AU2017292854B2 - Methods for fragmentome profiling of cell-free nucleic acids - Google Patents

Methods for fragmentome profiling of cell-free nucleic acids Download PDF

Info

Publication number
AU2017292854B2
AU2017292854B2 AU2017292854A AU2017292854A AU2017292854B2 AU 2017292854 B2 AU2017292854 B2 AU 2017292854B2 AU 2017292854 A AU2017292854 A AU 2017292854A AU 2017292854 A AU2017292854 A AU 2017292854A AU 2017292854 B2 AU2017292854 B2 AU 2017292854B2
Authority
AU
Australia
Prior art keywords
dna
cell
genome
parametric
fragments
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
AU2017292854A
Other languages
English (en)
Other versions
AU2017292854A1 (en
Inventor
Diana ABDUEVA
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Guardant Health Inc
Original Assignee
Guardant Health Inc
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 Guardant Health Inc filed Critical Guardant Health Inc
Publication of AU2017292854A1 publication Critical patent/AU2017292854A1/en
Application granted granted Critical
Publication of AU2017292854B2 publication Critical patent/AU2017292854B2/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Classifications

    • 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
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Computation (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Organic Chemistry (AREA)
  • Pathology (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Hospice & Palliative Care (AREA)
  • Biochemistry (AREA)
  • Oncology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
AU2017292854A 2016-07-06 2017-07-06 Methods for fragmentome profiling of cell-free nucleic acids Active AU2017292854B2 (en)

Applications Claiming Priority (9)

Application Number Priority Date Filing Date Title
US201662359151P 2016-07-06 2016-07-06
US62/359,151 2016-07-06
US201662420167P 2016-11-10 2016-11-10
US62/420,167 2016-11-10
US201662437172P 2016-12-21 2016-12-21
US62/437,172 2016-12-21
US201762489399P 2017-04-24 2017-04-24
US62/489,399 2017-04-24
PCT/US2017/040986 WO2018009723A1 (en) 2016-07-06 2017-07-06 Methods for fragmentome profiling of cell-free nucleic acids

Publications (2)

Publication Number Publication Date
AU2017292854A1 AU2017292854A1 (en) 2019-01-24
AU2017292854B2 true AU2017292854B2 (en) 2023-08-17

Family

ID=60913158

Family Applications (1)

Application Number Title Priority Date Filing Date
AU2017292854A Active AU2017292854B2 (en) 2016-07-06 2017-07-06 Methods for fragmentome profiling of cell-free nucleic acids

Country Status (11)

Country Link
EP (2) EP3481966B1 (enExample)
JP (3) JP7448310B2 (enExample)
KR (1) KR102610098B1 (enExample)
CN (1) CN109689891B (enExample)
AU (1) AU2017292854B2 (enExample)
BR (1) BR112019000296A2 (enExample)
CA (1) CA3030038A1 (enExample)
ES (1) ES2967443T3 (enExample)
MX (1) MX2019000037A (enExample)
SG (1) SG11201811556RA (enExample)
WO (1) WO2018009723A1 (enExample)

