CA3079389A1 - 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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Publication number
CA3079389A1
CA3079389A1 CA3079389A CA3079389A CA3079389A1 CA 3079389 A1 CA3079389 A1 CA 3079389A1 CA 3079389 A CA3079389 A CA 3079389A CA 3079389 A CA3079389 A CA 3079389A CA 3079389 A1 CA3079389 A1 CA 3079389A1
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Prior art keywords
data
evidence
variant
aspects
model
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English (en)
French (fr)
Inventor
Alexandre Colavin
Carlos L. Araya
Jason A. Reuter
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Invitae Corp
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Jungla LLC
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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
    • 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
    • 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
    • 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)
  • Computer Networks & Wireless Communication (AREA)
  • Signal Processing (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)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Physiology (AREA)
  • Power Engineering (AREA)
  • Mathematical Physics (AREA)
  • Computing Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Peptides Or Proteins (AREA)
CA3079389A 2017-10-17 2018-10-17 Molecular evidence platform for auditable, continuous optimization of variant interpretation in genetic and genomic testing and analysis Pending CA3079389A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
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

Publications (1)

Publication Number Publication Date
CA3079389A1 true CA3079389A1 (en) 2019-04-25

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Application Number Title Priority Date Filing Date
CA3079389A Pending CA3079389A1 (en) 2017-10-17 2018-10-17 Molecular evidence platform for auditable, continuous optimization of variant interpretation in genetic and genomic testing and analysis

Country Status (10)

Country Link
US (4) US11462299B2 (https=)
EP (1) EP3701534B1 (https=)
JP (1) JP7258871B2 (https=)
CN (1) CN112074909B (https=)
AU (1) AU2018350975B2 (https=)
BR (1) BR112020007449A2 (https=)
CA (1) CA3079389A1 (https=)
IL (1) IL274001A (https=)
MX (1) MX2020003709A (https=)
WO (1) WO2019079464A1 (https=)

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Also Published As

Publication number Publication date
WO2019079464A1 (en) 2019-04-25
US11462299B2 (en) 2022-10-04
US12136472B2 (en) 2024-11-05
EP3701534B1 (en) 2024-04-10
AU2018350975B2 (en) 2023-11-23
MX2020003709A (es) 2020-07-22
AU2018350975A1 (en) 2020-05-07
CN112074909A (zh) 2020-12-11
EP3701534C0 (en) 2024-04-10
JP2020537795A (ja) 2020-12-24
BR112020007449A2 (pt) 2020-10-20
US20200251179A1 (en) 2020-08-06
CN112074909B (zh) 2024-03-19
IL274001A (en) 2020-05-31
US20240006021A1 (en) 2024-01-04
US20190189246A1 (en) 2019-06-20
JP7258871B2 (ja) 2023-04-17
EP3701534A4 (en) 2021-08-04
US11798651B2 (en) 2023-10-24
EP3701534A1 (en) 2020-09-02
US20230117854A1 (en) 2023-04-20

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