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1. 发明申请

WO2009049166A2 GENOMIC LANDSCAPES OF HUMAN BREAST AND COLORECTAL CANCERS 审中-公开
标题翻译：人类乳腺癌和色素沉着病的基因组学观察
公开(公告)号：WO2009049166A2
公开(公告)日：2009-04-16
申请号：PCT/US2008079526
申请日：2008-10-10
申请人： UNIV JOHNS HOPKINS , WOOD LAURA D , PARSONS D WILLIAMS , JONES SIAN , LIN JIMMY , SJOEBLOM TOBIAS , BARBER THOMAS , PARMIGIANI GIOVANNI , VELCULESCU VICTOR , KINZLER KENNETH W , VOGELSTEIN BERT
发明人： WOOD LAURA D , PARSONS D WILLIAMS , JONES SIAN , LIN JIMMY , SJOEBLOM TOBIAS , BARBER THOMAS , PARMIGIANI GIOVANNI , VELCULESCU VICTOR , KINZLER KENNETH W , VOGELSTEIN BERT
IPC分类号： C12Q1/68 , C12Q1/02
CPC分类号： C12Q1/6886 , C12Q2600/112 , C12Q2600/156
摘要： Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalogue the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene "mountains" and a much larger number of gene "hills" that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.
摘要翻译：人类癌症是由致癌基因和肿瘤抑制基因突变的积累引起的。为了列出肿瘤发生过程中发生的遗传变化，我们从11个乳腺和11个结肠直肠肿瘤中分离出DNA，并在这些样品中确定了参考序列数据库中的基因序列。根据对18,191个基因的20,857个转录本的外显子的分析，我们得出结论，乳腺癌和结肠直肠癌的基因组景观由少数常见的突变基因“山”组成，更多的基因“山”在低位突变频率。我们描述了统计和生物信息学工具，可以帮助识别在肿瘤发生中发挥作用的突变。这些结果有助于了解人类癌症的性质和异质性以及使用个人基因组学进行肿瘤诊断和治疗。

2. 发明申请

WO2010028098A3 PATHWAYS UNDERLYING PANCREATIC TUMORIGENESIS AND AN HEREDITARY PANCREATIC CANCER GENE 审中-公开
标题翻译：基于胰腺癌和胰腺癌基因的途径
公开(公告)号：WO2010028098A3
公开(公告)日：2010-06-10
申请号：PCT/US2009055802
申请日：2009-09-03
申请人： UNIV JOHNS HOPKINS , VOGELSTEIN BERT , KINZLER KENNETH W , PARSONS D WILLIAMS , JONES SIAN , ZHANG XIAOSONG , LIN JIMMY CHANG-HO , LEARY REBECCA J , ANGENENDT PHILIPP , PAPADOPOULOS NICKOLAS , VELCULESCU VICTOR , PARMIGIANI GIOVANNI , KARCHIN RACHEL , KERN SCOTT , HRUBAN RALPH , ESHLEMAN JAMES R , GOGGINS MICHAEL , KLEIN ALISON
发明人： VOGELSTEIN BERT , KINZLER KENNETH W , PARSONS D WILLIAMS , JONES SIAN , ZHANG XIAOSONG , LIN JIMMY CHANG-HO , LEARY REBECCA J , ANGENENDT PHILIPP , PAPADOPOULOS NICKOLAS , VELCULESCU VICTOR , PARMIGIANI GIOVANNI , KARCHIN RACHEL , KERN SCOTT , HRUBAN RALPH , ESHLEMAN JAMES R , GOGGINS MICHAEL , KLEIN ALISON
IPC分类号： C12Q1/68
CPC分类号： G01N33/57438 , C12Q1/6886 , C12Q2600/156 , G01N2800/50
摘要： This invention relates to new insights into the pathogenesis of pancreatic cancers by analyzing 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：本发明涉及通过分析24个胰腺肿瘤中改变的基因对胰腺癌发病机理的新见解。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。其次，我们使用微阵列查询了每个样本中一百万个单核苷酸多态性的纯合缺失和扩增。第三，我们使用SAGE和下一代合成技术分析相同样品的转录组我们发现胰腺癌平均含有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。

