CN112074909B - 变体解释终端系统 - Google Patents

变体解释终端系统 Download PDF

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CN112074909B
CN112074909B CN201880081247.7A CN201880081247A CN112074909B CN 112074909 B CN112074909 B CN 112074909B CN 201880081247 A CN201880081247 A CN 201880081247A CN 112074909 B CN112074909 B CN 112074909B
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data
evidence
variant
aspects
performance
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CN112074909A (zh
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A·科拉维恩
C·L·阿拉亚
J·A·雷尤特
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Invet Corp
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    • 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
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/21—Design or setup of recognition systems or techniques; Extraction of features in feature space; Blind source separation
    • G06F18/211—Selection of the most significant subset of features
    • G06F18/2113—Selection of the most significant subset of features by ranking or filtering the set of features, e.g. using a measure of variance or of feature cross-correlation
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/21—Design or setup of recognition systems or techniques; Extraction of features in feature space; Blind source separation
    • G06F18/217—Validation; Performance evaluation; Active pattern learning techniques
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • 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
    • 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
    • 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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • 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
    • G16B50/00—ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/10—Ontologies; Annotations
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L67/00—Network arrangements or protocols for supporting network services or applications
    • H04L67/01—Protocols
    • H04L67/10—Protocols in which an application is distributed across nodes in the network
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L9/00—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols
    • H04L9/06—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols the encryption apparatus using shift registers or memories for block-wise or stream coding, e.g. DES systems or RC4; Hash functions; Pseudorandom sequence generators
    • H04L9/0618—Block ciphers, i.e. encrypting groups of characters of a plain text message using fixed encryption transformation
    • H04L9/0637—Modes of operation, e.g. cipher block chaining [CBC], electronic codebook [ECB] or Galois/counter mode [GCM]
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L9/00—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols
    • H04L9/06—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols the encryption apparatus using shift registers or memories for block-wise or stream coding, e.g. DES systems or RC4; Hash functions; Pseudorandom sequence generators
    • H04L9/0643—Hash functions, e.g. MD5, SHA, HMAC or f9 MAC
    • H—ELECTRICITY
    • H04—ELECTRIC COMMUNICATION TECHNIQUE
    • H04L—TRANSMISSION OF DIGITAL INFORMATION, e.g. TELEGRAPHIC COMMUNICATION
    • H04L9/00—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols
    • H04L9/50—Cryptographic mechanisms or cryptographic arrangements for secret or secure communications; Network security protocols using hash chains, e.g. blockchains or hash trees

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  • Engineering & Computer Science (AREA)
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  • Bioinformatics & Cheminformatics (AREA)
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  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Data Mining & Analysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Databases & Information Systems (AREA)
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  • Chemical & Material Sciences (AREA)
  • Bioethics (AREA)
  • Molecular Biology (AREA)
  • Signal Processing (AREA)
  • Computer Networks & Wireless Communication (AREA)
  • Artificial Intelligence (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Computation (AREA)
  • Genetics & Genomics (AREA)
  • Software Systems (AREA)
  • Computer Security & Cryptography (AREA)
  • General Engineering & Computer Science (AREA)
  • General Physics & Mathematics (AREA)
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  • Epidemiology (AREA)
  • Physiology (AREA)
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  • Computing Systems (AREA)
  • Mathematical Physics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Peptides Or Proteins (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
CN201880081247.7A 2017-10-17 2018-10-17 变体解释终端系统 Active CN112074909B (zh)

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US201762573458P 2017-10-17 2017-10-17
US62/573,458 2017-10-17
PCT/US2018/056304 WO2019079464A1 (en) 2017-10-17 2018-10-17 PLATFORM OF MOLECULAR EVIDENCE FOR CONTINUOUS AND VERIFY OPTIMIZATION OF INTERPRETATION OF VARIANTS IN TESTS AND GENETIC ANALYZES

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CN112074909B true CN112074909B (zh) 2024-03-19

