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1. 发明申请

WO2005017182A2 MULTI-COLOR IN VITRO TRANSLATION 审中-公开
标题翻译：多色翻译
公开(公告)号：WO2005017182A2
公开(公告)日：2005-02-24
申请号：PCT/US2004/019097
申请日：2004-07-21
申请人： THE JOHNS HOPINKS UNIVERSITY SCHOOL OF MEDICINE , TRAVERSO, Carlo, Giovanni , DIEHL, Frank , KINZLER, Kenneth, W. , VOGELSTEIN, Bert
发明人： TRAVERSO, Carlo, Giovanni , DIEHL, Frank , KINZLER, Kenneth, W. , VOGELSTEIN, Bert
IPC分类号： C12Q
CPC分类号： G01N33/6845 , G01N33/542
摘要： In vitro translation is a widely used tool for both analytical and preparative purposes. For analytical purposes, small amounts of proteins are synthesized and visualized through labeled amino acids incorporated during translation. The radioactively labeled amino acids originally used, such as [ 35 S]methionine or [ 14 C]leucine, have been superceded by the addition of antigenic tags or the incorporation of biotin-labeled or fluorescently-labeled amino acids. Such non-radioactive tags are simpler to visualize following translation and do not pose a radiation hazard. Among the non-radioactive tags, fluorescently labeled-lysine is the most convenient, as proteins that have incorporated this amino acid can be directly visualized following gel electrophoresis. Multiple fluorophores introduced into proteins significantly extend their utility, particularly for the comparison of in vitro translated proteins from related sources. This methodology can be employed for several purposes, including the simplified detection of rare truncating mutations in clinical samples from cancer patients.
摘要翻译：体外翻译是用于分析和制备目的的广泛使用的工具。为了分析的目的，通过在翻译过程中并入的标记氨基酸合成少量蛋白质并使其可视化。最初使用的放射性标记的氨基酸，例如[35 S]甲硫氨酸或[[14 C]亮氨酸）已经通过加入抗原标签或引入生物素标记或荧光标记的氨基酸而被替代。这种非放射性标签更容易可视化翻译，并且不会造成辐射危害。在非放射性标签中，荧光标记的赖氨酸是最方便的，因为结合了该氨基酸的蛋白质可以在凝胶电泳后直接显现。引入蛋白质的多种荧光团显着扩展其效用，特别是用于比较来自相关来源的体外翻译蛋白质。该方法可用于多种目的，包括简化检测癌症患者临床样品中罕见的截短突变。

2. 发明申请

WO2007050465A2 IMPROVED METHODS FOR BEAMING 审中-公开
标题翻译：改进的光束方法
公开(公告)号：WO2007050465A2
公开(公告)日：2007-05-03
申请号：PCT/US2006/041115
申请日：2006-10-20
申请人： THE JOHNS HOPKINS UNIVERSITY , VOGELSTEIN, Bert , DIEHL, Frank , KINZLER, Kenneth, W. , LI, Ming
发明人： VOGELSTEIN, Bert , DIEHL, Frank , KINZLER, Kenneth, W. , LI, Ming
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6858 , G01R31/025 , G01R31/3277 , C12Q2565/537 , C12Q2563/155 , C12Q2527/125
摘要： Improvements on the basic method used for BEAMing increase sensitivity and increase the signal-to-noise ratio. The improvements have permitted the determination of intrinsic error rates of various DNA polymerases and have permitted the detection of rare and subtle mutations in DNA isolated from plasma of cancer patients.
摘要翻译：
于用于整经增加的灵敏度和增加的信噪比的基本方法的改进。这些改进已批准的各种DNA聚合酶的固有误差率的确定和已批准来自癌症患者的血浆中分离的DNA中稀有和微妙的突变的检测。

