CA3151538A1 - Compositions and methods for analyzing cell-free dna in methylation partitioning assays - Google Patents
Compositions and methods for analyzing cell-free dna in methylation partitioning assays Download PDFInfo
- Publication number
- CA3151538A1 CA3151538A1 CA3151538A CA3151538A CA3151538A1 CA 3151538 A1 CA3151538 A1 CA 3151538A1 CA 3151538 A CA3151538 A CA 3151538A CA 3151538 A CA3151538 A CA 3151538A CA 3151538 A1 CA3151538 A1 CA 3151538A1
- Authority
- CA
- Canada
- Prior art keywords
- nucleobase
- dna
- subsample
- sequence
- target region
- 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
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
-
- 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
- C12Q1/6876—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
- 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
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Immunology (AREA)
- Analytical Chemistry (AREA)
- Genetics & Genomics (AREA)
- Physics & Mathematics (AREA)
- Biophysics (AREA)
- Biotechnology (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Biochemistry (AREA)
- Bioinformatics & Cheminformatics (AREA)
- General Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Pathology (AREA)
- Hospice & Palliative Care (AREA)
- Oncology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201962908569P | 2019-09-30 | 2019-09-30 | |
| US62/908,569 | 2019-09-30 | ||
| PCT/US2020/053610 WO2021067484A1 (en) | 2019-09-30 | 2020-09-30 | Compositions and methods for analyzing cell-free dna in methylation partitioning assays |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CA3151538A1 true CA3151538A1 (en) | 2021-04-08 |
Family
ID=72896163
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CA3151538A Pending CA3151538A1 (en) | 2019-09-30 | 2020-09-30 | Compositions and methods for analyzing cell-free dna in methylation partitioning assays |
Country Status (6)
| Country | Link |
|---|---|
| US (2) | US11891653B2 (https=) |
| EP (1) | EP4041919A1 (https=) |
| JP (2) | JP7717057B2 (https=) |
| CN (1) | CN114616343A (https=) |
| CA (1) | CA3151538A1 (https=) |
| WO (1) | WO2021067484A1 (https=) |
Families Citing this family (13)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| EP4567131A3 (en) * | 2019-01-31 | 2025-09-03 | Guardant Health, Inc. | Compositions and methods for isolating cell-free dna |
| GB202012433D0 (en) * | 2020-08-10 | 2020-09-23 | Univ Manchester | Nanoparticle-enabled analysis of cell-free nucleic acid in complex biological fluids |
| US12234518B2 (en) | 2020-10-23 | 2025-02-25 | Guardant Health, Inc. | Compositions and methods for analyzing DNA using partitioning and base conversion |
| JP2024523401A (ja) * | 2021-06-21 | 2024-06-28 | ガーダント ヘルス， インコーポレイテッド | コピー数情報に基づく組織起源分析のための方法および組成物 |
| WO2023086967A1 (en) * | 2021-11-12 | 2023-05-19 | Guardant Health, Inc. | Method of analysis of methylated dna-binding proteins |
| EP4453241A1 (en) * | 2021-12-21 | 2024-10-30 | Guardant Health, Inc. | Methods and systems for combinatorial chromatin-ip sequencing |
| EP4453240A1 (en) * | 2021-12-23 | 2024-10-30 | Guardant Health, Inc. | Compositions and methods for detection of metastasis |
| EP4634403A1 (en) * | 2022-12-16 | 2025-10-22 | Illumina, Inc. | Boranes on solid supports |
| AU2023409008A1 (en) * | 2022-12-21 | 2025-06-26 | Guardant Health, Inc. | Detecting homologous recombination deficiences based on methylation status of cell-free nucleic acid molecules |
| JP2025542261A (ja) * | 2022-12-22 | 2025-12-25 | ガーダント ヘルス， インコーポレイテッド | 統合された対象および全ゲノム体細胞およびｄｎａメチル化シーケンシングワークフロー |
| WO2025038399A1 (en) * | 2023-08-11 | 2025-02-20 | Guardant Health, Inc. | Methylated enrichment methods for single-molecule genetic and epigenetic sequencing |
