CN108351916A - 新生抗原分析 - Google Patents
新生抗原分析 Download PDFInfo
- Publication number
- CN108351916A CN108351916A CN201680050906.1A CN201680050906A CN108351916A CN 108351916 A CN108351916 A CN 108351916A CN 201680050906 A CN201680050906 A CN 201680050906A CN 108351916 A CN108351916 A CN 108351916A
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- China
- Prior art keywords
- neoantigens
- candidate
- candidate neoantigens
- peptide
- peptides
- 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.)
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1034—Isolating an individual clone by screening libraries
- C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1034—Isolating an individual clone by screening libraries
- C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
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- G—PHYSICS
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- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
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- 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
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
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- G—PHYSICS
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- 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
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
- G01N33/5758—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumours, cancers or neoplasias, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides or metabolites
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- G—PHYSICS
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- 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
- G01N33/6878—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids in epitope analysis
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- G—PHYSICS
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- 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
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- G—PHYSICS
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- 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
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- G16B20/30—Detection of binding sites or motifs
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- G16B35/20—Screening of libraries
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- G16C20/20—Identification of molecular entities, parts thereof or of chemical compositions
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- G16C20/50—Molecular design, e.g. of drugs
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- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
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- G16C20/70—Machine learning, data mining or chemometrics
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- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
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- 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
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/136—Screening for pharmacological compounds
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
- G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
- G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
- G01N2333/70503—Immunoglobulin superfamily, e.g. VCAMs, PECAM, LFA-3
- G01N2333/70539—MHC-molecules, e.g. HLA-molecules
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- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Engineering & Computer Science (AREA)
- Chemical & Material Sciences (AREA)
- Physics & Mathematics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Molecular Biology (AREA)
- General Health & Medical Sciences (AREA)
- Biotechnology (AREA)
- Genetics & Genomics (AREA)
- Immunology (AREA)
- Analytical Chemistry (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biomedical Technology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Theoretical Computer Science (AREA)
- Biophysics (AREA)
- Medical Informatics (AREA)
- Biochemistry (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Urology & Nephrology (AREA)
- Hematology (AREA)
- Organic Chemistry (AREA)
- Evolutionary Biology (AREA)
- Microbiology (AREA)
- Pathology (AREA)
- Wood Science & Technology (AREA)
- Zoology (AREA)
- Medicinal Chemistry (AREA)
- General Engineering & Computer Science (AREA)
- Crystallography & Structural Chemistry (AREA)
- Cell Biology (AREA)
- General Physics & Mathematics (AREA)
- Food Science & Technology (AREA)
- Library & Information Science (AREA)
