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.

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。

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。

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。

公开(公告)号：US20120115735A1

公开(公告)日：2012-05-10

申请号：US13060453

申请日：2009-09-03

申请人： Bert Vogelstein ,  Kenneth W. Kinzler ,  D. Williams Parsons ,  Sian Jones ,  Xiaosong Zhang ,  Jimmy Cheng-Ho Lin ,  Rebecca J. Leary ,  Philipp Angenendt ,  Nickolas Papadopoulos ,  Victor Velculescu ,  Giovanni Parmigiani ,  Rachel Karchin ,  Scott Kern ,  Ralph Hruban ,  James R. Eshleman ,  Michael Goggins ,  Alison Klein

发明人： Bert Vogelstein ,  Kenneth W. Kinzler ,  D. Williams Parsons ,  Sian Jones ,  Xiaosong Zhang ,  Jimmy Cheng-Ho Lin ,  Rebecca J. Leary ,  Philipp Angenendt ,  Nickolas Papadopoulos ,  Victor Velculescu ,  Giovanni Parmigiani ,  Rachel Karchin ,  Scott Kern ,  Ralph Hruban ,  James R. Eshleman ,  Michael Goggins ,  Alison Klein

IPC分类号： C12Q1/68 ,  C40B20/00 ,  C07H21/04

CPC分类号： G01N33/57438 ,  C12Q1/6886 ,  C12Q2600/156 ,  G01N2800/50

摘要： There are currently few therapeutic options for patients with pancreatic cancers and new insights into the pathogenesis of this lethal disease are urgently needed. To this end, we performed a comprehensive analysis of the genes altered in 24 pancreatic tumors. First, we determined the sequences of 23,781 transcripts, representing 20,583 protein-encoding genes, in DNA from these tumors. Second, we searched for homozygous deletions and amplifications using microarrays querying ˜one million single nucleotide polymorphisms in each sample. Third, we analyzed the transcriptomes of the same samples using SAGE and next-generation sequencing-by-synthesis technologies. We found that pancreatic cancers contain an average of 63 genetic alterations, of which 49 are point mutations, 8 are homozygous deletions, and 6 are amplifications. Further analyses revealed a core set of 12 regulatory processes or pathways that were each genetically altered in 70% to 100% of the samples. The data suggest that dysregulation of this core set of pathways is responsible for the major features of pancreatic tumorigenesis.

摘要翻译： 目前对胰腺癌患者几乎没有治疗选择，迫切需要对这种致死性疾病的发病机理的新见解。 为此，我们对24个胰腺肿瘤中改变的基因进行了综合分析。 首先，我们从这些肿瘤的DNA中确定了23,781个转录本，代表20,583个蛋白质编码基因的序列。 第二，我们使用微阵列查询每个样本中的百万个单核苷酸多态性的纯合缺失和扩增。 第三，我们使用SAGE和下一代按序合成技术分析了相同样品的转录组。 我们发现胰腺癌平均存在63个遗传改变，其中49个是点突变，8个是纯合缺失，6个是扩增。 进一步的分析揭示了一组核心的12个调节过程或途径，在70％至100％的样品中进行了遗传改变。 数据表明，这种核心途径的失调导致了胰腺肿瘤发生的主要特征。

公开(公告)号：US20120034318A1

公开(公告)日：2012-02-09

申请号：US13254610

申请日：2010-03-05

申请人： Bert Vogelstein ,  Kenneth W. Kinzler ,  D. Williams Parsons ,  Sian Jones ,  Scott Kern ,  Ralph Hruban ,  James R. Eshleman ,  Michael Goggins ,  Alison Klein ,  Manuel Hidalgo ,  Victor E. Velculescu

发明人： Bert Vogelstein ,  Kenneth W. Kinzler ,  D. Williams Parsons ,  Sian Jones ,  Scott Kern ,  Ralph Hruban ,  James R. Eshleman ,  Michael Goggins ,  Alison Klein ,  Manuel Hidalgo ,  Victor E. Velculescu