3. 发明申请

WO2007149432A2 SINGLE-MOLECULE PCR ON MICROPARTICLES IN WATER-IN-OIL EMULSIONS 审中-公开
标题翻译：单分子PCR在水中乳化液中的微量元素
公开(公告)号：WO2007149432A2
公开(公告)日：2007-12-27
申请号：PCT/US2007/014273
申请日：2007-06-19
申请人： THE JOHNS HOPKINS UNIVERSITY , DIEHL, Frank , KINZLER, Kenneth, W. , VOGELSTEIN, Bert
发明人： DIEHL, Frank , KINZLER, Kenneth, W. , VOGELSTEIN, Bert
IPC分类号： C12Q1/68
CPC分类号： C12Q1/686 , C12Q1/6876 , C12Q2600/16 , C12Q2527/125 , C12Q2527/153 , C12Q2565/537
摘要： Modulation of the viscosity of the oil phase of a microemulsion used for amplification of DNA on a bead increases the homogeneity of product beads and the amount of amplified DNA per bead. Moreover the number of separate microemulsion populations that can be formed in parallel is increased using multi-well plates and mixer mill disruptor machines designed to lyse biological samples.
摘要翻译：用于在珠上扩增DNA的微乳液的油相的粘度的调节增加了产物珠的均匀性和每个珠的扩增DNA的量。此外，可以使用设计用于裂解生物样品的多孔板和混合机研磨破碎机来增加可以平行形成的单独的微乳液种群的数量。

4. 发明申请

WO2010014920A1 CIRCULATING MUTANT DNA TO ASSESS TUMOR DYNAMICS 审中-公开
标题翻译：循环突变DNA评估肿瘤动力学
公开(公告)号：WO2010014920A1
公开(公告)日：2010-02-04
申请号：PCT/US2009/052436
申请日：2009-07-31
申请人： THE JOHNS HOPKINS UNIVERSITY , DIEHL, Frank , DIAZ, Luis , KINZLER, Kenneth, W. , VOGELSTEIN, Bert , SCHMIDT, Kerstin
发明人： DIEHL, Frank , DIAZ, Luis , KINZLER, Kenneth, W. , VOGELSTEIN, Bert , SCHMIDT, Kerstin
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q2525/197 , C12Q2535/131 , C12Q2549/119 , C12Q2600/112 , C12Q2600/118 , C12Q2600/136
摘要： DNA containing somatic mutations is highly tumor specific and thus, in theory, can provide optimum markers. However, the number of circulating mutant gene fragments is small compared to the number of normal circulating DNA fragments, making it difficult to detect and quantify them with the sensitivity required for meaningful clinical use. We apply a highly sensitive approach to quantify circulating tumor DNA (ctDNA) in body samples of patients. Measurements of ctDNA can be used to reliably monitor tumor dynamics in subjects with cancer, especially those who are undergoing surgery or chemotherapy. This personalized genetic approach can be generally applied.
摘要翻译：含有体细胞突变的DNA具有高度的肿瘤特异性，因此在理论上可以提供最佳的标记。然而，循环突变基因片段的数量与正常循环DNA片段的数量相比较小，使得难以用有意义的临床使用所需的灵敏度来检测和量化它们。我们应用高度敏感的方法来量化患者身体样本中的循环肿瘤DNA（ctDNA）。 ctDNA的测量可用于可靠地监测癌症患者的肿瘤动态，特别是正在接受手术或化疗的患者。这种个性化的遗传方法一般可以应用。

5. 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.

