-
公开(公告)号：US20100136560A1
公开(公告)日：2010-06-03
申请号：US12619726
申请日：2009-11-17
IPC分类号： C12Q1/68
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 analyses 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 analyses 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。 这些数据与这些相同肿瘤类型中的参考序列基因的先前突变分析相结合，以鉴定受拷贝数变化和点改变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排序变化的综合视图，并确定了可用于癌症诊断和治疗的基因和途径。
-
公开(公告)号：US09476095B2
公开(公告)日：2016-10-25
申请号：US14111715
申请日：2012-04-12
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。
-
公开(公告)号：US20130210645A1
公开(公告)日：2013-08-15
申请号：US13579964
申请日：2011-02-17
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q2600/156
摘要： Clinical management of human cancer is dependent on the accurate monitoring of residual and recurrent tumors. We have developed a method, called personalized analysis of rearranged ends (PARE), which can identify translocations in solid tumors. Analysis of four colorectal and two breast cancers revealed an average of nine rearranged sequences (range 4 to 15) per tumor. Polymerase chain reaction with primers spanning the breakpoints were able to detect mutant DNA molecules present at levels lower than 0.001% and readily identified mutated circulating DNA in patient plasma samples. This approach provides an exquisitely sensitive and broadly applicable approach for the development of personalized biomarkers to enhance the clinical management of cancer patients.
摘要翻译： 人类癌症的临床管理取决于对残留和复发性肿瘤的准确监测。 我们开发了一种称为重排末端（PARE）的个性化分析方法，可以识别实体瘤易位。 对4例结直肠癌和2例乳腺癌的分析显示，每个肿瘤平均有9个重排序列（范围4至15）。 与跨越断点的引物的聚合酶链反应能够检测出低于0.001％的突变型DNA分子，并且容易鉴定出患者血浆样品中突变的循环DNA。 这种方法为个性化生物标志物的开发提供了一种非常灵敏和广泛适用的方法，以加强癌症患者的临床管理。
-
公开(公告)号：US20140154683A1
公开(公告)日：2014-06-05
申请号：US14130007
申请日：2012-06-28
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6806 , C12Q2535/122 , C12Q2563/131 , C12Q2563/149 , C12Q2565/518
摘要： Assays can be used to detect mutations found in neoplasms of the pancreas, as well as for other neoplasms and other uses. Nucleic acids can be captured from body fluids such as cyst fluids. Thousands of oligonucleotides can be synthesized in parallel, amplified and ligated together. The ligated products can be further amplified. The amplified, ligated products are used to capture complementary DNA sequences, which can be analyzed, for example by massively parallel sequencing.
摘要翻译： 检测可用于检测胰腺肿瘤中发现的突变，以及其他肿瘤和其他用途。 核酸可以从体液如囊液中捕获。 数千个寡核苷酸可以并行合成，扩增并连接在一起。 连接的产物可以进一步扩增。 扩增的连接产物用于捕获互补DNA序列，其可以例如通过大规模并行测序来分析。
-
公开(公告)号：US20120164638A1
公开(公告)日：2012-06-28
申请号：US13263020
申请日：2010-04-06
申请人： Bert Vogelstein , Kenneth W. Kinzler , Meng Li , Luis Diaz , Nickolas Papadopoulos , Sanford Markowitz
发明人： Bert Vogelstein , Kenneth W. Kinzler , Meng Li , Luis Diaz , Nickolas Papadopoulos , Sanford Markowitz
CPC分类号： C12Q1/6816 , C12Q1/6886 , C12Q2600/154 , C12Q2565/501 , C12Q2527/125 , C12Q2523/125
摘要： Abnormal DNA methylation can be used as a biomarker in cancer patients. For such purposes, it is important to determine precisely the fraction of methylated molecules in an analyzed sample. A technology we term Methyl-BEAMing achieves this goal. Individual bisulfite-treated DNA molecules can be PCR-amplified within aqueous nanocompartments containing beads, resulting in a population of beads each containing thousands of copies of the template molecule. After hybridization with probes specific for methylated sequences, the beads can be analyzed by flow cytometry. This approach enables detection and enumeration of one methylated molecule in a population of ˜5000 unmethylated molecules. Methyl-BEAMing provides digital quantification of rare methylation events and is generally applicable to the assessment of methylated genes in clinical samples.
摘要翻译： DNA甲基化异常可用作癌症患者的生物标志物。 为此目的，重要的是精确测定分析样品中甲基化分子的分数。 我们称之为甲基BEAMing的技术实现了这一目标。 单独的亚硫酸氢盐处理的DNA分子可以在含有珠粒的含水纳米间隔内进行PCR扩增，导致每个珠粒群含有数千份拷贝的模板分子。 与特异于甲基化序列的探针杂交后，可以通过流式细胞术分析珠粒。 这种方法能够检测和计数一个约5000个非甲基化分子的群体中的一个甲基化分子。 甲基BEAMing提供罕见甲基化事件的数字量化，通常适用于临床样品中甲基化基因的评估。
-
公开(公告)号：US5750352A
公开(公告)日：1998-05-12
申请号：US519059
申请日：1995-08-23
IPC分类号： C12Q1/68 , G01N33/50 , G01N33/68 , G01N33/567
CPC分类号： G01N33/68 , C12Q1/6827 , G01N33/5005
摘要： A diagnostic strategy for detection of inherited diseases caused by germline mutations is based on somatic cell hybridization. Each allele of a human gene involved in the inherited disease is isolated in a somatic cell hybrid. The products of the isolated human allele are then observed in the absence of the other allele of the human.