IPC分类号： A61K33/24 ,  A61P35/00 ,  C40B20/08 ,  G01N33/577 ,  G01N33/566 ,  C12Q1/68

CPC分类号： C12Q1/6886 ,  A61K31/407 ,  C12Q2600/106 ,  C12Q2600/156 ,  C12Q2600/158 ,  G01N33/57438 ,  G01N2333/47

摘要： The present invention provides a method for detecting mutations in the PALB2 gene in pancreatic cancer patients and in individuals having a family history of pancreatic cancer. Methods are also provided for diagnosing a predisposition to pancreatic cancer, for predicting a patient's response to pancreatic cancer therapies, and for treating pancreatic cancer, based on presence of a PALB2 mutation or abberant PALB2 gene expression in a patient.

摘要翻译： 本发明提供了一种检测胰腺癌患者和具有胰腺癌家族史的个体中PALB2基因突变的方法。 还提供了用于诊断患有胰腺癌的倾向，用于预测患者对胰腺癌治疗的反应以及用于治疗患者胰腺癌的方法，其基于在患者体内PALB2突变或异常PALB2基因表达的存在。

公开(公告)号：US08026053B2

公开(公告)日：2011-09-27

申请号：US10591347

申请日：2005-02-18

申请人： Yardena Samuels ,  Victor Velculescu ,  Kenneth W. Kinzler ,  Bert Vogelstein

发明人： Yardena Samuels ,  Victor Velculescu ,  Kenneth W. Kinzler ,  Bert Vogelstein

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6886 ,  C12Q2600/156

摘要： Phosphatidylinositol 3-kinases (PI3Ks) are known to be important regulators of signaling pathways. To determine whether PI3Ks are genetically altered in cancers, we analyzed the sequences of the P13K gene family and discovered that one family member, PIK3CA, is frequently mutated in cancers of the colon and other organs. The majority of mutations clustered near two positions within the P13K helical or kinase domains. PIK3CA represents one of the most highly mutated oncogenes yet identified in human cancers and is useful as a diagnostic and therapeutic target.

摘要翻译： 已知磷脂酰肌醇3-激酶（PI3K）是信号通路的重要调控因子。 为了确定PI3K在癌症中的遗传改变，我们分析了P13K基因家族的序列，发现一个家族成员PIK3CA在结肠癌和其他器官的癌症中经常发生突变。 大多数突变聚集在P13K螺旋或激酶结构域内的两个位置附近。 PIK3CA代表人类癌症中尚未鉴定的最高突变型癌基因之一，可用作诊断和治疗靶点。

公开(公告)号：US20110033466A1

公开(公告)日：2011-02-10

申请号：US12858717

申请日：2010-08-18

申请人： Victor E. Velculescu ,  Bert Vogelstein ,  Kenneth W. Kinzler

发明人： Victor E. Velculescu ,  Bert Vogelstein ,  Kenneth W. Kinzler

IPC分类号： C12Q1/68 ,  C07H21/00 ,  C12N5/071 ,  C12N15/00 ,  A61K31/7088 ,  A61K39/395 ,  A61P35/00 ,  A61P43/00

CPC分类号： C12Q1/6886 ,  C12Q2600/136

摘要： Global gene expression patterns have been characterized in normal and cancerous human cells using serial analysis of gene expression (SAGE). Cancer cell-specific, cell-type specific, and ubiquitously expressed genes have been identified. This information can be used to provide combinations of cell type- and cancer-specific gene probes, as well as methods of using these probes to identify particular cell types, screen for useful drugs, reduce cancer-specific gene expression, standardize gene expression, and restore function to a diseased cell or tissue.

摘要翻译： 使用基因表达（SAGE）的连续分析，在正常和癌性人类细胞中表征全球基因表达模式。 已经鉴定了癌细胞特异性，细胞型特异性和普遍表达的基因。 该信息可用于提供细胞类型和癌症特异性基因探针的组合，以及使用这些探针来鉴定特定细胞类型，筛选有用药物，降低癌症特异性基因表达，标准化基因表达的方法，以及 恢复功能到病变细胞或组织。

