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11. 发明申请

US20140179538A1 MUTATIONS IN PANCREATIC NEOPLASMS 有权
标题翻译：。。。。。。。。。
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。

12. 发明授权

US09637779B2 Antisense transcriptomes of cells 有权
公开(公告)号：US09637779B2
公开(公告)日：2017-05-02
申请号：US13131413
申请日：2009-12-02
申请人： Bert Vogelstein , Kenneth W. Kinzler , Yiping He , Victor Velculescu , Nickolas Papadopoulos
发明人： Bert Vogelstein , Kenneth W. Kinzler , Yiping He , Victor Velculescu , Nickolas Papadopoulos
IPC分类号： C12Q1/68 , G06F19/22
CPC分类号： C12Q1/6844 , G06F19/22 , C12Q2539/113 , C12Q2523/125 , C12Q2521/107
摘要： Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the Plus- or Minus-strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was non-random across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, suggesting that they are a fundamental component of gene regulation.

13. 发明申请

US20120009573A1 Antisense Transcriptomes of Cells 有权
标题翻译：细胞反义转录组
公开(公告)号：US20120009573A1
公开(公告)日：2012-01-12
申请号：US13131413
申请日：2009-12-02
申请人： Bert Vogelstein , Kenneth W. Kinzler , Yiping He , Victor Velculescu , Nickolas Papadopoulos
发明人： Bert Vogelstein , Kenneth W. Kinzler , Yiping He , Victor Velculescu , Nickolas Papadopoulos
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6844 , G06F19/22 , C12Q2539/113 , C12Q2523/125 , C12Q2521/107
摘要： Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the Plus- or Minus-strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was non-random across the genome, and differed among cell types. Anti-sense transcripts thus appear to be a pervasive feature of human cells, suggesting that they are a fundamental component of gene regulation.
摘要翻译：哺乳动物细胞中的转录可以在全基因组范围内进行评估，但是难以可靠地确定个体转录本是否衍生自染色体的加号或阴影链。这种区别对于了解已知转录物（有义）和可能调节它们的互补反义转录物之间的关系可能是至关重要的。在这里，我们描述了一种可用于（i）识别任何特定RNA转录物的DNA链起源的技术，（ii）在全球范围内量化来自表达基因的正义和反义转录本的数量。我们检查了五种不同的人类细胞类型，并且在每种情况下都发现2900至6400个人类基因中的反义转录物的证据。反义转录物的分布与有义转录物的分布不同，在基因组中是非随机的，并且在细胞类型之间不同。因此，反义转录物似乎是人类细胞的普遍特征，表明它们是基因调控的基本组成部分。

14. 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。

15. 发明申请

US20140154683A1 Enrichment of Nucleic Acids by Complimentary Capture 有权
标题翻译：通过免费捕获富集核酸
公开(公告)号：US20140154683A1
公开(公告)日：2014-06-05
申请号：US14130007
申请日：2012-06-28
申请人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos , Jian WU
发明人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos , Jian WU
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。

16. 发明申请

US20120164638A1 Digital Quantification of DNA Methylation 审中-公开
标题翻译： DNA甲基化的数字定量
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
IPC分类号： C12Q1/68 , C07H21/04
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。

17. 发明授权

US07045352B2 Converting diploidy to haploidy for genetic diagnosis 失效
公开(公告)号：US07045352B2
公开(公告)日：2006-05-16
申请号：US10210066
申请日：2002-08-02
申请人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos , Hai Yan
发明人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos , Hai Yan
IPC分类号： C12N5/12 , C12Q1/00 , C12N15/06 , C12N15/87
CPC分类号： C12N5/166 , C12Q1/6886 , C12Q2600/156
摘要： Detection of mutations associated with hereditary diseases is complicated by the diploid nature of mammalian cells. Mutations present in one allele are often masked by the wild-type sequence of the other allele. Individual alleles can be isolated from every chromosome within somatic cell hybrids generated from a single fusion. Nucleic acids from the hybrids can be analyzed for mutations in an unambiguous manner. This approach was used to detect two cancer-causing mutations that had previously defied genetic diagnosis. One of the families studied, Warthin Family G, was the first kindred with a hereditary colon cancer syndrome described in the biomedical literature.

18. 发明授权

US5750352A Mono-allelic mutation analysis for identifying germline mutations 失效
公开(公告)号：US5750352A
公开(公告)日：1998-05-12
申请号：US519059
申请日：1995-08-23
申请人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos
发明人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos
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.

19. 发明授权

US09670527B2 Enrichment of nucleic acids by complimentary capture 有权
公开(公告)号：US09670527B2
公开(公告)日：2017-06-06
申请号：US14130007
申请日：2012-06-28
申请人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos , Jian Wu
发明人： Bert Vogelstein , Kenneth W. Kinzler , Nickolas Papadopoulos , Jian Wu
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.

20. 发明申请

US20140227705A1 SAFE SEQUENCING SYSTEM 有权
标题翻译：安全排序系统
公开(公告)号：US20140227705A1
公开(公告)日：2014-08-14
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
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。

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