-
公开(公告)号：US09670527B2
公开(公告)日：2017-06-06
申请号：US14130007
申请日：2012-06-28
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6806 , C12Q2535/122 , C12Q2563/131 , C12Q2563/149 , C12Q2565/518
摘要： Assays can be used to detect mutations found in neoplasms of the pancreas, as well as for other neoplasms and other uses. Nucleic acids can be captured from body fluids such as cyst fluids. Thousands of oligonucleotides can be synthesized in parallel, amplified and ligated together. The ligated products can be further amplified. The amplified, ligated products are used to capture complementary DNA sequences, which can be analyzed, for example by massively parallel sequencing.
-
公开(公告)号：US20140227705A1
公开(公告)日：2014-08-14
申请号：US14111715
申请日：2012-04-12
IPC分类号： C12Q1/68
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≥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。
-
公开(公告)号：US09976184B2
公开(公告)日：2018-05-22
申请号：US14128478
申请日：2012-06-22
申请人： Bert Vogelstein , Kenneth W. Kinzler , Jian Wu , Luis Diaz , Nickolas Papadopoulos , Hanno Matthaei , Ralph Hruban , Anirban Maitra
发明人： Bert Vogelstein , Kenneth W. Kinzler , Jian Wu , Luis Diaz , Nickolas Papadopoulos , Hanno Matthaei , Ralph Hruban , Anirban Maitra
CPC分类号： C12Q1/6886 , C12Q2600/112 , C12Q2600/156
摘要： To help reveal the pathogenesis of these lesions, we purified the DNA from Intraductal Papillary Mucinous Neoplasm (IPMN) cyst fluids from 19 patients and searched for mutations in 169 genes commonly altered in human cancers. We identified recurrent mutations at codon 201 of GNAS. We found that GNAS mutations were present in 66% of IPMNs and that either KRAS or GNAS mutations could be identified in 96%. In eight cases, we could investigate invasive adenocarcinomas that developed in association with IPMNs containing GNAS mutations. In seven of these eight cases, the GNAS mutations present in the IPMNs were also found in the invasive lesion. GNAS mutations were not found in other types of cystic neoplasms of the pancreas or in invasive adenocarcinomas not associated with IPMNs. These data suggest that GNAS mutations can inform the diagnosis and management of patients with cystic pancreatic lesions.
-
公开(公告)号：US20140179538A1
公开(公告)日：2014-06-26
申请号：US14128478
申请日：2012-06-22
申请人： Bert Vogelstein , Kenneth W. Kinzler , Jian Wu , Luis Diaz , Nickolas Papadopoulos , Hanno Matthaei , Ralph Hruban , Anirban Maitra
发明人： Bert Vogelstein , Kenneth W. Kinzler , Jian Wu , Luis Diaz , Nickolas Papadopoulos , Hanno Matthaei , Ralph Hruban , Anirban Maitra
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q2600/112 , C12Q2600/156
摘要： To help reveal the pathogenesis of these lesions, we purified the DNA from Intraductal Papillary Mucinous Neoplasm (IPMN) cyst fluids from 19 patients and searched for mutations in 169 genes commonly altered in human cancers. We identified recurrent mutations at codon 201 of GNAS. We found that GNAS mutations were present in 66% of IPMNs and that either KRAS or GNAS mutations could be identified in 96%. In eight cases, we could investigate invasive adenocarcinomas that developed in association with IPMNs containing GNAS mutations. In seven of these eight cases, the GNAS mutations present in the IPMNs were also found in the invasive lesion. GNAS mutations were not found in other types of cystic neoplasms of the pancreas or in invasive adenocarcinomas not associated with IPMNs. These data suggest that GNAS mutations can inform the diagnosis and management of patients with cystic pancreatic lesions.
摘要翻译： 为了揭示这些病变的发病机制，我们从19名患者的导管内乳头状粘液性肿瘤（IPMN）囊肿液中纯化DNA，并搜索了在人类癌症中通常改变的169种基因中的突变。 我们发现GNAS密码子201的复发性突变。 我们发现GNAS突变存在于66％的IPMNs中，KRAS或GNAS突变可以在96％中鉴定。 在8例中，我们可以调查与含有GNAS突变的IPMN相关的侵袭性腺癌。 在这8例中有7例中，存在于IPMNs中的GNAS突变也在侵袭性损伤中发现。 在其他类型的胰腺囊性肿瘤或与IPMN无关的侵袭性腺癌中未发现GNAS突变。 这些数据表明，GNAS突变可以通过诊断和管理囊性胰腺病变患者。
-
-
-
-
-
-
-
-
-
搜索结果
170 条记录 (耗时 0.055 秒)
