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1. 发明申请

US20110059435A1 Methods for Beaming 有权
标题翻译： Beaming方法
公开(公告)号：US20110059435A1
公开(公告)日：2011-03-10
申请号：US12091395
申请日：2006-02-06
申请人： Bert Vogelstein , Frank Diehl , Kenneth W. Kinzler , Ming Li
发明人： Bert Vogelstein , Frank Diehl , Kenneth W. Kinzler , Ming Li
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：用于BEAMing的基本方法的改进提高了灵敏度并提高了信噪比。这些改进允许确定各种DNA聚合酶的固有错误率，并允许检测从癌症患者血浆中分离的DNA中罕见且微妙的突变。

2. 发明申请

US20100041048A1 Circulating Mutant DNA to Assess Tumor Dynamics 审中-公开
标题翻译：循环突变体DNA评估肿瘤动力学
公开(公告)号：US20100041048A1
公开(公告)日：2010-02-18
申请号：US12512585
申请日：2009-07-30
申请人： Frank DIEHL , Luis Diaz , Kenneth W. Kinzler , Bert Vogelstein , Kerstin Schmidt
发明人： Frank DIEHL , Luis Diaz , Kenneth W. Kinzler , Bert Vogelstein , Kerstin Schmidt
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。

3. 发明申请

US20100190153A1 SINGLE-MOLECULE PCR ON MICROPARTICLES IN WATER-IN-OIL EMULSIONS 有权
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：US20100190153A1
公开(公告)日：2010-07-29
申请号：US12305825
申请日：2007-06-19
申请人： Frank Diehl , Kenneth W. Kinzler , Bert Vogelstein
发明人： Frank Diehl , Kenneth W. Kinzler , Bert Vogelstein
IPC分类号： C12Q1/68 , C12P19/34
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. 发明授权

US09360526B2 Methods for beaming 有权
标题翻译：辐射方法
公开(公告)号：US09360526B2
公开(公告)日：2016-06-07
申请号：US12091395
申请日：2006-10-20
申请人： Bert Vogelstein , Frank Diehl , Kenneth W Kinzler , Meng Li
发明人： Bert Vogelstein , Frank Diehl , Kenneth W Kinzler , Meng Li
IPC分类号： C12Q1/68 , C12P19/34 , G01R31/327 , G01R31/02
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：用于BEAMing的基本方法的改进提高了灵敏度并提高了信噪比。这些改进允许确定各种DNA聚合酶的固有错误率，并允许检测从癌症患者血浆中分离的DNA中罕见且微妙的突变。

5. 发明授权

US08715934B2 Single-molecule PCR on microparticles in water-in-oil emulsions 有权
标题翻译：油包水乳剂中微粒子上的单分子PCR
公开(公告)号：US08715934B2
公开(公告)日：2014-05-06
申请号：US12305825
申请日：2007-06-19
申请人： Frank Diehl , Kenneth W. Kinzler , Bert Vogelstein
发明人： Frank Diehl , Kenneth W. Kinzler , Bert Vogelstein
IPC分类号： C12Q1/68 , C12P19/34
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。

6. 发明申请

US20130040300A9 Methods for Beaming 有权
标题翻译： Beaming方法
公开(公告)号：US20130040300A9
公开(公告)日：2013-02-14
申请号：US12091395
申请日：2006-10-20
申请人： Bert Vogelstein , Frank Diehl , Kenneth W. Kinzler , Meng Li
发明人： Bert Vogelstein , Frank Diehl , Kenneth W. Kinzler , Meng Li
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：用于BEAMing的基本方法的改进提高了灵敏度并提高了信噪比。这些改进允许确定各种DNA聚合酶的固有错误率，并允许检测从癌症患者血浆中分离的DNA中罕见且微妙的突变。

7. 发明授权

US09982306B2 Somatic mutations in ATRX in brain cancer 有权
公开(公告)号：US09982306B2
公开(公告)日：2018-05-29
申请号：US14129850
申请日：2012-06-28
申请人： Hai Yan , Darell Bigner , Bert Vogelstein , Kenneth W. Kinzler , Alan Meeker , Ralph Hruban , Nickolas Papadopoulos , Luis Diaz , Yuchen Jiao
发明人： Hai Yan , Darell Bigner , Bert Vogelstein , Kenneth W. Kinzler , Alan Meeker , Ralph Hruban , Nickolas Papadopoulos , Luis Diaz , Yuchen Jiao
IPC分类号： G01N33/68 , C12Q1/68 , G01N33/574 , C07K16/40 , C12N15/113
CPC分类号： C12Q1/6886 , C07K16/40 , C12N15/1137 , C12Q2600/118 , C12Q2600/156 , G01N33/57407
摘要： We determined the sequence of ATRX and DAXX in 447 cancers from various sites. We found mutations most commonly in pediatric glioblastoma multiformae (GBM) (11.1%), adult GBM (6.5%), oligodendrogliomas (7.7%) and medulloblastomas (1.5%); and showed that Alternative Lengthening of Telomeres (ALT), a telomerase-independent telomere maintenance mechanism found in cancers that have not activated telomerase, perfectly correlated with somatic mutations of either gene. In contrast, neuroblastomas, and adenocarcinomas of the ovary, breast, and pancreas were negative for mutations in ATRX and DAXX. Alterations in ATRX or DAXX define a specific molecular pathway that is closely associated with an alternative telomere maintenance function in human cancers.

