CN118711654A - 无细胞dna的体细胞来源或种系来源的鉴定 - Google Patents

无细胞dna的体细胞来源或种系来源的鉴定 Download PDF

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Publication number
CN118711654A
CN118711654A CN202410873100.9A CN202410873100A CN118711654A CN 118711654 A CN118711654 A CN 118711654A CN 202410873100 A CN202410873100 A CN 202410873100A CN 118711654 A CN118711654 A CN 118711654A
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Prior art keywords
cancer
cfdna
genomic
sequencing
threshold
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CN202410873100.9A
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English (en)
Chinese (zh)
Inventor
理查德·B·兰曼
杰弗里·R·奥克斯纳德
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Dana Farber Cancer Institute Inc
Guardant Health Inc
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Dana Farber Cancer Institute Inc
Guardant Health Inc
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Publication of CN118711654A publication Critical patent/CN118711654A/zh
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    • 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
    • G16B20/10—Ploidy or copy number 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
    • C12Q1/6869—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
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/12—Computing arrangements based on biological models using genetic models
    • G06N3/123—DNA computing
    • 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
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20—Sequence assembly
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • 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
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • 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

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  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • General Engineering & Computer Science (AREA)
  • Data Mining & Analysis (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Immunology (AREA)
  • Mathematical Physics (AREA)
  • Microbiology (AREA)
  • Computational Linguistics (AREA)
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  • General Physics & Mathematics (AREA)
  • Biomedical Technology (AREA)
  • Biochemistry (AREA)
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  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
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CN202410873100.9A 2017-05-16 2018-05-16 无细胞dna的体细胞来源或种系来源的鉴定 Pending CN118711654A (zh)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US201762507127P 2017-05-16 2017-05-16
US62/507,127 2017-05-16
CN201880047621.1A CN110914450B (zh) 2017-05-16 2018-05-16 无细胞dna的体细胞来源或种系来源的鉴定
PCT/US2018/033038 WO2018213498A1 (en) 2017-05-16 2018-05-16 Identification of somatic or germline origin for cell-free dna

Related Parent Applications (1)

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CN201880047621.1A Division CN110914450B (zh) 2017-05-16 2018-05-16 无细胞dna的体细胞来源或种系来源的鉴定

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CN118711654A true CN118711654A (zh) 2024-09-27

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CN202410873100.9A Pending CN118711654A (zh) 2017-05-16 2018-05-16 无细胞dna的体细胞来源或种系来源的鉴定

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US (2) US20200202224A1 (enExample)
EP (2) EP3625341B1 (enExample)
JP (3) JP7123975B2 (enExample)
CN (2) CN110914450B (enExample)
ES (1) ES2991960T3 (enExample)
WO (1) WO2018213498A1 (enExample)

Families Citing this family (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105190656B (zh) 2013-01-17 2018-01-16 佩索纳里斯公司 用于遗传分析的方法和系统
ES3022582T3 (en) 2013-05-10 2025-05-28 Found Medicine Inc Analysis of genetic variants
EP3443066B1 (en) * 2016-04-14 2024-10-02 Guardant Health, Inc. Methods for early detection of cancer
US20210125683A1 (en) * 2017-09-15 2021-04-29 The Regents Of The University Of California Detecting somatic single nucleotide variants from cell-free nucleic acid with application to minimal residual disease monitoring
US11814750B2 (en) 2018-05-31 2023-11-14 Personalis, Inc. Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples
US10801064B2 (en) 2018-05-31 2020-10-13 Personalis, Inc. Compositions, methods and systems for processing or analyzing multi-species nucleic acid samples
CN114945987A (zh) 2019-11-05 2022-08-26 佩索纳里斯公司 从单一样品预估肿瘤纯度
GB2611640A (en) * 2020-04-17 2023-04-12 Los Angeles Childrens Hospital Watermarking of genomic sequencing data
EP4162073A4 (en) * 2020-06-05 2024-06-19 Foundation Medicine, Inc. METHODS AND SYSTEMS FOR DISTINGUISHING SOMATIC GENOME SEQUENCES FROM GERMLINE GENOME SEQUENCES
CN115497556A (zh) * 2021-06-18 2022-12-20 广州燃石医学检验所有限公司 一种用于区分体细胞突变和种系突变的方法
CN114242172B (zh) * 2021-07-12 2025-04-25 广州燃石医学检验所有限公司 基于血液测序的肿瘤内异质性的评估方法及其用于预测免疫疗法的应答
CN113278706B (zh) * 2021-07-23 2021-11-12 广州燃石医学检验所有限公司 一种用于区分体细胞突变和种系突变的方法
CN113462768B (zh) * 2021-07-29 2023-05-30 中国医学科学院整形外科医院 一种利用ddPCR检测小耳畸形患者ECR区域的拷贝数的引物及试剂盒
WO2023059654A1 (en) 2021-10-05 2023-04-13 Personalis, Inc. Customized assays for personalized cancer monitoring
CN114613432B (zh) * 2021-12-14 2024-10-22 中国科学院动物研究所 一种基于基因组稀有突变负荷变化和基因功能关联发现分子标志物的方法及系统
US20230323449A1 (en) * 2021-12-17 2023-10-12 Twist Bioscience Corporation Compositions and methods for detection of variants
US20230215513A1 (en) * 2021-12-31 2023-07-06 Sophia Genetics S.A. Methods and systems for detecting tumor mutational burden
KR102544002B1 (ko) * 2022-03-10 2023-06-16 주식회사 아이엠비디엑스 체세포 변이 및 생식세포 변이를 구별하는 방법
CN114898802B (zh) * 2022-07-14 2022-09-30 臻和(北京)生物科技有限公司 基于血浆游离dna甲基化测序数据的末端序列频率分布特征确定方法、评价方法及装置
US20240071628A1 (en) * 2022-08-24 2024-02-29 Guardant Health, Inc. Database for therapeutic interventions
US20250140343A1 (en) * 2023-10-30 2025-05-01 Myriad Women's Health, Inc. Methods for improving minimal residual disease assays

