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1. 发明授权

US07070932B2 Methods and devices for detecting printhead misalignment of an in situ polymeric array synthesis device 失效
标题翻译：用于检测原位聚合物阵列合成装置的打印头未对准的方法和装置
公开(公告)号：US07070932B2
公开(公告)日：2006-07-04
申请号：US10374307
申请日：2003-02-25
申请人： Eric M. Leproust , Douglas A. Amorese , Mel N. Kronick
发明人： Eric M. Leproust , Douglas A. Amorese , Mel N. Kronick
IPC分类号： C07H21/04 , C12Q1/68
CPC分类号： C12Q1/6837 , C12Q2525/173
摘要： Methods and devices for detecting deposition unit misalignment, e.g., printhead misalignment, of an in situ polymeric, e.g., a nucleic acid, array synthesis device are provided. In accordance with the subject methods, at least one test probe feature is synthesized on a substrate using an in situ polymeric array, e.g., nucleic acid array or protein array, synthesis device. The at least one test probe feature is then contacted with at least two different distinguishably labeled targets, e.g., target nucleic acids. The binding of the targets to the at least one test probe feature is then evaluated to detect any misalignment, e.g., deposition unit or pulse jet misalignments, of the synthesis device. Also provided are substrates having at least one test probe feature and at least one polymeric array, as well as methods of using the substrates in array assays. Also included are kits for use in practicing the subject methods.
摘要翻译：提供了用于检测原位聚合物例如核酸阵列合成装置的沉积单元未对准（例如，打印头未对准）的方法和装置。根据本发明的方法，使用原位聚合物阵列，例如核酸阵列或蛋白质阵列，合成装置，在底物上合成至少一种测试探针特征。然后将至少一个测试探针特征与至少两个不同的可区分标记的靶，例如靶核酸接触。然后评估目标与至少一个测试探针特征的结合以检测合成装置的任何未对准，例如沉积单元或脉冲射流未对准。还提供了具有至少一个测试探针特征和至少一个聚合物阵列的基底，以及在阵列测定中使用底物的方法。还包括用于实践主题方法的工具包。

2. 发明申请

US20070259344A1 Compound probes and methods of increasing the effective probe densities of arrays 审中-公开
标题翻译：复合探针和增加阵列有效探针密度的方法
公开(公告)号：US20070259344A1
公开(公告)日：2007-11-08
申请号：US11417313
申请日：2006-05-03
申请人： Eric M. Leproust , Douglas A. Amorese , Michael P. Caren , David B. Gordon , Andrew Payne
发明人： Eric M. Leproust , Douglas A. Amorese , Michael P. Caren , David B. Gordon , Andrew Payne
IPC分类号： C12Q1/68 , C07H21/04 , C12M3/00
CPC分类号： C12Q1/6837 , C12Q2565/507 , C12Q2525/197
摘要： Methods and articles for analyzing nucleotide sequences of nucleic acid molecules, e.g., using multiple probes per spot of an array, are described. In some embodiments, the methods and articles can reduce the numbers of arrays necessary to probe regions of interest in a biological sample, and/or increase the resolution at which biological events are probed. In some cases, these methods exploit the vertical aspect of an array in order to decrease the number of arrays or spots required for an assay. These probes may be in the form of compound probes, which comprise at least first and second probes, including first and second nucleotide sequences capable of hybridizing to first and second target nucleotide sequences, respectively, in a nucleic acid molecule of interest.
摘要翻译：描述了分析核酸分子的核苷酸序列的方法和制品，例如每个阵列点使用多个探针。在一些实施方案中，所述方法和制品可以减少探测生物样品中感兴趣区域所需的阵列数量和/或增加探测生物学事件的分辨率。在某些情况下，这些方法利用阵列的垂直方面，以减少测定所需的阵列数或点数。这些探针可以是化合物探针的形式，其包含至少第一和第二探针，包括分别在目的核酸分子中能够与第一和第二靶核苷酸序列杂交的第一和第二核苷酸序列。

