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11.发明授权Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process 有权通过DNA聚合过程产生的全基因组和整个转录组文库的扩增和分析公开(公告)号：US08206913B1
公开(公告)日：2012-06-26
申请号：US12716681
申请日：2010-03-03
申请人： Emmanuel Kamberov , Tong Sun , Eric Bruening , Jonathon H. Pinter , Irina Sleptsova , Takao Kurihara , Vladimir L. Makarov
发明人： Emmanuel Kamberov , Tong Sun , Eric Bruening , Jonathon H. Pinter , Irina Sleptsova , Takao Kurihara , Vladimir L. Makarov
CPC分类号： C12Q1/6853 , C12N15/10 , C12N15/1093 , C12Q1/6806 , C12Q1/686 , C12Q1/6876 , C12Q2525/161 , C12Q2525/179 , C12Q2525/15
摘要： The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.
摘要翻译： 本发明涉及用于全基因组扩增和全转录组扩增的多种方法和组合物。 在本发明的特定方面，存在扩增包含文库产生步骤之后是文库扩增步骤的基因组的方法。 在具体实施方案中，文库产生步骤使用特异性引物混合物和DNA聚合酶，其中特异性引物混合物被设计为消除混合物内其它引物自我杂交和/或杂交的能力，但有效且频繁引发核酸模板。
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12.发明申请DNA AMPLIFICATION AND SEQUENCING USING DNA MOLECULES GENERATED BY RANDOM FRAGMENTATION 有权使用随机分解产生的DNA分子进行DNA扩增和测序公开(公告)号：US20100145037A1
公开(公告)日：2010-06-10
申请号：US12697886
申请日：2010-02-01
IPC分类号： C07H21/04
CPC分类号： C12Q1/6855 , C12Q1/6844 , C12Q1/6846 , C12Q1/6869 , C12Q2531/113 , C12Q2525/191 , C12Q2521/301 , C12Q2523/107
摘要： The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3′ end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.
摘要翻译： 本发明涉及通过随机碎裂制备DNA分子或多个DNA分子的方法。 在一些实施方案中，本发明涉及通过随机断裂制备用于DNA测序的模板。 在具体实施方案中，随机碎裂包括化学断裂，机械破碎或酶促碎裂。 在进一步的具体实施方案中，通用序列附着于DNA片段的3'末端，例如通过连接衔接子序列或通过与末端脱氧核苷酸转移酶的均聚尾料连接。 在其它实施方案中，使用本发明的方法制备文库。
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13.发明授权DNA amplification and sequencing using DNA molecules generated by random fragmentation 有权DNA扩增和使用随机碎裂产生的DNA分子进行测序公开(公告)号：US08815504B2
公开(公告)日：2014-08-26
申请号：US12697886
申请日：2010-02-01
CPC分类号： C12Q1/6855 , C12Q1/6844 , C12Q1/6846 , C12Q1/6869 , C12Q2531/113 , C12Q2525/191 , C12Q2521/301 , C12Q2523/107
摘要： The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3′ end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.
摘要翻译： 本发明涉及通过随机碎裂制备DNA分子或多个DNA分子的方法。 在一些实施方案中，本发明涉及通过随机断裂制备用于DNA测序的模板。 在具体实施方案中，随机碎裂包括化学断裂，机械破碎或酶促碎裂。 在进一步的具体实施方案中，通用序列附着于DNA片段的3'末端，例如通过连接衔接子序列或通过与末端脱氧核苷酸转移酶的均聚尾料连接。 在其它实施方案中，使用本发明的方法制备文库。
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14.发明授权DNA amplification and sequencing using DNA molecules generated by random fragmentation 有权DNA扩增和使用随机碎裂产生的DNA分子进行测序公开(公告)号：US07655791B2
公开(公告)日：2010-02-02
申请号：US10293048
申请日：2002-11-13
CPC分类号： C12Q1/6855 , C12Q1/6844 , C12Q1/6846 , C12Q1/6869 , C12Q2531/113 , C12Q2525/191 , C12Q2521/301 , C12Q2523/107
摘要： The present invention is directed to methods to prepare a DNA molecule or a plurality of DNA molecules by random fragmentation. In some embodiments, the present invention regards preparing a template for DNA sequencing by random fragmentation. In specific embodiments, the random fragmentation comprises chemical fragmentation, mechanical fragmentation, or enzymatic fragmentation. In further specific embodiments, a universal sequence is attached to the 3′ end of the DNA fragments, such as by ligation of an adaptor sequence or by homopolymeric tailing with terminal deoxynucleotidyltransferase. In other embodiments, a library is prepared with methods of the present invention.
