HK1252804B - 用於基於測序的變型檢測的方法和系統 - Google Patents

用於基於測序的變型檢測的方法和系統

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Publication number
HK1252804B
HK1252804B HK18112105.7A HK18112105A HK1252804B HK 1252804 B HK1252804 B HK 1252804B HK 18112105 A HK18112105 A HK 18112105A HK 1252804 B HK1252804 B HK 1252804B
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HK
Hong Kong
Prior art keywords
sequencing
systems
methods
variant detection
based variant
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HK18112105.7A
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English (en)
Other versions
HK1252804A1 (zh
Inventor
格蘭達‧G‧安德森
查理‧C‧金
Original Assignee
遠見基因組系統公司
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Application filed by 遠見基因組系統公司 filed Critical 遠見基因組系統公司
Publication of HK1252804A1 publication Critical patent/HK1252804A1/zh
Publication of HK1252804B publication Critical patent/HK1252804B/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
    • 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
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
    • C—CHEMISTRY; METALLURGY
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    • 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
    • C—CHEMISTRY; METALLURGY
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    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6848—Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
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    • 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
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
    • 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
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/40—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
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    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • 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
    • C12Q2600/166—Oligonucleotides used as internal standards, controls or normalisation probes
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Analytical Chemistry (AREA)
  • Organic Chemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Medical Informatics (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Molecular Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Pathology (AREA)
  • Public Health (AREA)
  • Biomedical Technology (AREA)
  • Epidemiology (AREA)
  • Primary Health Care (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
HK18112105.7A 2015-07-07 2018-09-20 用於基於測序的變型檢測的方法和系統 HK1252804B (zh)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201562189555P 2015-07-07 2015-07-07
PCT/US2016/041288 WO2017007903A1 (en) 2015-07-07 2016-07-07 Methods and systems for sequencing-based variant detection

Publications (2)

Publication Number Publication Date
HK1252804A1 HK1252804A1 (zh) 2019-06-06
HK1252804B true HK1252804B (zh) 2020-02-28

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HK18112105.7A HK1252804B (zh) 2015-07-07 2018-09-20 用於基於測序的變型檢測的方法和系統

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US (2) US20180218789A1 (zh)
CN (1) CN107922973B (zh)
GB (2) GB2555551A (zh)
HK (1) HK1252804B (zh)
WO (1) WO2017007903A1 (zh)

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WO2017007903A1 (en) * 2015-07-07 2017-01-12 Farsight Genome Systems, Inc. Methods and systems for sequencing-based variant detection
CN105567811A (zh) * 2015-12-30 2016-05-11 广州金域检测科技股份有限公司 一种dpyd基因多态性的引物及其检测方法
US11514289B1 (en) * 2016-03-09 2022-11-29 Freenome Holdings, Inc. Generating machine learning models using genetic data
US20190198172A1 (en) * 2016-08-22 2019-06-27 Robert P. Nelson, JR. Systems, methods, and diagnostic support tools for facilitating the diagnosis of medical conditions
CN106834107A (zh) * 2017-03-10 2017-06-13 首度生物科技（苏州）有限公司 一种基于二代测序的预测肿瘤系统
CN107743121A (zh) * 2017-09-28 2018-02-27 深圳多特医疗技术有限公司 一种电子检伤分类方法和系统
CN109251927B (zh) * 2018-06-13 2022-04-08 南京医科大学第二附属医院 一种长链非编码rna及其组合物在诊断/治疗胆管癌中的应用
JP6920251B2 (ja) * 2018-06-29 2021-08-18 シスメックス株式会社 解析方法、情報処理装置、プログラム
CN112424380A (zh) 2018-11-01 2021-02-26 Illumina公司 用于体细胞变体检测的方法和组合物
CN109504751B (zh) * 2018-11-28 2022-03-11 锦州医科大学 一种肿瘤复杂克隆结构的缺失变异识别及克隆计数方法
CN109337976A (zh) * 2018-12-24 2019-02-15 中国医学科学院北京协和医院 用于检测pik3cd基因e1021k位点突变的探针和引物组合及试剂盒
CN110241215B (zh) * 2019-07-03 2020-05-19 上海润安医学科技有限公司 一种用于检测甲状腺结节良恶性相关基因变异的引物及试剂盒
CN110379465A (zh) * 2019-07-19 2019-10-25 元码基因科技（北京）股份有限公司 基于rna靶向测序和机器学习的癌症组织溯源方法
EP4041924A1 (en) 2019-10-08 2022-08-17 Illumina, Inc. Fragment size characterization of cell-free dna mutations from clonal hematopoiesis
EP4142730A4 (en) * 2020-04-30 2024-05-01 Cedars Sinai Medical Center METHODS AND SYSTEMS FOR ASSESSING FIBROTIC DISEASE USING DEEP LEARNING
CN111549132A (zh) * 2020-05-07 2020-08-18 南京实践医学检验有限公司 一种慢性淋巴细胞白血病基因突变检测试剂盒及方法
CN112086130B (zh) * 2020-08-13 2021-07-27 东南大学 一种基于测序和数据分析的肥胖风险预测装置的预测方法
US20240013858A1 (en) * 2020-09-24 2024-01-11 Foundation Medicine, Inc. Methods for determining variant frequency and monitoring disease progression
CN112908470B (zh) * 2021-02-08 2023-10-03 深圳市人民医院 一种基于rna结合蛋白基因的肝细胞癌预后评分系统及其应用
CN112852966A (zh) * 2021-03-23 2021-05-28 复旦大学附属肿瘤医院 基于二代测序技术的胰腺癌检测panel、试剂盒及其应用
CN113136424B (zh) * 2021-05-21 2022-04-08 广州合一生物科技有限公司 一种用于抗癫痫药物个体化用药的基因检测试剂盒及其应用
EP4374376A1 (en) * 2021-07-23 2024-05-29 Foundation Medicine, Inc. Methods for determining variant frequency and monitoring disease progression
EP4258268A1 (en) * 2022-04-05 2023-10-11 Biomérieux Detection of a genomic sequence in a microorganism genome by whole genome sequencing
CN115691672B (zh) * 2022-12-20 2023-06-16 臻和(北京)生物科技有限公司 针对测序平台特征的碱基质量值矫正方法、装置、电子设备和存储介质

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US20160034638A1 (en) * 2013-03-14 2016-02-04 University Of Rochester System and Method for Detecting Population Variation from Nucleic Acid Sequencing Data
WO2015051006A2 (en) * 2013-10-01 2015-04-09 Complete Genomics, Inc. Phasing and linking processes to identify variations in a genome
WO2017007903A1 (en) * 2015-07-07 2017-01-12 Farsight Genome Systems, Inc. Methods and systems for sequencing-based variant detection

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Publication number Publication date
US20200203014A1 (en) 2020-06-25
CN107922973B (zh) 2019-06-14
WO2017007903A1 (en) 2017-01-12
GB2555551A (en) 2018-05-02
US20180218789A1 (en) 2018-08-02
HK1252804A1 (zh) 2019-06-06
GB201800793D0 (en) 2018-03-07
CN107922973A (zh) 2018-04-17
GB201819855D0 (en) 2019-01-23

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