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1. 发明申请

WO2021163546A1 METHODS AND MATERIALS FOR ASSESSING NUCLEIC ACIDS 审中-公开
公开(公告)号：WO2021163546A1
公开(公告)日：2021-08-19
申请号：PCT/US2021/017937
申请日：2021-02-12
申请人： THE JOHNS HOPKINS UNIVERSITY , PAPADOPOULOS, Nickolas , KINZLER, Kenneth W. , VOGELSTEIN, Bert , COHEN, Joshua David
发明人： PAPADOPOULOS, Nickolas , KINZLER, Kenneth W. , VOGELSTEIN, Bert , COHEN, Joshua David
IPC分类号： C12Q1/686
摘要： Provided herein are systems, kits, compositions and methods for sequencing library preparation and sequencing workflow (e.g., for the identification of mutations). In certain embodiments, provides herein systems and methods to identically barcode both strands of templates, and PCR-based enrichment of each strand that does not require hybridization capture.

2. 发明申请

WO2019133245A1 PREVENTING CYTOKINE RELEASE SYNDROME 审中-公开
公开(公告)号：WO2019133245A1
公开(公告)日：2019-07-04
申请号：PCT/US2018/064969
申请日：2018-12-11
申请人： THE JOHNS HOPKINS UNIVERSITY
发明人： VOGELSTEIN, Bert , KINZLER, Kenneth W. , PAPADOPOULOS, Nickolas , ZHOU, Shibin , STAEDTKE, Verena , BAI, Renyuan , RIGGINS, Gregory J.
IPC分类号： A61K31/198 , A61K39/395 , A61K38/22 , A61P19/02 , A61P37/00
摘要： This document relates to methods and materials for preventing cytokine release syndrome (CRS). For example, methods and materials for using one or more catecholamine inhibitors to prevent a mammal from developing CRS are provided.

3. 发明申请

WO2019100059A1 METHODS AND MATERIALS FOR ASSESSING AND TREATING CANCER 审中-公开
公开(公告)号：WO2019100059A1
公开(公告)日：2019-05-23
申请号：PCT/US2018/062007
申请日：2018-11-20
申请人： THE JOHNS HOPKINS UNIVERSITY
发明人： VOGELSTEIN, Bert , KINZLER, Kenneth W. , WANG, Qing , PAPADOPOULOS, Nickolas , ZHANG, Ming
IPC分类号： G01N33/574
摘要： This document provides methods and materials for identifying biomarkers (e.g., peptide biomarkers) that can be used to identify a mammal as having a disease (e.g., cancer). This document also provides methods and materials for identifying and/or treating cancer. For example, this document provides methods and materials for using one or more peptide fragments derived from a peptidyl-prolyl cis-trans isomerase A (PPIA) polypeptide to identify a mammal as having cancer (e.g., ovarian cancer).

4. 发明申请

WO2019067092A1 METHODS AND MATERIALS FOR ASSESSING AND TREATING CANCER 审中-公开
公开(公告)号：WO2019067092A1
公开(公告)日：2019-04-04
申请号：PCT/US2018/045669
申请日：2018-08-07
申请人： THE JOHNS HOPKINS UNIVERSITY , BOARD OF REGENTS, THE UNIVERSITY OF TEXAS SYSTEMS , THE RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK
发明人： VOGELSTEIN, Bert , KINZLER, Kenneth W. , COHEN, Joshua , PAPADOPOULOS, Nickolas , LENNON, Anne Marie , TOMASETTI, Cristian , WANG, Yuxuan , NETTO, Georges Jabboure , KARCHIN, Rachel , DOUVILLE, Chris , HANASH, Samir , SPRINGER, Simeon , GROLLMAN, Arthur , DICKMAN, Kathleen
IPC分类号： C12Q1/6886
摘要： Provided herein are methods and materials for detecting and/or treating subject (e.g. a human) having cancer. In some embodiments, methods and materials for identifying a subject as having cancer (e.g., a localized cancer) are provided in which the presence of member(s) of two or more classes of biomarkers are detected. In some embodiments, methods and materials for identifying a subject as having cancer (e.g. a localized cancer) are provided in which the presence of member(s) of at least one class of biomarkers and the presence of aneuploidy are detected. In some embodiments, methods described herein provide increased sensitivity and/or specificity in the detection of cancer in a subject (e.g. a human).