公开(公告)号：US07745165B2

公开(公告)日：2010-06-29

申请号：US10868658

申请日：2004-06-16

申请人： Bert Vogelstein ,  Kenneth W. Kinzler ,  Saurabh Saha ,  Alberto Bardelli

发明人： Bert Vogelstein ,  Kenneth W. Kinzler ,  Saurabh Saha ,  Alberto Bardelli

IPC分类号： C12Q1/48 ,  G01N33/567

CPC分类号： C12N9/16 ,  A61K39/00 ,  C12Q1/6886 ,  C12Q2600/112 ,  C12Q2600/136 ,  C12Q2600/158

摘要： Among the genes identified, in a comparison of the global gene expression profile of metastatic colorectal cancer to that of primary cancers, benign colorectal tumors, and normal colorectal epithelium, the PRL-3 protein tyrosine phosphatase gene was of particular interest. It was expressed at high levels in each of 18 cancer metastases studied but at lower levels in non-metastatic tumors and normal colorectal epithelium. In three of twelve metastases examined, multiple copies of the PRL-3 gene were found within a small amplicon located at chromosome 8q24.3. These data suggest that the PRL-3 gene is important for colorectal cancer metastasis and provides a new therapeutic target for these intractable lesions.

摘要翻译： 在确定的基因中，在转移性结肠直肠癌与原发性癌症，良性结肠直肠肿瘤和正常结肠直肠上皮的全球基因表达谱比较中，PRL-3蛋白酪氨酸磷酸酶基因特别引人关注。 在所研究的18个癌症转移中的每一个中表达高水平，但在非转移性肿瘤和正常结肠直肠上皮中的水平较低。 在检查的十二个转移中的三个中，在位于染色体8q24.3的小扩增子中发现了PRL-3基因的多个拷贝。 这些数据表明，PRL-3基因对结肠直肠癌转移很重要，为这些难治性病变提供了新的治疗靶点。

公开(公告)号：US20100137413A1

公开(公告)日：2010-06-03

申请号：US12521695

申请日：2007-02-16

申请人： Jordan Cummins ,  Victor Velculescu ,  Kenneth W. Kinzler ,  Bert Vogelstein

发明人： Jordan Cummins ,  Victor Velculescu ,  Kenneth W. Kinzler ,  Bert Vogelstein

IPC分类号： A61K31/711 ,  C07H21/02 ,  C12N5/071 ,  C12Q1/68 ,  G01N33/574 ,  C07H21/04 ,  A61K31/7105 ,  C12N5/09 ,  A61P35/00

CPC分类号： C12N15/113 ,  C12N2310/141 ,  C12N2320/11 ,  C12N2330/10 ,  C12N2510/00 ,  C12Q1/6886

摘要： MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. The public miRNA database contains 321 human miRNA sequences, 234 of which have been experimentally verified. To explore the possibility that additional miRNAs are present in the human genome, we have developed an experimental approach called miRNA serial analysis of gene expression (miRAGE) and used it to perform the largest experimental analysis of human miRNAs to date. Sequence analysis of 273,966 small RNA tags from human colorectal cells allowed us to identify 200 known mature miRNAs, 133 novel miRNA candidates, and 112 previously uncharacterized miRNA* forms. To aid in the evaluation of candidate miRNAs, we disrupted the Dicer locus in three human colorectal cancer cell lines and examined known and novel miRNAs in these cells. The miRNAs are useful to diagnose and treat cancers.

摘要翻译： 微小RNA（miRNA）是一类在多细胞生物体中具有重要调节作用的小型非编码RNA。 公共miRNA数据库包含321个人类miRNA序列，其中234个已经通过实验验证。 为了探讨其他miRNA存在于人类基因组中的可能性，我们开发了一种称为miRNA序列分析基因表达（miRAGE）的实验方法，并将其用于迄今为止对人类miRNA进行最大的实验分析。 来自人结肠直肠细胞的273,966个小RNA标签的序列分析允许我们鉴定200个已知的成熟miRNA，133个新型miRNA候选物和112个先前未表征的miRNA *形式。 为了帮助评估候选miRNA，我们破坏了三种人结肠直肠癌细胞系中Dicer基因座，并检测了这些细胞中已知和新型的miRNA。 这些miRNA可用于诊断和治疗癌症。