SG11201909652WA - Neoantigen identification, manufacture, and use - Google Patents

Neoantigen identification, manufacture, and use

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Publication number
SG11201909652WA
SG11201909652WA SG11201909652WA SG11201909652WA SG 11201909652W A SG11201909652W A SG 11201909652WA SG 11201909652W A SG11201909652W A SG 11201909652WA SG 11201909652W A SG11201909652W A SG 11201909652WA
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Singapore
Prior art keywords
international
gritstone
emeryville
suite
oncology
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Inventor
Thomas Boucher
Brendan Bulik-Sullivan
Jennifer Busby
Roman Yelensky
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Gritstone Oncology Inc
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Application filed by Gritstone Oncology Inc filed Critical Gritstone Oncology Inc
Publication of SG11201909652WA publication Critical patent/SG11201909652WA/en

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    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K39/0005Vertebrate antigens
    • A61K39/0011Cancer antigens
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B50/00ICT programming tools or database systems specially adapted for bioinformatics
    • G16B50/40Encryption of genetic data
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/14Blood; Artificial blood
    • A61K35/17Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K39/46Cellular immunotherapy
    • A61K39/461Cellular immunotherapy characterised by the cell type used
    • A61K39/4611T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K39/46Cellular immunotherapy
    • A61K39/463Cellular immunotherapy characterised by recombinant expression
    • A61K39/4632T-cell receptors [TCR]; antibody T-cell receptor constructs
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K39/46Cellular immunotherapy
    • A61K39/464Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643Vertebrate antigens
    • A61K39/4644Cancer antigens
    • A61K39/464401Neoantigens
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    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5044Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving specific cell types
    • G01N33/5047Cells of the immune system
    • G01N33/505Cells of the immune system involving T-cells
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B20/00ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30Detection of binding sites or motifs
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • GPHYSICS
    • G16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K2039/51Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/515Animal cells
    • A61K2039/5158Antigen-pulsed cells, e.g. T-cells
    • AHUMAN NECESSITIES
    • A61MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61KPREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00Medicinal preparations containing antigens or antibodies
    • A61K2039/58Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation
    • A61K2039/585Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation wherein the target is cancer
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/156Polymorphic or mutational markers
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/158Expression markers

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Immunology (AREA)
  • Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Cell Biology (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
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  • Animal Behavior & Ethology (AREA)
  • Veterinary Medicine (AREA)
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  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • Mycology (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Medical Informatics (AREA)
  • Zoology (AREA)
  • Oncology (AREA)
  • Hematology (AREA)
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  • Theoretical Computer Science (AREA)
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  • Spectroscopy & Molecular Physics (AREA)
  • Organic Chemistry (AREA)
  • Pathology (AREA)
  • Wood Science & Technology (AREA)
  • Biochemistry (AREA)
  • Urology & Nephrology (AREA)
  • Bioethics (AREA)
  • Virology (AREA)
  • Developmental Biology & Embryology (AREA)

