AU2020334901A1 - Systems and methods for detecting cellular pathway dysregulation in cancer specimens - Google Patents

Systems and methods for detecting cellular pathway dysregulation in cancer specimens Download PDF

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Publication number
AU2020334901A1
AU2020334901A1 AU2020334901A AU2020334901A AU2020334901A1 AU 2020334901 A1 AU2020334901 A1 AU 2020334901A1 AU 2020334901 A AU2020334901 A AU 2020334901A AU 2020334901 A AU2020334901 A AU 2020334901A AU 2020334901 A1 AU2020334901 A1 AU 2020334901A1
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Australia
Prior art keywords
pathway
disruption
data
trained
gene
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AU2020334901A
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English (en)
Inventor
Nike T. Beaubier
Joshua SK Bell
Joshua Drews
Catherine Igartua
Lee F. Langer
Hailey B. Lefkofsky
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Tempus AI Inc
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Tempus AI Inc
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Publication of AU2020334901A1 publication Critical patent/AU2020334901A1/en
Assigned to TEMPUS AI, INC. reassignment TEMPUS AI, INC. Amend patent request/document other than specification (104) Assignors: TEMPUS LABS, INC.
Pending legal-status Critical Current

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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
    • 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
    • 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
    • G16B40/20—Supervised data analysis
    • 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
    • G16B40/30—Unsupervised data analysis
    • 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
    • G16B5/20—Probabilistic models

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  • Physics & Mathematics (AREA)
  • Engineering & Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Medical Informatics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Data Mining & Analysis (AREA)
  • Bioethics (AREA)
  • Evolutionary Computation (AREA)
  • Software Systems (AREA)
  • Genetics & Genomics (AREA)
  • Artificial Intelligence (AREA)
  • Molecular Biology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
  • Probability & Statistics with Applications (AREA)
  • Physiology (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Medical Treatment And Welfare Office Work (AREA)
AU2020334901A 2019-08-16 2020-08-14 Systems and methods for detecting cellular pathway dysregulation in cancer specimens Pending AU2020334901A1 (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
US201962888163P 2019-08-16 2019-08-16
US62/888,163 2019-08-16
US201962904300P 2019-09-23 2019-09-23
US62/904,300 2019-09-23
US202062986201P 2020-03-06 2020-03-06
US62/986,201 2020-03-06
PCT/US2020/046513 WO2021034712A1 (en) 2019-08-16 2020-08-14 Systems and methods for detecting cellular pathway dysregulation in cancer specimens

Publications (1)

Publication Number Publication Date
AU2020334901A1 true AU2020334901A1 (en) 2022-03-24

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Family Applications (1)

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AU2020334901A Pending AU2020334901A1 (en) 2019-08-16 2020-08-14 Systems and methods for detecting cellular pathway dysregulation in cancer specimens

Country Status (6)

Country Link
US (2) US11367508B2 (https=)
EP (2) EP4013866A4 (https=)
JP (3) JP2022544604A (https=)
AU (1) AU2020334901A1 (https=)
CA (1) CA3148023A1 (https=)
WO (2) WO2021034712A1 (https=)

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EP4275208A1 (en) 2021-01-07 2023-11-15 Tempus Labs, Inc. Systems and methods for joint low-coverage whole genome sequencing and whole exome sequencing inference of copy number variation for clinical diagnostics
US11481235B2 (en) * 2021-01-11 2022-10-25 Evicore Healthcare MSI, LLC Database framework model transformation for pathway identification
WO2022159774A2 (en) 2021-01-21 2022-07-28 Tempus Labs, Inc. METHODS AND SYSTEMS FOR mRNA BOUNDARY ANALYSIS IN NEXT GENERATION SEQUENCING
US12412100B2 (en) * 2021-01-22 2025-09-09 International Business Machines Corporation Cell state transition features from single cell data
US12361542B2 (en) 2021-03-03 2025-07-15 Tempus Ai, Inc. Systems and methods for deep orthogonal fusion for multimodal prognostic biomarker discovery
CN113421613B (zh) * 2021-06-08 2024-06-18 吴安华 一种基于铁死亡水平评价胶质母细胞瘤患者免疫治疗反应性的系统及分析方法
WO2023064309A1 (en) 2021-10-11 2023-04-20 Tempus Labs, Inc. Methods and systems for detecting alternative splicing in sequencing data
EP4430615A4 (en) * 2021-11-10 2026-01-21 Albert Einstein College Medicine METHOD FOR MEASURING SOMATIC DNA MUTATION AND DNA DAMAGE PROFILES AND APPROPRIATE DIAGNOSTIC KIT
WO2023091316A1 (en) 2021-11-19 2023-05-25 Tempus Labs, Inc. Methods and systems for accurate genotyping of repeat polymorphisms
WO2023100181A1 (en) * 2021-12-01 2023-06-08 Hadasit Medical Research Services And Development Ltd. Machine learning prediction of genetic mutations impact
JP2023091970A (ja) * 2021-12-21 2023-07-03 行正 塩津 提示装置及びプログラム
EP4239647A1 (en) 2022-03-03 2023-09-06 Tempus Labs, Inc. Systems and methods for deep orthogonal fusion for multimodal prognostic biomarker discovery
WO2023168049A2 (en) * 2022-03-04 2023-09-07 Bostongene Corporation Cytokine gene expression signatures
CN115273966B (zh) * 2022-08-29 2023-03-31 西安交通大学 谱系树中可变剪接模式和染色质状态动态变化的分析方法
US20240393932A1 (en) * 2023-02-16 2024-11-28 XAI.health, Inc. Visualization methods and systems for evaluating performance of a classifier and selection of optimal working thresholds
EP4689172A1 (en) * 2023-03-24 2026-02-11 Foundation Medicine, Inc. Systems and methods for identifying hla variants
US20240355485A1 (en) 2023-04-13 2024-10-24 Tempus Ai, Inc. Systems and methods for predicting clinical response
WO2024263404A1 (en) * 2023-06-22 2024-12-26 23Andme, Inc. Analyzing and merging data from genome-wide association studies
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EP2549399A1 (en) * 2011-07-19 2013-01-23 Koninklijke Philips Electronics N.V. Assessment of Wnt pathway activity using probabilistic modeling of target gene expression
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Also Published As

Publication number Publication date
WO2023224709A1 (en) 2023-11-23
US20220351805A1 (en) 2022-11-03
EP4526885A1 (en) 2025-03-26
CA3148023A1 (en) 2021-02-25
JP2025143491A (ja) 2025-10-01
JP2025517450A (ja) 2025-06-05
US20210057042A1 (en) 2021-02-25
US11367508B2 (en) 2022-06-21
WO2023224709A9 (en) 2024-10-10
WO2021034712A1 (en) 2021-02-25
EP4013866A1 (en) 2022-06-22
EP4013866A4 (en) 2023-08-30
JP2022544604A (ja) 2022-10-19

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