CA3175126A1 - Systems and methods for deconvolution of expression data - Google Patents

Systems and methods for deconvolution of expression data

Info

Publication number
CA3175126A1
CA3175126A1 CA3175126A CA3175126A CA3175126A1 CA 3175126 A1 CA3175126 A1 CA 3175126A1 CA 3175126 A CA3175126 A CA 3175126A CA 3175126 A CA3175126 A CA 3175126A CA 3175126 A1 CA3175126 A1 CA 3175126A1
Authority
CA
Canada
Prior art keywords
expression data
cell
rna
cell type
linear regression
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
CA3175126A
Other languages
English (en)
French (fr)
Inventor
Aleksandr Zaitsev
Maksim Chelushkin
Ekaterina Nuzhdina
Vladimir ZYRIN
Daniiar DYIKANOV
Alexander BAGAEV
Ravshan Ataullakhanov
Ilya CHEREMUSHKIN
Boris SHPAK
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
BostonGene Corp
Original Assignee
BostonGene Corp
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by BostonGene Corp filed Critical BostonGene Corp
Publication of CA3175126A1 publication Critical patent/CA3175126A1/en
Pending legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/18—Complex mathematical operations for evaluating statistical data, e.g. average values, frequency distributions, probability functions, regression 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
    • 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
    • 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
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Medical Informatics (AREA)
  • Data Mining & Analysis (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Genetics & Genomics (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Molecular Biology (AREA)
  • General Physics & Mathematics (AREA)
  • Mathematical Analysis (AREA)
  • Computational Mathematics (AREA)
  • Mathematical Optimization (AREA)
  • Pure & Applied Mathematics (AREA)
  • Mathematical Physics (AREA)
  • Operations Research (AREA)
  • Probability & Statistics with Applications (AREA)
  • Algebra (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Medical Treatment And Welfare Office Work (AREA)
CA3175126A 2020-03-12 2021-03-12 Systems and methods for deconvolution of expression data Pending CA3175126A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202062988700P 2020-03-12 2020-03-12
US62/988,700 2020-03-12
US202063108262P 2020-10-30 2020-10-30
US63/108,262 2020-10-30
PCT/US2021/022155 WO2021183917A1 (en) 2020-03-12 2021-03-12 Systems and methods for deconvolution of expression data

Publications (1)

Publication Number Publication Date
CA3175126A1 true CA3175126A1 (en) 2021-09-16

Family

ID=75396875

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3175126A Pending CA3175126A1 (en) 2020-03-12 2021-03-12 Systems and methods for deconvolution of expression data

Country Status (7)

Country Link
US (3) US11315658B2 (https=)
EP (2) EP4383262A3 (https=)
JP (2) JP7541585B2 (https=)
AU (1) AU2021233926B2 (https=)
CA (1) CA3175126A1 (https=)
IL (1) IL296316A (https=)
WO (1) WO2021183917A1 (https=)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP7541585B2 (ja) 2020-03-12 2024-08-28 ボストンジーン コーポレイション 発現データのデコンボリューションのためのシステム及び方法
JP2024517745A (ja) 2021-04-29 2024-04-23 ボストンジーン コーポレイション 複合腫瘍組織における腫瘍細胞発現を推定するための機械学習技法
AU2022275923A1 (en) 2021-05-18 2023-11-23 Bostongene Corporation Techniques for single sample expression projection to an expression cohort sequenced with another protocol
CN114038505B (zh) * 2021-10-19 2024-06-14 清华大学 一种在线整合多来源单细胞数据的方法和系统
EP4423301B1 (en) 2021-10-29 2025-12-10 BostonGene Corporation Tumor microenvironment types in breast cancer
US20240177803A1 (en) 2022-11-17 2024-05-30 Bostongene Corporation Comprehensive immunoprofiling of peripheral blood
EP4673723A1 (en) 2023-03-01 2026-01-07 BostonGene Corporation Systems and methods for analyzing cytometry data
EP4695425A1 (en) 2023-04-13 2026-02-18 BostonGene Corporation Pan-cancer tumor microenvironment classification based on immune escape mechanisms and immune infiltration
CN116779043A (zh) * 2023-06-30 2023-09-19 京东方科技集团股份有限公司 细胞比例预测方法、模型生成方法、设备及介质
US20260120879A1 (en) 2023-10-31 2026-04-30 Bostongene Corporation Machine learning technique for identifying ici responders and non-responders

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2971129A1 (en) * 2015-01-22 2016-07-28 The Board Of Trustees Of The Leland Stanford Junior University Methods and systems for determining proportions of distinct cell subsets
US10636512B2 (en) * 2017-07-14 2020-04-28 Cofactor Genomics, Inc. Immuno-oncology applications using next generation sequencing
EP3655955B1 (en) * 2017-07-21 2025-04-09 The Board of Trustees of the Leland Stanford Junior University Systems and methods for analyzing mixed cell populations
JP7421475B2 (ja) * 2018-06-29 2024-01-24 株式会社Preferred Networks 学習方法、混合率予測方法及び学習装置
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
WO2020142563A1 (en) 2018-12-31 2020-07-09 Tempus Labs, Inc. Transcriptome deconvolution of metastatic tissue samples
JP7541585B2 (ja) 2020-03-12 2024-08-28 ボストンジーン コーポレイション 発現データのデコンボリューションのためのシステム及び方法

Also Published As

Publication number Publication date
WO2021183917A1 (en) 2021-09-16
US11315658B2 (en) 2022-04-26
JP2023518185A (ja) 2023-04-28
JP2024174879A (ja) 2024-12-17
IL296316A (en) 2022-11-01
JP7541585B2 (ja) 2024-08-28
EP4383262A3 (en) 2024-08-14
EP4383262A2 (en) 2024-06-12
US20230178178A1 (en) 2023-06-08
US11587642B2 (en) 2023-02-21
WO2021183917A8 (en) 2021-12-16
EP4118657B1 (en) 2024-05-01
EP4118657A1 (en) 2023-01-18
US20210287759A1 (en) 2021-09-16
AU2021233926A1 (en) 2022-09-29
WO2021183917A9 (en) 2021-11-04
AU2021233926B2 (en) 2025-12-18
JP7818662B2 (ja) 2026-02-20
US20220230707A1 (en) 2022-07-21

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