KR20180087244A - 체크포인트 억제제에 대한 감도를 예측하는 msi 및 네오에피토프를 발견하기 위한 위한 시스템, 조성물 및 방법 - Google Patents

체크포인트 억제제에 대한 감도를 예측하는 msi 및 네오에피토프를 발견하기 위한 위한 시스템, 조성물 및 방법 Download PDF

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KR20180087244A
KR20180087244A KR1020187013060A KR20187013060A KR20180087244A KR 20180087244 A KR20180087244 A KR 20180087244A KR 1020187013060 A KR1020187013060 A KR 1020187013060A KR 20187013060 A KR20187013060 A KR 20187013060A KR 20180087244 A KR20180087244 A KR 20180087244A
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neoepitope
hla
patient
matched
tumor
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앤드류 응유옌
카이반 니아치
패트릭 순-시옹
스티븐 찰스 벤츠
샤흐루즈 라비자데흐
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난토믹스, 엘엘씨
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KR1020187013060A 2015-10-12 2016-10-12 체크포인트 억제제에 대한 감도를 예측하는 msi 및 네오에피토프를 발견하기 위한 위한 시스템, 조성물 및 방법 Withdrawn KR20180087244A (ko)

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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

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US (2) US11626187B2 (https=)
EP (1) EP3362930A4 (https=)
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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 (2)

* 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

Families Citing this family (18)

* 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
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

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 (2)

* 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

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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
CN108701173A (zh) 2018-10-23
JP2018532736A (ja) 2018-11-08
EP3362930A1 (en) 2018-08-22

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