CA3066635A1 - Neoantigen identification, manufacture, and use - Google Patents

Neoantigen identification, manufacture, and use

Info

Publication number
CA3066635A1
CA3066635A1 CA3066635A CA3066635A CA3066635A1 CA 3066635 A1 CA3066635 A1 CA 3066635A1 CA 3066635 A CA3066635 A CA 3066635A CA 3066635 A CA3066635 A CA 3066635A CA 3066635 A1 CA3066635 A1 CA 3066635A1
Authority
CA
Canada
Prior art keywords
allele
peptide
presentation
neoantigens
patient
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
CA3066635A
Other languages
English (en)
French (fr)
Inventor
Brendan BULIK-SULLIVAN
Roman YELENSKY
Jennifer BUSBY
Adnan Derti
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.)
Gritstone Bio Inc
Original Assignee
Gritstone Oncology Inc
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 Gritstone Oncology Inc filed Critical Gritstone Oncology Inc
Publication of CA3066635A1 publication Critical patent/CA3066635A1/en
Pending legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides 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
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • 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
    • 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
    • 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
    • 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
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/40—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/60—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for patient-specific data, e.g. for electronic patient records
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
    • G16H20/10—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to drugs or medications, e.g. for ensuring correct administration to patients
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16H—HEALTHCARE INFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR THE HANDLING OR PROCESSING OF MEDICAL OR HEALTHCARE DATA
    • G16H70/00—ICT specially adapted for the handling or processing of medical references
    • G16H70/60—ICT specially adapted for the handling or processing of medical references relating to pathologies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2570/00—Omics, e.g. proteomics, glycomics or lipidomics; Methods of analysis focusing on the entire complement of classes of biological molecules or subsets thereof, i.e. focusing on proteomes, glycomes or lipidomes
    • 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

Landscapes

  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Public Health (AREA)
  • Chemical & Material Sciences (AREA)
  • Epidemiology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Theoretical Computer Science (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Primary Health Care (AREA)
  • Data Mining & Analysis (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Software Systems (AREA)
  • Medicinal Chemistry (AREA)
  • Immunology (AREA)
  • Analytical Chemistry (AREA)
  • Biomedical Technology (AREA)
  • Databases & Information Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Genetics & Genomics (AREA)
  • Pathology (AREA)
  • Urology & Nephrology (AREA)
  • Organic Chemistry (AREA)
  • Biochemistry (AREA)
  • Hematology (AREA)
  • Bioethics (AREA)
  • General Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • Veterinary Medicine (AREA)
  • Animal Behavior & Ethology (AREA)
CA3066635A 2017-06-09 2018-06-08 Neoantigen identification, manufacture, and use Pending CA3066635A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201762517786P 2017-06-09 2017-06-09
US62/517,786 2017-06-09
PCT/US2018/036571 WO2018227030A1 (en) 2017-06-09 2018-06-08 Neoantigen identification, manufacture, and use

Publications (1)

Publication Number Publication Date
CA3066635A1 true CA3066635A1 (en) 2018-12-13

Family

ID=64566322

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3066635A Pending CA3066635A1 (en) 2017-06-09 2018-06-08 Neoantigen identification, manufacture, and use

Country Status (10)

Country Link
US (1) US20200105377A1 (https=)
EP (2) EP3635594B1 (https=)
JP (3) JP7795291B2 (https=)
KR (2) KR20240165471A (https=)
CN (1) CN110720127A (https=)
AU (1) AU2018279627B2 (https=)
CA (1) CA3066635A1 (https=)
IL (1) IL271038A (https=)
SG (1) SG11201911620PA (https=)
WO (1) WO2018227030A1 (https=)

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CN112210596A (zh) * 2020-09-08 2021-01-12 中生康元生物科技(北京)有限公司 基于基因融合事件的肿瘤新生抗原预测方法及其应用

