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1. 发明申请

US20060257893A1 Devices and methods for monitoring genomic DNA of organisms 有权
公开(公告)号：US20060257893A1
公开(公告)日：2006-11-16
申请号：US11356807
申请日：2006-02-17
申请人： Toru Takahashi , Hiroshi Inoue
发明人： Toru Takahashi , Hiroshi Inoue
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： C12Q1/6888 , B01L3/502715 , B01L3/502738 , B01L3/502784 , B01L7/525 , B01L7/54 , B01L2200/0673 , B01L2200/10 , B01L2300/0636 , B01L2300/0645 , B01L2300/0816 , B01L2300/087 , B01L2300/0877 , B01L2300/1827 , B01L2400/0415 , B01L2400/0487 , C12Q1/6839 , C12Q1/686 , G01N1/34 , G01N35/08 , G01N2001/4088 , G01N2035/00237 , C12Q2565/629 , C12Q2535/139 , C12Q2525/179 , C12Q2525/161 , C12Q2563/173
摘要： The invention provides an apparatus that can be used in methods of preparing, amplifying, detecting, and/or optionally selecting for further analysis the genomic material from an organism for the rapid detection and/or classification of an organism in a sample (e.g., screening for, identifying, quantifying, and/or optionally further analyzing, e.g., sequencing, the genomic material of the organism). The invention further provides methods of using the apparatus, e.g., in combination with novel SGP primers for improved use in waveform-profiling methods of DNA amplification. It is an object of the invention to provide an apparatus for fully automated analysis of genomic material, and multiple methods of using the apparatus that are beneficial to society, e.g., the apparatus may be used in methods of screening for, identifying, quantifying, and/or selecting genomic material for further analysis (e.g., sequencing) in relation to monitoring a source for the presence of contaminating organisms.

2. 发明授权

US08697852B2 Genetic fingerprinting and identification method 有权
标题翻译：遗传指纹识别方法
公开(公告)号：US08697852B2
公开(公告)日：2014-04-15
申请号：US13914987
申请日：2013-06-11
申请人： E. I. du Pont de Nemours and Company
发明人： Frank R. Burns , Xuan Peng
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6895 , C12Q1/686 , C12Q1/6888 , C12Q1/689 , C12Q2600/158 , G06F19/18 , C12Q2545/101 , C12Q2539/107 , C12Q2535/139
摘要： The present disclosure provides methods for molecular fingerprinting for the characterization and identification of organisms. More specifically, in one aspect the present invention provides a method of identifying an organism in a sample comprising: (a) providing a sample comprising said organism, said organism comprising at least one nucleic acid; (b) combining said sample or the at least one nucleic acid therefrom with an amplification mix comprising at least one labeled oligonucleotide primer; (c) generating at least one labeled amplification product from the at least one nucleic acid of said organism using a nucleotide amplification technique employing said at least one labeled oligonucleotide primer; (d) combining said at least one labeled amplification product with products of a DNA sequencing reaction to create a separation mix; and (e) separating said separation mix on the basis of oligonucleotide length in a fluorescent DNA sequencing instrument to generate a sequence embedded fingerprint pattern for said organism.
摘要翻译：本公开提供了用于表征和鉴定生物体的分子指纹图谱的方法。更具体地说，在一个方面，本发明提供了一种鉴定样品中生物体的方法，包括：（a）提供包含所述生物体的样品，所述生物体包含至少一种核酸; （b）将所述样品或其至少一种核酸与包含至少一种标记的寡核苷酸引物的扩增混合物结合; （c）使用所述至少一种标记的寡核苷酸引物的核苷酸扩增技术从所述生物体的至少一种核酸产生至少一种标记的扩增产物; （d）将所述至少一个标记的扩增产物与DNA测序反应的产物组合以产生分离混合物; 和（e）在荧光DNA测序仪器中基于寡核苷酸长度分离所述分离混合物，以产生所述生物体的嵌入指纹图案序列。

