ES2991960T3 - Identificación del origen somático o germinal del ADN libre de células - Google Patents

Identificación del origen somático o germinal del ADN libre de células Download PDF

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Publication number
ES2991960T3
ES2991960T3 ES18802961T ES18802961T ES2991960T3 ES 2991960 T3 ES2991960 T3 ES 2991960T3 ES 18802961 T ES18802961 T ES 18802961T ES 18802961 T ES18802961 T ES 18802961T ES 2991960 T3 ES2991960 T3 ES 2991960T3
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Prior art keywords
cancer
dna
sequencing
panel
cfdna
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ES18802961T
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English (en)
Spanish (es)
Inventor
Richard B Lanman
Geoffrey R Oxnard
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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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    • 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)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (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)
  • General Engineering & Computer Science (AREA)
  • Data Mining & Analysis (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Software Systems (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Immunology (AREA)
  • Computational Linguistics (AREA)
  • General Physics & Mathematics (AREA)
  • Biomedical Technology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Mathematical Physics (AREA)
  • Computing Systems (AREA)
  • Pathology (AREA)
  • Bioethics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
ES18802961T 2017-05-16 2018-05-16 Identificación del origen somático o germinal del ADN libre de células Active ES2991960T3 (es)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762507127P 2017-05-16 2017-05-16
PCT/US2018/033038 WO2018213498A1 (en) 2017-05-16 2018-05-16 Identification of somatic or germline origin for cell-free dna

Publications (1)

Publication Number Publication Date
ES2991960T3 true ES2991960T3 (es) 2024-12-05

Family

ID=64274641

Family Applications (1)

Application Number Title Priority Date Filing Date
ES18802961T Active ES2991960T3 (es) 2017-05-16 2018-05-16 Identificación del origen somático o germinal del ADN libre de células

Country Status (6)

Country Link
US (2) US20200202224A1 (enExample)
EP (2) EP4461826A3 (enExample)
JP (3) JP7123975B2 (enExample)
CN (2) CN110914450B (enExample)
ES (1) ES2991960T3 (enExample)
WO (1) WO2018213498A1 (enExample)

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EP2946345B1 (en) 2013-01-17 2024-04-03 Personalis, Inc. Methods and systems for genetic analysis
EP4524972A3 (en) 2013-05-10 2025-06-18 Foundation Medicine, Inc. Analysis of genetic variants
EP4488686A3 (en) * 2016-04-14 2025-04-30 Guardant Health, Inc. Methods for early detection of cancer
EP3682035B1 (en) * 2017-09-15 2025-02-05 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
EP4055610A4 (en) 2019-11-05 2023-11-29 Personalis, Inc. ESTIMATION OF TUMOR PURITY FROM SINGLE SAMPLES
US20240004969A1 (en) * 2020-04-17 2024-01-04 Children's Hospital Los Angeles Watermarking of genomic sequencing data
JP2023529838A (ja) * 2020-06-05 2023-07-12 ファウンデーション・メディシン・インコーポレイテッド 生殖系列ゲノム配列から体細胞ゲノム配列を区別するための方法及びシステム
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
WO2023284260A1 (zh) * 2021-07-12 2023-01-19 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
EP4413580A4 (en) 2021-10-05 2025-08-13 Personalis Inc PERSONALIZED TESTS 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

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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
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
WO2014149134A2 (en) 2013-03-15 2014-09-25 Guardant Health Inc. Systems and methods to detect rare mutations and copy number variation
KR102393608B1 (ko) 2012-09-04 2022-05-03 가던트 헬쓰, 인크. 희귀 돌연변이 및 카피수 변이를 검출하기 위한 시스템 및 방법
EP4253558B1 (en) * 2013-03-15 2025-07-02 The Board of Trustees of the Leland Stanford Junior University Identification and use of circulating nucleic acid tumor markers
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
ES2923602T3 (es) * 2014-12-31 2022-09-28 Guardant Health Inc Detección y tratamiento de enfermedades que muestran heterogeneidad celular de enfermedad y sistemas y métodos para comunicar los resultados de las pruebas
EP4012715B1 (en) * 2015-02-10 2025-09-24 The Chinese University Of Hong Kong Detecting mutations for cancer screening and fetal analysis
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EP3334834B1 (en) * 2015-08-12 2020-05-13 Circulogene Theranostics, LLC Method of preparing cell free nucleic acid molecules by in situ amplification
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

Also Published As

Publication number Publication date
EP3625341B1 (en) 2024-09-25
JP7123975B2 (ja) 2022-08-23
CN110914450B (zh) 2024-07-02
EP4461826A3 (en) 2025-05-14
JP7513653B2 (ja) 2024-07-09
JP2020521442A (ja) 2020-07-27
EP3625341A4 (en) 2021-05-19
JP2022110013A (ja) 2022-07-28
WO2018213498A1 (en) 2018-11-22
US20200202224A1 (en) 2020-06-25
EP3625341C0 (en) 2024-09-25
EP3625341A1 (en) 2020-03-25
US20250292103A1 (en) 2025-09-18
CN110914450A (zh) 2020-03-24
EP4461826A2 (en) 2024-11-13
JP2024105539A (ja) 2024-08-06
CN118711654A (zh) 2024-09-27

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