- Computing Systems (AREA)
- Oncology (AREA)
- Hospice & Palliative Care (AREA)
- Plant Pathology (AREA)
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Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| US201562192373P | 2015-07-14 | 2015-07-14 | |
| US62/192,373 | 2015-07-14 | ||
| PCT/US2016/042288 WO2017011660A1 (en) | 2015-07-14 | 2016-07-14 | Neoantigen analysis |
Related Child Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN202511758884.1A Division CN121963858A (en) | 2015-07-14 | 2016-07-14 | Neoantigen analysis |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| CN108351916A true CN108351916A (zh) | 2018-07-31 |
Family
ID=57757739
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN201680050906.1A Pending CN108351916A (zh) | 2015-07-14 | 2016-07-14 | 新生抗原分析 |
Country Status (6)
| Country | Link |
|---|---|
| US (3) | US10563266B2 (https=) |
| EP (2) | EP3323070B1 (https=) |
| JP (1) | JP2018524008A (https=) |
| CN (1) | CN108351916A (https=) |
| CA (2) | CA3255210A1 (https=) |
| WO (1) | WO2017011660A1 (https=) |
Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN109706065A (zh) * | 2018-12-29 | 2019-05-03 | 深圳裕策生物科技有限公司 | 肿瘤新生抗原负荷检测装置及存储介质 |
| CN110706742A (zh) * | 2019-09-30 | 2020-01-17 | 中生康元生物科技(北京)有限公司 | 泛癌种肿瘤新生抗原高通量预测方法及其应用 |
| CN111755067A (zh) * | 2019-03-28 | 2020-10-09 | 格源致善(上海)生物科技有限公司 | 一种肿瘤新生抗原的筛选方法 |
| CN112309502A (zh) * | 2020-10-14 | 2021-02-02 | 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 |
| CN112771214A (zh) * | 2018-09-27 | 2021-05-07 | 瓦西博迪公司 | 用于选择新表位的方法 |
| CN113039612A (zh) * | 2018-08-28 | 2021-06-25 | 赛科维有限两合公司 | 分级和/或选择肿瘤特异性新抗原的方法 |
| CN113424264A (zh) * | 2018-11-15 | 2021-09-21 | Nouscom股份公司 | 用于生成个性化癌症疫苗的癌症突变选择 |
Families Citing this family (27)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2016128060A1 (en) * | 2015-02-12 | 2016-08-18 | Biontech Ag | Predicting t cell epitopes useful for vaccination |
| GB201516047D0 (en) | 2015-09-10 | 2015-10-28 | Cancer Rec Tech Ltd | Method |
| US11514289B1 (en) | 2016-03-09 | 2022-11-29 | Freenome Holdings, Inc. | Generating machine learning models using genetic data |
| JP7155470B2 (ja) * | 2017-03-31 | 2022-10-19 | エーシーティー ジェノミックス (アイピー) カンパニー リミテッド | 免疫原性がん特異的エピトープのためのランク付けシステム |
| 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 |
| EP3688165A4 (en) | 2017-09-25 | 2021-09-29 | Nant Holdings IP, LLC | VALIDATION OF THE PRESENTATION OF NEOEPITOPES |
| CN108388773B (zh) * | 2018-02-01 | 2019-11-19 | 杭州纽安津生物科技有限公司 | 一种肿瘤新生抗原的鉴定方法 |
| CN108491689B (zh) * | 2018-02-01 | 2019-07-09 | 杭州纽安津生物科技有限公司 | 基于转录组的肿瘤新抗原鉴定方法 |
| CN108796055B (zh) * | 2018-06-12 | 2022-04-08 | 深圳裕策生物科技有限公司 | 基于二代测序的肿瘤新生抗原检测方法、装置和存储介质 |
| EP3815091A4 (en) * | 2018-06-29 | 2022-03-23 | Rady Children's Hospital Research Center | Method and system for sample identity assurance |
| EP3618071A1 (en) * | 2018-08-28 | 2020-03-04 | CeCaVa GmbH & Co. KG | Methods for selecting tumor-specific neoantigens |
| CA3120200A1 (en) | 2018-11-15 | 2020-05-22 | Personal Genome Diagnostics Inc. | Method of improving prediction of response for cancer patients treated with immunotherapy |
| CN109801678B (zh) * | 2019-01-25 | 2023-07-25 | 上海鲸舟基因科技有限公司 | 基于全转录组的肿瘤抗原预测方法及其应用 |
| CN111696628A (zh) * | 2019-03-15 | 2020-09-22 | 痕准生物科技有限公司 | 新生抗原的鉴定方法 |
| WO2020221783A1 (en) * | 2019-04-29 | 2020-11-05 | Vaccibody As | Methods for pre-selection of neoepitopes |
| CN110600077B (zh) * | 2019-08-29 | 2022-07-12 | 北京优迅医学检验实验室有限公司 | 肿瘤新抗原的预测方法及其应用 |
| EP4062177A1 (en) * | 2019-11-18 | 2022-09-28 | Epivax Therapeutics, Inc. | Improved compositions and methods for shared neo-epitope vaccines |
| CN114929899B (zh) * | 2020-01-07 | 2026-03-10 | 韩国科学技术院 | 一种新抗原的筛选方法、系统及其用途 |
| GB202006760D0 (en) * | 2020-05-07 | 2020-06-24 | Univ Helsinki | Bioinformatics |
| JP2024508677A (ja) * | 2021-02-05 | 2024-02-28 | アマゾン テクノロジーズ インコーポレイテッド | 個別化がんワクチン用ネオアンチゲンのランク付け |
| EP4330380A1 (en) | 2021-04-30 | 2024-03-06 | Tigen Pharma SA | Single vessel expansion of lymphocytes |
| US12537072B1 (en) | 2021-05-27 | 2026-01-27 | Amazon Technologies, Inc. | Immunogenic response prediction based on major histocompatibility complex (MHC) data |
| US20220383996A1 (en) * | 2021-05-27 | 2022-12-01 | Amazon Technologies, Inc. | Assigning peptides to peptide groups for vaccine development |
| US12518851B2 (en) * | 2021-09-07 | 2026-01-06 | Nec Corporation | Binding peptide generation for MHC class I proteins with deep reinforcement learning for immunotherapy decision making |
| JP2025541604A (ja) | 2022-11-02 | 2025-12-22 | ティゲン・ファーマ・ソシエテ・アノニム | リンパ球の拡大 |
