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1. 发明授权

US07006927B2 Method and system for extracting data from surface array deposited features 有权
公开(公告)号：US07006927B2
公开(公告)日：2006-02-28
申请号：US10086839
申请日：2002-02-28
申请人： Zohar Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas , Herbert F. Cattell , Scott D. Connell
发明人： Zohar Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas , Herbert F. Cattell , Scott D. Connell
IPC分类号： G06F11/32
CPC分类号： G06T7/73 , G06T2207/30072
摘要： A method and system for extracting data signals from a scanned image resulting from optical, radiometric, or other types of analysis of a molecular array. The positions of corner features are first located. Then, an initial feature coordinate grid is determined from the positions of the corner features. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features. Finally, signal intensity values are extracted from the features and their respective local background regions in the scanned image, and background-subtracted signal intensity values, background-subtracted and normalized signal intensity ratios, and variability information and confidence intervals are determined based on the extracted values.

2. 发明授权

US06591196B1 Method and system for extracting data from surface array deposited features 有权
公开(公告)号：US06591196B1
公开(公告)日：2003-07-08
申请号：US09589046
申请日：2000-06-06
申请人： Zohar Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas
发明人： Zohar Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas
IPC分类号： G01J102
CPC分类号： G06K9/3275 , G06T7/73 , G06T2207/30072
摘要： A method and system for extracting data signals from a scanned image resulting from optical, radiometric, or other types of analysis of a molecular array. The positions of corner features are first located. Then, an initial feature coordinate grid is determined from the positions of the corner features. A refined feature coordinate grid is then calculated based on the positions of strong features, and is used to identify the positions of weak features and the positions of the local background regions surrounding all features. Finally, signal intensity values are extracted from the features and their respective local background regions in the scanned image, and background-subtracted signal intensity values, background-subtracted and normalized signal intensity ratios, and variability information and confidence intervals are determined based on the extracted values.

3. 发明授权

US07330606B2 Method and system for extracting data from surface array deposited features 失效
标题翻译：从表面阵列沉积特征提取数据的方法和系统
公开(公告)号：US07330606B2
公开(公告)日：2008-02-12
申请号：US10894943
申请日：2004-07-19
申请人： Zohar H. Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas
发明人： Zohar H. Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas
IPC分类号： G06K9/34
CPC分类号： G06K9/00 , G06K2209/07 , G06T7/73 , G06T2207/20068 , G06T2207/30072
摘要： A method for evaluating an orientation of a molecular array having features arranged in a pattern. An image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.
摘要翻译：一种用于评估具有以图案排列的特征的分子阵列的取向的方法。通过扫描分子阵列以确定从分子阵列的表面上的离散位置发出的数据信号来获得分子阵列的图像。计算像素处于第二图案的图像的像素的函数的实际结果。将该实际结果与如果第二图案在阵列上具有预定取向将获得的预期结果进行比较。然后可以基于结果来评估阵列取向。

4. 发明授权

US06768820B1 Method and system for extracting data from surface array deposited features 失效
标题翻译：从表面阵列沉积特征提取数据的方法和系统
公开(公告)号：US06768820B1
公开(公告)日：2004-07-27
申请号：US09659415
申请日：2000-09-11
申请人： Zohar H. Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas
发明人： Zohar H. Yakhini , Cynthia Y. Enderwick , Glenda C. Delenstarr , Paul K. Wolber , Nicholas M. Sampas
IPC分类号： G06K936
CPC分类号： G06K9/3275 , G06T7/73 , G06T2207/30072
摘要： A method for evaluating an orientation of a molecular array having features arranged in a pattern. An image of the molecular array is obtained by scanning the molecular array to determine data signals emanating from discrete positions on a surface of the molecular array. An actual result of a function on pixels of the image which pixels lie in a second pattern, is calculated. This actual result is compared with an expected result which would be obtained if the second pattern had a predetermined orientation on the array. Array orientation can then be evaluated based on the result.
摘要翻译：一种用于评估具有以图案排列的特征的分子阵列的取向的方法。通过扫描分子阵列以确定从分子阵列的表面上的离散位置发出的数据信号来获得分子阵列的图像。计算像素处于第二图案的图像的像素的函数的实际结果。将该实际结果与如果第二图案在阵列上具有预定取向将获得的预期结果进行比较。然后可以基于结果来评估阵列取向。