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Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3701534B1 (en) 2017-10-17 2024-04-10 Invitae Corporation Molecular evidence platform for auditable, continuous optimization of variant interpretation in genetic and genomic testing and analysis
US10959277B2 (en) * 2019-04-01 2021-03-23 T-Mobile Usa, Inc. Mobile device network performance restoration and improvement
US10764062B2 (en) * 2019-06-03 2020-09-01 Alibaba Group Holding Limited Blockchain ledger compression
CN110602162B (zh) * 2019-08-06 2022-11-01 苏州龙信信息科技有限公司 终端取证方法、装置、设备和存储介质
CN110957006B (zh) * 2019-12-14 2023-08-11 杭州联川基因诊断技术有限公司 一种brca1/2基因变异的解读方法
CN112489812B (zh) * 2020-11-30 2021-07-06 北京华彬立成科技有限公司 药物开发分析方法、装置、电子设备和存储介质
US20230351337A1 (en) * 2022-04-29 2023-11-02 Bank Of America Corporation Generating and securing digital checks using distributed ledger and embedded chip methods
US12211039B2 (en) * 2022-09-20 2025-01-28 Veiovia Limited Externally validated proof of work for appending a block record to a blockchain with a data broker server
US11652650B1 (en) * 2022-09-20 2023-05-16 Veiovia Limited Externally validated proof of work for appending a block record to a blockchain with a commitment database server
US12216661B2 (en) 2022-09-20 2025-02-04 Veiovia Ltd. Externally validated proof of work for appending a block record to a blockchain with a mining node
WO2025115360A1 (ja) * 2023-11-30 2025-06-05 富士フイルム株式会社 木構造生成方法、情報処理装置、情報処理システム、及び木構造生成プログラム
CN119719955B (zh) * 2024-12-17 2025-09-05 四川大学华西医院 一种基于贝叶斯模型的证据优化方法、装置、计算机设备及存储介质

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR20120044100A (ko) * 2010-10-27 2012-05-07 삼성에스디에스 주식회사 바이오 마커 추출 장치 및 방법
CN105074463A (zh) * 2013-01-31 2015-11-18 科德克希思公司 使用相乘形式的模型鉴定生物分子的方法、系统和软件
CN105378104A (zh) * 2013-03-15 2016-03-02 威拉赛特公司 用于样品分类的方法和组合物
WO2016154584A1 (en) * 2015-03-26 2016-09-29 Quest Diagnostics Investments Incorporated Alignment and variant sequencing analysis pipeline
CN106796620A (zh) * 2014-06-30 2017-05-31 凯杰雷德伍德城公司 用于解释和报告基于序列的基因测试的方法和系统

