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31. 发明申请

US20160333401A1 Computational Methods for Translating a Sequence of Multi-Base Color Calls to a Sequence of Bases 审中-公开
标题翻译：用于将多基色调序列翻译为基序列的计算方法
公开(公告)号：US20160333401A1
公开(公告)日：2016-11-17
申请号：US15099685
申请日：2016-04-15
申请人： LIFE TECHNOLOGIES CORPORATION
发明人： Heinz BREU , Danwei GUO
IPC分类号： C12Q1/68 , G06F19/22
CPC分类号： C12Q1/6869 , G16B30/00 , C12Q2535/131 , C12Q2565/1025
摘要： Disclosed are systems and methods for resequencing using color calls. A DNA sample is encoded and sequenced according to a multi-base code producing a string of read color calls for a fragment of the sample. A reference sequence is obtained. The string of read color calls is mapped to the reference sequence. A base sequence is extracted from the reference sequence. The base sequence is encoded as a string of reference color codes according to the multi-base code. The string of read color calls is aligned with the string of reference color codes and mismatches in the alignment are detected. One or more mismatches of the string of read color calls are annotated as inconsistent. The one or more inconsistent mismatches of the string of read color calls are corrected. The string of corrected read color calls is decoded to bases producing a read sequence.
摘要翻译：公开了使用颜色调用重新测序的系统和方法。 DNA样本根据多基因码进行编码和测序，产生样本片段的一系列读取颜色调用。得到参考序列。读取颜色调用的字符串映射到参考序列。从参考序列中提取碱基序列。基本序列根据多基本码被编码为参考颜色码串。读取颜色调用的字符串与参考颜色代码的字符串对齐，并且检测到对齐中的不匹配。读取颜色调用字符串的一个或多个不匹配被注释为不一致。读取颜色调用串的一个或多个不一致的不匹配被更正。将经校正的读取颜色调用的字符串解码为产生读取序列的基准。

32. 发明申请

US20160298182A1 NUCLEIC ACID DETECTION AND QUANTIFICATION 审中-公开
标题翻译：核酸检测和定量
公开(公告)号：US20160298182A1
公开(公告)日：2016-10-13
申请号：US15102685
申请日：2014-12-09
申请人： QIAGEN GMBH
发明人： Nan Fang , Andreas Missel , Katja Heitz , Holger Wedler
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6851 , C12Q1/6818 , C12Q1/686 , C12Q2561/113 , C12Q2563/107 , C12Q2563/173 , C12Q2565/1025
摘要： The present invention relates to methods and uses for the detection or quantification of newly-synthesized double-stranded target nucleic acid molecules in a sample during quantitative real-time polymerase chain reaction (qPCR) amplification. According to the invention, an intercalating dye recognizing double-stranded DNA molecules with higher affinity than single-stranded DNA molecules and a fluorophore-labeled oligonucleotide-probe being sequence specific for a target nucleic acid molecule are simultaneously employed, thus enabling quantification a specific target and total amount of a mixed nucleic acid population, and enabling assessing the cause of suboptimal PCR performance.
摘要翻译：本发明涉及用于在定量实时聚合酶链反应（qPCR）扩增过程中检测或定量样品中新合成的双链靶核酸分子的方法和用途。根据本发明，同时使用识别比单链DNA分子更高亲和力的双链DNA分子的插入染料和靶核酸分子具有序列特异性的荧光团标记的寡核苷酸探针，从而能够定量特异性靶和混合核酸群体的总量，并且能够评估次优PCR性能的原因。