3. 发明申请

WO2010028098A4 PATHWAYS UNDERLYING PANCREATIC TUMORIGENESIS AND AN HEREDITARY PANCREATIC CANCER GENE 审中-公开
标题翻译：胰岛素瘤和遗传性胰腺癌基因途径
公开(公告)号：WO2010028098A4
公开(公告)日：2010-08-19
申请号：PCT/US2009055802
申请日：2009-09-03
申请人： UNIV JOHNS HOPKINS , VOGELSTEIN BERT , KINZLER KENNETH W , PARSONS D WILLIAMS , JONES SIAN , ZHANG XIAOSONG , LIN JIMMY CHANG-HO , LEARY REBECCA J , ANGENENDT PHILIPP , PAPADOPOULOS NICKOLAS , VELCULESCU VICTOR , PARMIGIANI GIOVANNI , KARCHIN RACHEL , KERN SCOTT , HRUBAN RALPH , ESHLEMAN JAMES R , GOGGINS MICHAEL , KLEIN ALISON
发明人： VOGELSTEIN BERT , KINZLER KENNETH W , PARSONS D WILLIAMS , JONES SIAN , ZHANG XIAOSONG , LIN JIMMY CHANG-HO , LEARY REBECCA J , ANGENENDT PHILIPP , PAPADOPOULOS NICKOLAS , VELCULESCU VICTOR , PARMIGIANI GIOVANNI , KARCHIN RACHEL , KERN SCOTT , HRUBAN RALPH , ESHLEMAN JAMES R , GOGGINS MICHAEL , KLEIN ALISON
IPC分类号： C12Q1/68
CPC分类号： G01N33/57438 , C12Q1/6886 , C12Q2600/156 , G01N2800/50
摘要： This invention relates to new insights into the pathogenesis of pancreatic cancers by analyzing 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：本发明涉及通过分析在24个胰腺肿瘤中改变的基因而对胰腺癌的发病机理的新见解。首先，我们确定了来自这些肿瘤的DNA中23,781个转录物的序列，代表20,583个蛋白质编码基因。其次，我们使用微阵列查询每个样本中一百万个单核苷酸多态性来寻找纯合子缺失和扩增。第三，我们使用SAGE和下一代合成测序技术分析了相同样品的转录组我们发现胰腺癌平均含有63个基因改变，其中49个是点突变，8个是纯合子缺失，6个是扩增。进一步的分析揭示了12个监管程序或途径的核心组合，每个过程或途径在70％到100％的样本中均被遗传改变。数据表明这种核心途径的失调调节是胰腺肿瘤发生的主要特征的原因。

4. 发明申请

WO2008021288A3 CONSENSUS CODING SEQUENCES OF HUMAN BREAST AND COLORECTAL CANCERS 审中-公开
标题翻译：人乳腺癌和结直肠癌共识编码序列
公开(公告)号：WO2008021288A3
公开(公告)日：2008-11-13
申请号：PCT/US2007017866
申请日：2007-08-13
申请人： UNIV JOHNS HOPKINS , SJOBLOM TOBIAS , JONES SIAN , PARSONS D WILLIAMS , WOOD LAURA D , LIN JIMMY , BARBER THOMAS , MANDELKER DIANA , VOGELSTEIN BERT , KINZLER KENNETH W , VELCULESU VICTOR E
发明人： SJOBLOM TOBIAS , JONES SIAN , PARSONS D WILLIAMS , WOOD LAURA D , LIN JIMMY , BARBER THOMAS , MANDELKER DIANA , VOGELSTEIN BERT , KINZLER KENNETH W , VELCULESU VICTOR E
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6886 , C12Q2600/106 , C12Q2600/156
摘要： Analysis of 13,023 genes in 11 breast and 11 colorectal cancers revealed that individual tumors accumulate an average of ~90 mutant genes but that only a subset of these contribute to the neoplastic process. Using stringent criteria to delineate this subset, we identified 189 genes (average of 11 per tumor) that were mutated at significant frequency. The vast majority of these genes were not known to be genetically altered in tumors and are predicted to affect a wide range of cellular functions, including transcription, adhesion, and invasion. These data define the genetic landscape of two human cancer types, provide new targets for diagnostic and therapeutic intervention and monitoring.
摘要翻译：对11个乳腺癌和11个结直肠癌中的13023个基因的分析显示，个体肿瘤累积平均约90个突变基因，但是只有这些基因的一部分有助于肿瘤过程。使用严格的标准划定这个子集，我们确定了189个基因（平均每个肿瘤11个）以显着频率突变。绝大多数这些基因在肿瘤中并不知晓是遗传改变的，预计会影响广泛的细胞功能，包括转录，粘附和侵袭。这些数据定义了两种人类癌症类型的遗传情况，为诊断和治疗干预和监测提供了新的目标。