3. 发明授权

US07252938B2 Methods and devices for producing a polymer at a location of a substrate 失效
标题翻译：在基材的位置处制备聚合物的方法和装置
公开(公告)号：US07252938B2
公开(公告)日：2007-08-07
申请号：US10374857
申请日：2003-02-25
申请人： Eric M. Leproust , Douglas A. Amorese
发明人： Eric M. Leproust , Douglas A. Amorese
IPC分类号： C12Q1/00 , C12Q1/68 , C12M1/36 , C12M3/00 , G01N33/53 , G01N33/566 , G01N33/543 , G01N33/551 , G01N33/544 , G01N21/00 , G01N21/75 , G01N21/76
CPC分类号： B01J19/0046 , B01J2219/00378 , B01J2219/00576 , B01J2219/00691 , B01J2219/00693 , B01J2219/00722 , B01J2219/00725 , C40B40/06 , C40B40/10 , C40B60/14 , Y10S436/807 , Y10S436/809
摘要： Methods and devices for producing a polymer at a location of a substrate are provided. In the subject methods, a fluid droplet containing a first monomer labeled with a first detectable label is deposited from a fluid deposition device onto a location of a substrate surface having a second monomer labeled with a second detectable label. The first and second detectable labels are then detected to determine any misalignment between the fluid deposition device and the location of the substrate surface during deposition. Also provided are algorithms that perform the subject methods, as well as fluid deposition devices that include the subject algorithms. The subject invention also includes arrays produced according to the subject methods and kits that include the subject arrays.
摘要翻译：提供了在基板的位置处制造聚合物的方法和装置。在本发明方法中，将含有用第一可检测标记物标记的第一单体的流体液滴从流体沉积装置沉积到具有用第二可检测标记物标记的第二单体的基底表面的位置。然后检测第一和第二可检测标记以确定在沉积期间流体沉积装置与基底表面的位置之间的任何未对准。还提供了执行主题方法的算法，以及包括主题算法的流体沉积设备。本发明还包括根据主题方法和包括主题阵列的试剂盒制备的阵列。

4. 发明申请

US20120231968A1 Comparative Genomic Hybridization Assays Using Immobilized Oligonucleotide Features and Compositions for Practicing the Same 审中-公开
标题翻译：使用固定的寡核苷酸特征和组合物进行比较的基因组杂交测定
公开(公告)号：US20120231968A1
公开(公告)日：2012-09-13
申请号：US13480348
申请日：2012-05-24
申请人： Laurakay Bruhn , Alicia F. Scheffer , Michael T. Barrett , Douglas A. Amorese , Stephen S. Laderman
发明人： Laurakay Bruhn , Alicia F. Scheffer , Michael T. Barrett , Douglas A. Amorese , Stephen S. Laderman
IPC分类号： C40B30/04
CPC分类号： C12Q1/6837 , C12Q1/6809 , C12Q2565/501
摘要： Comparative genomic hybridization assays and compositions for use in practicing the same are provided. A characteristic of the subject comparative genomic hybridization assays is that solid support immobilized oligonucleotide feature elements, e.g., in the form of an array, are employed. Specifically, at least first and second nucleic acid populations prepared from genomic templates are contacted with a plurality of distinct oligonucleotide feature elements immobilized on a solid support surface and the binding of the at least first and second populations is then evaluated. Also provided are kits for use in practicing the subject methods.
摘要翻译：提供了比较基因组杂交测定法和用于实践其的组合物。本发明比较基因组杂交测定法的特征在于使用固体支持物固定的寡核苷酸特征元件，例如阵列形式。具体地，从基因组模板制备的至少第一和第二核酸群体与固定在固体支持物表面上的多个不同的寡核苷酸特征元件接触，然后评估至少第一和第二群体的结合。还提供了用于实践主题方法的套件。

