反応の共役法 |
| 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 |
| US7501245B2 (en) | 1999-06-28 | 2009-03-10 | Helicos Biosciences Corp. | Methods and apparatuses for analyzing polynucleotide sequences |
| WO2001023610A2 (en) | 1999-09-29 | 2001-04-05 | Solexa Ltd. | Polynucleotide sequencing |
| WO2002004680A2 (en) | 2000-07-07 | 2002-01-17 | Visigen Biotechnologies, Inc. | Real-time sequence determination |
| AU2002359522A1 (en) | 2001-11-28 | 2003-06-10 | Applera Corporation | Compositions and methods of selective nucleic acid isolation |
| CA2519860C (en) | 2003-03-21 | 2018-01-16 | Santaris Pharma A/S | Short interfering rna (sirna) analogues |
| 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 |
| US7315019B2 (en) | 2004-09-17 | 2008-01-01 | Pacific Biosciences Of California, Inc. | Arrays of optical confinements and uses thereof |
| EP1817430B1 (en) | 2004-11-29 | 2009-09-16 | Klinikum der Universität Regensburg | Means and methods for detecting methylated dna |
| US7482120B2 (en) | 2005-01-28 | 2009-01-27 | Helicos Biosciences Corporation | Methods and compositions for improving fidelity in a nucleic acid synthesis reaction |
| EP1693468A1 (en) | 2005-02-16 | 2006-08-23 | Epigenomics AG | Method for determining the methylation pattern of a polynucleic acid |
| DE102005034628B4 (de) | 2005-07-19 | 2007-08-23 | Epigenomics Ag | Verfahren zur Untersuchung von Cytosin-Methylierungen in DNA |
| US7282337B1 (en) | 2006-04-14 | 2007-10-16 | Helicos Biosciences Corporation | Methods for increasing accuracy of nucleic acid sequencing |
| US8476013B2 (en) | 2008-09-16 | 2013-07-02 | Sequenom, Inc. | Processes and compositions for methylation-based acid enrichment of fetal nucleic acid from a maternal sample useful for non-invasive prenatal diagnoses |
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| US8486630B2 (en) | 2008-11-07 | 2013-07-16 | Industrial Technology Research Institute | Methods for accurate sequence data and modified base position determination |
| 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 |
| CN102971434B (zh) | 2010-08-11 | 2014-04-09 | 中国科学院心理研究所 | 一种甲基化dna的高通量测序方法及其应用 |
| EP2675913B1 (en) | 2011-02-15 | 2016-12-14 | Bio-Rad Laboratories, Inc. | Detecting methylation in a subpopulation of genomic dna |
| EP2694686B2 (en) | 2011-04-06 | 2023-07-19 | The University of Chicago | COMPOSITION AND METHODS RELATED TO MODIFICATION OF 5-METHYLCYTOSINE (5mC) |
| ES3018861T3 (en) | 2011-12-13 | 2025-05-19 | Univ Oslo Hf | Method for detection of hydroxymethylation status |
| EP3744857A1 (en) | 2012-03-20 | 2020-12-02 | University Of Washington Through Its Center For Commercialization | Methods of lowering the error rate of massively parallel dna sequencing using duplex consensus sequencing |
| EP2698436A1 (en) | 2012-08-14 | 2014-02-19 | Max-Planck-Gesellschaft zur Förderung der Wissenschaften e.V. | Colorectal cancer markers |
| US20160040229A1 (en) | 2013-08-16 | 2016-02-11 | Guardant Health, Inc. | Systems and methods to detect rare mutations and copy number variation |
| GB2533006B (en) | 2012-09-04 | 2017-06-07 | Guardant Health Inc | Systems and methods to detect copy number variation |
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| EP2983693A4 (en) | 2013-04-08 | 2016-10-26 | Univ Carmel Haifa Economic Cor | SEPT4 / ARTS AS TUMOR SUPPRESSOR IN THE DIAGNOSIS, FORECASTING AND TREATMENT OF LIVER DISEASES |
| EP2805769A1 (en) | 2013-05-24 | 2014-11-26 | European Molecular Biology Laboratory | Methods for nano-scale single cell analysis |
| KR102429186B1 (ko) | 2013-10-21 | 2022-08-03 | 베리나타 헬스, 인코포레이티드 | 사본수 변동을 결정함에 있어서 검출의 감수성을 향상시키기 위한 방법 |
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| EP3132055A2 (en) | 2014-04-14 | 2017-02-22 | Yissum Research and Development Company of the Hebrew University of Jerusalem Ltd. | A method and kit for determining the tissue or cell origin of dna |
| CN107002122B (zh) | 2014-07-25 | 2023-09-19 | 华盛顿大学 | 确定导致无细胞dna的产生的组织和/或细胞类型的方法以及使用其鉴定疾病或紊乱的方法 |
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| JP6897970B2 (ja) * | 2015-09-08 | 2021-07-07 | 国立大学法人山口大学 | 大腸腫瘍の有無を検査する方法 |
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| EP4257701A3 (en) | 2016-06-30 | 2023-12-20 | Grail, LLC | Differential tagging of rna for preparation of a cell-free dna/rna sequencing library |
| KR102610098B1 (ko) | 2016-07-06 | 2023-12-04 | 가던트 헬쓰, 인크. | 무세포 핵산의 프래그멘톰 프로파일링을 위한 방법 |
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| JP7136899B2 (ja) * | 2018-01-08 | 2022-09-13 | ルドウイグ インスティテュート フォー キャンサー リサーチ エルティーディー | シトシン修飾の、亜硫酸水素塩非含有、塩基分解能特定 |
| WO2020006369A1 (en) | 2018-06-29 | 2020-01-02 | Guardant Health, Inc. | Methods and systems for analysis of ctcf binding regions in cell-free dna |
| EP4567131A3 (en) * | 2019-01-31 | 2025-09-03 | Guardant Health, Inc. | Compositions and methods for isolating cell-free dna |
| US11891653B2 (en) | 2019-09-30 | 2024-02-06 | Guardant Health, Inc. | Compositions and methods for analyzing cell-free DNA in methylation partitioning assays |
| US20220154285A1 (en) | 2020-09-30 | 2022-05-19 | Guardant Health, Inc. | Analysis of methylated dna comprising methylation-sensitive or methylation-dependent restrictions |
-
2021
- 2021-10-21 US US17/507,697 patent/US12234518B2/en active Active
- 2021-10-21 WO PCT/US2021/056106 patent/WO2022087309A1/en not_active Ceased
- 2021-10-21 EP EP21807429.2A patent/EP4232599A1/en active Pending
- 2021-10-21 CA CA3195797A patent/CA3195797A1/en active Pending
- 2021-10-21 JP JP2023524623A patent/JP2023547620A/ja active Pending
-
2024
- 2024-10-21 US US18/922,116 patent/US20250188546A1/en active Pending
Also Published As
| Publication number | Publication date |
|---|---|
| JP2023547620A (ja) | 2023-11-13 |
| US20250188546A1 (en) | 2025-06-12 |
| WO2022087309A1 (en) | 2022-04-28 |
| US12234518B2 (en) | 2025-02-25 |
| US20220154286A1 (en) | 2022-05-19 |
| EP4232599A1 (en) | 2023-08-30 |
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