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1. 发明授权

US07361468B2 Methods for genotyping polymorphisms in humans 失效
标题翻译：人类基因分型多态性的方法
公开(公告)号：US07361468B2
公开(公告)日：2008-04-22
申请号：US11175859
申请日：2005-07-05
申请人： Guoying Liu , Simon Cawley , Hajime Matsuzaki , Earl A. Hubbell , Geoffrey Yang , Teresa A. Webster , Rui Mei , Xiaojun Di , Richard Chiles
发明人： Guoying Liu , Simon Cawley , Hajime Matsuzaki , Earl A. Hubbell , Geoffrey Yang , Teresa A. Webster , Rui Mei , Xiaojun Di , Richard Chiles
IPC分类号： C12Q1/68 , C07H21/04 , C12M3/00 , C12M1/34
CPC分类号： C12Q1/6883 , C12Q2600/156
摘要： Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.
摘要翻译：提供了用于并行分析大量人类SNP的核酸探针的方法，试剂盒和阵列。提供了一组超过100,000个人类SNP，已知在至少两个人群中是双向的。为一组人类SNP中的每个双重性SNP的每个等位基因提供等位基因特异性完全匹配探针和基因分型探针组，其可用于群体内和跨群体的遗传分析。提供包括完美匹配和不匹配探针的探针组。探头组适合包含在阵列中。本发明提供了SNP和周围序列，并提供了这样的序列，使得它们可用于各种分析，包括基因分型。因此，本发明涉及受遗传学性质影响的不同领域，包括生物学，医学和医学诊断。

2. 发明申请

US20080287308A1 SYSTEM, METHOD, AND COMPUTER SOFTWARE PRODUCT FOR GENOTYPE DETERMINATION USING PROBE ARRAY DATA 有权
标题翻译：系统，方法和计算机软件产品使用探针阵列数据进行基因组测定
公开(公告)号：US20080287308A1
公开(公告)日：2008-11-20
申请号：US12123463
申请日：2008-05-19
申请人： Earl A. Hubbell , Simon Cawley
发明人： Earl A. Hubbell , Simon Cawley
IPC分类号： C40B30/02
CPC分类号： G06F19/18 , G06F19/20 , G06F19/24
摘要： An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.
摘要翻译：描述了从生物探针阵列的处理图像分析数据的方法的实施例，其包括：接收包括与生物探针阵列上的探针相关联的多个强度值的多个文件; 对每个数据文件中的强度值进行归一化; 使用来自每个文件的每个分配的一个或多个强度值来确定多个基因型的初始分配; 使用所述多个初始分配估计聚类中心的分布; 将归一化强度值与聚类中心组合以确定每个聚类中心的后验估计; 以及使用来自所述后验估计的所述一个或多个强度值的距离来分配多个基因型呼叫。

3. 发明授权

US09760675B2 System, method, and computer software product for genotype determination using probe array data 有权
公开(公告)号：US09760675B2
公开(公告)日：2017-09-12
申请号：US13468604
申请日：2012-05-10
申请人： Earl A. Hubbell , Simon Cawley
发明人： Earl A. Hubbell , Simon Cawley
IPC分类号： G01N33/48 , G06F19/00 , G06F19/18 , G06F19/20 , G06F19/24
CPC分类号： G06F19/18 , G06F19/20 , G06F19/24
摘要： An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.

4. 发明申请

US20120221255A1 System, Method, and Computer Software Product for Genotype Determination Using Probe Array Data 有权
标题翻译：使用探针阵列数据进行基因型测定的系统，方法和计算机软件产品
公开(公告)号：US20120221255A1
公开(公告)日：2012-08-30
申请号：US13468604
申请日：2012-05-10
申请人： Earl A. Hubbell , Simon Cawley
发明人： Earl A. Hubbell , Simon Cawley
IPC分类号： G06F19/20
CPC分类号： G06F19/18 , G06F19/20 , G06F19/24
摘要： An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.
摘要翻译：描述了从生物探针阵列的处理图像分析数据的方法的实施例，其包括：接收包括与生物探针阵列上的探针相关联的多个强度值的多个文件; 对每个数据文件中的强度值进行归一化; 使用来自每个文件的每个分配的一个或多个强度值来确定多个基因型的初始分配; 使用所述多个初始分配估计聚类中心的分布; 将归一化强度值与聚类中心组合以确定每个聚类中心的后验估计; 以及使用来自所述后验估计的所述一个或多个强度值的距离来分配多个基因型呼叫。

