SG11201907738UA - Ranking system for immunogenic cancer-specific epitopes - Google Patents
Ranking system for immunogenic cancer-specific epitopesInfo
- Publication number
- SG11201907738UA SG11201907738UA SG11201907738UA SG11201907738UA SG11201907738UA SG 11201907738U A SG11201907738U A SG 11201907738UA SG 11201907738U A SG11201907738U A SG 11201907738UA SG 11201907738U A SG11201907738U A SG 11201907738UA SG 11201907738U A SG11201907738U A SG 11201907738UA
- Authority
- SG
- Singapore
- Prior art keywords
- international
- dist
- rule
- taipei city
- epitopes
- Prior art date
Links
- 206010028980 Neoplasm Diseases 0.000 title abstract 4
- 230000002163 immunogen Effects 0.000 title abstract 3
- 201000011510 cancer Diseases 0.000 title abstract 2
- 210000001744 T-lymphocyte Anatomy 0.000 abstract 2
- 238000000034 method Methods 0.000 abstract 2
- 230000035772 mutation Effects 0.000 abstract 2
- 108090000765 processed proteins & peptides Proteins 0.000 abstract 2
- 108700028369 Alleles Proteins 0.000 abstract 1
- 102000043129 MHC class I family Human genes 0.000 abstract 1
- 108091054437 MHC class I family Proteins 0.000 abstract 1
- 102000043131 MHC class II family Human genes 0.000 abstract 1
- 108091054438 MHC class II family Proteins 0.000 abstract 1
- 230000005867 T cell response Effects 0.000 abstract 1
- 210000001151 cytotoxic T lymphocyte Anatomy 0.000 abstract 1
- 201000010099 disease Diseases 0.000 abstract 1
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 abstract 1
- 210000002443 helper t lymphocyte Anatomy 0.000 abstract 1
- 230000028993 immune response Effects 0.000 abstract 1
- 230000005847 immunogenicity Effects 0.000 abstract 1
- 230000008520 organization Effects 0.000 abstract 1
- 238000007482 whole exome sequencing Methods 0.000 abstract 1
Classifications
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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
- A61K39/0005—Vertebrate antigens
- A61K39/0011—Cancer antigens
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
- C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
- C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
- C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
- C07K16/2833—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against MHC-molecules, e.g. HLA-molecules
-
- 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
- C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
- C07K14/70503—Immunoglobulin superfamily
- C07K14/70539—MHC-molecules, e.g. HLA-molecules
-
- 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
- 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
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K38/00—Medicinal preparations containing peptides
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2317/00—Immunoglobulins specific features
- C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
- C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
Landscapes
- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Chemical & Material Sciences (AREA)
- Immunology (AREA)
- Engineering & Computer Science (AREA)
- General Health & Medical Sciences (AREA)
- Physics & Mathematics (AREA)
- Biophysics (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Organic Chemistry (AREA)
- Molecular Biology (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Genetics & Genomics (AREA)
- Medical Informatics (AREA)
- Medicinal Chemistry (AREA)
- Evolutionary Biology (AREA)
- Biotechnology (AREA)
- Spectroscopy & Molecular Physics (AREA)
- Theoretical Computer Science (AREA)
- Bioinformatics & Computational Biology (AREA)
- Biochemistry (AREA)
- Analytical Chemistry (AREA)
- Public Health (AREA)
- Epidemiology (AREA)
- Data Mining & Analysis (AREA)
- Zoology (AREA)
- Gastroenterology & Hepatology (AREA)
- Cell Biology (AREA)
- Toxicology (AREA)
