HRP20210773T1 - Predviđanje imunogenosti epitopa t stanica - Google Patents
Predviđanje imunogenosti epitopa t stanica Download PDFInfo
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- HRP20210773T1 HRP20210773T1 HRP20210773TT HRP20210773T HRP20210773T1 HR P20210773 T1 HRP20210773 T1 HR P20210773T1 HR P20210773T T HRP20210773T T HR P20210773TT HR P20210773 T HRP20210773 T HR P20210773T HR P20210773 T1 HRP20210773 T1 HR P20210773T1
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- 230000005847 immunogenicity Effects 0.000 title claims 4
- 238000000034 method Methods 0.000 claims 29
- 108091005601 modified peptides Proteins 0.000 claims 23
- 238000012986 modification Methods 0.000 claims 20
- 230000004048 modification Effects 0.000 claims 20
- 150000001413 amino acids Chemical class 0.000 claims 10
- 108090000765 processed proteins & peptides Proteins 0.000 claims 9
- 239000000126 substance Substances 0.000 claims 8
- 239000012634 fragment Substances 0.000 claims 6
- 230000035772 mutation Effects 0.000 claims 5
- 102000004169 proteins and genes Human genes 0.000 claims 4
- 108090000623 proteins and genes Proteins 0.000 claims 4
- 210000004027 cell Anatomy 0.000 claims 3
- 108091005573 modified proteins Proteins 0.000 claims 3
- 102000035118 modified proteins Human genes 0.000 claims 3
- 206010028980 Neoplasm Diseases 0.000 claims 2
- 108700026244 Open Reading Frames Proteins 0.000 claims 2
- 201000011510 cancer Diseases 0.000 claims 2
- 229920001184 polypeptide Polymers 0.000 claims 2
- 102000004196 processed proteins & peptides Human genes 0.000 claims 2
- 238000006467 substitution reaction Methods 0.000 claims 2
- 229960005486 vaccine Drugs 0.000 claims 2
- 206010069754 Acquired gene mutation Diseases 0.000 claims 1
- 108700028369 Alleles Proteins 0.000 claims 1
- 102000043129 MHC class I family Human genes 0.000 claims 1
- 108091054437 MHC class I family Proteins 0.000 claims 1
- 102000043131 MHC class II family Human genes 0.000 claims 1
- 108091054438 MHC class II family Proteins 0.000 claims 1
- 108091008874 T cell receptors Proteins 0.000 claims 1
- 102000016266 T-Cell Antigen Receptors Human genes 0.000 claims 1
- 230000002163 immunogen Effects 0.000 claims 1
- 102000039446 nucleic acids Human genes 0.000 claims 1
- 108020004707 nucleic acids Proteins 0.000 claims 1
- 150000007523 nucleic acids Chemical class 0.000 claims 1
- 238000012163 sequencing technique Methods 0.000 claims 1
- 230000037439 somatic mutation Effects 0.000 claims 1
Classifications
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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
- 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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- 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
-
- 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
- A61K39/0005—Vertebrate antigens
- A61K39/0011—Cancer antigens
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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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
-
- 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
-
- 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
- A61K2039/80—Vaccine for a specifically defined cancer
-
- 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
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
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- Life Sciences & Earth Sciences (AREA)
- Chemical & Material Sciences (AREA)
- General Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Physics & Mathematics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Immunology (AREA)
- Genetics & Genomics (AREA)
- Analytical Chemistry (AREA)
- Biophysics (AREA)
- Microbiology (AREA)
- Molecular Biology (AREA)
- Medicinal Chemistry (AREA)
- Biotechnology (AREA)
- Organic Chemistry (AREA)
- Public Health (AREA)
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- Pharmacology & Pharmacy (AREA)
- Animal Behavior & Ethology (AREA)
- Mycology (AREA)
- Epidemiology (AREA)
- Medical Informatics (AREA)
- Theoretical Computer Science (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Bioinformatics & Computational Biology (AREA)
