FI3536807T3 - Kasvaimen metylomin noninvasiivinen määritys plasmasta - Google Patents
Kasvaimen metylomin noninvasiivinen määritys plasmasta Download PDFInfo
- Publication number
- FI3536807T3 FI3536807T3 FIEP19171630.7T FI19171630T FI3536807T3 FI 3536807 T3 FI3536807 T3 FI 3536807T3 FI 19171630 T FI19171630 T FI 19171630T FI 3536807 T3 FI3536807 T3 FI 3536807T3
- Authority
- FI
- Finland
- Prior art keywords
- cell
- free dna
- methylation
- sequencing
- dna molecules
- Prior art date
Links
- 206010028980 Neoplasm Diseases 0.000 title claims 4
- 238000000034 method Methods 0.000 claims 17
- 108020004414 DNA Proteins 0.000 claims 14
- 230000011987 methylation Effects 0.000 claims 14
- 238000007069 methylation reaction Methods 0.000 claims 14
- 238000012163 sequencing technique Methods 0.000 claims 8
- 108091029523 CpG island Proteins 0.000 claims 5
- 102000053602 DNA Human genes 0.000 claims 5
- 108091029430 CpG site Proteins 0.000 claims 4
- 239000000523 sample Substances 0.000 claims 4
- 201000011510 cancer Diseases 0.000 claims 3
- RYVNIFSIEDRLSJ-UHFFFAOYSA-N 5-(hydroxymethyl)cytosine Chemical compound NC=1NC(=O)N=CC=1CO RYVNIFSIEDRLSJ-UHFFFAOYSA-N 0.000 claims 2
- DWAQJAXMDSEUJJ-UHFFFAOYSA-M Sodium bisulfite Chemical compound [Na+].OS([O-])=O DWAQJAXMDSEUJJ-UHFFFAOYSA-M 0.000 claims 2
- 239000012472 biological sample Substances 0.000 claims 2
- 210000004027 cell Anatomy 0.000 claims 2
- 235000010267 sodium hydrogen sulphite Nutrition 0.000 claims 2
- LSNNMFCWUKXFEE-UHFFFAOYSA-M Bisulfite Chemical compound OS([O-])=O LSNNMFCWUKXFEE-UHFFFAOYSA-M 0.000 claims 1
- 238000001369 bisulfite sequencing Methods 0.000 claims 1
- 238000006243 chemical reaction Methods 0.000 claims 1
- 210000000349 chromosome Anatomy 0.000 claims 1
- 238000004590 computer program Methods 0.000 claims 1
- 238000013507 mapping Methods 0.000 claims 1
- 230000001590 oxidative effect Effects 0.000 claims 1
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
- C12Q1/6876—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
- 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
- C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
-
- 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
-
- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
-
- 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
- C12Q2523/00—Reactions characterised by treatment of reaction samples
- C12Q2523/10—Characterised by chemical treatment
- C12Q2523/125—Bisulfite(s)
-
- 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
- C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
- C12Q2535/122—Massive parallel 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
- 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
Landscapes
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Health & Medical Sciences (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Organic Chemistry (AREA)
- Engineering & Computer Science (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Analytical Chemistry (AREA)
- Genetics & Genomics (AREA)
- Immunology (AREA)
- Physics & Mathematics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Biophysics (AREA)
- Molecular Biology (AREA)
- General Health & Medical Sciences (AREA)
- Biotechnology (AREA)
- Biochemistry (AREA)