3. 发明授权

US07604938B2 Devices and methods for monitoring genomic DNA of organisms 有权
标题翻译：用于监测生物体基因组DNA的装置和方法
公开(公告)号：US07604938B2
公开(公告)日：2009-10-20
申请号：US11356807
申请日：2006-02-17
申请人： Toru Takahashi , Hiroshi Inoue
发明人： Toru Takahashi , Hiroshi Inoue
IPC分类号： C12Q1/68 , C12M1/00
CPC分类号： C12Q1/6888 , B01L3/502715 , B01L3/502738 , B01L3/502784 , B01L7/525 , B01L7/54 , B01L2200/0673 , B01L2200/10 , B01L2300/0636 , B01L2300/0645 , B01L2300/0816 , B01L2300/087 , B01L2300/0877 , B01L2300/1827 , B01L2400/0415 , B01L2400/0487 , C12Q1/6839 , C12Q1/686 , G01N1/34 , G01N35/08 , G01N2001/4088 , G01N2035/00237 , C12Q2565/629 , C12Q2535/139 , C12Q2525/179 , C12Q2525/161 , C12Q2563/173
摘要： The invention provides an apparatus that can be used in methods of preparing, amplifying, detecting, and/or optionally selecting for further analysis the genomic material from an organism for the rapid detection and/or classification of an organism in a sample (e.g., screening for, identifying, quantifying, and/or optionally further analyzing, e.g., sequencing, the genomic material of the organism). The invention further provides methods of using the apparatus, e.g., in combination with novel SGP primers for improved use in waveform-profiling methods of DNA amplification. It is an object of the invention to provide an apparatus for fully automated analysis of genomic material, and multiple methods of using the apparatus that are beneficial to society, e.g., the apparatus may be used in methods of screening for, identifying, quantifying, and/or selecting genomic material for further analysis (e.g., sequencing) in relation to monitoring a source for the presence of contaminating organisms.
摘要翻译：本发明提供一种可用于制备，扩增，检测和/或任选地选择用于进一步分析来自生物体的基因组材料用于快速检测和/或分类样品中生物体的方法的装置（例如，筛选用于，鉴定，定量和/或可选地进一步分析，例如测序生物体的基因组材料）。本发明进一步提供了使用该装置的方法，例如与新型SGP引物组合以改进在DNA扩增的波形分析方法中的用途。本发明的一个目的是提供用于基因组材料的完全自动化分析的装置，以及使用有益于社会的装置的多种方法，例如该装置可用于筛选，鉴定，定量和 /或选择用于进一步分析（例如，测序）的基因组材料，用于监测污染生物体的存在来源。

4. 发明授权

US08481267B2 Genetic fingerprinting and identification method 有权
标题翻译：遗传指纹识别方法
公开(公告)号：US08481267B2
公开(公告)日：2013-07-09
申请号：US12858508
申请日：2010-08-18
申请人： Frank R. Burns , Xuan Peng
发明人： Frank R. Burns , Xuan Peng
IPC分类号： C12Q1/68 , C07H19/00 , C07H21/00
CPC分类号： C12Q1/6895 , C12Q1/686 , C12Q1/6888 , C12Q1/689 , C12Q2600/158 , G06F19/18 , C12Q2545/101 , C12Q2539/107 , C12Q2535/139
摘要： The present disclosure provides methods for molecular fingerprinting for the characterization and identification of organisms. More specifically, in one aspect the present invention provides a method of identifying an organism in a sample by embedding fingerprint bands from any amplification based fingerprinting method within a DNA sequence so that small differences in size are resolvable. Fingerprint output is provided in a text file format that can then be analyzed by bioinformatics tools.
摘要翻译：本公开提供了用于表征和鉴定生物体的分子指纹图谱的方法。更具体地说，一方面，本发明提供了一种通过从DNA序列中嵌入来自任何基于扩增的指纹图谱的指纹带来鉴定样品中的生物体的方法，从而小尺寸差异是可分辨的。指纹输出以文本文件格式提供，然后可以通过生物信息学工具进行分析。

5. 发明授权

US07759057B2 Method for analyzing microbial communities 失效
标题翻译：微生物群落分析方法
公开(公告)号：US07759057B2
公开(公告)日：2010-07-20
申请号：US10943067
申请日：2004-09-16
申请人： Jizhong Zhou , Liyou Wu
发明人： Jizhong Zhou , Liyou Wu
IPC分类号： C12Q1/68
CPC分类号： C12Q1/689 , C12Q1/6851 , C12Q2565/607 , C12Q2539/107 , C12Q2535/139
摘要： The present invention provides a method for quantitatively analyzing microbial genes, species, or strains in a sample that contains at least two species or strains of microorganisms. The method involves using an isothermal DNA polymerase to randomly and representatively amplify genomic DNA of the microorganisms in the sample, hybridizing the resultant polynucleotide amplification product to a polynucleotide microarray that can differentiate different genes, species, or strains of microorganisms of interest, and measuring hybridization signals on the microarray to quantify the genes, species, or strains of interest.
摘要翻译：本发明提供了一种定量分析含有至少两种微生物种类或菌株的样品中的微生物基因，物种或菌株的方法。该方法包括使用等温DNA聚合酶随机和代表性地扩增样品中微生物的基因组DNA，将得到的多核苷酸扩增产物与能够区分感兴趣的微生物的不同基因，物种或菌株的多核苷酸微阵列杂交，并测量杂交信号在微阵列上定量感兴趣的基因，物种或菌株。