5. 发明申请

WO2012142213A2 SAFE SEQUENCING SYSTEM 审中-公开
标题翻译：安全排序系统
公开(公告)号：WO2012142213A2
公开(公告)日：2012-10-18
申请号：PCT/US2012/033207
申请日：2012-04-12
申请人： THE JOHNS HOPKINS UNIVERSITY , VOGELSTEIN, Bert , KINZLER, Kenneth W. , PAPADOPOULOS, Nickolas , KINDE, Isaac
发明人： VOGELSTEIN, Bert , KINZLER, Kenneth W. , PAPADOPOULOS, Nickolas , KINDE, Isaac
IPC分类号： C12Q1/68 , C12N15/11
CPC分类号： C12Q1/6874 , C12Q1/6806 , C12Q1/6869 , C12Q1/6876 , C12Q2563/179 , C12Q2600/158 , C12Q2535/122 , C12Q2565/514
摘要： The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called "Safe-SeqS" for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant ("super-mutants") if ≥95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro , and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.
摘要翻译：存在于DNA模板的一小部分中的突变的鉴定对于在几个生物医学研究领域的进展是必不可少的。尽管大规模并行测序仪器原则上非常适合于此任务，但是这些仪器中的错误率通常太高，无法确定罕见的变体。我们在这里描述了一种可以显着增加大规模并行测序仪器对此目的的灵敏度的方法。这种方法的一个例子是（Safe-Sequencing System），称为“Safe-SeqS”，包括（i）将唯一标识符（UID）分配给每个模板分子; （ii）每个唯一标记的模板分子的扩增以产生UID家族; 和（iii）扩增产物的冗余测序。具有相同UID的PCR片段是真正的突变体（“超突变体”），如果其中95％含有相同的突变。我们说明了这种方法用于确定聚合酶的保真度，体外合成的寡核苷酸的准确性以及正常细胞的核和线粒体基因组中突变的流行率的效用。

6. 发明申请

WO2012071096A2 ARID1A AND PPP2R1A MUTATIONS IN CANCER 审中-公开
标题翻译： ARID1A和PPP2R1A突变在癌症中
公开(公告)号：WO2012071096A2
公开(公告)日：2012-05-31
申请号：PCT/US2011/050487
申请日：2011-09-06
申请人： THE JOHNS HOPKINS UNIVERSITY , VOGELSTEIN, Bert , KINZLER, Kenneth W. , VELCULESCU, Victor , PAPADOPOULOS, Nickolas , JONES, Sian
发明人： VOGELSTEIN, Bert , KINZLER, Kenneth W. , VELCULESCU, Victor , PAPADOPOULOS, Nickolas , JONES, Sian
IPC分类号： C12Q1/68 , C12N5/09 , G01N33/68 , A61K31/7088 , C12N15/11
CPC分类号： C12Q1/6886 , A61K31/7088 , A61K31/711 , C12Q2600/156 , G01N33/5011
摘要： Two genes, ARID1A (AT-rich interactive domain-containing protein 1A) and PPP2R1A (protein-phosphatase 2, regulatory subunit 1, alpha), can be used in methods which are useful for detecting cancer, diagnosing cancer, contributing to a diagnosis of cancer, confirming a diagnosis of cancer, identifying appropriate treatments for cancer, monitoring treatment of cancer, and evaluating treatment protocols for cancer, including ovarian clear cell carcinoma, breast cancer, colon cancer, gastric cancer, lung cancer, medulloblastoma, pancreatic cancer, and prostate cancer.
摘要翻译：在可用于检测癌症的方法中可以使用两种基因，即ARID1A（富含AT的交互结构域的蛋白质1A）和PPP2R1A（蛋白质磷酸酶2，调节亚基1，α）诊断癌症，有助于诊断癌症，确认癌症的诊断，鉴别癌症的适当治疗，监测癌症的治疗，以及评估癌症的治疗方案，包括卵巢透明细胞癌，乳腺癌，结肠癌，胃癌，肺癌癌症，成神经管细胞瘤，胰腺癌和前列腺癌。

7. 发明申请

WO2022192691A1 ENGINEERED IMMUNE CELLS AND USES THEREOF 审中-公开
公开(公告)号：WO2022192691A1
公开(公告)日：2022-09-15
申请号：PCT/US2022/019980
申请日：2022-03-11
申请人： THE JOHNS HOPKINS UNIVERSITY
发明人： HWANG, Michael S. , DOUGLASS, Jacqueline , HSIUE, Emily Han-Chung , KINZLER, Kenneth W. , MOG, Brian J. , PAPADOPOULOS, Nickolas , PEARLMAN, Alexander H. , VOGELSTEIN, Bert , ZHOU, Shibin
IPC分类号： C12N5/22 , C12N5/0783 , A61K35/17 , A61K38/17 , A61K39/395 , A61P35/00 , A61P35/02
摘要： Provided herein are immune cells and methods of use, wherein the immune cells include a chimeric antigen receptor (CAR), wherein the CAR comprises an extracellular antigen binding domain that binds specifically to a first epitope; and an inhibitory chimeric antigen receptor (iCAR), wherein the iCAR comprises an extracellular antigen binding domain that binds specifically to a second epitope, wherein the immune cell is activated when the immune cells binds to the first epitope and does not bind to the second epitope; and wherein the immune cell is inactivated when the immune cell binds to the first and second epitopes.