- Evolutionary Biology (AREA)
- Oncology (AREA)
- Wood Science & Technology (AREA)
- Zoology (AREA)
- Pathology (AREA)
- Biochemistry (AREA)
- General Engineering & Computer Science (AREA)
- Hospice & Palliative Care (AREA)
- Chemical Kinetics & Catalysis (AREA)
- General Chemical & Material Sciences (AREA)
- Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
- Gastroenterology & Hepatology (AREA)
- Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)
Claims (26)
1. Kompjuterizirani postupak predviđanja imunogenosti izmijenjenih peptida koji sadrže aminokiselinske modifikacije, pri čemu su navedene modifikacije supstitucije, gdje postupak obuhvaća korake:
a) utvrđivanje rezultata vezanja modificiranog peptida za jednu ili više MHC molekula,
b) utvrđivanje rezultata vezanja nemodificiranog peptida za jednu ili više MHC molekula, i
c) utvrđivanje rezultata vezanja modificiranog peptida, kada se nalazi u kompleksu MHC-peptid, za jedan ili više T-staničnih receptora, što obuhvaća utvrđivanje rezultata kemijskih i fizičkih sličnosti između nemodificiranih i modificiranih aminokiselina, pri čemu se rezultat međusobnih kemijskih i fizičkih sličnosti određuje na osnovu vjerojatnosti izmjene tih aminokiselina u prirodi, pri čemu aminokiseline koje se češće izmjenjuju u prirodi smatraju međusobno sličnijima, gdje se kemijske i fizičke sličnosti određuju primjenom supstitucijskih matrica,
pri čemu su nemodificirani i modificirani peptidi međusobno identični, sa izuzetkom navedene modifikacije(a),
gdje su nemodificirani i modificirani peptidi dužine 8 do 15 aminokiselina, i pri čemu je predviđeno da je modificirani peptid imunogen ako (i) nemodificirani peptid ima rezultat vezanja za jednu ili više MHC molekula koji zadovoljava prag koji ukazuje na vezanje jedne ili više MHC molekula, i (ii) modificirani peptid ima rezultat vezanja za jednu ili više MHC molekula koji zadovoljava prag koji ukazuje na vezanje jedne ili više MHC molekula, i (iii) nemodificirane i modificirane aminokiseline imaju rezultat kemijskih i fizičkih sličnosti koji zadovoljava prag koji ukazuje na kemijsku i fizičku različitost.
2. Postupak prema zahtjevu 1, naznačen time što modificirani peptid sadrži fragment modificiranog proteina, gdje navedeni fragment obuhvaća modifikaciju(e) koja postoji u proteinu.
3. Postupak prema zahtjevu 1 ili 2, naznačen time što nemodificirani peptid ima izvornu aminokiselinu na poziciji(ama) koje odgovaraju poziciji(ama) modifikacije(a) u modificiranom peptidu.
4. Postupak prema bilo kojem zahtjevu 1 do 3, naznačen time što nemodificirani peptid i modificirani peptid imaju dužinu od 8 do 12 aminokiselina.
5. Postupak prema bilo kojem zahtjevu 1 do 4, naznačen time što jedna ili više MHC molekula obuhvaćaju različite tipove MHC molekula, konkretno različite MHC alele.
6. Postupak prema bilo kojem zahtjevu 1 do 5, naznačen time što su jedna ili više MHC molekula MHC molekule klase I i/ili MHC molekule klase II.
7. Postupak prema bilo kojem zahtjevu 1 do 6, naznačen time što je rezultat vezanja za jednu ili više MHC molekula utvrđen postupkom koji obuhvaća usporedbu sekvence sa bazom MHC-vezujućih motiva.
8. Postupak prema bilo kojem zahtjevu 1 do 7, naznačen time što i korak a) i korak b) obuhvaćaju utvrđivanje da li navedeni rezultat zadovoljava prethodno definiran prag vezanja za jednu ili više MHC molekula, i pri čemu je prag primijenjen u koraku a) različit od praga primijenjenog u koraku b).
9. Postupak prema zahtjevu 8, naznačen time što prethodno definiran prag vezanja za jednu ili više MHC molekula reflektira vjerojatnost vezanja za jednu ili više MHC molekula.
10. Postupak prema bilo kojem zahtjevu 1 do 9, naznačen time što se kemijske i fizičke sličnosti utvrđuju primjenom evolucijskih log-odd matrica.
11. Postupak prema bilo kojem zahtjevu 1 do 10, naznačen time što modifikacija nije na poziciji sidra za vezanje za jednu ili više MHC molekula.
12. Postupak prema bilo kojem zahtjevu 1 do 11, koji obuhvaća izvođenje koraka a) na dva ili više različitih modificiranih peptida, pri čemu navedena dva ili više različitih modificiranih peptida sadrže istu modifikaciju(e).