摘要翻译： 本发明涉及通过随机碎裂制备DNA分子或多个DNA分子的方法。 在一些实施方案中，本发明涉及通过随机断裂制备用于DNA测序的模板。 在具体实施方案中，随机碎裂包括化学断裂，机械破碎或酶促碎裂。 在进一步的具体实施方案中，通用序列附着于DNA片段的3'末端，例如通过连接衔接子序列或通过与末端脱氧核苷酸转移酶的均聚尾料连接。 在其它实施方案中，使用本发明的方法制备文库。
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15.发明授权Genome walking by selective amplification of nick-translate DNA library and amplification from complex mixtures of templates 有权通过选择性扩增切口翻译DNA文库并从模板的复杂混合物中扩增的基因组公开(公告)号：US06777187B2
公开(公告)日：2004-08-17
申请号：US09999018
申请日：2001-11-15
IPC分类号： C12Q168
CPC分类号： C12Q1/6869 , C12Q1/6876
摘要： Improved methods and reagents for chromosome walking of nucleic acid are discussed herein. A library of amplifiable nick translation molecules is generated, and a chromosome walk is initiated from a known sequence in the nucleic acid by producing at least one nick translate molecule, sequencing part of the nick translate molecule, and producing a second nick translate molecule by initiating the primer extension from the region of the obtained sequence of the prior nick translate molecule.
摘要翻译： 本文讨论了用于核酸染色体行走的改进方法和试剂。 产生可扩增切口平移分子的文库，通过产生至少一个切口平移分子，切割平移分子的测序部分，并通过引发产生第二切口平移分子，从核酸中的已知序列引发染色体步态 来自所获得的先前切口平移分子序列的区域的引物延伸。
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16.发明申请Methods and compositions for generating and amplifying DNA libraries for sensitive detection and analysis of DNA methylation 有权用于产生和扩增DNA文库以灵敏检测和分析DNA甲基化的方法和组合物公开(公告)号：US20050202490A1
公开(公告)日：2005-09-15
申请号：US11071864
申请日：2005-03-03
申请人： Vladimir Makarov , Emmanuel Kamberov , Tong Sun , Jonathon Pinter , Brendan Tarrier , Eric Bruening , Takao Kurihara , Tim Tesmer , Joseph M'Mwirichia
发明人： Vladimir Makarov , Emmanuel Kamberov , Tong Sun , Jonathon Pinter , Brendan Tarrier , Eric Bruening , Takao Kurihara , Tim Tesmer , Joseph M'Mwirichia
CPC分类号： C12Q1/6869 , C12N15/1072 , C12Q1/6827 , C12Q1/6855 , C12Q2525/301 , C12Q2525/191 , C12Q2521/331 , C12Q2523/125
摘要： The present invention regards a variety of methods and compositions for obtaining epigenetic information, such as DNA methylation patterns, through the preparation, amplification and analysis of Methylome libraries. In several aspects of the present invention, there are methods based on methylation-dependent enrichment or depletion of genomic DNA isolated from cellular and cell-free sources. In additional embodiments, there are methods and compositions for single-step high throughput preparations of Methylome libraries.