Families Citing this family (119)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11111543B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US11111544B2 (en) 2005-07-29 2021-09-07 Natera, Inc. System and method for cleaning noisy genetic data and determining chromosome copy number
US9424392B2 (en) 2005-11-26 2016-08-23 Natera, Inc. System and method for cleaning noisy genetic data from target individuals using genetic data from genetically related individuals
CA3207599A1 (en) 2010-05-18 2011-11-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11332785B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11408031B2 (en) 2010-05-18 2022-08-09 Natera, Inc. Methods for non-invasive prenatal paternity testing
US9677118B2 (en) 2014-04-21 2017-06-13 Natera, Inc. Methods for simultaneous amplification of target loci
US11332793B2 (en) 2010-05-18 2022-05-17 Natera, Inc. Methods for simultaneous amplification of target loci
US20190010543A1 (en) 2010-05-18 2019-01-10 Natera, Inc. Methods for simultaneous amplification of target loci
US12152275B2 (en) 2010-05-18 2024-11-26 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US12221653B2 (en) 2010-05-18 2025-02-11 Natera, Inc. Methods for simultaneous amplification of target loci
US11939634B2 (en) 2010-05-18 2024-03-26 Natera, Inc. Methods for simultaneous amplification of target loci
US11326208B2 (en) 2010-05-18 2022-05-10 Natera, Inc. Methods for nested PCR amplification of cell-free DNA
US11322224B2 (en) 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US11339429B2 (en) 2010-05-18 2022-05-24 Natera, Inc. Methods for non-invasive prenatal ploidy calling
US10316362B2 (en) 2010-05-18 2019-06-11 Natera, Inc. Methods for simultaneous amplification of target loci
BR112013020220B1 (pt) 2011-02-09 2020-03-17 Natera, Inc. Método para determinar o estado de ploidia de um cromossomo em um feto em gestação
DK3246416T3 (da) 2011-04-15 2024-09-02 Univ Johns Hopkins Sikkert sekventeringssystem
US20140100126A1 (en) 2012-08-17 2014-04-10 Natera, Inc. Method for Non-Invasive Prenatal Testing Using Parental Mosaicism Data
ES2886507T5 (es) 2012-10-29 2024-11-15 Univ Johns Hopkins Prueba de Papanicolaou para cánceres de ovario y de endometrio
EP3134541B1 (en) 2014-04-21 2020-08-19 Natera, Inc. Detecting copy number variations (cnv) of chromosomal segments in cancer
US20180173846A1 (en) 2014-06-05 2018-06-21 Natera, Inc. Systems and Methods for Detection of Aneuploidy
US11479812B2 (en) 2015-05-11 2022-10-25 Natera, Inc. Methods and compositions for determining ploidy
CN108026572B (zh) 2015-07-23 2022-07-01 香港中文大学 游离dna的片段化模式的分析
WO2017027653A1 (en) 2015-08-11 2017-02-16 The Johns Hopkins University Assaying ovarian cyst fluid
CN116987777A (zh) 2016-03-25 2023-11-03 凯锐思公司 合成核酸掺入物
RU2760913C2 (ru) 2016-04-15 2021-12-01 Натера, Инк. Способы выявления рака легкого
WO2018067517A1 (en) 2016-10-04 2018-04-12 Natera, Inc. Methods for characterizing copy number variation using proximity-litigation sequencing
GB201618485D0 (en) 2016-11-02 2016-12-14 Ucl Business Plc Method of detecting tumour recurrence
US10011870B2 (en) 2016-12-07 2018-07-03 Natera, Inc. Compositions and methods for identifying nucleic acid molecules
IL302912A (en) 2016-12-22 2023-07-01 Guardant Health Inc Methods and systems for analyzing nucleic acid molecules
MY197535A (en) 2017-01-25 2023-06-21 Univ Hong Kong Chinese Diagnostic applications using nucleic acid fragments
WO2019016353A1 (en) * 2017-07-21 2019-01-24 F. Hoffmann-La Roche Ag CLASSIFICATION OF SOMATIC MUTATIONS FROM A HETEROGENEOUS SAMPLE
CN111868260B (zh) 2017-08-07 2025-02-21 约翰斯霍普金斯大学 用于评估和治疗癌症的方法和材料
WO2019060716A1 (en) 2017-09-25 2019-03-28 Freenome Holdings, Inc. SAMPLE EXTRACTION METHODS AND SYSTEMS
US12084720B2 (en) 2017-12-14 2024-09-10 Natera, Inc. Assessing graft suitability for transplantation
EP3743518A4 (en) * 2018-01-24 2021-09-29 Freenome Holdings, Inc. METHODS AND SYSTEMS FOR DETECTING ANOMALY IN PATTERNS OF NUCLEIC ACIDS
EP3759238A4 (en) * 2018-02-27 2021-11-24 Cornell University SYSTEMS AND METHODS FOR DETECTING RESIDUAL DISEASES
JP2021514663A (ja) * 2018-03-08 2021-06-17 セント・ジョーンズ・ユニバーシティＳｔ． Ｊｏｈｎｓ Ｕｎｉｖｅｒｓｉｔｙ 循環性血清無細胞ｄｎａバイオマーカー及び方法
US20190287649A1 (en) * 2018-03-13 2019-09-19 Grail, Inc. Method and system for selecting, managing, and analyzing data of high dimensionality
US12087406B2 (en) 2018-03-15 2024-09-10 The Board Of Trustees Of The Leland Stanford Junior University Methods using chromatin-related nucleic acid signals for performing clinical actions
EP3776555A2 (en) * 2018-04-13 2021-02-17 Grail, Inc. Multi-assay prediction model for cancer detection
JP7455757B2 (ja) * 2018-04-13 2024-03-26 フリーノーム・ホールディングス・インコーポレイテッド 生体試料の多検体アッセイのための機械学習実装