| WO2025155895A1 (en) * | 2024-01-19 | 2025-07-24 | Guardant Health, Inc. | Nucleic acid modification profiling method |
| WO2026015607A1 (en) * | 2024-07-09 | 2026-01-15 | Guardant Health, Inc. | Methods for partitioning hyper-, hypo-, and non-methylated dna |
Family Cites Families (47)
| 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 |
| 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 |
| EP1817430B1 (en) | 2004-11-29 | 2009-09-16 | Klinikum der Universität Regensburg | Means and methods for detecting methylated dna |
| 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 |
| 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 |
| WO2010037001A2 (en) | 2008-09-26 | 2010-04-01 | Immune Disease Institute, Inc. | Selective oxidation of 5-methylcytosine by tet-family proteins |
| 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 |
| US10612088B2 (en) | 2013-03-14 | 2020-04-07 | The Broad Institute, Inc. | Massively multiplexed RNA sequencing |
| 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 |
| 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 |
| EP3191628B1 (en) | 2014-09-12 | 2022-05-25 | The Board of Trustees of the Leland Stanford Junior University | Identification and use of circulating nucleic acids |
| US10364467B2 (en) | 2015-01-13 | 2019-07-30 | The Chinese University Of Hong Kong | Using size and number aberrations in plasma DNA for detecting cancer |
| US9984201B2 (en) | 2015-01-18 | 2018-05-29 | Youhealth Biotech, Limited | Method and system for determining cancer status |
| CA2978616A1 (en) * | 2015-03-16 | 2016-09-22 | Cedars-Sinai Medical Center | Methods of treating inflammatory bowel disease with ifn-gamma therapy |
| US11384382B2 (en) | 2016-04-14 | 2022-07-12 | Guardant Health, Inc. | Methods of attaching adapters to sample nucleic acids |
| EP4488686A3 (en) * | 2016-04-14 | 2025-04-30 | Guardant Health, Inc. | Methods for early detection of cancer |
| US11702702B2 (en) | 2016-04-15 | 2023-07-18 | Predicine, Inc. | Systems and methods for detecting genetic alterations |
| JP2019515674A (ja) | 2016-04-19 | 2019-06-13 | プレジデント アンド フェローズ オブ ハーバード カレッジ | 遺伝的解析および他の適用のための固定化ベースのシステムおよび方法 |
| CN109415763A (zh) | 2016-05-03 | 2019-03-01 | 大学健康网络 | 捕获无细胞的甲基化dna的方法及其用途 |
| 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 |
| CN116445593A (zh) * | 2016-08-10 | 2023-07-18 | 格里尔公司 | 测定一生物样品的一甲基化图谱的方法 |
| US9850523B1 (en) | 2016-09-30 | 2017-12-26 | Guardant Health, Inc. | Methods for multi-resolution analysis of cell-free nucleic acids |
| CA3046007A1 (en) | 2016-12-22 | 2018-06-28 | Guardant Health, Inc. | Methods and systems for analyzing nucleic acid molecules |
| EP3366780B1 (en) * | 2017-02-23 | 2020-05-06 | Siemens Healthcare GmbH | Single-molecule sequence and high sensitivity methylation analysis for tissue-specific analysis |
| EP4134444B1 (en) * | 2017-03-23 | 2024-10-02 | University of Washington | Methods for targeted nucleic acid sequence enrichment with applications to error corrected nucleic acid sequencing |
| ES2868074T3 (es) * | 2017-04-14 | 2021-10-21 | Guardant Health Inc | Métodos para unir adaptadores a ácidos nucleicos de muestra |
| JP2020537487A (ja) | 2017-07-12 | 2020-12-24 | ユニバーシティー ヘルス ネットワーク | メチローム解析を用いる癌の検出及び分類 |
| EP4567131A3 (en) | 2019-01-31 | 2025-09-03 | Guardant Health, Inc. | Compositions and methods for isolating cell-free dna |
| EP4041888A4 (en) | 2019-10-11 | 2023-11-01 | Guardant Health, Inc. | USE OF CELLULAR BACTERIAL NUCLEIC ACIDS FOR CANCER DETECTION |
-
2020
- 2020-09-30 US US17/039,642 patent/US11891653B2/en active Active
- 2020-09-30 JP JP2022519473A patent/JP7717057B2/ja active Active
- 2020-09-30 WO PCT/US2020/053610 patent/WO2021067484A1/en not_active Ceased
- 2020-09-30 EP EP20792882.1A patent/EP4041919A1/en active Pending