- Bioethics (AREA)
- Pharmacology & Pharmacy (AREA)
- Computer Vision & Pattern Recognition (AREA)
- Evolutionary Computation (AREA)
- Artificial Intelligence (AREA)
- Software Systems (AREA)
- Oncology (AREA)
- Microbiology (AREA)
- Mycology (AREA)
- Databases & Information Systems (AREA)
- Animal Behavior & Ethology (AREA)
Abstract
Epitopeidentification Component computation 'Mathirieleething m odel Weight assignment Peptide-level score designation Sample-level score designation Immunogenicity score designation () INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 04 October 2018 (04.10.2018) W I PO I PCT ~~~~~~~~~~~~~ 011101010VIIIOH olo HE mil mo lio (10) International Publication Number WO 2018/183980 A3 (51) International Patent Classification: A61K 31/7052 (2006.01) A61K 39/02 (2006.01) A61K 31/7105 (2006.01) A61K 48/00 (2006.01) A61K 39/00 (2006.01) C07H 21/02 (2006.01) (21) International Application Number: PCT/US2018/025597 (22) International Filing Date: 31 March 2018 (31.03.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/479,320 31 March 2017 (31.03.2017) US (72) Inventors; and (71) Applicants: PEI-JIA, Yang; 4f, No.208, Xinhu 2nd Rd, Neihu Dist, Taipei City, 114 (TW). CHENG, Jen-Hao; 4f, No.208, Xinhu 2nd Rd, Neihu Dist, Taipei City, 114 (TW). CHEN, Ying-Ja [US/ ]; 4f, No.208, Xinhu 2nd Rd, Nei- hu Dist, Taipei City, 114 (TW). CHEN, Shu-Jen [US/ ]; 2f.-1, No.69-1, Hejiang St., Zhongshan Dist., Taipei City, 104 (TW). CHEN, Hua-Chien; 4f., No. 17, Ln. 63, Sec. 2, Dunhua S. Rd. Daan Dist., Taipei City, 106 (TW). (74) Agent: KAO, Laurence; OPES IP CONSULTING CO., LTD, 4f. No.203, Sec. 1, Fuxing S. Rd., Daan Dist., Taipei City, 10666 (TW). (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (54) Title: RANKING SYSTEM FOR IMMUNOGENIC CANCER-SPECIFIC EPITOPES Tumor 8f normal tis LIES Whole exome sequencing Variant deterrnina on Ranking FIGURE 1 (57) : This disclosure relates to systems and methods that identify, predict, and rank immunogenic T-cell epitopes. In particular, this disclosure identifies epitopes that arose from disease-associated mutations, wherein the epitopes are predicted to elicit immune response from T cells. Specifically, this disclosure simultaneously considers peptide-level information, including MHC Class I and II presentation, helper and cytotoxic T cell response and sample-level information, including mutation clonality and MHC allele dosage. In some embodiment, the systems and methods are used for personalized treatment of cancers. [Continued on next page] WO 2018/183980 A3 MIDEDIMOMOIDEIREEMOMiliMOIHMOMMEfin GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Declarations under Rule 4.17: as to the identity of the inventor (Rule 4.17(i)) as to applicant's entitlement to apply for and be granted a patent (Rule 4.17(11)) as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(iii)) of inventorship (Rule 4.17(iv)) Published: with international search report (Art. 21(3)) before the expiration of the time limit for amending the claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) (88) Date of publication of the international search report: 20 December 2018 (20.12.2018)
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US201762479320P | 2017-03-31 | 2017-03-31 | |
PCT/US2018/025597 WO2018183980A2 (en) | 2017-03-31 | 2018-03-31 | Ranking system for immunogenic cancer-specific epitopes |
Publications (1)
Publication Number | Publication Date |
---|---|
SG11201907738UA true SG11201907738UA (en) | 2019-09-27 |
Family
ID=63676910
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
SG11201907738UA SG11201907738UA (en) | 2017-03-31 | 2018-03-31 | Ranking system for immunogenic cancer-specific epitopes |
Country Status (7)
Country | Link |
---|---|
US (1) | US11485784B2 (en) |
EP (1) | EP3600340A4 (en) |
JP (1) | JP7155470B2 (en) |