US12024738B2 (en) 2018-04-14 2024-07-02 Natera, Inc. Methods for cancer detection and monitoring
US11482303B2 (en) 2018-06-01 2022-10-25 Grail, Llc Convolutional neural network systems and methods for data classification
WO2020006369A1 (en) * 2018-06-29 2020-01-02 Guardant Health, Inc. Methods and systems for analysis of ctcf binding regions in cell-free dna
US12234509B2 (en) 2018-07-03 2025-02-25 Natera, Inc. Methods for detection of donor-derived cell-free DNA
WO2020096691A2 (en) * 2018-09-04 2020-05-14 Guardant Health, Inc. Methods and systems for detecting allelic imbalance in cell-free nucleic acid samples
AU2019356497B2 (en) * 2018-10-08 2025-06-26 Freenome Holdings, Inc. Transcription factor profiling
GB201818159D0 (en) * 2018-11-07 2018-12-19 Cancer Research Tech Ltd Enhanced detection of target dna by fragment size analysis
WO2020106987A1 (en) * 2018-11-21 2020-05-28 Karius, Inc. Detection and prediction of infectious disease
CA3118990A1 (en) 2018-11-21 2020-05-28 Karius, Inc. Direct-to-library methods, systems, and compositions
US10468141B1 (en) * 2018-11-28 2019-11-05 Asia Genomics Pte. Ltd. Ancestry-specific genetic risk scores
US11581062B2 (en) 2018-12-10 2023-02-14 Grail, Llc Systems and methods for classifying patients with respect to multiple cancer classes
ES2968457T3 (es) * 2018-12-19 2024-05-09 Univ Hong Kong Chinese Características de los extremos del ADN extracelular circulante
EP3899049A1 (en) * 2018-12-21 2021-10-27 F. Hoffmann-La Roche AG Identification of global sequence features in whole genome sequence data from circulating nucelic acid
WO2020132499A2 (en) * 2018-12-21 2020-06-25 Grail, Inc. Systems and methods for using fragment lengths as a predictor of cancer
WO2020150258A1 (en) * 2019-01-15 2020-07-23 Luminist, Inc. Methods and systems for detecting liver disease
EP4632078A2 (en) * 2019-01-24 2025-10-15 Illumina, Inc. Methods and systems for monitoring organ health and disease
EP3918089B1 (en) 2019-01-31 2025-01-15 Guardant Health, Inc. Method for isolating and sequencing cell-free dna
US11475978B2 (en) 2019-02-12 2022-10-18 Tempus Labs, Inc. Detection of human leukocyte antigen loss of heterozygosity
WO2020168016A1 (en) 2019-02-12 2020-08-20 Tempus Labs, Inc. Detection of human leukocyte antigen loss of heterozygosity
WO2020176659A1 (en) * 2019-02-27 2020-09-03 Guardant Health, Inc. Methods and systems for determining the cellular origin of cell-free dna
EP3956466A1 (en) * 2019-04-15 2022-02-23 Natera, Inc. Improved liquid biopsy using size selection
US11869661B2 (en) 2019-05-22 2024-01-09 Grail, Llc Systems and methods for determining whether a subject has a cancer condition using transfer learning
EP3976822A1 (en) 2019-05-31 2022-04-06 Guardant Health, Inc. Methods and systems for improving patient monitoring after surgery
WO2020247263A1 (en) 2019-06-06 2020-12-10 Natera, Inc. Methods for detecting immune cell dna and monitoring immune system
US20220259647A1 (en) * 2019-07-09 2022-08-18 The Translational Genomics Research Institute METHODS OF DETECTING DISEASE AND TREATMENT RESPONSE IN cfDNA
US20220301654A1 (en) * 2019-08-28 2022-09-22 Grail, Llc Systems and methods for predicting and monitoring treatment response from cell-free nucleic acids
CN110706749B (zh) * 2019-09-10 2022-06-10 至本医疗科技（上海）有限公司 一种基于组织器官分化层次关系的癌症类型预测系统和方法
WO2021067484A1 (en) 2019-09-30 2021-04-08 Guardant Health, Inc. Compositions and methods for analyzing cell-free dna in methylation partitioning assays
WO2021072275A1 (en) * 2019-10-11 2021-04-15 Guardant Health, Inc. Use of cell free bacterial nucleic acids for detection of cancer
ES3031713T3 (en) 2019-11-26 2025-07-10 Guardant Health Inc Methods, compositions and systems for improving the binding of methylated polynucleotides
EP4068291A4 (en) * 2019-11-29 2023-12-20 GC Genome Corporation METHOD FOR DETECTING CHROMOSOMAL ANOMALIES USING ARTIFICIAL INTELLIGENCE
WO2021127208A1 (en) * 2019-12-20 2021-06-24 Accuragen Holdings Limited Methods and systems for disease detection
WO2021130356A1 (en) * 2019-12-24 2021-07-01 Vib Vzw Disease detection in liquid biopsies
CN115516108A (zh) 2020-02-14 2022-12-23 约翰斯霍普金斯大学 评估核酸的方法和材料
US20210285042A1 (en) * 2020-02-28 2021-09-16 Grail, Inc. Systems and methods for calling variants using methylation sequencing data
WO2021222828A1 (en) 2020-04-30 2021-11-04 Guardant Health, Inc. Methods for sequence determination using partitioned nucleic acids
AU2021276524A1 (en) * 2020-05-22 2023-01-05 Aqtual, Inc. Methods for characterizing cell-free nucleic acid fragments
WO2023282916A1 (en) 2021-07-09 2023-01-12 Guardant Health, Inc. Methods of detecting genomic rearrangements using cell free nucleic acids
EP4179111B1 (en) 2020-07-10 2024-04-03 Guardant Health, Inc. Methods of detecting genomic rearrangements using cell free nucleic acids