| WO2024261339A1 (en) | 2023-06-23 | 2024-12-26 | Tigen Pharma Sa | Lymphocyte-stimulatory matrix (lsm) and uses thereof for expansion of lymphocyte populations |
| WO2025049577A2 (en) * | 2023-08-29 | 2025-03-06 | Foundation Medicine, Inc. | Neoantigen feature selection for prioritization of potential immunotherapy targets |
Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1889086A (zh) * | 2006-07-20 | 2007-01-03 | 上海交通大学 | 交叉反应抗原计算机辅助筛选的方法 |
| WO2007101227A2 (en) * | 2006-02-27 | 2007-09-07 | Arizona Board Of Regents For And On Behalf Of Arizona State University | Identification and use of novopeptides for the treatment of cancer |
| WO2014052707A2 (en) * | 2012-09-28 | 2014-04-03 | The University Of Connecticut | Identification of tumor-protective epitopes for the treatment of cancers |
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| GB9620209D0 (en) | 1996-09-27 | 1996-11-13 | Cemu Bioteknik Ab | Method of sequencing DNA |
| US6054276A (en) | 1998-02-23 | 2000-04-25 | Macevicz; Stephen C. | DNA restriction site mapping |
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| WO2001023610A2 (en) | 1999-09-29 | 2001-04-05 | Solexa Ltd. | Polynucleotide sequencing |
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| WO2005042781A2 (en) | 2003-10-31 | 2005-05-12 | Agencourt Personal Genomics Corporation | Methods for producing a paired tag from a nucleic acid sequence and methods of use thereof |
| US7601499B2 (en) | 2005-06-06 | 2009-10-13 | 454 Life Sciences Corporation | Paired end sequencing |
| US7329860B2 (en) | 2005-11-23 | 2008-02-12 | Illumina, Inc. | Confocal imaging methods and apparatus |
| US7754429B2 (en) | 2006-10-06 | 2010-07-13 | Illumina Cambridge Limited | Method for pair-wise sequencing a plurity of target polynucleotides |
| US8262900B2 (en) | 2006-12-14 | 2012-09-11 | Life Technologies Corporation | Methods and apparatus for measuring analytes using large scale FET arrays |
| US7835871B2 (en) | 2007-01-26 | 2010-11-16 | Illumina, Inc. | Nucleic acid sequencing system and method |
| WO2008098014A2 (en) | 2007-02-05 | 2008-08-14 | Applied Biosystems, Llc | System and methods for indel identification using short read sequencing |
| US8271206B2 (en) | 2008-04-21 | 2012-09-18 | Softgenetics Llc | DNA sequence assembly methods of short reads |
| US20110257889A1 (en) | 2010-02-24 | 2011-10-20 | Pacific Biosciences Of California, Inc. | Sequence assembly and consensus sequence determination |
| BR112012029066A2 (pt) * | 2010-05-14 | 2020-09-01 | The General Hospital Corporation | composições e processos de identificação de neoantígenos específicos de tumor. |
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2016
- 2016-07-14 EP EP16825179.1A patent/EP3323070B1/en active Active
- 2016-07-14 CA CA3255210A patent/CA3255210A1/en active Pending
- 2016-07-14 JP JP2018501936A patent/JP2018524008A/ja active Pending
- 2016-07-14 WO PCT/US2016/042288 patent/WO2017011660A1/en not_active Ceased
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Cited By (9)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN113039612A (zh) * | 2018-08-28 | 2021-06-25 | 赛科维有限两合公司 | 分级和/或选择肿瘤特异性新抗原的方法 |
| CN112771214A (zh) * | 2018-09-27 | 2021-05-07 | 瓦西博迪公司 | 用于选择新表位的方法 |
| CN112771214B (zh) * | 2018-09-27 | 2025-06-13 | 耐考德治疗股份有限公司 | 用于选择新表位的方法 |
| CN113424264A (zh) * | 2018-11-15 | 2021-09-21 | Nouscom股份公司 | 用于生成个性化癌症疫苗的癌症突变选择 |
| CN113424264B (zh) * | 2018-11-15 | 2024-04-12 | Nouscom股份公司 | 用于生成个性化癌症疫苗的癌症突变选择 |
| CN109706065A (zh) * | 2018-12-29 | 2019-05-03 | 深圳裕策生物科技有限公司 | 肿瘤新生抗原负荷检测装置及存储介质 |
| CN111755067A (zh) * | 2019-03-28 | 2020-10-09 | 格源致善(上海)生物科技有限公司 | 一种肿瘤新生抗原的筛选方法 |
| CN110706742A (zh) * | 2019-09-30 | 2020-01-17 | 中生康元生物科技(北京)有限公司 | 泛癌种肿瘤新生抗原高通量预测方法及其应用 |
| CN112309502A (zh) * | 2020-10-14 | 2021-02-02 | 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 |
Also Published As
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|---|---|
| EP4407622A2 (en) | 2024-07-31 |
| US20250270656A1 (en) | 2025-08-28 |
| CA2992578A1 (en) | 2017-01-19 |
| EP3323070B1 (en) | 2024-05-08 |
| US10563266B2 (en) | 2020-02-18 |
| CA2992578C (en) | 2025-09-09 |
| EP3323070A4 (en) | 2019-03-13 |
| EP3323070A1 (en) | 2018-05-23 |
| WO2017011660A1 (en) | 2017-01-19 |
| US20200160939A1 (en) | 2020-05-21 |
| EP4407622A3 (en) | 2025-01-08 |
| JP2018524008A (ja) | 2018-08-30 |
| CA3255210A1 (en) | 2025-03-19 |
| US12331361B2 (en) | 2025-06-17 |
| US20170016075A1 (en) | 2017-01-19 |
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