Family Cites Families (16)

* Cited by examiner, † Cited by third party
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
US8835358B2 (en) 2009-12-15 2014-09-16 Cellular Research, Inc. Digital counting of individual molecules by stochastic attachment of diverse labels
US10388403B2 (en) * 2010-01-19 2019-08-20 Verinata Health, Inc. Analyzing copy number variation in the detection of cancer
US10196681B2 (en) * 2011-10-06 2019-02-05 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US11261494B2 (en) * 2012-06-21 2022-03-01 The Chinese University Of Hong Kong Method of measuring a fractional concentration of tumor DNA
EP4036247B1 (en) * 2012-09-04 2024-04-10 Guardant Health, Inc. Methods to detect rare mutations and copy number variation
EP3421613B1 (en) * 2013-03-15 2020-08-19 The Board of Trustees of the Leland Stanford Junior University Identification and use of circulating nucleic acid tumor markers
GB2528205B (en) 2013-03-15 2020-06-03 Guardant Health Inc Systems and methods to detect rare mutations and copy number variation
WO2015164432A1 (en) * 2014-04-21 2015-10-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
US20160201131A1 (en) * 2014-10-11 2016-07-14 Yan Wang Method for Identifying Drug Resistance Related Mutations
GB2552267B (en) * 2014-12-31 2020-06-10 Guardant Health Inc Detection and treatment of disease exhibiting disease cell heterogeneity and systems and methods for communicating test results
CA2976303A1 (en) * 2015-02-10 2016-08-18 The Chinese University Of Hong Kong Detecting mutations for cancer screening and fetal analysis
CA2980078C (en) * 2015-03-16 2024-03-12 Personal Genome Diagnostics Inc. Systems and methods for analyzing nucleic acid
CN108138209B (zh) * 2015-08-12 2022-06-10 环基因治疗诊断有限责任公司 通过原位扩增制备细胞游离核酸分子的方法
US20170058332A1 (en) * 2015-09-02 2017-03-02 Guardant Health, Inc. Identification of somatic mutations versus germline variants for cell-free dna variant calling applications

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Publication number Publication date
WO2018213498A1 (en) 2018-11-22
ES2991960T3 (es) 2024-12-05
EP4461826A3 (en) 2025-05-14
JP2022110013A (ja) 2022-07-28
EP3625341B1 (en) 2024-09-25
JP7513653B2 (ja) 2024-07-09
CN110914450A (zh) 2020-03-24
US20200202224A1 (en) 2020-06-25
EP4461826A2 (en) 2024-11-13
EP3625341A4 (en) 2021-05-19
CN110914450B (zh) 2024-07-02
EP3625341C0 (en) 2024-09-25
JP7123975B2 (ja) 2022-08-23
EP3625341A1 (en) 2020-03-25
US20250292103A1 (en) 2025-09-18
JP2020521442A (ja) 2020-07-27
JP2024105539A (ja) 2024-08-06

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