CA3148023A1 - 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
CA3148023A1
CA3148023A1 CA3148023A CA3148023A CA3148023A1 CA 3148023 A1 CA3148023 A1 CA 3148023A1 CA 3148023 A CA3148023 A CA 3148023A CA 3148023 A CA3148023 A CA 3148023A CA 3148023 A1 CA3148023 A1 CA 3148023A1
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Canada
Prior art keywords
pathway
disruption
data
gene
trained
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Pending
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CA3148023A
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English (en)
French (fr)
Inventor
Nike T. Beaubier
Hailey B. Lefkofsky
Lee F. Langer
Joshua SK Bell
Catherine Igartua
Joshua Drews
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Tempus AI Inc
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Tempus Labs Inc
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Publication of CA3148023A1 publication Critical patent/CA3148023A1/en
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)
CA3148023A 2019-08-16 2020-08-14 Systems and methods for detecting cellular pathway dysregulation in cancer specimens Pending CA3148023A1 (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
CA3148023A1 true CA3148023A1 (en) 2021-02-25

Family

ID=74646007

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3148023A Pending CA3148023A1 (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=)

Families Citing this family (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2020334901A1 (en) * 2019-08-16 2022-03-24 Tempus Ai, Inc. Systems and methods for detecting cellular pathway dysregulation in cancer specimens
US11645555B2 (en) 2019-10-12 2023-05-09 International Business Machines Corporation Feature selection using Sobolev Independence Criterion
US11373760B2 (en) * 2019-10-12 2022-06-28 International Business Machines Corporation False detection rate control with null-hypothesis
CA3174332A1 (en) 2020-04-21 2021-10-28 Jason PERERA Tcr/bcr profiling
WO2021231713A2 (en) 2020-05-14 2021-11-18 Ampel Biosolutions, Llc Methods and systems for machine learning analysis of single nucleotide polymorphisms in lupus
EP4271837A4 (en) 2020-12-31 2025-10-15 Tempus Ai Inc SYSTEMS AND METHODS FOR DETECTING MULTIMOLECULAR BIOMARKERS
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
US20250111910A1 (en) 2023-09-29 2025-04-03 Tempus Al, Inc. Methods and systems for disease phenotyping using multimodal ehr data and weak supervision

Family Cites Families (18)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090299646A1 (en) * 2004-07-30 2009-12-03 Soheil Shams System and method for biological pathway perturbation analysis
EP2419540B1 (en) * 2009-04-18 2017-05-17 Merck Sharp & Dohme Corp. Methods and gene expression signature for assessing ras pathway activity
WO2015077725A1 (en) 2013-11-22 2015-05-28 Dignity Health Diagnosing idh1 related subgroups and treatment of cancer
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
HK1205767A1 (en) * 2012-07-26 2015-12-24 The Regents Of The University Of California Screening, diagnosis and prognosis of autism and other developmental disorders
WO2014116881A1 (en) * 2013-01-23 2014-07-31 Reproductive Genetics And Technology Solutions, Llc Compositions and methods for genetic analysis of embryos
US20170335396A1 (en) * 2014-11-05 2017-11-23 Veracyte, Inc. Systems and methods of diagnosing idiopathic pulmonary fibrosis on transbronchial biopsies using machine learning and high dimensional transcriptional data
KR101785795B1 (ko) 2015-10-30 2017-10-13 가톨릭대학교 산학협력단 두경부암 예후 예측용 바이오마커 마이크로 rna
GB202209539D0 (en) 2017-06-13 2022-08-10 Bostongene Corp Systems and methods for identifying cancer treatments from normalized biomarker scores
DE102017216112A1 (de) 2017-09-12 2019-03-14 Thyssenkrupp Ag Aussetz-System und Aussetz-Verfahren mit zusammenziehbarem Vorleinenausleger
FR3072170B1 (fr) 2017-10-05 2020-10-16 Spade Dispositif de surveillance pour la detection, en continu, de defauts dans une section de canalisation et systeme de surveillance equipe d’au moins deux dispositifs de surveillance
AU2019317440B2 (en) 2018-08-06 2026-01-22 Tempus Ai, Inc. A multi-modal approach to predicting immune infiltration based on integrated RNA expression and imaging features
AU2019346427A1 (en) 2018-09-24 2021-05-13 Tempus Ai, Inc. Methods of normalizing and correcting RNA expression data
WO2020081607A1 (en) 2018-10-15 2020-04-23 Tempus Labs, Inc. Microsatellite instability determination system and related methods
CA3119749A1 (en) * 2018-11-15 2020-05-22 Ampel Biosolutions, Llc Machine learning disease prediction and treatment prioritization
WO2020142563A1 (en) 2018-12-31 2020-07-09 Tempus Labs, Inc. Transcriptome deconvolution of metastatic tissue samples
WO2020210487A1 (en) * 2019-04-12 2020-10-15 Cipher Genetics Inc. Systems and methods for nutrigenomics and nutrigenetic analysis
AU2020334901A1 (en) * 2019-08-16 2022-03-24 Tempus Ai, Inc. Systems and methods for detecting cellular pathway dysregulation in cancer specimens

Also Published As

Publication number Publication date
WO2023224709A1 (en) 2023-11-23
US20220351805A1 (en) 2022-11-03
EP4526885A1 (en) 2025-03-26
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
AU2020334901A1 (en) 2022-03-24
EP4013866A4 (en) 2023-08-30
JP2022544604A (ja) 2022-10-19

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