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21. 发明授权

US09551026B2 Method for nucleic acid detection using voltage enhancement 有权
标题翻译：使用电压增强的核酸检测方法
公开(公告)号：US09551026B2
公开(公告)日：2017-01-24
申请号：US13337968
申请日：2011-12-27
申请人： Andres Fernandez , Bryan Staker , Radoje Drmanac
发明人： Andres Fernandez , Bryan Staker , Radoje Drmanac
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6832 , C12Q1/6825 , C12Q2523/307 , C12Q2565/501 , C12Q2565/607
摘要： Methods are provided for carrying out DNA sequencing on a device having upper and lower conductive layers separated by an insulative layer. Holes in the upper conductive layer create discrete attachment sites for DNA fragments. Voltage is applied to the surface to control affinity between the attachment sites and the DNA fragments, and to compact the DNA fragments for discrete optical detection.
摘要翻译：提供了用于在具有由绝缘层隔开的上导电层和下导电层的器件上进行DNA测序的方法。上导电层中的孔为DNA片段产生离散的附着位点。将电压施加到表面以控制附着位点和DNA片段之间的亲和力，并压缩DNA片段以进行离散的光学检测。

22. 发明授权

US09023769B2 cDNA library for nucleic acid sequencing 有权
标题翻译：用于核酸测序的cDNA文库
公开(公告)号：US09023769B2
公开(公告)日：2015-05-05
申请号：US12956802
申请日：2010-11-30
申请人： Radoje Drmanac , Fredrik Dahl , Evan Hurowitz , Fredrie Dahl
发明人： Radoje Drmanac , Fredrik Dahl , Evan Hurowitz , Fredrie Dahl
IPC分类号： C40B50/06 , C12Q1/68 , C12N15/10 , C40B20/00
CPC分类号： C12Q1/6869 , B01J2219/00621 , B01J2219/00637 , B01J2219/00659 , B01J2219/00722 , C12N15/10 , C12Q1/6853 , C40B20/00
摘要： The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.
摘要翻译：本发明涉及用于核酸鉴定和检测的组合物和方法。本发明的组合物和方法包括从样品中提取和分离靶核酸，使用片段化的靶核酸产生靶核酸模板，并使这些靶核酸模板进行扩增方法以形成核酸纳米棒。本发明还包括使用各种测序应用检测和鉴定序列的方法，包括通过连接方法测序。

23. 发明授权

US08617811B2 Methods and compositions for efficient base calling in sequencing reactions 有权
公开(公告)号：US08617811B2
公开(公告)日：2013-12-31
申请号：US12361507
申请日：2009-01-28
申请人： Radoje Drmanac
发明人： Radoje Drmanac
IPC分类号： C12Q1/68 , C12P19/34 , C12M1/34 , C12M3/00 , C07H21/02 , C07H21/04
CPC分类号： C12Q1/6874 , C12Q1/68 , C12Q1/686 , C12Q1/6869 , C12Q1/6876 , C12Q2565/102 , C12Q2565/1025 , C12Q2565/518
摘要： The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.

24. 发明授权

US08592150B2 Methods and compositions for long fragment read sequencing 有权
标题翻译：用于长片段读取测序的方法和组合物
公开(公告)号：US08592150B2
公开(公告)日：2013-11-26
申请号：US12816365
申请日：2010-06-15
申请人： Radoje Drmanac , Brock A. Peters , Andrei Alexeev , Peter Hong
发明人： Radoje Drmanac , Brock A. Peters , Andrei Alexeev , Peter Hong
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： B01J19/0046 , B01J2219/00722 , C12P19/34 , C12Q1/6869 , C12Q1/6874 , C12Q2525/101 , C12Q2521/101
摘要： The present invention is directed to methods and compositions for long fragment read sequencing. The present invention encompasses methods and compositions for preparing long fragments of genomic DNA, for processing genomic DNA for long fragment read sequencing methods, as well as software and algorithms for processing and analyzing sequence data.
摘要翻译：本发明涉及用于长片段读取测序的方法和组合物。本发明包括用于制备基因组DNA长片段的方法和组合物，用于处理长片段读取测序方法的基因组DNA，以及用于处理和分析序列数据的软件和算法。

