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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Australia
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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    • 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
    • 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
    • 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
    • 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
    • G01N33/575—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • 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)
  • Immunology (AREA)
  • Medical Informatics (AREA)
  • Biotechnology (AREA)
  • Biomedical Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biophysics (AREA)
  • Public Health (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Pathology (AREA)
  • Cell Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Epidemiology (AREA)
  • Primary Health Care (AREA)
  • Biochemistry (AREA)
  • Food Science & Technology (AREA)
  • Microbiology (AREA)
  • General Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Surgery (AREA)
  • Virology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Zoology (AREA)
  • Organic Chemistry (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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Family Applications (1)

Application Number Title Priority Date Filing Date
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)

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

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CA3003251A1 (en) 2015-10-12 2017-04-20 Nantomics, Llc Systems, compositions, and methods for discovery of msi and neoepitopes that predict sensitivity to checkpoint inhibitors
WO2017139694A1 (en) 2016-02-12 2017-08-17 Nantomics, Llc High-throughput identification of patient-specific neoepitopes as therapeutic targets for cancer immunotherapies
EP3500966B1 (en) 2016-08-25 2021-04-21 Nantomics, LLC Immunotherapy markers and uses therefor
CN110651189B (zh) * 2017-03-03 2024-10-25 特雷斯生物有限公司 肽疫苗
WO2018237088A1 (en) * 2017-06-20 2018-12-27 Bio-Rad Laboratories, Inc. DIGITAL AMPLIFICATION ASSAYS FOR GENETIC INSTABILITY
US11918634B2 (en) * 2017-08-10 2024-03-05 Good T Cells, Inc. Method for activating T cells for cancer treatment
US11773449B2 (en) 2017-09-01 2023-10-03 The Hospital For Sick Children Profiling and treatment of hypermutant cancer
WO2019133391A1 (en) * 2017-12-20 2019-07-04 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
CA3106564A1 (en) 2018-07-26 2020-01-30 Frame Pharmaceuticals B.V. Cancer vaccines for breast cancer
US20220349010A1 (en) 2018-07-26 2022-11-03 Frame Pharmaceuticals B.V. Method of preparing subject-specific immunogenic compositions based on a neo open-reading-frame peptide database
WO2020041561A1 (en) * 2018-08-23 2020-02-27 Nantcell, Inc. Assessing microsatellite instability by liquid biopsy
JP7642530B2 (ja) 2018-09-04 2025-03-10 トレオス バイオ リミテッド ペプチドワクチン
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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CA3003251A1 (en) 2015-10-12 2017-04-20 Nantomics, Llc Systems, compositions, and methods for discovery of msi and neoepitopes that predict sensitivity to checkpoint inhibitors

Also Published As

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

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