5. 发明授权

US08200440B2 System, method, and computer software product for genotype determination using probe array data 有权
标题翻译：使用探针阵列数据进行基因型确定的系统，方法和计算机软件产品
公开(公告)号：US08200440B2
公开(公告)日：2012-06-12
申请号：US12123463
申请日：2008-05-19
申请人： Earl A. Hubbell , Simon Cawley
发明人： Earl A. Hubbell , Simon Cawley
IPC分类号： G06F19/00 , G06F19/18
CPC分类号： G06F19/18 , G06F19/20 , G06F19/24
摘要： An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.
摘要翻译：描述了从生物探针阵列的处理图像分析数据的方法的实施例，其包括接收多个文件，所述多个文件包括与生物探针阵列上的探针相关联的多个强度值; 对每个数据文件中的强度值进行归一化; 使用来自每个文件的每个分配的一个或多个强度值来确定多个基因型的初始分配; 使用所述多个初始分配估计聚类中心的分布; 将归一化强度值与聚类中心组合以确定每个聚类中心的后验估计; 以及使用来自所述后验估计的所述一个或多个强度值的距离来分配多个基因型呼叫。

6. 发明申请

US20110160092A1 Methods for Selecting a Collection of Single Nucleotide Polymorphisms 审中-公开
标题翻译：选择单核苷酸多态性集合的方法
公开(公告)号：US20110160092A1
公开(公告)日：2011-06-30
申请号：US13007471
申请日：2011-01-14
申请人： Teresa A. Webster , Hajime Matsuzaki , Xiaojun Di , Earl A. Hubbell , Rui Mei , Simon Cawley , Gregory Marcus , Keith W. Jones
发明人： Teresa A. Webster , Hajime Matsuzaki , Xiaojun Di , Earl A. Hubbell , Rui Mei , Simon Cawley , Gregory Marcus , Keith W. Jones
IPC分类号： C40B40/06 , C40B50/02
CPC分类号： C12Q1/6837 , B01J2219/00317 , B01J2219/00504 , B01J2219/00527 , B01J2219/00695 , B01J2219/00722 , B01J2219/00725 , G16B25/00 , G16B30/00
摘要： The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.
摘要翻译：本发明涉及跨基因组选择相关单核苷酸多态性集合以设计核酸探针阵列。因此，本发明涉及受遗传学性质影响的不同领域，包括生物学，医学和医学诊断。

7. 发明授权

US07881875B2 Methods for selecting a collection of single nucleotide polymorphisms 有权
标题翻译：选择单核苷酸多态性集合的方法
公开(公告)号：US07881875B2
公开(公告)日：2011-02-01
申请号：US11457452
申请日：2006-07-13
申请人： Teresa A. Webster , Hajime Matsuzaki , Xiaojun Di , Earl A. Hubbell , Rui Mei , Simon Cawley , Gregory Marcus , Keith W. Jones
发明人： Teresa A. Webster , Hajime Matsuzaki , Xiaojun Di , Earl A. Hubbell , Rui Mei , Simon Cawley , Gregory Marcus , Keith W. Jones
IPC分类号： G06F7/00
CPC分类号： C12Q1/6837 , B01J2219/00317 , B01J2219/00504 , B01J2219/00527 , B01J2219/00695 , B01J2219/00722 , B01J2219/00725 , G06F19/20 , G06F19/22
摘要： The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.
摘要翻译：本发明涉及跨基因组选择相关单核苷酸多态性集合以设计核酸探针阵列。因此，本发明涉及受遗传学性质影响的不同领域，包括生物学，医学和医学诊断。