5. 发明申请

WO2010102160A3 DIAGNOSTIC METHOD USING PALB2 审中-公开
标题翻译：诊断方法使用PALB2
公开(公告)号：WO2010102160A3
公开(公告)日：2011-01-13
申请号：PCT/US2010026290
申请日：2010-03-05
申请人： UNIV JOHNS HOPKINS , VOGELSTEIN BERT , KINZLER KENNETH W , PARSONS D WILLIAMS , JONES SIAN , KERN SCOTT , HRUBAN RALPH , ESHLEMAN JAMES R , GOGGINS MICHAEL , KLEIN ALISON , HIDALGO MANUEL , VELCULESCU VICTOR E
发明人： VOGELSTEIN BERT , KINZLER KENNETH W , PARSONS D WILLIAMS , JONES SIAN , KERN SCOTT , HRUBAN RALPH , ESHLEMAN JAMES R , GOGGINS MICHAEL , KLEIN ALISON , HIDALGO MANUEL , VELCULESCU VICTOR E
IPC分类号： C12Q1/68 , G01N33/574 , G01N33/68
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。

6. 发明申请

WO2012064721A2 MEDULLOBLASTOMA GENES AS TARGETS FOR DIAGNOSIS AND THERAPEUTICS 审中-公开
标题翻译：作为诊断和治疗目标的MEDLOBLASTOMA基因
公开(公告)号：WO2012064721A2
公开(公告)日：2012-05-18
申请号：PCT/US2011059751
申请日：2011-11-08
申请人： UNIV JOHNS HOPKINS , UNIV DUKE , VOGELSTEIN BERT , KINZLER KENNETH W , PAPADOPOULOS NICKOLAS , PARSONS DONALD WILLIAMS , LEARY REBECCA J , LI MENG , ZHANG XIAOSONG , JONES SIAN , RIGGINS GREGORY J , VELCULESCU VICTOR , BIGNER DARELL , YAN HAI
发明人： VOGELSTEIN BERT , KINZLER KENNETH W , PAPADOPOULOS NICKOLAS , PARSONS DONALD WILLIAMS , LEARY REBECCA J , LI MENG , ZHANG XIAOSONG , JONES SIAN , RIGGINS GREGORY J , VELCULESCU VICTOR , BIGNER DARELL , YAN HAI
IPC分类号： G01N33/574 , C12Q1/68 , G01N33/50
CPC分类号： C12Q1/6886 , C12Q2600/112 , C12Q2600/156 , G01N33/57407
摘要： Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high density microarrays and sequenced all known protein-coding genes and miRNA genes using Sanger sequencing. We found that, on average, each tumor had 11 gene alterations, markedly fewer than in common adult cancers. In addition to alterations in the Hedgehog and Wnt pathways, our analysis led to the discovery of genes not previously known to be altered in MBs. Most notably, inactivating mutations of the histone H3K4 trimethylase genes MLL2 or MLL3 were identified in 16% of MB patients. These results demonstrate key differences between the genetic landscapes of adult and childhood cancers, highlight dysregulation of developmental pathways as an important mechanism underlying MBs, and identify a role for a specific type of histone methylation in human tumorigenesis.
摘要翻译：髓母细胞瘤（MB）是儿童最常见的恶性脑肿瘤。为了鉴定这种肿瘤类型的遗传改变，我们使用高密度微阵列搜索拷贝数改变，并使用Sanger测序对所有已知的蛋白质编码基因和miRNA基因进行测序。我们发现平均而言，每个肿瘤有11个基因改变，明显少于常见的成人癌症。除了Hedgehog和Wnt途径的改变之外，我们的分析还导致发现以前不知道在MB中改变的基因。最值得注意的是，在16％的MB患者中鉴定出组蛋白H3K4三甲基化酶基因MLL2或MLL3的失活突变。这些结果表明成人和儿童癌症的遗传景观之间的主要区别，突出发展途径的失调作为潜在的MB的重要机制，并确定在人类肿瘤特定类型的组蛋白甲基化的作用。

