JP7123975B2 - 無細胞dnaについての体細胞起源または生殖系列起源の識別 - Google Patents

無細胞dnaについての体細胞起源または生殖系列起源の識別 Download PDF

Info

Publication number
JP7123975B2
JP7123975B2 JP2019563118A JP2019563118A JP7123975B2 JP 7123975 B2 JP7123975 B2 JP 7123975B2 JP 2019563118 A JP2019563118 A JP 2019563118A JP 2019563118 A JP2019563118 A JP 2019563118A JP 7123975 B2 JP7123975 B2 JP 7123975B2
Authority
JP
Japan
Prior art keywords
cancer
sequencing
dna
threshold
cfdna
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.)
Active
Application number
JP2019563118A
Other languages
English (en)
Japanese (ja)
Other versions
JP2020521442A (ja
JP2020521442A5 (enExample
Inventor
リチャード ビー. ランマン,
ジェフリー アール. オックスナード,
Original Assignee
ガーダント ヘルス, インコーポレイテッド
デイナ ファーバー キャンサー インスティチュート,インコーポレイテッド
Priority date (The priority date 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 date listed.)
Filing date
Publication date
Application filed by ガーダント ヘルス, インコーポレイテッド, デイナ ファーバー キャンサー インスティチュート,インコーポレイテッド filed Critical ガーダント ヘルス, インコーポレイテッド
Publication of JP2020521442A publication Critical patent/JP2020521442A/ja
Publication of JP2020521442A5 publication Critical patent/JP2020521442A5/ja
Priority to JP2022074644A priority Critical patent/JP7513653B2/ja
Application granted granted Critical
Publication of JP7123975B2 publication Critical patent/JP7123975B2/ja
Priority to JP2024078860A priority patent/JP2024105539A/ja
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

Classifications

    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/10Ploidy or copy number detection
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • GPHYSICS
    • G06COMPUTING OR CALCULATING; COUNTING
    • G06NCOMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00Computing arrangements based on biological models
    • G06N3/12Computing arrangements based on biological models using genetic models
    • G06N3/123DNA computing
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10Sequence alignment; Homology search
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/20Sequence assembly
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20Supervised data analysis
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/106Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers

Landscapes

  • 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)
JP2019563118A 2017-05-16 2018-05-16 無細胞dnaについての体細胞起源または生殖系列起源の識別 Active JP7123975B2 (ja)

Priority Applications (2)

Application Number Priority Date Filing Date Title
JP2022074644A JP7513653B2 (ja) 2017-05-16 2022-04-28 無細胞dnaについての体細胞起源または生殖系列起源の識別
JP2024078860A JP2024105539A (ja) 2017-05-16 2024-05-14 無細胞dnaについての体細胞起源または生殖系列起源の識別

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201762507127P 2017-05-16 2017-05-16
US62/507,127 2017-05-16
PCT/US2018/033038 WO2018213498A1 (en) 2017-05-16 2018-05-16 Identification of somatic or germline origin for cell-free dna

Related Child Applications (1)

Application Number Title Priority Date Filing Date
JP2022074644A Division JP7513653B2 (ja) 2017-05-16 2022-04-28 無細胞dnaについての体細胞起源または生殖系列起源の識別

Publications (3)

Publication Number Publication Date
JP2020521442A JP2020521442A (ja) 2020-07-27
JP2020521442A5 JP2020521442A5 (enExample) 2021-07-26
JP7123975B2 true JP7123975B2 (ja) 2022-08-23

Family

ID=64274641

Family Applications (3)

Application Number Title Priority Date Filing Date
JP2019563118A Active JP7123975B2 (ja) 2017-05-16 2018-05-16 無細胞dnaについての体細胞起源または生殖系列起源の識別
JP2022074644A Active JP7513653B2 (ja) 2017-05-16 2022-04-28 無細胞dnaについての体細胞起源または生殖系列起源の識別
JP2024078860A Pending JP2024105539A (ja) 2017-05-16 2024-05-14 無細胞dnaについての体細胞起源または生殖系列起源の識別

Family Applications After (2)