EP4585697A3 (en) 2020-07-30 2025-08-06 Guardant Health, Inc. Methods for isolating cell-free dna
JP2023540221A (ja) 2020-08-25 2023-09-22 ガーダント ヘルス， インコーポレイテッド バリアントの起源を予測するための方法およびシステム
WO2022061080A1 (en) * 2020-09-17 2022-03-24 The Regents Of The University Of Colorado, A Body Corporate Signatures in cell-free dna to detect disease, track treatment response, and inform treatment decisions
US20220162670A1 (en) 2020-09-30 2022-05-26 Guardant Health, Inc. Methods and systems to improve the signal to noise ratio of dna methylation partitioning assays
CA3195797A1 (en) 2020-10-23 2022-04-28 Andrew Kennedy Compositions and methods for analyzing dna using partitioning and base conversion
CA3199829A1 (en) 2020-11-30 2022-06-02 Guardant Health, Inc. Compositions and methods for enriching methylated polynucleotides
CN114634982A (zh) * 2020-12-15 2022-06-17 广州市基准医疗有限责任公司 一种检测多核苷酸变异的方法
EP4015650A1 (en) * 2020-12-18 2022-06-22 Nipd Genetics Biotech Limited Methods for classifying a sample into clinically relevant categories
WO2022140629A1 (en) 2020-12-23 2022-06-30 Guardant Health, Inc. Methods and systems for analyzing methylated polynucleotides
EP4291679A1 (en) 2021-02-12 2023-12-20 Guardant Health, Inc. Methods and compositions for detecting nucleic acid variants
WO2022204730A1 (en) 2021-03-25 2022-09-29 Guardant Health, Inc. Methods and compositions for quantifying immune cell dna
WO2022248844A1 (en) * 2021-05-24 2022-12-01 University Of Essex Enterprises Limited Method and system for identifying genomic regions with condition sensitive occupancy/positioning of nucleosomes and/or chromatin
KR20220160805A (ko) * 2021-05-28 2022-12-06 한국과학기술원 조직 특이적 조절지역의 무세포 dna 분포를 이용한 인공지능 기반 암 조기진단 방법
CN113838533B (zh) * 2021-08-17 2024-03-12 福建和瑞基因科技有限公司 一种癌症检测模型及其构建方法和试剂盒
WO2023091517A2 (en) * 2021-11-17 2023-05-25 The Board Of Trustees Of The Leland Stanford Junior University Systems and methods for gene expression and tissue of origin inference from cell-free dna
KR102884871B1 (ko) * 2022-01-26 2025-11-11 권창혁 암 판별 장치 및 암 판별 방법
JP2025513786A (ja) 2022-04-07 2025-04-30 ガーダント ヘルス， インコーポレイテッド 無細胞核酸分子のメチル化状態に基づいた腫瘍の存在の検出
US20250313898A1 (en) * 2022-06-02 2025-10-09 The Board Of Trustees Of The Leland Stanford Junior University Single molecule sequencing and methylation profiling of cell-free dna
EP4547857A1 (en) 2022-06-30 2025-05-07 Guardant Health, Inc. Enrichment of aberrantly methylated dna
US20240043935A1 (en) * 2022-07-29 2024-02-08 Centre For Novostics Limited Epigenetics analysis of cell-free dna
WO2024073508A2 (en) 2022-09-27 2024-04-04 Guardant Health, Inc. Methods and compositions for quantifying immune cell dna
CN115295074B (zh) * 2022-10-08 2022-12-16 南京世和基因生物技术股份有限公司 基因标志物在恶性肺结节筛查中的应用、筛查模型的构建方法和检测装置
EP4638782A2 (en) 2022-12-22 2025-10-29 Guardant Health, Inc. Integrated targeted and whole genome somatic and dna methylation sequencing workflows
WO2024137880A2 (en) 2022-12-22 2024-06-27 Guardant Health, Inc. Methods involving methylation preserving amplification with error correction
WO2024233502A1 (en) 2023-05-05 2024-11-14 Guardant Health, Inc. Cell-free dna blood-based test for cancer screening
WO2025019370A1 (en) * 2023-07-14 2025-01-23 Natera, Inc. Methods for assaying circulating tumor dna
WO2025029475A1 (en) 2023-07-28 2025-02-06 Guardant Health, Inc. Methods to enrich nucleotide variants by negative selection
WO2025038399A1 (en) 2023-08-11 2025-02-20 Guardant Health, Inc. Methylated enrichment methods for single-molecule genetic and epigenetic sequencing
CN117230165A (zh) * 2023-09-01 2023-12-15 深圳湾实验室 一种无创产前检测胎儿染色体拷贝数异常的优化方法
WO2025064706A1 (en) 2023-09-19 2025-03-27 Guardant Health, Inc. Detecting the presence of a tumor based on methylation status of cell-free nucleic acid molecules
WO2025076452A1 (en) 2023-10-06 2025-04-10 Guardant Health, Inc. Detecting tumor-related information based on methylation status of cell-free nucleic acid molecules
WO2025207817A1 (en) 2024-03-26 2025-10-02 Guardant Health, Inc. Method of determining the likelihood of a disease by combining biomarkers and imaging
WO2025208044A1 (en) 2024-03-28 2025-10-02 Guardant Health, Inc. Methods for cancer detection using molecular patterns
WO2025205006A1 (ja) * 2024-03-29 2025-10-02 ソニーグループ株式会社 分析方法、クロマチン状態を分類する方法、がん検査方法、分析システム、がん又は微小残存病変の検査システムおよび分析キット
WO2025235889A1 (en) 2024-05-10 2025-11-13 Guardant Health, Inc. Methods involving multiplexed pooled pcr
WO2025250544A1 (en) 2024-05-31 2025-12-04 Guardant Health, Inc. Methods for analyzing chromatin architecture in tissue to boost detection of cancer associated signals in cell-free dna
CN120334449B (zh) * 2025-06-20 2025-09-05 陕西右任故里茯砖茶股份有限公司 基于液相色谱的茯砖茶中金花菌发酵检测方法