33. 发明授权

US09342651B2 Computational methods for translating a sequence of multi-base color calls to a sequence of bases 有权
标题翻译：用于将多基色调序列转换为基序的计算方法
公开(公告)号：US09342651B2
公开(公告)日：2016-05-17
申请号：US13106998
申请日：2011-05-13
申请人： Heinz Breu , Danwei Guo
发明人： Heinz Breu , Danwei Guo
IPC分类号： G06F19/22 , G06F15/00 , C12Q1/68
CPC分类号： C12Q1/6869 , G06F19/22 , C12Q2535/131 , C12Q2565/1025
摘要： Disclosed are systems and methods for resequencing using color calls. A DNA sample is encoded and sequenced according to a multi-base code producing a string of read color calls for a fragment of the sample. A reference sequence is obtained. The string of read color calls is mapped to the reference sequence. A base sequence is extracted from the reference sequence. The base sequence is encoded as a string of reference color codes according to the multi-base code. The string of read color calls is aligned with the string of reference color codes and mismatches in the alignment are detected. One or more mismatches of the string of read color calls are annotated as inconsistent. The one or more inconsistent mismatches of the string of read color calls are corrected. The string of corrected read color calls is decoded to bases producing a read sequence.
摘要翻译：公开了使用颜色调用重新测序的系统和方法。 DNA样本根据多基因码进行编码和测序，产生样本片段的一系列读取颜色调用。得到参考序列。读取颜色调用的字符串映射到参考序列。从参考序列中提取碱基序列。基本序列根据多基本码被编码为参考颜色码串。读取颜色调用的字符串与参考颜色代码的字符串对齐，并且检测到对齐中的不匹配。读取颜色调用字符串的一个或多个不匹配被注释为不一致。读取颜色调用串的一个或多个不一致的不匹配被更正。将经校正的读取颜色调用的字符串解码为产生读取序列的基准。

34. 发明申请

US20140356865A1 Methods and Compositions for Efficient Base Calling in Sequencing Reactions 有权
公开(公告)号：US20140356865A1
公开(公告)日：2014-12-04
申请号：US14094630
申请日：2013-12-02
申请人： Complete Genomics, Inc.
发明人： Radoje Drmanac
IPC分类号： C12Q1/68
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.

35. 发明申请

US20140221218A1 METHODS FOR SINGLE-MOLECULE ANALYSIS 审中-公开
标题翻译：单分子分析方法
公开(公告)号：US20140221218A1
公开(公告)日：2014-08-07
申请号：US14171369
申请日：2014-02-03
申请人： Bionano Genomics, Inc.
发明人： Han Cao , Ming Xiao , Alex Hastie , Michael G. Saghbini , Henry B. Sadowski
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6869 , C12Q1/6806 , C12Q1/6809 , C12Q2521/301 , C12Q2565/1025
摘要： Methods for single-molecule preparation and analysis are disclosed herein. The methods can, for example, be used for isolating and analyzing DNA from various biological samples.
摘要翻译：本文公开了单分子制备和分析的方法。该方法可以例如用于分离和分析来自各种生物样品的DNA。

36. 发明授权

US08323929B2 Methods for detecting nucleic acid sequence variations 有权
标题翻译：检测核酸序列变异的方法
公开(公告)号：US08323929B2
公开(公告)日：2012-12-04
申请号：US12419737
申请日：2009-04-07
申请人： Sha-Sha Wang , Keith Thornton , James G. Nadeau , Tobin J. Hellyer
发明人： Sha-Sha Wang , Keith Thornton , James G. Nadeau , Tobin J. Hellyer
IPC分类号： C12P19/34 , C12Q1/68 , C07H21/02 , C07H21/04 , C07H21/00
CPC分类号： C12Q1/6827 , C12Q2565/1025 , C12Q2535/125 , C12Q2531/119 , C12Q2531/101
摘要： The invention employs an unlabeled signal primer comprising a 5′ adapter sequence for detection of variations in nucleic acid target sequences. The detection system further comprises a reporter probe, the 3′ end of which hybridizes to the complement of the 5′ adapter sequence of the signal primer to produce a 5′ overhang. Polymerase is used to fill in the overhang and synthesize the complement of the 5′ overhang of the reporter probe. Synthesis of the reporter probe complement is detected, either directly or indirectly, as an indication of the presence of the target.
摘要翻译：本发明采用包含5'衔接子序列的未标记信号引物来检测核酸靶序列的变异。检测系统还包括报道探针，其3'末端与信号引物的5'衔接子序列的互补体杂交以产生5'突出端。聚合酶用于填充突出端并合成报告基因探针的5'突出端的互补体。直接或间接检测报道探针补体的合成，作为目标存在的指示。