13. Postupak prema zahtjevu 12, naznačen time što dva ili više modificiranih peptida koji sadrže istu modifikaciju(e), sadrže različite fragmente modificiranog proteina, gdje navedeni različiti fragmenti sadrže istu modifikaciju(e) koja se nalazi u proteinu.
14. Postupak prema zahtjevima 12 ili 13, naznačen time što dva ili više različitih modificiranih peptida, koji sadrže istu modifikaciju(e), sadrže sve potencijalne MHC-vezujuće fragmente modificiranog proteina, gdje navedeni fragmenti sadrže istu modifikaciju(e) koja se nalazi u proteinu.
15. Postupak prema bilo kojem zahtjevu 12 do 14, koji dalje obuhvaća odabir (tog/tih) modificiranog peptida, iz grupe dva ili više različitih modificiranih peptida koji sadrže istu modifikaciju(e), koji imaju vjerojatnost ili imaju najveću vjerojatnost vezanja za jednu ili više MHC molekula.
16. Postupak prema bilo kojem zahtjevu 12 do 15, naznačen time što se dva ili više različitih modificiranih peptida koji sadrže istu modifikaciju(e), razlikuju u dužinu i/ili poziciji modifikacije(a).
17. Postupak prema bilo kojem zahtjevu 1 do 16, koji obuhvaća izvođenje koraka a) i izborno, jednog ili oba koraka b) i c) na dva ili više različitih modificiranih peptida.
18. Postupak prema zahtjevu 17, naznačen time što navedena dva ili više različitih modificiranih peptida sadrže istu modifikaciju(e) i/ili sadrže različite modifikacije.
19. Postupak prema zahtjevu 18, naznačen time što su različite modifikacije prisutne u istom i/ili različitim proteinima.
20. Postupak prema zahtjevima 12 do 19, koji obuhvaća uspoređivanje rezultata dva ili više navedenih različitih modificiranih peptida.
21. Postupak prema zahtjevu 20, naznačen time što je rezultat vezanja modificiranog peptida za jednu ili više MHC molekula ponderiran više od rezultata kemijske i fizičke sličnosti između nemodificiranih i modificiranih aminokiselina i rezultat kemijske i fizičke sličnosti između nemodificiranih i modificiranih aminokiselina je ponderiran više od rezultata vezanja nemodificiranog peptida za jednu ili više MHC molekula.
22. Postupak prema bilo kojem zahtjevu 1 do 21, koji dalje obuhvaća identificiranje nesinonimnih mutacija u jednom ili više protein-kodirajućih područja.
23. Postupak prema bilo kojem zahtjevu 1 do 22, naznačen time što su modifikacije identificirane parcijalnim ili potpunim sekvenciranjem genoma ili transkriptoma jedne ili više stanica, kao što su jedna ili više stanica raka i izborno, jedna ili više ne-kanceroznih stanica i identificiranjem mutacija u jednom ili više protein-kodirajućih područja.