5. 发明授权

US07537936B2 Method of testing multiple fluid samples with multiple biopolymer arrays 失效
标题翻译：用多个生物聚合物阵列测试多个流体样品的方法
公开(公告)号：US07537936B2
公开(公告)日：2009-05-26
申请号：US11136227
申请日：2005-05-23
申请人： SueAnn C. Dahm , Arthur Schleifer , Carol T. Schembri , Douglas A. Amorese
发明人： SueAnn C. Dahm , Arthur Schleifer , Carol T. Schembri , Douglas A. Amorese
IPC分类号： G01N30/00
CPC分类号： B01L3/502 , B01L3/5025 , B01L7/00 , B01L2200/027 , B01L2200/0689 , B01L2300/0636 , B01L2300/0803 , B01L2300/0822 , B01L2300/0877 , B01L2400/0487 , Y10T436/2575
摘要： A method of testing multiple fluid samples with multiple biopolymer arrays. A cover is assembled to a contiguous substrate carrying on a first side, multiple arrays each with multiple regions of biopolymers linked to the substrate, such that the cover and the substrate together form a plurality of chambers each containing a biopolymer array and each being accessible through its own port. Multiple fluid samples are introduced into respective chambers through a port of each such that the fluid samples contact respective arrays. A binding pattern of the arrays is observed. An apparatus and kit useful in such methods, are also provided.
摘要翻译：用多个生物聚合物阵列测试多个流体样品的方法。将盖组装到承载在第一侧上的连续基底，多个阵列，每个阵列具有连接到基底的多个生物聚合区域，使得盖和基底一起形成多个腔室，每个腔室包含生物聚合物阵列，并且每个腔室可通过自己的港口多个流体样品通过各自的端口引入相应的室中，使得流体样品与相应的阵列接触。观察到阵列的绑定模式。还提供了一种在这些方法中有用的装置和试剂盒。

6. 发明授权

US07247497B2 Testing multiple fluid samples with multiple biopolymer arrays 有权
标题翻译：用多个生物聚合物阵列测试多个流体样品
公开(公告)号：US07247497B2
公开(公告)日：2007-07-24
申请号：US10160620
申请日：2002-05-31
申请人： SueAnn C. Dahm , Arthur Schleifer , Carol T. Schembri , Douglas A. Amorese
发明人： SueAnn C. Dahm , Arthur Schleifer , Carol T. Schembri , Douglas A. Amorese
IPC分类号： G01N30/00
CPC分类号： B01L3/5025 , B01L3/5027 , B01L9/52 , B01L2200/027 , B01L2200/0689 , B01L2300/044 , B01L2300/0636 , B01L2300/0803 , B01L2300/0816 , B01L2300/0877 , B01L2400/0487 , Y10T436/2575
摘要： A method of testing multiple fluid samples with multiple biopolymer arrays. A cover is assembled to a contiguous substrate carrying on a first side, multiple arrays each with multiple regions of biopolymers linked to the substrate, such that the cover and the substrate together form a plurality of chambers each containing a biopolymer array and each being accessible through its own port. Multiple fluid samples are introduced into respective chambers through a port of each such that the fluid samples contact respective arrays. A binding pattern of the arrays is observed. An apparatus and kit useful in such methods, are also provided.
摘要翻译：用多个生物聚合物阵列测试多个流体样品的方法。将盖组装到承载在第一侧上的连续基底，多个阵列，每个阵列具有连接到基底的多个生物聚合区域，使得盖和基底一起形成多个腔室，每个腔室包含生物聚合物阵列，并且每个腔室可通过自己的港口多个流体样品通过各自的端口引入相应的室中，使得流体样品与相应的阵列接触。观察到阵列的绑定模式。还提供了一种在这些方法中有用的装置和试剂盒。

7. 发明授权

US08232055B2 Comparative genomic hybridization assays using immobilized oligonucleotide features and compositions for practicing the same 有权
标题翻译：使用固定的寡核苷酸特征和组合物进行比较的基因组杂交测定
公开(公告)号：US08232055B2
公开(公告)日：2012-07-31
申请号：US10744595
申请日：2003-12-22
申请人： Laurakay Bruhn , Alicia F. Scheffer , Michael T. Barrett , Douglas A. Amorese , Stephen S. Laderman
发明人： Laurakay Bruhn , Alicia F. Scheffer , Michael T. Barrett , Douglas A. Amorese , Stephen S. Laderman
IPC分类号： C12Q1/68 , G01N33/50
CPC分类号： C12Q1/6837 , C12Q1/6809 , C12Q2565/501
摘要： Comparative genomic hybridization assays and compositions for use in practicing the same are provided. A characteristic of the subject comparative genomic hybridization assays is that solid support immobilized oligonucleotide feature elements, e.g., in the form of an array, are employed. Specifically, at least first and second nucleic acid populations prepared from genomic templates are contacted with a plurality of distinct oligonucleotide feature elements immobilized on a solid support surface and the binding of the at least first and second populations is then evaluated. Also provided are kits for use in practicing the subject methods.
摘要翻译：提供了比较基因组杂交测定法和用于实践其的组合物。本发明比较基因组杂交测定法的特征在于使用固体支持物固定的寡核苷酸特征元件，例如阵列形式。具体地，从基因组模板制备的至少第一和第二核酸群体与固定在固体支持物表面上的多个不同的寡核苷酸特征元件接触，然后评估至少第一和第二群体的结合。还提供了用于实践主题方法的套件。