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015048535A1 (en) * 2013-09-27 2015-04-02 Natera, Inc. Prenatal diagnostic resting standards
US20160019338A1 (en) * 2014-05-30 2016-01-21 Verinata Health, Inc. Detecting fetal sub-chromosomal aneuploidies
WO2016015058A2 (en) * 2014-07-25 2016-01-28 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

Family Cites Families (18)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2741117A1 (en) * 2008-10-30 2010-05-06 Centre De Recherche Public De La Sante Biomarkers for heart failure
CN101901345B (zh) * 2009-05-27 2013-02-27 复旦大学 一种差异蛋白质组学的分类方法
US11322224B2 (en) * 2010-05-18 2022-05-03 Natera, Inc. Methods for non-invasive prenatal ploidy calling
EP2426217A1 (en) * 2010-09-03 2012-03-07 Centre National de la Recherche Scientifique (CNRS) Analytical methods for cell free nucleic acids and applications
GB2485635B (en) * 2011-07-26 2012-11-28 Verinata Health Inc Method for determining the presence or absence of different aneuploidies in a sample
US9367663B2 (en) * 2011-10-06 2016-06-14 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
JP6073902B2 (ja) * 2011-10-06 2017-02-01 セクエノム， インコーポレイテッド 遺伝的変異の非侵襲的評価のための方法およびプロセス
EP3736339B1 (en) * 2012-02-16 2022-07-27 Oxford Nanopore Technologies plc Analysis of measurements of a polymer
EP3573066B1 (en) * 2012-03-13 2023-09-27 The Chinese University Of Hong Kong Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
CN107435070A (zh) * 2012-04-12 2017-12-05 维里纳塔健康公司 拷贝数变异的检测和分类
US10497461B2 (en) * 2012-06-22 2019-12-03 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
US20160040229A1 (en) * 2013-08-16 2016-02-11 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
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
US20130309666A1 (en) * 2013-01-25 2013-11-21 Sequenom, Inc. Methods and processes for non-invasive assessment of genetic variations
CN105722994B (zh) * 2013-06-17 2020-12-18 维里纳塔健康公司 用于确定性染色体中的拷贝数变异的方法
EP3378952B1 (en) 2013-12-28 2020-02-05 Guardant Health, Inc. Methods and systems for detecting genetic variants
WO2016094853A1 (en) * 2014-12-12 2016-06-16 Verinata Health, Inc. Using cell-free dna fragment size to determine copy number variations