8. 发明授权

US09476095B2 Safe sequencing system 有权
标题翻译：安全排序系统
公开(公告)号：US09476095B2
公开(公告)日：2016-10-25
申请号：US14111715
申请日：2012-04-12
申请人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos , Isaac Kinde
发明人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos , Isaac Kinde
IPC分类号： C12Q1/68 , C07H21/02
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片段是真实的突变体（“超突变体”），如果其≥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。

9. 发明授权

US08709723B2 Integrated analyses of breast and colorectal cancers 有权
标题翻译：乳腺癌和结肠直肠癌的综合分析
公开(公告)号：US08709723B2
公开(公告)日：2014-04-29
申请号：US13461268
申请日：2012-05-01
申请人： Bert Vogelstein , Kenneth W. Kinzler , Rebecca J. Leary , Victor E. Velculescu
发明人： Bert Vogelstein , Kenneth W. Kinzler , Rebecca J. Leary , Victor E. Velculescu
IPC分类号： C12Q1/66 , C12P19/34 , C07H21/02
CPC分类号： C12Q1/6886 , C12Q2600/156
摘要： Genome-wide analysis of copy number changes in breast and colorectal tumors used approaches that can reliably detect homozygous deletions and amplifications. The number of genes altered by major copy number changes—deletion of all copies or amplification of at least twelve copies per cell—averaged thirteen per tumor. These data were integrated with previous mutation analysis of the Reference Sequence genes in these same tumor types to identify genes and cellular pathways affected by both copy number changes and point alterations. Pathways enriched for genetic alterations include those controlling cell adhesion, intracellular signaling, DNA topological change, and cell cycle control. These analysis provide an integrated view of copy number and sequencing alterations on a genome-wide scale and identify genes and pathways that are useful for cancer diagnosis and therapy.
摘要翻译：使用可以可靠地检测纯合缺失和扩增的方法对乳腺和结肠直肠肿瘤的拷贝数变化进行全基因组分析。通过主要拷贝数变化改变的基因数量 - 全部拷贝的缺失或每个细胞至少12个拷贝的扩增，平均每个肿瘤13个。这些数据与以前相同肿瘤类型的参考序列基因的突变分析结合起来，以鉴定受拷贝数变化和点变化影响的基因和细胞途径。富含遗传改变的途径包括控制细胞粘附，细胞内信号转导，DNA拓扑变化和细胞周期控制的途径。这些分析提供了在全基因组范围内的拷贝数和测序改变的综合视图，并确定了可用于癌症诊断和治疗的基因和途径。

10. 发明授权

US08394598B2 Tyrosine kinome 有权
标题翻译：酪氨酸激酶
公开(公告)号：US08394598B2
公开(公告)日：2013-03-12
申请号：US12705760
申请日：2010-02-15
申请人： Alberto Bardelli , Will Parsons , Victor Velculescu , Kenneth W. Kinzler , Bert Vogelstein
发明人： Alberto Bardelli , Will Parsons , Victor Velculescu , Kenneth W. Kinzler , Bert Vogelstein
IPC分类号： C12Q1/68 , G01N33/574
CPC分类号： C12Q1/6886 , A61K31/506 , C12N9/1205 , C12Q1/025 , C12Q1/485 , C12Q1/6809 , C12Q1/6827 , C12Q2600/136 , C12Q2600/156 , G01N33/574
摘要： Protein kinases are important signaling molecules involved in tumorigenesis. Mutational analysis of the human tyrosine kinase gene family (98 genes) identified somatic alterations in -20% of colorectal cancers, with the majority of mutations occurring in NTRK3, FES, GUCY2F and a previously uncharacterized tyrosine kinase gene called MCCK/MLK4. Most alterations were in conserved residues affecting key regions of the kinase domain. These data represent a paradigm for the unbiased analysis of signal transducing genes in cancer and provide useful targets for therapeutic intervention.
摘要翻译：蛋白激酶是参与肿瘤发生的重要信号分子。人类酪氨酸激酶基因家族（98个基因）的突变分析鉴定了-20％的结肠直肠癌的体细胞变化，大部分突变发生在NTRK3，FES，GUCY2F和以前称为MCCK / MLK4的未表征的酪氨酸激酶基因。大多数改变是保守的残基影响激酶结构域的关键区域。这些数据代表了癌症中信号转导基因的无偏见分析的范例，并为治疗干预提供了有用的目标。

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