8. 发明申请

US20110281772A1 Methods, systems and computer software for designing and synthesizing sequence arrays 审中-公开
标题翻译：用于设计和合成序列数组的方法，系统和计算机软件
公开(公告)号：US20110281772A1
公开(公告)日：2011-11-17
申请号：US13180006
申请日：2011-07-11
申请人： Earl A. Hubbell
发明人： Earl A. Hubbell
IPC分类号： C40B50/02
CPC分类号： C40B40/06 , B01J19/0046 , B01J2219/00432 , B01J2219/00529 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00605 , B01J2219/00612 , B01J2219/00626 , B01J2219/00659 , B01J2219/00689 , B01J2219/00695 , B01J2219/00711 , B01J2219/00722 , B82Y30/00 , C40B40/10 , C40B60/14 , G16B25/00 , G16B35/00 , G16B40/00 , G16C20/60
摘要： Embodiments of the invention provides methods, computer software products and systems for arranging polymers during combinatorial polymer synthesis so that the border or edge between synthesis site is minimized. In one embodiment, travelling salesman algorithm is used to minimize the edges. In another embodiment, a locally greedy optimization method is provided. In addition, methods and software products are provided for solving the robust arrangement problem for multi-probe gene expression arrays.
摘要翻译：本发明的实施例提供了在组合聚合物合成期间用于布置聚合物的方法，计算机软件产品和系统，使得合成位点之间的边界或边缘最小化。在一个实施例中，使用旅行推销员算法来使边缘最小化。在另一个实施例中，提供了局部贪心优化方法。此外，提供方法和软件产品，用于解决多探针基因表达阵列的鲁棒排列问题。

9. 发明授权

US08009889B2 Feature intensity reconstruction of biological probe array 有权
标题翻译：生物探针阵列特征强度重建
公开(公告)号：US08009889B2
公开(公告)日：2011-08-30
申请号：US11769600
申请日：2007-06-27
申请人： Earl A. Hubbell
发明人： Earl A. Hubbell
IPC分类号： G06K9/00 , G01N33/50
CPC分类号： G06K9/0014 , G06F19/20 , G06K9/00 , G06K2209/07
摘要： The invention provides methods and systems for reconstructing feature intensities from pixel level data. In certain embodiments, the invention uses an empirically determined transfer function to construct a theoretical estimate of pixel level data and then iteratively updates feature intensities based on a minimum multiplicative error between the pixel level data and the theoretical estimate of the pixel level data.
摘要翻译：本发明提供了用于从像素级数据重建特征强度的方法和系统。在某些实施例中，本发明使用经验确定的传递函数来构建像素级数据的理论估计，然后基于像素级数据与像素级数据的理论估计之间的最小乘法误差迭代地更新特征强度。

10. 发明申请

US20080261832A1 Arrays of nucleic acid probes for detecting cystic fibrosis 审中-公开
标题翻译：用于检测囊性纤维化的核酸探针阵列
公开(公告)号：US20080261832A1
公开(公告)日：2008-10-23
申请号：US11506176
申请日：2006-08-18
申请人： Maureen T. Cronin , Charles Garrett Miyada , Earl A. Hubbell , Mark Chee , Stephen P.A. Fodor , Xiaohua C. Huang , Robert J. Lipshutz , Peter E. Lobban , MacDonald S. Morris , Edward L. Sheldon
发明人： Maureen T. Cronin , Charles Garrett Miyada , Earl A. Hubbell , Mark Chee , Stephen P.A. Fodor , Xiaohua C. Huang , Robert J. Lipshutz , Peter E. Lobban , MacDonald S. Morris , Edward L. Sheldon
IPC分类号： C40B40/06 , C40B50/14
CPC分类号： C12Q1/6874 , C12Q1/6886
摘要： The invention provides arrays of immobilized probes, and methods employing the arrays, for detecting mutations in the CFTR gene.
摘要翻译：本发明提供了固定化探针的阵列，以及采用阵列的方法，用于检测CFTR基因中的突变。

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