- General Engineering & Computer Science (AREA)
- Microbiology (AREA)
- Pathology (AREA)
- Hospice & Palliative Care (AREA)
- Oncology (AREA)
- Cell Biology (AREA)
- Bioinformatics & Computational Biology (AREA)
- Evolutionary Biology (AREA)
- Medical Informatics (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Theoretical Computer Science (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Investigating Or Analysing Biological Materials (AREA)
- Apparatus Associated With Microorganisms And Enzymes (AREA)
- Ultra Sonic Daignosis Equipment (AREA)
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201261703512P | 2012-09-20 | 2012-09-20 | |
| US13/842,209 US9732390B2 (en) | 2012-09-20 | 2013-03-15 | Non-invasive determination of methylome of fetus or tumor from plasma |
| US201361830571P | 2013-06-03 | 2013-06-03 |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| FI3536807T3 true FI3536807T3 (fi) | 2024-02-01 |
Family
ID=50340462
Family Applications (2)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| FIEP19171630.7T FI3536807T3 (fi) | 2012-09-20 | 2013-09-20 | Kasvaimen metylomin noninvasiivinen määritys plasmasta |
| FIEP22171427.2T FI4056712T3 (fi) | 2012-09-20 | 2013-09-20 | Kasvaimen metyloomin nonivasiivinen määrittäminen plasmasta |
Family Applications After (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| FIEP22171427.2T FI4056712T3 (fi) | 2012-09-20 | 2013-09-20 | Kasvaimen metyloomin nonivasiivinen määrittäminen plasmasta |
Country Status (28)
| Country | Link |
|---|---|
| EP (6) | EP3536807B1 (enExample) |
| JP (6) | JP6317354B2 (enExample) |
| KR (5) | KR102390711B1 (enExample) |
| CN (2) | CN117757932A (enExample) |
| AU (5) | AU2013317708C1 (enExample) |
| BR (3) | BR112015006183B1 (enExample) |
| CA (2) | CA2884066C (enExample) |
| CY (1) | CY1124139T1 (enExample) |
| DK (4) | DK3536807T3 (enExample) |
| EA (1) | EA201500327A1 (enExample) |
| ES (4) | ES2862726T3 (enExample) |
| FI (2) | FI3536807T3 (enExample) |
| HR (3) | HRP20240210T1 (enExample) |
| HU (3) | HUE053822T2 (enExample) |
| IL (4) | IL299444B2 (enExample) |
| LT (2) | LT3354747T (enExample) |
| MX (1) | MX360034B (enExample) |
| MY (2) | MY187444A (enExample) |
| NZ (2) | NZ717423A (enExample) |
| PH (2) | PH12022552061A1 (enExample) |
| PL (4) | PL3536807T3 (enExample) |
| PT (4) | PT3354747T (enExample) |
| SG (2) | SG11201501927VA (enExample) |
| SI (1) | SI4056712T1 (enExample) |
| SM (1) | SMT202100256T1 (enExample) |
| TW (4) | TWI806621B (enExample) |
| WO (1) | WO2014043763A1 (enExample) |
| ZA (1) | ZA201501772B (enExample) |
Families Citing this family (94)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101153336B (zh) | 2006-09-27 | 2011-09-07 | 香港中文大学 | 检测dna甲基化程度的方法和试剂盒 |
| US9892230B2 (en) | 2012-03-08 | 2018-02-13 | The Chinese University Of Hong Kong | Size-based analysis of fetal or tumor DNA fraction in plasma |
| US9732390B2 (en) | 2012-09-20 | 2017-08-15 | The Chinese University Of Hong Kong | Non-invasive determination of methylome of fetus or tumor from plasma |
| BR112015006183B1 (pt) | 2012-09-20 | 2022-04-26 | The Chinese University Of Hong Kong | Métodos para analisar uma amostra biológica de um organismo, para determinar um primeiro perfil de metilação de uma amostra biológica de um organismo, para detecção de uma anormalidade cromossômica de uma amostra biológica de um organismo e para estimar um nível de metilação do dna em uma amostra biológica de um organismo, produto de computador, e, kit para análise de dna fetal |