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015048535A1 (en) * 2013-09-27 2015-04-02 Natera, Inc. Prenatal diagnostic resting standards
US20160019338A1 (en) * 2014-05-30 2016-01-21 Verinata Health, Inc. Detecting fetal sub-chromosomal aneuploidies
WO2016015058A2 (en) * 2014-07-25 2016-01-28 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

Also Published As

Publication number Publication date
CA3030038A1 (en) 2018-01-11
KR20190026837A (ko) 2019-03-13
AU2017292854A1 (en) 2019-01-24
BR112019000296A2 (pt) 2019-04-16
EP4322168A2 (en) 2024-02-14
MX2019000037A (es) 2019-07-10
JP2024119898A (ja) 2024-09-03
EP3481966A4 (en) 2019-08-07
EP3481966B1 (en) 2023-11-08
JP2019531700A (ja) 2019-11-07
CN109689891A (zh) 2019-04-26
ES2967443T3 (es) 2024-04-30
EP3481966A1 (en) 2019-05-15
JP2022025101A (ja) 2022-02-09
KR102610098B1 (ko) 2023-12-04
WO2018009723A1 (en) 2018-01-11
CN109689891B (zh) 2024-06-18
EP4322168A3 (en) 2024-05-15
JP7448310B2 (ja) 2024-03-12
SG11201811556RA (en) 2019-01-30

Similar Documents

Publication Publication Date Title
AU2017292854B2 (en) Methods for fragmentome profiling of cell-free nucleic acids
US20190287645A1 (en) Methods for fragmentome profiling of cell-free nucleic acids
JP7689557B2 (ja) 相同組換え欠損を推定するための統合された機械学習フレームワーク
JP7458360B2 (ja) 疾患細胞不均一性を示す疾患の検出および処置、ならびに通信試験結果のためのシステムおよび方法
US20190352695A1 (en) Methods for fragmentome profiling of cell-free nucleic acids
Hardiman et al. Intra-tumor genetic heterogeneity in rectal cancer
Alkodsi et al. Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data
US20190264291A1 (en) Sequence variant analysis of cell-free dna for cancer screening
JP7340021B2 (ja) 予測腫瘍遺伝子変異量に基づいた腫瘍分類
CN115287348A (zh) Dna混合物中组织的单倍型的甲基化模式分析
HK40008790A (en) Methods for fragmentome profiling of cell-free nucleic acids
HK40008790B (en) Methods for fragmentome profiling of cell-free nucleic acids
WO2025113619A1 (en) Enrichment of clinically-relevant nucleic acids
US20250137063A1 (en) Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing
Ensminger Early Cancer Detection in Hereditary Breast and Ovarian Cancer Syndrome with Cell-Free DNA
Rashid Making sense of cancer mutations
Luo Accurate and Integrative Detection of Copy Number Variants With High-Throughput Data
HK40082326A (en) Methylation pattern analysis of haplotypes in tissues in dna mixture
HK40056499A (en) Mutational analysis of plasma dna for cancer detection
Chi Recurrent copy number alteration analysis identifies risk genes in young women with breast cancer
Parker et al. Effects of germline and somatic events in candidate
HK1252222B (en) Methylation pattern analysis of haplotypes in tissues in dna mixture
HK1205533B (en) Mutational analysis of plasma dna for cancer detection

Legal Events

Date Code Title Description
FGA Letters patent sealed or granted (standard patent)