37. 发明申请

US20120190030A1 Detection of Target Nucleic Acid Sequences by Cyclic Exonucleolytic Reactions 有权
标题翻译：通过循环核酸内切酶反应检测靶核酸序列
公开(公告)号：US20120190030A1
公开(公告)日：2012-07-26
申请号：US13497310
申请日：2010-04-09
申请人： Jong Yoon Chun , In Taek Hwang
发明人： Jong Yoon Chun , In Taek Hwang
IPC分类号： G01N21/64
CPC分类号： C12Q1/682 , C12Q2565/1025 , C12Q2521/319
摘要： The present invention relates to the detection of a target nucleic acid sequence by a cyclic exonucleolytic reaction. The present method enabling to generate signals by probe digestion with no help of primers and to amplify signals with no help of simultaneous target amplification reactions may enable to detect multiple target sequences without any problems accounted in the conventional real-time PCR methods such as false positive signals and difficulties in oligonucleotides (primer and probe) selection and reaction condition optimization.
摘要翻译：本发明涉及通过循环核酸内切酶反应检测靶核酸序列。通过探针消化而不用引物帮助产生信号并且在没有同时靶扩增反应的帮助下扩增信号的本发明方法可以使得能够检测多个靶序列，而不存在常规实时PCR方法中所存在的任何问题，例如假阳性寡核苷酸（引物和探针）选择和反应条件优化的信号和困难。

38. 发明申请

US20110306504A1 POLYNUCLEOTIDE MAPPING AND SEQUENCING 有权
标题翻译：多核苷酸映射和测序
公开(公告)号：US20110306504A1
公开(公告)日：2011-12-15
申请号：US13129634
申请日：2009-11-18
申请人： Ming Xiao , Han Cao , Parikshit A. Deshpande , Michael Boyce-Jacino
发明人： Ming Xiao , Han Cao , Parikshit A. Deshpande , Michael Boyce-Jacino
IPC分类号： C40B20/08 , C40B40/06 , C12Q1/68 , G01N21/64
CPC分类号： C12Q1/6874 , C12Q1/68 , C12Q1/6806 , C12Q1/6869 , C12Q2565/133 , C12Q2565/1025 , C12Q2521/301 , C12Q2563/107 , C12Q2535/101
摘要： The present invention provides methods of obtaining structural information about a biopolymer sample. The methods include labeling portions of a biopolymer, such as DNA or RNA, linearizing the biopolymer in some cases, and determining the distance between the labels. The user can then compare different samples' between-label distances to qualitatively compare different samples and to assay a given sample for additions or deletions of nucleotides in the regions flanked by the labels. The methods also permit sequencing of biopolymers.
摘要翻译：本发明提供获得关于生物聚合物样品的结构信息的方法。所述方法包括在一些情况下标记生物聚合物（例如DNA或RNA）的部分线性化生物聚合物，并确定标签之间的距离。然后，用户可以比较不同样品的标记间距离，以定性比较不同的样品，并测定给定的样品，用于在标签侧翼的区域中添加或缺失核苷酸。该方法还允许对生物聚合物进行测序。