6. 发明申请

US20060115830A1 Methods for monitoring genomic DNA of organisms 有权
公开(公告)号：US20060115830A1
公开(公告)日：2006-06-01
申请号：US11190942
申请日：2005-07-28
申请人： Toru Takahashi , Deborah Boles
发明人： Toru Takahashi , Deborah Boles
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6858 , C12Q1/686 , C12Q2600/156 , C12Q2535/139 , C12Q2527/113 , C12Q2525/204 , C12Q2527/101
摘要： The invention provides novel SGP primers for improved use in waveform-profiling methods of DNA amplification. In one embodiment, use of an SGP primer in a method of DNA amplification results in exponential amplification of several distinct products. In another embodiment, the methods of the invention further comprise a novel half-time elongation step. In another embodiment, the distinct products may be detected via melting temperature analysis. The primers and methods of the invention may be combined to determine an organism in a sample.

7. 发明授权

US08841093B2 Devices and methods for monitoring genomic DNA of organisms 有权
标题翻译：用于监测生物体基因组DNA的装置和方法
公开(公告)号：US08841093B2
公开(公告)日：2014-09-23
申请号：US12466779
申请日：2009-05-15
申请人： Toru Takahashi , Hiroshi Inoue
发明人： Toru Takahashi , Hiroshi Inoue
IPC分类号： C12P19/34 , C12Q1/68 , G01N35/08 , B01L3/00 , G01N35/00 , B01L7/00 , G01N1/40 , G01N1/34
CPC分类号： C12Q1/6888 , B01L3/502715 , B01L3/502738 , B01L3/502784 , B01L7/525 , B01L7/54 , B01L2200/0673 , B01L2200/10 , B01L2300/0636 , B01L2300/0645 , B01L2300/0816 , B01L2300/087 , B01L2300/0877 , B01L2300/1827 , B01L2400/0415 , B01L2400/0487 , C12Q1/6839 , C12Q1/686 , G01N1/34 , G01N35/08 , G01N2001/4088 , G01N2035/00237 , C12Q2565/629 , C12Q2535/139 , C12Q2525/179 , C12Q2525/161 , C12Q2563/173
摘要： The invention provides an apparatus that can be used in methods of preparing, amplifying, detecting, and/or optionally selecting for further analysis the genomic material from an organism for the rapid detection and/or classification of an organism in a sample (e.g., screening for, identifying, quantifying, and/or optionally further analyzing, e.g., sequencing, the genomic material of the organism). The invention further provides methods of using the apparatus, e.g., in combination with novel SGP primers for improved use in waveform-profiling methods of DNA amplification. It is an object of the invention to provide an apparatus for fully automated analysis of genomic material, and multiple methods of using the apparatus that are beneficial to society, e.g., the apparatus may be used in methods of screening for, identifying, quantifying, and/or selecting genomic material for further analysis (e.g., sequencing) in relation to monitoring a source for the presence of contaminating organisms.
摘要翻译：本发明提供一种可用于制备，扩增，检测和/或任选地选择用于进一步分析来自生物体的基因组材料用于快速检测和/或分类样品中生物体的方法的装置（例如，筛选用于，鉴定，定量和/或可选地进一步分析，例如测序生物体的基因组材料）。本发明进一步提供了使用该装置的方法，例如与新型SGP引物组合以改进在DNA扩增的波形分析方法中的用途。本发明的一个目的是提供用于基因组材料的完全自动化分析的装置，以及使用有益于社会的装置的多种方法，例如该装置可用于筛选，鉴定，定量和 /或选择用于进一步分析（例如，测序）的基因组材料，用于监测污染生物体的存在来源。