Application Number Title Priority Date Filing Date
JP2022074644A Active JP7513653B2 (ja) 2017-05-16 2022-04-28 無細胞dnaについての体細胞起源または生殖系列起源の識別
JP2024078860A Pending JP2024105539A (ja) 2017-05-16 2024-05-14 無細胞dnaについての体細胞起源または生殖系列起源の識別

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)

Families Citing this family (21)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015164432A1 (en) 2014-04-21 2015-10-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
JP2015535681A (ja) 2012-09-04 2015-12-17 ガーダント ヘルス, インコーポレイテッド まれな変異およびコピー数多型を検出するためのシステムおよび方法
WO2016109452A1 (en) 2014-12-31 2016-07-07 Guardant Health , Inc. Detection and treatment of disease exhibiting disease cell heterogeneity and systems and methods for communicating test results
WO2016127944A1 (en) 2015-02-10 2016-08-18 The Chinese University Of Hong Kong Detecting mutations for cancer screening and fetal analysis
WO2016149261A1 (en) 2015-03-16 2016-09-22 Personal Genome Diagnostics, Inc. Systems and methods for analyzing nucleic acid

Family Cites Families (11)

* 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
WO2014149134A2 (en) 2013-03-15 2014-09-25 Guardant Health Inc. Systems and methods to detect rare mutations and copy number variation
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
US20160201131A1 (en) * 2014-10-11 2016-07-14 Yan Wang Method for Identifying Drug Resistance Related Mutations
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

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2015535681A (ja) 2012-09-04 2015-12-17 ガーダント ヘルス, インコーポレイテッド まれな変異およびコピー数多型を検出するためのシステムおよび方法
WO2015164432A1 (en) 2014-04-21 2015-10-29 Natera, Inc. Detecting mutations and ploidy in chromosomal segments
WO2016109452A1 (en) 2014-12-31 2016-07-07 Guardant Health , Inc. Detection and treatment of disease exhibiting disease cell heterogeneity and systems and methods for communicating test results
WO2016127944A1 (en) 2015-02-10 2016-08-18 The Chinese University Of Hong Kong Detecting mutations for cancer screening and fetal analysis
WO2016149261A1 (en) 2015-03-16 2016-09-22 Personal Genome Diagnostics, Inc. Systems and methods for analyzing nucleic acid

Also Published As

Publication number Publication date
EP3625341B1 (en) 2024-09-25
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
ES2991960T3 (es) 2024-12-05
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

Similar Documents

Publication Publication Date Title
JP7513653B2 (ja) 無細胞dnaについての体細胞起源または生殖系列起源の識別
US12116640B2 (en) Methods for early detection of cancer
US12435368B2 (en) Methods and systems for detecting genetic variants
US20240290423A1 (en) Methods for non-invasive assessment of genetic alterations
US20210125685A1 (en) Methods and systems for analysis of ctcf binding regions in cell-free dna

Legal Events

Date Code Title Description
A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20200206

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20210514

A621 Written request for application examination

Free format text: JAPANESE INTERMEDIATE CODE: A621

Effective date: 20210514

A977 Report on retrieval

Free format text: JAPANESE INTERMEDIATE CODE: A971007

Effective date: 20220126

A131 Notification of reasons for refusal

Free format text: JAPANESE INTERMEDIATE CODE: A131

Effective date: 20220207

A521 Request for written amendment filed

Free format text: JAPANESE INTERMEDIATE CODE: A523

Effective date: 20220428

TRDD Decision of grant or rejection written
A01 Written decision to grant a patent or to grant a registration (utility model)

Free format text: JAPANESE INTERMEDIATE CODE: A01

Effective date: 20220808

A61 First payment of annual fees (during grant procedure)

Free format text: JAPANESE INTERMEDIATE CODE: A61

Effective date: 20220810

R150 Certificate of patent or registration of utility model

Ref document number: 7123975

Country of ref document: JP

Free format text: JAPANESE INTERMEDIATE CODE: R150

R250 Receipt of annual fees

Free format text: JAPANESE INTERMEDIATE CODE: R250