24. Postupak prema zahtjevima 22 ili 23, naznačen time što su navedene mutacije, somatske mutacije.
25. Postupak prema bilo kojem zahtjevu 22 do 24, naznačen time što su navedene mutacije, mutacije raka.
26. Postupak osiguravanja cjepiva, koji obuhvaća sljedeće korake:
a) identificiranje modifikacije(a) ili modificiranog(ih) peptida, čija je imunogenost predviđena postupkom prema bilo kojem zahtjevu 1 do 25, i
b) osiguravanje cjepiva koje sadrži peptid ili polipeptid koji sadrže modifikaciju(e) ili modificirani peptid(e), sa predviđenom imunogenošću, ili nukleinsku kiselinu koja kodira taj peptid ili polipeptid.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| PCT/EP2013/001400 WO2014180490A1 (en) | 2013-05-10 | 2013-05-10 | Predicting immunogenicity of t cell epitopes |
| EP14722117.0A EP2994159B1 (en) | 2013-05-10 | 2014-05-07 | Predicting immunogenicity of t cell epitopes |
| PCT/EP2014/001232 WO2014180569A1 (en) | 2013-05-10 | 2014-05-07 | Predicting immunogenicity of t cell epitopes |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| HRP20210773T1 true HRP20210773T1 (hr) | 2021-09-17 |
Family
ID=48539078
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| HRP20210773TT HRP20210773T1 (hr) | 2013-05-10 | 2021-05-13 | Predviđanje imunogenosti epitopa t stanica |
Country Status (24)
| Country | Link |
|---|---|
| US (2) | US11222711B2 (hr) |
| EP (2) | EP2994159B1 (hr) |
| JP (4) | JP6710634B2 (hr) |
| KR (1) | KR102399419B1 (hr) |
| CN (2) | CN105451759B (hr) |
| AU (3) | AU2014264943B2 (hr) |
| CA (1) | CA2911945C (hr) |
| CY (1) | CY1124176T1 (hr) |
| DK (1) | DK2994159T3 (hr) |
| ES (1) | ES2871384T3 (hr) |
| HK (1) | HK1215169A1 (hr) |
| HR (1) | HRP20210773T1 (hr) |
| HU (1) | HUE055146T2 (hr) |
| IL (2) | IL242281B (hr) |
| LT (1) | LT2994159T (hr) |
| MX (1) | MX2015015511A (hr) |
| PL (1) | PL2994159T3 (hr) |
| PT (1) | PT2994159T (hr) |
| RS (1) | RS61868B1 (hr) |
| RU (2) | RU2724370C2 (hr) |
| SG (1) | SG11201508816RA (hr) |
| SI (1) | SI2994159T1 (hr) |
| WO (2) | WO2014180490A1 (hr) |
| ZA (1) | ZA201508048B (hr) |
Families Citing this family (56)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| WO2014180490A1 (en) | 2013-05-10 | 2014-11-13 | Biontech Ag | Predicting immunogenicity of t cell epitopes |
| CN113791220A (zh) | 2014-09-10 | 2021-12-14 | 豪夫迈·罗氏有限公司 | 免疫原性突变体肽筛选平台 |
| WO2016128060A1 (en) * | 2015-02-12 | 2016-08-18 | Biontech Ag | Predicting t cell epitopes useful for vaccination |
| US10568948B2 (en) | 2015-05-13 | 2020-02-25 | Agenus Inc. | Vaccines for treatment and prevention of cancer |
| RU2729116C2 (ru) | 2015-12-16 | 2020-08-04 | Гритстоун Онколоджи, Инк. | Идентификация, производство и применение неоантигенов |
| JP2019505512A (ja) | 2016-01-08 | 2019-02-28 | バッシボディ アクスイェ セルスカプ | 治療用抗癌ネオエピトープワクチン |
| US20170224796A1 (en) | 2016-02-05 | 2017-08-10 | Xeme Biopharma Inc. | Therapeutic Cancer Vaccine Containing Tumor-Associated Neoantigens and Immunostimulants in a Delivery System |
| CN109072227A (zh) * | 2016-03-15 | 2018-12-21 | 组库创世纪株式会社 | 用于免疫治疗的监测和诊断及治疗剂的设计 |
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| US20190237158A1 (en) * | 2016-08-31 | 2019-08-01 | Medgenome, Inc. | Methods to analyze genetic alterations in cancer to identify therapeutic peptide vaccines and kits therefore |
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| CA3059645A1 (en) | 2017-04-10 | 2018-10-18 | Immatics Biotechnologies Gmbh | Peptides and combination of peptides for use in immunotherapy against leukemias and other cancers |
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| CN109081867B (zh) * | 2017-06-13 | 2021-05-28 | 北京大学 | 癌症特异性tcr及其分析技术和应用 |
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2019
- 2019-12-06 AU AU2019275637A patent/AU2019275637A1/en not_active Abandoned
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2020
- 2020-02-14 JP JP2020023610A patent/JP6882550B2/ja active Active
- 2020-04-02 IL IL273785A patent/IL273785A/en unknown
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2021
- 2021-05-06 JP JP2021078360A patent/JP7405792B2/ja active Active
- 2021-05-13 HR HRP20210773TT patent/HRP20210773T1/hr unknown
- 2021-05-19 CY CY20211100436T patent/CY1124176T1/el unknown
- 2021-11-30 US US17/539,157 patent/US20220093209A1/en active Pending
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2022
- 2022-02-10 AU AU2022200863A patent/AU2022200863A1/en active Pending
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2023
- 2023-12-14 JP JP2023210801A patent/JP2024037890A/ja active Pending
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