公开(公告)号：US07267966B2

公开(公告)日：2007-09-11

申请号：US09904039

申请日：2001-07-12

申请人： Shoulian Dong ,  Robert J. Lipshutz ,  David Lockhart

发明人： Shoulian Dong ,  Robert J. Lipshutz ,  David Lockhart

IPC分类号： C12P19/34 ,  C12Q1/68

CPC分类号： C12Q1/6837 ,  C12Q1/6855 ,  C12Q1/6858 ,  C12Q2600/156 ,  Y10S977/924 ,  C12Q2531/113 ,  C12Q2525/191 ,  C12Q2521/313 ,  C12Q2563/143

摘要： The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to model enzymatic reactions in order to determine experimental conditions before conducting actual experiments.

摘要翻译： 本发明提供了重复地降低核酸样品的复杂性的样品制备和分析的新方法。 本发明进一步提供了通过与阵列的杂交来分析上述样品，所述阵列可被特别设计成询问特定特征的期望片段，例如多态性的存在或不存在。 本发明进一步提供了使用计算机系统来模拟酶反应以便在进行实际实验之前确定实验条件的新方法。

公开(公告)号：US20060063158A1

公开(公告)日：2006-03-23

申请号：US10942364

申请日：2004-09-16

申请人： Shoulian Dong ,  Robert Lipshutz ,  David Lockhart

发明人： Shoulian Dong ,  Robert Lipshutz ,  David Lockhart

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6837 ,  C12Q1/6855 ,  C12Q1/6858 ,  C12Q2600/156 ,  Y10S977/924 ,  C12Q2531/113 ,  C12Q2525/191 ,  C12Q2521/313 ,  C12Q2563/143

摘要： The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to model enzymatic reactions in order to determine experimental conditions before conducting actual experiments.

摘要翻译： 本发明提供了重复地降低核酸样品的复杂性的样品制备和分析的新方法。 本发明进一步提供了通过与阵列的杂交来分析上述样品，所述阵列可被特别设计成询问特定特征的期望片段，例如多态性的存在或不存在。 本发明进一步提供了使用计算机系统来模拟酶反应以便在进行实际实验之前确定实验条件的新方法。

公开(公告)号：US06632611B2

公开(公告)日：2003-10-14

申请号：US09910292

申请日：2001-07-20

申请人： Xing Su ,  Shoulian Dong

发明人： Xing Su ,  Shoulian Dong

IPC分类号： C12Q168

CPC分类号： C12Q1/6855 ,  C12Q2565/501 ,  C12Q2521/107 ,  C12Q2521/319

摘要： The presently claimed invention provides methods and kits for amplifying a target sequence from within a nucleic acid population. The presently claimed invention provides selection probes which are complementary to at least a portion of said target sequence and mechanisms for adding a probe sequence to the 3′ end of a target sequence that is hybridized to a selection probe. The added 3′ probe sequence and a probe sequence added at the 5′ end of the target by adaptor ligation allow for selective amplification of the target sequence.

摘要翻译： 本发明提供了用于从核酸群体内扩增靶序列的方法和试剂盒。 目前要求保护的发明提供了与所述靶序列的至少一部分互补的选择探针和用于将探针序列添加到与选择探针杂交的靶序列的3'末端的机制。 添加的3'探针序列和通过衔接子连接在靶的5'末端添加的探针序列允许选择性扩增靶序列。

公开(公告)号：US20130084574A1

公开(公告)日：2013-04-04

申请号：US13617230

申请日：2012-09-14

申请人： Shoulian Dong ,  Junko F. Stevens ,  Chunmei Liu ,  Cora L. Woo ,  Luz Montesclaros

发明人： Shoulian Dong ,  Junko F. Stevens ,  Chunmei Liu ,  Cora L. Woo ,  Luz Montesclaros

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q1/6827 ,  C12Q1/6848 ,  C12Q1/6886 ,  C12Q2600/154 ,  C12Q2600/158 ,  C12Q2600/178 ,  C12Q2523/101 ,  C12Q2537/164 ,  C12Q2565/133 ,  C12Q2545/113 ,  C12Q2525/173 ,  C12Q2525/191

摘要： Disclosed herein are compositions, methods and kits for analyzing three-dimensional chromatin and/or chromosome conformation. Method are also disclosed for using the methods disclosed herein for diagnosing diseases such as cancer.

摘要翻译： 本文公开了用于分析三维染色质和/或染色体构象的组合物，方法和试剂盒。 还公开了使用本文公开的用于诊断疾病如癌症的方法的方法。

公开(公告)号：US20100292097A1

公开(公告)日：2010-11-18

申请号：US12822896

申请日：2010-06-24

申请人： Shoulian Dong

发明人： Shoulian Dong

IPC分类号： C40B30/04

CPC分类号： C12Q1/6855 ,  C12N15/1093 ,  C12Q1/6806 ,  C12Q1/683 ,  C12Q1/686 ,  Y10T436/143333 ,  C12Q2521/301

摘要： The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the above amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.

