AU2016339035A1 - Systems, compositions, and methods for discovery of MSI and neoepitopes that predict sensitivity to checkpoint inhibitors - Google Patents

Systems, compositions, and methods for discovery of MSI and neoepitopes that predict sensitivity to checkpoint inhibitors Download PDF

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Publication number
AU2016339035A1
AU2016339035A1 AU2016339035A AU2016339035A AU2016339035A1 AU 2016339035 A1 AU2016339035 A1 AU 2016339035A1 AU 2016339035 A AU2016339035 A AU 2016339035A AU 2016339035 A AU2016339035 A AU 2016339035A AU 2016339035 A1 AU2016339035 A1 AU 2016339035A1
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Prior art keywords
neoepitopes
hla
matched
patient
tumor
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Abandoned
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AU2016339035A
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English (en)
Inventor
Stephen Charles BENZ
Andrew Nguyen
Kayvan Niazi
Shahrooz Rabizadeh
Patrick Soon-Shiong
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Nantomics LLC
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Nantomics LLC
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    • 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
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • 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
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56966—Animal cells
    • G01N33/56977—HLA or MHC typing
    • 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
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/575—
    • 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
    • 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
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or 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
    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
    • G16H20/40—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance relating to mechanical, radiation or invasive therapies, e.g. surgery, laser therapy, dialysis or acupuncture
    • 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
    • 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
    • G01N2333/70532—B7 molecules, e.g. CD80, CD86
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Medical Informatics (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Urology & Nephrology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Public Health (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Hematology (AREA)
  • Pathology (AREA)
  • Cell Biology (AREA)
  • Epidemiology (AREA)
  • Medicinal Chemistry (AREA)
  • Primary Health Care (AREA)
  • Food Science & Technology (AREA)
  • Microbiology (AREA)
  • General Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Genetics & Genomics (AREA)
  • Data Mining & Analysis (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Databases & Information Systems (AREA)
  • Zoology (AREA)
  • Surgery (AREA)
  • Virology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Animal Behavior & Ethology (AREA)
AU2016339035A 2015-10-12 2016-10-12 Systems, compositions, and methods for discovery of MSI and neoepitopes that predict sensitivity to checkpoint inhibitors Abandoned AU2016339035A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562240494P 2015-10-12 2015-10-12
US62/240,494 2015-10-12
PCT/US2016/056692 WO2017066357A1 (en) 2015-10-12 2016-10-12 Systems, compositions, and methods for discovery of msi and neoepitopes that predict sensitivity to checkpoint inhibitors

Publications (1)

Publication Number Publication Date
AU2016339035A1 true AU2016339035A1 (en) 2018-05-10

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AU2016339035A Abandoned AU2016339035A1 (en) 2015-10-12 2016-10-12 Systems, compositions, and methods for discovery of MSI and neoepitopes that predict sensitivity to checkpoint inhibitors

Country Status (10)

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US (2) US11626187B2 (enExample)
EP (1) EP3362930A4 (enExample)
JP (1) JP2018532736A (enExample)
KR (1) KR20180087244A (enExample)
CN (1) CN108701173A (enExample)
AU (1) AU2016339035A1 (enExample)
CA (1) CA3003251A1 (enExample)
HK (1) HK1258091A1 (enExample)
IL (1) IL258679A (enExample)
WO (1) WO2017066357A1 (enExample)

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CN108701173A (zh) 2015-10-12 2018-10-23 南托米克斯有限责任公司 用于发现预测对检查点抑制剂敏感的msi和新表位的系统、组合物和方法
KR20180091119A (ko) 2016-02-12 2018-08-14 난토믹스, 엘엘씨 암 면역요법을 위한 치료 표적으로 환자 특이적 네오에피토프의 높은 스루풋 식별 (high-throughput identification of patient-specific neoepitopes as therapeutic targets for cancer immunotherapies)
SG11201901432YA (en) 2016-08-25 2019-03-28 Nantomics Llc Immunotherapy markers and uses therefor
JP7437939B2 (ja) * 2017-03-03 2024-02-26 トレオス バイオ リミテッド 集団に基づいた免疫原性ペプチドの同定のプラットフォーム
US11104938B2 (en) 2017-06-20 2021-08-31 Bio-Rad Laboratories, Inc. Digital amplification assays for genetic instability
EP3666887A4 (en) * 2017-08-10 2021-09-01 Good T Cells, Inc. T-CELL ACTIVATION METHOD FOR CANCER TREATMENT
US11773449B2 (en) 2017-09-01 2023-10-03 The Hospital For Sick Children Profiling and treatment of hypermutant cancer
US20200385815A1 (en) * 2017-12-20 2020-12-10 Nantomics, Llc Using cfRNA for Diagnosing Minimal Residual Disease
WO2019206725A1 (en) * 2018-04-25 2019-10-31 Koninklijke Philips N.V. Tumor functional mutation and epitope loads as improved predictive biomarkers for immunotherapy response
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US20210189505A1 (en) * 2018-08-23 2021-06-24 Nantcell, Inc. Assessing microsatellite instability by liquid biopsy
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WO2020091944A1 (en) * 2018-10-31 2020-05-07 Nantomics, Llc Genomic and immune infiltration differences between msi and mss gi tumors
CN110556164B (zh) * 2019-09-09 2023-02-07 深圳裕策生物科技有限公司 用于目标区域捕获测序检测msi的方法、装置和存储介质
CN110910957B (zh) * 2019-12-31 2023-06-27 求臻医学科技(浙江)有限公司 一种基于单肿瘤样本高通量测序微卫星不稳定性探测位点筛选方法
CN111785324B (zh) * 2020-07-02 2021-02-02 深圳市海普洛斯生物科技有限公司 一种微卫星不稳定分析方法及装置
CN112183557A (zh) * 2020-09-29 2021-01-05 山西医科大学 基于胃癌组织病理图像纹理特征的msi预测模型构建方法
CN114974420A (zh) * 2021-10-29 2022-08-30 无锡臻和生物科技有限公司 预测胃肠肿瘤免疫检查点抑制剂疗效的标志物及其应用

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Publication number Publication date
CN108701173A (zh) 2018-10-23
HK1258091A1 (zh) 2019-11-01
US20170032082A1 (en) 2017-02-02
KR20180087244A (ko) 2018-08-01
US11626187B2 (en) 2023-04-11
EP3362930A1 (en) 2018-08-22
WO2017066357A1 (en) 2017-04-20
EP3362930A4 (en) 2019-06-19
JP2018532736A (ja) 2018-11-08
US20230307090A1 (en) 2023-09-28
IL258679A (en) 2018-06-28
CA3003251A1 (en) 2017-04-20

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