AU2018350975B2 - Molecular evidence platform for auditable, continuous optimization of variant interpretation in genetic and genomic testing and analysis - Google Patents

Molecular evidence platform for auditable, continuous optimization of variant interpretation in genetic and genomic testing and analysis Download PDF

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AU2018350975B2
AU2018350975B2 AU2018350975A AU2018350975A AU2018350975B2 AU 2018350975 B2 AU2018350975 B2 AU 2018350975B2 AU 2018350975 A AU2018350975 A AU 2018350975A AU 2018350975 A AU2018350975 A AU 2018350975A AU 2018350975 B2 AU2018350975 B2 AU 2018350975B2
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evidence
variant
performance
test
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AU2018350975A1 (en
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Carlos L. Araya
Alexandre Colavin
Jason A. Reuter
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Invitae Corp
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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
    • G16B20/20—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)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Data Mining & Analysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
  • Analytical Chemistry (AREA)
  • Chemical & Material Sciences (AREA)
  • Molecular Biology (AREA)
  • Signal Processing (AREA)
  • Computer Networks & Wireless Communication (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Genetics & Genomics (AREA)
  • Software Systems (AREA)
  • Computer Security & Cryptography (AREA)
  • General Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Power Engineering (AREA)
  • Physiology (AREA)
  • 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)
AU2018350975A 2017-10-17 2018-10-17 Molecular evidence platform for auditable, continuous optimization of variant interpretation in genetic and genomic testing and analysis Active AU2018350975B2 (en)

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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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AU2018350975A1 AU2018350975A1 (en) 2020-05-07
AU2018350975B2 true AU2018350975B2 (en) 2023-11-23

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JP (1) JP7258871B2 (enExample)
CN (1) CN112074909B (enExample)
AU (1) AU2018350975B2 (enExample)
BR (1) BR112020007449A2 (enExample)
CA (1) CA3079389A1 (enExample)
IL (1) IL274001A (enExample)
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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

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US11798651B2 (en) 2023-10-24
EP3701534A1 (en) 2020-09-02
US12136472B2 (en) 2024-11-05
US20190189246A1 (en) 2019-06-20
CA3079389A1 (en) 2019-04-25
JP2020537795A (ja) 2020-12-24
US20200251179A1 (en) 2020-08-06
AU2018350975A1 (en) 2020-05-07
EP3701534A4 (en) 2021-08-04
BR112020007449A2 (pt) 2020-10-20
US20240006021A1 (en) 2024-01-04
MX2020003709A (es) 2020-07-22
JP7258871B2 (ja) 2023-04-17
US20230117854A1 (en) 2023-04-20
IL274001A (en) 2020-05-31
CN112074909B (zh) 2024-03-19
CN112074909A (zh) 2020-12-11
EP3701534C0 (en) 2024-04-10
US11462299B2 (en) 2022-10-04
EP3701534B1 (en) 2024-04-10
WO2019079464A1 (en) 2019-04-25

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