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 PDFInfo
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| US201562240494P | 2015-10-12 | 2015-10-12 | |
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| 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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| CN108701173A true CN108701173A (zh) | 2018-10-23 |
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| HK (1) | HK1258091A1 (enExample) |
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Cited By (4)
| 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 |
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| Publication number | Priority date | Publication date | Assignee | Title |
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| EP3414692A4 (en) | 2016-02-12 | 2020-07-29 | Nantomics, LLC | HIGH-RATE IDENTIFICATION OF PATIENT-SPECIFIC NEOEPITOPES AS THERAPEUTIC TARGETS FOR CANCER IMMUNOTHERAPIES |
| US11875877B2 (en) | 2016-08-25 | 2024-01-16 | Nantomics, Llc | Immunotherapy markers and uses therefor |
| IL268919B2 (en) * | 2017-03-03 | 2023-10-01 | Treos Bio Zrt | A personalized immunogenic peptide identification platform |
| CN111373050A (zh) * | 2017-06-20 | 2020-07-03 | 生物辐射实验室股份有限公司 | 用于遗传不稳定性的数字扩增试验 |
| WO2019031939A2 (ko) * | 2017-08-10 | 2019-02-14 | 주식회사 굳티셀 | 암 치료를 위한 t 세포의 활성화 방법 |
| 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 |
| EP3784802A1 (en) * | 2018-04-25 | 2021-03-03 | Koninklijke Philips N.V. | Tumor functional mutation and epitope loads as improved predictive biomarkers for immunotherapy response |
| EP3826669A2 (en) | 2018-07-26 | 2021-06-02 | Frame Pharmaceuticals B.V. | Off-the-shelf cancer vaccines |
| 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)
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|---|---|---|---|---|
| EP1461001A4 (en) | 2002-01-03 | 2010-03-31 | Scripps Research Inst | ASSOCIATED WITH CANCER EPITOP |
| PL1601450T3 (pl) | 2003-03-10 | 2014-03-31 | Expression Pathology Inc | Ciekły preparat tkankowy z próbek biologicznych, tkanek i komórek poddanych obróbce histopatologicznej |
| WO2005019432A2 (en) | 2003-08-20 | 2005-03-03 | Cleveland Clinic Foundation Innovations | 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 |
| US8906367B2 (en) | 2007-01-05 | 2014-12-09 | University Of Zurich | Method of providing disease-specific binding molecules and targets |
| KR102315754B1 (ko) | 2010-05-14 | 2021-10-22 | 더 제너럴 하스피톨 코포레이션 | 종양 특이적 신생항원을 확인하는 조성물 및 방법 |
| US9646134B2 (en) | 2010-05-25 | 2017-05-09 | The Regents Of The University Of California | Bambam: parallel comparative analysis of high-throughput sequencing data |
| KR102042253B1 (ko) | 2010-05-25 | 2019-11-07 | 더 리젠츠 오브 더 유니버시티 오브 캘리포니아 | Ｂａｍｂａｍ：고처리율 서열분석 데이터의 병렬 비교 분석 |
| US9856320B2 (en) | 2012-05-15 | 2018-01-02 | Bristol-Myers Squibb Company | Cancer immunotherapy by disrupting PD-1/PD-L1 signaling |
| AU2013323368B2 (en) | 2012-09-28 | 2019-03-21 | The University Of Connecticut | Identification of tumor-protective epitopes for the treatment of cancers |
| CA2908434C (en) | 2013-04-07 | 2021-12-28 | 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 |
| EP3082853A2 (en) * | 2013-12-20 | 2016-10-26 | The Broad Institute, Inc. | Combination therapy with neoantigen vaccine |
| KR20160102314A (ko) | 2014-01-02 | 2016-08-29 | 메모리얼 슬로안-케터링 캔서 센터 | 면역 치료요법에 대한 암 반응의 결정인자 |
| US20190099475A1 (en) | 2015-04-08 | 2019-04-04 | Nantomics, Llc | Cancer neoepitopes |
| WO2016172722A1 (en) | 2015-04-23 | 2016-10-27 | Nantomics, Llc | Cancer neoepitopes |
| RU2018106934A (ru) | 2015-08-25 | 2019-09-26 | Нантомикс, Ллс | Системы и способы высокоточного определения вариантов |
| JP2018532736A (ja) | 2015-10-12 | 2018-11-08 | ナントミクス，エルエルシー | チェックポイント阻害物質への感受性を予測するｍｓｉおよびネオエピトープの探索のための系、組成物、および方法 |
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2016
- 2016-10-12 JP JP2018519039A patent/JP2018532736A/ja active Pending
- 2016-10-12 HK HK19100475.3A patent/HK1258091A1/zh unknown
- 2016-10-12 CA CA3003251A patent/CA3003251A1/en active Pending
- 2016-10-12 CN CN201680065549.6A patent/CN108701173A/zh not_active Withdrawn
- 2016-10-12 US US15/292,021 patent/US11626187B2/en active Active
- 2016-10-12 EP EP16856134.8A patent/EP3362930A4/en not_active Withdrawn
- 2016-10-12 AU AU2016339035A patent/AU2016339035A1/en not_active Abandoned
- 2016-10-12 WO PCT/US2016/056692 patent/WO2017066357A1/en not_active Ceased
- 2016-10-12 KR KR1020187013060A patent/KR20180087244A/ko not_active Withdrawn
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2018
- 2018-04-12 IL IL258679A patent/IL258679A/en unknown
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2023
- 2023-02-02 US US18/163,664 patent/US20230307090A1/en active Pending
Cited By (4)
| 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 |
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| CA3003251A1 (en) | 2017-04-20 |
| US11626187B2 (en) | 2023-04-11 |
| AU2016339035A1 (en) | 2018-05-10 |
| WO2017066357A1 (en) | 2017-04-20 |
| US20170032082A1 (en) | 2017-02-02 |
| HK1258091A1 (zh) | 2019-11-01 |
| EP3362930A4 (en) | 2019-06-19 |
| KR20180087244A (ko) | 2018-08-01 |
| US20230307090A1 (en) | 2023-09-28 |
| EP3362930A1 (en) | 2018-08-22 |
| JP2018532736A (ja) | 2018-11-08 |
| IL258679A (en) | 2018-06-28 |
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