CN108701173A - 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 - Google Patents

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 Download PDF

Info

Publication number
CN108701173A
CN108701173A CN201680065549.6A CN201680065549A CN108701173A CN 108701173 A CN108701173 A CN 108701173A CN 201680065549 A CN201680065549 A CN 201680065549A CN 108701173 A CN108701173 A CN 108701173A
Authority
CN
China
Prior art keywords
neo
epitopes
hla
matched
patient
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
CN201680065549.6A
Other languages
English (en)
Chinese (zh)
Inventor
A·阮
K·尼亚齐
P·宋世宗
S·C·奔驰
S·拉比扎德
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Nantomics LLC
Original Assignee
Nantomics LLC
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Nantomics LLC filed Critical Nantomics LLC
Publication of CN108701173A publication Critical patent/CN108701173A/zh
Withdrawn legal-status Critical Current

Links

Classifications

    • 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
    • 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
    • G01N33/575—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

Landscapes

  • 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)
CN201680065549.6A 2015-10-12 2016-10-12 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 Withdrawn CN108701173A (zh)

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
CN108701173A true CN108701173A (zh) 2018-10-23

Family

ID=57882841

Family Applications (1)

Application Number Title Priority Date Filing Date
CN201680065549.6A Withdrawn CN108701173A (zh) 2015-10-12 2016-10-12 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

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=)

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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
US11504420B2 (en) 2015-04-08 2022-11-22 Nantomics, Llc AGGF1 immunogenic compositions
US11626187B2 (en) 2015-10-12 2023-04-11 Nantomics Llc Systems, compositions, and methods for discovery of MSI and neoepitopes that predict sensitivity to checkpoint inhibitors

Families Citing this family (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
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

Family Cites Families (20)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
AU2003207459A1 (en) 2002-01-03 2003-07-24 The Scripps Research Institute Cancer-associated epitope
DK1601450T3 (da) 2003-03-10 2013-09-08 Expression Pathology Inc Flydende vævspræparat ud fra histopatologisk bearbejdede biologiske prøver, væv og celler
CA2535976A1 (en) 2003-08-20 2005-03-03 Cleveland Clinic Foundation A novel gene and protein associated with angiogenesis and endothelial apoptosis
US7767792B2 (en) 2004-02-20 2010-08-03 Ludwig Institute For Cancer Research Ltd. Antibodies to EGF receptor epitope peptides
JP4852046B2 (ja) 2004-10-12 2012-01-11 クルセル ホランド ベー ヴェー 癌の治療及び検出に用いる結合分子
US7811993B2 (en) 2005-06-29 2010-10-12 The Wistar Institute Of Anatomy And Biology Methods and compositions for treating melanoma
WO2008081008A1 (en) 2007-01-05 2008-07-10 University Of Zurich Method of providing disease-specific binding molecules and targets
EP2569633B1 (en) 2010-05-14 2016-02-10 The General Hospital Corporation Compositions and methods of identifying tumor specific neoantigens
KR102042253B1 (ko) 2010-05-25 2019-11-07 더 리젠츠 오브 더 유니버시티 오브 캘리포니아 Ｂａｍｂａｍ：고처리율 서열분석 데이터의 병렬 비교 분석
US9646134B2 (en) 2010-05-25 2017-05-09 The Regents Of The University Of California Bambam: parallel comparative analysis of high-throughput sequencing data
HK1203971A1 (en) 2012-05-15 2015-11-06 Bristol-Myers Squibb Company Cancer immunotherapy by disrupting pd-1/pd-l1 signaling
LT2901341T (lt) 2012-09-28 2019-09-25 The University Of Connecticut Protekcinių vėžio epitopų identifikavimas, skirtas vėžio gydymui
EP2983702A2 (en) 2013-04-07 2016-02-17 The Broad Institute, Inc. Compositions and methods for personalized neoplasia vaccines
AU2014337063A1 (en) 2013-10-18 2016-05-19 Adaptive Biotechnologies Corp. Predicting patient responsiveness to immune checkpoint inhibitors
KR20230076867A (ko) * 2013-12-20 2023-05-31 더 브로드 인스티튜트, 인코퍼레이티드 신생항원 백신과의 병용 요법
EP3090066A4 (en) * 2014-01-02 2017-08-30 Memorial Sloan Kettering Cancer Center Determinants of cancer response to immunotherapy
US20190099475A1 (en) 2015-04-08 2019-04-04 Nantomics, Llc Cancer neoepitopes
BR112017022845A2 (pt) 2015-04-23 2018-07-17 Nantomics, Llc neoepítopos de câncer
AU2016311444B2 (en) 2015-08-25 2019-02-07 Nantomics, Llc Systems and methods for high-accuracy variant calling
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

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11504420B2 (en) 2015-04-08 2022-11-22 Nantomics, Llc AGGF1 immunogenic compositions
US11626187B2 (en) 2015-10-12 2023-04-11 Nantomics Llc Systems, compositions, and methods for discovery of MSI and neoepitopes that predict sensitivity to checkpoint inhibitors
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

Also Published As

Publication number Publication date
KR20180087244A (ko) 2018-08-01
US20230307090A1 (en) 2023-09-28
AU2016339035A1 (en) 2018-05-10
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
JP2018532736A (ja) 2018-11-08
EP3362930A1 (en) 2018-08-22

Similar Documents

Publication Publication Date Title
US20230307090A1 (en) Systems, Compositions, And Methods For Discovery Of MSI And Neoepitopes That Predict Sensitivity To Checkpoint Inhibitors
US20220270709A1 (en) High-Throughput Identification of Patient-Specific Neoepitopes as Therapeutic Targets for Cancer Immunotherapies
Jiang et al. Multi-omics analysis identifies osteosarcoma subtypes with distinct prognosis indicating stratified treatment
US20240079089A1 (en) Immunotherapy Markers And Uses Therefor
Radovich et al. The integrated genomic landscape of thymic epithelial tumors
Martel-Jantin et al. Genetic variability and integration of Merkel cell polyomavirus in Merkel cell carcinoma
Ojesina et al. Landscape of genomic alterations in cervical carcinomas
CN110214275B (zh) 肿瘤抗原性加工和呈递
JP7034931B2 (ja) ネオエピトープのウイルス送達のための改善された組成物および方法ならびにその使用
Hoff et al. Novel RNA variants in colorectal cancers
Sverchkova et al. Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response
JP2023524048A (ja) 癌の免疫療法のための複合バイオマーカー
AU2017100960A4 (en) Method of identifying a gene associated with a disease or pathological condition of the disease
WO2023081117A1 (en) Immunotherapy targeting
US20220296642A1 (en) Methods of Making Therapeutic T Lymphocytes

Legal Events

Date Code Title Description
PB01 Publication
PB01 Publication
SE01 Entry into force of request for substantive examination
SE01 Entry into force of request for substantive examination
WW01 Invention patent application withdrawn after publication
WW01 Invention patent application withdrawn after publication

Application publication date: 20181023