Abstract

WO 18/ 195 357 Al Example 2 Example 3 / Example 1 / Example 2 • - Example 3 - Example 4 FIG. 13J Example 1 (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 25 October 2018 (25.10.2018) WIPO I PCT (51) International Patent Classification: GOOF 19/22 (2011.01) A61K 35/15 (2015.01) A61K 39/00 (2006.01) C07K 7/08 (2006.01) A61K 38/10 (2006.01) (21) International Application Number: PCT/US2018/028438 (22) International Filing Date: 19 April 2018 (19.04.2018) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/487,469 19 April 2017 (19.04.2017) US (71) Applicant: GRITSTONE ONCOLOGY, INC. [US/US]; 5858 Horton Street, Suite 210, Emeryville, CA 94608 (US). (72) Inventors: BOUCHER, Thomas; Gritstone Oncology, Inc., 5858 Horton Street, Suite 210, Emeryville, CA 94608 (US). BULIK-SULLIVAN, Brendan; Gritstone Oncolo- gy, Inc., 5858 Horton Street, Suite 210, Emeryville, CA 94608 (US). BUSBY, Jennifer; Gritstone Oncology, Inc., 5858 Horton Street, Suite 210, Emeryville, CA 94608 (US). YELENSKY, Roman; Gritstone Oncology, Inc., 5858 Horton Street, Suite 210, Emeryville, CA 94608 (US). (74) Agent: WHITEHEAD, Andrew P. et al.; Fenwick & West LLP, 801 California Street, Mountain View, CA 94041 (US). (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, 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). (54) Title: NEOANTIGEN IDENTIFICATION, MANUFACTURE, AND USE ill~~~~~~~~ 0111111010VIIIOH olo mull! omioommo oimIE (10) International Publication Number WO 2018/195357 Al (57) : Disclosed herein is a system and methods for de- termining the alleles, neoantigens, and vaccine composition as de- termined on the basis of an individual's tumor mutations. Also dis- closed are systems and methods for obtaining high quality sequenc- ing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines. [Continued on next page] WO 2018/195357 Al MIDEDIMOMMIDEFIEDMOMMEHOMINHINVOIMIE Declarations under Rule 4.17: — of inventorship (Rule 4.17(iv)) Published: — with international search report (Art. 21(3))
SG11201909652W 2017-04-19 2018-04-19 Neoantigen identification, manufacture, and use SG11201909652WA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762487469P 2017-04-19 2017-04-19
PCT/US2018/028438 WO2018195357A1 (en) 2017-04-19 2018-04-19 Neoantigen identification, manufacture, and use

Publications (1)

Publication Number Publication Date
SG11201909652WA true SG11201909652WA (en) 2019-11-28

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US (1) US20210113673A1 (en)
EP (1) EP3612965A4 (en)
JP (2) JP7217711B2 (en)
KR (1) KR20190140935A (en)
CN (1) CN110636852A (en)
AU (2) AU2018254526B2 (en)
BR (1) BR112019021782A2 (en)
CA (1) CA3060569A1 (en)
CO (1) CO2019012345A2 (en)
IL (1) IL269855B2 (en)
MX (1) MX2019012433A (en)
RU (1) RU2019136762A (en)
SG (1) SG11201909652WA (en)
WO (1) WO2018195357A1 (en)