- 2020-09-30 CN CN202080076649.5A patent/CN114616343A/zh active Pending
- 2020-09-30 CA CA3151538A patent/CA3151538A1/en active Pending
-
2024
- 2024-02-05 US US18/433,345 patent/US20240229112A1/en active Pending
-
2025
- 2025-07-22 JP JP2025122521A patent/JP2025148581A/ja active Pending
Also Published As
| Publication number | Publication date |
|---|---|
| US20210115502A1 (en) | 2021-04-22 |
| JP2022550131A (ja) | 2022-11-30 |
| EP4041919A1 (en) | 2022-08-17 |
| JP2025148581A (ja) | 2025-10-07 |
| JP7717057B2 (ja) | 2025-08-01 |
| CN114616343A (zh) | 2022-06-10 |
| WO2021067484A1 (en) | 2021-04-08 |
| US20240229112A1 (en) | 2024-07-11 |
| US11891653B2 (en) | 2024-02-06 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| US20240229112A1 (en) | Compositions and methods for analyzing cell-free dna in methylation partitioning assays | |
| US20230323474A1 (en) | Compositions and methods for isolating cell-free dna | |
| US11946106B2 (en) | Methods and systems to improve the signal to noise ratio of DNA methylation partitioning assays | |
| US20240150844A1 (en) | Compositions and methods for enriching methylated polynucleotides | |
| US12234518B2 (en) | Compositions and methods for analyzing DNA using partitioning and base conversion | |
| US20240167099A1 (en) | Detection of epigenetic status using sequence-specific degradation | |
| US20240229113A1 (en) | Methods and compositions for detecting nucleic acid variants | |
| US20250101494A1 (en) | Methods for analyzing cytosine methylation and hydroxymethylation | |
| US20240093292A1 (en) | Quality control method |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| EEER | Examination request |
Effective date: 20220929 |
|
| MFA | Maintenance fee for application paid |
Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 4TH ANNIV.) - STANDARD Year of fee payment: 4 |
|
| U00 | Fee paid |
Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED Effective date: 20240920 |
|
| U11 | Full renewal or maintenance fee paid |
Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT DETERMINED COMPLIANT Effective date: 20240920 Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL Effective date: 20240920 |
|
| D15 | Examination report completed |
Free format text: ST27 STATUS EVENT CODE: A-2-2-D10-D15-D126 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: EXAMINER'S REPORT Effective date: 20250318 |
|
| P11 | Amendment of application requested |
Free format text: ST27 STATUS EVENT CODE: A-2-2-P10-P11-P100 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: AMENDMENT RECEIVED - RESPONSE TO EXAMINER'S REQUISITION Effective date: 20250718 |
|
| P11 | Amendment of application requested |
Free format text: ST27 STATUS EVENT CODE: A-2-2-P10-P11-P102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: AMENDMENT DETERMINED COMPLIANT Effective date: 20250721 |
|
| P13 | Application amended |
Free format text: ST27 STATUS EVENT CODE: A-2-2-P10-P13-X000 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: APPLICATION AMENDED Effective date: 20250721 |
|
| W00 | Other event occurred |
Free format text: ST27 STATUS EVENT CODE: A-2-2-W10-W00-W111 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: CORRESPONDENT DETERMINED COMPLIANT Effective date: 20250721 |
|
| MFA | Maintenance fee for application paid |
Free format text: FEE DESCRIPTION TEXT: MF (APPLICATION, 5TH ANNIV.) - STANDARD Year of fee payment: 5 |
|
| U00 | Fee paid |
Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U00-U101 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE REQUEST RECEIVED Effective date: 20250926 |
|
| U11 | Full renewal or maintenance fee paid |
Free format text: ST27 STATUS EVENT CODE: A-2-2-U10-U11-U102 (AS PROVIDED BY THE NATIONAL OFFICE); EVENT TEXT: MAINTENANCE FEE PAYMENT PAID IN FULL Effective date: 20250926 |