CN (1) | CN110799196B (en) |
SG (1) | SG11201907738UA (en) |
TW (1) | TWI672503B (en) |
WO (1) | WO2018183980A2 (en) |
Families Citing this family (8)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
RU2729116C2 (en) * | 2015-12-16 | 2020-08-04 | Гритстоун Онколоджи, Инк. | Identification, production and use of neoantigens |
WO2018195357A1 (en) * | 2017-04-19 | 2018-10-25 | Gritstone Oncology, Inc. | Neoantigen identification, manufacture, and use |
US11885815B2 (en) | 2017-11-22 | 2024-01-30 | Gritstone Bio, Inc. | Reducing junction epitope presentation for neoantigens |
KR20210064229A (en) * | 2018-11-21 | 2021-06-02 | 닛본 덴끼 가부시끼가이샤 | Epitope targeting method and system for neoantigen-based immunotherapy |
CN113474840A (en) * | 2018-12-21 | 2021-10-01 | 百欧恩泰美国公司 | Methods and systems for predicting HLA class II specific epitopes and characterizing CD4+ T cells |
EP3931834A1 (en) | 2019-02-28 | 2022-01-05 | Universiteit Antwerpen | Method for determining responsiveness to an epitope |
WO2020223361A1 (en) * | 2019-04-30 | 2020-11-05 | Memorial Sloan Kettering Cancer Center | System and methods for identification of non-immunogenic epitopes and determining efficacy of epitopes in therapeutic regimens |
WO2023052917A1 (en) * | 2021-09-28 | 2023-04-06 | Act Genomics (ip) Limited | Methylation biomarker selection apparatuses and methods |
Family Cites Families (11)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
JP2005301523A (en) * | 2004-04-08 | 2005-10-27 | Celestar Lexico-Sciences Inc | Apparatus and method for predicting vaccine candidate partial sequence, apparatus and method for predicting mhc-binding partial sequence, program and recording medium |
EP2771349B1 (en) | 2011-09-16 | 2020-02-26 | Iogenetics, LLC. | Bioinformatic processes for determination of peptide binding |
PT2945647T (en) | 2013-01-15 | 2020-11-26 | Memorial Sloan Kettering Cancer Center | Immunogenic wt-1 peptides and methods of use thereof |
CN105377292A (en) | 2013-04-07 | 2016-03-02 | 博德研究所 | Compositions and methods for personalized neoplasia vaccines |
EP3998481A1 (en) * | 2014-09-10 | 2022-05-18 | F. Hoffmann-La Roche AG | Immunogenic mutant peptide screening platform |
WO2016128060A1 (en) | 2015-02-12 | 2016-08-18 | Biontech Ag | Predicting t cell epitopes useful for vaccination |
US11421016B2 (en) * | 2015-04-23 | 2022-08-23 | Nantomics Llc | Cancer neoepitopes |
EP3603666A1 (en) * | 2015-04-27 | 2020-02-05 | Cancer Research Technology Limited | Method for treating cancer |
WO2017011660A1 (en) | 2015-07-14 | 2017-01-19 | Personal Genome Diagnostics, Inc. | Neoantigen analysis |
GB201516047D0 (en) * | 2015-09-10 | 2015-10-28 | Cancer Rec Tech Ltd | Method |
CN107704727B (en) | 2017-11-03 | 2020-01-31 | 杭州风起智能科技有限公司 | Neoantigen activity prediction and sequencing method based on tumor neoantigen characteristic value |
-
2018
- 2018-03-31 TW TW107111453A patent/TWI672503B/en active
- 2018-03-31 WO PCT/US2018/025597 patent/WO2018183980A2/en active Application Filing
- 2018-03-31 SG SG11201907738UA patent/SG11201907738UA/en unknown
- 2018-03-31 JP JP2020502531A patent/JP7155470B2/en active Active
- 2018-03-31 EP EP18776882.5A patent/EP3600340A4/en active Pending
- 2018-03-31 CN CN201880019637.1A patent/CN110799196B/en active Active
- 2018-03-31 US US16/497,442 patent/US11485784B2/en active Active
Also Published As
Publication number | Publication date |
---|---|
CN110799196A (en) | 2020-02-14 |
JP2020518083A (en) | 2020-06-18 |
TW201903411A (en) | 2019-01-16 |
JP7155470B2 (en) | 2022-10-19 |
WO2018183980A3 (en) | 2018-12-20 |
CN110799196B (en) | 2024-02-13 |
US20210284738A1 (en) | 2021-09-16 |
EP3600340A4 (en) | 2021-01-20 |
WO2018183980A2 (en) | 2018-10-04 |
TWI672503B (en) | 2019-09-21 |
US11485784B2 (en) | 2022-11-01 |
EP3600340A2 (en) | 2020-02-05 |
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