5. 发明授权

US07122303B2 Arrays comprising background features that provide for a measure of a non-specific binding and methods for using the same 失效
标题翻译：包含提供非特异性结合度量的背景特征的数组和使用该特征的方法
公开(公告)号：US07122303B2
公开(公告)日：2006-10-17
申请号：US09398399
申请日：1999-09-17
申请人： Glenda C. Delenstarr , Steven M. Lefkowitz , Kevin J. Luebke , Leslie B. Overman , Nicholas M. Sampas , Jeffery R. Sampson , Paul K. Wolber
发明人： Glenda C. Delenstarr , Steven M. Lefkowitz , Kevin J. Luebke , Leslie B. Overman , Nicholas M. Sampas , Jeffery R. Sampson , Paul K. Wolber
IPC分类号： C12Q1/68 , C12M1/34 , C07H21/02 , C07H21/04
CPC分类号： C12Q1/6837 , Y10T436/143333 , C12Q2545/107
摘要： Methods for substantially improved detection and analysis in nucleic acid hybridization assays are described. The methods provide the reliable estimation of background signal which derives primarily from nonspecific hybridization. The invention is useful in chemical, biological, medical and diagnostic techniques, as well as for drug discovery.
摘要翻译：描述了在核酸杂交测定中基本上改进的检测和分析的方法。该方法提供了主要来自非特异性杂交的背景信号的可靠估计。本发明可用于化学，生物，医学和诊断技术以及用于药物发现。

6. 发明授权

US07078167B2 Arrays having background features and methods for using the same 有权
公开(公告)号：US07078167B2
公开(公告)日：2006-07-18
申请号：US09899381
申请日：2001-07-02
申请人： Glenda C. Delenstarr , Paul K. Wolber , Theodore R. Sana
发明人： Glenda C. Delenstarr , Paul K. Wolber , Theodore R. Sana
IPC分类号： C12Q1/68 , G01N33/00 , C07H21/02 , C07H21/04
CPC分类号： C12Q1/6837 , Y10T436/143333 , C12Q2545/107
摘要： Nucleic acid arrays that have background features, and methods for using the same, are provided. The subject nucleic acid arrays include both hybridization features and background features, where the background features provide a background signal in a hybridization assay that is made up of a feature substrate component, a nucleic acid probe component and a nucleic acid probe non-specific binding component. In practicing the subject methods, the arrays are contacted with a sample and signals are observed for both hybridization features and background features. The background feature signal is then subtracted from the hybridization feature signal to obtain a background corrected hybridization feature signal that is employed as the output of the assay, e.g., to determine the presence, either qualitatively or quantitatively, of the analyte target nucleic acid in the sample. Also provided are kits for use in practicing the subject methods.

7. 发明授权

US06251588B1 Method for evaluating oligonucleotide probe sequences 失效
标题翻译：评价寡核苷酸探针序列的方法
公开(公告)号：US06251588B1
公开(公告)日：2001-06-26
申请号：US09021701
申请日：1998-02-10
申请人： Karen W. Shannon , Paul K. Wolber , Glenda C. Delenstarr , Peter G. Webb , Robert H. Kincaid
发明人： Karen W. Shannon , Paul K. Wolber , Glenda C. Delenstarr , Peter G. Webb , Robert H. Kincaid
IPC分类号： C12Q168
CPC分类号： G06F19/20 , G06F19/24
摘要： Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.
摘要翻译：公开了用于预测寡核苷酸与靶核苷酸序列杂交的潜力的方法。鉴定出预定数量的唯一寡核苷酸。选择独特的寡核苷酸来对可与靶核苷酸序列杂交的核苷酸序列的整个长度进行采样。确定并评估每种上述寡核苷酸的至少一个独立地预测该组寡核苷酸与靶核苷酸序列杂交的能力的参数。基于参数的评估来鉴定预定数量的唯一寡核苷酸内的寡核苷酸的子集。鉴定了亚群中的寡核苷酸，其沿着与靶核苷酸序列可杂交的核苷酸序列的区域聚集。该方法可以借助于计算机进行。

8. 发明授权

US06403314B1 Computational method and system for predicting fragmented hybridization and for identifying potential cross-hybridization 失效
标题翻译：用于预测片段化杂交和鉴定潜在交叉杂交的计算方法和系统
公开(公告)号：US06403314B1
公开(公告)日：2002-06-11
申请号：US09498608
申请日：2000-02-04
申请人： Daniel H. Lange , Nicholas M. Sampas , Paul K. Wolber , Zohar H. Yakhini
发明人： Daniel H. Lange , Nicholas M. Sampas , Paul K. Wolber , Zohar H. Yakhini
IPC分类号： C12Q168
CPC分类号： G06F19/20 , C12Q1/6813
摘要： A computational method and system for predicting the hybridization potential for two polymers. A probe/target interaction matrix is prepared to contain indications of all possible probe/target subunit interaction stabilities. The probe/target interaction matrix is analyzed to create a list of possible single-fragment hybridizations. A graph is then generated with vertices representing fragments, and edges representing possible loops in one or both of the probe and target sequences that allow the pair of fragments interconnected by the edge to coexist within a multi-fragment cross-hybridization. Finally, the graph is analyzed to construct a list of all possible single-fragment and multi-fragment cross-hybridizations possible between the probe molecule and the target molecule. The different hybridizations are scored and sorted by score.
摘要翻译：一种用于预测两种聚合物杂交势的计算方法和系统。准备探针/靶相互作用矩阵以包含所有可能的探针/靶亚单位相互作用稳定性的指示。分析探针/靶相互作用矩阵以创建可能的单片段杂交的列表。然后，生成具有表示片段的顶点的图形，以及表示探针和靶序列中的一个或两个中的可能环的边缘，其允许边缘互连的片段在多片段交叉杂交中共存。最后，分析该图以构建探针分子和靶分子之间可能的所有可能的单片段和多片段交叉杂交的列表。不同的杂交被评分并按分数排序。

