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1.发明授权公开(公告)号：US07031846B2
公开(公告)日：2006-04-18
申请号：US10219882
申请日：2002-08-15
申请人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
发明人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
CPC分类号： G06F19/20 , B01J2219/007 , G01N2035/00158 , G06F19/18 , G06F19/26 , Y10S707/99943
摘要： A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data, The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.
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2.发明授权System, method, and computer software for genotyping analysis and identification of allelic imbalance 有权系统，方法和计算机软件进行基因分型分析和鉴定等位基因不平衡公开(公告)号：US07280922B2
公开(公告)日：2007-10-09
申请号：US11181584
申请日：2005-07-14
申请人： Rui Mei , Teresa Webster
发明人： Rui Mei , Teresa Webster
摘要： Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.
摘要翻译： 提供了使用多个探针来确定样品的基因型的方法，系统和计算机软件产品。 在一个优选实施方案中，基于相对等位基因信号进行临时基因型呼叫。 然后使用模式识别来验证暂定呼叫。
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3.发明授权公开(公告)号：US07991560B2
公开(公告)日：2011-08-02
申请号：US11352008
申请日：2006-02-10
IPC分类号： G06F7/00
CPC分类号： G06F19/20 , B01J2219/007 , G01N2035/00158 , G06F19/18 , G06F19/26 , Y10S707/99943
摘要： A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.
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4.发明申请System, method, and computer software for genotyping analysis and identification of allelic imbalance 有权系统，方法和计算机软件进行基因分型分析和鉴定等位基因不平衡公开(公告)号：US20050250151A1
公开(公告)日：2005-11-10
申请号：US11181584
申请日：2005-07-14
申请人： Rui Mei , Teresa Webster
发明人： Rui Mei , Teresa Webster
摘要： Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.
摘要翻译： 提供了使用多个探针来确定样品的基因型的方法，系统和计算机软件产品。 在一个优选实施方案中，基于相对等位基因信号进行临时基因型呼叫。 然后使用模式识别来验证暂定呼叫。
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5.发明申请公开(公告)号：US20060167636A1
公开(公告)日：2006-07-27
申请号：US11352008
申请日：2006-02-10
申请人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
发明人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
IPC分类号： G06F19/00
CPC分类号： G06F19/20 , B01J2219/007 , G01N2035/00158 , G06F19/18 , G06F19/26 , Y10S707/99943
摘要： A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.
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公开(公告)号：US06988040B2
公开(公告)日：2006-01-17
申请号：US10219503
申请日：2002-08-15
申请人： Rui Mei , Teresa Webster
发明人： Rui Mei , Teresa Webster
IPC分类号： G06F17/00
摘要： Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.
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7.发明申请System, method, and computer software for the presentation and storage of analysis results 有权系统，方法和计算机软件，用于演示和存储分析结果公开(公告)号：US20110246085A1
公开(公告)日：2011-10-06
申请号：US13161150
申请日：2011-06-15
申请人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
发明人： Shantanu Kaushikkar , Teresa Webster , Rui Mei , Linda McAllister
IPC分类号： G06F19/00
CPC分类号： G06F19/20 , B01J2219/007 , G01N2035/00158 , G06F19/18 , G06F19/26 , Y10S707/99943
摘要： A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.
摘要翻译： 描述了计算机程序产品以及相关系统和方法，其处理对应于生物探针阵列的探针的发射强度数据。 所述计算机程序包括基因型和统计分析管理器，所述基因型和统计分析管理器至少部分地基于所述发射强度数据和至少一个用户可选择的统计参数的统计测量来确定绝对或相对表达值。 至少部分地基于发射强度数据，分析管理器还可以确定对一个或多个探针的基因型呼叫。 至少部分地基于至少一个用户可选显示参数和/或基因型呼叫之间的归一化变化的量度，分析管理器可进一步显示绝对或相对表达值。 归一化变化的度量可以至少部分地基于基因型呼叫和参考值的比较。
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公开(公告)号：US20070016382A1
公开(公告)日：2007-01-18
申请号：US11457452
申请日：2006-07-13
申请人： Teresa Webster , Hajime Matsuzaki , Xiaojun Di , Earl Hubbell , Rui Mei , Simon Cawley , Gregory Marcus , Keith Jones
发明人： Teresa Webster , Hajime Matsuzaki , Xiaojun Di , Earl Hubbell , Rui Mei , Simon Cawley , Gregory Marcus , Keith Jones
IPC分类号： G06F19/00
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。
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公开(公告)号：US20060024715A1
公开(公告)日：2006-02-02
申请号：US11175859
申请日：2005-07-05
申请人： Guoying Liu , Simon Cawley , Hajime Matsuzaki , Earl Hubbell , Geoffrey Yang , Teresa Webster , Rui Mei , Xiaojun Di , Richard Chiles
发明人： Guoying Liu , Simon Cawley , Hajime Matsuzaki , Earl Hubbell , Geoffrey Yang , Teresa Webster , Rui Mei , Xiaojun Di , Richard Chiles
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。
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10.发明申请公开(公告)号：US20050158790A1
公开(公告)日：2005-07-21
申请号：US11078138
申请日：2005-03-10
申请人： Rui Mei , Teresa Webster
发明人： Rui Mei , Teresa Webster
CPC分类号： C12Q1/6813 , G16B25/00 , C12Q2527/107
摘要： Methods and computer software products are provided for selecting nucleic acid probes. In one embodiment, perfect match intensity, mismatch intensity and the slope of quantitative response of a probe are predicted. A unified quality score is calculated. Probes are selected based on the unified quality score.
摘要翻译： 提供了用于选择核酸探针的方法和计算机软件产品。 在一个实施例中，预测了探针的完美匹配强度，不匹配强度和定量响应的斜率。 计算统一的质量得分。 根据统一的质量得分选择探针。
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