| US10706957B2 (en) | 2012-09-20 | 2020-07-07 | The Chinese University Of Hong Kong | Non-invasive determination of methylome of tumor from plasma |
| US20130309666A1 (en) | 2013-01-25 | 2013-11-21 | Sequenom, Inc. | Methods and processes for non-invasive assessment of genetic variations |
| WO2015013885A1 (zh) * | 2013-07-30 | 2015-02-05 | 深圳华大基因科技有限公司 | 确定核酸混合物中核酸组成的方法 |
| US10174375B2 (en) | 2013-09-20 | 2019-01-08 | The Chinese University Of Hong Kong | Sequencing analysis of circulating DNA to detect and monitor autoimmune diseases |
| WO2015126840A1 (en) * | 2014-02-18 | 2015-08-27 | Bionano Genomics, Inc. | Improved methods of determining nucleic acid structural information |
| EP3561075A1 (en) * | 2014-04-21 | 2019-10-30 | Natera, Inc. | Detecting mutations in tumour biopsies and cell-free samples |
| US12492429B2 (en) | 2014-04-21 | 2025-12-09 | Natera, Inc. | Detecting mutations and ploidy in chromosomal segments |
| EP2942400A1 (en) | 2014-05-09 | 2015-11-11 | Lifecodexx AG | Multiplex detection of DNA that originates from a specific cell-type |
| CA2985134A1 (en) | 2014-05-09 | 2015-11-12 | Sebastian Gromminger | Detection of dna that originates from a specific cell-type and related methods |
| TWI727156B (zh) * | 2014-07-18 | 2021-05-11 | 香港中文大學 | Ｄｎａ混合物中之組織甲基化模式分析 |
| WO2016010401A1 (ko) * | 2014-07-18 | 2016-01-21 | 에스케이텔레콘 주식회사 | 산모의 혈청 dna를 이용한 태아의 단일유전자 유전변이의 예측방법 |
| 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 |
| EP4574996B1 (en) | 2014-12-31 | 2025-11-05 | Guardant Health, Inc. | Detection and treatment of disease exhibiting disease cell heterogeneity and systems and methods for communicating test results |
| 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 |
| ES2908347T3 (es) | 2015-02-10 | 2022-04-28 | Univ Hong Kong Chinese | Detección de mutaciones para cribado de cáncer y análisis fetal |
| WO2017012544A1 (en) * | 2015-07-20 | 2017-01-26 | The Chinese University Of Hong Kong | Methylation pattern analysis of haplotypes in tissues in dna mixture |
| EP4279612B1 (en) * | 2015-07-23 | 2025-07-02 | The Chinese University of Hong Kong | Analysis of fragmentation patterns of cell-free dna |
| CA2995422A1 (en) | 2015-08-12 | 2017-02-16 | The Chinese University Of Hong Kong | Single-molecule sequencing of plasma dna |
| CN108026576B (zh) | 2015-09-22 | 2022-06-28 | 香港中文大学 | 通过母亲血浆dna的浅深度测序准确定量胎儿dna分数 |
| US10260088B2 (en) * | 2015-10-30 | 2019-04-16 | New England Biolabs, Inc. | Compositions and methods for analyzing modified nucleotides |
| CN108368548A (zh) * | 2015-11-09 | 2018-08-03 | 普罗格尼迪公司 | 用于确定dna分子的来源的方法 |
| EP3168309B8 (en) | 2015-11-10 | 2020-06-03 | Eurofins LifeCodexx GmbH | Detection of foetal chromosomal aneuploidies using dna regions that are differentially methylated between the foetus and the pregnant female |
| AU2016370835B2 (en) | 2015-12-17 | 2020-02-13 | Illumina, Inc. | Distinguishing methylation levels in complex biological samples |
| CN116640847A (zh) * | 2016-02-02 | 2023-08-25 | 夸登特健康公司 | 癌症进化检测和诊断 |