25. 发明授权

US08440397B2 High throughput genome sequencing on DNA arrays 有权
公开(公告)号：US08440397B2
公开(公告)日：2013-05-14
申请号：US11981761
申请日：2007-10-31
申请人： Radoje Drmanac , Matthew J. Callow , Snezana Drmanac
发明人： Radoje Drmanac , Matthew J. Callow , Snezana Drmanac
IPC分类号： C12Q1/68 , C12P19/34 , C12M1/36
CPC分类号： C12Q1/6874 , C12N15/64 , C12N15/66 , Y10T436/143333 , C12Q2521/313 , C12Q2525/191 , C12Q2525/151 , C12Q2525/131 , C12Q2565/518 , C12Q2533/107 , C12Q2531/125
摘要： The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences using adaptors interspersed in target polynucleotides. The sequence information can be new, e.g. sequencing unknown nucleic acids, re-sequencing, or genotyping. The invention preferably includes methods for inserting a plurality of adaptors at spaced locations within a target polynucleotide or a fragment of a polynucleotide. Such adaptors may serve as platforms for interrogating adjacent sequences using various sequencing chemistries, such as those that identify nucleotides by primer extension, probe ligation, and the like. Encompassed in the invention are methods and compositions for the insertion of known adaptor sequences into target sequences, such that there is an interruption of contiguous target sequence with the adaptors. By sequencing both “upstream” and “downstream” of the adaptors, identification of entire target sequences may be accomplished.

26. 发明申请

US20130059740A1 Sequencing Small Amounts of Complex Nucleic Acids 审中-公开
标题翻译：测序小量的复杂核酸
公开(公告)号：US20130059740A1
公开(公告)日：2013-03-07
申请号：US13448279
申请日：2012-04-16
申请人： Radoje Drmanac , Brock A. Peters , Bahram Ghaffarzadeh Kermani
发明人： Radoje Drmanac , Brock A. Peters , Bahram Ghaffarzadeh Kermani
IPC分类号： C40B20/00 , C40B20/04
CPC分类号： G16B30/00
摘要： The present invention provides methods and compositions for sequencing small amounts of complex nucleic acids such as human genomes and for analyzing the resulting sequence information in order to reduce sequencing errors and perform haplotype phasing, for example.
摘要翻译：本发明提供了用于测序少量复合核酸如人类基因组的方法和组合物，并且用于分析所得序列信息以减少测序误差并进行例如单倍型定相。

27. 发明申请

US20120100534A1 EFFICIENT BASE DETERMINATION IN SEQUENCING REACTIONS 有权
标题翻译：顺序反应中有效的碱基测定
公开(公告)号：US20120100534A1
公开(公告)日：2012-04-26
申请号：US12329365
申请日：2008-12-05
申请人： Radoje Drmanac , Andrew Sparks , Fredrik Dahl , Matthew J. Callow , Clifford Reid
发明人： Radoje Drmanac , Andrew Sparks , Fredrik Dahl , Matthew J. Callow , Clifford Reid
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6874 , C12Q1/6855 , C12Q2531/125 , C12Q2521/313 , C12Q2521/125 , C12Q2537/163 , C12Q2525/191 , C12Q2521/531 , C12Q2521/501 , C12Q2525/307 , C12Q2525/151
摘要： The present invention is directed to compositions and methods for nucleic acid identification and detection. Compositions and methods of the present invention include extracting and fragmenting target nucleic acids from a sample, using the fragmented target nucleic acids to produce target nucleic acid templates and subjecting those target nucleic acid templates to amplification methods to form nucleic acid nanoballs. The invention also includes methods of detecting and identifying sequences using various sequencing applications, including sequencing by ligation methods.
摘要翻译：本发明涉及用于核酸鉴定和检测的组合物和方法。本发明的组合物和方法包括从样品中提取和分离靶核酸，使用片段化的靶核酸产生靶核酸模板，并使这些靶核酸模板进行扩增方法以形成核酸纳米棒。本发明还包括使用各种测序应用检测和鉴定序列的方法，包括通过连接方法测序。

28. 发明申请

US20110319281A1 Nucleic Acid Analysis by Random Mixtures of Non-Overlapping Fragments 有权
标题翻译：通过非重叠片段的随机混合进行核酸分析
公开(公告)号：US20110319281A1
公开(公告)日：2011-12-29
申请号：US13017244
申请日：2011-01-31
申请人： Radoje DRMANAC
发明人： Radoje DRMANAC
IPC分类号： C40B30/04
CPC分类号： C12Q1/6874 , C07H21/04 , C07K1/047 , C12Q1/6806 , C12Q1/682 , C12Q1/6837 , C12Q1/6869 , C12Q2525/151 , C12Q2525/313 , C12Q2531/125 , C12Q2565/513 , G01N15/1404 , G01N15/1434 , Y10S977/778 , Y10S977/789 , Y10S977/792 , Y10S977/88 , Y10S977/882 , C12Q2521/307 , C12Q2525/161 , C12Q2535/122 , C12Q2563/179 , C12Q2565/514
摘要： The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like.
摘要翻译：本发明提供了用于排序从一个或多个目标多核苷酸衍生的序列信息的方法和试剂盒。在一个方面，产生一个或多个分层或等级的碎片和等分试样，之后从最终级别或层级的片段获得序列信息。这样的最后一层中的每个片段都来自特定的等分试样，而这些等分试样又是来自先前层的特定等分试样，等等。对于最后一层中的等分试样的每个片段，从每个先前的层次派生的等分试样是已知的，或者可以被辨别出来。因此，来自不同等分试样的重叠片段的相同序列可以被区分并分组为从与先前层相同或不同的片段衍生的。当最终层中的片段被排序时，使用不同等分试样的片段的重叠序列区域来登记片段，使得非重叠区域被排序。在一个方面，该方法以分级方式进行，直到一个或多个目标多核苷酸被表征为例如。通过其核酸序列，或通过序列片段的排序，或通过单核苷酸多态性（SNP）等的排序。