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WO2016128060A1 (en) 2015-02-12 2016-08-18 Biontech Ag Predicting t cell epitopes useful for vaccination
RU2729116C2 (ru) 2015-12-16 2020-08-04 Гритстоун Онколоджи, Инк. Идентификация, производство и применение неоантигенов
WO2017194170A1 (en) 2016-05-13 2017-11-16 Biontech Rna Pharmaceuticals Gmbh Methods for predicting the usefulness of proteins or protein fragments for immunotherapy
MX2019013259A (es) 2017-05-08 2020-01-13 Gritstone Oncology Inc Vectores de neoantigeno de alfavirus.
WO2018224166A1 (en) 2017-06-09 2018-12-13 Biontech Rna Pharmaceuticals Gmbh Methods for predicting the usefulness of disease specific amino acid modifications for immunotherapy
KR20260039788A (ko) 2017-10-10 2026-03-20 시애틀 프로젝트 코포레이션 핫스팟을 이용한 신생항원 동정
CA3083097A1 (en) 2017-11-22 2019-05-31 Gritstone Oncology, Inc. Reducing junction epitope presentation for neoantigens
CN112368386A (zh) * 2018-05-23 2021-02-12 磨石肿瘤生物技术公司 共有抗原
US11599774B2 (en) * 2019-03-29 2023-03-07 International Business Machines Corporation Training machine learning model
MX2021014525A (es) 2019-05-30 2022-03-17 Gritstone Bio Inc Adenovirus modificados.
CN114761041A (zh) 2019-07-16 2022-07-15 吉利德科学公司 Hiv疫苗及其制备和使用方法
CN111303268B (zh) * 2020-03-10 2021-08-27 江苏兰恩生物治疗技术研究院有限公司 子宫肌瘤新抗原、其应用和子宫肌瘤疫苗
KR102159921B1 (ko) * 2020-03-24 2020-09-25 주식회사 테라젠바이오 펩타이드 서열 및 hla 대립유전자 서열을 이용하여 신생항원을 예측하는 방법 및 컴퓨터 프로그램
WO2022013154A1 (en) * 2020-07-14 2022-01-20 Myneo Nv Method, system and computer program product for determining presentation likelihoods of neoantigens
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CN114333998B (zh) * 2020-10-10 2024-10-15 格源致善(上海)生物科技有限公司 一种基于深度学习模型的肿瘤新抗原预测方法及新生抗原预测系统
CN112309502B (zh) * 2020-10-14 2024-09-20 深圳市新合生物医疗科技有限公司 一种计算肿瘤新抗原负荷的方法及系统
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JP7057003B1 (ja) 2021-02-26 2022-04-19 国立大学法人東京工業大学 予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム
JP7057004B1 (ja) 2021-03-05 2022-04-19 国立大学法人東京工業大学 予測装置、学習済みモデルの生成装置、予測方法、学習済みモデルの生成方法、予測プログラム、及び学習済みモデルの生成プログラム
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EP4148146A1 (en) * 2021-09-13 2023-03-15 OncoDNA Method to generate personalized neoantigens of a tumor of a patient
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Publication number Priority date Publication date Assignee Title
CN112210596A (zh) * 2020-09-08 2021-01-12 中生康元生物科技(北京)有限公司 基于基因融合事件的肿瘤新生抗原预测方法及其应用
CN112210596B (zh) * 2020-09-08 2022-04-26 中生康元生物科技(北京)有限公司 基于基因融合事件的肿瘤新生抗原预测方法及其应用

Also Published As

Publication number Publication date
KR102729393B1 (ko) 2024-11-13
CN110720127A (zh) 2020-01-21
AU2018279627A1 (en) 2020-01-16
JP2020523010A (ja) 2020-08-06
KR20240165471A (ko) 2024-11-22
SG11201911620PA (en) 2020-01-30
EP4512817A2 (en) 2025-02-26
NZ759958A (en) 2024-03-22
JP7651623B2 (ja) 2025-03-26
EP3635594A1 (en) 2020-04-15
EP3635594B1 (en) 2024-10-09
EP4512817A3 (en) 2025-08-20
AU2018279627B2 (en) 2023-08-10
JP7795291B2 (ja) 2026-01-07
EP3635594A4 (en) 2021-03-03
US20200105377A1 (en) 2020-04-02
KR20200016265A (ko) 2020-02-14
JP2023134542A (ja) 2023-09-27
WO2018227030A1 (en) 2018-12-13
IL271038A (en) 2020-01-30
JP2025094018A (ja) 2025-06-24

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