6. 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。

7. 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。

8. 发明申请

WO2005113824A2 PROTEIN TYROSINE PHOSPHATASE MUTATIONS IN CANCERS 审中-公开
标题翻译：蛋白质酪氨酸磷酸酶突变体
公开(公告)号：WO2005113824A2
公开(公告)日：2005-12-01
申请号：PCT/US2005/017105
申请日：2005-05-16
申请人： WANG, Zhenghe , VELCULESCU, Victor , KINZLER, Kenneth, W. , VOGELSTEIN, Bert
发明人： WANG, Zhenghe , VELCULESCU, Victor , KINZLER, Kenneth, W. , VOGELSTEIN, Bert
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12N9/16 , C12Q2600/112 , C12Q2600/136 , C12Q2600/156 , C12Q2600/158 , C12Y301/03048 , G01N33/5011 , G01N2333/916
摘要： Tyrosine phosphorylation, regulated by protein tyrosine phosphatases (PTPs) and kinases (PTKs), is important in signaling pathways underlying tumorigenesis. A mutational analysis of the tyrosine phosphatase gene superfamily in human cancers identified 83 somatic mutations in six PTPs ( PTPRF, PTPRG, PTPRT, PTPN3, PTPN13, PTPN14 ) affecting 26 % of colorectal cancers and a smaller fraction of lung, breast and gastric cancers. Fifteen mutations were nonsense, frameshift or splice site alterations predicted to result in truncated proteins lacking phosphatase activity. Five missense mutations in the most commonly altered PTP ( PTPRP ) were biochemically examined and found to reduce phosphatase activity. Expression of wild-type but not a mutant PTPRT in human cancer cells inhibited cell growth. These observations suggest that the tyrosine phosphatase genes are tumor suppressor genes, regulating cellular pathways that may be amenable to therapeutic intervention.
摘要翻译：由蛋白酪氨酸磷酸酶（PTP）和激酶（PTK）调节的酪氨酸磷酸化在肿瘤发生的信号通路中是重要的。人类癌症中酪氨酸磷酸酶基因超家族的突变分析鉴定了影响26％结肠直肠癌和较小部分肺癌，乳腺癌和胃癌的6种PTPs（PTPRF，PTPRG，PTPRT，PTPN3，PTPN13，PTPN14）中的83个体细胞突变。十五个突变是无义，移位或剪接位点改变，预计会导致截短的蛋白质缺乏磷酸酶活性。在生物化学检查中发现最常改变的PTP（PTPRP）中的五个错义突变被发现可以降低磷酸酶活性。野生型但不是突变PTPRT在人类癌细胞中的表达抑制细胞生长。这些观察表明，酪氨酸磷酸酶基因是肿瘤抑制基因，调节可能适合于治疗性干预的细胞途径。

9. 发明申请

WO2005076984A2 THYMIDYLATE SYNTHASE GENE AND METASTASIS 审中-公开
标题翻译：甲基合成酶基因和METASTASIS
公开(公告)号：WO2005076984A2
公开(公告)日：2005-08-25
申请号：PCT/US2005/003776
申请日：2005-02-07
申请人： THE JOHN HOPKINS UNIVERSITY , WANG, Tian-LI , DIAZ, Luis , LENGAUER, Christoph , VELCULESCU, Victor , KINZLER, Kenneth, W. , VOGELSTEIN, Bert
发明人： WANG, Tian-LI , DIAZ, Luis , LENGAUER, Christoph , VELCULESCU, Victor , KINZLER, Kenneth, W. , VOGELSTEIN, Bert
IPC分类号： C12Q1/68 , G01N33/48 , G01N33/50 , G06F19/00
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/136
摘要： Thymidylate synthase (TYMS) gene amplification was observed in 23% of 31 5-FU resistant liver metastases, while no amplification was observed in metastases of patients that had not been treated with 5-FU. Patients with metastases containing TYMS amplification had a substantially shorter median survival (329 days) than those without amplification (1021 days, p
摘要翻译：在31例5-FU耐药性肝转移患者中，23例患者观察到胸苷酸合成酶（TYMS）基因扩增，而未用5-FU治疗的患者转移灶未观察到扩增。含有TYMS扩增的转移患者的中位生存期（329天）比没有扩增的患者显着更短（1021天，p <0.01）。 TYMS的遗传扩增对复发性结肠直肠癌患者的治疗具有重要意义。

10. 发明申请

WO2005062812A3 A rAAV-BASED SYSTEM FOR SOMATIC CELL GENE DISRUPTION 审中-公开
公开(公告)号：WO2005062812A3
公开(公告)日：2005-07-14
申请号：PCT/US2004/042597
申请日：2004-12-21
申请人： THE JOHNS HOPKINS UNIVERSITY , VOGELSTEIN, Bert , KINZLER, Kenneth, W. , KOHLI, Manu , RAGO, Carlo
发明人： VOGELSTEIN, Bert , KINZLER, Kenneth, W. , KOHLI, Manu , RAGO, Carlo
IPC分类号： C12N15/63
摘要： Emerging evidence suggests that recombinant adeno-associated viral (rAAV) vectors can be used for specific gene targeting in human somatic cells. We have developed an rAAV vector construction procedure employing fusion PCR and a single cloning step that considerably simplifies the knockout process. We demonstrate its utility by disrupting genes at specific positions within human colon cancer cells as well as within immortalized normal epithelial cells. This technology should be broadly applicable to in vitro studies that require the manipulation of the human genome.

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