29. 发明申请

US20110281738A1 SELF-ASSEMBLED SINGLE MOLECULE ARRAYS AND USES THEREOF 有权
标题翻译：自组装单分子阵列及其用途
公开(公告)号：US20110281738A1
公开(公告)日：2011-11-17
申请号：US13098965
申请日：2011-05-02
申请人： Radoje Drmanac , Matthew J. Callow , Brian K. Hauser , George Yeung
发明人： Radoje Drmanac , Matthew J. Callow , Brian K. Hauser , George Yeung
IPC分类号： C40B30/04 , C40B20/00
CPC分类号： C12Q1/6837 , C12N15/1093 , C12Q1/682 , C12Q1/6869 , C12Q1/6874 , C12Q2531/125 , C12Q2525/313 , C12Q2525/151 , C12Q2521/313 , C12Q2565/513 , C12Q2521/307
摘要： The present invention provides methods of making and using self-assembled arrays of single polynucleotide molecules for carrying out a variety of large-scale genetic measurements, such as gene expression analysis, gene copy number assessment, and the like. Random arrays used in the invention are “self-assembled” in the sense that they are formed by deposition of polynucleotide molecules onto a surface where they become fixed at random locations. The polynucleotide molecules fixed on the surface are then identified by direct sequence determination of component nucleic acids, such as incorporated probe sequences, or by other decoding schemes. Such identification converts a random array of determinable polynucleotides, and their respective probes into an addressable array of probe sequences.
摘要翻译：本发明提供制造和使用单个多核苷酸分子的自组装阵列进行各种大规模遗传测量的方法，例如基因表达分析，基因拷贝数评估等。在本发明中使用的随机阵列是“自组装”的意思，即它们通过将多核苷酸分子沉积到其随机位置固定的表面上而形成。然后通过直接序列测定组分核酸，例如并入的探针序列或其他解码方案来鉴定固定在表面上的多核苷酸分子。这种鉴定将随机阵列的可测定多核苷酸及其各自的探针转换成可寻址的探针序列阵列。

30. 发明授权

US07901891B2 Nucleic acid analysis by random mixtures of non-overlapping fragments 有权
标题翻译：通过非重叠片段的随机混合物进行核酸分析
公开(公告)号：US07901891B2
公开(公告)日：2011-03-08
申请号：US12335168
申请日：2008-12-15
申请人： Radoje Drmanac
发明人： Radoje Drmanac
IPC分类号： C12Q1/68 , C12P19/34 , C07H21/02
CPC分类号： C12Q1/6874 , C07H21/04 , C07K1/047 , C12Q1/6806 , C12Q1/682 , C12Q1/6837 , C12Q1/6869 , C12Q2525/151 , C12Q2525/313 , C12Q2531/125 , C12Q2565/513 , G01N15/1404 , G01N15/1434 , Y10S977/778 , Y10S977/789 , Y10S977/792 , Y10S977/88 , Y10S977/882 , C12Q2521/307 , C12Q2525/161 , C12Q2535/122 , C12Q2563/179 , C12Q2565/514
摘要： The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like.
摘要翻译：本发明提供了用于排序从一个或多个目标多核苷酸衍生的序列信息的方法和试剂盒。在一个方面，产生一个或多个分层或等级的碎片和等分试样，之后从最终级别或层级的片段获得序列信息。这样的最后一层中的每个片段都来自特定的等分试样，而这些等分试样又是来自先前层的特定等分试样，等等。对于最后一层中的等分试样的每个片段，从每个先前的层次派生的等分试样是已知的，或者可以被辨别出来。因此，来自不同等分试样的重叠片段的相同序列可以被区分并分组为从与先前层相同或不同的片段衍生的。当最终层中的片段被排序时，使用不同等分试样的片段的重叠序列区域来登记片段，使得非重叠区域被排序。在一个方面，该方法以分级方式进行，直到一个或多个目标多核苷酸被表征为例如。通过其核酸序列，或通过序列片段的排序，或通过单核苷酸多态性（SNP）等的排序。

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