8. 发明申请

US20070292842A1 Detection of viral or viral vector integration sites in genomic DNA 审中-公开
标题翻译：检测基因组DNA中的病毒或病毒载体整合位点
公开(公告)号：US20070292842A1
公开(公告)日：2007-12-20
申请号：US11453205
申请日：2006-06-14
申请人： Stephanie B. Fulmer-Smentek , Douglas N. Roberts , Douglas A. Amorese
发明人： Stephanie B. Fulmer-Smentek , Douglas N. Roberts , Douglas A. Amorese
IPC分类号： C12Q1/70 , C12Q1/68 , C12N15/86
CPC分类号： C12Q1/701 , C12Q2565/501 , C12Q2531/131
摘要： Methods for detecting the integration of viral nucleic acids into a host cell, and methods for determining the locus of integration using microarrays are described. The methods can also be used in conjunction with viral vectors used in gene therapy.
摘要翻译：描述了用于检测病毒核酸与宿主细胞的整合的方法，以及使用微阵列确定整合位点的方法。该方法也可以与用于基因治疗的病毒载体结合使用。

9. 发明申请

US20060008836A1 Composite arrays 审中-公开
公开(公告)号：US20060008836A1
公开(公告)日：2006-01-12
申请号：US11193107
申请日：2005-07-29
申请人： Douglas A. Amorese , Karen W. Shannon , Patrick J. Collins , Paul K. Wolber
发明人： Douglas A. Amorese , Karen W. Shannon , Patrick J. Collins , Paul K. Wolber
IPC分类号： C12Q1/68 , C12M1/34
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/00527 , B01J2219/00585 , B01J2219/00596 , B01J2219/00605 , B01J2219/00608 , B01J2219/00612 , B01J2219/00659 , B01J2219/00675 , B01J2219/00707 , C40B50/14
摘要： A polynucleotide array, and methods of making and using such arrays. The array may include a first set of multiple features each of which has first polynucleotide molecules of at least 400 nucleotides in length, and a second set of features each of which has second polynucleotide molecules of no more than 100 nucleotides in length. The second set of features can be used as control features, or to replace failed sequences in an enzymatic amplification to produce first polynucleotides, or to detect polymorphisms or splice variants which may not be detected by a particular first polynucleotide.

10. 发明申请

US20070141584A1 Methods for assessment of native chromatin on microarrays 审中-公开
标题翻译：用于评估微阵列上天然染色质的方法
公开(公告)号：US20070141584A1
公开(公告)日：2007-06-21
申请号：US11313522
申请日：2005-12-20
申请人： Douglas N. Roberts , Douglas A. Amorese , Stephanie Fulmer-Smentek
发明人： Douglas N. Roberts , Douglas A. Amorese , Stephanie Fulmer-Smentek
IPC分类号： C12Q1/68 , C12P19/34
CPC分类号： C12Q1/6837 , C12Q2521/301
摘要： A method for determining chromatin accessibility of nucleic acids in a cell by expressing an effective amount of a nuclease in a cell to digest chromatin at chromatin accessible sites to form chromatin fragments; isolating chromatin fragments from the cell; and hybridizing the chromatin fragments on a microarray to determine the location and/or sequence of the chromatin fragments.
摘要翻译：一种通过在细胞中表达有效量的核酸酶以消化染色质可接近部位的染色质以形成染色质片段来确定细胞中核酸的染色质可及性的方法; 从细胞中分离染色质片段; 并在微阵列上杂交染色质片段以确定染色质片段的位置和/或序列。

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