8. 发明申请

US20130029341A1 METHOD TO AMPLIFY NUCLEIC ACIDS TO GENERATE FLUORESCENCE LABELED FRAGMENTS OF CONSERVED AND ARBITRARY PRODUCTS 有权
标题翻译：放大核酸生成保存和仲裁产品的荧光标记片段的方法
公开(公告)号：US20130029341A1
公开(公告)日：2013-01-31
申请号：US13553256
申请日：2012-07-19
申请人： Anjana AGARWAL , Mark A. Jensen
发明人： Anjana AGARWAL , Mark A. Jensen
IPC分类号： G01N21/64
CPC分类号： C12Q1/689 , C12Q1/6846 , C12Q1/686 , C12Q2527/101 , C12Q2535/139
摘要： Disclosed herein are methods for the identification of the species, serotype, and strain of a microorganism. Also disclosed are primers for use in detecting such microorganisms and kits comprising such primers.
摘要翻译：本文公开了用于鉴定微生物的物种，血清型和菌株的方法。还公开了用于检测这些微生物的引物和包含这种引物的试剂盒。

9. 发明申请

US20110045478A1 Genetic Fingerprinting And Identification Method 有权
标题翻译：遗传指纹识别方法
公开(公告)号：US20110045478A1
公开(公告)日：2011-02-24
申请号：US12858508
申请日：2010-08-18
申请人： Frank R. Burns , Xuan Peng
发明人： Frank R. Burns , Xuan Peng
IPC分类号： C12Q1/68 , C07H21/04
CPC分类号： C12Q1/6895 , C12Q1/686 , C12Q1/6888 , C12Q1/689 , C12Q2600/158 , G06F19/18 , C12Q2545/101 , C12Q2539/107 , C12Q2535/139
摘要： The present disclosure provides methods for molecular fingerprinting for the characterization and identification of organisms. More specifically, in one aspect the present invention provides a method of identifying an organism in a sample comprising: (a) providing a sample comprising said organism, said organism comprising at least one nucleic acid; (b) combining said sample or the at least one nucleic acid therefrom with an amplification mix comprising at least one labeled oligonucleotide primer; (c) generating at least one labeled amplification product from the at least one nucleic acid of said organism using a nucleotide amplification technique employing said at least one labeled oligonucleotide primer; (d) combining said at least one labeled amplification product with products of a DNA sequencing reaction to create a separation mix; and (e) separating said separation mix on the basis of oligonucleotide length in a fluorescent DNA sequencing instrument to generate a sequence embedded fingerprint pattern for said organism.
摘要翻译：本公开提供了用于表征和鉴定生物体的分子指纹图谱的方法。更具体地说，在一个方面，本发明提供了一种鉴定样品中生物体的方法，包括：（a）提供包含所述生物体的样品，所述生物体包含至少一种核酸; （b）将所述样品或其至少一种核酸与包含至少一种标记的寡核苷酸引物的扩增混合物结合; （c）使用所述至少一种标记的寡核苷酸引物的核苷酸扩增技术从所述生物体的至少一种核酸产生至少一种标记的扩增产物; （d）将所述至少一个标记的扩增产物与DNA测序反应的产物组合以产生分离混合物; 和（e）在荧光DNA测序仪器中基于寡核苷酸长度分离所述分离混合物，以产生所述生物体的嵌入指纹图案序列。

10. 发明授权

US07547514B2 Methods for monitoring genomic DNA of organisms 有权
标题翻译：监测生物体基因组DNA的方法
公开(公告)号：US07547514B2
公开(公告)日：2009-06-16
申请号：US11190942
申请日：2005-07-28
申请人： Toru Takahashi , Deborah John Boles
发明人： Toru Takahashi , Deborah John Boles
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6858 , C12Q1/686 , C12Q2600/156 , C12Q2535/139 , C12Q2527/113 , C12Q2525/204 , C12Q2527/101
摘要： The invention provides novel SGP primers for improved use in waveform-profiling methods of DNA amplification. In one embodiment, use of an SGP primer in a method of DNA amplification results in exponential amplification of several distinct products. In another embodiment, the methods of the invention further comprise a novel half-time elongation step. In another embodiment, the distinct products may be detected via melting temperature analysis. The primers and methods of the invention may be combined to determine an organism in a sample.
摘要翻译：本发明提供了用于改进在DNA扩增波形分析方法中使用的新型SGP引物。在一个实施方案中，在DNA扩增方法中使用SGP引物导致几种不同产物的指数扩增。在另一个实施方案中，本发明的方法还包括新的半时间延伸步骤。在另一个实施方案中，可以通过熔融温度分析来检测不同的产物。本发明的引物和方法可以组合以确定样品中的生物体。

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