9. 发明授权

US07534561B2 Nucleic acid array in situ fabrication methods and arrays produced using the same 有权
标题翻译：核酸阵列原位制备方法和使用其制备的阵列
公开(公告)号：US07534561B2
公开(公告)日：2009-05-19
申请号：US10407080
申请日：2003-04-02
申请人： Theodore R. Sana , Eric M. Leproust , Michel G. M. Perbost , Paul K. Wolber
发明人： Theodore R. Sana , Eric M. Leproust , Michel G. M. Perbost , Paul K. Wolber
IPC分类号： C12Q1/68 , C12N11/16 , C07H21/04 , C12P19/34
CPC分类号： B82Y30/00 , B01J19/0046 , B01J2219/0036 , B01J2219/00378 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00608 , B01J2219/0061 , B01J2219/00612 , B01J2219/00626 , B01J2219/00637 , B01J2219/00659 , B01J2219/00675 , B01J2219/00689 , B01J2219/00693 , B01J2219/00695 , B01J2219/00707 , B01J2219/00722 , C12Q1/6837 , C40B40/06 , C40B50/14 , C40B60/14 , C12Q2565/513 , C12Q2545/101
摘要： Methods and devices for producing a nucleic acid arrays using in situ nucleic acid array synthesis protocols are provided. A feature of certain embodiments of the invention is that control probes are produced in collections of features, e.g., columns, of the arrays that have been selected according to a particular efficient control probe feature/column selection protocol. A feature of certain other embodiments of the invention is that an “all-bases-all-layers” probe set is produced in at least one of column of the arrays. Also provided are devices configured for use in the subject methods, as well as arrays produced using the subject methods and devices as well as methods for using such arrays.
摘要翻译：提供了使用原位核酸阵列合成方案制备核酸阵列的方法和装置。本发明的某些实施例的特征在于，控制探针是根据特定的有效控制探针特征/列选择协议选择的阵列的特征（例如列）的集合产生的。本发明的某些其他实施例的特征在于，在全部阵列中的至少一列中产生“全基底全层”探针组。还提供了被配置为在主题方法中使用的装置以及使用主题方法和装置产生的阵列以及使用这些阵列的方法。

10. 发明申请

US20110263445A1 Multidentate Arrays 审中-公开
标题翻译：多数数组
公开(公告)号：US20110263445A1
公开(公告)日：2011-10-27
申请号：US12423740
申请日：2009-04-14
申请人： Paul K. Wolber
发明人： Paul K. Wolber
IPC分类号： C40B30/04 , C40B40/06
CPC分类号： C12Q1/6837 , C12Q2525/161 , C12Q2565/513 , C12Q2565/107
摘要： A method of evaluating for the presence of a target polynucleotide in a sample, using an addressable array of multiple polynucleotide probes linked to a substrate. The sample is exposed to the array and a set of polynucleotide target probes, such that target polynucleotide which may be present will bind to a predetermined feature of the array through multiple target probes of the set by forming at respective target regions on a target molecule, simultaneous hybrids with anti-target regions of the multiple target probes. A binding pattern on the array is observed and the presence of the target polynucleotide evaluated based on the observed binding pattern. Kits using such arrays, and methods for selecting target probes are further provided.
摘要翻译：使用连接到底物的多个多核苷酸探针的可寻址阵列来评估样品中靶多核苷酸的存在的方法。将样品暴露于阵列和一组多核苷酸靶探针，使得可存在的靶多核苷酸通过在靶分子上的各个靶区域形成而通过该组的多个靶探针结合阵列的预定特征，同时具有多个目标探针的抗靶区域的杂交体。观察到阵列上的结合模式，并且基于观察到的结合模式评价靶多核苷酸的存在。进一步提供使用这种阵列的套件以及用于选择目标探针的方法。

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