| US11514289B1 (en) | 2016-03-09 | 2022-11-29 | Freenome Holdings, Inc. | Generating machine learning models using genetic data |
| EP4425178A3 (en) | 2016-05-03 | 2024-12-18 | University Health Network | Methods of capturing cell-free methylated dna and uses of same |
| WO2017201606A1 (en) * | 2016-05-04 | 2017-11-30 | Queen's University At Kingston | Cell-free detection of methylated tumour dna |
| SG11201810544WA (en) | 2016-05-30 | 2018-12-28 | Univ Hong Kong Chinese | Detecting hematological disorders using cell-free dna in blood |
| WO2017218908A2 (en) * | 2016-06-16 | 2017-12-21 | The Johns Hopkins University | Methods and system for epigenetic analysis |
| US11999998B2 (en) | 2016-08-24 | 2024-06-04 | Center For Excellence In Molecular Cell Science, Chinese Academy Of Sciences | Modification of 5-methylcytosine catalyzed by Cmd1 enzyme and application thereof |
| EP3529377B1 (en) | 2016-10-19 | 2023-04-05 | The Chinese University Of Hong Kong | Gestational age assessment by methylation and size profiling of maternal plasma dna |
| WO2018081130A1 (en) | 2016-10-24 | 2018-05-03 | The Chinese University Of Hong Kong | Methods and systems for tumor detection |
| JP2020503003A (ja) * | 2016-11-30 | 2020-01-30 | ザ チャイニーズ ユニバーシティ オブ ホンコン | 尿および他のサンプルにおける無細胞ｄｎａの分析 |
| WO2018112100A2 (en) * | 2016-12-13 | 2018-06-21 | Bellwether Bio, Inc. | Determining a physiological condition in an individual by analyzing cell-free dna fragment endpoints in a biological sample |
| BR112019014208A2 (pt) * | 2017-01-11 | 2020-03-17 | Quest Diagnostics Investments Llc | Métodos para detectar diagnóstico falso-positivo de aneuploidia cromossômica em um feto e para detectar diagnóstico aneuploidiadiagnóstico de aneuploidia cromossômica falso-positiva em um feto. |
| PL3575407T3 (pl) * | 2017-01-24 | 2024-07-29 | Bgi Genomics Co., Ltd. | Sposób oznaczania udziału frakcji bezkomórkowych kwasów nukleinowych z wcześniej określonego źródła w próbce biologicznej |
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| CN107247873B (zh) * | 2017-03-29 | 2020-04-14 | 电子科技大学 | 一种差异甲基化位点识别方法 |
| CN111417731A (zh) * | 2017-05-12 | 2020-07-14 | 哈佛学院校长同事会 | 通用早期癌症诊断 |
| US12031184B2 (en) | 2017-07-12 | 2024-07-09 | University Health Network | Cancer detection and classification using methylome analysis |
| US12227737B2 (en) | 2017-07-12 | 2025-02-18 | University Health Network | Cancer detection and classification using methylome analysis |
| CN118782138A (zh) * | 2017-07-12 | 2024-10-15 | 安德股份有限公司 | 模式识别系统 |
| CN111051536A (zh) | 2017-07-26 | 2020-04-21 | 香港中文大学 | 利用不含细胞的病毒核酸改善癌症筛选 |
| WO2019055819A1 (en) | 2017-09-14 | 2019-03-21 | Grail, Inc. | METHODS FOR PREPARING A SEQUENCING LIBRARY FROM SINGLE STRANDED DNA |
| US11851650B2 (en) | 2017-09-28 | 2023-12-26 | Grail, Llc | Enrichment of short nucleic acid fragments in sequencing library preparation |
| US11168356B2 (en) * | 2017-11-02 | 2021-11-09 | The Chinese University Of Hong Kong | Using nucleic acid size range for noninvasive cancer detection |
| TW202434742A (zh) | 2018-03-13 | 2024-09-01 | 美商格瑞爾有限責任公司 | 異常片段偵測及分類 |
| KR20210023804A (ko) * | 2018-03-15 | 2021-03-04 | 그레일, 인코포레이티드. | 조직 특이적 메틸화 마커 |
| CN119753091A (zh) | 2018-04-02 | 2025-04-04 | 格里尔公司 | 用于扩增与癌症相关联的cfDNA分子的化验板 |
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