7. 发明申请

WO2012071096A3 ARID1A AND PPP2R1A MUTATIONS IN CANCER 审中-公开
标题翻译：癌症中的ARID1A和PPP2R1A突变
公开(公告)号：WO2012071096A3
公开(公告)日：2012-08-16
申请号：PCT/US2011050487
申请日：2011-09-06
申请人： UNIV JOHNS HOPKINS , 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 , A61K31/7088 , C12N5/09 , C12N15/11 , G01N33/68
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：可用于检测癌症，诊断癌症，有助于诊断癌症的方法中使用两种基因ARID1A（含AT富含交互结构域的蛋白质1A）和PPP2R1A（蛋白质磷酸酶2，调节亚单位1，α）确定癌症的诊断，确定癌症的适当治疗，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，成神经管细胞瘤，胰腺癌和前列腺癌。

8. 发明申请

WO2005091849A3 MUTATIONS OF THE PIK3CA GENE IN HUMAN CANCERS 审中-公开
标题翻译：人类癌症中PIK3CA基因的突变
公开(公告)号：WO2005091849A3
公开(公告)日：2009-04-16
申请号：PCT/US2005005193
申请日：2005-02-18
申请人： UNIV JOHNS HOPKINS , SAMUELS YARDENA , VELCULESCU VICTOR , KINZLER KENNETH W , VOGELSTEIN BERT
发明人： SAMUELS YARDENA , VELCULESCU VICTOR , KINZLER KENNETH W , VOGELSTEIN BERT
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）是信号传导途径的重要调控因子。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代表人类癌症中鉴定出来的最突变的癌基因之一，可用作诊断和治疗靶点。

9. 发明申请

WO2008103135A3 THE MICRORNAOME 审中-公开
标题翻译：微笑
公开(公告)号：WO2008103135A3
公开(公告)日：2008-12-24
申请号：PCT/US2007004518
申请日：2007-02-16
申请人： UNIV JOHNS HOPKINS , CUMMINS JORDAN , VELCULESCU VICTOR , KINZLER KENNETH W , VOGELSTEIN BERT
发明人： CUMMINS JORDAN , VELCULESCU VICTOR , KINZLER KENNETH W , VOGELSTEIN BERT
IPC分类号： C07H21/02 , A01N43/04 , A61K31/70 , C07H21/04 , C12N15/113
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。

10. 发明申请

WO2004082458A2 TYROSINE KINOME 审中-公开
公开(公告)号：WO2004082458A2
公开(公告)日：2004-09-30
申请号：PCT/US2004004452
申请日：2004-02-18
申请人： UNIV JOHNS HOPKINS , BARDELLI ALBERTO , PARSONS WILL , VELCULESCU VICTOR , KINZLER KENNETH W , VOGELSTEIN BERT
发明人： BARDELLI ALBERTO , PARSONS WILL , VELCULESCU VICTOR , KINZLER KENNETH W , VOGELSTEIN BERT
IPC分类号： A61B20060101 , C12N9/12 , C12Q1/68 , A61B
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。这些数据代表了对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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