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WO2014180490A1 (en) 2013-05-10 2014-11-13 Biontech Ag Predicting immunogenicity of t cell epitopes
WO2016128060A1 (en) 2015-02-12 2016-08-18 Biontech Ag Predicting t cell epitopes useful for vaccination
TWI765875B (en) 2015-12-16 2022-06-01 美商磨石生物公司 Neoantigen identification, manufacture, and use
SI3580561T1 (en) 2017-02-12 2024-04-30 Biontech Us Inc. Hla-based methods and compositions and uses thereof
US11634773B2 (en) * 2017-07-14 2023-04-25 The Francis Crick Institute Limited Analysis of HLA alleles in tumours and the uses thereof
EP3694532A4 (en) 2017-10-10 2021-07-14 Gritstone Oncology, Inc. Neoantigen identification using hotspots
JP2021503897A (en) 2017-11-22 2021-02-15 グリットストーン オンコロジー インコーポレイテッド Reduced junction epitope presentation for nascent antigens
JP2021509823A (en) 2018-01-04 2021-04-08 アイコニック セラピューティクス インコーポレイテッド Anti-tissue factor antibody, antibody drug conjugate, and related methods
WO2020041748A1 (en) * 2018-08-24 2020-02-27 The Regents Of The University Of California Mhc-ii genotype restricts the oncogenic mutational landscape
US10936768B2 (en) * 2018-10-15 2021-03-02 Aible, Inc. Interface for visualizing and improving model performance
AU2019374874A1 (en) * 2018-11-07 2021-06-10 Gritstone Bio, Inc. Alphavirus neoantigen vectors and interferon inhibitors
EP3906045A1 (en) 2019-01-03 2021-11-10 Evaxion Biotech ApS Vaccines targeting neoepitopes
CN111621564B (en) * 2019-02-28 2022-03-25 武汉大学 Method for identifying effective tumor neoantigen
CA3132041A1 (en) * 2019-03-06 2020-09-10 Gritstone Bio, Inc. Identification of neoantigens with mhc class ii model
AU2020234003A1 (en) 2019-03-11 2021-11-11 Evaxion Biotech A/S Nucleic acid vaccination using neo-epitope encoding constructs
WO2020185010A1 (en) * 2019-03-12 2020-09-17 (주)신테카바이오 System and method for providing neoantigen immunotherapy information by using artificial-intelligence-model-based molecular dynamics big data
JP2022533861A (en) * 2019-05-03 2022-07-26 ギレム リチャード Neoantigens in cancer
AU2020298552A1 (en) * 2019-07-02 2022-03-03 Gritstone Bio, Inc. HIV antigens and MHC complexes
WO2021011544A1 (en) 2019-07-16 2021-01-21 Gilead Sciences, Inc. Hiv vaccines and methods of making and using
EP4028763A1 (en) 2019-09-13 2022-07-20 Evaxion Biotech A/S Method for identifying t-cell epitopes
US20230072079A1 (en) 2019-12-18 2023-03-09 Evaxion Biotech A/S Nucleic acid vaccination using neo-epitope encoding constructs
EP4116436A4 (en) * 2020-01-07 2024-01-31 Korea Advanced Inst Sci & Tech Method and system for screening for neoantigens, and uses thereof
CN115698051A (en) 2020-04-07 2023-02-03 伊沃逊生物科技股份公司 Novel epitopic immunotherapy with APC targeting units
WO2021257879A1 (en) * 2020-06-18 2021-12-23 Personalis Inc. Machine-learning techniques for predicting surface-presenting peptides
AU2021307553A1 (en) 2020-07-14 2023-02-16 Evaxion Biotech A/S APC targeting units for immunotherapy
EP4213158A1 (en) 2020-11-13 2023-07-19 Ahead Biocomputing, Co. Ltd Information processing device, information processing method, recording medium recording information processing program, and information processing system
JP7057003B1 (en) 2021-02-26 2022-04-19 国立大学法人東京工業大学 Predictor, trained model generator, predictor, trained model generator, predictor, and trained model generator
JP7057004B1 (en) 2021-03-05 2022-04-19 国立大学法人東京工業大学 Predictor, trained model generator, predictor, trained model generator, predictor, and trained model generator
JP2024518302A (en) 2021-04-29 2024-05-01 イェダ リサーチ アンド デベロップメント カンパニー リミテッド T cell receptors for RAS-induced recurrent neoantigens and methods for identifying them
CN113762416B (en) * 2021-10-15 2023-05-30 南京澄实生物科技有限公司 Antigen immunogenicity prediction method and system based on multi-modal depth coding

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AU2014251207B2 (en) * 2013-04-07 2019-06-13 Dana-Farber Cancer Institute, Inc. Compositions and methods for personalized neoplasia vaccines
WO2014180490A1 (en) * 2013-05-10 2014-11-13 Biontech Ag Predicting immunogenicity of t cell epitopes
TWI765875B (en) * 2015-12-16 2022-06-01 美商磨石生物公司 Neoantigen identification, manufacture, and use
WO2017184590A1 (en) * 2016-04-18 2017-10-26 The Broad Institute Inc. Improved hla epitope prediction
CN110799196B (en) * 2017-03-31 2024-02-13 行动基因(智财)有限公司 Ranking system for immunogenic cancer specific epitope

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JP2023055775A (en) 2023-04-18
IL269855B2 (en) 2023-05-01
CN110636852A (en) 2019-12-31
JP7217711B2 (en) 2023-02-03
EP3612965A4 (en) 2021-01-13
JP2020519246A (en) 2020-07-02
IL269855B1 (en) 2023-01-01
AU2018254526A1 (en) 2019-11-14
AU2018254526B2 (en) 2024-02-15
CO2019012345A2 (en) 2020-01-17
RU2019136762A (en) 2021-05-19
KR20190140935A (en) 2019-12-20
BR112019021782A2 (en) 2020-08-18
MX2019012433A (en) 2019-12-11
CA3060569A1 (en) 2018-10-25
AU2024202903A1 (en) 2024-05-23
IL269855A (en) 2019-11-28
EP3612965A1 (en) 2020-02-26
US20210113673A1 (en) 2021-04-22
WO2018195357A1 (en) 2018-10-25

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