摘要翻译： 本发明涉及通过Methylome文库的制备，扩增和分析来获得表观遗传信息的各种方法和组合物，例如DNA甲基化模式。 在本发明的几个方面，存在基于从细胞和无细胞来源分离的基因组DNA的甲基化依赖性富集或消耗的方法。 在另外的实施方案中，存在Methylome文库的单步高通量制剂的方法和组合物。
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17.发明申请Amplification and analysis of whole genome and whole transcriptome libraries generated by a DNA polymerization process 审中-公开通过DNA聚合过程产生的全基因组和整个转录组文库的扩增和分析公开(公告)号：US20070054311A1
公开(公告)日：2007-03-08
申请号：US11593625
申请日：2006-11-06
申请人： Emmanuel Kamberov , Tong Sun , Eric Bruening , Jonathon Pinter , Irina Sleptsova , Takao Kurihara , Vladimir Makarov
发明人： Emmanuel Kamberov , Tong Sun , Eric Bruening , Jonathon Pinter , Irina Sleptsova , Takao Kurihara , Vladimir Makarov
CPC分类号： C12N15/1093 , C12N15/10 , C12Q1/686 , C40B40/06 , C40B50/06 , C12Q2525/161 , C12Q2525/179 , C12Q2525/15
摘要： The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.
摘要翻译： 本发明涉及用于全基因组扩增和全转录组扩增的多种方法和组合物。 在本发明的特定方面，存在扩增包含文库产生步骤之后是文库扩增步骤的基因组的方法。 在具体实施方案中，文库产生步骤使用特异性引物混合物和DNA聚合酶，其中特异性引物混合物被设计为消除混合物内其它引物自我杂交和/或杂交的能力，但有效且频繁引发核酸模板。
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18.发明申请Genome walking by selective amplification of nick-translate DNA library and amplification from complex mixtures of templates 审中-公开通过选择性扩增切口翻译DNA文库并从模板的复杂混合物中扩增的基因组公开(公告)号：US20050032104A1
公开(公告)日：2005-02-10
申请号：US10909516
申请日：2004-08-02
CPC分类号： C12Q1/6869 , C12Q1/6876
摘要： Improved methods and reagents for chromosome walking of nucleic acid are discussed herein. A library of amplifiable nick translation molecules is generated, and a chromosome walk is initiated from a known sequence in the nucleic acid by producing at least one nick translate molecule, sequencing part of the nick translate molecule, and producing a second nick translate molecule by initiating the primer extension from the region of the obtained sequence of the prior nick translate molecule.
摘要翻译： 本文讨论了用于核酸染色体行走的改进方法和试剂。 产生可扩增切口平移分子的文库，通过产生至少一个切口平移分子，切割平移分子的测序部分，并通过引发产生第二切口平移分子，从核酸中的已知序列引发染色体步态 来自所获得的先前切口平移分子序列的区域的引物延伸。
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19.发明申请公开(公告)号：US20070031858A1
公开(公告)日：2007-02-08
申请号：US11367046
申请日：2006-03-02
CPC分类号： C12N15/1065 , C12N15/1003 , C12N15/1093 , C12Q1/6846 , C12Q1/6886 , C12Q2537/164 , C12Q2527/107
摘要： The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example.
摘要翻译： 本发明涉及分离，文库制备和从部分分子的DNA片段的组成不均一聚集体（例如源自启动子CpG岛的那些DNA片段）的选择性扩增，并且特征在于高GC含量。 特别地，该方法利用热分解DNA分子到GC-不良的单链分子级分和富含GC的双链分子级分，随后富含GC的双链DNA分子的酶转化 进入文库，可选地，扩增。 在具体实施方案中，例如，分离过程用于产生用于研究和诊断应用的富含启动子的基因组和甲基化文库。
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20.发明申请Compositions and methods for processing and amplification of DNA, including using multiple enzymes in a single reaction 审中-公开用于处理和扩增DNA的组合物和方法，包括在单次反应中使用多种酶公开(公告)号：US20070031857A1
公开(公告)日：2007-02-08
申请号：US11366222
申请日：2006-03-02
CPC分类号： C12Q1/6853 , C12N15/1068 , C12P19/34 , C12Q1/6855 , C12Q1/686 , C12Q1/6865 , C12Q2525/301 , C12Q2525/119 , C12Q2521/301 , C12Q2525/191 , C12Q2521/501
摘要： The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.
摘要翻译： 本发明涉及使用茎环寡核苷酸制备DNA分子，例如文库。 在具体实施方案中，本发明采用单一反应混合物和条件。 特别地，在制备分子期间，至少部分反向回文被去除以促进分子的扩增。 因此，在具体实施方案中，DNA分子适合于扩增，并且不受回文的存在的阻碍。
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