Family Cites Families (27)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5972693A (en) 1995-10-24 1999-10-26 Curagen Corporation Apparatus for identifying, classifying, or quantifying DNA sequences in a sample without sequencing
US5780236A (en) 1996-11-18 1998-07-14 Wisconsin Alumni Research Foundation Method for identifying mutants and molecules
US6949692B2 (en) 1996-11-18 2005-09-27 Wisconsin Alumni Research Foundation Method for identifying mutants and molecules
US7135286B2 (en) 2002-03-26 2006-11-14 Perlegen Sciences, Inc. Pharmaceutical and diagnostic business systems and methods
US20060223058A1 (en) * 2005-04-01 2006-10-05 Perlegen Sciences, Inc. In vitro association studies
US7702468B2 (en) 2006-05-03 2010-04-20 Population Diagnostics, Inc. Evaluating genetic disorders
WO2008033239A2 (en) 2006-09-11 2008-03-20 Applera Genetic polymorphisms associated with psoriasis, methods of detection and uses thereof
US20130338012A1 (en) 2010-11-18 2013-12-19 Illumina Inc. Genetic risk factors of sick sinus syndrome
WO2012155148A2 (en) 2011-05-12 2012-11-15 University Of Utah Research Foundation Predicting gene variant pathogenicity
US8718950B2 (en) * 2011-07-08 2014-05-06 The Medical College Of Wisconsin, Inc. Methods and apparatus for identification of disease associated mutations
US9773091B2 (en) * 2011-10-31 2017-09-26 The Scripps Research Institute Systems and methods for genomic annotation and distributed variant interpretation
US9235686B2 (en) 2012-01-06 2016-01-12 Molecular Health Gmbh Systems and methods for using adverse event data to predict potential side effects
US20140089009A1 (en) * 2012-09-27 2014-03-27 Wobblebase, Inc. Method for Personal Genome Data Management
US9792405B2 (en) * 2013-01-17 2017-10-17 Edico Genome, Corp. Bioinformatics systems, apparatuses, and methods executed on an integrated circuit processing platform
US20160048633A1 (en) * 2013-03-15 2016-02-18 Cypher Genomics, Inc. Systems and methods for genomic variant annotation
US10235496B2 (en) * 2013-03-15 2019-03-19 The Scripps Research Institute Systems and methods for genomic annotation and distributed variant interpretation
JP6566484B2 (ja) * 2013-06-14 2019-08-28 キージーン ナムローゼ フェンノートシャップ 表現形質改善のための制御された戦略
US20150025861A1 (en) * 2013-07-17 2015-01-22 The Johns Hopkins University Genetic screening computing systems and methods
WO2015027085A1 (en) * 2013-08-22 2015-02-26 Genomoncology, Llc Computer-based systems and methods for analyzing genomes based on discrete data structures corresponding to genetic variants therein
US20160314245A1 (en) 2014-06-17 2016-10-27 Genepeeks, Inc. Device, system and method for assessing risk of variant-specific gene dysfunction
EP3189619B1 (en) * 2014-09-03 2021-02-17 NantOmics, LLC Device, method and computer program product for synthetic genomic variant-based secure transaction
EP3286677A4 (en) * 2015-04-22 2019-07-24 Genepeeks, Inc. DEVICE, SYSTEM AND METHOD FOR ASSESSING THE RISK OF VARIATION SPECIFIC GENDYS FUNCTION
US10185803B2 (en) 2015-06-15 2019-01-22 Deep Genomics Incorporated Systems and methods for classifying, prioritizing and interpreting genetic variants and therapies using a deep neural network
EP3433781A4 (en) * 2016-03-21 2019-12-04 Human Longevity, Inc. GENOMIC, METABOLOMIC AND MICROBIOMICAL RESEARCH ENGINE
EP3701534B1 (en) 2017-10-17 2024-04-10 Invitae Corporation Molecular evidence platform for auditable, continuous optimization of variant interpretation in genetic and genomic testing and analysis
US10978196B2 (en) * 2018-10-17 2021-04-13 Tempus Labs, Inc. Data-based mental disorder research and treatment systems and methods
US20200121715A1 (en) 2018-10-20 2020-04-23 MC Technology Holdings, LLC Composition comprising aqueous medium with reduced size water clusters to improve bioavailability of the aqueous medium and methods for making and using the compositions

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR20120044100A (ko) * 2010-10-27 2012-05-07 삼성에스디에스 주식회사 바이오 마커 추출 장치 및 방법
CN105074463A (zh) * 2013-01-31 2015-11-18 科德克希思公司 使用相乘形式的模型鉴定生物分子的方法、系统和软件
CN105378104A (zh) * 2013-03-15 2016-03-02 威拉赛特公司 用于样品分类的方法和组合物
CN106796620A (zh) * 2014-06-30 2017-05-31 凯杰雷德伍德城公司 用于解释和报告基于序列的基因测试的方法和系统
WO2016154584A1 (en) * 2015-03-26 2016-09-29 Quest Diagnostics Investments Incorporated Alignment and variant sequencing analysis pipeline

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies;Chengliang Dong et al.;《Human Molecular Genetics》;第24卷(第8期);第2125-2137页 *
The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity;Dominik G. Grimm et al.;《Human Mutation》;第513-523页 *

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US20230117854A1 (en) 2023-04-20
MX2020003709A (es) 2020-07-22
CN112074909A (zh) 2020-12-11
US20200251179A1 (en) 2020-08-06
US20190189246A1 (en) 2019-06-20
US11798651B2 (en) 2023-10-24
AU2018350975A1 (en) 2020-05-07
US11462299B2 (en) 2022-10-04
EP3701534A4 (en) 2021-08-04
JP2020537795A (ja) 2020-12-24
BR112020007449A2 (pt) 2020-10-20
US12136472B2 (en) 2024-11-05
CA3079389A1 (en) 2019-04-25
US20240006021A1 (en) 2024-01-04
IL274001A (en) 2020-05-31
AU2018350975B2 (en) 2023-11-23
JP7258871B2 (ja) 2023-04-17
EP3701534C0 (en) 2024-04-10
EP3701534B1 (en) 2024-04-10
EP3701534A1 (en) 2020-09-02
WO2019079464A1 (en) 2019-04-25

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