39. 发明申请

US20110136122A1 NUCLEIC ACID DETECTION USING FLOW THROUGH METHODS 审中-公开
标题翻译：使用流动方法进行核酸检测
公开(公告)号：US20110136122A1
公开(公告)日：2011-06-09
申请号：US12440732
申请日：2007-09-12
申请人： Ian Garthwaite , Philip A. Myers , Christine M. Sadek
发明人： Ian Garthwaite , Philip A. Myers , Christine M. Sadek
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： C12Q1/6834 , C12Q1/6804 , C12Q1/689 , Y02A50/451 , C12Q2565/625 , C12Q2565/1025 , C12Q2563/131 , C12Q2563/155 , C12Q2563/137 , C12Q2563/149 , C12Q2545/101 , C12Q2565/102
摘要： Methods and kits for use in detecting a target nucleic acid in a sample are disclosed. In one particular application, the methods and kits allow for the detection of an undesirable micro-organism (e.g. Listeriaceae, Enterobacteriaceae, or Staphylococcaceae) in food or present on a food preparation surface.
摘要翻译：公开了用于检测样品中靶核酸的方法和试剂盒。在一个特定应用中，所述方法和试剂盒允许在食物中检测不期望的微生物（例如Listeriaceae，肠杆菌科或葡萄球菌）或存在于食物制剂表面上。

40. 发明申请

US20110003715A1 METHODS FOR DETECTION AND QUANTIFICATION OF ANALYTES IN COMPLEX MIXTURES 有权
标题翻译：用于复合混合物中分析物的检测和定量的方法
公开(公告)号：US20110003715A1
公开(公告)日：2011-01-06
申请号：US12819101
申请日：2010-06-18
申请人： Krassen Dimitrov
发明人： Krassen Dimitrov
IPC分类号： C40B40/06
CPC分类号： C12Q1/6888 , C12Q1/6816 , C12Q1/682 , C12Q1/6876 , C12Q2565/102 , C12Q2537/143 , C12Q2525/161 , C12Q2565/1025 , C12Q2563/179 , C12Q2525/151 , C12Q2525/101
摘要： The invention provides a diverse population of uniquely labeled probes, containing about thirty or more target specific nucleic acid probes each attached to a unique label bound to a nucleic acid. Also provided is a method of producing a population of uniquely labeled nucleic acid probes. The method consists of (a) synthesizing a population of target specific nucleic acid probes each having a different specifier; (b) synthesizing a corresponding population of anti-genedigits each having a unique label, the population having a diversity sufficient to uniquely hybridize to genedigits within the specifiers, and (c) hybridizing the populations of target nucleic acid probes to the anti-genedigits, to produce a population in which each of the target specific probes is uniquely labeled. Also provided is a method of detecting a nucleic acid analyte. The method consists of (a) contacting a mixture of nucleic acid analytes under conditions sufficient for hybridization with a plurality of target specific nucleic acid probes each having a different specifier; (b) contacting the mixture under conditions sufficient for hybridization with a corresponding plurality of anti-genedigits each having a unique label, the plurality of anti-genedigits having a diversity sufficient to uniquely hybridize to genedigits within the specifiers, and (c) uniquely detecting a hybridized complex between one or more analytes in the mixture, a target specific probe, and an anti-genedigit.
摘要翻译：本发明提供了多种独特标记的探针，其含有约30个或更多个目标特异性核酸探针，其各自附着于与核酸结合的唯一标记。还提供了生产独特标记的核酸探针群体的方法。该方法包括（a）合成具有不同说明符的目标特异性核酸探针群; （b）合成各自具有独特标记的相应群体的抗Genieigits，所述群体具有足以独特地与所述说明者内的Genesigits杂交的多样性，以及（c）将靶核酸探针的群体与抗Genieigits杂交，以产生其中每个靶特异性探针被唯一标记的群体。还提供了检测核酸分析物的方法。该方法包括（a）在足以与多个具有不同说明符的靶特异性核酸探针杂交的条件下使核酸分析物的混合物接触; （b）在足以与各自具有唯一标记的相应多个抗基因组杂交的条件下接触混合物，所述多个抗Genetigits具有足以独特地与指定剂内的Genesigits杂交的分集，以及（c）唯一检测混合物中一种或多种分析物之间的杂交复合物，靶标特异性探针和抗Genetigigit。

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