8. 发明申请

WO2022177889A1 METHODS AND MATERIALS FOR TREATING CLONAL T CELL EXPANSIONS 审中-公开
公开(公告)号：WO2022177889A1
公开(公告)日：2022-08-25
申请号：PCT/US2022/016423
申请日：2022-02-15
申请人： THE JOHNS HOPKINS UNIVERSITY
发明人： HWANG, Michael S. , KINZLER, Kenneth W. , MOG, Brian J. , PAPADOPOULOS, Nickolas , PARDOLL, Andrew , PAUL, Suman , VOGELSTEIN, Bert , ZHOU, Shibin
IPC分类号： C07K16/28 , C07K16/30 , A61P35/00
摘要： This document relates to methods and materials for treating T cell cancers. For example, a composition containing one or more bispecific molecules targeting T cell receptor £ chain constant region (TRBC) can be administered to a mammal having a T cell cancer to treat the mammal. For example, this document provides methods and materials for using one or more bispecific molecules to treat a mammal having a T cell cancer.

9. 发明申请

WO2021127184A1 MANAbodies TARGETING TUMOR ANTIGENS AND METHODS OF USING 审中-公开
公开(公告)号：WO2021127184A1
公开(公告)日：2021-06-24
申请号：PCT/US2020/065617
申请日：2020-12-17
申请人： THE JOHNS HOPKINS UNIVERSITY , VOGELSTEIN, Bert , KINZLER, Kenneth W. , HSIUE, Emily Han-Chung , DOUGLASS, Jacqueline , HWANG, Michael S. , PEARLMAN, Alexander , PAPADOPOULOS, Nickolas , ZHOU, Shibin , MOG, Brian , WRIGHT, Katharine M. , GABELLI, Sandra B.
发明人： VOGELSTEIN, Bert , KINZLER, Kenneth W. , HSIUE, Emily Han-Chung , DOUGLASS, Jacqueline , HWANG, Michael S. , PEARLMAN, Alexander , PAPADOPOULOS, Nickolas , ZHOU, Shibin , MOG, Brian , WRIGHT, Katharine M. , GABELLI, Sandra B.
IPC分类号： C07K14/82 , C07K16/32 , A61K39/395 , A61P35/00
摘要： This document provides methods and materials for assessing a mammal having or suspected of having cancer and/or for treating a mammal having cancer. For example, molecules including one or more antigen-binding domains (e.g., a single-chain variable fragment (scFv)) that can bind to a modified peptide (e.g., a tumor antigen), as well as method for using such molecules, are provided.

10. 发明申请

WO2017132438A1 BOTTLENECK SEQUENCING 审中-公开
标题翻译： BOTTLENECK测序
公开(公告)号：WO2017132438A1
公开(公告)日：2017-08-03
申请号：PCT/US2017/015229
申请日：2017-01-27
申请人： THE JOHNS HOPKINS UNIVERSITY
发明人： VOGELSTEIN, Bert , KINZLER, Kenneth , HOANG, Margaret , PAPADOPOULOS, Nickolas
IPC分类号： C12Q1/68 , C40B20/04
CPC分类号： C12Q1/6869 , C12Q1/6844 , C40B20/04 , C12Q2525/151 , C12Q2525/191 , C12Q2565/514
摘要： Bottleneck Sequencing System (BotSeqS) is a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately prior to library amplification. BotSeqS can be used to show age and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal tissues can vary by several orders of magnitude, depending on biologic and environmental factors. BotSeqS has been used to show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, BotSeqS has shown that the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them.
摘要翻译：瓶颈测序系统（BotSeqS）是一种新一代测序方法，可同时量化线粒体和核基因组中的罕见体细胞点突变。 BotSeqS在文库扩增之前将分子条形码与简单稀释步骤结合在一起。 BotSeqS可以用于显示年龄和组织依赖性罕见突变的累积，并且证明正常组织中的体细胞突变负荷可以根据生物和环境因素而变化几个数量级。 BotSeqS已被用于显示正常组织中线粒体和核基因组的突变模式之间的主要差异。最后，BotSeqS已经表明，正常组织的突变谱彼此不同，但与它们中出现的癌症的突变谱相似。

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