摘要翻译： 目前要求保护的发明提供了用于通过提供用于扩增样品中的序列的子集的非凝胶的方法来降低核酸样品的复杂性的新方法和试剂盒。 在一个优选的实施方案中，子集的扩增可以通过用两个或更多个限制性内切酶消化样品并将连接适配子连接到片段来实现，从而只能扩增片段的一个子集。 本发明进一步提供了通过与阵列杂交来分析上述扩增的样品，其可以被特别设计成询问特定特征的期望片段，例如多态性的存在或不存在。

公开(公告)号：US20060035274A1

公开(公告)日：2006-02-16

申请号：US11256505

申请日：2005-10-21

申请人： Shoulian Dong

发明人： Shoulian Dong

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6855 ,  C12N15/1093 ,  C12Q1/6806 ,  C12Q1/683 ,  C12Q1/686 ,  Y10T436/143333 ,  C12Q2521/301

摘要： The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified The invention further provides for analysis of the above amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism

摘要翻译： 目前要求保护的发明提供了用于通过提供用于扩增样品中的序列的子集的非基于凝胶的方法来降低核酸样品的复杂性的新方法和试剂盒。在一个优选实施方案中，子集的扩增可以通过 用两个或多个限制酶消化样品并将片段连接到该片段上，使得只有片段的一部分可以被扩增本发明进一步提供了通过与阵列杂交来分析上述扩增的样品，其可以专门设计成询问 用于特定特征的期望片段，例如多态性的存在或不存在

公开(公告)号：US08492121B2

公开(公告)日：2013-07-23

申请号：US13171892

申请日：2011-06-29

申请人： Shoulian Dong

发明人： Shoulian Dong

IPC分类号： C12Q1/68 ,  C12P19/34 ,  C07H21/02 ,  C07H21/04 ,  C07H21/00

CPC分类号： C12Q1/6855 ,  C12N15/1093 ,  C12Q1/6806 ,  C12Q1/683 ,  C12Q1/686 ,  Y10T436/143333 ,  C12Q2521/301

摘要： The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the above amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.

公开(公告)号：US20120149012A1

公开(公告)日：2012-06-14

申请号：US13180382

申请日：2011-07-11

申请人： Shoulian Dong ,  Junko F. Stevens

发明人： Shoulian Dong ,  Junko F. Stevens

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6827 ,  C12Q2537/164 ,  C12Q2522/101

摘要： The present teachings provide DNA methylation quantification methods that avoid bisulfite treatment of DNA. Methylation-specific binding proteins (MeDNA binding proteins) and non-methylation specific binding proteins (non-MeDNA binding proteins) are employed in various embodiments to modulate the accessibility of nucleic acids to primer extension reactions. After selectively removing the target nucleic acids, the extension products can be analyzed and methylation quantitated. In some embodiments, the analysis comprises real-time PCR.

摘要翻译： 本教导提供了避免亚硫酸氢盐处理DNA的DNA甲基化定量方法。 甲基化特异性结合蛋白（MeDNA结合蛋白）和非甲基化特异性结合蛋白（非MeDNA结合蛋白）用于各种实施方案中以调节核酸对引物延伸反应的可及性。 在选择性除去靶核酸后，可以分析延伸产物并定量甲基化。 在一些实施方案中，分析包括实时PCR。

公开(公告)号：US20110287491A1

公开(公告)日：2011-11-24

申请号：US13171892

申请日：2011-06-29

申请人： Shoulian Dong

发明人： Shoulian Dong

IPC分类号： C12P19/34

CPC分类号： C12Q1/6855 ,  C12N15/1093 ,  C12Q1/6806 ,  C12Q1/683 ,  C12Q1/686 ,  Y10T436/143333 ,  C12Q2521/301

摘要： The presently claimed invention provides for novel methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel based methods for amplification of a subset of the sequences in a sample. In a preferred embodiment, amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The invention further provides for analysis of the above amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism.

摘要翻译： 目前要求保护的发明提供了用于通过提供用于扩增样品中的序列的子集的非凝胶的方法来降低核酸样品的复杂性的新方法和试剂盒。 在一个优选的实施方案中，子集的扩增可以通过用两个或更多个限制性内切酶消化样品并将连接适配子连接到片段来实现，从而只能扩增片段的一个子集。 本发明进一步提供了通过与阵列杂交来分析上述扩增的样品，其可以被特别设计成询问特定特征的期望片段，例如多态性的存在或不存在。

公开(公告)号：US20100041057A1

公开(公告)日：2010-02-18

申请号：US12543450

申请日：2009-08-18

申请人： Shoulian Dong ,  Junko F. Stevens

发明人： Shoulian Dong ,  Junko F. Stevens

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6827 ,  C12Q2537/164 ,  C12Q2522/101

摘要： The present teachings provide DNA methylation quantification methods that avoid bisulfite treatment of DNA. Methylation-specific binding proteins (MeDNA binding proteins) and non-methylation specific binding proteins (non-MeDNA binding proteins) are employed in various embodiments to modulate the accessibility of nucleic acids to primer extension reactions. After selectively removing the target nucleic acids, the extension products can be analyzed and methylation quantitated. In some embodiments, the analysis comprises real-time PCR.

摘要翻译： 本教导提供了避免亚硫酸氢盐处理DNA的DNA甲基化定量方法。 在各种实施方案中使用甲基化特异性结合蛋白（MeDNA结合蛋白）和非甲基化特异性结合蛋白（非MeDNA结合蛋白）来调节核酸对引物延伸反应的可及性。 在选择性除去靶核酸后，可以分析延伸产物并定量甲基化。 在一些实施方案中，分析包括实时PCR。